From 50f953bcc575f55165c401a427abe9a4dba8dc0c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 09:41:37 +0200
Subject: [PATCH 001/228] PixelRefine: Work in progress

---
 image_analysis/CMakeLists.txt                 |   1 +
 .../pixel_refinement/CMakeLists.txt           |   2 +
 .../pixel_refinement/PixelRefine.cpp          | 133 ++++++++++++++++++
 image_analysis/pixel_refinement/PixelRefine.h |  36 +++++
 4 files changed, 172 insertions(+)
 create mode 100644 image_analysis/pixel_refinement/CMakeLists.txt
 create mode 100644 image_analysis/pixel_refinement/PixelRefine.cpp
 create mode 100644 image_analysis/pixel_refinement/PixelRefine.h

diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 9572d0b0..913870c5 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -50,5 +50,6 @@ ADD_SUBDIRECTORY(lattice_search)
 ADD_SUBDIRECTORY(scale_merge)
 ADD_SUBDIRECTORY(image_preprocessing)
 ADD_SUBDIRECTORY(azint)
+ADD_SUBDIRECTORY(pixel_refinement)
 
 TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge gemmi)
diff --git a/image_analysis/pixel_refinement/CMakeLists.txt b/image_analysis/pixel_refinement/CMakeLists.txt
new file mode 100644
index 00000000..5d5e3c6c
--- /dev/null
+++ b/image_analysis/pixel_refinement/CMakeLists.txt
@@ -0,0 +1,2 @@
+ADD_LIBRARY(JFJochPixelRefine PixelRefine.cpp PixelRefine.h)
+TARGET_LINK_LIBRARIES(JFJochPixelRefine JFJochBraggPrediction JFJochCommon ceres_static)
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
new file mode 100644
index 00000000..1e547b08
--- /dev/null
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -0,0 +1,133 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "PixelRefine.h"
+
+#include <ceres/ceres.h>
+#include <ceres/rotation.h>
+
+
+
+
+struct PixelRefineResidual {
+    ScalingPostRefResidual(int32_t h, int32_t k, int32_t l,
+                           double x, double y,
+                           double Itrue,
+                           const DiffractionGeometry &geometry,
+                           const CrystalLattice &lattice)
+    :
+          integration_center_x(r.predicted_x),
+          integration_center_y(r.predicted_y),
+          inv_lambda(SafeInv(geometry.GetWavelength_A(), 0.0)),
+          pixel_size(geometry.GetPixelSize_mm()),
+          det_dist_mm(geometry.GetDetectorDistance_mm()),
+          beam_x(geometry.GetBeamX_pxl()),
+          beam_y(geometry.GetBeamY_pxl()),
+          exp_h(r.h),
+          exp_k(r.k),
+          exp_l(r.l),
+          Astar(lattice.Astar()),
+          Bstar(lattice.Bstar()),
+          Cstar(lattice.Cstar()),
+          c1(std::cos(geometry.GetPoniRot1_rad())),
+          s1(std::sin(geometry.GetPoniRot1_rad())),
+          c2(std::cos(geometry.GetPoniRot2_rad())),
+          s2(std::sin(geometry.GetPoniRot2_rad())) {
+    }
+
+    template <typename T>
+    T CalcPartiality(const T *const R,
+                    const T *const beam_corr,
+                    const T *const p0) const {
+        // Detector coordinates in mm
+        const T det_x = (T(integration_center_x) - beam_x - beam_corr[0]) * T(pixel_size);
+        const T det_y = (T(integration_center_y) - beam_y - beam_corr[1]) * T(pixel_size);
+        const T det_z = T(det_dist_mm);
+
+        // Apply Ry(rot1) first: rotate around Y
+        const T t1_x = T(c1) * det_x + T(s1) * det_z;
+        const T t1_y = det_y;
+        const T t1_z = T(-s1) * det_x + T(c1) * det_z;
+
+        // Then apply Rx(-rot2): rotate around X
+        const T x = t1_x;
+        const T y = T(c2) * t1_y + T(s2) * t1_z;
+        const T z = - T(s2) * t1_y + T(c2) * t1_z;
+
+        // convert to recip space
+        const T lab_norm = ceres::sqrt(x * x + y * y + z * z);
+        const T inv_norm = T(1) / lab_norm;
+
+        T recip_obs[3];
+        recip_obs[0] = x * inv_norm * inv_lambda;
+        recip_obs[1] = y * inv_norm * inv_lambda;
+        recip_obs[2] = (z * inv_norm - T(1.0)) * inv_lambda;
+
+        const Eigen::Matrix<T, 3, 1> e_obs_recip(recip_obs[0], recip_obs[1], recip_obs[2]);
+
+        const T astar_unrot[3] = {T(Astar.x), T(Astar.y), T(Astar.z)};
+        const T bstar_unrot[3] = {T(Bstar.x), T(Bstar.y), T(Bstar.z)};
+        const T cstar_unrot[3] = {T(Cstar.x), T(Cstar.y), T(Cstar.z)};
+
+        T astar_rot[3], bstar_rot[3], cstar_rot[3];
+
+        ceres::AngleAxisRotatePoint(p0, astar_unrot, astar_rot);
+        ceres::AngleAxisRotatePoint(p0, bstar_unrot, bstar_rot);
+        ceres::AngleAxisRotatePoint(p0, cstar_unrot, cstar_rot);
+
+        const Eigen::Matrix<T, 3, 1> e_pred_recip(T(exp_h) * astar_rot[0] + T(exp_k) * bstar_rot[0] + T(exp_l) * cstar_rot[0],
+            T(exp_h) * astar_rot[1] + T(exp_k) * bstar_rot[1] + T(exp_l) * cstar_rot[1],
+            T(exp_h) * astar_rot[2] + T(exp_k) * bstar_rot[2] + T(exp_l) * cstar_rot[2]
+        );
+
+        // Ewald sphere centre is at -k_i = (0, 0, -inv_lambda)
+        // Radial direction: outward normal at g_hkl
+        const Eigen::Matrix<T, 3, 1> S_pred(
+            e_pred_recip[0],
+            e_pred_recip[1],
+            e_pred_recip[2] + T(inv_lambda)   // g_hkl + k_i
+        );
+        const T S_pred_norm = S_pred.norm();
+        if (S_pred_norm < T(1e-10))
+            return T(0);
+
+        const Eigen::Matrix<T, 3, 1> n_radial = S_pred / S_pred_norm;
+
+        const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
+        const T eps_radial        = delta_q.dot(n_radial);
+        const Eigen::Matrix<T, 3, 1> dq_tang = delta_q - eps_radial * n_radial;
+        const T eps_tangential_sq = dq_tang.squaredNorm();   // guaranteed ≥ 0
+        // ─────────────────────────────────────────────────────────────
+
+        return ceres::exp(- eps_radial * eps_radial / (R[0] * R[0]) - eps_tangential_sq / (R[1] * R[1]));
+    }
+
+    template<typename T>
+    bool operator()(const T *const G,
+                    const T *const B,
+                    const T *const R,
+                    const T *const beam_corr,
+                    const T *const p0,
+                    T *residual) const {
+        if (R[0] < T(1e-10) || R[1] < T(1e-10))
+            return false;
+
+        const T B_term = ceres::exp(B[0] * T(b_resolution_coeff));
+
+        const T partiality = CalcPartiality(R, beam_corr, p0);
+        residual[0] = (G[0] * partiality * B_term * T(lp) * T(Itrue)
+                       - T(Iobs)) * T(weight);
+        return true;
+    }
+
+    const double integration_center_x, integration_center_y;
+    const double inv_lambda;
+    const double pixel_size;
+    const double det_dist_mm;
+    const double beam_x, beam_y;
+    const double exp_h;
+    const double exp_k;
+    const double exp_l;
+    const Coord Astar, Bstar, Cstar;
+    const double c1,s1,c2,s2;
+};
\ No newline at end of file
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
new file mode 100644
index 00000000..1610ea9c
--- /dev/null
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -0,0 +1,36 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "../bragg_prediction/BraggPrediction.h"
+#include "../common/DiffractionExperiment.h"
+#include "../common/AzimuthalIntegrationMapping.h"
+
+struct PixelRefineData {
+    DiffractionGeometry geom;
+    CrystalLattice latt;
+    gemmi::CrystalSystem crystal_system = gemmi::CrystalSystem::Triclinic;
+    char centering = 'P';
+
+    double B_factor = 0.0;
+    double scale_factor = 1.0;
+    double R[2] = {0.001, 0.001};
+
+    bool refine_beam_center = false;
+    bool refine_unit_cell = false;
+};
+
+class PixelRefine {
+    BraggPrediction &prediction;
+    const AzimuthalIntegrationMapping &mapping;
+    const size_t xpixel, ypixel;
+
+public:
+    PixelRefine(const DiffractionExperiment &experiment,
+                const AzimuthalIntegrationMapping &mapping;
+                BraggPrediction &prediction);
+
+    template <class T>
+    void Run(const T *image, PixelRefineData &data);
+};
-- 
2.52.0


From 0d6b2787673e8e7ac9c4d741a44218d441293137 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 11:11:35 +0200
Subject: [PATCH 002/228] LatticeReduction: Move outside of XtalOptimizer

---
 image_analysis/geom_refinement/CMakeLists.txt |   2 +
 .../geom_refinement/LatticeReduction.cpp      | 257 +++++++++++++++++
 .../geom_refinement/LatticeReduction.h        |  19 ++
 .../geom_refinement/XtalOptimizer.cpp         | 260 +-----------------
 .../geom_refinement/XtalOptimizer.h           |  13 -
 tests/CMakeLists.txt                          |   1 +
 tests/LatticeReductionTest.cpp                | 225 +++++++++++++++
 tests/XtalOptimizerTest.cpp                   | 213 --------------
 8 files changed, 505 insertions(+), 485 deletions(-)
 create mode 100644 image_analysis/geom_refinement/LatticeReduction.cpp
 create mode 100644 image_analysis/geom_refinement/LatticeReduction.h
 create mode 100644 tests/LatticeReductionTest.cpp

diff --git a/image_analysis/geom_refinement/CMakeLists.txt b/image_analysis/geom_refinement/CMakeLists.txt
index a81b8b54..51df98fa 100644
--- a/image_analysis/geom_refinement/CMakeLists.txt
+++ b/image_analysis/geom_refinement/CMakeLists.txt
@@ -6,6 +6,8 @@ ADD_LIBRARY(JFJochGeomRefinement STATIC
         AssignSpotsToRings.h
         XtalOptimizer.cpp
         XtalOptimizer.h
+        LatticeReduction.cpp
+        LatticeReduction.h
 )
 
 TARGET_LINK_LIBRARIES(JFJochGeomRefinement Ceres::ceres Eigen3::Eigen JFJochCommon)
diff --git a/image_analysis/geom_refinement/LatticeReduction.cpp b/image_analysis/geom_refinement/LatticeReduction.cpp
new file mode 100644
index 00000000..7da10261
--- /dev/null
+++ b/image_analysis/geom_refinement/LatticeReduction.cpp
@@ -0,0 +1,257 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "LatticeReduction.h"
+
+#include <Eigen/Dense>
+
+void LatticeToRodriguesAndLengths_GS(const CrystalLattice &latt,
+                                            double rod[3],
+                                            double lengths[3]) {
+    // Load lattice columns
+    const Coord a = latt.Vec0();
+    const Coord b = latt.Vec1();
+    const Coord c = latt.Vec2();
+
+    Eigen::Vector3d A(a[0], a[1], a[2]);
+    Eigen::Vector3d B(b[0], b[1], b[2]);
+    Eigen::Vector3d C(c[0], c[1], c[2]);
+
+    // Lengths = column norms (orthorhombic assumption)
+    lengths[0] = A.norm();
+    lengths[1] = B.norm();
+    lengths[2] = C.norm();
+
+    auto safe_unit = [](const Eigen::Vector3d &v, double eps = 1e-15) -> Eigen::Vector3d {
+        double n = v.norm();
+        return (n > eps) ? (v / n) : Eigen::Vector3d(1.0, 0.0, 0.0);
+    };
+
+    // Gram–Schmidt with original order: x from A, y from B orthogonalized vs x
+    Eigen::Vector3d e1 = safe_unit(A);
+    Eigen::Vector3d y = B - (e1.dot(B)) * e1;
+    Eigen::Vector3d e2 = safe_unit(y);
+
+    // z from cross to ensure right-handed basis
+    Eigen::Vector3d e3 = e1.cross(e2);
+    double n3 = e3.norm();
+    if (n3 < 1e-15) {
+        // Degenerate case: B nearly collinear with A → use C instead
+        y = C - (e1.dot(C)) * e1;
+        e2 = safe_unit(y);
+        e3 = e1.cross(e2);
+        n3 = e3.norm();
+        if (n3 < 1e-15) {
+            // Still degenerate: pick any perpendicular to e1
+            e2 = safe_unit((std::abs(e1.x()) < 0.9)
+                               ? Eigen::Vector3d::UnitX().cross(e1)
+                               : Eigen::Vector3d::UnitY().cross(e1));
+            e3 = e1.cross(e2);
+        }
+    } else {
+        e3 /= n3;
+    }
+
+    Eigen::Matrix3d R;
+    R.col(0) = e1;
+    R.col(1) = e2;
+    R.col(2) = e3;
+
+    // Convert rotation to Rodrigues (axis * angle)
+    Eigen::AngleAxisd aa(R);
+    Eigen::Vector3d r = aa.angle() * aa.axis();
+    rod[0] = r.x();
+    rod[1] = r.y();
+    rod[2] = r.z();
+}
+
+void LatticeToRodriguesAndLengths_Hex(const CrystalLattice &latt, double rod[3], double ac[3]) {
+    const Coord a = latt.Vec0();
+    const Coord b = latt.Vec1();
+    const Coord c = latt.Vec2();
+
+    Eigen::Vector3d A(a[0], a[1], a[2]);
+    Eigen::Vector3d B(b[0], b[1], b[2]);
+    Eigen::Vector3d C(c[0], c[1], c[2]);
+
+    const double a_len = A.norm();
+    const double b_len = B.norm();
+    const double c_len = C.norm();
+
+    ac[0] = (a_len + b_len) / 2.0;
+    ac[1] = (a_len + b_len) / 2.0;
+    ac[2] = c_len;
+
+    Eigen::Vector3d e1;
+    Eigen::Vector3d e3;
+
+    if (a_len > 0.0)
+        e1 = A / a_len;
+    else
+        e1 = Eigen::Vector3d::UnitX();
+
+    if (c_len > 0.0)
+        e3 = C / c_len;
+    else
+        e3 = Eigen::Vector3d::UnitZ();
+
+    Eigen::Vector3d e2 = e3.cross(e1);
+    if (e2.norm() < 1e-15) {
+        e2 = (std::abs(e1.x()) < 0.9)
+                 ? Eigen::Vector3d::UnitX().cross(e1)
+                 : Eigen::Vector3d::UnitY().cross(e1);
+    }
+    e2.normalize();
+    e3 = e1.cross(e2).normalized();
+
+    Eigen::Matrix3d R;
+    R.col(0) = e1;
+    R.col(1) = e2;
+    R.col(2) = e3;
+
+    Eigen::AngleAxisd aa(R);
+    Eigen::Vector3d r = aa.angle() * aa.axis();
+    rod[0] = r.x();
+    rod[1] = r.y();
+    rod[2] = r.z();
+}
+
+// Extract rotation (Rodrigues), lengths (a,b,c) and beta (rad) for monoclinic (unique axis b).
+// Frame choice: e2 aligned with b; e1 from a projected orthogonal to e2; e3 = e1 x e2.
+void LatticeToRodriguesLengthsBeta_Mono(const CrystalLattice &latt,
+                                        double rod[3],
+                                        double lengths[3],
+                                        double &beta_rad) {
+    const Coord a = latt.Vec0();
+    const Coord b = latt.Vec1();
+    const Coord c = latt.Vec2();
+
+    const Eigen::Vector3d A(a[0], a[1], a[2]);
+    const Eigen::Vector3d Bv(b[0], b[1], b[2]);
+    const Eigen::Vector3d C(c[0], c[1], c[2]);
+
+    // Unit cell lengths
+    const double a_len = A.norm();
+    const double b_len = Bv.norm();
+    const double c_len = C.norm();
+
+    lengths[0] = a_len;
+    lengths[1] = b_len;
+    lengths[2] = c_len;
+
+    // Monoclinic beta = angle(a, c)
+    double cos_beta = 0.0;
+    if (a_len > 1e-15 && c_len > 1e-15) {
+        cos_beta = A.dot(C) / (a_len * c_len);
+        cos_beta = std::clamp(cos_beta, -1.0, 1.0);
+    }
+
+    beta_rad = std::acos(cos_beta);
+
+    // Protect against singular construction
+    const double sin_beta = std::max(std::abs(std::sin(beta_rad)), 1e-12);
+
+    // Canonical monoclinic basis:
+    //
+    // B =
+    // [ 1   0   cos(beta) ]
+    // [ 0   1        0     ]
+    // [ 0   0   sin(beta) ]
+    //
+    Eigen::Matrix3d Bmono = Eigen::Matrix3d::Zero();
+    Bmono(0,0) = 1.0;
+    Bmono(1,1) = 1.0;
+    Bmono(0,2) = std::cos(beta_rad);
+    Bmono(2,2) = sin_beta;
+
+    // Scale by lengths
+    Eigen::DiagonalMatrix<double,3> D(a_len, b_len, c_len);
+
+    // Ideal body-frame lattice
+    const Eigen::Matrix3d M = Bmono * D;
+
+    // Observed lattice
+    Eigen::Matrix3d L;
+    L.col(0) = A;
+    L.col(1) = Bv;
+    L.col(2) = C;
+
+    // Estimate rotation:
+    // R ≈ L * M^{-1}
+    Eigen::Matrix3d R_est = L * M.inverse();
+
+    // Project to nearest proper rotation matrix
+    Eigen::JacobiSVD<Eigen::Matrix3d> svd(R_est, Eigen::ComputeFullU | Eigen::ComputeFullV);
+
+    Eigen::Matrix3d R = svd.matrixU() * svd.matrixV().transpose();
+
+    // Enforce det(R)=+1
+    if (R.determinant() < 0.0) {
+        Eigen::Matrix3d U = svd.matrixU();
+        U.col(2) *= -1.0;
+        R = U * svd.matrixV().transpose();
+    }
+
+    // Rodrigues vector
+    Eigen::AngleAxisd aa(R);
+    const Eigen::Vector3d r = aa.angle() * aa.axis();
+
+    rod[0] = r.x();
+    rod[1] = r.y();
+    rod[2] = r.z();
+}
+
+static inline Eigen::Matrix3d B_from_angles(double alpha_rad, double beta_rad, double gamma_rad) {
+    const double ca = std::cos(alpha_rad);
+    const double cb = std::cos(beta_rad);
+    const double cg = std::cos(gamma_rad);
+    const double sg = std::sin(gamma_rad);
+
+    Eigen::Matrix3d B = Eigen::Matrix3d::Identity();
+
+    // a along x, b in x-y, c general
+    B(0, 0) = 1.0;  B(1, 0) = 0.0;  B(2, 0) = 0.0;
+    B(0, 1) = cg;   B(1, 1) = sg;   B(2, 1) = 0.0;
+
+    // c vector components (standard crystallography construction)
+    const double cx = cb;
+    const double cy = (ca - cb * cg) / sg;
+    const double cz = std::sqrt(std::max(0.0, 1.0 - cx * cx - cy * cy));
+
+    B(0, 2) = cx;
+    B(1, 2) = cy;
+    B(2, 2) = cz;
+
+    return B;
+}
+
+CrystalLattice AngleAxisAndCellToLattice(const double rod[3],
+                                         const double lengths[3],
+                                         double alpha_rad,
+                                         double beta_rad,
+                                         double gamma_rad) {
+    const Eigen::Vector3d r(rod[0], rod[1], rod[2]);
+    const double angle = r.norm();
+
+    Eigen::Matrix3d R = Eigen::Matrix3d::Identity();
+    if (angle > 0.0)
+        R = Eigen::AngleAxisd(angle, r / angle).toRotationMatrix();
+
+    const Eigen::DiagonalMatrix<double, 3> D(lengths[0], lengths[1], lengths[2]);
+    const Eigen::Matrix3d B = B_from_angles(alpha_rad, beta_rad, gamma_rad);
+
+    // IMPORTANT convention: L = R * B * D (scale columns by lengths)
+    const Eigen::Matrix3d latt = R * B * D;
+
+    return CrystalLattice(Coord(latt(0, 0), latt(1, 0), latt(2, 0)),
+                          Coord(latt(0, 1), latt(1, 1), latt(2, 1)),
+                          Coord(latt(0, 2), latt(1, 2), latt(2, 2)));
+}
+
+
+CrystalLattice AngleAxisAndLengthsToLattice(const double rod[3], const double lengths[3], bool hex) {
+    return AngleAxisAndCellToLattice(rod, lengths,
+                                     /*alpha=*/M_PI / 2.0,
+                                     /*beta =*/M_PI / 2.0,
+                                     /*gamma=*/hex ? 2.0 * M_PI / 3.0 : M_PI / 2.0);
+}
diff --git a/image_analysis/geom_refinement/LatticeReduction.h b/image_analysis/geom_refinement/LatticeReduction.h
new file mode 100644
index 00000000..bcf0d3d3
--- /dev/null
+++ b/image_analysis/geom_refinement/LatticeReduction.h
@@ -0,0 +1,19 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "../common/CrystalLattice.h"
+
+void LatticeToRodriguesAndLengths_GS(const CrystalLattice &latt,  double rod[3], double lengths[3]);
+void LatticeToRodriguesAndLengths_Hex(const CrystalLattice &latt, double rod[3], double ac[3]);
+void LatticeToRodriguesLengthsBeta_Mono(const CrystalLattice &latt,
+                                               double rod[3],
+                                               double lengths[3],
+                                               double &beta_rad);
+
+CrystalLattice AngleAxisAndCellToLattice(const double rod[3],
+                                         const double lengths[3],
+                                         double alpha_rad,
+                                         double beta_rad,
+                                         double gamma_rad);
diff --git a/image_analysis/geom_refinement/XtalOptimizer.cpp b/image_analysis/geom_refinement/XtalOptimizer.cpp
index cefb24cc..03d5ce08 100644
--- a/image_analysis/geom_refinement/XtalOptimizer.cpp
+++ b/image_analysis/geom_refinement/XtalOptimizer.cpp
@@ -6,6 +6,7 @@
 #include "XtalOptimizer.h"
 #include "ceres/ceres.h"
 #include "ceres/rotation.h"
+#include "LatticeReduction.h"
 
 struct XtalResidual {
     XtalResidual(double x, double y,
@@ -244,265 +245,6 @@ struct RotationNormRegularizer {
     const double weight;
 };
 
-inline void LatticeToRodriguesAndLengths_GS(const CrystalLattice &latt,
-                                            double rod[3],
-                                            double lengths[3]) {
-    // Load lattice columns
-    const Coord a = latt.Vec0();
-    const Coord b = latt.Vec1();
-    const Coord c = latt.Vec2();
-
-    Eigen::Vector3d A(a[0], a[1], a[2]);
-    Eigen::Vector3d B(b[0], b[1], b[2]);
-    Eigen::Vector3d C(c[0], c[1], c[2]);
-
-    // Lengths = column norms (orthorhombic assumption)
-    lengths[0] = A.norm();
-    lengths[1] = B.norm();
-    lengths[2] = C.norm();
-
-    auto safe_unit = [](const Eigen::Vector3d &v, double eps = 1e-15) -> Eigen::Vector3d {
-        double n = v.norm();
-        return (n > eps) ? (v / n) : Eigen::Vector3d(1.0, 0.0, 0.0);
-    };
-
-    // Gram–Schmidt with original order: x from A, y from B orthogonalized vs x
-    Eigen::Vector3d e1 = safe_unit(A);
-    Eigen::Vector3d y = B - (e1.dot(B)) * e1;
-    Eigen::Vector3d e2 = safe_unit(y);
-
-    // z from cross to ensure right-handed basis
-    Eigen::Vector3d e3 = e1.cross(e2);
-    double n3 = e3.norm();
-    if (n3 < 1e-15) {
-        // Degenerate case: B nearly collinear with A → use C instead
-        y = C - (e1.dot(C)) * e1;
-        e2 = safe_unit(y);
-        e3 = e1.cross(e2);
-        n3 = e3.norm();
-        if (n3 < 1e-15) {
-            // Still degenerate: pick any perpendicular to e1
-            e2 = safe_unit((std::abs(e1.x()) < 0.9)
-                               ? Eigen::Vector3d::UnitX().cross(e1)
-                               : Eigen::Vector3d::UnitY().cross(e1));
-            e3 = e1.cross(e2);
-        }
-    } else {
-        e3 /= n3;
-    }
-
-    Eigen::Matrix3d R;
-    R.col(0) = e1;
-    R.col(1) = e2;
-    R.col(2) = e3;
-
-    // Convert rotation to Rodrigues (axis * angle)
-    Eigen::AngleAxisd aa(R);
-    Eigen::Vector3d r = aa.angle() * aa.axis();
-    rod[0] = r.x();
-    rod[1] = r.y();
-    rod[2] = r.z();
-}
-
-void LatticeToRodriguesAndLengths_Hex(const CrystalLattice &latt, double rod[3], double ac[3]) {
-    const Coord a = latt.Vec0();
-    const Coord b = latt.Vec1();
-    const Coord c = latt.Vec2();
-
-    Eigen::Vector3d A(a[0], a[1], a[2]);
-    Eigen::Vector3d B(b[0], b[1], b[2]);
-    Eigen::Vector3d C(c[0], c[1], c[2]);
-
-    const double a_len = A.norm();
-    const double b_len = B.norm();
-    const double c_len = C.norm();
-
-    ac[0] = (a_len + b_len) / 2.0;
-    ac[1] = (a_len + b_len) / 2.0;
-    ac[2] = c_len;
-
-    Eigen::Vector3d e1;
-    Eigen::Vector3d e3;
-
-    if (a_len > 0.0)
-        e1 = A / a_len;
-    else
-        e1 = Eigen::Vector3d::UnitX();
-
-    if (c_len > 0.0)
-        e3 = C / c_len;
-    else
-        e3 = Eigen::Vector3d::UnitZ();
-
-    Eigen::Vector3d e2 = e3.cross(e1);
-    if (e2.norm() < 1e-15) {
-        e2 = (std::abs(e1.x()) < 0.9)
-                 ? Eigen::Vector3d::UnitX().cross(e1)
-                 : Eigen::Vector3d::UnitY().cross(e1);
-    }
-    e2.normalize();
-    e3 = e1.cross(e2).normalized();
-
-    Eigen::Matrix3d R;
-    R.col(0) = e1;
-    R.col(1) = e2;
-    R.col(2) = e3;
-
-    Eigen::AngleAxisd aa(R);
-    Eigen::Vector3d r = aa.angle() * aa.axis();
-    rod[0] = r.x();
-    rod[1] = r.y();
-    rod[2] = r.z();
-}
-
-// Extract rotation (Rodrigues), lengths (a,b,c) and beta (rad) for monoclinic (unique axis b).
-// Frame choice: e2 aligned with b; e1 from a projected orthogonal to e2; e3 = e1 x e2.
-void LatticeToRodriguesLengthsBeta_Mono(const CrystalLattice &latt,
-                                        double rod[3],
-                                        double lengths[3],
-                                        double &beta_rad) {
-    const Coord a = latt.Vec0();
-    const Coord b = latt.Vec1();
-    const Coord c = latt.Vec2();
-
-    const Eigen::Vector3d A(a[0], a[1], a[2]);
-    const Eigen::Vector3d Bv(b[0], b[1], b[2]);
-    const Eigen::Vector3d C(c[0], c[1], c[2]);
-
-    // Unit cell lengths
-    const double a_len = A.norm();
-    const double b_len = Bv.norm();
-    const double c_len = C.norm();
-
-    lengths[0] = a_len;
-    lengths[1] = b_len;
-    lengths[2] = c_len;
-
-    // Monoclinic beta = angle(a, c)
-    double cos_beta = 0.0;
-    if (a_len > 1e-15 && c_len > 1e-15) {
-        cos_beta = A.dot(C) / (a_len * c_len);
-        cos_beta = std::clamp(cos_beta, -1.0, 1.0);
-    }
-
-    beta_rad = std::acos(cos_beta);
-
-    // Protect against singular construction
-    const double sin_beta = std::max(std::abs(std::sin(beta_rad)), 1e-12);
-
-    // Canonical monoclinic basis:
-    //
-    // B =
-    // [ 1   0   cos(beta) ]
-    // [ 0   1        0     ]
-    // [ 0   0   sin(beta) ]
-    //
-    Eigen::Matrix3d Bmono = Eigen::Matrix3d::Zero();
-    Bmono(0,0) = 1.0;
-    Bmono(1,1) = 1.0;
-    Bmono(0,2) = std::cos(beta_rad);
-    Bmono(2,2) = sin_beta;
-
-    // Scale by lengths
-    Eigen::DiagonalMatrix<double,3> D(a_len, b_len, c_len);
-
-    // Ideal body-frame lattice
-    const Eigen::Matrix3d M = Bmono * D;
-
-    // Observed lattice
-    Eigen::Matrix3d L;
-    L.col(0) = A;
-    L.col(1) = Bv;
-    L.col(2) = C;
-
-    // Estimate rotation:
-    // R ≈ L * M^{-1}
-    Eigen::Matrix3d R_est = L * M.inverse();
-
-    // Project to nearest proper rotation matrix
-    Eigen::JacobiSVD<Eigen::Matrix3d> svd(R_est, Eigen::ComputeFullU | Eigen::ComputeFullV);
-
-    Eigen::Matrix3d R = svd.matrixU() * svd.matrixV().transpose();
-
-    // Enforce det(R)=+1
-    if (R.determinant() < 0.0) {
-        Eigen::Matrix3d U = svd.matrixU();
-        U.col(2) *= -1.0;
-        R = U * svd.matrixV().transpose();
-    }
-
-    // Rodrigues vector
-    Eigen::AngleAxisd aa(R);
-    const Eigen::Vector3d r = aa.angle() * aa.axis();
-
-    rod[0] = r.x();
-    rod[1] = r.y();
-    rod[2] = r.z();
-}
-
-static inline Eigen::Matrix3d B_from_angles(double alpha_rad, double beta_rad, double gamma_rad) {
-    const double ca = std::cos(alpha_rad);
-    const double cb = std::cos(beta_rad);
-    const double cg = std::cos(gamma_rad);
-    const double sg = std::sin(gamma_rad);
-
-    Eigen::Matrix3d B = Eigen::Matrix3d::Identity();
-
-    // a along x, b in x-y, c general
-    B(0, 0) = 1.0;  B(1, 0) = 0.0;  B(2, 0) = 0.0;
-    B(0, 1) = cg;   B(1, 1) = sg;   B(2, 1) = 0.0;
-
-    // c vector components (standard crystallography construction)
-    const double cx = cb;
-    const double cy = (ca - cb * cg) / sg;
-    const double cz = std::sqrt(std::max(0.0, 1.0 - cx * cx - cy * cy));
-
-    B(0, 2) = cx;
-    B(1, 2) = cy;
-    B(2, 2) = cz;
-
-    return B;
-}
-
-CrystalLattice AngleAxisAndCellToLattice(const double rod[3],
-                                         const double lengths[3],
-                                         double alpha_rad,
-                                         double beta_rad,
-                                         double gamma_rad) {
-    const Eigen::Vector3d r(rod[0], rod[1], rod[2]);
-    const double angle = r.norm();
-
-    Eigen::Matrix3d R = Eigen::Matrix3d::Identity();
-    if (angle > 0.0)
-        R = Eigen::AngleAxisd(angle, r / angle).toRotationMatrix();
-
-    const Eigen::DiagonalMatrix<double, 3> D(lengths[0], lengths[1], lengths[2]);
-    const Eigen::Matrix3d B = B_from_angles(alpha_rad, beta_rad, gamma_rad);
-
-    // IMPORTANT convention: L = R * B * D (scale columns by lengths)
-    const Eigen::Matrix3d latt = R * B * D;
-
-    return CrystalLattice(Coord(latt(0, 0), latt(1, 0), latt(2, 0)),
-                          Coord(latt(0, 1), latt(1, 1), latt(2, 1)),
-                          Coord(latt(0, 2), latt(1, 2), latt(2, 2)));
-}
-
-
-CrystalLattice AngleAxisAndLengthsToLattice(const double rod[3], const double lengths[3], bool hex) {
-    if (!hex) {
-        return AngleAxisAndCellToLattice(rod, lengths,
-                                         /*alpha=*/M_PI / 2.0,
-                                         /*beta =*/M_PI / 2.0,
-                                         /*gamma=*/M_PI / 2.0);
-    }
-
-    // Hexagonal: caller must already enforce a=b in `lengths`.
-    return AngleAxisAndCellToLattice(rod, lengths,
-                                     /*alpha=*/M_PI / 2.0,
-                                     /*beta =*/M_PI / 2.0,
-                                     /*gamma=*/2.0 * M_PI / 3.0);
-}
-
 bool XtalOptimizerInternal(XtalOptimizerData &data,
                            const std::vector<std::vector<SpotToSave>> &spots,
                            const float tolerance) {
diff --git a/image_analysis/geom_refinement/XtalOptimizer.h b/image_analysis/geom_refinement/XtalOptimizer.h
index c472e8ab..7dbaae47 100644
--- a/image_analysis/geom_refinement/XtalOptimizer.h
+++ b/image_analysis/geom_refinement/XtalOptimizer.h
@@ -43,19 +43,6 @@ struct XtalOptimizerData {
     std::optional<Coord> angle_axis;
 };
 
-void LatticeToRodriguesAndLengths_GS(const CrystalLattice &latt,  double rod[3], double lengths[3]);
-void LatticeToRodriguesAndLengths_Hex(const CrystalLattice &latt, double rod[3], double ac[3]);
-void LatticeToRodriguesLengthsBeta_Mono(const CrystalLattice &latt,
-                                               double rod[3],
-                                               double lengths[3],
-                                               double &beta_rad);
-
-CrystalLattice AngleAxisAndCellToLattice(const double rod[3],
-                                         const double lengths[3],
-                                         double alpha_rad,
-                                         double beta_rad,
-                                         double gamma_rad);
-
 bool XtalOptimizer(XtalOptimizerData &data, const std::vector<std::vector<SpotToSave>> &spots);
 bool XtalOptimizerRotationOnly(XtalOptimizerData &data, const std::vector<SpotToSave> &spots, float tolerance);
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index f4868b12..751e8f64 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -71,6 +71,7 @@ ADD_EXECUTABLE(jfjoch_test
         UnitCellTest.cpp
         CCTest.cpp
         MultiLatticeSearchTest.cpp
+        LatticeReductionTest.cpp
 )
 
 target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochWriter
diff --git a/tests/LatticeReductionTest.cpp b/tests/LatticeReductionTest.cpp
new file mode 100644
index 00000000..8ad8aa93
--- /dev/null
+++ b/tests/LatticeReductionTest.cpp
@@ -0,0 +1,225 @@
+// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include <Eigen/Dense>
+
+#include "../image_analysis/geom_refinement/LatticeReduction.h"
+
+
+namespace {
+    Eigen::Vector3d to_eigen(const Coord& v) {
+        return {v[0], v[1], v[2]};
+    }
+
+    double angle_rad(const Eigen::Vector3d& a, const Eigen::Vector3d& b) {
+        const double na = a.norm();
+        const double nb = b.norm();
+        if (na == 0.0 || nb == 0.0)
+            return 0.0;
+        double c = a.dot(b) / (na * nb);
+        c = std::max(-1.0, std::min(1.0, c));
+        return std::acos(c);
+    }
+
+    // Compare two lattices up to a global rotation: compare Gram matrices G = L^T L (rotation-invariant).
+    Eigen::Matrix3d gram(const CrystalLattice& latt) {
+        const Eigen::Vector3d A = to_eigen(latt.Vec0());
+        const Eigen::Vector3d B = to_eigen(latt.Vec1());
+        const Eigen::Vector3d C = to_eigen(latt.Vec2());
+        Eigen::Matrix3d G;
+        G(0,0) = A.dot(A); G(0,1) = A.dot(B); G(0,2) = A.dot(C);
+        G(1,0) = B.dot(A); G(1,1) = B.dot(B); G(1,2) = B.dot(C);
+        G(2,0) = C.dot(A); G(2,1) = C.dot(B); G(2,2) = C.dot(C);
+        return G;
+    }
+
+    void check_gram_close(const CrystalLattice& a,
+                          const CrystalLattice& b,
+                          double abs_eps,
+                          double rel_eps) {
+        const Eigen::Matrix3d Ga = gram(a);
+        const Eigen::Matrix3d Gb = gram(b);
+
+        for (int r = 0; r < 3; ++r) {
+            for (int c = 0; c < 3; ++c) {
+                const double va = Ga(r, c);
+                const double vb = Gb(r, c);
+
+                // Scale for relative error; avoid blowing up around zero.
+                const double scale = std::max({1.0, std::abs(va), std::abs(vb)});
+                const double tol = std::max(abs_eps, rel_eps * scale);
+
+                INFO("G(" << r << "," << c << ") va=" << va << " vb=" << vb
+                          << " scale=" << scale << " tol=" << tol);
+
+                CHECK(va == Catch::Approx(vb).margin(tol));
+            }
+        }
+    }
+} // namespace
+
+
+TEST_CASE("LatticeToRodrigues") {
+    double rod[3];
+    double lengths[3];
+
+    CrystalLattice latt_i(40,50,80,90,90,90);
+
+    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
+    CHECK(lengths[0] == Catch::Approx(40.0));
+    CHECK(lengths[1] == Catch::Approx(50.0));
+    CHECK(lengths[2] == Catch::Approx(80.0));
+    CHECK(fabs(rod[0]) < 0.001);
+    CHECK(fabs(rod[1]) < 0.001);
+    CHECK(fabs(rod[2]) < 0.001);
+
+    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
+
+    CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
+    CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
+    CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
+}
+
+
+TEST_CASE("LatticeToRodrigues_irregular") {
+    double rod[3];
+    double lengths[3];
+
+    CrystalLattice latt_i(Coord(40,0,0),
+                          Coord(0, 50 / sqrt(2), -50 / sqrt(2)),
+                          Coord(0, 80 / sqrt(2), 80 / sqrt(2)));
+
+    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
+    CHECK(lengths[0] == Catch::Approx(40.0));
+    CHECK(lengths[1] == Catch::Approx(50.0));
+    CHECK(lengths[2] == Catch::Approx(80.0));
+
+    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
+
+    CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
+    CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
+    CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
+}
+
+TEST_CASE("LatticeToRodrigues_Hex") {
+    double rod[3];
+    double lengths[3];
+
+    Coord a = Coord(40,0,0);
+    Coord b = Coord(40 / 2, 40 * sqrt(3)/ 2.0, 0);
+    Coord c = Coord(0, 0, 70);
+
+    RotMatrix R(1.0, Coord(0,1,1));
+    CrystalLattice latt_i(R*a,R*b,R*c);
+
+    LatticeToRodriguesAndLengths_Hex(latt_i, rod, lengths);
+    CHECK(lengths[0] == Catch::Approx(40.0));
+    CHECK(lengths[1] == Catch::Approx(40.0));
+    CHECK(lengths[2] == Catch::Approx(70.0));
+
+    auto latt_o = AngleAxisAndCellToLattice(rod, lengths,M_PI / 2.0, M_PI / 2.0, 2.0 * M_PI / 3.0);
+    auto uc_o = latt_o.GetUnitCell();
+    CHECK(uc_o.a == Catch::Approx(40.0));
+    CHECK(uc_o.b == Catch::Approx(40.0));
+    CHECK(uc_o.c == Catch::Approx(70.0));
+    CHECK(uc_o.alpha == Catch::Approx(90.0));
+    CHECK(uc_o.beta == Catch::Approx(90.0));
+    CHECK(uc_o.gamma == Catch::Approx(120.0));
+}
+
+
+TEST_CASE("LatticeReduction Lattice param roundtrip (GS) preserves Gram matrix") {
+    // Non-orthogonal, irregular basis, but still a valid lattice
+    CrystalLattice latt_i(Coord(40,  1,  2),
+                          Coord( 3, 50, -4),
+                          Coord(-5,  6, 80));
+
+    double rod[3]{}, lengths[3]{};
+    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
+    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
+
+    // This parametrization only keeps "lengths + rotation", i.e. it cannot reproduce shear.
+    // So we *do not* compare Gram matrices here.
+    // Instead, sanity-check: reconstructed vectors have the requested lengths.
+    CHECK(latt_o.Vec0().Length() == Catch::Approx(lengths[0]).margin(1e-9));
+    CHECK(latt_o.Vec1().Length() == Catch::Approx(lengths[1]).margin(1e-9));
+    CHECK(latt_o.Vec2().Length() == Catch::Approx(lengths[2]).margin(1e-9));
+}
+
+TEST_CASE("LatticeReduction Lattice param roundtrip (Hex) preserves unit cell") {
+    Coord a = Coord(40, 0, 0);
+    Coord b = Coord(40 / 2.0, 40 * std::sqrt(3) / 2.0, 0);
+    Coord c = Coord(0, 0, 70);
+
+    // Apply an arbitrary rotation to ensure the rod extraction is meaningful
+    RotMatrix R(1.0, Coord(0, 1, 1));
+    CrystalLattice latt_i(R * a, R * b, R * c);
+
+    double rod[3]{}, ac[3]{};
+    LatticeToRodriguesAndLengths_Hex(latt_i, rod, ac);
+    auto latt_o = AngleAxisAndCellToLattice(rod, ac, M_PI/2, M_PI/2, 2*M_PI/3);
+
+    auto uc_o = latt_o.GetUnitCell();
+    CHECK(uc_o.a == Catch::Approx(40.0).margin(1e-6));
+    CHECK(uc_o.b == Catch::Approx(40.0).margin(1e-6));
+    CHECK(uc_o.c == Catch::Approx(70.0).margin(1e-6));
+    CHECK(uc_o.alpha == Catch::Approx(90.0).margin(1e-6));
+    CHECK(uc_o.beta  == Catch::Approx(90.0).margin(1e-6));
+    CHECK(uc_o.gamma == Catch::Approx(120.0).margin(1e-6));
+}
+
+TEST_CASE("LatticeReduction Monoclinic param roundtrip") {
+    struct Case { double beta_deg; };
+    const std::vector<Case> cases = {
+        {60.0}, {75.0}, {115.0}, {130.0}
+    };
+
+    for (const auto& cs : cases) {
+        INFO("beta_deg=" << cs.beta_deg);
+
+        // Start from a clean monoclinic cell in its conventional setting (unique axis b).
+        CrystalLattice latt0(50, 60, 70, 90, cs.beta_deg, 90);
+
+        // Now apply a TRUE global rotation: rotate each basis vector (left-multiply).
+        RotMatrix R(0.7, Coord(0.3, 0.9, 0.1));
+        CrystalLattice latt_i(R * latt0.Vec0(),
+                              R * latt0.Vec1(),
+                              R * latt0.Vec2());
+
+        double rod[3]{}, lengths[3]{}, beta_rad = 0.0;
+        LatticeToRodriguesLengthsBeta_Mono(latt_i, rod, lengths, beta_rad);
+
+        // Basic sanity
+        CHECK(lengths[0] == Catch::Approx(50.0).margin(1e-6));
+        CHECK(lengths[1] == Catch::Approx(60.0).margin(1e-6));
+        CHECK(lengths[2] == Catch::Approx(70.0).margin(1e-6));
+        CHECK(beta_rad * 180.0 / M_PI == Catch::Approx(cs.beta_deg).margin(1e-6));
+
+        auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, beta_rad, M_PI/2);
+
+        // Rotation-invariant check: Gram matrices match.
+        check_gram_close(latt_i, latt_o, /*abs_eps=*/5e-4, /*rel_eps=*/1e-10);
+
+        // Also check the unit-cell angles we expect for monoclinic(unique b).
+        auto uc_o = latt_o.GetUnitCell();
+        CHECK(uc_o.alpha == Catch::Approx(90.0).margin(1e-4));
+        CHECK(uc_o.gamma == Catch::Approx(90.0).margin(1e-4));
+        CHECK(uc_o.beta  == Catch::Approx(cs.beta_deg).margin(1e-4));
+    }
+}
+
+TEST_CASE("LatticeReduction monoclinic") {
+    // This isolates only the beta definition, independent of other choices.
+    CrystalLattice latt_i(50, 60, 70, 90, 130, 90);
+
+    const Eigen::Vector3d A = to_eigen(latt_i.Vec0());
+    const Eigen::Vector3d C = to_eigen(latt_i.Vec2());
+    const double beta_geom = angle_rad(A, C);
+
+    double rod[3]{}, lengths[3]{}, beta_rad = 0.0;
+    LatticeToRodriguesLengthsBeta_Mono(latt_i, rod, lengths, beta_rad);
+
+    CHECK(beta_rad == Catch::Approx(beta_geom).margin(1e-12));
+}
diff --git a/tests/XtalOptimizerTest.cpp b/tests/XtalOptimizerTest.cpp
index 8b90983b..5a809a87 100644
--- a/tests/XtalOptimizerTest.cpp
+++ b/tests/XtalOptimizerTest.cpp
@@ -489,73 +489,6 @@ TEST_CASE("XtalOptimizer_monoclinic") {
     CHECK(fabs(uc_o.gamma - 90) < 0.05);
 }
 
-TEST_CASE("LatticeToRodrigues") {
-    double rod[3];
-    double lengths[3];
-
-    CrystalLattice latt_i(40,50,80,90,90,90);
-
-    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
-    CHECK(lengths[0] == Catch::Approx(40.0));
-    CHECK(lengths[1] == Catch::Approx(50.0));
-    CHECK(lengths[2] == Catch::Approx(80.0));
-    CHECK(fabs(rod[0]) < 0.001);
-    CHECK(fabs(rod[1]) < 0.001);
-    CHECK(fabs(rod[2]) < 0.001);
-
-    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
-
-    CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
-    CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
-    CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
-}
-
-TEST_CASE("LatticeToRodrigues_irregular") {
-    double rod[3];
-    double lengths[3];
-
-    CrystalLattice latt_i(Coord(40,0,0),
-                          Coord(0, 50 / sqrt(2), -50 / sqrt(2)),
-                          Coord(0, 80 / sqrt(2), 80 / sqrt(2)));
-
-    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
-    CHECK(lengths[0] == Catch::Approx(40.0));
-    CHECK(lengths[1] == Catch::Approx(50.0));
-    CHECK(lengths[2] == Catch::Approx(80.0));
-
-    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
-
-    CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
-    CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
-    CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
-}
-
-TEST_CASE("LatticeToRodrigues_Hex") {
-    double rod[3];
-    double lengths[3];
-
-    Coord a = Coord(40,0,0);
-    Coord b = Coord(40 / 2, 40 * sqrt(3)/ 2.0, 0);
-    Coord c = Coord(0, 0, 70);
-
-    RotMatrix R(1.0, Coord(0,1,1));
-    CrystalLattice latt_i(R*a,R*b,R*c);
-
-    LatticeToRodriguesAndLengths_Hex(latt_i, rod, lengths);
-    CHECK(lengths[0] == Catch::Approx(40.0));
-    CHECK(lengths[1] == Catch::Approx(40.0));
-    CHECK(lengths[2] == Catch::Approx(70.0));
-
-    auto latt_o = AngleAxisAndCellToLattice(rod, lengths,M_PI / 2.0, M_PI / 2.0, 2.0 * M_PI / 3.0);
-    auto uc_o = latt_o.GetUnitCell();
-    CHECK(uc_o.a == Catch::Approx(40.0));
-    CHECK(uc_o.b == Catch::Approx(40.0));
-    CHECK(uc_o.c == Catch::Approx(70.0));
-    CHECK(uc_o.alpha == Catch::Approx(90.0));
-    CHECK(uc_o.beta == Catch::Approx(90.0));
-    CHECK(uc_o.gamma == Catch::Approx(120.0));
-}
-
 TEST_CASE("XtalOptimizer_rotation") {
     // Geometry
     DiffractionExperiment exp_i;
@@ -736,149 +669,3 @@ TEST_CASE("XtalOptimizer_refine_rotation_axis") {
 
 // --- helpers for lattice sanity tests ---
 #include <Eigen/Dense>
-
-namespace {
-Eigen::Vector3d to_eigen(const Coord& v) {
-    return {v[0], v[1], v[2]};
-}
-
-double angle_rad(const Eigen::Vector3d& a, const Eigen::Vector3d& b) {
-    const double na = a.norm();
-    const double nb = b.norm();
-    if (na == 0.0 || nb == 0.0)
-        return 0.0;
-    double c = a.dot(b) / (na * nb);
-    c = std::max(-1.0, std::min(1.0, c));
-    return std::acos(c);
-}
-
-// Compare two lattices up to a global rotation: compare Gram matrices G = L^T L (rotation-invariant).
-Eigen::Matrix3d gram(const CrystalLattice& latt) {
-    const Eigen::Vector3d A = to_eigen(latt.Vec0());
-    const Eigen::Vector3d B = to_eigen(latt.Vec1());
-    const Eigen::Vector3d C = to_eigen(latt.Vec2());
-    Eigen::Matrix3d G;
-    G(0,0) = A.dot(A); G(0,1) = A.dot(B); G(0,2) = A.dot(C);
-    G(1,0) = B.dot(A); G(1,1) = B.dot(B); G(1,2) = B.dot(C);
-    G(2,0) = C.dot(A); G(2,1) = C.dot(B); G(2,2) = C.dot(C);
-    return G;
-}
-
-    void check_gram_close(const CrystalLattice& a,
-                          const CrystalLattice& b,
-                          double abs_eps,
-                          double rel_eps) {
-    const Eigen::Matrix3d Ga = gram(a);
-    const Eigen::Matrix3d Gb = gram(b);
-
-    for (int r = 0; r < 3; ++r) {
-        for (int c = 0; c < 3; ++c) {
-            const double va = Ga(r, c);
-            const double vb = Gb(r, c);
-
-            // Scale for relative error; avoid blowing up around zero.
-            const double scale = std::max({1.0, std::abs(va), std::abs(vb)});
-            const double tol = std::max(abs_eps, rel_eps * scale);
-
-            INFO("G(" << r << "," << c << ") va=" << va << " vb=" << vb
-                      << " scale=" << scale << " tol=" << tol);
-
-            CHECK(va == Catch::Approx(vb).margin(tol));
-        }
-    }
-}
-} // namespace
-
-TEST_CASE("XtalOptimizer Lattice param roundtrip (GS) preserves Gram matrix") {
-    // Non-orthogonal, irregular basis, but still a valid lattice
-    CrystalLattice latt_i(Coord(40,  1,  2),
-                          Coord( 3, 50, -4),
-                          Coord(-5,  6, 80));
-
-    double rod[3]{}, lengths[3]{};
-    LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
-    auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, M_PI/2, M_PI/2);
-
-    // This parametrization only keeps "lengths + rotation", i.e. it cannot reproduce shear.
-    // So we *do not* compare Gram matrices here.
-    // Instead, sanity-check: reconstructed vectors have the requested lengths.
-    CHECK(latt_o.Vec0().Length() == Catch::Approx(lengths[0]).margin(1e-9));
-    CHECK(latt_o.Vec1().Length() == Catch::Approx(lengths[1]).margin(1e-9));
-    CHECK(latt_o.Vec2().Length() == Catch::Approx(lengths[2]).margin(1e-9));
-}
-
-TEST_CASE("XtalOptimizer Lattice param roundtrip (Hex) preserves unit cell") {
-    Coord a = Coord(40, 0, 0);
-    Coord b = Coord(40 / 2.0, 40 * std::sqrt(3) / 2.0, 0);
-    Coord c = Coord(0, 0, 70);
-
-    // Apply an arbitrary rotation to ensure the rod extraction is meaningful
-    RotMatrix R(1.0, Coord(0, 1, 1));
-    CrystalLattice latt_i(R * a, R * b, R * c);
-
-    double rod[3]{}, ac[3]{};
-    LatticeToRodriguesAndLengths_Hex(latt_i, rod, ac);
-    auto latt_o = AngleAxisAndCellToLattice(rod, ac, M_PI/2, M_PI/2, 2*M_PI/3);
-
-    auto uc_o = latt_o.GetUnitCell();
-    CHECK(uc_o.a == Catch::Approx(40.0).margin(1e-6));
-    CHECK(uc_o.b == Catch::Approx(40.0).margin(1e-6));
-    CHECK(uc_o.c == Catch::Approx(70.0).margin(1e-6));
-    CHECK(uc_o.alpha == Catch::Approx(90.0).margin(1e-6));
-    CHECK(uc_o.beta  == Catch::Approx(90.0).margin(1e-6));
-    CHECK(uc_o.gamma == Catch::Approx(120.0).margin(1e-6));
-}
-
-TEST_CASE("XtalOptimizer Monoclinic param roundtrip") {
-    struct Case { double beta_deg; };
-    const std::vector<Case> cases = {
-        {60.0}, {75.0}, {115.0}, {130.0}
-    };
-
-    for (const auto& cs : cases) {
-        INFO("beta_deg=" << cs.beta_deg);
-
-        // Start from a clean monoclinic cell in its conventional setting (unique axis b).
-        CrystalLattice latt0(50, 60, 70, 90, cs.beta_deg, 90);
-
-        // Now apply a TRUE global rotation: rotate each basis vector (left-multiply).
-        RotMatrix R(0.7, Coord(0.3, 0.9, 0.1));
-        CrystalLattice latt_i(R * latt0.Vec0(),
-                              R * latt0.Vec1(),
-                              R * latt0.Vec2());
-
-        double rod[3]{}, lengths[3]{}, beta_rad = 0.0;
-        LatticeToRodriguesLengthsBeta_Mono(latt_i, rod, lengths, beta_rad);
-
-        // Basic sanity
-        CHECK(lengths[0] == Catch::Approx(50.0).margin(1e-6));
-        CHECK(lengths[1] == Catch::Approx(60.0).margin(1e-6));
-        CHECK(lengths[2] == Catch::Approx(70.0).margin(1e-6));
-        CHECK(beta_rad * 180.0 / M_PI == Catch::Approx(cs.beta_deg).margin(1e-6));
-
-        auto latt_o = AngleAxisAndCellToLattice(rod, lengths, M_PI/2, beta_rad, M_PI/2);
-
-        // Rotation-invariant check: Gram matrices match.
-        check_gram_close(latt_i, latt_o, /*abs_eps=*/5e-4, /*rel_eps=*/1e-10);
-
-        // Also check the unit-cell angles we expect for monoclinic(unique b).
-        auto uc_o = latt_o.GetUnitCell();
-        CHECK(uc_o.alpha == Catch::Approx(90.0).margin(1e-4));
-        CHECK(uc_o.gamma == Catch::Approx(90.0).margin(1e-4));
-        CHECK(uc_o.beta  == Catch::Approx(cs.beta_deg).margin(1e-4));
-    }
-}
-
-TEST_CASE("XtalOptimizer Monoclinic beta geometry: extracted beta equals angle(a,c)") {
-    // This isolates only the beta definition, independent of other choices.
-    CrystalLattice latt_i(50, 60, 70, 90, 130, 90);
-
-    const Eigen::Vector3d A = to_eigen(latt_i.Vec0());
-    const Eigen::Vector3d C = to_eigen(latt_i.Vec2());
-    const double beta_geom = angle_rad(A, C);
-
-    double rod[3]{}, lengths[3]{}, beta_rad = 0.0;
-    LatticeToRodriguesLengthsBeta_Mono(latt_i, rod, lengths, beta_rad);
-
-    CHECK(beta_rad == Catch::Approx(beta_geom).margin(1e-12));
-}
-- 
2.52.0


From 9a991b6614d81cb5cf7e5c46753e4687d228f325 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 11:59:48 +0200
Subject: [PATCH 003/228] PixelRefine: Work in progress

---
 .../pixel_refinement/CMakeLists.txt           |   2 +-
 .../pixel_refinement/PixelRefine.cpp          | 317 ++++++++++++++----
 image_analysis/pixel_refinement/PixelRefine.h |  14 +-
 3 files changed, 257 insertions(+), 76 deletions(-)

diff --git a/image_analysis/pixel_refinement/CMakeLists.txt b/image_analysis/pixel_refinement/CMakeLists.txt
index 5d5e3c6c..5eb253dc 100644
--- a/image_analysis/pixel_refinement/CMakeLists.txt
+++ b/image_analysis/pixel_refinement/CMakeLists.txt
@@ -1,2 +1,2 @@
 ADD_LIBRARY(JFJochPixelRefine PixelRefine.cpp PixelRefine.h)
-TARGET_LINK_LIBRARIES(JFJochPixelRefine JFJochBraggPrediction JFJochCommon ceres_static)
+TARGET_LINK_LIBRARIES(JFJochPixelRefine JFJochBraggPrediction JFJochCommon JFJochScaleMerge ceres_static)
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 1e547b08..fe1d2089 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -7,78 +7,177 @@
 #include <ceres/rotation.h>
 
 
-
-
-struct PixelRefineResidual {
-    ScalingPostRefResidual(int32_t h, int32_t k, int32_t l,
-                           double x, double y,
-                           double Itrue,
-                           const DiffractionGeometry &geometry,
-                           const CrystalLattice &lattice)
-    :
-          integration_center_x(r.predicted_x),
-          integration_center_y(r.predicted_y),
-          inv_lambda(SafeInv(geometry.GetWavelength_A(), 0.0)),
-          pixel_size(geometry.GetPixelSize_mm()),
-          det_dist_mm(geometry.GetDetectorDistance_mm()),
-          beam_x(geometry.GetBeamX_pxl()),
-          beam_y(geometry.GetBeamY_pxl()),
-          exp_h(r.h),
-          exp_k(r.k),
-          exp_l(r.l),
-          Astar(lattice.Astar()),
-          Bstar(lattice.Bstar()),
-          Cstar(lattice.Cstar()),
-          c1(std::cos(geometry.GetPoniRot1_rad())),
-          s1(std::sin(geometry.GetPoniRot1_rad())),
-          c2(std::cos(geometry.GetPoniRot2_rad())),
-          s2(std::sin(geometry.GetPoniRot2_rad())) {
+struct PixelResidual {
+    // Assume that Itrue and Ibkg are already corrected with solid angle and polarization correction
+    PixelResidual(double x, double y,
+                  double Itrue, double Iobs,
+                  double Ibkg, double Ibkg_sigma,
+                  double lambda,
+                  double pixel_size,
+                  double angle_rad,
+                  double exp_h, double exp_k,
+                  double exp_l,
+                  gemmi::CrystalSystem symmetry)
+        : Itrue(Itrue), Iobs(Iobs),
+          Ibkg(Ibkg), Ibkg_sigma(Ibkg_sigma), obs_x(x),
+          obs_y(y),
+          inv_lambda(1.0 / lambda),
+          pixel_size(pixel_size),
+          exp_h(exp_h),
+          exp_k(exp_k),
+          exp_l(exp_l),
+          angle_rad(angle_rad),
+          symmetry(symmetry) {
+        if (std::fabs(lambda) < 1e-6)
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "Lambda cannot be close to zero");
     }
 
-    template <typename T>
-    T CalcPartiality(const T *const R,
-                    const T *const beam_corr,
-                    const T *const p0) const {
+    template<typename T>
+    bool operator()(const T *const beam,
+                    const T *const distance_mm,
+                    const T *const detector_rot,
+                    const T *const rotation_axis,
+                    const T *const p0,
+                    const T *const p1,
+                    const T *const p2,
+                    const T *const scale_factor,
+                    const T *const B,
+                    const T *const R,
+                    T *residual) const {
+        // PyFAI convention (left-handed for rot1/rot2):
+        // poni_rot = Rz(-rot3) * Rx(-rot2) * Ry(+rot1)
+        // detector_rot[0] = rot1, detector_rot[1] = rot2 (rot3 = 0 assumed)
+
+        const T rot1 = detector_rot[0];
+        const T rot2 = detector_rot[1];
+
+        // Ry(+rot1): rotation around Y-axis
+        const T c1 = ceres::cos(rot1);
+        const T s1 = ceres::sin(rot1);
+
+        // Rx(-rot2): rotation around X-axis with inverted sign (PyFAI left-handed)
+        const T c2 = ceres::cos(rot2);
+        const T s2 = ceres::sin(rot2);
+
         // Detector coordinates in mm
-        const T det_x = (T(integration_center_x) - beam_x - beam_corr[0]) * T(pixel_size);
-        const T det_y = (T(integration_center_y) - beam_y - beam_corr[1]) * T(pixel_size);
-        const T det_z = T(det_dist_mm);
+        const T det_x = (T(obs_x) - beam[0]) * T(pixel_size);
+        const T det_y = (T(obs_y) - beam[1]) * T(pixel_size);
+        const T det_z = T(distance_mm[0]);
 
         // Apply Ry(rot1) first: rotate around Y
-        const T t1_x = T(c1) * det_x + T(s1) * det_z;
+        const T t1_x = c1 * det_x + s1 * det_z;
         const T t1_y = det_y;
-        const T t1_z = T(-s1) * det_x + T(c1) * det_z;
+        const T t1_z = -s1 * det_x + c1 * det_z;
 
         // Then apply Rx(-rot2): rotate around X
         const T x = t1_x;
-        const T y = T(c2) * t1_y + T(s2) * t1_z;
-        const T z = - T(s2) * t1_y + T(c2) * t1_z;
+        const T y = c2 * t1_y + s2 * t1_z;
+        const T z = -s2 * t1_y + c2 * t1_z;
 
         // convert to recip space
         const T lab_norm = ceres::sqrt(x * x + y * y + z * z);
         const T inv_norm = T(1) / lab_norm;
 
+        T recip_raw[3];
+        recip_raw[0] = x * inv_norm * T(inv_lambda);
+        recip_raw[1] = y * inv_norm * T(inv_lambda);
+        recip_raw[2] = (z * inv_norm - T(1.0)) * T(inv_lambda);
+
+        // Apply goniometer "back-to-start" rotation:
+        // brings observed reciprocal from image orientation into reference crystal frame
+        const T aa_back[3] = {
+            T(angle_rad) * rotation_axis[0],
+            T(angle_rad) * rotation_axis[1],
+            T(angle_rad) * rotation_axis[2]
+        };
+
         T recip_obs[3];
-        recip_obs[0] = x * inv_norm * inv_lambda;
-        recip_obs[1] = y * inv_norm * inv_lambda;
-        recip_obs[2] = (z * inv_norm - T(1.0)) * inv_lambda;
+        ceres::AngleAxisRotatePoint(aa_back, recip_raw, recip_obs);
 
         const Eigen::Matrix<T, 3, 1> e_obs_recip(recip_obs[0], recip_obs[1], recip_obs[2]);
 
-        const T astar_unrot[3] = {T(Astar.x), T(Astar.y), T(Astar.z)};
-        const T bstar_unrot[3] = {T(Bstar.x), T(Bstar.y), T(Bstar.z)};
-        const T cstar_unrot[3] = {T(Cstar.x), T(Cstar.y), T(Cstar.z)};
+        // Build unit cell lengths and B (convention: columns are a, b, c prior to global rotation)
+        Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
+        Eigen::Matrix<T, 3, 3> B = Eigen::Matrix<T, 3, 3>::Identity();
 
-        T astar_rot[3], bstar_rot[3], cstar_rot[3];
+        if (symmetry == gemmi::CrystalSystem::Hexagonal) {
+            e_uc_len << p1[0], p1[0], p1[2];
+            B(0, 1) = T(-0.5); // cos(120)
+            B(1, 1) = T(sqrt(3.0) / 2.0); // sin(120)
+        } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
+            e_uc_len << p1[0], p1[1], p1[2];
+        } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
+            e_uc_len << p1[0], p1[0], p1[2];
+        } else if (symmetry == gemmi::CrystalSystem::Cubic) {
+            e_uc_len << p1[0], p1[0], p1[0];
+        } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
+            // Unique axis b: alpha = gamma = 90°, beta free (angle between a and c)
+            e_uc_len << p1[0], p1[1], p1[2];
+            B(0, 2) = ceres::cos(p2[0]);
+            B(2, 2) = ceres::sin(p2[0]);
+        } else {
+            // Triclinic: p1 = (a,b,c), p2 = (alpha, beta, gamma) in radians
+            const T ca = ceres::cos(p2[0]);
+            const T cb = ceres::cos(p2[1]);
+            const T cg = ceres::cos(p2[2]);
+            const T sg = ceres::sin(p2[2]);
 
-        ceres::AngleAxisRotatePoint(p0, astar_unrot, astar_rot);
-        ceres::AngleAxisRotatePoint(p0, bstar_unrot, bstar_rot);
-        ceres::AngleAxisRotatePoint(p0, cstar_unrot, cstar_rot);
+            e_uc_len << p1[0], p1[1], p1[2];
 
-        const Eigen::Matrix<T, 3, 1> e_pred_recip(T(exp_h) * astar_rot[0] + T(exp_k) * bstar_rot[0] + T(exp_l) * cstar_rot[0],
-            T(exp_h) * astar_rot[1] + T(exp_k) * bstar_rot[1] + T(exp_l) * cstar_rot[1],
-            T(exp_h) * astar_rot[2] + T(exp_k) * bstar_rot[2] + T(exp_l) * cstar_rot[2]
-        );
+            B(0, 0) = T(1);
+            B(1, 0) = T(0);
+            B(2, 0) = T(0);
+            B(0, 1) = cg;
+            B(1, 1) = sg;
+            B(2, 1) = T(0);
+
+            // c vector components:
+            const T cx = cb;
+            const T cy = (ca - cb * cg) / sg;
+            const T v = T(1) - cx * cx - cy * cy;
+            const T cz = (v >= T(0)) ? ceres::sqrt(v) : T(0);
+
+            B(0, 2) = cx;
+            B(1, 2) = cy;
+            B(2, 2) = cz;
+        }
+
+        // Build unrotated direct lattice columns: (B * D), then rotate them by p0.
+        // This avoids AngleAxisToRotationMatrix + matrix multiplications.
+        const T L0 = e_uc_len[0];
+        const T L1 = e_uc_len[1];
+        const T L2 = e_uc_len[2];
+
+        T col0_unrot[3] = {B(0, 0) * L0, B(1, 0) * L0, B(2, 0) * L0};
+        T col1_unrot[3] = {B(0, 1) * L1, B(1, 1) * L1, B(2, 1) * L1};
+        T col2_unrot[3] = {B(0, 2) * L2, B(1, 2) * L2, B(2, 2) * L2};
+
+        T col0_rot[3], col1_rot[3], col2_rot[3];
+        ceres::AngleAxisRotatePoint(p0, col0_unrot, col0_rot);
+        ceres::AngleAxisRotatePoint(p0, col1_unrot, col1_rot);
+        ceres::AngleAxisRotatePoint(p0, col2_unrot, col2_rot);
+
+        const Eigen::Matrix<T, 3, 1> A(col0_rot[0], col0_rot[1], col0_rot[2]);
+        const Eigen::Matrix<T, 3, 1> Bv(col1_rot[0], col1_rot[1], col1_rot[2]);
+        const Eigen::Matrix<T, 3, 1> C(col2_rot[0], col2_rot[1], col2_rot[2]);
+
+        const Eigen::Matrix<T, 3, 1> BxC = Bv.cross(C);
+        const Eigen::Matrix<T, 3, 1> CxA = C.cross(A);
+        const Eigen::Matrix<T, 3, 1> AxB = A.cross(Bv);
+
+        const T V = A.dot(BxC);
+        const T invV = T(1) / V;
+
+        const Eigen::Matrix<T, 3, 1> Astar = BxC * invV;
+        const Eigen::Matrix<T, 3, 1> Bstar = CxA * invV;
+        const Eigen::Matrix<T, 3, 1> Cstar = AxB * invV;
+
+        const T h = T(exp_h);
+        const T k = T(exp_k);
+        const T l = T(exp_l);
+
+        const Eigen::Matrix<T, 3, 1> e_pred_recip = Astar * h + Bstar * k + Cstar * l;
 
         // Ewald sphere centre is at -k_i = (0, 0, -inv_lambda)
         // Radial direction: outward normal at g_hkl
@@ -99,35 +198,109 @@ struct PixelRefineResidual {
         const T eps_tangential_sq = dq_tang.squaredNorm();   // guaranteed ≥ 0
         // ─────────────────────────────────────────────────────────────
 
-        return ceres::exp(- eps_radial * eps_radial / (R[0] * R[0]) - eps_tangential_sq / (R[1] * R[1]));
-    }
+        const T B_term = ceres::exp(- B[0] * e_pred_recip.squaredNorm() / 4.0);
 
-    template<typename T>
-    bool operator()(const T *const G,
-                    const T *const B,
-                    const T *const R,
-                    const T *const beam_corr,
-                    const T *const p0,
-                    T *residual) const {
-        if (R[0] < T(1e-10) || R[1] < T(1e-10))
-            return false;
+        // Need to normalize by R[0] and R[1]
+        const T partiality = ceres::exp(- eps_radial * eps_radial / (R[0] * R[0]) - eps_tangential_sq / (R[1] * R[1]));
 
-        const T B_term = ceres::exp(B[0] * T(b_resolution_coeff));
+        const T Ipred = partiality * Itrue * scale_factor[0] * B_term - Ibkg;
+
+        // Need to weight by sigma
+        // I would like to use sigma based on Ipred and Ibkg_sigma - need to come up with a better approach
+        residual[0] = (Ipred - Iobs) / Ibkg_sigma;
 
-        const T partiality = CalcPartiality(R, beam_corr, p0);
-        residual[0] = (G[0] * partiality * B_term * T(lp) * T(Itrue)
-                       - T(Iobs)) * T(weight);
         return true;
     }
 
-    const double integration_center_x, integration_center_y;
+    const double Itrue, Iobs, Ibkg, Ibkg_sigma;
+    const double obs_x, obs_y;
     const double inv_lambda;
     const double pixel_size;
-    const double det_dist_mm;
-    const double beam_x, beam_y;
     const double exp_h;
     const double exp_k;
     const double exp_l;
-    const Coord Astar, Bstar, Cstar;
-    const double c1,s1,c2,s2;
-};
\ No newline at end of file
+    const double angle_rad;
+    gemmi::CrystalSystem symmetry;
+};
+
+PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
+                         const AzimuthalIntegrationMapping &mapping,
+                         const std::vector<MergedReflection> &reference,
+                         BraggPrediction &prediction)
+    : prediction(prediction),
+      mapping(mapping),
+      xpixel(experiment.GetXPixelsNum()),
+      ypixel(experiment.GetYPixelsNum()),
+      experiment(experiment),
+      hkl_key_generator(experiment.GetScalingSettings().GetMergeFriedel(),
+                        experiment.GetSpaceGroupNumber().value_or(1)) {
+    for (const auto &ref: reference)
+        reference_data[hkl_key_generator(ref)] = ref.I;
+}
+
+template<class T>
+void PixelRefine::Run(const T *image,
+         const AzimuthalIntegrationProfile &profile,
+         PixelRefineData &data) {
+
+    ceres::Problem problem;
+
+    // We predict reflections based on initial geometry and default settings
+    // To be tuned later
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .max_hkl = 100,
+        .centering = data.centering
+    };
+    prediction.Calc(experiment, data.latt, settings_prediction);
+
+    auto azim_result = profile.GetResult();
+    auto azim_std = profile.GetStd();
+
+    // For each reflection we select some area (3-5 pixels around it)
+    const int radius = 3;
+
+    for (const auto &refl : prediction.GetReflections()) {
+        auto hkl = hkl_key_generator(refl);
+        // We only handle reflections that are present in the reference set
+        if (!reference_data.contains(hkl))
+            continue;
+        const double I_true = reference_data[hkl];
+
+        int min_y = std::max<int>(refl.predicted_y - radius, 0);
+        int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
+        int min_x = std::max<int>(refl.predicted_x - radius, 0);
+        int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+
+        for (int y = min_y; y <= max_y; ++y) {
+            for (int x = min_x; x <= max_x; ++x) {
+                const size_t npixel = xpixel * y + x;
+                int azim_bin = mapping.GetPixelToBin()[npixel];
+                // If pixel is not mapped to azimuthal bin
+                // or pixel has special value (lowest/highest integer)
+                // it should be ignored for the purpose of this try
+                // We should check if pixel mask is needed, but for most workflows it is already applied
+
+                if (azim_bin >= mapping.GetAzimuthalBinCount())
+                    continue;
+                if (image[npixel] == std::numeric_limits<T>::max())
+                    continue;
+                if (std::is_signed_v<T>() && (image[npixel] == std::numeric_limits<T>::min()))
+                    continue;
+
+                // Get per-pixel polarization and solid angle correction for the pixel from the AzimuthalIntegrationMapping
+                // Warning! this is missing Lorentz correction, but we don't worry at the moment about it
+                // Important is -> this correction is also applied to background, so we must be consistent here
+                float correction = mapping.Corrections()[npixel];
+
+                // Get mean pixel value for background in the azimuthal bin + sigma
+                float bkg_value = azim_result[azim_bin];
+                float bkg_sigma = azim_std[azim_bin];
+                float pixel_value = image[npixel];
+
+
+            }
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 1610ea9c..1ee0a9f1 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -6,6 +6,8 @@
 #include "../bragg_prediction/BraggPrediction.h"
 #include "../common/DiffractionExperiment.h"
 #include "../common/AzimuthalIntegrationMapping.h"
+#include "../common/AzimuthalIntegrationProfile.h"
+#include "../scale_merge/HKLKey.h"
 
 struct PixelRefineData {
     DiffractionGeometry geom;
@@ -25,12 +27,18 @@ class PixelRefine {
     BraggPrediction &prediction;
     const AzimuthalIntegrationMapping &mapping;
     const size_t xpixel, ypixel;
+    const DiffractionExperiment &experiment;
 
+    const HKLKeyGenerator hkl_key_generator;
+    std::map<HKLKey, double> reference_data;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
-                const AzimuthalIntegrationMapping &mapping;
+                const AzimuthalIntegrationMapping &mapping,
+                const std::vector<MergedReflection> &reference,
                 BraggPrediction &prediction);
 
-    template <class T>
-    void Run(const T *image, PixelRefineData &data);
+    template<class T>
+    void Run(const T *image,
+             const AzimuthalIntegrationProfile &profile,
+             PixelRefineData &data);
 };
-- 
2.52.0


From 66a48c426637ac4704ac95d3195a1e946e709aee Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 12:43:10 +0200
Subject: [PATCH 004/228] PixelRefine: Work in progress (Claude)

---
 .../pixel_refinement/CMakeLists.txt           |   2 +-
 .../pixel_refinement/PixelRefine.cpp          | 589 ++++++++++++++----
 image_analysis/pixel_refinement/PixelRefine.h |  32 +-
 3 files changed, 488 insertions(+), 135 deletions(-)

diff --git a/image_analysis/pixel_refinement/CMakeLists.txt b/image_analysis/pixel_refinement/CMakeLists.txt
index 5eb253dc..5e94b562 100644
--- a/image_analysis/pixel_refinement/CMakeLists.txt
+++ b/image_analysis/pixel_refinement/CMakeLists.txt
@@ -1,2 +1,2 @@
 ADD_LIBRARY(JFJochPixelRefine PixelRefine.cpp PixelRefine.h)
-TARGET_LINK_LIBRARIES(JFJochPixelRefine JFJochBraggPrediction JFJochCommon JFJochScaleMerge ceres_static)
+TARGET_LINK_LIBRARIES(JFJochPixelRefine JFJochBraggPrediction JFJochCommon JFJochScaleMerge JFJochGeomRefinement ceres_static)
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index fe1d2089..e734516c 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -3,79 +3,114 @@
 
 #include "PixelRefine.h"
 
+#include <Eigen/Dense>
 #include <ceres/ceres.h>
 #include <ceres/rotation.h>
 
+#include "../geom_refinement/LatticeReduction.h"
 
+namespace {
+
+// Per-pixel observation, in *corrected* intensity units (solid-angle and
+// polarization correction already folded in, consistently for signal and
+// background). Geometry-independent quantities are precomputed here so that the
+// Ceres cost functor stays cheap.
+struct PixelObs {
+    double x, y;          // detector pixel coordinate
+    double Iobs;          // corrected pixel value (signal + background)
+    double Ibkg;          // corrected background estimate (azimuthal bin mean)
+    double weight;        // 1 / sigma_pixel
+    double A_recip;       // reciprocal-space area subtended by the pixel (Jacobian)
+    double angle_rad;     // goniometer angle of this observation
+};
+
+// One reflection together with the pixels of its shoebox.
+struct ReflGroup {
+    int h, k, l;
+    double d;
+    double Itrue;             // reference intensity (held fixed)
+    double predicted_x, predicted_y;
+    std::vector<PixelObs> pixels;
+};
+
+double SafeInv(double x, double fallback) {
+    if (!std::isfinite(x) || std::fabs(x) < 1e-30)
+        return fallback;
+    return 1.0 / x;
+}
+
+} // namespace
+
+// ---------------------------------------------------------------------------
+// Cost functor
+//
+//   I_pred(pixel) = G * Itrue * B_term * P_radial * P_tangential + I_bkg
+//
+//   B_term       = exp(-B |q|^2 / 4)                    (Debye-Waller)
+//   P_radial     = exp(-eps_r^2 / R0^2)                 (partiality: fraction of
+//                                                        the mosaic blob on the
+//                                                        Ewald sphere; NOT
+//                                                        normalized, <= 1)
+//   P_tangential = A_recip/(pi R1^2) * exp(-eps_t^2/R1^2)(spatial profile on the
+//                                                        detector, normalized so
+//                                                        that sum over pixels ~ 1)
+//
+// The tangential factor is what makes this "profile fitting": summing
+// I_pred - I_bkg over the shoebox reproduces G * Itrue * B_term * P_radial.
+// The 1/(pi R1^2) normalization is the missing piece that decouples the profile
+// width R1 from the overall scale G.
+// ---------------------------------------------------------------------------
 struct PixelResidual {
-    // Assume that Itrue and Ibkg are already corrected with solid angle and polarization correction
-    PixelResidual(double x, double y,
-                  double Itrue, double Iobs,
-                  double Ibkg, double Ibkg_sigma,
-                  double lambda,
-                  double pixel_size,
-                  double angle_rad,
-                  double exp_h, double exp_k,
-                  double exp_l,
+    PixelResidual(const PixelObs &obs, double Itrue,
+                  double lambda, double pixel_size,
+                  double exp_h, double exp_k, double exp_l,
                   gemmi::CrystalSystem symmetry)
-        : Itrue(Itrue), Iobs(Iobs),
-          Ibkg(Ibkg), Ibkg_sigma(Ibkg_sigma), obs_x(x),
-          obs_y(y),
-          inv_lambda(1.0 / lambda),
-          pixel_size(pixel_size),
-          exp_h(exp_h),
-          exp_k(exp_k),
-          exp_l(exp_l),
-          angle_rad(angle_rad),
-          symmetry(symmetry) {
+        : Itrue(Itrue), Iobs(obs.Iobs), Ibkg(obs.Ibkg), weight(obs.weight),
+          A_recip(obs.A_recip), obs_x(obs.x), obs_y(obs.y),
+          inv_lambda(1.0 / lambda), pixel_size(pixel_size),
+          exp_h(exp_h), exp_k(exp_k), exp_l(exp_l),
+          angle_rad(obs.angle_rad), symmetry(symmetry) {
         if (std::fabs(lambda) < 1e-6)
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Lambda cannot be close to zero");
     }
 
+    // Maps a detector pixel through the current geometry + lattice into the
+    // reference reciprocal frame and returns:
+    //   q_sq        = |g_hkl|^2                 (predicted node, for B-factor)
+    //   eps_radial  = deviation along Ewald normal (partiality direction)
+    //   eps_tang_sq = squared deviation in the detector-tangential plane (profile)
     template<typename T>
-    bool operator()(const T *const beam,
-                    const T *const distance_mm,
-                    const T *const detector_rot,
-                    const T *const rotation_axis,
-                    const T *const p0,
-                    const T *const p1,
-                    const T *const p2,
-                    const T *const scale_factor,
-                    const T *const B,
-                    const T *const R,
-                    T *residual) const {
+    bool GeometryTerms(const T *const beam,
+                       const T *const distance_mm,
+                       const T *const detector_rot,
+                       const T *const rotation_axis,
+                       const T *const p0,
+                       const T *const p1,
+                       const T *const p2,
+                       T &q_sq, T &eps_radial, T &eps_tang_sq) const {
         // PyFAI convention (left-handed for rot1/rot2):
-        // poni_rot = Rz(-rot3) * Rx(-rot2) * Ry(+rot1)
-        // detector_rot[0] = rot1, detector_rot[1] = rot2 (rot3 = 0 assumed)
-
+        // poni_rot = Rz(-rot3) * Rx(-rot2) * Ry(+rot1), rot3 = 0 assumed.
         const T rot1 = detector_rot[0];
         const T rot2 = detector_rot[1];
 
-        // Ry(+rot1): rotation around Y-axis
         const T c1 = ceres::cos(rot1);
         const T s1 = ceres::sin(rot1);
-
-        // Rx(-rot2): rotation around X-axis with inverted sign (PyFAI left-handed)
         const T c2 = ceres::cos(rot2);
         const T s2 = ceres::sin(rot2);
 
-        // Detector coordinates in mm
         const T det_x = (T(obs_x) - beam[0]) * T(pixel_size);
         const T det_y = (T(obs_y) - beam[1]) * T(pixel_size);
         const T det_z = T(distance_mm[0]);
 
-        // Apply Ry(rot1) first: rotate around Y
         const T t1_x = c1 * det_x + s1 * det_z;
         const T t1_y = det_y;
         const T t1_z = -s1 * det_x + c1 * det_z;
 
-        // Then apply Rx(-rot2): rotate around X
         const T x = t1_x;
         const T y = c2 * t1_y + s2 * t1_z;
         const T z = -s2 * t1_y + c2 * t1_z;
 
-        // convert to recip space
         const T lab_norm = ceres::sqrt(x * x + y * y + z * z);
         const T inv_norm = T(1) / lab_norm;
 
@@ -84,27 +119,25 @@ struct PixelResidual {
         recip_raw[1] = y * inv_norm * T(inv_lambda);
         recip_raw[2] = (z * inv_norm - T(1.0)) * T(inv_lambda);
 
-        // Apply goniometer "back-to-start" rotation:
-        // brings observed reciprocal from image orientation into reference crystal frame
+        // Goniometer "back-to-start" rotation: image frame -> reference frame.
         const T aa_back[3] = {
             T(angle_rad) * rotation_axis[0],
             T(angle_rad) * rotation_axis[1],
             T(angle_rad) * rotation_axis[2]
         };
-
         T recip_obs[3];
         ceres::AngleAxisRotatePoint(aa_back, recip_raw, recip_obs);
-
         const Eigen::Matrix<T, 3, 1> e_obs_recip(recip_obs[0], recip_obs[1], recip_obs[2]);
 
-        // Build unit cell lengths and B (convention: columns are a, b, c prior to global rotation)
+        // Build cell lengths and the (unit) B matrix from the symmetry-specific
+        // parametrization (identical convention to XtalOptimizer::XtalResidual).
         Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
-        Eigen::Matrix<T, 3, 3> B = Eigen::Matrix<T, 3, 3>::Identity();
+        Eigen::Matrix<T, 3, 3> Bmat = Eigen::Matrix<T, 3, 3>::Identity();
 
         if (symmetry == gemmi::CrystalSystem::Hexagonal) {
             e_uc_len << p1[0], p1[0], p1[2];
-            B(0, 1) = T(-0.5); // cos(120)
-            B(1, 1) = T(sqrt(3.0) / 2.0); // sin(120)
+            Bmat(0, 1) = T(-0.5);
+            Bmat(1, 1) = T(sqrt(3.0) / 2.0);
         } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
             e_uc_len << p1[0], p1[1], p1[2];
         } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
@@ -112,12 +145,10 @@ struct PixelResidual {
         } else if (symmetry == gemmi::CrystalSystem::Cubic) {
             e_uc_len << p1[0], p1[0], p1[0];
         } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
-            // Unique axis b: alpha = gamma = 90°, beta free (angle between a and c)
             e_uc_len << p1[0], p1[1], p1[2];
-            B(0, 2) = ceres::cos(p2[0]);
-            B(2, 2) = ceres::sin(p2[0]);
+            Bmat(0, 2) = ceres::cos(p2[0]);
+            Bmat(2, 2) = ceres::sin(p2[0]);
         } else {
-            // Triclinic: p1 = (a,b,c), p2 = (alpha, beta, gamma) in radians
             const T ca = ceres::cos(p2[0]);
             const T cb = ceres::cos(p2[1]);
             const T cg = ceres::cos(p2[2]);
@@ -125,33 +156,26 @@ struct PixelResidual {
 
             e_uc_len << p1[0], p1[1], p1[2];
 
-            B(0, 0) = T(1);
-            B(1, 0) = T(0);
-            B(2, 0) = T(0);
-            B(0, 1) = cg;
-            B(1, 1) = sg;
-            B(2, 1) = T(0);
+            Bmat(0, 1) = cg;
+            Bmat(1, 1) = sg;
 
-            // c vector components:
             const T cx = cb;
             const T cy = (ca - cb * cg) / sg;
             const T v = T(1) - cx * cx - cy * cy;
             const T cz = (v >= T(0)) ? ceres::sqrt(v) : T(0);
 
-            B(0, 2) = cx;
-            B(1, 2) = cy;
-            B(2, 2) = cz;
+            Bmat(0, 2) = cx;
+            Bmat(1, 2) = cy;
+            Bmat(2, 2) = cz;
         }
 
-        // Build unrotated direct lattice columns: (B * D), then rotate them by p0.
-        // This avoids AngleAxisToRotationMatrix + matrix multiplications.
         const T L0 = e_uc_len[0];
         const T L1 = e_uc_len[1];
         const T L2 = e_uc_len[2];
 
-        T col0_unrot[3] = {B(0, 0) * L0, B(1, 0) * L0, B(2, 0) * L0};
-        T col1_unrot[3] = {B(0, 1) * L1, B(1, 1) * L1, B(2, 1) * L1};
-        T col2_unrot[3] = {B(0, 2) * L2, B(1, 2) * L2, B(2, 2) * L2};
+        T col0_unrot[3] = {Bmat(0, 0) * L0, Bmat(1, 0) * L0, Bmat(2, 0) * L0};
+        T col1_unrot[3] = {Bmat(0, 1) * L1, Bmat(1, 1) * L1, Bmat(2, 1) * L1};
+        T col2_unrot[3] = {Bmat(0, 2) * L2, Bmat(1, 2) * L2, Bmat(2, 2) * L2};
 
         T col0_rot[3], col1_rot[3], col2_rot[3];
         ceres::AngleAxisRotatePoint(p0, col0_unrot, col0_rot);
@@ -167,58 +191,92 @@ struct PixelResidual {
         const Eigen::Matrix<T, 3, 1> AxB = A.cross(Bv);
 
         const T V = A.dot(BxC);
+        if (ceres::abs(V) < T(1e-12))
+            return false;
         const T invV = T(1) / V;
 
         const Eigen::Matrix<T, 3, 1> Astar = BxC * invV;
         const Eigen::Matrix<T, 3, 1> Bstar = CxA * invV;
         const Eigen::Matrix<T, 3, 1> Cstar = AxB * invV;
 
-        const T h = T(exp_h);
-        const T k = T(exp_k);
-        const T l = T(exp_l);
+        const Eigen::Matrix<T, 3, 1> e_pred_recip =
+            Astar * T(exp_h) + Bstar * T(exp_k) + Cstar * T(exp_l);
 
-        const Eigen::Matrix<T, 3, 1> e_pred_recip = Astar * h + Bstar * k + Cstar * l;
+        q_sq = e_pred_recip.squaredNorm();
 
-        // Ewald sphere centre is at -k_i = (0, 0, -inv_lambda)
-        // Radial direction: outward normal at g_hkl
+        // Ewald sphere centre at -k_i = (0,0,-inv_lambda); radial normal at g_hkl.
         const Eigen::Matrix<T, 3, 1> S_pred(
             e_pred_recip[0],
             e_pred_recip[1],
-            e_pred_recip[2] + T(inv_lambda)   // g_hkl + k_i
-        );
+            e_pred_recip[2] + T(inv_lambda));
         const T S_pred_norm = S_pred.norm();
         if (S_pred_norm < T(1e-10))
-            return T(0);
+            return false;
 
         const Eigen::Matrix<T, 3, 1> n_radial = S_pred / S_pred_norm;
-
         const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-        const T eps_radial        = delta_q.dot(n_radial);
+
+        eps_radial = delta_q.dot(n_radial);
         const Eigen::Matrix<T, 3, 1> dq_tang = delta_q - eps_radial * n_radial;
-        const T eps_tangential_sq = dq_tang.squaredNorm();   // guaranteed ≥ 0
-        // ─────────────────────────────────────────────────────────────
-
-        const T B_term = ceres::exp(- B[0] * e_pred_recip.squaredNorm() / 4.0);
-
-        // Need to normalize by R[0] and R[1]
-        const T partiality = ceres::exp(- eps_radial * eps_radial / (R[0] * R[0]) - eps_tangential_sq / (R[1] * R[1]));
-
-        const T Ipred = partiality * Itrue * scale_factor[0] * B_term - Ibkg;
-
-        // Need to weight by sigma
-        // I would like to use sigma based on Ipred and Ibkg_sigma - need to come up with a better approach
-        residual[0] = (Ipred - Iobs) / Ibkg_sigma;
-
+        eps_tang_sq = dq_tang.squaredNorm();
         return true;
     }
 
-    const double Itrue, Iobs, Ibkg, Ibkg_sigma;
+    // Assembles the full model intensity for the pixel from the geometry terms.
+    template<typename T>
+    bool Model(const T *const beam, const T *const distance_mm,
+               const T *const detector_rot, const T *const rotation_axis,
+               const T *const p0, const T *const p1, const T *const p2,
+               const T *const scale_factor, const T *const B, const T *const R,
+               T &Ipred) const {
+        T q_sq, eps_radial, eps_tang_sq;
+        if (!GeometryTerms(beam, distance_mm, detector_rot, rotation_axis,
+                           p0, p1, p2, q_sq, eps_radial, eps_tang_sq))
+            return false;
+
+        if (R[0] < T(1e-10) || R[1] < T(1e-10))
+            return false;
+
+        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
+        const T P_radial = ceres::exp(-eps_radial * eps_radial / (R[0] * R[0]));
+
+        // Normalized 2D Gaussian profile in the detector-tangential plane,
+        // weighted by the reciprocal-space area of the pixel so that the sum of
+        // the profile over the shoebox is ~1 (intensity-conserving).
+        const T norm_tang = T(A_recip) / (T(M_PI) * R[1] * R[1]);
+        const T P_tang = norm_tang * ceres::exp(-eps_tang_sq / (R[1] * R[1]));
+
+        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
+        Ipred = signal + T(Ibkg);
+        return true;
+    }
+
+    template<typename T>
+    bool operator()(const T *const beam,
+                    const T *const distance_mm,
+                    const T *const detector_rot,
+                    const T *const rotation_axis,
+                    const T *const p0,
+                    const T *const p1,
+                    const T *const p2,
+                    const T *const scale_factor,
+                    const T *const B,
+                    const T *const R,
+                    T *residual) const {
+        T Ipred;
+        if (!Model(beam, distance_mm, detector_rot, rotation_axis,
+                   p0, p1, p2, scale_factor, B, R, Ipred))
+            return false;
+
+        residual[0] = (Ipred - T(Iobs)) * T(weight);
+        return true;
+    }
+
+    const double Itrue, Iobs, Ibkg, weight, A_recip;
     const double obs_x, obs_y;
     const double inv_lambda;
     const double pixel_size;
-    const double exp_h;
-    const double exp_k;
-    const double exp_l;
+    const double exp_h, exp_k, exp_l;
     const double angle_rad;
     gemmi::CrystalSystem symmetry;
 };
@@ -240,13 +298,23 @@ PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
 
 template<class T>
 void PixelRefine::Run(const T *image,
-         const AzimuthalIntegrationProfile &profile,
-         PixelRefineData &data) {
+                      const AzimuthalIntegrationProfile &profile,
+                      PixelRefineData &data) {
+    data.solved = false;
+    data.reflections.clear();
 
-    ceres::Problem problem;
+    const auto geom = data.geom;
+    const double lambda = geom.GetWavelength_A();
+    const double pixel_size = geom.GetPixelSize_mm();
+    const double distance_mm = geom.GetDetectorDistance_mm();
 
-    // We predict reflections based on initial geometry and default settings
-    // To be tuned later
+    // Reciprocal-space area subtended by one pixel (small-angle approximation):
+    // |dq/dpixel| ~ pixel_size / (lambda * distance), so the area is its square.
+    // Used to normalize the tangential profile. Good enough for a prototype; a
+    // proper treatment would use the per-reflection 2-theta dependent Jacobian.
+    const double A_recip = std::pow(pixel_size / (lambda * distance_mm), 2.0);
+
+    // Predict reflection positions with the current lattice/geometry.
     const BraggPredictionSettings settings_prediction{
         .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
         .max_hkl = 100,
@@ -254,53 +322,316 @@ void PixelRefine::Run(const T *image,
     };
     prediction.Calc(experiment, data.latt, settings_prediction);
 
-    auto azim_result = profile.GetResult();
-    auto azim_std = profile.GetStd();
+    const auto azim_result = profile.GetResult();
+    const auto azim_std = profile.GetStd();
+    const auto &pixel_to_bin = mapping.GetPixelToBin();
+    const auto &corrections = mapping.Corrections();
+    const int azim_bin_count = mapping.GetAzimuthalBinCount();
 
-    // For each reflection we select some area (3-5 pixels around it)
-    const int radius = 3;
+    const double angle_rad = data.angle_deg * M_PI / 180.0;
+    const int radius = data.shoebox_radius;
 
+    // ---- Collect per-reflection shoebox pixels --------------------------------
+    std::vector<ReflGroup> groups;
     for (const auto &refl : prediction.GetReflections()) {
-        auto hkl = hkl_key_generator(refl);
-        // We only handle reflections that are present in the reference set
+        const auto hkl = hkl_key_generator(refl);
         if (!reference_data.contains(hkl))
             continue;
-        const double I_true = reference_data[hkl];
 
-        int min_y = std::max<int>(refl.predicted_y - radius, 0);
-        int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
-        int min_x = std::max<int>(refl.predicted_x - radius, 0);
-        int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+        ReflGroup g;
+        g.h = refl.h;
+        g.k = refl.k;
+        g.l = refl.l;
+        g.d = refl.d;
+        g.Itrue = reference_data[hkl];
+        g.predicted_x = refl.predicted_x;
+        g.predicted_y = refl.predicted_y;
+
+        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
+        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
+        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
+        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
 
         for (int y = min_y; y <= max_y; ++y) {
             for (int x = min_x; x <= max_x; ++x) {
                 const size_t npixel = xpixel * y + x;
-                int azim_bin = mapping.GetPixelToBin()[npixel];
-                // If pixel is not mapped to azimuthal bin
-                // or pixel has special value (lowest/highest integer)
-                // it should be ignored for the purpose of this try
-                // We should check if pixel mask is needed, but for most workflows it is already applied
+                const int azim_bin = pixel_to_bin[npixel];
 
-                if (azim_bin >= mapping.GetAzimuthalBinCount())
+                // Skip pixels not mapped to an azimuthal bin or carrying a
+                // sentinel (masked / saturated) value. We assume the pixel mask
+                // is already applied upstream.
+                if (azim_bin >= azim_bin_count)
                     continue;
                 if (image[npixel] == std::numeric_limits<T>::max())
                     continue;
-                if (std::is_signed_v<T>() && (image[npixel] == std::numeric_limits<T>::min()))
+                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
                     continue;
 
-                // Get per-pixel polarization and solid angle correction for the pixel from the AzimuthalIntegrationMapping
-                // Warning! this is missing Lorentz correction, but we don't worry at the moment about it
-                // Important is -> this correction is also applied to background, so we must be consistent here
-                float correction = mapping.Corrections()[npixel];
-
-                // Get mean pixel value for background in the azimuthal bin + sigma
-                float bkg_value = azim_result[azim_bin];
-                float bkg_sigma = azim_std[azim_bin];
-                float pixel_value = image[npixel];
+                const double correction = corrections[npixel];
+                const double Ibkg = azim_result[azim_bin] * 1.0; // already corrected units
+                const double Ibkg_sigma = azim_std[azim_bin];
+                const double raw = static_cast<double>(image[npixel]);
+                const double Iobs = raw * correction;
 
+                // Per-pixel variance: Poisson noise of the corrected counts
+                // (var(c*N) = c^2 * N = c * Iobs) plus the background spread.
+                double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
+                if (!(var > 1.0))
+                    var = 1.0;
 
+                PixelObs obs{
+                    .x = static_cast<double>(x),
+                    .y = static_cast<double>(y),
+                    .Iobs = Iobs,
+                    .Ibkg = Ibkg,
+                    .weight = 1.0 / std::sqrt(var),
+                    .A_recip = A_recip,
+                    .angle_rad = angle_rad
+                };
+                g.pixels.push_back(obs);
             }
         }
+
+        if (!g.pixels.empty())
+            groups.push_back(std::move(g));
+    }
+
+    if (groups.empty())
+        return;
+
+    // ---- Set up parameter blocks (mirrors XtalOptimizer for the geometry part) -
+    double beam[2] = {geom.GetBeamX_pxl(), geom.GetBeamY_pxl()};
+    double dist_mm = distance_mm;
+    double detector_rot[2] = {geom.GetPoniRot1_rad(), geom.GetPoniRot2_rad()};
+    double rot_vec[3] = {1.0, 0.0, 0.0};
+    if (auto axis = geom.GetRotation()) {
+        rot_vec[0] = axis->GetAxis().x;
+        rot_vec[1] = axis->GetAxis().y;
+        rot_vec[2] = axis->GetAxis().z;
+    }
+
+    double latt_vec0[3] = {0, 0, 0}; // orientation (Rodrigues)
+    double latt_vec1[3] = {0, 0, 0}; // lengths
+    double latt_vec2[3] = {0, 0, 0}; // angles (rad)
+    double beta = data.latt.GetUnitCell().beta;
+
+    switch (data.crystal_system) {
+        case gemmi::CrystalSystem::Orthorhombic:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            break;
+        case gemmi::CrystalSystem::Tetragonal:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
+            break;
+        case gemmi::CrystalSystem::Cubic:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
+            break;
+        case gemmi::CrystalSystem::Hexagonal:
+            LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
+            break;
+        case gemmi::CrystalSystem::Monoclinic:
+            LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
+            latt_vec2[0] = beta;
+            break;
+        default: {
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            const auto uc = data.latt.GetUnitCell();
+            latt_vec2[0] = uc.alpha * M_PI / 180.0;
+            latt_vec2[1] = uc.beta * M_PI / 180.0;
+            latt_vec2[2] = uc.gamma * M_PI / 180.0;
+            break;
+        }
     }
 
-}
\ No newline at end of file
+    ceres::Problem problem;
+
+    for (const auto &g : groups) {
+        for (const auto &obs : g.pixels) {
+            auto *cost = new ceres::AutoDiffCostFunction<
+                PixelResidual, 1, 2, 1, 2, 3, 3, 3, 3, 1, 1, 2>(
+                new PixelResidual(obs, g.Itrue, lambda, pixel_size,
+                                  g.h, g.k, g.l, data.crystal_system));
+            problem.AddResidualBlock(cost, new ceres::HuberLoss(3.0),
+                                     beam, &dist_mm, detector_rot, rot_vec,
+                                     latt_vec0, latt_vec1, latt_vec2,
+                                     &data.scale_factor, &data.B_factor, data.R);
+        }
+    }
+
+    data.residual_count = problem.NumResidualBlocks();
+
+    // ---- Constrain / bound parameter blocks -----------------------------------
+    if (!data.refine_orientation)
+        problem.SetParameterBlockConstant(latt_vec0);
+
+    if (!data.refine_unit_cell) {
+        problem.SetParameterBlockConstant(latt_vec1);
+        problem.SetParameterBlockConstant(latt_vec2);
+    } else {
+        for (int i = 0; i < 3; ++i) {
+            problem.SetParameterLowerBound(latt_vec1, i, 5.0);
+            problem.SetParameterUpperBound(latt_vec1, i, 1000.0);
+        }
+        if (data.crystal_system != gemmi::CrystalSystem::Monoclinic &&
+            data.crystal_system != gemmi::CrystalSystem::Triclinic)
+            problem.SetParameterBlockConstant(latt_vec2);
+    }
+
+    if (!data.refine_beam_center)
+        problem.SetParameterBlockConstant(beam);
+
+    if (!data.refine_distance) {
+        problem.SetParameterBlockConstant(&dist_mm);
+    } else {
+        problem.SetParameterLowerBound(&dist_mm, 0, dist_mm * 0.9);
+        problem.SetParameterUpperBound(&dist_mm, 0, dist_mm * 1.1);
+    }
+
+    if (!data.refine_detector_angles) {
+        problem.SetParameterBlockConstant(detector_rot);
+    } else {
+        const double rng = 3.0 / 180.0 * M_PI;
+        for (int i = 0; i < 2; ++i) {
+            problem.SetParameterLowerBound(detector_rot, i, detector_rot[i] - rng);
+            problem.SetParameterUpperBound(detector_rot, i, detector_rot[i] + rng);
+        }
+    }
+
+    if (!data.refine_rotation_axis)
+        problem.SetParameterBlockConstant(rot_vec);
+
+    if (data.refine_scale)
+        problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
+    else
+        problem.SetParameterBlockConstant(&data.scale_factor);
+
+    if (!data.refine_B)
+        problem.SetParameterBlockConstant(&data.B_factor);
+
+    if (data.refine_R) {
+        problem.SetParameterLowerBound(data.R, 0, 1e-5);
+        problem.SetParameterLowerBound(data.R, 1, 1e-5);
+    } else {
+        problem.SetParameterBlockConstant(data.R);
+    }
+
+    // ---- Solve ----------------------------------------------------------------
+    ceres::Solver::Options options;
+    options.linear_solver_type = ceres::DENSE_QR;
+    options.minimizer_progress_to_stdout = false;
+    options.logging_type = ceres::LoggingType::SILENT;
+    options.max_solver_time_in_seconds = data.max_time_s;
+    options.num_threads = 1;
+
+    ceres::Solver::Summary summary;
+    ceres::Solve(options, &problem, &summary);
+
+    data.final_cost = summary.final_cost;
+    data.solved = summary.IsSolutionUsable();
+
+    // ---- Write back refined geometry + lattice --------------------------------
+    if (data.refine_beam_center)
+        data.geom.BeamX_pxl(beam[0]).BeamY_pxl(beam[1]);
+    if (data.refine_distance)
+        data.geom.DetectorDistance_mm(dist_mm);
+    if (data.refine_detector_angles)
+        data.geom.PoniRot1_rad(detector_rot[0]).PoniRot2_rad(detector_rot[1]);
+
+    if (data.refine_orientation || data.refine_unit_cell) {
+        switch (data.crystal_system) {
+            case gemmi::CrystalSystem::Orthorhombic:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Tetragonal:
+                latt_vec1[1] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Cubic:
+                latt_vec1[1] = latt_vec1[0];
+                latt_vec1[2] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Hexagonal:
+                latt_vec1[1] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
+                break;
+            case gemmi::CrystalSystem::Monoclinic:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
+                break;
+            default:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
+                                                      latt_vec2[0], latt_vec2[1], latt_vec2[2]);
+                break;
+        }
+    }
+
+    // ---- Extract integrated reflections ---------------------------------------
+    // Profile-fitted intensity with the optimized profile P (shape only):
+    //     I = sum_p [ P_p (Iobs_p - Ibkg_p) / v_p ] / sum_p [ P_p^2 / v_p ]
+    //     var(I) = 1 / sum_p [ P_p^2 / v_p ]
+    // where P_p is the *shape* of the model per pixel (signal at G=Itrue=B=1).
+    data.reflections.reserve(groups.size());
+    for (const auto &g : groups) {
+        double num = 0.0, den = 0.0, partiality_sum = 0.0, bkg_sum = 0.0;
+        size_t n = 0;
+
+        for (const auto &obs : g.pixels) {
+            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system);
+            double q_sq, eps_r, eps_t_sq;
+            if (!pr.GeometryTerms(beam, &dist_mm, detector_rot, rot_vec,
+                                  latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                continue;
+            if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
+                continue;
+
+            const double P_radial = std::exp(-eps_r * eps_r / (data.R[0] * data.R[0]));
+            const double norm_tang = obs.A_recip / (M_PI * data.R[1] * data.R[1]);
+            const double P_tang = norm_tang * std::exp(-eps_t_sq / (data.R[1] * data.R[1]));
+            const double P = P_radial * P_tang; // model shape per pixel (unit scale)
+            const double v = SafeInv(obs.weight * obs.weight, 1.0); // pixel variance
+            const double signal = obs.Iobs - obs.Ibkg;
+
+            num += P * signal / v;
+            den += P * P / v;
+            partiality_sum += P_tang;   // tangential profile sums to ~partiality
+            bkg_sum += obs.Ibkg;
+            ++n;
+        }
+
+        Reflection r{};
+        r.h = g.h;
+        r.k = g.k;
+        r.l = g.l;
+        r.d = static_cast<float>(g.d);
+        r.predicted_x = static_cast<float>(g.predicted_x);
+        r.predicted_y = static_cast<float>(g.predicted_y);
+        r.observed_x = NAN;
+        r.observed_y = NAN;
+        r.rlp = 1.0f;
+        r.partiality = static_cast<float>(partiality_sum);
+
+        if (den > 0.0 && n > 0) {
+            const double I = num / den;
+            r.I = static_cast<float>(I);
+            r.sigma = static_cast<float>(std::sqrt(1.0 / den));
+            r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
+            r.observed = true;
+            r.image_scale_corr = (r.partiality > 0.0f) ? r.rlp / r.partiality : NAN;
+        } else {
+            r.I = 0.0f;
+            r.sigma = NAN;
+            r.bkg = 0.0f;
+            r.observed = false;
+        }
+        data.reflections.push_back(r);
+    }
+}
+
+// Explicit instantiations for the supported (uncompressed) image pixel types.
+template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 1ee0a9f1..5848cf15 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -10,17 +10,39 @@
 #include "../scale_merge/HKLKey.h"
 
 struct PixelRefineData {
+    // --- model state (input as initial guess, output as refined result) ---
     DiffractionGeometry geom;
     CrystalLattice latt;
     gemmi::CrystalSystem crystal_system = gemmi::CrystalSystem::Triclinic;
     char centering = 'P';
 
-    double B_factor = 0.0;
-    double scale_factor = 1.0;
-    double R[2] = {0.001, 0.001};
+    double B_factor = 0.0;      // Debye-Waller B (A^2)
+    double scale_factor = 1.0;  // overall scale G
+    double R[2] = {0.005, 0.005}; // R[0] = radial (partiality) width, R[1] = tangential (profile) width (A^-1)
 
-    bool refine_beam_center = false;
-    bool refine_unit_cell = false;
+    // Goniometer: for a still image keep angle_deg = 0. For a wedge, pass the
+    // angle (deg) of the slice centre relative to the reference (phi=0) frame.
+    double angle_deg = 0.0;
+
+    // --- what to refine ---
+    bool refine_orientation     = true;  // crystal orientation (p0)
+    bool refine_unit_cell       = false; // cell lengths + angles
+    bool refine_beam_center     = false;
+    bool refine_distance        = false;
+    bool refine_detector_angles = false;
+    bool refine_rotation_axis   = false;
+    bool refine_scale           = true;
+    bool refine_B               = false;
+    bool refine_R               = true;
+
+    double max_time_s = 5.0;
+    int    shoebox_radius = 3; // half-size of the per-reflection pixel box
+
+    // --- output ---
+    std::vector<Reflection> reflections; // profile-fitted integration result
+    bool   solved = false;
+    double final_cost = NAN;
+    size_t residual_count = 0;
 };
 
 class PixelRefine {
-- 
2.52.0


From 6f6098d5083bfd2d08c413f5c3068066b53e8212 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 13:44:39 +0200
Subject: [PATCH 005/228] PixelRefine: Work in progress (Claude)

---
 .../pixel_refinement/PixelRefine.cpp          | 536 ++++++++++--------
 image_analysis/pixel_refinement/PixelRefine.h |  67 +++
 2 files changed, 360 insertions(+), 243 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index e734516c..63971bf2 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -238,15 +238,27 @@ struct PixelResidual {
             return false;
 
         const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
-        const T P_radial = ceres::exp(-eps_radial * eps_radial / (R[0] * R[0]));
 
-        // Normalized 2D Gaussian profile in the detector-tangential plane,
-        // weighted by the reciprocal-space area of the pixel so that the sum of
-        // the profile over the shoebox is ~1 (intensity-conserving).
-        const T norm_tang = T(A_recip) / (T(M_PI) * R[1] * R[1]);
-        const T P_tang = norm_tang * ceres::exp(-eps_tang_sq / (R[1] * R[1]));
+        // Full 3D reciprocal-space spot density modelled as a separable Gaussian,
+        // normalized so that its integral is 1 (intensity-conserving):
+        //   radial:     g_r(e) = exp(-e^2/R0^2) / (sqrt(pi) R0)     [1/A^-1]
+        //   tangential: g_t(e) = exp(-|e|^2/R1^2) / (pi R1^2)        [1/A^-2]
+        // The detector pixel captures the fraction g_t * A_recip of the tangential
+        // profile (A_recip = reciprocal area the pixel subtends; sum over shoebox
+        // ~ 1). The radial factor is the still-image partiality: how far this
+        // reflection sits from the Ewald sphere.
+        //
+        // Caveat: a still samples the radial direction at a single offset, so the
+        // sqrt(pi) R0 normalization makes g_r a density (1/A^-1) rather than a
+        // dimensionless fraction. The leftover dimensional factor is absorbed by
+        // the free scale G; completing it physically needs an effective radial
+        // sampling width from the energy bandwidth + beam divergence (TODO).
+        const T g_radial = ceres::exp(-eps_radial * eps_radial / (R[0] * R[0]))
+                           / (ceres::sqrt(T(M_PI)) * R[0]);
+        const T P_tang = T(A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
+                         / (T(M_PI) * R[1] * R[1]);
 
-        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
+        const T signal = scale_factor[0] * T(Itrue) * B_term * g_radial * P_tang;
         Ipred = signal + T(Ibkg);
         return true;
     }
@@ -303,24 +315,14 @@ void PixelRefine::Run(const T *image,
     data.solved = false;
     data.reflections.clear();
 
-    const auto geom = data.geom;
-    const double lambda = geom.GetWavelength_A();
-    const double pixel_size = geom.GetPixelSize_mm();
-    const double distance_mm = geom.GetDetectorDistance_mm();
+    const double lambda = data.geom.GetWavelength_A();
+    const double pixel_size = data.geom.GetPixelSize_mm();
 
-    // Reciprocal-space area subtended by one pixel (small-angle approximation):
-    // |dq/dpixel| ~ pixel_size / (lambda * distance), so the area is its square.
-    // Used to normalize the tangential profile. Good enough for a prototype; a
-    // proper treatment would use the per-reflection 2-theta dependent Jacobian.
-    const double A_recip = std::pow(pixel_size / (lambda * distance_mm), 2.0);
-
-    // Predict reflection positions with the current lattice/geometry.
     const BraggPredictionSettings settings_prediction{
         .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
         .max_hkl = 100,
         .centering = data.centering
     };
-    prediction.Calc(experiment, data.latt, settings_prediction);
 
     const auto azim_result = profile.GetResult();
     const auto azim_std = profile.GetStd();
@@ -331,249 +333,295 @@ void PixelRefine::Run(const T *image,
     const double angle_rad = data.angle_deg * M_PI / 180.0;
     const int radius = data.shoebox_radius;
 
-    // ---- Collect per-reflection shoebox pixels --------------------------------
+    // Exact reciprocal-space area a 1x1 pixel subtends, |dq/dx x dq/dy|, via
+    // finite differences of the detector->reciprocal map. This is the Jacobian
+    // between the curved Ewald-sphere sampling and flat reciprocal space, and it
+    // is exactly the geometric factor that plays the role of the Lorentz factor
+    // for stills: where the sphere grazes reciprocal space obliquely, a pixel
+    // covers more reciprocal volume and the captured fraction grows. It tracks
+    // the refined geometry because it reads the current data.geom each iteration.
+    auto recip_area = [&](double x, double y) -> double {
+        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
+        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
+        return (qx % qy).Length();
+    };
+
+    // Mutable experiment whose geometry is re-synced from the refined data.geom
+    // before each prediction, so shoeboxes track the refined geometry/cell.
+    DiffractionExperiment exp_iter = experiment;
+
+    // State retained after the loop for the final reflection extraction.
     std::vector<ReflGroup> groups;
-    for (const auto &refl : prediction.GetReflections()) {
-        const auto hkl = hkl_key_generator(refl);
-        if (!reference_data.contains(hkl))
-            continue;
-
-        ReflGroup g;
-        g.h = refl.h;
-        g.k = refl.k;
-        g.l = refl.l;
-        g.d = refl.d;
-        g.Itrue = reference_data[hkl];
-        g.predicted_x = refl.predicted_x;
-        g.predicted_y = refl.predicted_y;
-
-        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
-        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
-        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
-        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
-
-        for (int y = min_y; y <= max_y; ++y) {
-            for (int x = min_x; x <= max_x; ++x) {
-                const size_t npixel = xpixel * y + x;
-                const int azim_bin = pixel_to_bin[npixel];
-
-                // Skip pixels not mapped to an azimuthal bin or carrying a
-                // sentinel (masked / saturated) value. We assume the pixel mask
-                // is already applied upstream.
-                if (azim_bin >= azim_bin_count)
-                    continue;
-                if (image[npixel] == std::numeric_limits<T>::max())
-                    continue;
-                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
-                    continue;
-
-                const double correction = corrections[npixel];
-                const double Ibkg = azim_result[azim_bin] * 1.0; // already corrected units
-                const double Ibkg_sigma = azim_std[azim_bin];
-                const double raw = static_cast<double>(image[npixel]);
-                const double Iobs = raw * correction;
-
-                // Per-pixel variance: Poisson noise of the corrected counts
-                // (var(c*N) = c^2 * N = c * Iobs) plus the background spread.
-                double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
-                if (!(var > 1.0))
-                    var = 1.0;
-
-                PixelObs obs{
-                    .x = static_cast<double>(x),
-                    .y = static_cast<double>(y),
-                    .Iobs = Iobs,
-                    .Ibkg = Ibkg,
-                    .weight = 1.0 / std::sqrt(var),
-                    .A_recip = A_recip,
-                    .angle_rad = angle_rad
-                };
-                g.pixels.push_back(obs);
-            }
-        }
-
-        if (!g.pixels.empty())
-            groups.push_back(std::move(g));
-    }
-
-    if (groups.empty())
-        return;
-
-    // ---- Set up parameter blocks (mirrors XtalOptimizer for the geometry part) -
-    double beam[2] = {geom.GetBeamX_pxl(), geom.GetBeamY_pxl()};
-    double dist_mm = distance_mm;
-    double detector_rot[2] = {geom.GetPoniRot1_rad(), geom.GetPoniRot2_rad()};
+    double beam[2] = {0, 0};
+    double dist_mm = data.geom.GetDetectorDistance_mm();
+    double detector_rot[2] = {0, 0};
     double rot_vec[3] = {1.0, 0.0, 0.0};
-    if (auto axis = geom.GetRotation()) {
-        rot_vec[0] = axis->GetAxis().x;
-        rot_vec[1] = axis->GetAxis().y;
-        rot_vec[2] = axis->GetAxis().z;
-    }
-
     double latt_vec0[3] = {0, 0, 0}; // orientation (Rodrigues)
     double latt_vec1[3] = {0, 0, 0}; // lengths
     double latt_vec2[3] = {0, 0, 0}; // angles (rad)
-    double beta = data.latt.GetUnitCell().beta;
 
-    switch (data.crystal_system) {
-        case gemmi::CrystalSystem::Orthorhombic:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            break;
-        case gemmi::CrystalSystem::Tetragonal:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
-            break;
-        case gemmi::CrystalSystem::Cubic:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
-            break;
-        case gemmi::CrystalSystem::Hexagonal:
-            LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
-            break;
-        case gemmi::CrystalSystem::Monoclinic:
-            LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
-            latt_vec2[0] = beta;
-            break;
-        default: {
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            const auto uc = data.latt.GetUnitCell();
-            latt_vec2[0] = uc.alpha * M_PI / 180.0;
-            latt_vec2[1] = uc.beta * M_PI / 180.0;
-            latt_vec2[2] = uc.gamma * M_PI / 180.0;
-            break;
+    const int n_iter = std::max(1, data.max_iterations);
+    for (int iter = 0; iter < n_iter; ++iter) {
+        // ---- 1. Re-sync prediction geometry from the (refined) model ----------
+        exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+                .BeamY_pxl(data.geom.GetBeamY_pxl())
+                .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+                .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+                .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+
+        prediction.Calc(exp_iter, data.latt, settings_prediction);
+
+        // ---- 2. Collect per-reflection shoebox pixels -------------------------
+        groups.clear();
+        for (const auto &refl : prediction.GetReflections()) {
+            const auto hkl = hkl_key_generator(refl);
+            if (!reference_data.contains(hkl))
+                continue;
+
+            ReflGroup g;
+            g.h = refl.h;
+            g.k = refl.k;
+            g.l = refl.l;
+            g.d = refl.d;
+            g.Itrue = reference_data[hkl];
+            g.predicted_x = refl.predicted_x;
+            g.predicted_y = refl.predicted_y;
+
+            const int min_y = std::max<int>(refl.predicted_y - radius, 0);
+            const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
+            const int min_x = std::max<int>(refl.predicted_x - radius, 0);
+            const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+
+            for (int y = min_y; y <= max_y; ++y) {
+                for (int x = min_x; x <= max_x; ++x) {
+                    const size_t npixel = xpixel * y + x;
+                    const int azim_bin = pixel_to_bin[npixel];
+
+                    // Skip pixels not mapped to an azimuthal bin or carrying a
+                    // sentinel (masked / saturated) value. We assume the pixel
+                    // mask is already applied upstream.
+                    if (azim_bin >= azim_bin_count)
+                        continue;
+                    if (image[npixel] == std::numeric_limits<T>::max())
+                        continue;
+                    if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
+                        continue;
+
+                    const double correction = corrections[npixel];
+                    const double Ibkg = azim_result[azim_bin]; // already in corrected units
+                    const double Ibkg_sigma = azim_std[azim_bin];
+                    const double raw = static_cast<double>(image[npixel]);
+                    const double Iobs = raw * correction;
+
+                    // Per-pixel variance: Poisson noise of the corrected counts
+                    // (var(c*N) = c^2 * N = c * Iobs) plus the background spread.
+                    double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
+                    if (!(var > 1.0))
+                        var = 1.0;
+
+                    PixelObs obs{
+                        .x = static_cast<double>(x),
+                        .y = static_cast<double>(y),
+                        .Iobs = Iobs,
+                        .Ibkg = Ibkg,
+                        .weight = 1.0 / std::sqrt(var),
+                        .A_recip = recip_area(x, y),
+                        .angle_rad = angle_rad
+                    };
+                    g.pixels.push_back(obs);
+                }
+            }
+
+            if (!g.pixels.empty())
+                groups.push_back(std::move(g));
         }
-    }
 
-    ceres::Problem problem;
+        if (groups.empty())
+            return;
 
-    for (const auto &g : groups) {
-        for (const auto &obs : g.pixels) {
-            auto *cost = new ceres::AutoDiffCostFunction<
-                PixelResidual, 1, 2, 1, 2, 3, 3, 3, 3, 1, 1, 2>(
-                new PixelResidual(obs, g.Itrue, lambda, pixel_size,
-                                  g.h, g.k, g.l, data.crystal_system));
-            problem.AddResidualBlock(cost, new ceres::HuberLoss(3.0),
-                                     beam, &dist_mm, detector_rot, rot_vec,
-                                     latt_vec0, latt_vec1, latt_vec2,
-                                     &data.scale_factor, &data.B_factor, data.R);
+        // ---- 3. Set up parameter blocks (geometry part mirrors XtalOptimizer) -
+        beam[0] = data.geom.GetBeamX_pxl();
+        beam[1] = data.geom.GetBeamY_pxl();
+        dist_mm = data.geom.GetDetectorDistance_mm();
+        detector_rot[0] = data.geom.GetPoniRot1_rad();
+        detector_rot[1] = data.geom.GetPoniRot2_rad();
+        rot_vec[0] = 1.0; rot_vec[1] = 0.0; rot_vec[2] = 0.0;
+        if (auto axis = data.geom.GetRotation()) {
+            rot_vec[0] = axis->GetAxis().x;
+            rot_vec[1] = axis->GetAxis().y;
+            rot_vec[2] = axis->GetAxis().z;
         }
-    }
 
-    data.residual_count = problem.NumResidualBlocks();
-
-    // ---- Constrain / bound parameter blocks -----------------------------------
-    if (!data.refine_orientation)
-        problem.SetParameterBlockConstant(latt_vec0);
-
-    if (!data.refine_unit_cell) {
-        problem.SetParameterBlockConstant(latt_vec1);
-        problem.SetParameterBlockConstant(latt_vec2);
-    } else {
-        for (int i = 0; i < 3; ++i) {
-            problem.SetParameterLowerBound(latt_vec1, i, 5.0);
-            problem.SetParameterUpperBound(latt_vec1, i, 1000.0);
-        }
-        if (data.crystal_system != gemmi::CrystalSystem::Monoclinic &&
-            data.crystal_system != gemmi::CrystalSystem::Triclinic)
-            problem.SetParameterBlockConstant(latt_vec2);
-    }
-
-    if (!data.refine_beam_center)
-        problem.SetParameterBlockConstant(beam);
-
-    if (!data.refine_distance) {
-        problem.SetParameterBlockConstant(&dist_mm);
-    } else {
-        problem.SetParameterLowerBound(&dist_mm, 0, dist_mm * 0.9);
-        problem.SetParameterUpperBound(&dist_mm, 0, dist_mm * 1.1);
-    }
-
-    if (!data.refine_detector_angles) {
-        problem.SetParameterBlockConstant(detector_rot);
-    } else {
-        const double rng = 3.0 / 180.0 * M_PI;
-        for (int i = 0; i < 2; ++i) {
-            problem.SetParameterLowerBound(detector_rot, i, detector_rot[i] - rng);
-            problem.SetParameterUpperBound(detector_rot, i, detector_rot[i] + rng);
-        }
-    }
-
-    if (!data.refine_rotation_axis)
-        problem.SetParameterBlockConstant(rot_vec);
-
-    if (data.refine_scale)
-        problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
-    else
-        problem.SetParameterBlockConstant(&data.scale_factor);
-
-    if (!data.refine_B)
-        problem.SetParameterBlockConstant(&data.B_factor);
-
-    if (data.refine_R) {
-        problem.SetParameterLowerBound(data.R, 0, 1e-5);
-        problem.SetParameterLowerBound(data.R, 1, 1e-5);
-    } else {
-        problem.SetParameterBlockConstant(data.R);
-    }
-
-    // ---- Solve ----------------------------------------------------------------
-    ceres::Solver::Options options;
-    options.linear_solver_type = ceres::DENSE_QR;
-    options.minimizer_progress_to_stdout = false;
-    options.logging_type = ceres::LoggingType::SILENT;
-    options.max_solver_time_in_seconds = data.max_time_s;
-    options.num_threads = 1;
-
-    ceres::Solver::Summary summary;
-    ceres::Solve(options, &problem, &summary);
-
-    data.final_cost = summary.final_cost;
-    data.solved = summary.IsSolutionUsable();
-
-    // ---- Write back refined geometry + lattice --------------------------------
-    if (data.refine_beam_center)
-        data.geom.BeamX_pxl(beam[0]).BeamY_pxl(beam[1]);
-    if (data.refine_distance)
-        data.geom.DetectorDistance_mm(dist_mm);
-    if (data.refine_detector_angles)
-        data.geom.PoniRot1_rad(detector_rot[0]).PoniRot2_rad(detector_rot[1]);
-
-    if (data.refine_orientation || data.refine_unit_cell) {
+        double beta = data.latt.GetUnitCell().beta;
         switch (data.crystal_system) {
             case gemmi::CrystalSystem::Orthorhombic:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                 break;
             case gemmi::CrystalSystem::Tetragonal:
-                latt_vec1[1] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
                 break;
             case gemmi::CrystalSystem::Cubic:
-                latt_vec1[1] = latt_vec1[0];
-                latt_vec1[2] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
                 break;
             case gemmi::CrystalSystem::Hexagonal:
-                latt_vec1[1] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
+                LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
                 break;
             case gemmi::CrystalSystem::Monoclinic:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
+                LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
+                latt_vec2[0] = beta;
                 break;
-            default:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
-                                                      latt_vec2[0], latt_vec2[1], latt_vec2[2]);
+            default: {
+                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+                const auto uc = data.latt.GetUnitCell();
+                latt_vec2[0] = uc.alpha * M_PI / 180.0;
+                latt_vec2[1] = uc.beta * M_PI / 180.0;
+                latt_vec2[2] = uc.gamma * M_PI / 180.0;
                 break;
+            }
         }
-    }
+
+        // ---- 4. Build the problem ---------------------------------------------
+        ceres::Problem problem;
+        for (const auto &g : groups) {
+            for (const auto &obs : g.pixels) {
+                auto *cost = new ceres::AutoDiffCostFunction<
+                    PixelResidual, 1, 2, 1, 2, 3, 3, 3, 3, 1, 1, 2>(
+                    new PixelResidual(obs, g.Itrue, lambda, pixel_size,
+                                      g.h, g.k, g.l, data.crystal_system));
+                problem.AddResidualBlock(cost, new ceres::HuberLoss(3.0),
+                                         beam, &dist_mm, detector_rot, rot_vec,
+                                         latt_vec0, latt_vec1, latt_vec2,
+                                         &data.scale_factor, &data.B_factor, data.R);
+            }
+        }
+        data.residual_count = problem.NumResidualBlocks();
+
+        // ---- 5. Constrain / bound parameter blocks ----------------------------
+        if (!data.refine_orientation)
+            problem.SetParameterBlockConstant(latt_vec0);
+
+        if (!data.refine_unit_cell) {
+            problem.SetParameterBlockConstant(latt_vec1);
+            problem.SetParameterBlockConstant(latt_vec2);
+        } else {
+            for (int i = 0; i < 3; ++i) {
+                problem.SetParameterLowerBound(latt_vec1, i, 5.0);
+                problem.SetParameterUpperBound(latt_vec1, i, 1000.0);
+            }
+            if (data.crystal_system != gemmi::CrystalSystem::Monoclinic &&
+                data.crystal_system != gemmi::CrystalSystem::Triclinic)
+                problem.SetParameterBlockConstant(latt_vec2);
+        }
+
+        if (!data.refine_beam_center)
+            problem.SetParameterBlockConstant(beam);
+
+        if (!data.refine_distance) {
+            problem.SetParameterBlockConstant(&dist_mm);
+        } else {
+            problem.SetParameterLowerBound(&dist_mm, 0, dist_mm * 0.9);
+            problem.SetParameterUpperBound(&dist_mm, 0, dist_mm * 1.1);
+        }
+
+        if (!data.refine_detector_angles) {
+            problem.SetParameterBlockConstant(detector_rot);
+        } else {
+            const double rng = 3.0 / 180.0 * M_PI;
+            for (int i = 0; i < 2; ++i) {
+                problem.SetParameterLowerBound(detector_rot, i, detector_rot[i] - rng);
+                problem.SetParameterUpperBound(detector_rot, i, detector_rot[i] + rng);
+            }
+        }
+
+        if (!data.refine_rotation_axis)
+            problem.SetParameterBlockConstant(rot_vec);
+
+        if (data.refine_scale)
+            problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
+        else
+            problem.SetParameterBlockConstant(&data.scale_factor);
+
+        if (!data.refine_B)
+            problem.SetParameterBlockConstant(&data.B_factor);
+
+        if (data.refine_R) {
+            problem.SetParameterLowerBound(data.R, 0, 1e-5);
+            problem.SetParameterLowerBound(data.R, 1, 1e-5);
+        } else {
+            problem.SetParameterBlockConstant(data.R);
+        }
+
+        // ---- 6. Solve ---------------------------------------------------------
+        ceres::Solver::Options options;
+        options.linear_solver_type = ceres::DENSE_QR;
+        options.minimizer_progress_to_stdout = false;
+        options.logging_type = ceres::LoggingType::SILENT;
+        options.max_solver_time_in_seconds = data.max_time_s;
+        options.num_threads = 1;
+
+        ceres::Solver::Summary summary;
+        ceres::Solve(options, &problem, &summary);
+
+        data.final_cost = summary.final_cost;
+        data.solved = summary.IsSolutionUsable();
+
+        // ---- 7. Write refined geometry + lattice back into data ---------------
+        if (data.refine_beam_center)
+            data.geom.BeamX_pxl(beam[0]).BeamY_pxl(beam[1]);
+        if (data.refine_distance)
+            data.geom.DetectorDistance_mm(dist_mm);
+        if (data.refine_detector_angles)
+            data.geom.PoniRot1_rad(detector_rot[0]).PoniRot2_rad(detector_rot[1]);
+
+        if (data.refine_orientation || data.refine_unit_cell) {
+            switch (data.crystal_system) {
+                case gemmi::CrystalSystem::Orthorhombic:
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                    break;
+                case gemmi::CrystalSystem::Tetragonal:
+                    latt_vec1[1] = latt_vec1[0];
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                    break;
+                case gemmi::CrystalSystem::Cubic:
+                    latt_vec1[1] = latt_vec1[0];
+                    latt_vec1[2] = latt_vec1[0];
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                    break;
+                case gemmi::CrystalSystem::Hexagonal:
+                    latt_vec1[1] = latt_vec1[0];
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
+                    break;
+                case gemmi::CrystalSystem::Monoclinic:
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
+                    break;
+                default:
+                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
+                                                          latt_vec2[0], latt_vec2[1], latt_vec2[2]);
+                    break;
+            }
+        }
+    } // predict<->refine iterations
 
     // ---- Extract integrated reflections ---------------------------------------
-    // Profile-fitted intensity with the optimized profile P (shape only):
-    //     I = sum_p [ P_p (Iobs_p - Ibkg_p) / v_p ] / sum_p [ P_p^2 / v_p ]
-    //     var(I) = 1 / sum_p [ P_p^2 / v_p ]
-    // where P_p is the *shape* of the model per pixel (signal at G=Itrue=B=1).
+    // Two quantities are read back per reflection, using the *optimized* model:
+    //
+    //  * Recorded (partial) intensity J by profile fitting against the normalized
+    //    tangential profile P_t (sum over the shoebox ~ 1):
+    //        J       = sum_p [ P_t,p (Iobs_p - Ibkg_p) / v_p ] / sum_p [ P_t,p^2 / v_p ]
+    //        var(J)  = 1 / sum_p [ P_t,p^2 / v_p ]
+    //    Because P_t is area-normalized, J estimates the integrated intensity
+    //    actually recorded on this image (not the full-spot intensity).
+    //
+    //  * Partiality: the profile-weighted mean of the *peak-normalized* radial
+    //    factor exp(-eps_r^2/R0^2) in (0,1], i.e. how close to the Ewald sphere
+    //    the reflection sits. Kept dimensionless for consistency with the rest of
+    //    the pipeline (image_scale_corr = rlp / partiality, full I = J / partiality).
     data.reflections.reserve(groups.size());
     for (const auto &g : groups) {
-        double num = 0.0, den = 0.0, partiality_sum = 0.0, bkg_sum = 0.0;
+        double num = 0.0, den = 0.0, bkg_sum = 0.0;
+        double radial_sum = 0.0, radial_w = 0.0;
         size_t n = 0;
 
         for (const auto &obs : g.pixels) {
@@ -585,16 +633,19 @@ void PixelRefine::Run(const T *image,
             if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
                 continue;
 
+            // Normalized tangential profile (sum over shoebox ~ 1) -> fit weight.
+            const double P_t = obs.A_recip * std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
+                               / (M_PI * data.R[1] * data.R[1]);
+            // Peak-normalized radial factor (the partiality), in (0,1].
             const double P_radial = std::exp(-eps_r * eps_r / (data.R[0] * data.R[0]));
-            const double norm_tang = obs.A_recip / (M_PI * data.R[1] * data.R[1]);
-            const double P_tang = norm_tang * std::exp(-eps_t_sq / (data.R[1] * data.R[1]));
-            const double P = P_radial * P_tang; // model shape per pixel (unit scale)
+
             const double v = SafeInv(obs.weight * obs.weight, 1.0); // pixel variance
             const double signal = obs.Iobs - obs.Ibkg;
 
-            num += P * signal / v;
-            den += P * P / v;
-            partiality_sum += P_tang;   // tangential profile sums to ~partiality
+            num += P_t * signal / v;
+            den += P_t * P_t / v;
+            radial_sum += P_radial * P_t;   // weight partiality by the spot core
+            radial_w += P_t;
             bkg_sum += obs.Ibkg;
             ++n;
         }
@@ -609,11 +660,10 @@ void PixelRefine::Run(const T *image,
         r.observed_x = NAN;
         r.observed_y = NAN;
         r.rlp = 1.0f;
-        r.partiality = static_cast<float>(partiality_sum);
+        r.partiality = (radial_w > 0.0) ? static_cast<float>(radial_sum / radial_w) : 1.0f;
 
         if (den > 0.0 && n > 0) {
-            const double I = num / den;
-            r.I = static_cast<float>(I);
+            r.I = static_cast<float>(num / den);
             r.sigma = static_cast<float>(std::sqrt(1.0 / den));
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 5848cf15..44ae21c8 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -9,6 +9,72 @@
 #include "../common/AzimuthalIntegrationProfile.h"
 #include "../scale_merge/HKLKey.h"
 
+// =============================================================================
+// PixelRefine — one optimization to rule geometry, integration and scaling
+// =============================================================================
+//
+// Intent
+// ------
+// Classical crystallographic data processing is a one-way pipeline:
+//
+//     spot finding -> indexing -> geometry refinement -> integration -> scaling -> merging
+//
+// Each stage consumes the previous stage's output and never talks back. The
+// integrator trusts the refined geometry; the scaler trusts the integrated
+// intensities; nothing downstream is ever allowed to correct an upstream
+// parameter. Post-refinement and profile fitting were the field's partial
+// answers to this: post-refinement lets merged intensities nudge per-image
+// orientation/cell/mosaicity, and profile fitting lets a learned spot shape
+// improve weak-reflection intensities. But both are narrow back-channels bolted
+// onto a feed-forward pipeline — there is no end-to-end gradient that flows from
+// the raw detector pixels all the way back to every parameter at once.
+//
+// PixelRefine is an experiment in doing the whole thing as a *single* least
+// squares problem. We write down, for every pixel in a reflection's shoebox, the
+// expected counts as an explicit forward model
+//
+//     I_pred(pixel) = G * I_true * B_term * P_radial * P_tangential + I_bkg
+//
+// and let Ceres autodiff back-propagate the per-pixel residuals into ALL of:
+//   * detector geometry  (beam centre, distance, tilt)
+//   * crystal orientation + unit cell
+//   * overall scale G and Debye-Waller B
+//   * the reciprocal-space spot widths R = (radial, tangential)
+// simultaneously. Geometry refinement, profile-fitted integration and scaling
+// then stop being separate stages: they are different parameters of one model,
+// coupled through the same pixels, with full backpropagation between them. Once
+// the model is differentiable end-to-end, things that used to need bespoke code
+// — mosaicity refinement, profile fitting, partiality — fall out "for free" as
+// extra parameters of the same forward model.
+//
+// How I_true enters
+// -----------------
+// I_true is NOT refined here. It is a *fixed hypothesis* for the duration of a
+// pass: the current best merged estimate of each reflection's full intensity.
+// The intended outer loop is iterative, like EM / self-consistent field:
+//
+//     repeat over the whole dataset:
+//         run PixelRefine on every image with the current I_true reference
+//         re-merge the resulting intensities -> new I_true
+//     until the reference stops changing
+//
+// So a single PixelRefine call answers "given this intensity hypothesis, what
+// geometry/scale/profile best explains these pixels, and what intensities do I
+// read back out?", and the dataset-level loop refines the hypothesis itself.
+//
+// Inner predict<->refine loop
+// ---------------------------
+// Within one image we also iterate (max_iterations): Bragg prediction places the
+// shoeboxes, we refine, the refined geometry/cell feed the next prediction, etc.
+// Initially the model geometry equals the experiment's DiffractionGeometry, but
+// as refinement proceeds it diverges, so later predictions must use the *refined*
+// data.geom rather than the static experiment geometry.
+//
+// Status: experimental prototype. The forward model (esp. the still-image
+// Lorentz/partiality normalization) is deliberately simple and expected to
+// evolve. See PixelRefine.cpp for the physics conventions and known caveats.
+// =============================================================================
+
 struct PixelRefineData {
     // --- model state (input as initial guess, output as refined result) ---
     DiffractionGeometry geom;
@@ -37,6 +103,7 @@ struct PixelRefineData {
 
     double max_time_s = 5.0;
     int    shoebox_radius = 3; // half-size of the per-reflection pixel box
+    int    max_iterations = 3; // inner predict<->refine cycles (re-predict with refined geom/latt)
 
     // --- output ---
     std::vector<Reflection> reflections; // profile-fitted integration result
-- 
2.52.0


From 6f311596078e99e92520aa667d9f66d62a02f121 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 13:59:01 +0200
Subject: [PATCH 006/228] PixelRefine: Add bandwidth contribution

---
 .../pixel_refinement/PixelRefine.cpp          | 49 ++++++++++++++-----
 image_analysis/pixel_refinement/PixelRefine.h | 29 +++++++++++
 2 files changed, 67 insertions(+), 11 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 63971bf2..933edb40 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -29,6 +29,7 @@ struct ReflGroup {
     int h, k, l;
     double d;
     double Itrue;             // reference intensity (held fixed)
+    double R_bw_sq;           // bandwidth radial-width^2 contribution (0 = monochromatic)
     double predicted_x, predicted_y;
     std::vector<PixelObs> pixels;
 };
@@ -47,10 +48,9 @@ double SafeInv(double x, double fallback) {
 //   I_pred(pixel) = G * Itrue * B_term * P_radial * P_tangential + I_bkg
 //
 //   B_term       = exp(-B |q|^2 / 4)                    (Debye-Waller)
-//   P_radial     = exp(-eps_r^2 / R0^2)                 (partiality: fraction of
+//   P_radial     = exp(-eps_r^2 / R0_eff^2)             (partiality: fraction of
 //                                                        the mosaic blob on the
-//                                                        Ewald sphere; NOT
-//                                                        normalized, <= 1)
+//                                                        Ewald sphere; <= 1)
 //   P_tangential = A_recip/(pi R1^2) * exp(-eps_t^2/R1^2)(spatial profile on the
 //                                                        detector, normalized so
 //                                                        that sum over pixels ~ 1)
@@ -59,17 +59,28 @@ double SafeInv(double x, double fallback) {
 // I_pred - I_bkg over the shoebox reproduces G * Itrue * B_term * P_radial.
 // The 1/(pi R1^2) normalization is the missing piece that decouples the profile
 // width R1 from the overall scale G.
+//
+// X-ray bandwidth: a spread in lambda is a spread in the Ewald-sphere radius,
+// i.e. a purely *radial* thickening of the shell. It adds (in quadrature) a
+// resolution-dependent term to the radial width:
+//     R0_eff^2 = R0^2 + R_bw^2 ,   R_bw^2 = (b*lambda)^2 / (2 d^4)
+// where b = relative bandwidth (sigma of dlambda/lambda). R_bw grows like 1/d^2,
+// so bandwidth leaves low-resolution spots sharp and smears high-resolution ones
+// radially - the pink-beam/DMM signature. R_bw_sq is a fixed per-reflection
+// constant (b is known), so R0 keeps meaning "intrinsic" width (mosaic +
+// divergence + beam). b = 0 makes R_bw = 0: a monochromatic no-op.
 // ---------------------------------------------------------------------------
 struct PixelResidual {
     PixelResidual(const PixelObs &obs, double Itrue,
                   double lambda, double pixel_size,
                   double exp_h, double exp_k, double exp_l,
+                  double R_bw_sq,
                   gemmi::CrystalSystem symmetry)
         : Itrue(Itrue), Iobs(obs.Iobs), Ibkg(obs.Ibkg), weight(obs.weight),
           A_recip(obs.A_recip), obs_x(obs.x), obs_y(obs.y),
           inv_lambda(1.0 / lambda), pixel_size(pixel_size),
           exp_h(exp_h), exp_k(exp_k), exp_l(exp_l),
-          angle_rad(obs.angle_rad), symmetry(symmetry) {
+          R_bw_sq(R_bw_sq), angle_rad(obs.angle_rad), symmetry(symmetry) {
         if (std::fabs(lambda) < 1e-6)
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Lambda cannot be close to zero");
@@ -251,10 +262,11 @@ struct PixelResidual {
         // Caveat: a still samples the radial direction at a single offset, so the
         // sqrt(pi) R0 normalization makes g_r a density (1/A^-1) rather than a
         // dimensionless fraction. The leftover dimensional factor is absorbed by
-        // the free scale G; completing it physically needs an effective radial
-        // sampling width from the energy bandwidth + beam divergence (TODO).
-        const T g_radial = ceres::exp(-eps_radial * eps_radial / (R[0] * R[0]))
-                           / (ceres::sqrt(T(M_PI)) * R[0]);
+        // the free scale G. The energy-bandwidth contribution to the radial width
+        // is folded in here via R_bw_sq (beam divergence is still TODO).
+        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
+        const T g_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq)
+                           / (ceres::sqrt(T(M_PI)) * ceres::sqrt(R0_eff_sq));
         const T P_tang = T(A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
                          / (T(M_PI) * R[1] * R[1]);
 
@@ -289,6 +301,7 @@ struct PixelResidual {
     const double inv_lambda;
     const double pixel_size;
     const double exp_h, exp_k, exp_l;
+    const double R_bw_sq;   // bandwidth radial-width^2 contribution (0 = monochromatic)
     const double angle_rad;
     gemmi::CrystalSystem symmetry;
 };
@@ -346,6 +359,17 @@ void PixelRefine::Run(const T *image,
         return (qx % qy).Length();
     };
 
+    // Bandwidth radial-width^2 (in the code's R = sqrt(2)*sigma convention):
+    //   R_bw^2 = (b*lambda)^2 / (2 d^4),   b = relative bandwidth (sigma).
+    // A fixed per-reflection constant; data.bandwidth == 0 -> monochromatic no-op.
+    const double bw = data.bandwidth;
+    auto bandwidth_radial_sq = [&](double d) -> double {
+        if (bw <= 0.0 || d <= 0.0)
+            return 0.0;
+        const double bl = bw * lambda;
+        return bl * bl / (2.0 * d * d * d * d);
+    };
+
     // Mutable experiment whose geometry is re-synced from the refined data.geom
     // before each prediction, so shoeboxes track the refined geometry/cell.
     DiffractionExperiment exp_iter = experiment;
@@ -384,6 +408,7 @@ void PixelRefine::Run(const T *image,
             g.l = refl.l;
             g.d = refl.d;
             g.Itrue = reference_data[hkl];
+            g.R_bw_sq = bandwidth_radial_sq(refl.d);
             g.predicted_x = refl.predicted_x;
             g.predicted_y = refl.predicted_y;
 
@@ -489,7 +514,7 @@ void PixelRefine::Run(const T *image,
                 auto *cost = new ceres::AutoDiffCostFunction<
                     PixelResidual, 1, 2, 1, 2, 3, 3, 3, 3, 1, 1, 2>(
                     new PixelResidual(obs, g.Itrue, lambda, pixel_size,
-                                      g.h, g.k, g.l, data.crystal_system));
+                                      g.h, g.k, g.l, g.R_bw_sq, data.crystal_system));
                 problem.AddResidualBlock(cost, new ceres::HuberLoss(3.0),
                                          beam, &dist_mm, detector_rot, rot_vec,
                                          latt_vec0, latt_vec1, latt_vec2,
@@ -625,7 +650,7 @@ void PixelRefine::Run(const T *image,
         size_t n = 0;
 
         for (const auto &obs : g.pixels) {
-            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system);
+            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, g.R_bw_sq, data.crystal_system);
             double q_sq, eps_r, eps_t_sq;
             if (!pr.GeometryTerms(beam, &dist_mm, detector_rot, rot_vec,
                                   latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
@@ -637,7 +662,9 @@ void PixelRefine::Run(const T *image,
             const double P_t = obs.A_recip * std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
                                / (M_PI * data.R[1] * data.R[1]);
             // Peak-normalized radial factor (the partiality), in (0,1].
-            const double P_radial = std::exp(-eps_r * eps_r / (data.R[0] * data.R[0]));
+            // Bandwidth-broadened radial width, matching the model in Model().
+            const double R0_eff_sq = data.R[0] * data.R[0] + g.R_bw_sq;
+            const double P_radial = std::exp(-eps_r * eps_r / R0_eff_sq);
 
             const double v = SafeInv(obs.weight * obs.weight, 1.0); // pixel variance
             const double signal = obs.Iobs - obs.Ibkg;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 44ae21c8..07b280cf 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -70,6 +70,30 @@
 // as refinement proceeds it diverges, so later predictions must use the *refined*
 // data.geom rather than the static experiment geometry.
 //
+// On shoeboxes, tails, and gatekeeping
+// ------------------------------------
+// We deliberately do NOT chase the full spot. A shoebox only needs to cover
+// enough of a reflection for the fit to be meaningful; clipped tails are fine,
+// because the partiality term already downweights whatever falls outside the
+// well-modelled core. The premise - especially for serial crystallography - is
+// that the problem is rarely *missing* information; it is *failing to gate out*
+// information that is not meaningful. As long as the model knows a piece is
+// missing (low partiality), it is safe to leave it missing. That flips the usual
+// trade-off: rather than shrinking boxes to avoid contamination, we can grow them
+// and let partiality decide, per pixel and per reflection, what actually carries
+// signal. (For downstream integration this pixel-level gating is the point - keep
+// only meaningful pixels, instead of a fixed geometric mask.) The bandwidth term
+// below is part of the same idea: it tells the model where the radial tails are
+// *expected* to be, so it can weight rather than blindly include them.
+//
+// X-ray bandwidth (optional)
+// --------------------------
+// A finite bandwidth thickens the Ewald shell radially and smears spots along the
+// radial direction, growing like 1/d^2 (the pink-beam/DMM signature). It enters
+// as a fixed, resolution-dependent addition to the radial width R0 (see
+// PixelRefineData::bandwidth and PixelRefine.cpp). It is OFF by default
+// (bandwidth = 0, monochromatic); set it for DMM-type data, leave it for Si.
+//
 // Status: experimental prototype. The forward model (esp. the still-image
 // Lorentz/partiality normalization) is deliberately simple and expected to
 // evolve. See PixelRefine.cpp for the physics conventions and known caveats.
@@ -86,6 +110,11 @@ struct PixelRefineData {
     double scale_factor = 1.0;  // overall scale G
     double R[2] = {0.005, 0.005}; // R[0] = radial (partiality) width, R[1] = tangential (profile) width (A^-1)
 
+    // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1%
+    // FWHM DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening
+    // to R[0]. 0 = monochromatic (the term switches off entirely).
+    double bandwidth = 0.0;
+
     // Goniometer: for a still image keep angle_deg = 0. For a wedge, pass the
     // angle (deg) of the slice centre relative to the reference (phi=0) frame.
     double angle_deg = 0.0;
-- 
2.52.0


From 155c53acd8d971a8d017d88437a3a363e25cf06c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 15:37:27 +0200
Subject: [PATCH 007/228] jfjoch_process: First pixel refine integration

---
 common/DatasetSettings.cpp                    |   9 ++
 common/DatasetSettings.h                      |   3 +
 common/DiffractionExperiment.cpp              |   9 ++
 common/DiffractionExperiment.h                |   2 +
 common/IndexingSettings.h                     |   2 +-
 image_analysis/CMakeLists.txt                 |   2 +-
 image_analysis/IndexAndRefine.cpp             | 115 +++++++++++++++---
 image_analysis/IndexAndRefine.h               |  26 +++-
 image_analysis/MXAnalysisWithoutFPGA.cpp      |   2 +-
 .../pixel_refinement/PixelRefine.cpp          |  26 ++--
 image_analysis/pixel_refinement/PixelRefine.h |   8 +-
 tools/jfjoch_process.cpp                      |  34 +++++-
 12 files changed, 203 insertions(+), 35 deletions(-)

diff --git a/common/DatasetSettings.cpp b/common/DatasetSettings.cpp
index 85bb81d5..2bcb144b 100644
--- a/common/DatasetSettings.cpp
+++ b/common/DatasetSettings.cpp
@@ -389,6 +389,15 @@ std::optional<float> DatasetSettings::GetPolarizationFactor() const {
     return polarization_factor;
 }
 
+DatasetSettings &DatasetSettings::BandwidthFWHM(const std::optional<float> &input) {
+    bandwidth_fwhm = input;
+    return *this;
+}
+
+std::optional<float> DatasetSettings::GetBandwidthFWHM() const {
+    return bandwidth_fwhm;
+}
+
 float DatasetSettings::GetPoniRot3_rad() const {
     return poni_rot_3_rad;
 }
diff --git a/common/DatasetSettings.h b/common/DatasetSettings.h
index 9ec5672e..3d91c630 100644
--- a/common/DatasetSettings.h
+++ b/common/DatasetSettings.h
@@ -55,6 +55,7 @@ class DatasetSettings {
     bool write_nxmx_hdf5_master;
 
     std::optional<float> polarization_factor;
+    std::optional<float> bandwidth_fwhm; // relative X-ray bandwidth, FWHM of dlambda/lambda (e.g. 0.01 for 1%)
     float poni_rot_1_rad;
     float poni_rot_2_rad;
     float poni_rot_3_rad;
@@ -99,6 +100,7 @@ public:
     DatasetSettings& PixelValueLowThreshold(const std::optional<int64_t> &input);
     DatasetSettings& PixelValueHighThreshold(const std::optional<int64_t> &input);
     DatasetSettings& PolarizationFactor(const std::optional<float> &input);
+    DatasetSettings& BandwidthFWHM(const std::optional<float> &input);
     DatasetSettings& PoniRot1_rad(float input);
     DatasetSettings& PoniRot2_rad(float input);
     DatasetSettings& PoniRot3_rad(float input);
@@ -150,6 +152,7 @@ public:
     std::optional<bool> IsSaveCalibration() const;
 
     std::optional<float> GetPolarizationFactor() const;
+    std::optional<float> GetBandwidthFWHM() const;
     float GetPoniRot1_rad() const;
     float GetPoniRot2_rad() const;
     float GetPoniRot3_rad() const;
diff --git a/common/DiffractionExperiment.cpp b/common/DiffractionExperiment.cpp
index ffd5f4ad..6b1a3b66 100644
--- a/common/DiffractionExperiment.cpp
+++ b/common/DiffractionExperiment.cpp
@@ -1310,6 +1310,15 @@ std::optional<float> DiffractionExperiment::GetPolarizationFactor() const {
     return dataset.GetPolarizationFactor();
 }
 
+DiffractionExperiment &DiffractionExperiment::BandwidthFWHM(const std::optional<float> &input) {
+    dataset.BandwidthFWHM(input);
+    return *this;
+}
+
+std::optional<float> DiffractionExperiment::GetBandwidthFWHM() const {
+    return dataset.GetBandwidthFWHM();
+}
+
 DiffractionExperiment &DiffractionExperiment::SaveCalibration(const std::optional<bool> &input) {
     dataset.SaveCalibration(input);
     return *this;
diff --git a/common/DiffractionExperiment.h b/common/DiffractionExperiment.h
index 131c3bff..a8bbb9a8 100644
--- a/common/DiffractionExperiment.h
+++ b/common/DiffractionExperiment.h
@@ -281,9 +281,11 @@ public:
 
     DiffractionExperiment& ApplySolidAngleCorr(bool input);
     DiffractionExperiment& PolarizationFactor(const std::optional<float> &input);
+    DiffractionExperiment& BandwidthFWHM(const std::optional<float> &input);
 
     bool GetApplySolidAngleCorr() const;
     std::optional<float> GetPolarizationFactor() const;
+    std::optional<float> GetBandwidthFWHM() const;
 
     int64_t GetUDPInterfaceCount() const;
     std::vector<DetectorModuleConfig> GetDetectorModuleConfig(const std::vector<AcquisitionDeviceNetConfig>& net_config) const;
diff --git a/common/IndexingSettings.h b/common/IndexingSettings.h
index 6e900440..c428f02e 100644
--- a/common/IndexingSettings.h
+++ b/common/IndexingSettings.h
@@ -6,7 +6,7 @@
 #include <cstdint>
 
 enum class IndexingAlgorithmEnum {FFBIDX, FFT, FFTW, Auto, None};
-enum class GeomRefinementAlgorithmEnum {None, OrientationOnly, BeamCenter};
+enum class GeomRefinementAlgorithmEnum {None, OrientationOnly, BeamCenter, PixelRefine};
 
 class IndexingSettings {
     IndexingAlgorithmEnum algorithm;
diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 913870c5..1bf6e448 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -52,4 +52,4 @@ ADD_SUBDIRECTORY(image_preprocessing)
 ADD_SUBDIRECTORY(azint)
 ADD_SUBDIRECTORY(pixel_refinement)
 
-TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge gemmi)
+TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochPixelRefine gemmi)
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index d436f2a7..5dc02d55 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -175,6 +175,10 @@ void IndexAndRefine::RefineGeometryIfNeeded(DataMessage &msg, IndexAndRefine::In
             XtalOptimizerRotationOnly(data, msg.spots, 0.05);
             break;
         case GeomRefinementAlgorithmEnum::BeamCenter:
+        case GeomRefinementAlgorithmEnum::PixelRefine:
+            // PixelRefine still benefits from the classical beam-center + cell
+            // refinement as a starting point; the pixel-level refinement runs
+            // later, during integration.
             if (XtalOptimizer(data, {msg.spots})) {
                 outcome.experiment.BeamX_pxl(data.geom.GetBeamX_pxl())
                         .BeamY_pxl(data.geom.GetBeamY_pxl());
@@ -234,7 +238,9 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                                               const SpotFindingSettings &spot_finding_settings,
                                               const CompressedImage &image,
                                               BraggPrediction &prediction,
-                                              const IndexAndRefine::IndexingOutcome &outcome) {
+                                              const IndexAndRefine::IndexingOutcome &outcome,
+                                              const AzimuthalIntegrationMapping *mapping,
+                                              const AzimuthalIntegrationProfile *profile) {
     if (!outcome.lattice_candidate)
         return;
 
@@ -286,14 +292,31 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
         .mosaicity_deg = std::fabs(mos_deg)
     };
 
-    auto pred_start_time = std::chrono::steady_clock::now();
-    auto nrefl = prediction.Calc(outcome.experiment, latt, settings_prediction);
-    auto pred_end_time = std::chrono::steady_clock::now();
-    msg.bragg_prediction_time_s = std::chrono::duration<float>(pred_end_time - pred_start_time).count();
+    // Select the integration path: classical 2D integration, or the experimental
+    // PixelRefine joint geometry/profile/scale refinement (which also produces the
+    // integrated reflections that flow into the normal save/merge).
+    const bool use_pixel_refine =
+        experiment.GetIndexingSettings().GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::PixelRefine
+        && !pixel_reference_.empty() && mapping && profile;
 
-    auto integration_start_time = std::chrono::steady_clock::now();
-    i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), nrefl, msg.number);
-    msg.integrated_reflections = i_outcome.reflections.size();
+    if (use_pixel_refine) {
+        auto integration_start_time = std::chrono::steady_clock::now();
+        PixelRefineIntegrate(msg, image, prediction, outcome, *mapping, *profile, i_outcome);
+        msg.integrated_reflections = i_outcome.reflections.size();
+        auto integration_end_time = std::chrono::steady_clock::now();
+        msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
+    } else {
+        auto pred_start_time = std::chrono::steady_clock::now();
+        auto nrefl = prediction.Calc(outcome.experiment, latt, settings_prediction);
+        auto pred_end_time = std::chrono::steady_clock::now();
+        msg.bragg_prediction_time_s = std::chrono::duration<float>(pred_end_time - pred_start_time).count();
+
+        auto integration_start_time = std::chrono::steady_clock::now();
+        i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), nrefl, msg.number);
+        msg.integrated_reflections = i_outcome.reflections.size();
+        auto integration_end_time = std::chrono::steady_clock::now();
+        msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
+    }
 
     constexpr size_t kMaxReflections = 10000;
     if (i_outcome.reflections.size() > kMaxReflections) {
@@ -314,10 +337,10 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
     CalcISigma(msg, i_outcome.reflections);
     CalcWilsonBFactor(msg, i_outcome.reflections);
 
-    auto integration_end_time = std::chrono::steady_clock::now();
-    msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
-
-    ScaleImage(msg, i_outcome);
+    // PixelRefine produces already-scaled reflections; only the classical path
+    // needs the separate ScaleOnTheFly step.
+    if (!use_pixel_refine)
+        ScaleImage(msg, i_outcome);
 
     // Copy reflections to outgoing message
     msg.reflections = i_outcome.reflections;
@@ -331,7 +354,9 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
 void IndexAndRefine::ProcessImage(DataMessage &msg,
                                   const SpotFindingSettings &spot_finding_settings,
                                   const CompressedImage &image,
-                                  BraggPrediction &prediction) {
+                                  BraggPrediction &prediction,
+                                  const AzimuthalIntegrationMapping *mapping,
+                                  const AzimuthalIntegrationProfile *profile) {
     if (!indexer_ || !spot_finding_settings.indexing)
         return;
 
@@ -361,7 +386,7 @@ void IndexAndRefine::ProcessImage(DataMessage &msg,
     msg.lattice_type = outcome.symmetry;
 
     if (spot_finding_settings.quick_integration)
-        QuickPredictAndIntegrate(msg, spot_finding_settings, image, prediction, outcome);
+        QuickPredictAndIntegrate(msg, spot_finding_settings, image, prediction, outcome, mapping, profile);
 }
 
 std::optional<RotationIndexerResult> IndexAndRefine::FinalizeRotationIndexing() {
@@ -377,6 +402,7 @@ std::optional<RotationIndexerResult> IndexAndRefine::FinalizeRotationIndexing()
 
 IndexAndRefine &IndexAndRefine::ReferenceIntensities(std::vector<MergedReflection> &reference) {
     scaling_engine = std::make_unique<ScaleOnTheFly>(experiment, reference);
+    pixel_reference_ = reference; // kept for the experimental PixelRefine path
     return *this;
 }
 
@@ -396,6 +422,67 @@ void IndexAndRefine::ScaleImage(DataMessage &msg, IntegrationOutcome& outcome) {
     msg.image_scale_time_s = std::chrono::duration<float>(scaling_end_time - scaling_start_time).count();
 }
 
+bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
+                                          const CompressedImage &image,
+                                          BraggPrediction &prediction,
+                                          const IndexAndRefine::IndexingOutcome &outcome,
+                                          const AzimuthalIntegrationMapping &mapping,
+                                          const AzimuthalIntegrationProfile &profile,
+                                          IntegrationOutcome &i_outcome) {
+    if (!outcome.lattice_candidate)
+        return false;
+
+    // Build the engine once (lazy: needs the azimuthal mapping, known only here).
+    std::call_once(pixel_refine_once_, [&] {
+        pixel_refine_ = std::make_unique<PixelRefine>(experiment, mapping, pixel_reference_);
+    });
+    if (!pixel_refine_)
+        return false;
+
+    PixelRefineData prd;
+    prd.geom = outcome.experiment.GetDiffractionGeometry();
+    prd.latt = *outcome.lattice_candidate;
+    prd.crystal_system = outcome.symmetry.crystal_system;
+    if (prd.crystal_system == gemmi::CrystalSystem::Trigonal)
+        prd.crystal_system = gemmi::CrystalSystem::Hexagonal;
+    prd.centering = outcome.symmetry.centering;
+    if (const auto bw = experiment.GetBandwidthFWHM())
+        prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
+
+    std::vector<uint8_t> buffer;
+    const uint8_t *ptr = image.GetUncompressedPtr(buffer);
+    switch (image.GetMode()) {
+        case CompressedImageMode::Int8:
+            pixel_refine_->Run(reinterpret_cast<const int8_t *>(ptr), profile, prediction, prd); break;
+        case CompressedImageMode::Int16:
+            pixel_refine_->Run(reinterpret_cast<const int16_t *>(ptr), profile, prediction, prd); break;
+        case CompressedImageMode::Int32:
+            pixel_refine_->Run(reinterpret_cast<const int32_t *>(ptr), profile, prediction, prd); break;
+        case CompressedImageMode::Uint8:
+            pixel_refine_->Run(reinterpret_cast<const uint8_t *>(ptr), profile, prediction, prd); break;
+        case CompressedImageMode::Uint16:
+            pixel_refine_->Run(reinterpret_cast<const uint16_t *>(ptr), profile, prediction, prd); break;
+        case CompressedImageMode::Uint32:
+            pixel_refine_->Run(reinterpret_cast<const uint32_t *>(ptr), profile, prediction, prd); break;
+        default:
+            return false;
+    }
+
+    // PixelRefine output flows into the normal save/merge path: the refined
+    // geometry/lattice and the already-scaled reflections become the outcome.
+    i_outcome.reflections = std::move(prd.reflections);
+    i_outcome.geom = prd.geom;
+    i_outcome.latt = prd.latt;
+    i_outcome.image_scale_g = static_cast<float>(prd.scale_factor);
+    i_outcome.image_scale_b_factor_Ang2 = static_cast<float>(prd.B_factor);
+
+    msg.image_scale_factor = static_cast<float>(prd.scale_factor);
+    if (prd.B_factor != 0.0)
+        msg.image_scale_b_factor = static_cast<float>(prd.B_factor);
+
+    return true;
+}
+
 ScalingResult IndexAndRefine::ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads) {
     ScaleOnTheFly scaling(experiment, reference);
     scaling.Scale(integration_outcome, nthreads);
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index 0f03ee97..7674392e 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -8,7 +8,10 @@
 
 #include "../common/DiffractionSpot.h"
 #include "../common/DiffractionExperiment.h"
+#include "../common/AzimuthalIntegrationMapping.h"
+#include "../common/AzimuthalIntegrationProfile.h"
 #include "bragg_prediction/BraggPrediction.h"
+#include "pixel_refinement/PixelRefine.h"
 #include "indexing/IndexerThreadPool.h"
 #include "lattice_search/LatticeSearch.h"
 #include "rotation_indexer/RotationIndexer.h"
@@ -62,17 +65,36 @@ class IndexAndRefine {
                                  const SpotFindingSettings &spot_finding_settings,
                                  const CompressedImage &image,
                                  BraggPrediction &prediction,
-                                 const IndexingOutcome &outcome);
+                                 const IndexingOutcome &outcome,
+                                 const AzimuthalIntegrationMapping *mapping,
+                                 const AzimuthalIntegrationProfile *profile);
 
     std::unique_ptr<ScaleOnTheFly> scaling_engine;
     void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
+
+    // Experimental PixelRefine integration path (selected via
+    // GeomRefinementAlgorithmEnum::PixelRefine). Needs reference intensities; the
+    // engine is built lazily on first use (when the azimuthal mapping is known)
+    // and is safe to share across threads (prediction is supplied per call).
+    std::vector<MergedReflection> pixel_reference_;
+    std::unique_ptr<PixelRefine> pixel_refine_;
+    std::once_flag pixel_refine_once_;
+    bool PixelRefineIntegrate(DataMessage &msg,
+                              const CompressedImage &image,
+                              BraggPrediction &prediction,
+                              const IndexingOutcome &outcome,
+                              const AzimuthalIntegrationMapping &mapping,
+                              const AzimuthalIntegrationProfile &profile,
+                              IntegrationOutcome &i_outcome);
 public:
     IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer);
 
     void AddImageToRotationIndexer(DataMessage &msg);
     void ForceRotationIndexerLattice(const CrystalLattice& lattice);
 
-    void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction);
+    void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction,
+                      const AzimuthalIntegrationMapping *mapping = nullptr,
+                      const AzimuthalIntegrationProfile *profile = nullptr);
     IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
 
     ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index 7bade492..6a638213 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -92,7 +92,7 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
         if (spot_finding_settings.indexing)
             indexer.ProcessImage(output, spot_finding_settings,
                 CompressedImage(preprocessor_buffer->getBuffer(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum()),
-                *prediction);
+                *prediction, &integration, &profile);
     }
 
     output.max_viable_pixel_value = ret.max_value;
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 933edb40..f2e4f93c 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -308,10 +308,8 @@ struct PixelResidual {
 
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
                          const AzimuthalIntegrationMapping &mapping,
-                         const std::vector<MergedReflection> &reference,
-                         BraggPrediction &prediction)
-    : prediction(prediction),
-      mapping(mapping),
+                         const std::vector<MergedReflection> &reference)
+    : mapping(mapping),
       xpixel(experiment.GetXPixelsNum()),
       ypixel(experiment.GetYPixelsNum()),
       experiment(experiment),
@@ -324,6 +322,7 @@ PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
 template<class T>
 void PixelRefine::Run(const T *image,
                       const AzimuthalIntegrationProfile &profile,
+                      BraggPrediction &prediction,
                       PixelRefineData &data) {
     data.solved = false;
     data.reflections.clear();
@@ -694,7 +693,12 @@ void PixelRefine::Run(const T *image,
             r.sigma = static_cast<float>(std::sqrt(1.0 / den));
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
-            r.image_scale_corr = (r.partiality > 0.0f) ? r.rlp / r.partiality : NAN;
+            // Put I onto a common (merge-ready) scale: I * image_scale_corr is the
+            // full-spot, scale/DW-corrected intensity. Fold in the refined G, the
+            // per-reflection B_term and the partiality (rlp = 1 here).
+            const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
+            const double denom = static_cast<double>(r.partiality) * data.scale_factor * B_term;
+            r.image_scale_corr = (denom > 0.0) ? static_cast<float>(r.rlp / denom) : NAN;
         } else {
             r.I = 0.0f;
             r.sigma = NAN;
@@ -706,9 +710,9 @@ void PixelRefine::Run(const T *image,
 }
 
 // Explicit instantiations for the supported (uncompressed) image pixel types.
-template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
-template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
-template void PixelRefine::Run<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
-template void PixelRefine::Run<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
-template void PixelRefine::Run<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
-template void PixelRefine::Run<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, PixelRefineData &);
+template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 07b280cf..fec77c46 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -142,7 +142,6 @@ struct PixelRefineData {
 };
 
 class PixelRefine {
-    BraggPrediction &prediction;
     const AzimuthalIntegrationMapping &mapping;
     const size_t xpixel, ypixel;
     const DiffractionExperiment &experiment;
@@ -152,11 +151,14 @@ class PixelRefine {
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const AzimuthalIntegrationMapping &mapping,
-                const std::vector<MergedReflection> &reference,
-                BraggPrediction &prediction);
+                const std::vector<MergedReflection> &reference);
 
+    // The BraggPrediction is supplied per call (it is mutated): this keeps a
+    // single PixelRefine instance usable from several threads, each passing its
+    // own prediction buffer. Only `data` is written; PixelRefine state is const.
     template<class T>
     void Run(const T *image,
              const AzimuthalIntegrationProfile &profile,
+             BraggPrediction &prediction,
              PixelRefineData &data);
 };
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index f0f32aab..b01c05b1 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -58,7 +58,7 @@ void print_usage() {
     std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
     std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" << std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
-    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice)" << std::endl;
+    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)" << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Scaling and merging" << std::endl;
@@ -73,6 +73,10 @@ void print_usage() {
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
+    std::cout << std::endl;
+
+    std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
+    std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
     }
 
 enum {
@@ -87,7 +91,8 @@ enum {
     OPT_SCALING_OUTPUT,
     OPT_SINGLE_PASS_ROTATION,
     OPT_REDO_ROTATION_SPOTS,
-    OPT_FORCE_ROTATION_LATTICE
+    OPT_FORCE_ROTATION_LATTICE,
+    OPT_BANDWIDTH
 };
 
 static option long_options[] = {
@@ -123,6 +128,7 @@ static option long_options[] = {
     {"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
     {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
     {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
+    {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -293,6 +299,8 @@ int main(int argc, char **argv) {
     int64_t scaling_iter = 3;
     std::optional<CrystalLattice> forced_rotation_lattice;
 
+    std::optional<float> bandwidth_fwhm; // relative FWHM of dlambda/lambda
+
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
     GeomRefinementAlgorithmEnum refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
 
@@ -410,6 +418,8 @@ int main(int argc, char **argv) {
                 refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
             else if (alg == "orientation")
                 refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
+            else if (alg == "pixelrefine")
+                refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
             else {
                 logger.Error("Invalid geom refinement algorithm: {}", alg);
                 print_usage();
@@ -515,6 +525,13 @@ int main(int argc, char **argv) {
                 exit(EXIT_FAILURE);
             }
             break;
+        case OPT_BANDWIDTH:
+            bandwidth_fwhm = atof(optarg);
+            if (!(bandwidth_fwhm.value() >= 0.0f)) {
+                logger.Error("Invalid bandwidth: {}", optarg);
+                exit(EXIT_FAILURE);
+            }
+            break;
 
         default:
             print_usage();
@@ -616,6 +633,19 @@ int main(int argc, char **argv) {
         logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
     }
 
+    // X-ray bandwidth: CLI overrides the value carried in the dataset; otherwise
+    // keep whatever the dataset provided (0 / none -> monochromatic).
+    if (bandwidth_fwhm)
+        experiment.BandwidthFWHM(bandwidth_fwhm);
+    if (experiment.GetBandwidthFWHM())
+        logger.Info("X-ray bandwidth FWHM set to {:.4f}", experiment.GetBandwidthFWHM().value());
+
+    // PixelRefine integration needs reference intensities (the I_true hypothesis).
+    if (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine && reference_data.empty()) {
+        logger.Warning("-r pixelrefine needs --reference-mtz; falling back to beam_and_lattice");
+        refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
+    }
+
     // Configure Indexing
     IndexingSettings indexing_settings;
     indexing_settings.Algorithm(indexing_algorithm);
-- 
2.52.0


From 96edee9b2d8e6fe08d305f54d5b3c5027adac7a3 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 15:47:12 +0200
Subject: [PATCH 008/228] jfjoch_writer: Add incident_wavelength_spread

---
 common/DiffractionExperiment.cpp            | 5 +++++
 common/JFJochMessages.h                     | 1 +
 docs/CBOR.md                                | 1 +
 frame_serialize/CBORStream2Deserializer.cpp | 2 ++
 frame_serialize/CBORStream2Serializer.cpp   | 1 +
 writer/HDF5NXmx.cpp                         | 2 ++
 6 files changed, 12 insertions(+)

diff --git a/common/DiffractionExperiment.cpp b/common/DiffractionExperiment.cpp
index 6b1a3b66..3fac1a9c 100644
--- a/common/DiffractionExperiment.cpp
+++ b/common/DiffractionExperiment.cpp
@@ -641,6 +641,11 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
     message.beam_center_y = GetBeamY_pxl();
     message.detector_distance = GetDetectorDistance_mm() * 1e-3f;
     message.incident_wavelength = GetWavelength_A();
+    // NXmx incident_wavelength_spread is the FWHM of the wavelength distribution,
+    // in wavelength units. We store bandwidth as a relative FWHM (dlambda/lambda),
+    // so convert to absolute: dlambda = (dlambda/lambda) * lambda.
+    if (const auto bw = GetBandwidthFWHM())
+        message.incident_wavelength_spread = bw.value() * GetWavelength_A();
     message.incident_energy = GetIncidentEnergy_keV() * 1e3f;
     message.image_size_x = GetXPixelsNum();
     message.image_size_y = GetYPixelsNum();
diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index aa0b703f..067f938c 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -208,6 +208,7 @@ struct StartMessage {
 
     float incident_energy;
     float incident_wavelength;
+    std::optional<float> incident_wavelength_spread; // NXmx incident_wavelength_spread: FWHM of dlambda (Angstrom)
 
     float frame_time;
     float count_time;
diff --git a/docs/CBOR.md b/docs/CBOR.md
index bdca03d4..58339cc6 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -27,6 +27,7 @@ There are minor differences at the moment:
 | image_size_y                     | uint64               | Image height \[pixels\]                                                                                                                        |             X             |
 | incident_energy                  | float                | X-ray energy \[eV\]                                                                                                                            |             X             |
 | incident_wavelength              | float                | X-ray wavelength \[Angstrom\]                                                                                                                  |             X             |
+| incident_wavelength_spread       | float (optional)     | FWHM of the X-ray wavelength distribution \[Angstrom\] (NXmx incident_wavelength_spread); omitted when the beam is monochromatic               |                           |
 | frame_time                       | float                | Frame time, if multiple frames per trigger \[s\]                                                                                               |             X             |
 | count_time                       | float                | Exposure time \[s\]                                                                                                                            |             X             |
 | saturation_value                 | int64                | Maximum valid sample value                                                                                                                     |             X             |
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index 0d2c70ae..2a598de6 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -1182,6 +1182,8 @@ namespace {
                 message.incident_energy = GetCBORFloat(value);
             else if (key == "incident_wavelength")
                 message.incident_wavelength = GetCBORFloat(value);
+            else if (key == "incident_wavelength_spread")
+                message.incident_wavelength_spread = GetCBORFloat(value);
             else if (key == "frame_time")
                 message.frame_time = GetCBORFloat(value);
             else if (key == "count_time")
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index 6debfc5c..a79370f1 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -632,6 +632,7 @@ void CBORStream2Serializer::SerializeSequenceStart(const StartMessage& message)
 
     CBOR_ENC(mapEncoder, "incident_energy", message.incident_energy);
     CBOR_ENC(mapEncoder, "incident_wavelength", message.incident_wavelength);
+    CBOR_ENC(mapEncoder, "incident_wavelength_spread", message.incident_wavelength_spread);
 
     CBOR_ENC(mapEncoder, "frame_time", message.frame_time);
     CBOR_ENC(mapEncoder, "count_time", message.count_time);
diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index d2a3372d..2196dd56 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -480,6 +480,8 @@ void NXmx::Beam(const StartMessage &start) {
     HDF5Group group(*hdf5_file, "/entry/instrument/beam");
     group.NXClass("NXbeam");
     SaveScalar(group, "incident_wavelength", start.incident_wavelength)->Units("angstrom");
+    if (start.incident_wavelength_spread)
+        SaveScalar(group, "incident_wavelength_spread", start.incident_wavelength_spread.value())->Units("angstrom");
     if (start.total_flux)
         SaveScalar(group, "total_flux", start.total_flux.value())->Units("Hz");
 }
-- 
2.52.0


From 32e91f7287790835f4ae74ec160d8549c5d5523e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 15:56:20 +0200
Subject: [PATCH 009/228] Minor fixes

---
 image_analysis/UpdateReflectionResolution.h  |  6 ++++--
 image_analysis/indexing/FitProfileRadius.cpp |  3 ---
 image_analysis/scale_merge/Merge.cpp         |  2 +-
 image_analysis/scale_merge/ScalingResult.cpp |  4 ++--
 reader/JFJochHDF5Reader.cpp                  | 10 ++++++++--
 5 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/image_analysis/UpdateReflectionResolution.h b/image_analysis/UpdateReflectionResolution.h
index 46f909e1..695d2ba0 100644
--- a/image_analysis/UpdateReflectionResolution.h
+++ b/image_analysis/UpdateReflectionResolution.h
@@ -9,8 +9,10 @@
 #include "IntegrationOutcome.h"
 
 struct ResolutionStats {
-    float d_low = std::numeric_limits<float>::max();
-    float d_high = 0.0f;
+    // d_high = highest resolution = smallest d (tracked via `d_high > d`);
+    // d_low  = lowest  resolution = largest  d (tracked via `d_low  < d`).
+    float d_low = 0.0f;
+    float d_high = std::numeric_limits<float>::max();
     int n_reflections = 0;
     int n_images = 0;
 };
diff --git a/image_analysis/indexing/FitProfileRadius.cpp b/image_analysis/indexing/FitProfileRadius.cpp
index bef1f2a6..2c3ca8c2 100644
--- a/image_analysis/indexing/FitProfileRadius.cpp
+++ b/image_analysis/indexing/FitProfileRadius.cpp
@@ -1,9 +1,6 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
 #include "FitProfileRadius.h"
 #include <algorithm>  // std::nth_element
 #include <cmath>      // std::fabs
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index d455129e..8d69f811 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -406,7 +406,7 @@ std::ostream &operator<<(std::ostream &output, const MergeStatistics &in) {
     output << std::endl;
     output << fmt::format("  {:>8s} {:>8s} {:>8s} {:>8s} {:>8s} {:>8s} {:>8s} {:>8s}",
         "d_min", "N_obs", "N_uniq", "N_possib", "Compl","<I/sig>", "CC1/2", "CCref")
-    << std::endl;;
+    << std::endl;
     output << fmt::format("  {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->8s}",
         "", "", "", "", "", "", "", "") << std::endl;
     for (const auto &sh: in.shells) {
diff --git a/image_analysis/scale_merge/ScalingResult.cpp b/image_analysis/scale_merge/ScalingResult.cpp
index 318948b9..c01b88e5 100644
--- a/image_analysis/scale_merge/ScalingResult.cpp
+++ b/image_analysis/scale_merge/ScalingResult.cpp
@@ -36,8 +36,8 @@ void ScalingResult::SaveToFile(const std::string &filename) {
     const std::string img_path = filename + "_image.dat";
     std::ofstream img_file(img_path,  std::ofstream::out | std::ofstream::trunc);
     if (!img_file) {
-        throw JFJochException(JFJochExceptionCategory::FileWriteError
-                              , "Cannot open {} for writing");
+        throw JFJochException(JFJochExceptionCategory::FileWriteError,
+                              "Cannot open " + img_path + " for writing");
     }
 
     for (size_t i = 0; i < image_scale_g.size(); ++i) {
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index ce997918..cefbba4e 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -498,8 +498,14 @@ void JFJochHDF5Reader::ReadFile(const std::string &filename) {
             det_distance = 0.1; // Set to 100 mm, if det distance is less than 1 mm
         dataset->experiment.DetectorDistance_mm(det_distance * 1000.0);
 
-        dataset->experiment.IncidentEnergy_keV(
-            WVL_1A_IN_KEV / master_file->GetFloat("/entry/instrument/beam/incident_wavelength"));
+        const float incident_wavelength_A = master_file->GetFloat("/entry/instrument/beam/incident_wavelength");
+        dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / incident_wavelength_A);
+
+        // NXmx incident_wavelength_spread is the absolute FWHM (Angstrom); store it
+        // as the relative bandwidth FWHM (dlambda/lambda) used internally.
+        if (const auto spread = master_file->GetOptFloat("/entry/instrument/beam/incident_wavelength_spread"))
+            if (incident_wavelength_A > 0.0f)
+                dataset->experiment.BandwidthFWHM(spread.value() / incident_wavelength_A);
 
         dataset->error_value = master_file->GetOptInt("/entry/instrument/detector/error_value");
 
-- 
2.52.0


From 698a98be359b293aa9dfe220afb124309b578b28 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 20:06:53 +0200
Subject: [PATCH 010/228] PixelRefine: Claude fixed my bugs

---
 .../pixel_refinement/PixelRefine.cpp          | 222 ++++++++++++++----
 image_analysis/pixel_refinement/PixelRefine.h |  19 ++
 2 files changed, 193 insertions(+), 48 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index f2e4f93c..8a59a64c 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -319,6 +319,56 @@ PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
         reference_data[hkl_key_generator(ref)] = ref.I;
 }
 
+void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
+                                       double beam[2], double &dist_mm,
+                                       double detector_rot[2], double rot_vec[3],
+                                       double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const {
+    beam[0] = data.geom.GetBeamX_pxl();
+    beam[1] = data.geom.GetBeamY_pxl();
+    dist_mm = data.geom.GetDetectorDistance_mm();
+    detector_rot[0] = data.geom.GetPoniRot1_rad();
+    detector_rot[1] = data.geom.GetPoniRot2_rad();
+    rot_vec[0] = 1.0; rot_vec[1] = 0.0; rot_vec[2] = 0.0;
+    if (auto axis = data.geom.GetRotation()) {
+        rot_vec[0] = axis->GetAxis().x;
+        rot_vec[1] = axis->GetAxis().y;
+        rot_vec[2] = axis->GetAxis().z;
+    }
+
+    for (int i = 0; i < 3; ++i)
+        latt_vec0[i] = latt_vec1[i] = latt_vec2[i] = 0.0;
+
+    double beta = data.latt.GetUnitCell().beta;
+    switch (data.crystal_system) {
+        case gemmi::CrystalSystem::Orthorhombic:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            break;
+        case gemmi::CrystalSystem::Tetragonal:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
+            break;
+        case gemmi::CrystalSystem::Cubic:
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
+            break;
+        case gemmi::CrystalSystem::Hexagonal:
+            LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
+            break;
+        case gemmi::CrystalSystem::Monoclinic:
+            LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
+            latt_vec2[0] = beta;
+            break;
+        default: {
+            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
+            const auto uc = data.latt.GetUnitCell();
+            latt_vec2[0] = uc.alpha * M_PI / 180.0;
+            latt_vec2[1] = uc.beta * M_PI / 180.0;
+            latt_vec2[2] = uc.gamma * M_PI / 180.0;
+            break;
+        }
+    }
+}
+
 template<class T>
 void PixelRefine::Run(const T *image,
                       const AzimuthalIntegrationProfile &profile,
@@ -340,7 +390,10 @@ void PixelRefine::Run(const T *image,
     const auto azim_std = profile.GetStd();
     const auto &pixel_to_bin = mapping.GetPixelToBin();
     const auto &corrections = mapping.Corrections();
-    const int azim_bin_count = mapping.GetAzimuthalBinCount();
+    // pixel_to_bin stores the *full* bin index (azimuthal_sector * q_bins + q_bin),
+    // so the valid range is the total number of bins, i.e. the profile size - NOT
+    // GetAzimuthalBinCount() (which is only the number of azimuthal sectors).
+    const int total_bin_count = static_cast<int>(azim_result.size());
 
     const double angle_rad = data.angle_deg * M_PI / 180.0;
     const int radius = data.shoebox_radius;
@@ -392,11 +445,15 @@ void PixelRefine::Run(const T *image,
                 .PoniRot1_rad(data.geom.GetPoniRot1_rad())
                 .PoniRot2_rad(data.geom.GetPoniRot2_rad());
 
-        prediction.Calc(exp_iter, data.latt, settings_prediction);
+        const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
 
         // ---- 2. Collect per-reflection shoebox pixels -------------------------
+        // GetReflections() returns the full pre-sized buffer; only the first
+        // nrefl entries are valid for this image (the rest are stale/zeroed).
         groups.clear();
-        for (const auto &refl : prediction.GetReflections()) {
+        const auto &predicted = prediction.GetReflections();
+        for (int ri = 0; ri < nrefl; ++ri) {
+            const auto &refl = predicted[ri];
             const auto hkl = hkl_key_generator(refl);
             if (!reference_data.contains(hkl))
                 continue;
@@ -421,10 +478,10 @@ void PixelRefine::Run(const T *image,
                     const size_t npixel = xpixel * y + x;
                     const int azim_bin = pixel_to_bin[npixel];
 
-                    // Skip pixels not mapped to an azimuthal bin or carrying a
-                    // sentinel (masked / saturated) value. We assume the pixel
-                    // mask is already applied upstream.
-                    if (azim_bin >= azim_bin_count)
+                    // Skip pixels not mapped to a bin or carrying a sentinel
+                    // (masked / saturated) value. We assume the pixel mask is
+                    // already applied upstream.
+                    if (azim_bin >= total_bin_count)
                         continue;
                     if (image[npixel] == std::numeric_limits<T>::max())
                         continue;
@@ -464,47 +521,8 @@ void PixelRefine::Run(const T *image,
             return;
 
         // ---- 3. Set up parameter blocks (geometry part mirrors XtalOptimizer) -
-        beam[0] = data.geom.GetBeamX_pxl();
-        beam[1] = data.geom.GetBeamY_pxl();
-        dist_mm = data.geom.GetDetectorDistance_mm();
-        detector_rot[0] = data.geom.GetPoniRot1_rad();
-        detector_rot[1] = data.geom.GetPoniRot2_rad();
-        rot_vec[0] = 1.0; rot_vec[1] = 0.0; rot_vec[2] = 0.0;
-        if (auto axis = data.geom.GetRotation()) {
-            rot_vec[0] = axis->GetAxis().x;
-            rot_vec[1] = axis->GetAxis().y;
-            rot_vec[2] = axis->GetAxis().z;
-        }
-
-        double beta = data.latt.GetUnitCell().beta;
-        switch (data.crystal_system) {
-            case gemmi::CrystalSystem::Orthorhombic:
-                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-                break;
-            case gemmi::CrystalSystem::Tetragonal:
-                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
-                break;
-            case gemmi::CrystalSystem::Cubic:
-                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-                latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
-                break;
-            case gemmi::CrystalSystem::Hexagonal:
-                LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
-                break;
-            case gemmi::CrystalSystem::Monoclinic:
-                LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
-                latt_vec2[0] = beta;
-                break;
-            default: {
-                LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-                const auto uc = data.latt.GetUnitCell();
-                latt_vec2[0] = uc.alpha * M_PI / 180.0;
-                latt_vec2[1] = uc.beta * M_PI / 180.0;
-                latt_vec2[2] = uc.gamma * M_PI / 180.0;
-                break;
-            }
-        }
+        BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec,
+                             latt_vec0, latt_vec1, latt_vec2);
 
         // ---- 4. Build the problem ---------------------------------------------
         ceres::Problem problem;
@@ -709,6 +727,114 @@ void PixelRefine::Run(const T *image,
     }
 }
 
+std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &profile,
+                                             BraggPrediction &prediction,
+                                             const PixelRefineData &data,
+                                             bool include_background) const {
+    std::vector<float> img(xpixel * ypixel, 0.0f);
+
+    const double lambda = data.geom.GetWavelength_A();
+    const double pixel_size = data.geom.GetPixelSize_mm();
+    const auto azim_result = profile.GetResult();
+    const auto &pixel_to_bin = mapping.GetPixelToBin();
+    const auto &corrections = mapping.Corrections();
+    const int total_bin_count = static_cast<int>(azim_result.size());
+    const double angle_rad = data.angle_deg * M_PI / 180.0;
+    const int radius = data.shoebox_radius;
+    const double bw = data.bandwidth;
+
+    auto recip_area = [&](double x, double y) -> double {
+        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
+        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
+        return (qx % qy).Length();
+    };
+    auto bandwidth_radial_sq = [&](double d) -> double {
+        if (bw <= 0.0 || d <= 0.0)
+            return 0.0;
+        const double bl = bw * lambda;
+        return bl * bl / (2.0 * d * d * d * d);
+    };
+
+    // The model works in solid-angle/polarization-corrected units (as in Run,
+    // where Iobs = raw * correction). Map back to raw detector units (/ correction)
+    // so the predicted image overlays directly on the original image.
+    auto to_raw = [&](size_t npixel, double corrected) -> float {
+        const double corr = corrections[npixel];
+        return (corr > 0.0) ? static_cast<float>(corrected / corr) : 0.0f;
+    };
+
+    // Background base layer (per-pixel azimuthal mean), full-frame pass.
+    if (include_background) {
+        for (size_t p = 0; p < img.size(); ++p) {
+            const int bin = pixel_to_bin[p];
+            if (bin >= 0 && bin < total_bin_count)
+                img[p] = to_raw(p, azim_result[bin]);
+        }
+    }
+
+    double beam[2], dist_mm, detector_rot[2], rot_vec[3];
+    double latt_vec0[3], latt_vec1[3], latt_vec2[3];
+    BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec, latt_vec0, latt_vec1, latt_vec2);
+
+    DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+            .BeamY_pxl(data.geom.GetBeamY_pxl())
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .max_hkl = 100,
+        .centering = data.centering
+    };
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+    const auto &predicted = prediction.GetReflections();
+
+    for (int ri = 0; ri < nrefl; ++ri) {
+        const auto &refl = predicted[ri];
+        const auto it = reference_data.find(hkl_key_generator(refl));
+        if (it == reference_data.end())
+            continue;
+
+        const double Itrue = it->second;
+        const double R_bw_sq = bandwidth_radial_sq(refl.d);
+
+        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
+        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
+        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
+        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+
+        for (int y = min_y; y <= max_y; ++y) {
+            for (int x = min_x; x <= max_x; ++x) {
+                const size_t npixel = xpixel * y + x;
+
+                // Pure Bragg signal: Ibkg = 0 so Model() returns signal only; the
+                // background is already laid down above. Same code path as Run.
+                PixelObs obs{
+                    .x = static_cast<double>(x),
+                    .y = static_cast<double>(y),
+                    .Iobs = 0.0,
+                    .Ibkg = 0.0,
+                    .weight = 1.0,
+                    .A_recip = recip_area(x, y),
+                    .angle_rad = angle_rad
+                };
+                PixelResidual pr(obs, Itrue, lambda, pixel_size,
+                                 refl.h, refl.k, refl.l, R_bw_sq, data.crystal_system);
+
+                double signal = 0.0;
+                if (pr.Model(beam, &dist_mm, detector_rot, rot_vec,
+                             latt_vec0, latt_vec1, latt_vec2,
+                             &data.scale_factor, &data.B_factor, data.R, signal))
+                    img[npixel] += to_raw(npixel, signal);
+            }
+        }
+    }
+
+    return img;
+}
+
 // Explicit instantiations for the supported (uncompressed) image pixel types.
 template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index fec77c46..ae805f4e 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -148,6 +148,14 @@ class PixelRefine {
 
     const HKLKeyGenerator hkl_key_generator;
     std::map<HKLKey, double> reference_data;
+
+    // Fills the Ceres parameter blocks (geometry + symmetry-aware lattice
+    // parametrization) from the current model state. Shared by Run and
+    // PredictImage so both walk identical geometry/lattice code.
+    void BuildParameterBlocks(const PixelRefineData &data,
+                              double beam[2], double &dist_mm,
+                              double detector_rot[2], double rot_vec[3],
+                              double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const AzimuthalIntegrationMapping &mapping,
@@ -161,4 +169,15 @@ public:
              const AzimuthalIntegrationProfile &profile,
              BraggPrediction &prediction,
              PixelRefineData &data);
+
+    // Render the forward model as a full detector image (raw detector units, so
+    // it overlays directly on the original image). Uses the *same* per-pixel
+    // model path (PixelResidual::Model) as the optimizer, evaluated in double
+    // precision - slow but exact. For each reference reflection it adds the Bragg
+    // signal over its shoebox; with include_background it also lays down the
+    // azimuthal background. Diagnostic tool, not on the hot path.
+    std::vector<float> PredictImage(const AzimuthalIntegrationProfile &profile,
+                                    BraggPrediction &prediction,
+                                    const PixelRefineData &data,
+                                    bool include_background = true) const;
 };
-- 
2.52.0


From 05711a107702faf387243c38848fead091235565 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 21:22:19 +0200
Subject: [PATCH 011/228] jfjoch_viewer: Add pixel refinw and magnifier windows
 (to be tested)

---
 .../pixel_refinement/PixelRefine.cpp          |  33 ++--
 viewer/CMakeLists.txt                         |   5 +
 viewer/JFJochImageReadingWorker.cpp           | 172 +++++++++++++++-
 viewer/JFJochImageReadingWorker.h             |  26 +++
 viewer/JFJochViewerWindow.cpp                 |  37 ++++
 viewer/image_viewer/JFJochImage.cpp           |  21 ++
 viewer/image_viewer/JFJochImage.h             |  10 +
 viewer/windows/JFJochMagnifierWindow.cpp      |  35 ++++
 viewer/windows/JFJochMagnifierWindow.h        |  28 +++
 viewer/windows/JFJochPixelRefineWindow.cpp    | 186 ++++++++++++++++++
 viewer/windows/JFJochPixelRefineWindow.h      |  73 +++++++
 viewer/windows/PixelRefineParams.h            |  33 ++++
 12 files changed, 646 insertions(+), 13 deletions(-)
 create mode 100644 viewer/windows/JFJochMagnifierWindow.cpp
 create mode 100644 viewer/windows/JFJochMagnifierWindow.h
 create mode 100644 viewer/windows/JFJochPixelRefineWindow.cpp
 create mode 100644 viewer/windows/JFJochPixelRefineWindow.h
 create mode 100644 viewer/windows/PixelRefineParams.h

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 8a59a64c..cf64c993 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -436,6 +436,7 @@ void PixelRefine::Run(const T *image,
     double latt_vec1[3] = {0, 0, 0}; // lengths
     double latt_vec2[3] = {0, 0, 0}; // angles (rad)
 
+    const bool eval_only = (data.max_iterations <= 0);
     const int n_iter = std::max(1, data.max_iterations);
     for (int iter = 0; iter < n_iter; ++iter) {
         // ---- 1. Re-sync prediction geometry from the (refined) model ----------
@@ -595,19 +596,29 @@ void PixelRefine::Run(const T *image,
             problem.SetParameterBlockConstant(data.R);
         }
 
-        // ---- 6. Solve ---------------------------------------------------------
-        ceres::Solver::Options options;
-        options.linear_solver_type = ceres::DENSE_QR;
-        options.minimizer_progress_to_stdout = false;
-        options.logging_type = ceres::LoggingType::SILENT;
-        options.max_solver_time_in_seconds = data.max_time_s;
-        options.num_threads = 1;
+        // ---- 6. Solve (or, for max_iterations<=0, just evaluate the cost) -----
+        // Evaluate-only is the live-residual path: it reports the current cost
+        // without moving any parameter, so a UI can show how good the present
+        // R0/R1/bandwidth/geometry are as the user drags sliders.
+        if (eval_only) {
+            double cost = 0.0;
+            problem.Evaluate(ceres::Problem::EvaluateOptions(), &cost, nullptr, nullptr, nullptr);
+            data.final_cost = cost;
+            data.solved = true;
+        } else {
+            ceres::Solver::Options options;
+            options.linear_solver_type = ceres::DENSE_QR;
+            options.minimizer_progress_to_stdout = false;
+            options.logging_type = ceres::LoggingType::SILENT;
+            options.max_solver_time_in_seconds = data.max_time_s;
+            options.num_threads = 1;
 
-        ceres::Solver::Summary summary;
-        ceres::Solve(options, &problem, &summary);
+            ceres::Solver::Summary summary;
+            ceres::Solve(options, &problem, &summary);
 
-        data.final_cost = summary.final_cost;
-        data.solved = summary.IsSolutionUsable();
+            data.final_cost = summary.final_cost;
+            data.solved = summary.IsSolutionUsable();
+        }
 
         // ---- 7. Write refined geometry + lattice back into data ---------------
         if (data.refine_beam_center)
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 0db42e76..70981081 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -86,6 +86,11 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         ${APP_RESOURCES}
         windows/JFJochViewerReciprocalSpaceWindow.cpp
         windows/JFJochViewerReciprocalSpaceWindow.h
+        windows/JFJochPixelRefineWindow.cpp
+        windows/JFJochPixelRefineWindow.h
+        windows/JFJochMagnifierWindow.cpp
+        windows/JFJochMagnifierWindow.h
+        windows/PixelRefineParams.h
 )
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::DBus Qt6::Concurrent
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 6d7cf8c7..1ad60bd0 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -8,6 +8,8 @@
 #include <cstring>
 
 #include "JFJochImageReadingWorker.h"
+#include "../image_analysis/LoadFCalcFromMtz.h"
+#include "../image_analysis/bragg_prediction/BraggPredictionFactory.h"
 #include "../image_analysis/geom_refinement/AssignSpotsToRings.h"
 #include "../image_analysis/spot_finding/StrongPixelSet.h"
 #include "../image_analysis/spot_finding/SpotUtils.h"
@@ -66,6 +68,7 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
     : QObject(parent),
       indexing_settings(experiment.GetIndexingSettings()),
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
+    qRegisterMetaType<PixelRefineParams>("PixelRefineParams");
     spot_finding_settings = settings;;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
@@ -300,6 +303,14 @@ void JFJochImageReadingWorker::UpdateAzint_i(const JFJochReaderDataset *dataset)
         index_and_refine = std::make_unique<IndexAndRefine>(curr_experiment, indexing.get());
         image_analysis = std::make_unique<MXAnalysisWithoutFPGA>(curr_experiment, *azint_mapping, dataset->pixel_mask,
             *index_and_refine.get());
+
+        // PixelRefine state is tied to the experiment/mapping; rebuild lazily.
+        pixel_refine_.reset();
+        pixel_pred_.reset();
+        last_profile_.reset();
+        // Keep scale-on-the-fly alive across dataset reloads.
+        if (!pixel_reference_.empty())
+            index_and_refine->ReferenceIntensities(pixel_reference_);
     }
 }
 
@@ -444,8 +455,10 @@ void JFJochImageReadingWorker::ReanalyzeImage_i() {
     new_image_dataset->azimuthal_bins = azint_mapping->GetAzimuthalBinCount();
     new_image_dataset->q_bins = azint_mapping->GetQBinCount();
 
-    AzimuthalIntegrationProfile azint_profile(*azint_mapping);
-    image_analysis->Analyze(new_image->ImageData(),azint_profile, spot_finding_settings);
+    // Retain the profile (PixelRefine needs it). AzimuthalIntegrationProfile holds
+    // a mutex (non-copyable), so keep it via unique_ptr re-created each analysis.
+    last_profile_ = std::make_unique<AzimuthalIntegrationProfile>(*azint_mapping);
+    image_analysis->Analyze(new_image->ImageData(), *last_profile_, spot_finding_settings);
 
     current_image_ptr = new_image;
     auto end_time = std::chrono::high_resolution_clock::now();
@@ -705,3 +718,158 @@ void JFJochImageReadingWorker::LoadSpots(int64_t start_image, int64_t end_image,
         result = file_reader.ReadAllSpots(start_image, end_image, stride);
     emit spotsLoaded(result);
 }
+
+// ---------------------------------------------------------------------------
+// Experimental PixelRefine
+// ---------------------------------------------------------------------------
+void JFJochImageReadingWorker::EnsurePixelRefine_i() {
+    if (!pixel_refine_ && azint_mapping && !pixel_reference_.empty())
+        pixel_refine_ = std::make_unique<PixelRefine>(curr_experiment, *azint_mapping, pixel_reference_);
+    if (!pixel_pred_)
+        pixel_pred_ = CreateBraggPrediction(curr_experiment.IsRotationIndexing());
+}
+
+bool JFJochImageReadingWorker::BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p) const {
+    if (!current_image_ptr || !index_and_refine || !current_image.has_value())
+        return false;
+
+    const auto &outcomes = index_and_refine->GetIntegrationOutcome();
+    const int64_t n = current_image.value();
+    if (n < 0 || n >= static_cast<int64_t>(outcomes.size()))
+        return false;
+
+    const auto &io = outcomes[n];
+    if (io.reflections.empty()) // image not indexed/integrated
+        return false;
+
+    d.geom = io.geom;
+    d.latt = io.latt;
+
+    const auto &lt = current_image_ptr->ImageData().lattice_type;
+    if (lt) {
+        d.crystal_system = lt->crystal_system;
+        d.centering = lt->centering;
+    }
+    if (d.crystal_system == gemmi::CrystalSystem::Trigonal)
+        d.crystal_system = gemmi::CrystalSystem::Hexagonal;
+
+    d.R[0] = p.R0;
+    d.R[1] = p.R1;
+    d.bandwidth = p.bandwidth_fwhm / 2.3548; // FWHM -> sigma
+    d.scale_factor = p.scale_factor;
+    d.B_factor = p.B_factor;
+    if (std::isfinite(p.beam_x) && std::isfinite(p.beam_y))
+        d.geom.BeamX_pxl(static_cast<float>(p.beam_x)).BeamY_pxl(static_cast<float>(p.beam_y));
+
+    d.refine_orientation = p.refine_orientation;
+    d.refine_unit_cell = p.refine_unit_cell;
+    d.refine_beam_center = p.refine_beam_center;
+    d.refine_scale = p.refine_scale;
+    d.refine_B = p.refine_B;
+    d.refine_R = p.refine_R;
+    d.max_iterations = p.max_iterations;
+    return true;
+}
+
+std::shared_ptr<SimpleImage> JFJochImageReadingWorker::WrapFloatImage_i(const std::vector<float> &img) const {
+    auto si = std::make_shared<SimpleImage>();
+    si->image = CompressedImage(img, curr_experiment.GetXPixelsNum(), curr_experiment.GetYPixelsNum());
+    return si;
+}
+
+void JFJochImageReadingWorker::LoadReference(QString path) {
+    QMutexLocker ul(&m);
+    try {
+        pixel_reference_ = LoadFCalcFromMtz(path.toStdString());
+        if (index_and_refine)
+            index_and_refine->ReferenceIntensities(pixel_reference_); // enables scale-on-the-fly too
+        pixel_refine_.reset();                                        // rebuild with new reference
+        emit pixelRefineStatus(QString("Loaded %1 reference reflections").arg(pixel_reference_.size()));
+    } catch (const std::exception &e) {
+        emit pixelRefineStatus(QString("Failed to load reference: %1").arg(e.what()));
+    }
+}
+
+void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
+    QMutexLocker ul(&m);
+    if (!last_profile_) {
+        emit pixelRefineStatus("Analyze an image first");
+        return;
+    }
+    EnsurePixelRefine_i();
+    if (!pixel_refine_) {
+        emit pixelRefineStatus("Load reference data first");
+        return;
+    }
+
+    PixelRefineData d;
+    if (!BuildPixelSeed_i(d, params)) {
+        emit pixelRefineStatus("Current image is not indexed");
+        return;
+    }
+
+    // Preview = evaluate only: do not move any parameter.
+    d.refine_orientation = d.refine_unit_cell = d.refine_beam_center = false;
+    d.refine_scale = d.refine_B = d.refine_R = false;
+    d.max_iterations = 0;
+
+    try {
+        const auto &img32 = current_image_ptr->Image();
+        pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
+        emit pixelRefineResidual(d.final_cost, static_cast<int64_t>(d.reflections.size()));
+
+        auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
+        emit predictedImageReady(WrapFloatImage_i(pred));
+    } catch (const std::exception &e) {
+        emit pixelRefineStatus(QString("PixelRefine preview failed: %1").arg(e.what()));
+    }
+}
+
+void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
+    QMutexLocker ul(&m);
+    if (!last_profile_) {
+        emit pixelRefineStatus("Analyze an image first");
+        return;
+    }
+    EnsurePixelRefine_i();
+    if (!pixel_refine_) {
+        emit pixelRefineStatus("Load reference data first");
+        return;
+    }
+
+    PixelRefineData d;
+    if (!BuildPixelSeed_i(d, params)) {
+        emit pixelRefineStatus("Current image is not indexed");
+        return;
+    }
+    if (d.max_iterations <= 0)
+        d.max_iterations = 3;
+
+    try {
+        const auto &img32 = current_image_ptr->Image();
+        pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
+
+        // Push refined values back so the sliders follow the optimizer.
+        PixelRefineParams out = params;
+        out.R0 = d.R[0];
+        out.R1 = d.R[1];
+        out.bandwidth_fwhm = d.bandwidth * 2.3548; // sigma -> FWHM
+        out.scale_factor = d.scale_factor;
+        out.B_factor = d.B_factor;
+        out.beam_x = d.geom.GetBeamX_pxl();
+        out.beam_y = d.geom.GetBeamY_pxl();
+        emit pixelRefineParamsRefined(out);
+        emit pixelRefineResidual(d.final_cost, static_cast<int64_t>(d.reflections.size()));
+
+        auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
+        emit predictedImageReady(WrapFloatImage_i(pred));
+
+        // Show the refined predictions on the main image too.
+        auto new_image = std::make_shared<JFJochReaderImage>(*current_image_ptr);
+        new_image->ImageData().reflections = d.reflections;
+        current_image_ptr = new_image;
+        emit imageLoaded(current_image_ptr);
+    } catch (const std::exception &e) {
+        emit pixelRefineStatus(QString("PixelRefine failed: %1").arg(e.what()));
+    }
+}
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 4d419f9d..6ab9e429 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -15,7 +15,10 @@
 #include "../common/Logger.h"
 #include "../reader/JFJochHttpReader.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
+#include "../image_analysis/pixel_refinement/PixelRefine.h"
+#include "../image_analysis/bragg_prediction/BraggPrediction.h"
 #include "SimpleImage.h"
+#include "windows/PixelRefineParams.h"
 #include "../common/MovingAverage.h"
 
 Q_DECLARE_METATYPE(std::shared_ptr<const JFJochReaderDataset>)
@@ -57,6 +60,18 @@ private:
     std::unique_ptr<MXAnalysisWithoutFPGA> image_analysis;
     std::unique_ptr<IndexAndRefine> index_and_refine;
 
+    // Experimental PixelRefine support. last_profile_ keeps the azimuthal profile
+    // of the most recently analyzed image (PixelRefine needs it); the engine and a
+    // dedicated prediction buffer are built lazily once a reference is loaded.
+    std::unique_ptr<AzimuthalIntegrationProfile> last_profile_;
+    std::vector<MergedReflection> pixel_reference_;
+    std::unique_ptr<PixelRefine> pixel_refine_;
+    std::unique_ptr<BraggPrediction> pixel_pred_;
+
+    void EnsurePixelRefine_i();
+    bool BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p) const;
+    std::shared_ptr<SimpleImage> WrapFloatImage_i(const std::vector<float> &img) const;
+
     std::unique_ptr<ROIElement> roi;
 
     SpotFindingSettings spot_finding_settings;
@@ -117,6 +132,12 @@ signals:
     void fileLoadError(QString title, QString message);
     void fileLoadRetryStatus(bool active, QString message);
 
+    // PixelRefine (experimental)
+    void predictedImageReady(std::shared_ptr<const SimpleImage> image);
+    void pixelRefineResidual(double cost, int64_t n_reflections);
+    void pixelRefineParamsRefined(PixelRefineParams params);
+    void pixelRefineStatus(QString message);
+
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
     ~JFJochImageReadingWorker() override = default;
@@ -153,4 +174,9 @@ public slots:
     void LoadCalibration(QString dataset);
     void setAutoLoadMode(AutoloadMode mode);
     void setAutoLoadJump(int64_t val);
+
+    // PixelRefine (experimental)
+    void LoadReference(QString path);
+    void PixelRefinePreview(PixelRefineParams params);
+    void PixelRefineRun(PixelRefineParams params);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index e43fcc76..de383008 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -25,6 +25,9 @@
 #include "toolbar/JFJochViewerToolbarImage.h"
 #include "windows/JFJoch2DAzintImageWindow.h"
 #include "windows/JFJochAzIntWindow.h"
+#include "windows/JFJochPixelRefineWindow.h"
+#include "windows/JFJochMagnifierWindow.h"
+#include "image_viewer/JFJochImage.h"
 #include <QMessageBox>
 
 JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString &file) : QMainWindow(parent) {
@@ -103,6 +106,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     auto azintWindow = new JFJochAzIntWindow(experiment.GetAzimuthalIntegrationSettings(), this);
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
+    auto pixelRefineWindow = new JFJochPixelRefineWindow(this);
+    auto magnifierWindow = new JFJochMagnifierWindow(this);
 
     menuBar->AddWindowEntry(tableWindow, "Image list");
     menuBar->AddWindowEntry(spotWindow, "Spot list");
@@ -113,6 +118,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(reciprocalWindow, "Reciprocal space viewer");
     menuBar->AddWindowEntry(azintWindow, "Azimuthal integration settings");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
+    menuBar->AddWindowEntry(pixelRefineWindow, "PixelRefine (experimental)");
+    menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
 
     if (dbus) {
         // Create adaptor attached to this window
@@ -333,6 +340,36 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(azintImageWindow, &JFJoch2DAzintImageWindow::zoomOnBin,
             viewer, &JFJochDiffractionImage::centerOnSpot);
 
+    // --- PixelRefine (experimental) ---
+    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+            pixelRefineWindow, &JFJochHelperWindow::imageLoaded);
+    connect(pixelRefineWindow, &JFJochPixelRefineWindow::paramsChanged,
+            reading_worker, &JFJochImageReadingWorker::PixelRefinePreview);
+    connect(pixelRefineWindow, &JFJochPixelRefineWindow::refineRequested,
+            reading_worker, &JFJochImageReadingWorker::PixelRefineRun);
+    connect(pixelRefineWindow, &JFJochPixelRefineWindow::loadReferenceRequested,
+            reading_worker, &JFJochImageReadingWorker::LoadReference);
+    connect(reading_worker, &JFJochImageReadingWorker::predictedImageReady,
+            pixelRefineWindow, &JFJochPixelRefineWindow::setPredictedImage);
+    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineResidual,
+            pixelRefineWindow, &JFJochPixelRefineWindow::setResidual);
+    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineParamsRefined,
+            pixelRefineWindow, &JFJochPixelRefineWindow::setRefinedParams);
+    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineStatus,
+            pixelRefineWindow, &JFJochPixelRefineWindow::setStatus);
+
+    // Lock the predicted-image viewport to the original image (both directions).
+    connect(viewer, &JFJochImage::viewportChanged,
+            pixelRefineWindow->imageView(), &JFJochImage::applyViewport);
+    connect(pixelRefineWindow->imageView(), &JFJochImage::viewportChanged,
+            viewer, &JFJochImage::applyViewport);
+
+    // --- Magnifier ---
+    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+            magnifierWindow, &JFJochHelperWindow::imageLoaded);
+    connect(viewer, &JFJochImage::hoverScenePos,
+            magnifierWindow, &JFJochMagnifierWindow::centerAt);
+
     // Ensure worker is deleted in its own thread when the thread stops
     connect(reading_thread, &QThread::finished, reading_worker, &QObject::deleteLater);
 
diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index 7700dc4f..ed030ef0 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -119,6 +119,7 @@ void JFJochImage::wheelEvent(QWheelEvent *event) {
         translate(delta.x(), delta.y()); // Shift the view
 
         updateOverlay();
+        emitViewportChanged();
     }
 }
 
@@ -188,6 +189,7 @@ void JFJochImage::mouseMoveEvent(QMouseEvent *event) {
 
     const QPointF scenePos = mapToScene(event->pos());
     mouseHover(event);
+    emit hoverScenePos(scenePos);
     QPointF delta;
 
     switch (mouse_event_type) {
@@ -199,6 +201,7 @@ void JFJochImage::mouseMoveEvent(QMouseEvent *event) {
             verticalScrollBar()->setValue(verticalScrollBar()->value() - viewDelta.y());
 
             updateOverlay();
+            emitViewportChanged();
             break;
         }
         case MouseEventType::DrawingROI:
@@ -679,6 +682,24 @@ void JFJochImage::centerOnSpot(QPointF point) {
     // If W or H = 0, then conditions are never satisfied
     if (point.x() >= 0 && point.x() < W && point.y() >= 0 && point.y() < H)
         centerOn(point);
+    emitViewportChanged();
+}
+
+void JFJochImage::emitViewportChanged() {
+    if (m_applyingViewport || !scene())
+        return;
+    emit viewportChanged(transform(), mapToScene(viewport()->rect().center()));
+}
+
+void JFJochImage::applyViewport(QTransform transform, QPointF center) {
+    if (m_applyingViewport || !scene())
+        return;
+    m_applyingViewport = true;
+    setTransform(transform);
+    scale_factor = transform.m11();
+    centerOn(center);
+    updateOverlay();
+    m_applyingViewport = false;
 }
 
 void JFJochImage::writePixelLabels() {
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index 4e8b1ad8..593cda04 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -5,6 +5,8 @@
 
 #include <QGraphicsView>
 #include <QMouseEvent>
+#include <QTransform>
+#include <QPointF>
 #include "../../common/ColorScale.h"
 #include "../../common/JFJochMessages.h"
 
@@ -15,6 +17,11 @@ class JFJochImage : public QGraphicsView {
 
     bool m_adjustForegroundWithWheel = false;
 
+    // Viewport-lock support: guard prevents the emit<->apply ping-pong between
+    // two linked views, and the helper broadcasts the current transform+center.
+    bool m_applyingViewport = false;
+    void emitViewportChanged();
+
     void DrawROI();
     virtual void addCustomOverlay();
     void updateROI();
@@ -106,6 +113,8 @@ signals:
     void roiBoxUpdated(QRect box);
     void roiCircleUpdated(double x, double y, double radius);
     void roiCalculated(ROIMessage &output);
+    void viewportChanged(QTransform transform, QPointF center);
+    void hoverScenePos(QPointF scenePos);
 private slots:
     void onScroll(int value);
 public slots:
@@ -118,6 +127,7 @@ public slots:
     void SetROICircle(double x, double y, double radius);
 
     void centerOnSpot(QPointF point);
+    void applyViewport(QTransform transform, QPointF center);
     void fitToView();
 
     void adjustForeground(bool input);
diff --git a/viewer/windows/JFJochMagnifierWindow.cpp b/viewer/windows/JFJochMagnifierWindow.cpp
new file mode 100644
index 00000000..266a5056
--- /dev/null
+++ b/viewer/windows/JFJochMagnifierWindow.cpp
@@ -0,0 +1,35 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochMagnifierWindow.h"
+#include "../image_viewer/JFJochSimpleImage.h"
+#include "../SimpleImage.h"
+
+#include <QTransform>
+
+JFJochMagnifierWindow::JFJochMagnifierWindow(QWidget *parent)
+    : JFJochHelperWindow(parent) {
+    setWindowTitle("Magnifier");
+    m_image = new JFJochSimpleImage(this);
+    setCentralWidget(m_image);
+    resize(320, 320);
+}
+
+void JFJochMagnifierWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage> image) {
+    if (!image) {
+        m_have_image = false;
+        m_image->setImage(nullptr);
+        return;
+    }
+    const auto &exp = image->Dataset().experiment;
+    auto si = std::make_shared<SimpleImage>();
+    si->image = CompressedImage(image->Image(), exp.GetXPixelsNum(), exp.GetYPixelsNum());
+    m_image->setImage(si);
+    m_have_image = true;
+}
+
+void JFJochMagnifierWindow::centerAt(QPointF scenePos) {
+    if (!m_have_image || !isVisible())
+        return;
+    m_image->applyViewport(QTransform::fromScale(m_magnification, m_magnification), scenePos);
+}
diff --git a/viewer/windows/JFJochMagnifierWindow.h b/viewer/windows/JFJochMagnifierWindow.h
new file mode 100644
index 00000000..91ec2621
--- /dev/null
+++ b/viewer/windows/JFJochMagnifierWindow.h
@@ -0,0 +1,28 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "JFJochHelperWindow.h"
+#include <QPointF>
+
+class JFJochSimpleImage;
+
+// ADXV-style magnifier: a small window showing a high-zoom close-up of the main
+// image that follows the cursor. Fed the original image (converted to a
+// SimpleImage) and re-centered on each hover position.
+class JFJochMagnifierWindow : public JFJochHelperWindow {
+    Q_OBJECT
+
+    JFJochSimpleImage *m_image;
+    double m_magnification = 12.0;
+    bool m_have_image = false;
+
+public:
+    explicit JFJochMagnifierWindow(QWidget *parent = nullptr);
+
+    void imageLoaded(std::shared_ptr<const JFJochReaderImage> image) override;
+
+public slots:
+    void centerAt(QPointF scenePos);
+};
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
new file mode 100644
index 00000000..364cf5df
--- /dev/null
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -0,0 +1,186 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochPixelRefineWindow.h"
+#include "../image_viewer/JFJochSimpleImage.h"
+
+#include <QWidget>
+#include <QHBoxLayout>
+#include <QVBoxLayout>
+#include <QFormLayout>
+#include <QGroupBox>
+#include <QFileDialog>
+#include <cmath>
+
+JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
+    : JFJochHelperWindow(parent) {
+    setWindowTitle("PixelRefine (experimental)");
+
+    auto central = new QWidget(this);
+    setCentralWidget(central);
+    auto layout = new QHBoxLayout(central);
+
+    // --- predicted image (left, expanding) ---------------------------------
+    m_image = new JFJochSimpleImage(this);
+    m_image->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
+    layout->addWidget(m_image, 1);
+
+    // --- control panel (right) ---------------------------------------------
+    auto controls = new QWidget(this);
+    controls->setMinimumWidth(320);
+    auto controlsLayout = new QVBoxLayout(controls);
+    layout->addWidget(controls, 0);
+
+    auto paramBox = new QGroupBox(tr("Model parameters"), this);
+    auto form = new QFormLayout(paramBox);
+
+    m_R0    = new SliderPlusBox(1e-4, 0.05, 1e-4, 4, this);                       m_R0->setValue(0.005);
+    m_R1    = new SliderPlusBox(1e-4, 0.05, 1e-4, 4, this);                       m_R1->setValue(0.005);
+    m_bw    = new SliderPlusBox(0.0, 0.05, 1e-4, 4, this);                        m_bw->setValue(0.0);
+    m_scale = new SliderPlusBox(1e-3, 1e4, 1e-3, 3, this, SliderPlusBox::Logarithmic); m_scale->setValue(1.0);
+    m_B     = new SliderPlusBox(0.0, 200.0, 0.1, 1, this);                        m_B->setValue(0.0);
+    m_beamx = new SliderPlusBox(0.0, 5000.0, 0.5, 1, this);                       m_beamx->setValue(0.0);
+    m_beamy = new SliderPlusBox(0.0, 5000.0, 0.5, 1, this);                       m_beamy->setValue(0.0);
+
+    form->addRow(tr("R0 radial [Å⁻¹]:"), m_R0);
+    form->addRow(tr("R1 tangential [Å⁻¹]:"), m_R1);
+    form->addRow(tr("Bandwidth FWHM (Δλ/λ):"), m_bw);
+    form->addRow(tr("Scale G:"), m_scale);
+    form->addRow(tr("B-factor [Ų]:"), m_B);
+
+    m_overrideBeam = new QCheckBox(tr("Override beam centre"), this);
+    form->addRow(QString(), m_overrideBeam);
+    form->addRow(tr("Beam X [px]:"), m_beamx);
+    form->addRow(tr("Beam Y [px]:"), m_beamy);
+    m_beamx->setEnabled(false);
+    m_beamy->setEnabled(false);
+
+    controlsLayout->addWidget(paramBox);
+
+    // --- what "Refine" is allowed to move ----------------------------------
+    auto refBox = new QGroupBox(tr("Refine (Ceres)"), this);
+    auto refLayout = new QVBoxLayout(refBox);
+    m_refOrientation = new QCheckBox(tr("Orientation"), this);   m_refOrientation->setChecked(true);
+    m_refCell        = new QCheckBox(tr("Unit cell"), this);
+    m_refBeam        = new QCheckBox(tr("Beam centre"), this);
+    m_refScale       = new QCheckBox(tr("Scale G"), this);       m_refScale->setChecked(true);
+    m_refB           = new QCheckBox(tr("B-factor"), this);
+    m_refR           = new QCheckBox(tr("Widths R0/R1"), this);  m_refR->setChecked(true);
+    for (auto *cb : {m_refOrientation, m_refCell, m_refBeam, m_refScale, m_refB, m_refR})
+        refLayout->addWidget(cb);
+    controlsLayout->addWidget(refBox);
+
+    // --- buttons + readouts -------------------------------------------------
+    m_loadRef = new QPushButton(tr("Load reference MTZ…"), this);
+    m_refine  = new QPushButton(tr("Refine"), this);
+    controlsLayout->addWidget(m_loadRef);
+    controlsLayout->addWidget(m_refine);
+
+    m_residual = new QLabel(tr("Residual: —"), this);
+    m_status   = new QLabel(QString(), this);
+    m_status->setWordWrap(true);
+    m_status->setStyleSheet("color: rgb(80, 80, 80);");
+    controlsLayout->addWidget(m_residual);
+    controlsLayout->addWidget(m_status);
+    controlsLayout->addStretch(1);
+
+    // --- debounce timer for live preview -----------------------------------
+    m_debounce = new QTimer(this);
+    m_debounce->setSingleShot(true);
+    m_debounce->setInterval(150);
+    connect(m_debounce, &QTimer::timeout, this, [this] {
+        emit paramsChanged(currentParams());
+    });
+
+    for (auto *s : {m_R0, m_R1, m_bw, m_scale, m_B, m_beamx, m_beamy})
+        connect(s, &SliderPlusBox::valueChanged, this, [this](double) { onControlChanged(); });
+
+    connect(m_overrideBeam, &QCheckBox::toggled, this, [this](bool on) {
+        m_beamx->setEnabled(on);
+        m_beamy->setEnabled(on);
+        onControlChanged();
+    });
+
+    connect(m_loadRef, &QPushButton::clicked, this, [this] {
+        const QString path = QFileDialog::getOpenFileName(
+            this, tr("Load reference MTZ"), QString(), tr("MTZ files (*.mtz);;All files (*)"));
+        if (!path.isEmpty())
+            emit loadReferenceRequested(path);
+    });
+
+    connect(m_refine, &QPushButton::clicked, this, [this] {
+        PixelRefineParams p = currentParams();
+        p.max_iterations = 5;
+        emit refineRequested(p);
+    });
+}
+
+PixelRefineParams JFJochPixelRefineWindow::currentParams() const {
+    PixelRefineParams p;
+    p.R0 = m_R0->value();
+    p.R1 = m_R1->value();
+    p.bandwidth_fwhm = m_bw->value();
+    p.scale_factor = m_scale->value();
+    p.B_factor = m_B->value();
+    if (m_overrideBeam->isChecked()) {
+        p.beam_x = m_beamx->value();
+        p.beam_y = m_beamy->value();
+    } else {
+        p.beam_x = NAN;
+        p.beam_y = NAN;
+    }
+    p.refine_orientation = m_refOrientation->isChecked();
+    p.refine_unit_cell   = m_refCell->isChecked();
+    p.refine_beam_center = m_refBeam->isChecked();
+    p.refine_scale       = m_refScale->isChecked();
+    p.refine_B           = m_refB->isChecked();
+    p.refine_R           = m_refR->isChecked();
+    return p;
+}
+
+void JFJochPixelRefineWindow::onControlChanged() {
+    if (m_suppress)
+        return;
+    m_debounce->start();
+}
+
+void JFJochPixelRefineWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage> image) {
+    if (m_beamInit || !image)
+        return;
+    const auto geom = image->Dataset().experiment.GetDiffractionGeometry();
+    m_beamx->setMax(static_cast<double>(image->Dataset().experiment.GetXPixelsNum()));
+    m_beamy->setMax(static_cast<double>(image->Dataset().experiment.GetYPixelsNum()));
+    m_suppress = true;
+    m_beamx->setValue(geom.GetBeamX_pxl());
+    m_beamy->setValue(geom.GetBeamY_pxl());
+    m_suppress = false;
+    m_beamInit = true;
+}
+
+void JFJochPixelRefineWindow::setPredictedImage(std::shared_ptr<const SimpleImage> image) {
+    m_image->setImage(std::move(image));
+}
+
+void JFJochPixelRefineWindow::setResidual(double cost, int64_t n_reflections) {
+    m_residual->setText(tr("Residual: %1   (%2 reflections)")
+                            .arg(cost, 0, 'g', 6)
+                            .arg(n_reflections));
+}
+
+void JFJochPixelRefineWindow::setRefinedParams(PixelRefineParams params) {
+    m_suppress = true;
+    m_R0->setValue(params.R0);
+    m_R1->setValue(params.R1);
+    m_bw->setValue(params.bandwidth_fwhm);
+    m_scale->setValue(params.scale_factor);
+    m_B->setValue(params.B_factor);
+    if (std::isfinite(params.beam_x) && std::isfinite(params.beam_y)) {
+        m_beamx->setValue(params.beam_x);
+        m_beamy->setValue(params.beam_y);
+    }
+    m_suppress = false;
+}
+
+void JFJochPixelRefineWindow::setStatus(QString message) {
+    m_status->setText(message);
+}
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
new file mode 100644
index 00000000..7e7f167c
--- /dev/null
+++ b/viewer/windows/JFJochPixelRefineWindow.h
@@ -0,0 +1,73 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "JFJochHelperWindow.h"
+#include "PixelRefineParams.h"
+#include "../SimpleImage.h"
+#include "../widgets/SliderPlusBox.h"
+
+#include <memory>
+#include <QCheckBox>
+#include <QLabel>
+#include <QPushButton>
+#include <QTimer>
+
+class JFJochSimpleImage;
+
+// Experimental PixelRefine control window: sliders for the forward-model
+// parameters, a live (debounced) predicted-image preview, a residual readout,
+// "Load reference" and "Refine" buttons. The predicted-image view is exposed so
+// the main window can lock its viewport to the original image.
+class JFJochPixelRefineWindow : public JFJochHelperWindow {
+    Q_OBJECT
+
+    JFJochSimpleImage *m_image;
+
+    SliderPlusBox *m_R0;
+    SliderPlusBox *m_R1;
+    SliderPlusBox *m_bw;
+    SliderPlusBox *m_scale;
+    SliderPlusBox *m_B;
+    SliderPlusBox *m_beamx;
+    SliderPlusBox *m_beamy;
+
+    QCheckBox *m_overrideBeam;
+    QCheckBox *m_refOrientation;
+    QCheckBox *m_refCell;
+    QCheckBox *m_refBeam;
+    QCheckBox *m_refScale;
+    QCheckBox *m_refB;
+    QCheckBox *m_refR;
+
+    QLabel *m_residual;
+    QLabel *m_status;
+    QPushButton *m_loadRef;
+    QPushButton *m_refine;
+
+    QTimer *m_debounce;
+    bool m_suppress = false;   // guard while pushing refined params into sliders
+    bool m_beamInit = false;   // beam-centre sliders initialised from geometry
+
+    PixelRefineParams currentParams() const;
+    void onControlChanged();
+
+public:
+    explicit JFJochPixelRefineWindow(QWidget *parent = nullptr);
+
+    JFJochSimpleImage *imageView() const { return m_image; }
+
+    void imageLoaded(std::shared_ptr<const JFJochReaderImage> image) override;
+
+signals:
+    void paramsChanged(PixelRefineParams params);       // debounced live preview
+    void refineRequested(PixelRefineParams params);     // "Refine" button
+    void loadReferenceRequested(QString path);          // "Load reference" button
+
+public slots:
+    void setPredictedImage(std::shared_ptr<const SimpleImage> image);
+    void setResidual(double cost, int64_t n_reflections);
+    void setRefinedParams(PixelRefineParams params);
+    void setStatus(QString message);
+};
diff --git a/viewer/windows/PixelRefineParams.h b/viewer/windows/PixelRefineParams.h
new file mode 100644
index 00000000..4b266e62
--- /dev/null
+++ b/viewer/windows/PixelRefineParams.h
@@ -0,0 +1,33 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <cmath>
+#include <QMetaType>
+
+// Parameters exchanged between the PixelRefine window (sliders/buttons) and the
+// reading worker. bandwidth here is the *FWHM* of dlambda/lambda (user-facing);
+// the worker converts it to the sigma that PixelRefineData expects. beam_x/beam_y
+// are NaN to mean "keep the current refined geometry".
+struct PixelRefineParams {
+    double R0 = 0.005;          // radial / partiality width (A^-1)
+    double R1 = 0.005;          // tangential / profile width (A^-1)
+    double bandwidth_fwhm = 0.0; // relative bandwidth FWHM (dlambda/lambda)
+    double scale_factor = 1.0;   // overall scale G
+    double B_factor = 0.0;       // Debye-Waller B (A^2)
+    double beam_x = NAN;         // detector beam centre X (px); NaN = keep current
+    double beam_y = NAN;         // detector beam centre Y (px); NaN = keep current
+
+    // What the "Refine" button is allowed to move (ignored by the preview path).
+    bool refine_orientation = true;
+    bool refine_unit_cell   = false;
+    bool refine_beam_center = false;
+    bool refine_scale       = true;
+    bool refine_B           = false;
+    bool refine_R           = true;
+
+    int max_iterations = 3; // <=0 means evaluate-only (preview / residual)
+};
+
+Q_DECLARE_METATYPE(PixelRefineParams)
-- 
2.52.0


From e8a9b1840d2a01a8aea55a5f09a5d35436643d22 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 8 Jun 2026 22:45:22 +0200
Subject: [PATCH 012/228] PixelRefine: Make it faster by doing one cell
 calculation per shoe-box

---
 .../pixel_refinement/PixelRefine.cpp          | 412 +++++++++++-------
 1 file changed, 260 insertions(+), 152 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index cf64c993..3b6ccdfe 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -40,6 +40,139 @@ double SafeInv(double x, double fallback) {
     return 1.0 / x;
 }
 
+// Per-pixel: map a detector pixel through the current geometry into the
+// reference reciprocal frame. Cheap (a few trig + one rotation); depends on the
+// pixel and the detector geometry, not on the lattice.
+template<typename T>
+void ObservedRecip(const T *beam, const T *distance_mm, const T *detector_rot,
+                   const T *rotation_axis, double obs_x, double obs_y,
+                   double pixel_size, double inv_lambda, double angle_rad,
+                   Eigen::Matrix<T, 3, 1> &e_obs_recip) {
+    // PyFAI convention (left-handed for rot1/rot2): rot3 = 0 assumed.
+    const T c1 = ceres::cos(detector_rot[0]);
+    const T s1 = ceres::sin(detector_rot[0]);
+    const T c2 = ceres::cos(detector_rot[1]);
+    const T s2 = ceres::sin(detector_rot[1]);
+
+    const T det_x = (T(obs_x) - beam[0]) * T(pixel_size);
+    const T det_y = (T(obs_y) - beam[1]) * T(pixel_size);
+    const T det_z = T(distance_mm[0]);
+
+    const T t1_x = c1 * det_x + s1 * det_z;
+    const T t1_y = det_y;
+    const T t1_z = -s1 * det_x + c1 * det_z;
+
+    const T x = t1_x;
+    const T y = c2 * t1_y + s2 * t1_z;
+    const T z = -s2 * t1_y + c2 * t1_z;
+
+    const T inv_norm = T(1) / ceres::sqrt(x * x + y * y + z * z);
+
+    T recip_raw[3] = {
+        x * inv_norm * T(inv_lambda),
+        y * inv_norm * T(inv_lambda),
+        (z * inv_norm - T(1.0)) * T(inv_lambda)
+    };
+    const T aa_back[3] = {
+        T(angle_rad) * rotation_axis[0],
+        T(angle_rad) * rotation_axis[1],
+        T(angle_rad) * rotation_axis[2]
+    };
+    T recip_obs[3];
+    ceres::AngleAxisRotatePoint(aa_back, recip_raw, recip_obs);
+    e_obs_recip = Eigen::Matrix<T, 3, 1>(recip_obs[0], recip_obs[1], recip_obs[2]);
+}
+
+// Per-reflection: predicted node g_hkl, |g_hkl|^2, and the Ewald-sphere normal.
+// This is the expensive part (symmetry-aware B matrix, three rotations, cross
+// products) - it depends only on the lattice (p0,p1,p2) and hkl, so for a whole
+// shoebox it can be computed once. Convention identical to XtalOptimizer.
+template<typename T>
+bool PredictedNode(const T *p0, const T *p1, const T *p2,
+                   double exp_h, double exp_k, double exp_l,
+                   gemmi::CrystalSystem symmetry, double inv_lambda,
+                   Eigen::Matrix<T, 3, 1> &e_pred_recip,
+                   Eigen::Matrix<T, 3, 1> &n_radial, T &q_sq) {
+    Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
+    Eigen::Matrix<T, 3, 3> Bmat = Eigen::Matrix<T, 3, 3>::Identity();
+
+    if (symmetry == gemmi::CrystalSystem::Hexagonal) {
+        e_uc_len << p1[0], p1[0], p1[2];
+        Bmat(0, 1) = T(-0.5);
+        Bmat(1, 1) = T(sqrt(3.0) / 2.0);
+    } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
+        e_uc_len << p1[0], p1[1], p1[2];
+    } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
+        e_uc_len << p1[0], p1[0], p1[2];
+    } else if (symmetry == gemmi::CrystalSystem::Cubic) {
+        e_uc_len << p1[0], p1[0], p1[0];
+    } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
+        e_uc_len << p1[0], p1[1], p1[2];
+        Bmat(0, 2) = ceres::cos(p2[0]);
+        Bmat(2, 2) = ceres::sin(p2[0]);
+    } else {
+        const T ca = ceres::cos(p2[0]);
+        const T cb = ceres::cos(p2[1]);
+        const T cg = ceres::cos(p2[2]);
+        const T sg = ceres::sin(p2[2]);
+
+        e_uc_len << p1[0], p1[1], p1[2];
+
+        Bmat(0, 1) = cg;
+        Bmat(1, 1) = sg;
+
+        const T cx = cb;
+        const T cy = (ca - cb * cg) / sg;
+        const T v = T(1) - cx * cx - cy * cy;
+        const T cz = (v >= T(0)) ? ceres::sqrt(v) : T(0);
+
+        Bmat(0, 2) = cx;
+        Bmat(1, 2) = cy;
+        Bmat(2, 2) = cz;
+    }
+
+    const T L0 = e_uc_len[0];
+    const T L1 = e_uc_len[1];
+    const T L2 = e_uc_len[2];
+
+    T col0_unrot[3] = {Bmat(0, 0) * L0, Bmat(1, 0) * L0, Bmat(2, 0) * L0};
+    T col1_unrot[3] = {Bmat(0, 1) * L1, Bmat(1, 1) * L1, Bmat(2, 1) * L1};
+    T col2_unrot[3] = {Bmat(0, 2) * L2, Bmat(1, 2) * L2, Bmat(2, 2) * L2};
+
+    T col0_rot[3], col1_rot[3], col2_rot[3];
+    ceres::AngleAxisRotatePoint(p0, col0_unrot, col0_rot);
+    ceres::AngleAxisRotatePoint(p0, col1_unrot, col1_rot);
+    ceres::AngleAxisRotatePoint(p0, col2_unrot, col2_rot);
+
+    const Eigen::Matrix<T, 3, 1> A(col0_rot[0], col0_rot[1], col0_rot[2]);
+    const Eigen::Matrix<T, 3, 1> Bv(col1_rot[0], col1_rot[1], col1_rot[2]);
+    const Eigen::Matrix<T, 3, 1> C(col2_rot[0], col2_rot[1], col2_rot[2]);
+
+    const Eigen::Matrix<T, 3, 1> BxC = Bv.cross(C);
+    const Eigen::Matrix<T, 3, 1> CxA = C.cross(A);
+    const Eigen::Matrix<T, 3, 1> AxB = A.cross(Bv);
+
+    const T Vol = A.dot(BxC);
+    if (ceres::abs(Vol) < T(1e-12))
+        return false;
+    const T invV = T(1) / Vol;
+
+    e_pred_recip = (BxC * T(exp_h) + CxA * T(exp_k) + AxB * T(exp_l)) * invV;
+    q_sq = e_pred_recip.squaredNorm();
+
+    // Ewald sphere centre at -k_i = (0,0,-inv_lambda); radial normal at g_hkl.
+    const Eigen::Matrix<T, 3, 1> S_pred(
+        e_pred_recip[0],
+        e_pred_recip[1],
+        e_pred_recip[2] + T(inv_lambda));
+    const T S_pred_norm = S_pred.norm();
+    if (S_pred_norm < T(1e-10))
+        return false;
+
+    n_radial = S_pred / S_pred_norm;
+    return true;
+}
+
 } // namespace
 
 // ---------------------------------------------------------------------------
@@ -100,136 +233,18 @@ struct PixelResidual {
                        const T *const p1,
                        const T *const p2,
                        T &q_sq, T &eps_radial, T &eps_tang_sq) const {
-        // PyFAI convention (left-handed for rot1/rot2):
-        // poni_rot = Rz(-rot3) * Rx(-rot2) * Ry(+rot1), rot3 = 0 assumed.
-        const T rot1 = detector_rot[0];
-        const T rot2 = detector_rot[1];
+        Eigen::Matrix<T, 3, 1> e_obs_recip;
+        ObservedRecip(beam, distance_mm, detector_rot, rotation_axis,
+                      obs_x, obs_y, pixel_size, inv_lambda, angle_rad, e_obs_recip);
 
-        const T c1 = ceres::cos(rot1);
-        const T s1 = ceres::sin(rot1);
-        const T c2 = ceres::cos(rot2);
-        const T s2 = ceres::sin(rot2);
-
-        const T det_x = (T(obs_x) - beam[0]) * T(pixel_size);
-        const T det_y = (T(obs_y) - beam[1]) * T(pixel_size);
-        const T det_z = T(distance_mm[0]);
-
-        const T t1_x = c1 * det_x + s1 * det_z;
-        const T t1_y = det_y;
-        const T t1_z = -s1 * det_x + c1 * det_z;
-
-        const T x = t1_x;
-        const T y = c2 * t1_y + s2 * t1_z;
-        const T z = -s2 * t1_y + c2 * t1_z;
-
-        const T lab_norm = ceres::sqrt(x * x + y * y + z * z);
-        const T inv_norm = T(1) / lab_norm;
-
-        T recip_raw[3];
-        recip_raw[0] = x * inv_norm * T(inv_lambda);
-        recip_raw[1] = y * inv_norm * T(inv_lambda);
-        recip_raw[2] = (z * inv_norm - T(1.0)) * T(inv_lambda);
-
-        // Goniometer "back-to-start" rotation: image frame -> reference frame.
-        const T aa_back[3] = {
-            T(angle_rad) * rotation_axis[0],
-            T(angle_rad) * rotation_axis[1],
-            T(angle_rad) * rotation_axis[2]
-        };
-        T recip_obs[3];
-        ceres::AngleAxisRotatePoint(aa_back, recip_raw, recip_obs);
-        const Eigen::Matrix<T, 3, 1> e_obs_recip(recip_obs[0], recip_obs[1], recip_obs[2]);
-
-        // Build cell lengths and the (unit) B matrix from the symmetry-specific
-        // parametrization (identical convention to XtalOptimizer::XtalResidual).
-        Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
-        Eigen::Matrix<T, 3, 3> Bmat = Eigen::Matrix<T, 3, 3>::Identity();
-
-        if (symmetry == gemmi::CrystalSystem::Hexagonal) {
-            e_uc_len << p1[0], p1[0], p1[2];
-            Bmat(0, 1) = T(-0.5);
-            Bmat(1, 1) = T(sqrt(3.0) / 2.0);
-        } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
-            e_uc_len << p1[0], p1[1], p1[2];
-        } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
-            e_uc_len << p1[0], p1[0], p1[2];
-        } else if (symmetry == gemmi::CrystalSystem::Cubic) {
-            e_uc_len << p1[0], p1[0], p1[0];
-        } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
-            e_uc_len << p1[0], p1[1], p1[2];
-            Bmat(0, 2) = ceres::cos(p2[0]);
-            Bmat(2, 2) = ceres::sin(p2[0]);
-        } else {
-            const T ca = ceres::cos(p2[0]);
-            const T cb = ceres::cos(p2[1]);
-            const T cg = ceres::cos(p2[2]);
-            const T sg = ceres::sin(p2[2]);
-
-            e_uc_len << p1[0], p1[1], p1[2];
-
-            Bmat(0, 1) = cg;
-            Bmat(1, 1) = sg;
-
-            const T cx = cb;
-            const T cy = (ca - cb * cg) / sg;
-            const T v = T(1) - cx * cx - cy * cy;
-            const T cz = (v >= T(0)) ? ceres::sqrt(v) : T(0);
-
-            Bmat(0, 2) = cx;
-            Bmat(1, 2) = cy;
-            Bmat(2, 2) = cz;
-        }
-
-        const T L0 = e_uc_len[0];
-        const T L1 = e_uc_len[1];
-        const T L2 = e_uc_len[2];
-
-        T col0_unrot[3] = {Bmat(0, 0) * L0, Bmat(1, 0) * L0, Bmat(2, 0) * L0};
-        T col1_unrot[3] = {Bmat(0, 1) * L1, Bmat(1, 1) * L1, Bmat(2, 1) * L1};
-        T col2_unrot[3] = {Bmat(0, 2) * L2, Bmat(1, 2) * L2, Bmat(2, 2) * L2};
-
-        T col0_rot[3], col1_rot[3], col2_rot[3];
-        ceres::AngleAxisRotatePoint(p0, col0_unrot, col0_rot);
-        ceres::AngleAxisRotatePoint(p0, col1_unrot, col1_rot);
-        ceres::AngleAxisRotatePoint(p0, col2_unrot, col2_rot);
-
-        const Eigen::Matrix<T, 3, 1> A(col0_rot[0], col0_rot[1], col0_rot[2]);
-        const Eigen::Matrix<T, 3, 1> Bv(col1_rot[0], col1_rot[1], col1_rot[2]);
-        const Eigen::Matrix<T, 3, 1> C(col2_rot[0], col2_rot[1], col2_rot[2]);
-
-        const Eigen::Matrix<T, 3, 1> BxC = Bv.cross(C);
-        const Eigen::Matrix<T, 3, 1> CxA = C.cross(A);
-        const Eigen::Matrix<T, 3, 1> AxB = A.cross(Bv);
-
-        const T V = A.dot(BxC);
-        if (ceres::abs(V) < T(1e-12))
-            return false;
-        const T invV = T(1) / V;
-
-        const Eigen::Matrix<T, 3, 1> Astar = BxC * invV;
-        const Eigen::Matrix<T, 3, 1> Bstar = CxA * invV;
-        const Eigen::Matrix<T, 3, 1> Cstar = AxB * invV;
-
-        const Eigen::Matrix<T, 3, 1> e_pred_recip =
-            Astar * T(exp_h) + Bstar * T(exp_k) + Cstar * T(exp_l);
-
-        q_sq = e_pred_recip.squaredNorm();
-
-        // Ewald sphere centre at -k_i = (0,0,-inv_lambda); radial normal at g_hkl.
-        const Eigen::Matrix<T, 3, 1> S_pred(
-            e_pred_recip[0],
-            e_pred_recip[1],
-            e_pred_recip[2] + T(inv_lambda));
-        const T S_pred_norm = S_pred.norm();
-        if (S_pred_norm < T(1e-10))
+        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
+        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
+                           e_pred_recip, n_radial, q_sq))
             return false;
 
-        const Eigen::Matrix<T, 3, 1> n_radial = S_pred / S_pred_norm;
         const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-
         eps_radial = delta_q.dot(n_radial);
-        const Eigen::Matrix<T, 3, 1> dq_tang = delta_q - eps_radial * n_radial;
-        eps_tang_sq = dq_tang.squaredNorm();
+        eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
         return true;
     }
 
@@ -250,27 +265,25 @@ struct PixelResidual {
 
         const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
 
-        // Full 3D reciprocal-space spot density modelled as a separable Gaussian,
-        // normalized so that its integral is 1 (intensity-conserving):
-        //   radial:     g_r(e) = exp(-e^2/R0^2) / (sqrt(pi) R0)     [1/A^-1]
-        //   tangential: g_t(e) = exp(-|e|^2/R1^2) / (pi R1^2)        [1/A^-2]
-        // The detector pixel captures the fraction g_t * A_recip of the tangential
-        // profile (A_recip = reciprocal area the pixel subtends; sum over shoebox
-        // ~ 1). The radial factor is the still-image partiality: how far this
-        // reflection sits from the Ewald sphere.
+        // Separable Gaussian spot model:
+        //   radial  P_r(e) = exp(-e^2/R0_eff^2)                      (peak-normalized, in (0,1])
+        //   tangent g_t(e) = exp(-|e|^2/R1^2) / (pi R1^2)            [1/A^-2]
+        // The pixel captures the fraction g_t * A_recip of the tangential profile
+        // (A_recip = reciprocal area the pixel subtends; sum over shoebox ~ 1).
+        // The radial factor is the still-image partiality (how far the reflection
+        // sits from the Ewald sphere); the overall scale is carried by the free G.
         //
-        // Caveat: a still samples the radial direction at a single offset, so the
-        // sqrt(pi) R0 normalization makes g_r a density (1/A^-1) rather than a
-        // dimensionless fraction. The leftover dimensional factor is absorbed by
-        // the free scale G. The energy-bandwidth contribution to the radial width
-        // is folded in here via R_bw_sq (beam divergence is still TODO).
+        // IMPORTANT: the radial factor MUST use the same convention here as the
+        // extraction's `partiality` (peak-normalized), otherwise image_scale_corr
+        // = 1/(partiality*G*B) does not invert the model and a leftover, R0_eff-
+        // dependent (hence resolution-dependent) factor biases the intensities.
+        // R0_eff folds in the energy-bandwidth broadening via R_bw_sq.
         const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
-        const T g_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq)
-                           / (ceres::sqrt(T(M_PI)) * ceres::sqrt(R0_eff_sq));
+        const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
         const T P_tang = T(A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
                          / (T(M_PI) * R[1] * R[1]);
 
-        const T signal = scale_factor[0] * T(Itrue) * B_term * g_radial * P_tang;
+        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
         Ipred = signal + T(Ibkg);
         return true;
     }
@@ -306,6 +319,85 @@ struct PixelResidual {
     gemmi::CrystalSystem symmetry;
 };
 
+// ---------------------------------------------------------------------------
+// Per-shoebox cost functor
+//
+// One residual block per reflection emitting N residuals (one per shoebox pixel).
+// The expensive per-reflection geometry (PredictedNode: symmetry-aware B matrix,
+// three rotations, cross products) is computed ONCE; only the cheap per-pixel
+// ObservedRecip + Gaussian profile run in the pixel loop. This is identical in
+// value to the old one-block-per-pixel formulation but ~(pixels-per-shoebox)x
+// fewer evaluations of the costly node computation. Uses the same shared helpers
+// (and hence the same conventions) as PixelResidual.
+// ---------------------------------------------------------------------------
+struct ShoeboxResidual {
+    ShoeboxResidual(const ReflGroup &g, double lambda, double pixel_size,
+                    gemmi::CrystalSystem symmetry)
+        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq),
+          exp_h(g.h), exp_k(g.k), exp_l(g.l),
+          inv_lambda(1.0 / lambda), pixel_size(pixel_size),
+          angle_rad(g.pixels.empty() ? 0.0 : g.pixels.front().angle_rad),
+          symmetry(symmetry) {}
+
+    template<typename T>
+    bool operator()(const T *const *params, T *residual) const {
+        // Parameter blocks (order matches AddParameterBlock in Run):
+        // 0 beam[2] 1 distance[1] 2 detector_rot[2] 3 rotation_axis[3]
+        // 4 p0[3] 5 p1[3] 6 p2[3] 7 scale[1] 8 B[1] 9 R[2]
+        const T *beam = params[0];
+        const T *distance_mm = params[1];
+        const T *detector_rot = params[2];
+        const T *rotation_axis = params[3];
+        const T *p0 = params[4];
+        const T *p1 = params[5];
+        const T *p2 = params[6];
+        const T *scale_factor = params[7];
+        const T *B = params[8];
+        const T *R = params[9];
+
+        if (R[0] < T(1e-10) || R[1] < T(1e-10))
+            return false;
+
+        // --- per-reflection: computed once ---------------------------------
+        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
+        T q_sq;
+        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
+                           e_pred_recip, n_radial, q_sq))
+            return false;
+
+        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
+        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
+
+        // --- per-pixel loop -------------------------------------------------
+        for (size_t i = 0; i < pixels.size(); ++i) {
+            const PixelObs &obs = pixels[i];
+
+            Eigen::Matrix<T, 3, 1> e_obs_recip;
+            ObservedRecip(beam, distance_mm, detector_rot, rotation_axis,
+                          obs.x, obs.y, pixel_size, inv_lambda, angle_rad, e_obs_recip);
+
+            const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
+            const T eps_radial = delta_q.dot(n_radial);
+            const T eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
+
+            const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
+            const T P_tang = T(obs.A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
+                             / (T(M_PI) * R[1] * R[1]);
+
+            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
+            const T Ipred = signal + T(obs.Ibkg);
+            residual[i] = (Ipred - T(obs.Iobs)) * T(obs.weight);
+        }
+        return true;
+    }
+
+    std::vector<PixelObs> pixels;
+    const double Itrue, R_bw_sq;
+    const double exp_h, exp_k, exp_l;
+    const double inv_lambda, pixel_size, angle_rad;
+    gemmi::CrystalSystem symmetry;
+};
+
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
                          const AzimuthalIntegrationMapping &mapping,
                          const std::vector<MergedReflection> &reference)
@@ -526,20 +618,36 @@ void PixelRefine::Run(const T *image,
                              latt_vec0, latt_vec1, latt_vec2);
 
         // ---- 4. Build the problem ---------------------------------------------
+        // One residual block per shoebox (N residuals), so the expensive
+        // per-reflection node geometry is evaluated once per reflection instead
+        // of once per pixel.
         ceres::Problem problem;
+        size_t residual_pixels = 0;
         for (const auto &g : groups) {
-            for (const auto &obs : g.pixels) {
-                auto *cost = new ceres::AutoDiffCostFunction<
-                    PixelResidual, 1, 2, 1, 2, 3, 3, 3, 3, 1, 1, 2>(
-                    new PixelResidual(obs, g.Itrue, lambda, pixel_size,
-                                      g.h, g.k, g.l, g.R_bw_sq, data.crystal_system));
-                problem.AddResidualBlock(cost, new ceres::HuberLoss(3.0),
-                                         beam, &dist_mm, detector_rot, rot_vec,
-                                         latt_vec0, latt_vec1, latt_vec2,
-                                         &data.scale_factor, &data.B_factor, data.R);
-            }
+            auto *cost = new ceres::DynamicAutoDiffCostFunction<ShoeboxResidual>(
+                new ShoeboxResidual(g, lambda, pixel_size, data.crystal_system));
+            cost->AddParameterBlock(2); // beam
+            cost->AddParameterBlock(1); // distance
+            cost->AddParameterBlock(2); // detector_rot
+            cost->AddParameterBlock(3); // rotation_axis
+            cost->AddParameterBlock(3); // p0 (orientation)
+            cost->AddParameterBlock(3); // p1 (lengths)
+            cost->AddParameterBlock(3); // p2 (angles)
+            cost->AddParameterBlock(1); // scale G
+            cost->AddParameterBlock(1); // B
+            cost->AddParameterBlock(2); // R
+            cost->SetNumResiduals(static_cast<int>(g.pixels.size()));
+            // No robust loss here: a per-block (whole-shoebox) Huber would act on
+            // the sum of ~N squared residuals and mis-scale, unlike the previous
+            // per-pixel Huber. Per-pixel sigma weighting is retained; per-pixel
+            // outlier rejection (zingers) is a TODO if needed.
+            problem.AddResidualBlock(cost, nullptr,
+                                     beam, &dist_mm, detector_rot, rot_vec,
+                                     latt_vec0, latt_vec1, latt_vec2,
+                                     &data.scale_factor, &data.B_factor, data.R);
+            residual_pixels += g.pixels.size();
         }
-        data.residual_count = problem.NumResidualBlocks();
+        data.residual_count = residual_pixels;
 
         // ---- 5. Constrain / bound parameter blocks ----------------------------
         if (!data.refine_orientation)
-- 
2.52.0


From 254462b9f202a7c61f7e06ce102416a6c0aa4d13 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 07:28:13 +0200
Subject: [PATCH 013/228] jfjoch_process: Clarify what happens in scaling when
 reference data provided

---
 tools/jfjoch_process.cpp | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index b01c05b1..47cd0736 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -932,10 +932,17 @@ int main(int argc, char **argv) {
     if (end_msg.indexing_rate.has_value()
         && end_msg.indexing_rate > 0
         && (run_scaling || !reference_data.empty())) {
-        logger.Info("Running scaling (mosaicity refinement) ...");
 
-        if (reference_data.empty()) {
-            // If reference data are given, there is live scaling (no need to go again)
+        const bool pixel_refine_path =
+            (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
+
+        // Scaling is only the classical, no-reference ScaleOnTheFly post-pass.
+        // - With a reference (classical path): per-image live scaling already ran.
+        // - With PixelRefine: each image was scaled by PixelRefine itself.
+        // In both of those cases we must NOT run ScaleOnTheFly again - we go
+        // straight to merging on the per-image image_scale_corr.
+        if (reference_data.empty() && !pixel_refine_path) {
+            logger.Info("Running scaling ...");
             ScalingResult scale_result(0);
 
             auto scale_start = std::chrono::steady_clock::now();
@@ -957,6 +964,10 @@ int main(int argc, char **argv) {
             auto scale_end = std::chrono::steady_clock::now();
             double scale_time = std::chrono::duration<double>(scale_end - scale_start).count();
             logger.Info("Scaling completed in {:.2f} s", scale_time);
+        } else if (pixel_refine_path) {
+            logger.Info("PixelRefine scaled each image during processing; merging directly (no ScaleOnTheFly)");
+        } else {
+            logger.Info("Reference provided: per-image live scaling already applied; merging directly");
         }
 
         auto merge_start = std::chrono::steady_clock::now();
-- 
2.52.0


From e4b66f9cd9a39ebbba1214cd2f65332d820faecc Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 08:04:27 +0200
Subject: [PATCH 014/228] PIxelRefine: Another iteration

---
 image_analysis/IndexAndRefine.cpp             |  5 ++
 .../pixel_refinement/PixelRefine.cpp          | 77 ++++++++++++++-----
 image_analysis/pixel_refinement/PixelRefine.h |  2 +
 viewer/JFJochImageReadingWorker.cpp           |  4 +-
 viewer/JFJochImageReadingWorker.h             |  2 +-
 viewer/windows/JFJochPixelRefineWindow.cpp    |  7 +-
 viewer/windows/JFJochPixelRefineWindow.h      |  2 +-
 7 files changed, 73 insertions(+), 26 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 5dc02d55..c297de04 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -475,8 +475,13 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     i_outcome.latt = prd.latt;
     i_outcome.image_scale_g = static_cast<float>(prd.scale_factor);
     i_outcome.image_scale_b_factor_Ang2 = static_cast<float>(prd.B_factor);
+    if (std::isfinite(prd.cc)) {
+        i_outcome.image_scale_cc = static_cast<float>(prd.cc);
+        i_outcome.image_scale_cc_n = prd.cc_n;
+    }
 
     msg.image_scale_factor = static_cast<float>(prd.scale_factor);
+    msg.image_scale_cc = i_outcome.image_scale_cc;
     if (prd.B_factor != 0.0)
         msg.image_scale_b_factor = static_cast<float>(prd.B_factor);
 
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 3b6ccdfe..b2d2578f 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -766,19 +766,20 @@ void PixelRefine::Run(const T *image,
     } // predict<->refine iterations
 
     // ---- Extract integrated reflections ---------------------------------------
-    // Two quantities are read back per reflection, using the *optimized* model:
+    // Profile fitting gives the recorded amplitude (against the normalized
+    // tangential profile P_t):
+    //     J      = sum_p[ P_t,p (Iobs_p - Ibkg_p)/v_p ] / sum_p[ P_t,p^2 / v_p ]
+    //            ~ G * Itrue * B_term * partiality            (recorded intensity)
+    //     var(J) = 1 / sum_p[ P_t,p^2 / v_p ]
     //
-    //  * Recorded (partial) intensity J by profile fitting against the normalized
-    //    tangential profile P_t (sum over the shoebox ~ 1):
-    //        J       = sum_p [ P_t,p (Iobs_p - Ibkg_p) / v_p ] / sum_p [ P_t,p^2 / v_p ]
-    //        var(J)  = 1 / sum_p [ P_t,p^2 / v_p ]
-    //    Because P_t is area-normalized, J estimates the integrated intensity
-    //    actually recorded on this image (not the full-spot intensity).
-    //
-    //  * Partiality: the profile-weighted mean of the *peak-normalized* radial
-    //    factor exp(-eps_r^2/R0^2) in (0,1], i.e. how close to the Ewald sphere
-    //    the reflection sits. Kept dimensionless for consistency with the rest of
-    //    the pipeline (image_scale_corr = rlp / partiality, full I = J / partiality).
+    // Output split (Merge multiplies r.I * image_scale_corr and weights by
+    // 1/(sigma*image_scale_corr)^2 - see Merge.cpp):
+    //   r.I              = J / (B_term * partiality)   = G * Itrue  (B/partiality corrected)
+    //   r.sigma          = sqrt(var(J)) / (B_term * partiality)
+    //   r.partiality     = profile-weighted peak radial factor in (0,1]  (Merge filter only)
+    //   r.image_scale_corr = 1/G                         (per-image scale ONLY)
+    // so r.I * image_scale_corr = Itrue. B and partiality live on the intensity,
+    // G lives on image_scale_corr - one clean meaning per field.
     data.reflections.reserve(groups.size());
     for (const auto &g : groups) {
         double num = 0.0, den = 0.0, bkg_sum = 0.0;
@@ -826,16 +827,22 @@ void PixelRefine::Run(const T *image,
         r.partiality = (radial_w > 0.0) ? static_cast<float>(radial_sum / radial_w) : 1.0f;
 
         if (den > 0.0 && n > 0) {
-            r.I = static_cast<float>(num / den);
-            r.sigma = static_cast<float>(std::sqrt(1.0 / den));
+            const double I_amp = num / den;             // ~ G*Itrue*B_term*partiality
+            const double sigma_amp = std::sqrt(1.0 / den);
+            const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
+            const double corr = static_cast<double>(r.partiality) * B_term; // B & partiality
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
-            // Put I onto a common (merge-ready) scale: I * image_scale_corr is the
-            // full-spot, scale/DW-corrected intensity. Fold in the refined G, the
-            // per-reflection B_term and the partiality (rlp = 1 here).
-            const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
-            const double denom = static_cast<double>(r.partiality) * data.scale_factor * B_term;
-            r.image_scale_corr = (denom > 0.0) ? static_cast<float>(r.rlp / denom) : NAN;
+
+            if (corr > 0.0 && data.scale_factor > 0.0) {
+                r.I = static_cast<float>(I_amp / corr);       // = G*Itrue
+                r.sigma = static_cast<float>(sigma_amp / corr);
+                r.image_scale_corr = static_cast<float>(1.0 / data.scale_factor); // G only
+            } else {
+                r.I = static_cast<float>(I_amp);
+                r.sigma = static_cast<float>(sigma_amp);
+                r.image_scale_corr = NAN;
+            }
         } else {
             r.I = 0.0f;
             r.sigma = NAN;
@@ -844,6 +851,36 @@ void PixelRefine::Run(const T *image,
         }
         data.reflections.push_back(r);
     }
+
+    // ---- Per-image CC vs reference (the half/ref correlation diagnostic) -------
+    // Pearson CC of the scaled estimate (r.I * image_scale_corr = Itrue_est)
+    // against the reference intensities, over the matched reflections.
+    {
+        double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
+        size_t cn = 0;
+        for (const auto &r : data.reflections) {
+            if (!r.observed || !std::isfinite(r.I) || !std::isfinite(r.image_scale_corr))
+                continue;
+            const auto it = reference_data.find(hkl_key_generator(r));
+            if (it == reference_data.end())
+                continue;
+            const double x = static_cast<double>(r.I) * static_cast<double>(r.image_scale_corr);
+            const double y = it->second;
+            if (!std::isfinite(x) || !std::isfinite(y))
+                continue;
+            sx += x; sy += y; sxx += x * x; syy += y * y; sxy += x * y; ++cn;
+        }
+        data.cc = NAN;
+        data.cc_n = static_cast<int64_t>(cn);
+        if (cn >= 3) {
+            const double nd = static_cast<double>(cn);
+            const double cov = sxy - sx * sy / nd;
+            const double vx = sxx - sx * sx / nd;
+            const double vy = syy - sy * sy / nd;
+            if (vx > 0.0 && vy > 0.0)
+                data.cc = cov / std::sqrt(vx * vy);
+        }
+    }
 }
 
 std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &profile,
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index ae805f4e..9522fc91 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -139,6 +139,8 @@ struct PixelRefineData {
     bool   solved = false;
     double final_cost = NAN;
     size_t residual_count = 0;
+    double cc = NAN;        // per-image CC of scaled intensities vs reference
+    int64_t cc_n = 0;       // number of reflections in the CC
 };
 
 class PixelRefine {
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 1ad60bd0..08eb7ad7 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -816,7 +816,7 @@ void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
     try {
         const auto &img32 = current_image_ptr->Image();
         pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
-        emit pixelRefineResidual(d.final_cost, static_cast<int64_t>(d.reflections.size()));
+        emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
 
         auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
         emit predictedImageReady(WrapFloatImage_i(pred));
@@ -859,7 +859,7 @@ void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
         out.beam_x = d.geom.GetBeamX_pxl();
         out.beam_y = d.geom.GetBeamY_pxl();
         emit pixelRefineParamsRefined(out);
-        emit pixelRefineResidual(d.final_cost, static_cast<int64_t>(d.reflections.size()));
+        emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
 
         auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
         emit predictedImageReady(WrapFloatImage_i(pred));
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 6ab9e429..a5b219df 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -134,7 +134,7 @@ signals:
 
     // PixelRefine (experimental)
     void predictedImageReady(std::shared_ptr<const SimpleImage> image);
-    void pixelRefineResidual(double cost, int64_t n_reflections);
+    void pixelRefineResidual(double cost, double cc, int64_t n_reflections);
     void pixelRefineParamsRefined(PixelRefineParams params);
     void pixelRefineStatus(QString message);
 
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index 364cf5df..6cce6a99 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -161,9 +161,12 @@ void JFJochPixelRefineWindow::setPredictedImage(std::shared_ptr<const SimpleImag
     m_image->setImage(std::move(image));
 }
 
-void JFJochPixelRefineWindow::setResidual(double cost, int64_t n_reflections) {
-    m_residual->setText(tr("Residual: %1   (%2 reflections)")
+void JFJochPixelRefineWindow::setResidual(double cost, double cc, int64_t n_reflections) {
+    const QString cc_str = std::isfinite(cc) ? QString::number(cc * 100.0, 'f', 1) + "%"
+                                             : QStringLiteral("—");
+    m_residual->setText(tr("Residual: %1   CC: %2   (%3 reflections)")
                             .arg(cost, 0, 'g', 6)
+                            .arg(cc_str)
                             .arg(n_reflections));
 }
 
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
index 7e7f167c..b508497e 100644
--- a/viewer/windows/JFJochPixelRefineWindow.h
+++ b/viewer/windows/JFJochPixelRefineWindow.h
@@ -67,7 +67,7 @@ signals:
 
 public slots:
     void setPredictedImage(std::shared_ptr<const SimpleImage> image);
-    void setResidual(double cost, int64_t n_reflections);
+    void setResidual(double cost, double cc, int64_t n_reflections);
     void setRefinedParams(PixelRefineParams params);
     void setStatus(QString message);
 };
-- 
2.52.0


From 5735302691dff3055f65dcf3b2a994ce9b9c6d94 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 11:06:16 +0200
Subject: [PATCH 015/228] Merge: CC1/2 limit adjustment

---
 image_analysis/scale_merge/Merge.cpp | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 8d69f811..4f4fd8ee 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -22,7 +22,14 @@ MergeOnTheFly::MergeOnTheFly(const DiffractionExperiment &x)
       scaling_settings(x.GetScalingSettings()),
       indexing_settings(x.GetIndexingSettings()),
       high_resolution_limit(scaling_settings.GetHighResolutionLimit_A()),
-      image_cc_limit(scaling_settings.GetMinCCForImage()),
+      // A min-image-CC of 0 (the default) means "no limit": leave the optional
+      // empty so the per-image CC cut is inactive. Otherwise a 0.0 threshold
+      // would silently drop every image with a non-positive per-image CC (which
+      // also wrongly zeroed N_obs in MergeStats, since it masks with cc_mask=true
+      // while the merge keeps all images).
+      image_cc_limit(scaling_settings.GetMinCCForImage() > 0.0
+                         ? std::optional<double>(scaling_settings.GetMinCCForImage())
+                         : std::nullopt),
       min_partiality(scaling_settings.GetMinPartiality()),
       generator(scaling_settings.GetMergeFriedel(), space_group_number) {
 }
-- 
2.52.0


From 30dcc98f896cebbcfa58fb64304a29522eaff729 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 12:03:45 +0200
Subject: [PATCH 016/228] JFJochMagnifierWindow: Zoom is saved ... it is not
 optimal (when image is first loaded, than it starts with weird zoom), but can
 be fixed later

---
 viewer/image_viewer/JFJochImage.cpp      | 13 +++++++++++++
 viewer/image_viewer/JFJochImage.h        |  3 ++-
 viewer/windows/JFJochMagnifierWindow.cpp |  5 ++++-
 3 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index ed030ef0..a11db19e 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -948,4 +948,17 @@ void JFJochImage::adjustForeground(bool input) {
 
 void JFJochImage::beforeOverlayCleared() {}
 
+double JFJochImage::GetScaleFactor() const {
+    return scale_factor;
+}
 
+void JFJochImage::setZoom(double input) {
+    if (std::isfinite(input) && input > 0) {
+        scale_factor = input;
+        if (!scene())
+            return;
+        scale(input, input);
+        updateOverlay();
+        emitViewportChanged();
+    }
+}
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index 593cda04..f16ec3ec 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -131,7 +131,8 @@ public slots:
     void fitToView();
 
     void adjustForeground(bool input);
-
+    void setZoom(double input);
 public:
     explicit JFJochImage(QWidget *parent = nullptr);
+    double GetScaleFactor() const;
 };
\ No newline at end of file
diff --git a/viewer/windows/JFJochMagnifierWindow.cpp b/viewer/windows/JFJochMagnifierWindow.cpp
index 266a5056..8027652e 100644
--- a/viewer/windows/JFJochMagnifierWindow.cpp
+++ b/viewer/windows/JFJochMagnifierWindow.cpp
@@ -11,6 +11,7 @@ JFJochMagnifierWindow::JFJochMagnifierWindow(QWidget *parent)
     : JFJochHelperWindow(parent) {
     setWindowTitle("Magnifier");
     m_image = new JFJochSimpleImage(this);
+    m_image->setZoom(m_magnification);
     setCentralWidget(m_image);
     resize(320, 320);
 }
@@ -25,11 +26,13 @@ void JFJochMagnifierWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage>
     auto si = std::make_shared<SimpleImage>();
     si->image = CompressedImage(image->Image(), exp.GetXPixelsNum(), exp.GetYPixelsNum());
     m_image->setImage(si);
+    m_image->setZoom(m_magnification);
     m_have_image = true;
 }
 
 void JFJochMagnifierWindow::centerAt(QPointF scenePos) {
     if (!m_have_image || !isVisible())
         return;
-    m_image->applyViewport(QTransform::fromScale(m_magnification, m_magnification), scenePos);
+    double scale = m_image->GetScaleFactor();
+    m_image->applyViewport(QTransform::fromScale(scale, scale), scenePos);
 }
-- 
2.52.0


From 8a582b8a90604ffc1c6201af22967d64d6be631e Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 12:09:40 +0200
Subject: [PATCH 017/228] JFJochMagnifierWindow: Fixed

---
 viewer/image_viewer/JFJochImage.cpp      | 2 +-
 viewer/windows/JFJochMagnifierWindow.cpp | 9 ++++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index a11db19e..0e278524 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -957,7 +957,7 @@ void JFJochImage::setZoom(double input) {
         scale_factor = input;
         if (!scene())
             return;
-        scale(input, input);
+        setTransform(QTransform::fromScale(input, input));
         updateOverlay();
         emitViewportChanged();
     }
diff --git a/viewer/windows/JFJochMagnifierWindow.cpp b/viewer/windows/JFJochMagnifierWindow.cpp
index 8027652e..06f1f109 100644
--- a/viewer/windows/JFJochMagnifierWindow.cpp
+++ b/viewer/windows/JFJochMagnifierWindow.cpp
@@ -22,11 +22,18 @@ void JFJochMagnifierWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage>
         m_image->setImage(nullptr);
         return;
     }
+
+    const double scale = m_have_image ? m_image->GetScaleFactor() : m_magnification;
+    const QPointF center = m_have_image
+                           ? m_image->mapToScene(m_image->viewport()->rect().center())
+                           : QPointF(image->Dataset().experiment.GetXPixelsNum() * 0.5,
+                                     image->Dataset().experiment.GetYPixelsNum() * 0.5);
+
     const auto &exp = image->Dataset().experiment;
     auto si = std::make_shared<SimpleImage>();
     si->image = CompressedImage(image->Image(), exp.GetXPixelsNum(), exp.GetYPixelsNum());
     m_image->setImage(si);
-    m_image->setZoom(m_magnification);
+    m_image->applyViewport(QTransform::fromScale(scale, scale), center);
     m_have_image = true;
 }
 
-- 
2.52.0


From feca63f4b9be1516cbdbaadb85b30f86af812a9d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 12:35:06 +0200
Subject: [PATCH 018/228] jfjoch_viewer: fixes to pixel refine

---
 viewer/JFJochImageReadingWorker.cpp        | 41 +++++++++++++++++-----
 viewer/JFJochImageReadingWorker.h          |  2 +-
 viewer/windows/JFJochPixelRefineWindow.cpp | 28 ++++++++++-----
 3 files changed, 52 insertions(+), 19 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 08eb7ad7..6582700c 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -729,18 +729,31 @@ void JFJochImageReadingWorker::EnsurePixelRefine_i() {
         pixel_pred_ = CreateBraggPrediction(curr_experiment.IsRotationIndexing());
 }
 
-bool JFJochImageReadingWorker::BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p) const {
-    if (!current_image_ptr || !index_and_refine || !current_image.has_value())
+bool JFJochImageReadingWorker::BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p, QString &reason) const {
+    if (!current_image_ptr || !index_and_refine || !current_image.has_value()) {
+        reason = "No image loaded";
         return false;
+    }
 
     const auto &outcomes = index_and_refine->GetIntegrationOutcome();
     const int64_t n = current_image.value();
-    if (n < 0 || n >= static_cast<int64_t>(outcomes.size()))
+    if (n < 0 || n >= static_cast<int64_t>(outcomes.size())) {
+        reason = "No analysis result for current image";
         return false;
+    }
 
     const auto &io = outcomes[n];
-    if (io.reflections.empty()) // image not indexed/integrated
+    if (io.reflections.empty()) {
+        // The "indexed" badge in the viewer comes from indexing (lattice_type);
+        // PixelRefine instead seeds from the *integration* outcome, which is only
+        // populated when Quick integration is enabled and succeeds for this image.
+        // Distinguish the two so the user knows what to turn on.
+        if (current_image_ptr->ImageData().lattice_type.has_value())
+            reason = "Image is indexed but not integrated - enable Quick integration";
+        else
+            reason = "Current image is not indexed";
         return false;
+    }
 
     d.geom = io.geom;
     d.latt = io.latt;
@@ -773,7 +786,15 @@ bool JFJochImageReadingWorker::BuildPixelSeed_i(PixelRefineData &d, const PixelR
 
 std::shared_ptr<SimpleImage> JFJochImageReadingWorker::WrapFloatImage_i(const std::vector<float> &img) const {
     auto si = std::make_shared<SimpleImage>();
-    si->image = CompressedImage(img, curr_experiment.GetXPixelsNum(), curr_experiment.GetYPixelsNum());
+    // CompressedImage is a non-owning view over its data pointer. predictedImageReady
+    // is a queued cross-thread connection, so the source float vector must outlive the
+    // emit: copy it into SimpleImage::buffer (which the shared_ptr keeps alive) instead
+    // of aliasing the caller's temporary, otherwise loadImageInternal() reads freed
+    // memory in the GUI thread (SIGSEGV).
+    si->buffer.resize(img.size() * sizeof(float));
+    std::memcpy(si->buffer.data(), img.data(), si->buffer.size());
+    si->image = CompressedImage(si->buffer, curr_experiment.GetXPixelsNum(), curr_experiment.GetYPixelsNum(),
+                                CompressedImageMode::Float32);
     return si;
 }
 
@@ -803,8 +824,9 @@ void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
     }
 
     PixelRefineData d;
-    if (!BuildPixelSeed_i(d, params)) {
-        emit pixelRefineStatus("Current image is not indexed");
+    QString seed_reason;
+    if (!BuildPixelSeed_i(d, params, seed_reason)) {
+        emit pixelRefineStatus(seed_reason);
         return;
     }
 
@@ -838,8 +860,9 @@ void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
     }
 
     PixelRefineData d;
-    if (!BuildPixelSeed_i(d, params)) {
-        emit pixelRefineStatus("Current image is not indexed");
+    QString seed_reason;
+    if (!BuildPixelSeed_i(d, params, seed_reason)) {
+        emit pixelRefineStatus(seed_reason);
         return;
     }
     if (d.max_iterations <= 0)
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index a5b219df..93d4240b 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -69,7 +69,7 @@ private:
     std::unique_ptr<BraggPrediction> pixel_pred_;
 
     void EnsurePixelRefine_i();
-    bool BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p) const;
+    bool BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p, QString &reason) const;
     std::shared_ptr<SimpleImage> WrapFloatImage_i(const std::vector<float> &img) const;
 
     std::unique_ptr<ROIElement> roi;
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index 6cce6a99..bd4e1927 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -145,16 +145,26 @@ void JFJochPixelRefineWindow::onControlChanged() {
 }
 
 void JFJochPixelRefineWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage> image) {
-    if (m_beamInit || !image)
+    if (!image)
         return;
-    const auto geom = image->Dataset().experiment.GetDiffractionGeometry();
-    m_beamx->setMax(static_cast<double>(image->Dataset().experiment.GetXPixelsNum()));
-    m_beamy->setMax(static_cast<double>(image->Dataset().experiment.GetYPixelsNum()));
-    m_suppress = true;
-    m_beamx->setValue(geom.GetBeamX_pxl());
-    m_beamy->setValue(geom.GetBeamY_pxl());
-    m_suppress = false;
-    m_beamInit = true;
+
+    // Initialise the beam-centre sliders from the geometry once.
+    if (!m_beamInit) {
+        const auto geom = image->Dataset().experiment.GetDiffractionGeometry();
+        m_beamx->setMax(static_cast<double>(image->Dataset().experiment.GetXPixelsNum()));
+        m_beamy->setMax(static_cast<double>(image->Dataset().experiment.GetYPixelsNum()));
+        m_suppress = true;
+        m_beamx->setValue(geom.GetBeamX_pxl());
+        m_beamy->setValue(geom.GetBeamY_pxl());
+        m_suppress = false;
+        m_beamInit = true;
+    }
+
+    // Request a predicted-image preview for the (re)loaded image. Without this the
+    // preview only refreshed on a slider change, so opening/reanalyzing an image
+    // left the predicted view empty. The worker no-ops if there is no reference or
+    // the image is not integrated yet.
+    onControlChanged();
 }
 
 void JFJochPixelRefineWindow::setPredictedImage(std::shared_ptr<const SimpleImage> image) {
-- 
2.52.0


From 2d202f1d44ed1a7afb6ab12b2cd38af1c39de4e5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 13:20:46 +0200
Subject: [PATCH 019/228] jfjoch_viewer: fixes to pixel refine window

---
 viewer/image_viewer/JFJochImage.cpp        | 4 ++--
 viewer/image_viewer/JFJochImage.h          | 6 ++++++
 viewer/image_viewer/JFJochSimpleImage.cpp  | 3 +++
 viewer/windows/JFJochPixelRefineWindow.cpp | 4 ++++
 4 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index 0e278524..7f151a92 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -752,9 +752,9 @@ void JFJochImage::writePixelLabels() {
                     if (std::abs(val - nearest) < 1e-6)
                         numBuf = QString::number(static_cast<qint64>(val));
                     else if (absVal < 1e4)
-                        numBuf = QString::number(val, 'f', 3);
+                        numBuf = QString::number(val, 'f', label_decimals_);
                     else
-                        numBuf = QString::number(val, 'f', 2);
+                        numBuf = QString::number(val, 'f', std::min(label_decimals_, 2));
                     pText = &numBuf;
                 } else {
                     numBuf = QString::number(val, 'e', 1);
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index f16ec3ec..5b3816ea 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -54,6 +54,12 @@ protected:
     bool initial_fit_done_ = false;
 
     QColor feature_color = Qt::magenta;
+
+    // Decimal places for non-integer per-pixel value labels. Float images (e.g. the
+    // PixelRefine prediction) are unreadable with many decimals, so subclasses can
+    // lower this.
+    int label_decimals_ = 3;
+
     float foreground = 10.0;
     float background = 0.0;
     ColorScale color_scale;
diff --git a/viewer/image_viewer/JFJochSimpleImage.cpp b/viewer/image_viewer/JFJochSimpleImage.cpp
index 700537f8..24bdcad6 100644
--- a/viewer/image_viewer/JFJochSimpleImage.cpp
+++ b/viewer/image_viewer/JFJochSimpleImage.cpp
@@ -18,6 +18,9 @@ JFJochSimpleImage::JFJochSimpleImage(QWidget *parent)
 
     // Keep overlays in pixel units independent of zoom (for labels font sizing)
     setViewportUpdateMode(QGraphicsView::FullViewportUpdate);
+
+    // The predicted/float image is unreadable with 3-decimal per-pixel labels.
+    label_decimals_ = 1;
 }
 
 void JFJochSimpleImage::setImage(std::shared_ptr<const SimpleImage> img) {
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index bd4e1927..5ff21ea6 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -109,6 +109,10 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
     });
 
     connect(m_refine, &QPushButton::clicked, this, [this] {
+        // Cancel any pending live-preview: otherwise a debounce armed by a slider
+        // move just before this click fires after the refine and overwrites the
+        // refined residual/preview with the stale pre-refine slider values.
+        m_debounce->stop();
         PixelRefineParams p = currentParams();
         p.max_iterations = 5;
         emit refineRequested(p);
-- 
2.52.0


From 003fea1b1e6acc9e8c03bb162985a6ec1f52b2b0 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 13:28:35 +0200
Subject: [PATCH 020/228] jfjoch_viewer: fix sorting by indexing status

---
 viewer/windows/JFJochViewerImageListWindow.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/viewer/windows/JFJochViewerImageListWindow.cpp b/viewer/windows/JFJochViewerImageListWindow.cpp
index bf5bf698..abd2dc5c 100644
--- a/viewer/windows/JFJochViewerImageListWindow.cpp
+++ b/viewer/windows/JFJochViewerImageListWindow.cpp
@@ -84,6 +84,12 @@ void JFJochViewerImageListWindow::addDataRow(int imageNumber, double backgroundE
     rowItems.append(bgItem);
 
     QStandardItem *indexingItem = new QStandardItem(indexingResult);
+    if (indexingResult == "Yes")
+        indexingItem->setData(1, ScaleSortRole);
+    else if (indexingResult == "No")
+        indexingItem->setData(0, ScaleSortRole);
+    else
+        indexingItem->setData(-1, ScaleSortRole);
     rowItems.append(indexingItem);
 
     QStandardItem *spotItem = new QStandardItem();
-- 
2.52.0


From 6af22b6a0ccd88744c45298d8978dafaa5a3b8b0 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 13:28:56 +0200
Subject: [PATCH 021/228] jfjoch_viewer: show image CC based on standard
 pipeline

---
 viewer/windows/JFJochPixelRefineWindow.cpp | 12 ++++++++++++
 viewer/windows/JFJochPixelRefineWindow.h   |  1 +
 2 files changed, 13 insertions(+)

diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index 5ff21ea6..230d4974 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -77,10 +77,12 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
     controlsLayout->addWidget(m_refine);
 
     m_residual = new QLabel(tr("Residual: —"), this);
+    m_pipelineCC = new QLabel(tr("Pipeline CC (ref): —"), this);
     m_status   = new QLabel(QString(), this);
     m_status->setWordWrap(true);
     m_status->setStyleSheet("color: rgb(80, 80, 80);");
     controlsLayout->addWidget(m_residual);
+    controlsLayout->addWidget(m_pipelineCC);
     controlsLayout->addWidget(m_status);
     controlsLayout->addStretch(1);
 
@@ -164,6 +166,16 @@ void JFJochPixelRefineWindow::imageLoaded(std::shared_ptr<const JFJochReaderImag
         m_beamInit = true;
     }
 
+    // Show the standard ScaleOnTheFly pipeline's per-image CC vs the reference (set
+    // on the message during analysis when a reference is loaded), as a baseline to
+    // compare PixelRefine against.
+    const auto pipeline_cc = image->ImageData().image_scale_cc;
+    if (pipeline_cc.has_value() && std::isfinite(pipeline_cc.value()))
+        m_pipelineCC->setText(tr("Pipeline CC (ref): %1%")
+                                  .arg(pipeline_cc.value() * 100.0, 0, 'f', 1));
+    else
+        m_pipelineCC->setText(tr("Pipeline CC (ref): —"));
+
     // Request a predicted-image preview for the (re)loaded image. Without this the
     // preview only refreshed on a slider change, so opening/reanalyzing an image
     // left the predicted view empty. The worker no-ops if there is no reference or
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
index b508497e..7940ce16 100644
--- a/viewer/windows/JFJochPixelRefineWindow.h
+++ b/viewer/windows/JFJochPixelRefineWindow.h
@@ -42,6 +42,7 @@ class JFJochPixelRefineWindow : public JFJochHelperWindow {
     QCheckBox *m_refR;
 
     QLabel *m_residual;
+    QLabel *m_pipelineCC;   // first-image CC vs reference from the standard ScaleOnTheFly pipeline
     QLabel *m_status;
     QPushButton *m_loadRef;
     QPushButton *m_refine;
-- 
2.52.0


From 6c85aaba2b6bbcbdf3d73ce5718875e9b811aa02 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 15:01:44 +0200
Subject: [PATCH 022/228] BraggPrediction: Include X-ray bandwidth

---
 image_analysis/IndexAndRefine.cpp             |  4 +++-
 .../bragg_prediction/BraggPrediction.cpp      | 20 ++++++++++++++++++-
 .../bragg_prediction/BraggPrediction.h        |  6 ++++++
 .../bragg_prediction/BraggPredictionGPU.cu    | 20 ++++++++++++++++---
 .../bragg_prediction/BraggPredictionGPU.h     |  1 +
 .../pixel_refinement/PixelRefine.cpp          |  6 ++++--
 6 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index c297de04..98b1aed6 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -289,7 +289,9 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
         .max_hkl = 100,
         .centering = outcome.symmetry.centering,
         .wedge_deg = std::fabs(wedge_deg),
-        .mosaicity_deg = std::fabs(mos_deg)
+        .mosaicity_deg = std::fabs(mos_deg),
+        // FWHM -> sigma; 0 when monochromatic, leaving the prediction unchanged.
+        .bandwidth_sigma = experiment.GetBandwidthFWHM().value_or(0.0f) / 2.3548f
     };
 
     // Select the integration path: classical 2D integration, or the experimental
diff --git a/image_analysis/bragg_prediction/BraggPrediction.cpp b/image_analysis/bragg_prediction/BraggPrediction.cpp
index 962ae45d..4c134e38 100644
--- a/image_analysis/bragg_prediction/BraggPrediction.cpp
+++ b/image_analysis/bragg_prediction/BraggPrediction.cpp
@@ -4,6 +4,13 @@
 #include "BraggPrediction.h"
 #include "../bragg_integration/SystematicAbsence.h"
 
+namespace {
+    // Number of bandwidth sigmas included in the (radially thickened) Ewald-shell
+    // acceptance window. 3σ captures essentially the whole pink-beam smear; matches
+    // the conservative end of the mosaicity cutoff used by callers.
+    constexpr float kBandwidthCutoffSigmas = 3.0f;
+}
+
 BraggPrediction::BraggPrediction(int max_reflections)
     : max_reflections(max_reflections), reflections(max_reflections) {}
 
@@ -76,7 +83,18 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
                 float S_len = sqrtf(S_x * S_x + S_y * S_y + S_z * S_z);
                 float dist_ewald_sphere = std::fabs(S_len - one_over_wavelength);
 
-                if (dist_ewald_sphere <= settings.ewald_dist_cutoff ) {
+                // Energy bandwidth thickens the Ewald shell radially: at the
+                // diffraction condition |S|-1/λ shifts by recip_z·(Δλ/λ), i.e.
+                // σ_bw = |recip_z|·bandwidth_sigma (= bλ/2d², identical to
+                // PixelRefine's R_bw). Broaden the acceptance window in quadrature so
+                // high-resolution shells (smeared most, ∝1/d²) are not clipped.
+                float radial_cutoff = settings.ewald_dist_cutoff;
+                if (settings.bandwidth_sigma > 0.0f) {
+                    const float bw_tol = kBandwidthCutoffSigmas * settings.bandwidth_sigma * std::fabs(recip_z);
+                    radial_cutoff = std::sqrt(radial_cutoff * radial_cutoff + bw_tol * bw_tol);
+                }
+
+                if (dist_ewald_sphere <= radial_cutoff ) {
                     const float s0_p0 = S0.x * recip_x + S0.y * recip_y + S0.z * recip_z;
                     const float val = s0_sq * recip_sq - s0_p0 * s0_p0;
 
diff --git a/image_analysis/bragg_prediction/BraggPrediction.h b/image_analysis/bragg_prediction/BraggPrediction.h
index 6aaf4fc5..13d1c7ed 100644
--- a/image_analysis/bragg_prediction/BraggPrediction.h
+++ b/image_analysis/bragg_prediction/BraggPrediction.h
@@ -18,6 +18,12 @@ struct BraggPredictionSettings {
     float mosaicity_deg = 0.2f;
     float min_zeta = 0.05;
     float mosaicity_multiplier = 4.0;
+    // Relative X-ray bandwidth Δλ/λ expressed as a Gaussian sigma (0 = monochromatic).
+    // When > 0 the Ewald-shell acceptance is thickened radially per reflection by
+    // σ_bw = |recip_z|·bandwidth_sigma (= bλ/2d²), so the 1/d² pink-beam smear no
+    // longer clips high-resolution reflections. Must stay the last member so existing
+    // designated initializers remain valid.
+    float bandwidth_sigma = 0.0f;
 };
 
 class BraggPrediction {
diff --git a/image_analysis/bragg_prediction/BraggPredictionGPU.cu b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
index b15c34bc..cf8f8cc6 100644
--- a/image_analysis/bragg_prediction/BraggPredictionGPU.cu
+++ b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
@@ -8,6 +8,10 @@
 #include <cuda_runtime.h>
 
 namespace {
+    // Number of bandwidth sigmas included in the (radially thickened) Ewald-shell
+    // acceptance window. Mirrors the CPU BraggPrediction path.
+    constexpr float kBandwidthCutoffSigmas = 3.0f;
+
     __device__ inline bool is_odd(int v) { return (v & 1) != 0; }
 
     __device__ inline float angle_from_ewald_sphere_deg(const Coord &S0, float recip_x, float recip_y, float recip_z, float recip_sq) {
@@ -95,7 +99,14 @@ namespace {
         float Sz = recip_z + C.S0.z;
         float S_len = sqrtf(Sx * Sx + Sy * Sy + Sz * Sz);
         float dist_ewald = fabsf(S_len - C.one_over_wavelength);
-        if (dist_ewald > C.ewald_cutoff) return false;
+        // Energy bandwidth thickens the Ewald shell radially: σ_bw = |recip_z|·(Δλ/λ)
+        // (= bλ/2d²). Broaden the acceptance window in quadrature (see CPU path).
+        float radial_cutoff = C.ewald_cutoff;
+        if (C.bandwidth_sigma > 0.0f) {
+            const float bw_tol = kBandwidthCutoffSigmas * C.bandwidth_sigma * fabsf(recip_z);
+            radial_cutoff = sqrtf(radial_cutoff * radial_cutoff + bw_tol * bw_tol);
+        }
+        if (dist_ewald > radial_cutoff) return false;
         float Srx = C.rot[0] * Sx + C.rot[1] * Sy + C.rot[2] * Sz;
         float Sry = C.rot[3] * Sx + C.rot[4] * Sy + C.rot[5] * Sz;
         float Srz = C.rot[6] * Sx + C.rot[7] * Sy + C.rot[8] * Sz;
@@ -145,7 +156,8 @@ namespace {
                                           const CrystalLattice &lattice,
                                           float high_res_A,
                                           float ewald_dist_cutoff,
-                                          char centering) {
+                                          char centering,
+                                          float bandwidth_sigma) {
         KernelConsts kc{};
         auto geom = experiment.GetDiffractionGeometry();
         kc.det_width_pxl = static_cast<float>(experiment.GetXPixelsNum());
@@ -157,6 +169,7 @@ namespace {
         kc.one_over_dmax_sq = one_over_dmax * one_over_dmax;
         kc.one_over_wavelength = 1.0f / geom.GetWavelength_A();
         kc.ewald_cutoff = ewald_dist_cutoff;
+        kc.bandwidth_sigma = bandwidth_sigma;
         kc.Astar = lattice.Astar();
         kc.Bstar = lattice.Bstar();
         kc.Cstar = lattice.Cstar();
@@ -178,7 +191,8 @@ int BraggPredictionGPU::Calc(const DiffractionExperiment &experiment,
                              const CrystalLattice &lattice,
                              const BraggPredictionSettings &settings) {
     // Build constants on host
-    KernelConsts hK = BuildKernelConsts(experiment, lattice, settings.high_res_A, settings.ewald_dist_cutoff, settings.centering);
+    KernelConsts hK = BuildKernelConsts(experiment, lattice, settings.high_res_A, settings.ewald_dist_cutoff,
+                                        settings.centering, settings.bandwidth_sigma);
     cudaMemcpyAsync(dK, &hK, sizeof(KernelConsts), cudaMemcpyHostToDevice, stream);
     cudaMemsetAsync(d_count, 0, sizeof(int), stream);
 
diff --git a/image_analysis/bragg_prediction/BraggPredictionGPU.h b/image_analysis/bragg_prediction/BraggPredictionGPU.h
index 2bf7a27b..8c6a8486 100644
--- a/image_analysis/bragg_prediction/BraggPredictionGPU.h
+++ b/image_analysis/bragg_prediction/BraggPredictionGPU.h
@@ -18,6 +18,7 @@ struct KernelConsts {
     float one_over_wavelength;
     float one_over_dmax_sq;
     float ewald_cutoff;
+    float bandwidth_sigma;   // relative Δλ/λ (sigma); 0 = monochromatic
     Coord Astar, Bstar, Cstar, S0;
     float rot[9];
     char centering;
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index b2d2578f..8f78e16c 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -475,7 +475,8 @@ void PixelRefine::Run(const T *image,
     const BraggPredictionSettings settings_prediction{
         .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
         .max_hkl = 100,
-        .centering = data.centering
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
     };
 
     const auto azim_result = profile.GetResult();
@@ -942,7 +943,8 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
     const BraggPredictionSettings settings_prediction{
         .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
         .max_hkl = 100,
-        .centering = data.centering
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
     };
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
-- 
2.52.0


From efe882f4b689f38c7bcbc01eba68d58960557377 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 16:28:17 +0200
Subject: [PATCH 023/228] jfjoch_viewer: Better display (to be tested) of pixel
 refine

---
 .../pixel_refinement/PixelRefine.cpp          | 123 ++++++++++++++++++
 image_analysis/pixel_refinement/PixelRefine.h |  12 ++
 viewer/JFJochImageReadingWorker.cpp           |  80 +++++++++++-
 viewer/JFJochImageReadingWorker.h             |  12 ++
 viewer/JFJochViewerWindow.cpp                 |   3 +
 viewer/image_viewer/JFJochSimpleImage.cpp     |  25 ++++
 viewer/image_viewer/JFJochSimpleImage.h       |   8 ++
 viewer/windows/JFJochPixelRefineWindow.cpp    |  12 ++
 viewer/windows/JFJochPixelRefineWindow.h      |   3 +
 viewer/windows/PixelRefineParams.h            |   8 ++
 10 files changed, 282 insertions(+), 4 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 8f78e16c..225778f7 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -993,6 +993,122 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
     return img;
 }
 
+template<class T>
+std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
+                                                const AzimuthalIntegrationProfile &profile,
+                                                BraggPrediction &prediction,
+                                                const PixelRefineData &data) const {
+    std::vector<float> img(xpixel * ypixel, 0.0f);
+
+    const double lambda = data.geom.GetWavelength_A();
+    const double pixel_size = data.geom.GetPixelSize_mm();
+    const auto azim_result = profile.GetResult();
+    const auto azim_std = profile.GetStd();
+    const auto &pixel_to_bin = mapping.GetPixelToBin();
+    const auto &corrections = mapping.Corrections();
+    const int total_bin_count = static_cast<int>(azim_result.size());
+    const double angle_rad = data.angle_deg * M_PI / 180.0;
+    const int radius = data.shoebox_radius;
+    const double bw = data.bandwidth;
+
+    auto recip_area = [&](double x, double y) -> double {
+        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
+        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
+        return (qx % qy).Length();
+    };
+    auto bandwidth_radial_sq = [&](double d) -> double {
+        if (bw <= 0.0 || d <= 0.0)
+            return 0.0;
+        const double bl = bw * lambda;
+        return bl * bl / (2.0 * d * d * d * d);
+    };
+
+    double beam[2], dist_mm, detector_rot[2], rot_vec[3];
+    double latt_vec0[3], latt_vec1[3], latt_vec2[3];
+    BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec, latt_vec0, latt_vec1, latt_vec2);
+
+    DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+            .BeamY_pxl(data.geom.GetBeamY_pxl())
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)
+    };
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+    const auto &predicted = prediction.GetReflections();
+
+    for (int ri = 0; ri < nrefl; ++ri) {
+        const auto &refl = predicted[ri];
+        const auto it = reference_data.find(hkl_key_generator(refl));
+        if (it == reference_data.end())
+            continue;
+
+        const double Itrue = it->second;
+        const double R_bw_sq = bandwidth_radial_sq(refl.d);
+
+        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
+        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
+        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
+        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+
+        for (int y = min_y; y <= max_y; ++y) {
+            for (int x = min_x; x <= max_x; ++x) {
+                const size_t npixel = xpixel * y + x;
+                const int azim_bin = pixel_to_bin[npixel];
+
+                // Same gating as Run(): only pixels that actually enter the fit.
+                if (azim_bin >= total_bin_count)
+                    continue;
+                if (image[npixel] == std::numeric_limits<T>::max())
+                    continue;
+                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
+                    continue;
+
+                const double correction = corrections[npixel];
+                const double Ibkg = azim_result[azim_bin];
+                const double Ibkg_sigma = azim_std[azim_bin];
+                const double raw = static_cast<double>(image[npixel]);
+                const double Iobs = raw * correction;
+
+                double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
+                if (!(var > 1.0))
+                    var = 1.0;
+                const double weight = 1.0 / std::sqrt(var);
+
+                PixelObs obs{
+                    .x = static_cast<double>(x),
+                    .y = static_cast<double>(y),
+                    .Iobs = Iobs,
+                    .Ibkg = Ibkg,
+                    .weight = weight,
+                    .A_recip = recip_area(x, y),
+                    .angle_rad = angle_rad
+                };
+                PixelResidual pr(obs, Itrue, lambda, pixel_size,
+                                 refl.h, refl.k, refl.l, R_bw_sq, data.crystal_system);
+
+                double Ipred = 0.0;
+                if (pr.Model(beam, &dist_mm, detector_rot, rot_vec,
+                             latt_vec0, latt_vec1, latt_vec2,
+                             &data.scale_factor, &data.B_factor, data.R, Ipred)) {
+                    // residual_i = (I_pred - I_obs) * weight (== Ceres residual);
+                    // its square is this pixel's contribution to the cost.
+                    const double rw = (Ipred - Iobs) * weight;
+                    img[npixel] += static_cast<float>(rw * rw);
+                }
+            }
+        }
+    }
+
+    return img;
+}
+
 // Explicit instantiations for the supported (uncompressed) image pixel types.
 template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
@@ -1000,3 +1116,10 @@ template void PixelRefine::Run<int32_t>(const int32_t *, const AzimuthalIntegrat
 template void PixelRefine::Run<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+
+template std::vector<float> PixelRefine::ChiSquaredImage<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 9522fc91..73a63094 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -182,4 +182,16 @@ public:
                                     BraggPrediction &prediction,
                                     const PixelRefineData &data,
                                     bool include_background = true) const;
+
+    // Render the per-pixel chi-square (cost density) that the optimizer actually
+    // minimizes: for every shoebox pixel that enters the fit it stores the squared
+    // weighted residual ((I_pred - I_obs)/sigma)^2 in *corrected* units - identical
+    // to the Ceres residual_i^2 - accumulating where shoeboxes overlap. Pixels that
+    // are not part of any shoebox stay 0; masked/saturated pixels (skipped by the
+    // fit) also stay 0. Summing the image gives ~2*final_cost. Diagnostic tool.
+    template<class T>
+    std::vector<float> ChiSquaredImage(const T *image,
+                                       const AzimuthalIntegrationProfile &profile,
+                                       BraggPrediction &prediction,
+                                       const PixelRefineData &data) const;
 };
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 6582700c..8f90cb11 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -8,6 +8,7 @@
 #include <cstring>
 
 #include "JFJochImageReadingWorker.h"
+#include "../reader/JFJochReaderImage.h"   // JFJochReaderImage + GAP/ERROR/SATURATED sentinels
 #include "../image_analysis/LoadFCalcFromMtz.h"
 #include "../image_analysis/bragg_prediction/BraggPredictionFactory.h"
 #include "../image_analysis/geom_refinement/AssignSpotsToRings.h"
@@ -69,6 +70,7 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
       indexing_settings(experiment.GetIndexingSettings()),
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
     qRegisterMetaType<PixelRefineParams>("PixelRefineParams");
+    qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
     spot_finding_settings = settings;;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
@@ -798,6 +800,74 @@ std::shared_ptr<SimpleImage> JFJochImageReadingWorker::WrapFloatImage_i(const st
     return si;
 }
 
+void JFJochImageReadingWorker::SquaredResidualWithImage_i(std::vector<float> &pred) const {
+    // PredictImage() returns raw detector units (same as the measured counts), so
+    // pred - measured is the per-pixel residual the model fails to explain. We plot
+    // |pred - measured|^2: sign-free, so it needs no diverging colour scale and just
+    // highlights where the model disagrees most. Masked / saturated pixels carry
+    // sentinels rather than counts, so no comparison is possible -> NaN (gap).
+    if (!current_image_ptr)
+        return;
+    const auto &img = current_image_ptr->Image();
+    const size_t n = std::min(pred.size(), img.size());
+    for (size_t i = 0; i < n; ++i) {
+        const int32_t v = img[i];
+        if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE || v == SATURATED_PXL_VALUE) {
+            pred[i] = NAN;
+        } else {
+            const float diff = pred[i] - static_cast<float>(v);
+            pred[i] = diff * diff;
+        }
+    }
+}
+
+void JFJochImageReadingWorker::MaskMeasuredSentinels_i(std::vector<float> &img) const {
+    // The chi^2 image is 0 outside shoeboxes; show masked/saturated pixels as a gap
+    // (NaN) instead, so they read as "not comparable" rather than "zero cost".
+    if (!current_image_ptr)
+        return;
+    const auto &measured = current_image_ptr->Image();
+    const size_t n = std::min(img.size(), measured.size());
+    for (size_t i = 0; i < n; ++i) {
+        const int32_t v = measured[i];
+        if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE || v == SATURATED_PXL_VALUE)
+            img[i] = NAN;
+    }
+}
+
+QVector<QRect> JFJochImageReadingWorker::BuildShoeboxes_i(const PixelRefineData &data) const {
+    // One rectangle per fitted reflection: the shoebox the optimizer summed over,
+    // centred on the predicted position with half-size data.shoebox_radius.
+    QVector<QRect> boxes;
+    boxes.reserve(static_cast<int>(data.reflections.size()));
+    const int r = data.shoebox_radius;
+    const int side = 2 * r + 1;
+    for (const auto &refl : data.reflections) {
+        if (!std::isfinite(refl.predicted_x) || !std::isfinite(refl.predicted_y))
+            continue;
+        const int cx = static_cast<int>(std::lround(refl.predicted_x));
+        const int cy = static_cast<int>(std::lround(refl.predicted_y));
+        boxes.push_back(QRect(cx - r, cy - r, side, side));
+    }
+    return boxes;
+}
+
+std::vector<float> JFJochImageReadingWorker::BuildDisplayImage_i(const PixelRefineData &data,
+                                                                 int display_mode) const {
+    if (display_mode == PixelRefineParams::ChiSquared) {
+        // The cost density the optimizer actually minimizes (weighted residual^2).
+        const auto &img32 = current_image_ptr->Image();
+        auto chi2 = pixel_refine_->ChiSquaredImage<int32_t>(img32.data(), *last_profile_, *pixel_pred_, data);
+        MaskMeasuredSentinels_i(chi2);
+        return chi2;
+    }
+
+    auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, data, true);
+    if (display_mode == PixelRefineParams::SquaredDifference)
+        SquaredResidualWithImage_i(pred);
+    return pred;
+}
+
 void JFJochImageReadingWorker::LoadReference(QString path) {
     QMutexLocker ul(&m);
     try {
@@ -840,8 +910,9 @@ void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
         pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
         emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
 
-        auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
-        emit predictedImageReady(WrapFloatImage_i(pred));
+        auto display = BuildDisplayImage_i(d, params.display_mode);
+        emit predictedImageReady(WrapFloatImage_i(display));
+        emit predictedShoeboxes(BuildShoeboxes_i(d));
     } catch (const std::exception &e) {
         emit pixelRefineStatus(QString("PixelRefine preview failed: %1").arg(e.what()));
     }
@@ -884,8 +955,9 @@ void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
         emit pixelRefineParamsRefined(out);
         emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
 
-        auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, d, true);
-        emit predictedImageReady(WrapFloatImage_i(pred));
+        auto display = BuildDisplayImage_i(d, params.display_mode);
+        emit predictedImageReady(WrapFloatImage_i(display));
+        emit predictedShoeboxes(BuildShoeboxes_i(d));
 
         // Show the refined predictions on the main image too.
         auto new_image = std::make_shared<JFJochReaderImage>(*current_image_ptr);
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 93d4240b..501b557d 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -71,6 +71,17 @@ private:
     void EnsurePixelRefine_i();
     bool BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p, QString &reason) const;
     std::shared_ptr<SimpleImage> WrapFloatImage_i(const std::vector<float> &img) const;
+    // Turn a predicted image into the squared residual |predicted - measured|^2 in
+    // place. Masked/saturated pixels become NaN (rendered as a gap: no comparison
+    // possible), not 0.
+    void SquaredResidualWithImage_i(std::vector<float> &pred) const;
+    // Mark masked/saturated pixels of the current image as NaN (gap) in a float
+    // image, leaving the rest untouched (used for the chi^2 view).
+    void MaskMeasuredSentinels_i(std::vector<float> &img) const;
+    // Build the per-reflection shoebox rectangles for the last refine/preview.
+    QVector<QRect> BuildShoeboxes_i(const PixelRefineData &data) const;
+    // Build the float image to display for the given PixelRefineParams::DisplayMode.
+    std::vector<float> BuildDisplayImage_i(const PixelRefineData &data, int display_mode) const;
 
     std::unique_ptr<ROIElement> roi;
 
@@ -134,6 +145,7 @@ signals:
 
     // PixelRefine (experimental)
     void predictedImageReady(std::shared_ptr<const SimpleImage> image);
+    void predictedShoeboxes(QVector<QRect> boxes); // per-reflection optimization windows
     void pixelRefineResidual(double cost, double cc, int64_t n_reflections);
     void pixelRefineParamsRefined(PixelRefineParams params);
     void pixelRefineStatus(QString message);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index de383008..9fa6a302 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -28,6 +28,7 @@
 #include "windows/JFJochPixelRefineWindow.h"
 #include "windows/JFJochMagnifierWindow.h"
 #include "image_viewer/JFJochImage.h"
+#include "image_viewer/JFJochSimpleImage.h"
 #include <QMessageBox>
 
 JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString &file) : QMainWindow(parent) {
@@ -351,6 +352,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::LoadReference);
     connect(reading_worker, &JFJochImageReadingWorker::predictedImageReady,
             pixelRefineWindow, &JFJochPixelRefineWindow::setPredictedImage);
+    connect(reading_worker, &JFJochImageReadingWorker::predictedShoeboxes,
+            pixelRefineWindow->imageView(), &JFJochSimpleImage::setShoeboxes);
     connect(reading_worker, &JFJochImageReadingWorker::pixelRefineResidual,
             pixelRefineWindow, &JFJochPixelRefineWindow::setResidual);
     connect(reading_worker, &JFJochImageReadingWorker::pixelRefineParamsRefined,
diff --git a/viewer/image_viewer/JFJochSimpleImage.cpp b/viewer/image_viewer/JFJochSimpleImage.cpp
index 24bdcad6..d3494a8f 100644
--- a/viewer/image_viewer/JFJochSimpleImage.cpp
+++ b/viewer/image_viewer/JFJochSimpleImage.cpp
@@ -40,6 +40,31 @@ void JFJochSimpleImage::setImage(std::shared_ptr<const SimpleImage> img) {
     }
 }
 
+void JFJochSimpleImage::setShoeboxes(QVector<QRect> boxes) {
+    shoeboxes_ = std::move(boxes);
+    // Redraw overlays on the current image (no-op if no image yet).
+    updateOverlay();
+}
+
+void JFJochSimpleImage::addCustomOverlay() {
+    if (shoeboxes_.isEmpty() || !scene())
+        return;
+
+    // Cosmetic 1-px outline so the box edges stay thin at any zoom; only draw the
+    // ones currently in view (there can be hundreds of reflections).
+    const QRectF visibleRect = mapToScene(viewport()->geometry()).boundingRect();
+    QPen pen(QColor(0, 220, 255), 0); // cyan, distinct from the prediction colours
+    pen.setCosmetic(true);
+
+    for (const QRect &b : shoeboxes_) {
+        const QRectF r(b.x(), b.y(), b.width(), b.height());
+        if (!visibleRect.intersects(r))
+            continue;
+        auto *item = scene()->addRect(r, pen);
+        addOverlayItem(item);
+    }
+}
+
 void JFJochSimpleImage::mouseHover(QMouseEvent *event) {
     if (image_) {
         const QPointF scenePos = mapToScene(event->pos());
diff --git a/viewer/image_viewer/JFJochSimpleImage.h b/viewer/image_viewer/JFJochSimpleImage.h
index 8d7251e4..40abac06 100644
--- a/viewer/image_viewer/JFJochSimpleImage.h
+++ b/viewer/image_viewer/JFJochSimpleImage.h
@@ -7,6 +7,7 @@
 #include <QVector>
 #include <QColor>
 #include <QPointF>
+#include <QRect>
 #include <QGraphicsTextItem>
 #include <vector>
 #include <QTimer>
@@ -18,14 +19,21 @@ class JFJochSimpleImage : public JFJochImage {
     Q_OBJECT
 
     std::shared_ptr<const SimpleImage> image_;
+
+    // Per-reflection shoebox rectangles (pixel coordinates) to overlay: the pixels
+    // PixelRefine actually summed over. Empty = nothing drawn.
+    QVector<QRect> shoeboxes_;
+
     // Prepare image
     template<class T>
     void loadImageInternal(const uint8_t *input);
     void loadImageInternal();
 
     void mouseHover(QMouseEvent *event) override;
+    void addCustomOverlay() override;
 public:
     explicit JFJochSimpleImage(QWidget *parent = nullptr);
 public slots:
     void setImage(std::shared_ptr<const SimpleImage> img);
+    void setShoeboxes(QVector<QRect> boxes);
 };
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index 230d4974..7f7a64ec 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -31,6 +31,15 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
     auto controlsLayout = new QVBoxLayout(controls);
     layout->addWidget(controls, 0);
 
+    // --- what the left image shows ------------------------------------------
+    m_displayMode = new QComboBox(this);
+    m_displayMode->addItem(tr("Prediction"));
+    m_displayMode->addItem(tr("Squared difference |pred - image|²"));
+    m_displayMode->addItem(tr("χ² (weighted residual = LSQ cost)"));
+    auto displayForm = new QFormLayout();
+    displayForm->addRow(tr("Display:"), m_displayMode);
+    controlsLayout->addLayout(displayForm);
+
     auto paramBox = new QGroupBox(tr("Model parameters"), this);
     auto form = new QFormLayout(paramBox);
 
@@ -97,6 +106,8 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
     for (auto *s : {m_R0, m_R1, m_bw, m_scale, m_B, m_beamx, m_beamy})
         connect(s, &SliderPlusBox::valueChanged, this, [this](double) { onControlChanged(); });
 
+    connect(m_displayMode, &QComboBox::currentIndexChanged, this, [this](int) { onControlChanged(); });
+
     connect(m_overrideBeam, &QCheckBox::toggled, this, [this](bool on) {
         m_beamx->setEnabled(on);
         m_beamy->setEnabled(on);
@@ -141,6 +152,7 @@ PixelRefineParams JFJochPixelRefineWindow::currentParams() const {
     p.refine_scale       = m_refScale->isChecked();
     p.refine_B           = m_refB->isChecked();
     p.refine_R           = m_refR->isChecked();
+    p.display_mode       = m_displayMode->currentIndex();
     return p;
 }
 
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
index 7940ce16..99c628c2 100644
--- a/viewer/windows/JFJochPixelRefineWindow.h
+++ b/viewer/windows/JFJochPixelRefineWindow.h
@@ -10,6 +10,7 @@
 
 #include <memory>
 #include <QCheckBox>
+#include <QComboBox>
 #include <QLabel>
 #include <QPushButton>
 #include <QTimer>
@@ -33,6 +34,8 @@ class JFJochPixelRefineWindow : public JFJochHelperWindow {
     SliderPlusBox *m_beamx;
     SliderPlusBox *m_beamy;
 
+    QComboBox *m_displayMode;   // Prediction vs. Difference (prediction - image)
+
     QCheckBox *m_overrideBeam;
     QCheckBox *m_refOrientation;
     QCheckBox *m_refCell;
diff --git a/viewer/windows/PixelRefineParams.h b/viewer/windows/PixelRefineParams.h
index 4b266e62..64f6e27b 100644
--- a/viewer/windows/PixelRefineParams.h
+++ b/viewer/windows/PixelRefineParams.h
@@ -28,6 +28,14 @@ struct PixelRefineParams {
     bool refine_R           = true;
 
     int max_iterations = 3; // <=0 means evaluate-only (preview / residual)
+
+    // Display only (no effect on the fit): what the preview/refine image shows.
+    enum DisplayMode : int {
+        Prediction        = 0, // forward-model image
+        SquaredDifference = 1, // |prediction - measured|^2 (raw, unweighted)
+        ChiSquared        = 2  // ((prediction - measured)/sigma)^2 = the LSQ cost density
+    };
+    int display_mode = Prediction;
 };
 
 Q_DECLARE_METATYPE(PixelRefineParams)
-- 
2.52.0


From e051eed033cd2e36ad85d725ea98bda4f9511648 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 9 Jun 2026 19:43:34 +0200
Subject: [PATCH 024/228] jfjoch_process: Remove postrefinement

---
 common/ScalingSettings.h                     |   2 +-
 image_analysis/scale_merge/ScaleOnTheFly.cpp | 170 +------------------
 tools/jfjoch_process.cpp                     |   2 -
 3 files changed, 2 insertions(+), 172 deletions(-)

diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index a20bcd21..f7c724f8 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -6,7 +6,7 @@
 #include <optional>
 #include "JFJochException.h"
 
-enum class PartialityModel { Fixed, Rotation, Unity, Postrefinement };
+enum class PartialityModel { Fixed, Rotation, Unity };
 enum class IntensityFormat { Text, mmCIF, MTZ};
 
 class ScalingSettings {
diff --git a/image_analysis/scale_merge/ScaleOnTheFly.cpp b/image_analysis/scale_merge/ScaleOnTheFly.cpp
index f5765374..46fc6cea 100644
--- a/image_analysis/scale_merge/ScaleOnTheFly.cpp
+++ b/image_analysis/scale_merge/ScaleOnTheFly.cpp
@@ -105,145 +105,6 @@ namespace {
         double partiality;
     };
 
-struct ScalingPostRefResidual : public ScalingResidual {
-    // Postrefinement for still images
-    //
-    // In this algorithm at the point of post-refinement we don't anymore care for where maximum of
-    // the reflection was located and if it fits the observed position.
-    // This reflections was already integrated and we cannot integrate it better at this point.
-    // But, we could adjust partiality to indicate that this reflection was wrongly predicted.
-    // I.e., integrated position was far away from true reflection, so partiality must be low.
-    // This is an empiric model and need to see if this will work in practice at all.
-    // I hope it will allow the model to find that reflections were misindexed.
-    // We assume at this point that initial indexing was done properly and integration was generally OK => most low resolution reflections fit correctly
-    // Yet we know, that small errors in indexing are inducing misalignment at high resolution - sometimes it is visible that high-resolution reflections
-    // are away from shoe-boxes observed in the image, if we can catch this at post-refinement/scaling step, this would be great.
-    // Next logical step is to do this pixel-wise - for each pixel refine partiality and merge pixels
-    // This should work for per-image scaling, or even, maybe, for full rotation datasets (3600 images)
-    // Then we could properly take into account misalignment of shoe-box center vs. partiality and also remove most pixels
-    // in the shoe-box that don't really contribute to the reflection.
-    // But...it could also drift to downweighting partiality for all high resolution reflections to make loss function "fake happy".
-
-    // We assume rot3 == 0. Rot3 is not really helping much in crystallography (other than fixing polarization correction)
-    ScalingPostRefResidual(const Reflection &r, double Itrue, double sigma,
-                           const DiffractionGeometry &geometry,
-                           const CrystalLattice &lattice)
-    : ScalingResidual(r, Itrue, sigma),
-          integration_center_x(r.predicted_x),
-          integration_center_y(r.predicted_y),
-          inv_lambda(SafeInv(geometry.GetWavelength_A(), 0.0)),
-          pixel_size(geometry.GetPixelSize_mm()),
-          det_dist_mm(geometry.GetDetectorDistance_mm()),
-          beam_x(geometry.GetBeamX_pxl()),
-          beam_y(geometry.GetBeamY_pxl()),
-          exp_h(r.h),
-          exp_k(r.k),
-          exp_l(r.l),
-          Astar(lattice.Astar()),
-          Bstar(lattice.Bstar()),
-          Cstar(lattice.Cstar()),
-          c1(std::cos(geometry.GetPoniRot1_rad())),
-          s1(std::sin(geometry.GetPoniRot1_rad())),
-          c2(std::cos(geometry.GetPoniRot2_rad())),
-          s2(std::sin(geometry.GetPoniRot2_rad())) {
-    }
-
-    template <typename T>
-    T CalcPartiality(const T *const R,
-                    const T *const beam_corr,
-                    const T *const p0) const {
-        // Detector coordinates in mm
-        const T det_x = (T(integration_center_x) - beam_x - beam_corr[0]) * T(pixel_size);
-        const T det_y = (T(integration_center_y) - beam_y - beam_corr[1]) * T(pixel_size);
-        const T det_z = T(det_dist_mm);
-
-        // Apply Ry(rot1) first: rotate around Y
-        const T t1_x = T(c1) * det_x + T(s1) * det_z;
-        const T t1_y = det_y;
-        const T t1_z = T(-s1) * det_x + T(c1) * det_z;
-
-        // Then apply Rx(-rot2): rotate around X
-        const T x = t1_x;
-        const T y = T(c2) * t1_y + T(s2) * t1_z;
-        const T z = - T(s2) * t1_y + T(c2) * t1_z;
-
-        // convert to recip space
-        const T lab_norm = ceres::sqrt(x * x + y * y + z * z);
-        const T inv_norm = T(1) / lab_norm;
-
-        T recip_obs[3];
-        recip_obs[0] = x * inv_norm * inv_lambda;
-        recip_obs[1] = y * inv_norm * inv_lambda;
-        recip_obs[2] = (z * inv_norm - T(1.0)) * inv_lambda;
-
-        const Eigen::Matrix<T, 3, 1> e_obs_recip(recip_obs[0], recip_obs[1], recip_obs[2]);
-
-        const T astar_unrot[3] = {T(Astar.x), T(Astar.y), T(Astar.z)};
-        const T bstar_unrot[3] = {T(Bstar.x), T(Bstar.y), T(Bstar.z)};
-        const T cstar_unrot[3] = {T(Cstar.x), T(Cstar.y), T(Cstar.z)};
-
-        T astar_rot[3], bstar_rot[3], cstar_rot[3];
-
-        ceres::AngleAxisRotatePoint(p0, astar_unrot, astar_rot);
-        ceres::AngleAxisRotatePoint(p0, bstar_unrot, bstar_rot);
-        ceres::AngleAxisRotatePoint(p0, cstar_unrot, cstar_rot);
-
-        const Eigen::Matrix<T, 3, 1> e_pred_recip(T(exp_h) * astar_rot[0] + T(exp_k) * bstar_rot[0] + T(exp_l) * cstar_rot[0],
-            T(exp_h) * astar_rot[1] + T(exp_k) * bstar_rot[1] + T(exp_l) * cstar_rot[1],
-            T(exp_h) * astar_rot[2] + T(exp_k) * bstar_rot[2] + T(exp_l) * cstar_rot[2]
-        );
-
-        // Ewald sphere centre is at -k_i = (0, 0, -inv_lambda)
-        // Radial direction: outward normal at g_hkl
-        const Eigen::Matrix<T, 3, 1> S_pred(
-            e_pred_recip[0],
-            e_pred_recip[1],
-            e_pred_recip[2] + T(inv_lambda)   // g_hkl + k_i
-        );
-        const T S_pred_norm = S_pred.norm();
-        if (S_pred_norm < T(1e-10))
-            return T(0);
-
-        const Eigen::Matrix<T, 3, 1> n_radial = S_pred / S_pred_norm;
-
-        const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-        const T eps_radial        = delta_q.dot(n_radial);
-        const Eigen::Matrix<T, 3, 1> dq_tang = delta_q - eps_radial * n_radial;
-        const T eps_tangential_sq = dq_tang.squaredNorm();   // guaranteed ≥ 0
-        // ─────────────────────────────────────────────────────────────
-
-        return ceres::exp(- eps_radial * eps_radial / (R[0] * R[0]) - eps_tangential_sq / (R[1] * R[1]));
-    }
-
-    template<typename T>
-    bool operator()(const T *const G,
-                    const T *const B,
-                    const T *const R,
-                    const T *const beam_corr,
-                    const T *const p0,
-                    T *residual) const {
-        if (R[0] < T(1e-10) || R[1] < T(1e-10))
-            return false;
-
-        const T B_term = ceres::exp(B[0] * T(b_resolution_coeff));
-
-        const T partiality = CalcPartiality(R, beam_corr, p0);
-        residual[0] = (G[0] * partiality * B_term * T(lp) * T(Itrue)
-                       - T(Iobs)) * T(weight);
-        return true;
-    }
-
-    const double integration_center_x, integration_center_y;
-    const double inv_lambda;
-    const double pixel_size;
-    const double det_dist_mm;
-    const double beam_x, beam_y;
-    const double exp_h;
-    const double exp_k;
-    const double exp_l;
-    const Coord Astar, Bstar, Cstar;
-    const double c1,s1,c2,s2;
-};
     struct RotationNormRegularizer {
         explicit RotationNormRegularizer(double weight) : weight(weight) {}
 
@@ -282,7 +143,6 @@ bool ScaleOnTheFly::Accept(const Reflection &r) const {
             return std::isfinite(r.zeta) && r.zeta > 0.0f;
         case PartialityModel::Fixed:
         case PartialityModel::Unity:
-        case PartialityModel::Postrefinement:
             return true;
     }
 
@@ -395,12 +255,6 @@ void ScaleOnTheFly::Scale(IntegrationOutcome &integration_outcome) const {
                 problem.AddResidualBlock(cost, nullptr, &result.G, &result.B);
             }
             break;
-            case PartialityModel::Postrefinement: {
-                auto *cost = new ceres::AutoDiffCostFunction<ScalingPostRefResidual, 1, 1, 1, 2, 2, 3>(
-                    new ScalingPostRefResidual(r, Itrue, sigma, integration_outcome.geom, integration_outcome.latt));
-                problem.AddResidualBlock(cost, nullptr, &result.G, &result.B, result.R, result.beam_corr, result.p0);
-            }
-            break;
             case PartialityModel::Rotation: {
                 auto *cost = new ceres::AutoDiffCostFunction<ScalingRotationResidual, 1, 1, 1, 1, 1>(
                     new ScalingRotationResidual(r, Itrue, sigma));
@@ -460,21 +314,6 @@ void ScaleOnTheFly::Scale(IntegrationOutcome &integration_outcome) const {
         problem.SetParameterUpperBound(&result.mos, 0, s.GetMaxMosaicity());
     }
 
-    if (model == PartialityModel::Postrefinement) {
-        problem.SetParameterLowerBound(result.R, 0, 1e-6);
-        problem.SetParameterLowerBound(result.R, 1, 1e-6);
-
-        // Beam center can be off by max 1 pixel
-        problem.SetParameterLowerBound(result.beam_corr, 0, -1);
-        problem.SetParameterUpperBound(result.beam_corr, 0, 1);
-        problem.SetParameterLowerBound(result.beam_corr, 1, -1);
-        problem.SetParameterUpperBound(result.beam_corr, 1, 1);
-
-        auto *angle_reg_cost = new ceres::AutoDiffCostFunction<RotationNormRegularizer, 3, 3>(
-            new RotationNormRegularizer(0.05));
-        problem.AddResidualBlock(angle_reg_cost, nullptr, result.p0);
-    }
-
     ceres::Solver::Options options;
     options.linear_solver_type = ceres::DENSE_QR;
     options.minimizer_progress_to_stdout = false;
@@ -495,19 +334,12 @@ void ScaleOnTheFly::Scale(IntegrationOutcome &integration_outcome) const {
                     r.partiality = RotationPartiality(r.delta_phi_deg, r.zeta, result.mos, result.wedge);
                 break;
             }
-            case PartialityModel::Postrefinement: {
-                ScalingPostRefResidual residual(r, 0, 0, integration_outcome.geom, integration_outcome.latt);
-                r.partiality = static_cast<float>(residual.CalcPartiality(result.R, result.beam_corr, result.p0));
-            }
-                break;
             default:
                 // For fixed partiality there is no need to change anything
                 break;
         }
         const double denom = B_term * r.partiality * result.G;
-        if (std::isfinite(r.rlp) &&
-            std::isfinite(denom) &&
-            denom > 0.0) {
+        if (std::isfinite(r.rlp) && std::isfinite(denom) && denom > 0.0) {
                 r.image_scale_corr = static_cast<float>(r.rlp / denom);
             } else {
                 r.image_scale_corr = NAN;
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 47cd0736..5876418b 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -469,8 +469,6 @@ int main(int argc, char **argv) {
                 partiality_model = PartialityModel::Fixed;
             else if (strcmp(optarg, "rot") == 0)
                 partiality_model = PartialityModel::Rotation;
-            else if (strcmp(optarg, "postref") == 0)
-                partiality_model = PartialityModel::Postrefinement;
             else {
                 logger.Error("Invalid partiality mode: {}", optarg);
                 print_usage();
-- 
2.52.0


From e4230bc14ee9a0b5a127d24d1cb71ca486820de4 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 14:41:36 +0200
Subject: [PATCH 025/228] Bragg integration: option to use azimuthal
 integration profile

---
 common/BraggIntegrationSettings.cpp           |   9 +
 common/BraggIntegrationSettings.h             |   5 +-
 image_analysis/IndexAndRefine.cpp             |  14 +-
 image_analysis/IndexAndRefine.h               |   8 +-
 image_analysis/MXAnalysisAfterFPGA.cpp        |  11 +-
 image_analysis/MXAnalysisAfterFPGA.h          |   5 +-
 image_analysis/MXAnalysisWithoutFPGA.cpp      |   2 +-
 .../bragg_integration/BraggIntegrate2D.cpp    | 219 +++++++++++++-----
 .../bragg_integration/BraggIntegrate2D.h      |  10 +-
 receiver/JFJochReceiver.cpp                   |  25 +-
 receiver/JFJochReceiver.h                     |   2 +-
 receiver/JFJochReceiverFPGA.cpp               |  11 +-
 receiver/JFJochReceiverLite.cpp               |   4 +-
 tests/BraggIntegrate2DTest.cpp                |   6 +-
 tools/jfjoch_scale.cpp                        |   2 -
 15 files changed, 218 insertions(+), 115 deletions(-)

diff --git a/common/BraggIntegrationSettings.cpp b/common/BraggIntegrationSettings.cpp
index 3fe0a861..0528084e 100644
--- a/common/BraggIntegrationSettings.cpp
+++ b/common/BraggIntegrationSettings.cpp
@@ -87,3 +87,12 @@ float BraggIntegrationSettings::GetDMinLimit_A() const {
 float BraggIntegrationSettings::GetMinimumSigmaInRegardsToI() const {
     return minimum_sigma_in_regards_to_i;
 }
+
+bool BraggIntegrationSettings::IsUseAzimProfile() const {
+    return use_azim_profile;
+}
+
+BraggIntegrationSettings &BraggIntegrationSettings::UseAzimProfile(bool input) {
+    use_azim_profile = input;
+    return *this;
+}
diff --git a/common/BraggIntegrationSettings.h b/common/BraggIntegrationSettings.h
index 60ab4059..2c15921d 100644
--- a/common/BraggIntegrationSettings.h
+++ b/common/BraggIntegrationSettings.h
@@ -12,14 +12,14 @@ class BraggIntegrationSettings {
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;
     float minimum_sigma_in_regards_to_i = 0.02;
-
+    bool use_azim_profile = false;
 public:
     BraggIntegrationSettings& R1(float input);
     BraggIntegrationSettings& R2(float input);
     BraggIntegrationSettings& R3(float input);
     BraggIntegrationSettings& DMinLimit_A(float input);
     BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
-
+    BraggIntegrationSettings& UseAzimProfile(bool input);
 
     [[nodiscard]] float GetR1() const;
     [[nodiscard]] float GetR2() const;
@@ -28,4 +28,5 @@ public:
     [[nodiscard]] float GetDMinLimit_A() const;
 
     [[nodiscard]] float GetMinimumSigmaInRegardsToI() const;
+    [[nodiscard]] bool IsUseAzimProfile() const;
 };
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 98b1aed6..459af31e 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -239,8 +239,8 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                                               const CompressedImage &image,
                                               BraggPrediction &prediction,
                                               const IndexAndRefine::IndexingOutcome &outcome,
-                                              const AzimuthalIntegrationMapping *mapping,
-                                              const AzimuthalIntegrationProfile *profile) {
+                                              const AzimuthalIntegrationMapping &mapping,
+                                              const AzimuthalIntegrationProfile &profile) {
     if (!outcome.lattice_candidate)
         return;
 
@@ -299,11 +299,11 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
     // integrated reflections that flow into the normal save/merge).
     const bool use_pixel_refine =
         experiment.GetIndexingSettings().GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::PixelRefine
-        && !pixel_reference_.empty() && mapping && profile;
+        && !pixel_reference_.empty();
 
     if (use_pixel_refine) {
         auto integration_start_time = std::chrono::steady_clock::now();
-        PixelRefineIntegrate(msg, image, prediction, outcome, *mapping, *profile, i_outcome);
+        PixelRefineIntegrate(msg, image, prediction, outcome, mapping, profile, i_outcome);
         msg.integrated_reflections = i_outcome.reflections.size();
         auto integration_end_time = std::chrono::steady_clock::now();
         msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
@@ -314,7 +314,7 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
         msg.bragg_prediction_time_s = std::chrono::duration<float>(pred_end_time - pred_start_time).count();
 
         auto integration_start_time = std::chrono::steady_clock::now();
-        i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), nrefl, msg.number);
+        i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), mapping, profile, nrefl, msg.number);
         msg.integrated_reflections = i_outcome.reflections.size();
         auto integration_end_time = std::chrono::steady_clock::now();
         msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
@@ -357,8 +357,8 @@ void IndexAndRefine::ProcessImage(DataMessage &msg,
                                   const SpotFindingSettings &spot_finding_settings,
                                   const CompressedImage &image,
                                   BraggPrediction &prediction,
-                                  const AzimuthalIntegrationMapping *mapping,
-                                  const AzimuthalIntegrationProfile *profile) {
+                                  const AzimuthalIntegrationMapping &mapping,
+                                  const AzimuthalIntegrationProfile &profile) {
     if (!indexer_ || !spot_finding_settings.indexing)
         return;
 
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index 7674392e..d73fc2f1 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -66,8 +66,8 @@ class IndexAndRefine {
                                  const CompressedImage &image,
                                  BraggPrediction &prediction,
                                  const IndexingOutcome &outcome,
-                                 const AzimuthalIntegrationMapping *mapping,
-                                 const AzimuthalIntegrationProfile *profile);
+                                 const AzimuthalIntegrationMapping &mapping,
+                                 const AzimuthalIntegrationProfile &profile);
 
     std::unique_ptr<ScaleOnTheFly> scaling_engine;
     void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
@@ -93,8 +93,8 @@ public:
     void ForceRotationIndexerLattice(const CrystalLattice& lattice);
 
     void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction,
-                      const AzimuthalIntegrationMapping *mapping = nullptr,
-                      const AzimuthalIntegrationProfile *profile = nullptr);
+                      const AzimuthalIntegrationMapping &mapping,
+                      const AzimuthalIntegrationProfile &profile);
     IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
 
     ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
diff --git a/image_analysis/MXAnalysisAfterFPGA.cpp b/image_analysis/MXAnalysisAfterFPGA.cpp
index a5347236..96d8430d 100644
--- a/image_analysis/MXAnalysisAfterFPGA.cpp
+++ b/image_analysis/MXAnalysisAfterFPGA.cpp
@@ -25,10 +25,12 @@ double stddev(const std::vector<float> &v) {
 }
 
 
-MXAnalysisAfterFPGA::MXAnalysisAfterFPGA(const DiffractionExperiment &in_experiment, IndexAndRefine &indexer)
+MXAnalysisAfterFPGA::MXAnalysisAfterFPGA(const DiffractionExperiment &in_experiment, IndexAndRefine &indexer,
+                                         AzimuthalIntegrationMapping &mapping)
     : experiment(in_experiment),
       indexer(indexer),
-      prediction(CreateBraggPrediction(experiment.IsRotationIndexing())) {
+      prediction(CreateBraggPrediction(experiment.IsRotationIndexing())),
+      mapping(mapping) {
     if (experiment.IsSpotFindingEnabled())
         find_spots = true;
 }
@@ -103,7 +105,8 @@ void MXAnalysisAfterFPGA::ReadFromCPU(DeviceOutput *output, const SpotFindingSet
     }
 }
 
-void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSettings& spot_finding_settings) {
+void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSettings &spot_finding_settings,
+                                  const AzimuthalIntegrationProfile &profile) {
     if (find_spots && (state == State::Enabled)) {
         const auto t0 = std::chrono::steady_clock::now();
         SpotAnalyze(experiment, spot_finding_settings, spots, message);
@@ -111,7 +114,7 @@ void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSetting
         spot_finding_time_total += (t1 - t0);
 
         if (spot_finding_settings.indexing)
-            indexer.ProcessImage(message, spot_finding_settings, message.image, *prediction);
+            indexer.ProcessImage(message, spot_finding_settings, message.image, *prediction, mapping, profile);
     }
 
     if (spot_finding_timing_active) {
diff --git a/image_analysis/MXAnalysisAfterFPGA.h b/image_analysis/MXAnalysisAfterFPGA.h
index ccddf87a..e3b708ac 100644
--- a/image_analysis/MXAnalysisAfterFPGA.h
+++ b/image_analysis/MXAnalysisAfterFPGA.h
@@ -28,9 +28,10 @@ class MXAnalysisAfterFPGA {
 
     std::chrono::duration<double, std::micro> spot_finding_time_total{0.0};
     bool spot_finding_timing_active = false;
+    const AzimuthalIntegrationMapping &mapping;
 public:
 
-    MXAnalysisAfterFPGA(const DiffractionExperiment& experiment, IndexAndRefine &indexer);
+    MXAnalysisAfterFPGA(const DiffractionExperiment& experiment, IndexAndRefine &indexer, AzimuthalIntegrationMapping &mapping);
 
     void ReadFromFPGA(const DeviceOutput* output,
                       const SpotFindingSettings& settings,
@@ -40,5 +41,5 @@ public:
                      const SpotFindingSettings &settings,
                      size_t module_number);
 
-    void Process(DataMessage &message, const SpotFindingSettings& settings);
+    void Process(DataMessage &message, const SpotFindingSettings& settings, const AzimuthalIntegrationProfile &profile);
 };
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index 6a638213..62b6379f 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -92,7 +92,7 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
         if (spot_finding_settings.indexing)
             indexer.ProcessImage(output, spot_finding_settings,
                 CompressedImage(preprocessor_buffer->getBuffer(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum()),
-                *prediction, &integration, &profile);
+                *prediction, integration, profile);
     }
 
     output.max_viable_pixel_value = ret.max_value;
diff --git a/image_analysis/bragg_integration/BraggIntegrate2D.cpp b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
index b616ecc1..35ec4849 100644
--- a/image_analysis/bragg_integration/BraggIntegrate2D.cpp
+++ b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
@@ -8,65 +8,62 @@
 #include <vector>
 
 namespace {
+    template<class T>
+    float Median(std::vector<T> &values) {
+        if (values.empty())
+            return 0.0f;
 
-template<class T>
-float Median(std::vector<T> &values) {
-    if (values.empty())
-        return 0.0f;
+        const size_t middle = values.size() / 2;
+        std::nth_element(values.begin(), values.begin() + middle, values.end());
 
-    const size_t middle = values.size() / 2;
-    std::nth_element(values.begin(), values.begin() + middle, values.end());
+        if (values.size() % 2 == 1)
+            return static_cast<float>(values[middle]);
 
-    if (values.size() % 2 == 1)
-        return static_cast<float>(values[middle]);
+        const T upper = values[middle];
+        std::nth_element(values.begin(), values.begin() + middle - 1, values.begin() + middle);
+        const T lower = values[middle - 1];
 
-    const T upper = values[middle];
-    std::nth_element(values.begin(), values.begin() + middle - 1, values.begin() + middle);
-    const T lower = values[middle - 1];
+        return 0.5f * static_cast<float>(lower + upper);
+    }
 
-    return 0.5f * static_cast<float>(lower + upper);
-}
+    void MarkReflectionMask(std::vector<uint8_t> &mask,
+                            size_t xpixel, size_t ypixel,
+                            const Reflection &r, float r_2, float r_2_sq) {
+        int64_t x0 = std::floor(r.predicted_x - r_2 - 1.0f);
+        int64_t x1 = std::ceil(r.predicted_x + r_2 + 1.0f);
+        int64_t y0 = std::floor(r.predicted_y - r_2 - 1.0f);
+        int64_t y1 = std::ceil(r.predicted_y + r_2 + 1.0f);
 
-void MarkReflectionMask(std::vector<uint8_t> &mask,
-                        size_t xpixel, size_t ypixel,
-                        const Reflection &r, float r_2, float r_2_sq) {
+        if (x0 < 0)
+            x0 = 0;
+        if (y0 < 0)
+            y0 = 0;
+        if (x1 >= static_cast<int64_t>(xpixel))
+            x1 = static_cast<int64_t>(xpixel) - 1;
+        if (y1 >= static_cast<int64_t>(ypixel))
+            y1 = static_cast<int64_t>(ypixel) - 1;
 
-    int64_t x0 = std::floor(r.predicted_x - r_2 - 1.0f);
-    int64_t x1 = std::ceil(r.predicted_x + r_2 + 1.0f);
-    int64_t y0 = std::floor(r.predicted_y - r_2 - 1.0f);
-    int64_t y1 = std::ceil(r.predicted_y + r_2 + 1.0f);
-
-    if (x0 < 0)
-        x0 = 0;
-    if (y0 < 0)
-        y0 = 0;
-    if (x1 >= static_cast<int64_t>(xpixel))
-        x1 = static_cast<int64_t>(xpixel) - 1;
-    if (y1 >= static_cast<int64_t>(ypixel))
-        y1 = static_cast<int64_t>(ypixel) - 1;
-
-    for (int64_t y = y0; y <= y1; y++) {
-        for (int64_t x = x0; x <= x1; x++) {
-            const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
-                                + (y - r.predicted_y) * (y - r.predicted_y);
-            if (dist_sq < r_2_sq)
-                mask[y * xpixel + x] = 1;
+        for (int64_t y = y0; y <= y1; y++) {
+            for (int64_t x = x0; x <= x1; x++) {
+                const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
+                                      + (y - r.predicted_y) * (y - r.predicted_y);
+                if (dist_sq < r_2_sq)
+                    mask[y * xpixel + x] = 1;
+            }
         }
     }
-}
 
-std::vector<uint8_t> BuildReflectionMask(const std::vector<Reflection> &predicted,
-                                         size_t npredicted,
-                                         size_t xpixel, size_t ypixel,
-                                         float r_2, float r_2_sq) {
-    std::vector<uint8_t> mask(xpixel * ypixel, 0);
+    std::vector<uint8_t> BuildReflectionMask(const std::vector<Reflection> &predicted,
+                                             size_t npredicted,
+                                             size_t xpixel, size_t ypixel,
+                                             float r_2, float r_2_sq) {
+        std::vector<uint8_t> mask(xpixel * ypixel, 0);
 
-    for (size_t i = 0; i < npredicted; i++)
-        MarkReflectionMask(mask, xpixel, ypixel, predicted.at(i), r_2, r_2_sq);
-
-    return mask;
-}
+        for (size_t i = 0; i < npredicted; i++)
+            MarkReflectionMask(mask, xpixel, ypixel, predicted.at(i), r_2, r_2_sq);
 
+        return mask;
+    }
 } // namespace
 
 template<class T>
@@ -75,7 +72,6 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
                          int64_t special_value, int64_t saturation,
                          float r_3, float r_1_sq, float r_2_sq, float r_3_sq,
                          float minimum_sigma_in_regards_to_i) {
-
     int64_t x0 = std::floor(r.predicted_x - r_3 - 1.0);
     int64_t x1 = std::ceil(r.predicted_x + r_3 + 1.0);
     int64_t y0 = std::floor(r.predicted_y - r_3 - 1.0);
@@ -146,15 +142,94 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
     }
 }
 
+template<class T>
+void IntegrateReflectionAzim(Reflection &r, const T *image,
+                             size_t xpixel, size_t ypixel,
+                             int64_t special_value, int64_t saturation,
+                             float r_1, float r_1_sq,
+                             const std::vector<uint16_t> &pixel_to_bin,
+                             const std::vector<float> &bkg_mean,
+                             float minimum_sigma_in_regards_to_i) {
+    int64_t x0 = std::floor(r.predicted_x - r_1 - 1.0);
+    int64_t x1 = std::ceil(r.predicted_x + r_1 + 1.0);
+    int64_t y0 = std::floor(r.predicted_y - r_1 - 1.0);
+    int64_t y1 = std::ceil(r.predicted_y + r_1 + 1.0);
+    x0 = std::max(0L, x0);
+    x1 = std::min(static_cast<int64_t>(xpixel - 1), x1);
+    y0 = std::max(0L, y0);
+    y1 = std::min(static_cast<int64_t>(ypixel - 1), y1);
+
+    int64_t I_sum = 0;
+    int64_t I_npixel_inner = 0;
+    int64_t I_npixel_integrated = 0;
+    int64_t I_sum_x = 0;
+    int64_t I_sum_y = 0;
+
+    std::vector<T> bkg_values;
+    bkg_values.reserve(static_cast<size_t>((x1 - x0 + 1) * (y1 - y0 + 1)));
+
+    float bkg = 0.0;
+
+    for (int64_t y = y0; y <= y1; y++) {
+        for (int64_t x = x0; x <= x1; x++) {
+            const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
+                                  + (y - r.predicted_y) * (y - r.predicted_y);
+            const auto pixel = image[y * xpixel + x];
+            auto azim_bint = pixel_to_bin[y * xpixel + x];
+
+            if (dist_sq < r_1_sq)
+                I_npixel_inner++;
+
+            if (azim_bint >= bkg_mean.size())
+                continue;
+
+            if (pixel == special_value || pixel == saturation)
+                continue;
+
+            if (dist_sq < r_1_sq) {
+                bkg += bkg_values.at(azim_bint);
+                I_sum += pixel;
+                I_sum_x += x * pixel;
+                I_sum_y += y * pixel;
+                I_npixel_integrated++;
+            }
+        }
+    }
+
+    if ((I_npixel_integrated == I_npixel_inner) && (bkg_values.size() > 5)) {
+        r.bkg = bkg / static_cast<float>(I_npixel_integrated);
+        r.I = static_cast<float>(I_sum) - bkg;
+        if (I_sum > 0) {
+            r.observed_x = static_cast<float>(I_sum_x) / static_cast<float>(I_sum);
+            r.observed_y = static_cast<float>(I_sum_y) / static_cast<float>(I_sum);
+        }
+
+        // sigma is max of the:
+        // - 1 (for zero photons)
+        // - Poisson noise (sqrt(I_sum)) (for in between)
+        // - minimum_sigma_in_regards_to_i of Intensity (for very large numbers)
+        r.sigma = std::max(1.0f, r.I * minimum_sigma_in_regards_to_i);
+        if (I_sum > 0)
+            r.sigma = std::max(r.sigma, std::sqrt(static_cast<float>(I_sum)));
+        r.observed = true;
+    } else {
+        r.I = 0;
+        r.bkg = 0;
+        r.sigma = NAN;
+        r.observed = false;
+    }
+}
+
 template<class T>
 std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experiment,
                                           const CompressedImage &image,
+                                          const AzimuthalIntegrationMapping &mapping,
+                                          const AzimuthalIntegrationProfile &profile,
                                           const std::vector<Reflection> &predicted,
                                           size_t npredicted,
                                           int64_t special_value,
                                           int64_t saturation,
                                           int64_t image_number) {
-
     std::vector<Reflection> ret;
     ret.reserve(npredicted);
 
@@ -164,24 +239,36 @@ std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experimen
     std::vector<uint8_t> buffer;
     auto ptr = reinterpret_cast<const T *>(image.GetUncompressedPtr(buffer));
 
-    const float r_3 = settings.GetR3();
-    const float r_1_sq = settings.GetR1() * settings.GetR1();
+    const float r_1 = settings.GetR1();
     const float r_2 = settings.GetR2();
-    const float r_2_sq = settings.GetR2() * settings.GetR2();
-    const float r_3_sq = settings.GetR3() * settings.GetR3();
+    const float r_3 = settings.GetR3();
+
+    const float r_1_sq = r_1 * r_1;
+    const float r_2_sq = r_2 * r_2;
+    const float r_3_sq = r_3 * r_3;
 
     const float minimum_sigma_in_regards_to_i = settings.GetMinimumSigmaInRegardsToI();
     const auto reflection_mask = BuildReflectionMask(predicted, npredicted,
                                                      image.GetWidth(), image.GetHeight(),
                                                      r_2, r_2_sq);
 
+    const auto &pixel_to_bin = mapping.GetPixelToBin();
+    const auto p = profile.GetResult();
+
     for (int i = 0; i < npredicted; i++) {
         auto r = predicted.at(i);
-        IntegrateReflection(r, ptr, reflection_mask, image.GetWidth(), image.GetHeight(), special_value, saturation,
-                            r_3, r_1_sq, r_2_sq, r_3_sq, minimum_sigma_in_regards_to_i);
+        if (settings.IsUseAzimProfile()) {
+            IntegrateReflectionAzim(r, ptr, image.GetWidth(), image.GetHeight(),
+                                    special_value, saturation,
+                                    r_1, r_1_sq, pixel_to_bin, p, minimum_sigma_in_regards_to_i);
+        } else {
+            IntegrateReflection(r, ptr, reflection_mask, image.GetWidth(), image.GetHeight(), special_value, saturation,
+                                r_3, r_1_sq, r_2_sq, r_3_sq, minimum_sigma_in_regards_to_i);
+        }
         if (r.observed) {
             if (experiment.GetPolarizationFactor())
-                r.rlp /= geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y, experiment.GetPolarizationFactor().value());
+                r.rlp /= geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y,
+                                                        experiment.GetPolarizationFactor().value());
             r.image_scale_corr = r.rlp / r.partiality;
             r.image_number = static_cast<float>(image_number);
             ret.emplace_back(r);
@@ -193,6 +280,8 @@ std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experimen
 std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
                                          const CompressedImage &image,
                                          const std::vector<Reflection> &predicted,
+                                         const AzimuthalIntegrationMapping &mapping,
+                                         const AzimuthalIntegrationProfile &profile,
                                          size_t npredicted,
                                          int64_t image_number) {
     if (image.GetCompressedSize() == 0 || predicted.empty())
@@ -200,17 +289,23 @@ std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment
 
     switch (image.GetMode()) {
         case CompressedImageMode::Int8:
-           return IntegrateInternal<int8_t>(experiment, image, predicted, npredicted, INT8_MIN, INT8_MAX, image_number);
+            return IntegrateInternal<int8_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                             INT8_MIN, INT8_MAX, image_number);
         case CompressedImageMode::Int16:
-            return IntegrateInternal<int16_t>(experiment, image, predicted, npredicted, INT16_MIN, INT16_MAX, image_number);
+            return IntegrateInternal<int16_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                              INT16_MIN, INT16_MAX, image_number);
         case CompressedImageMode::Int32:
-            return IntegrateInternal<int32_t>(experiment, image, predicted, npredicted, INT32_MIN, INT32_MAX, image_number);
+            return IntegrateInternal<int32_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                              INT32_MIN, INT32_MAX, image_number);
         case CompressedImageMode::Uint8:
-            return IntegrateInternal<uint8_t>(experiment, image, predicted, npredicted, UINT8_MAX, UINT8_MAX, image_number);
+            return IntegrateInternal<uint8_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                              UINT8_MAX, UINT8_MAX, image_number);
         case CompressedImageMode::Uint16:
-            return IntegrateInternal<uint16_t>(experiment, image, predicted, npredicted, UINT16_MAX, UINT16_MAX, image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                               UINT16_MAX, UINT16_MAX, image_number);
         case CompressedImageMode::Uint32:
-            return IntegrateInternal<uint32_t>(experiment, image, predicted, npredicted, UINT32_MAX, UINT32_MAX, image_number);
+            return IntegrateInternal<uint32_t>(experiment, image, mapping, profile, predicted, npredicted,
+                                               UINT32_MAX, UINT32_MAX, image_number);
         default:
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Image mode not supported");
diff --git a/image_analysis/bragg_integration/BraggIntegrate2D.h b/image_analysis/bragg_integration/BraggIntegrate2D.h
index 353757b5..3045ff7d 100644
--- a/image_analysis/bragg_integration/BraggIntegrate2D.h
+++ b/image_analysis/bragg_integration/BraggIntegrate2D.h
@@ -1,17 +1,17 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#ifndef JFJOCH_BRAGGINTEGRATE2D_H
-#define JFJOCH_BRAGGINTEGRATE2D_H
+#pragma once
 
 #include <vector>
 #include "../../common/DiffractionExperiment.h"
 #include "../../common/Reflection.h"
+#include "../../common/AzimuthalIntegrationProfile.h"
 
 std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
                                          const CompressedImage &image,
                                          const std::vector<Reflection> &predicted,
+                                         const AzimuthalIntegrationMapping &mapping,
+                                         const AzimuthalIntegrationProfile &profile,
                                          size_t npredicted,
-                                         int64_t image_number);
-
-#endif //JFJOCH_BRAGGINTEGRATE2D_H
+                                         int64_t image_number);
\ No newline at end of file
diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp
index 64e82e33..1aa8ce1e 100644
--- a/receiver/JFJochReceiver.cpp
+++ b/receiver/JFJochReceiver.cpp
@@ -31,7 +31,8 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
           serialmx_filter(in_experiment),
           numa_policy(in_numa_policy),
           pixel_mask(in_pixel_mask),
-          indexer(experiment, indexing_thread_pool) {
+          indexer(experiment, indexing_thread_pool),
+          az_int_mapping(experiment, pixel_mask) {
     logger.Info("Initializing receiver");
     // Ensure there is nothing running for now
     if (!image_buffer.Finalize(std::chrono::seconds(1)))
@@ -43,13 +44,7 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
     current_status.SetEfficiency({});
     current_status.SetStatus(JFJochReceiverStatus{}); // GetStatus() is virtual function and cannot be called yet!
 
-    auto start_time_point = std::chrono::steady_clock::now();
-    az_int_mapping = std::make_unique<AzimuthalIntegrationMapping>(experiment, pixel_mask);
-    auto end_time_point = std::chrono::steady_clock::now();
-    auto duration = std::chrono::duration<float>(end_time_point - start_time_point);
-    logger.Info("Azimuthal integration mapping done in {:.5f} s with {} threads", duration.count(), az_int_mapping->GetNThreads());
-
-    plots.Setup(experiment, *az_int_mapping);
+    plots.Setup(experiment, az_int_mapping);
 
     push_images_to_writer = (experiment.GetImageNum() > 0) && (!experiment.GetFilePrefix().empty());
 }
@@ -111,13 +106,13 @@ void JFJochReceiver::SendStartMessage() {
     StartMessage message{};
     experiment.FillMessage(message);
     message.arm_date = time_UTC(std::chrono::system_clock::now());
-    message.az_int_q_bin_count = az_int_mapping->GetQBinCount();
-    message.az_int_bin_to_q = az_int_mapping->GetBinToQ();
-    message.az_int_bin_to_two_theta = az_int_mapping->GetBinToTwoTheta();
-    message.az_int_phi_bin_count = az_int_mapping->GetAzimuthalBinCount();
-    if (az_int_mapping->GetAzimuthalBinCount() > 1) {
-        message.az_int_bin_to_phi = az_int_mapping->GetBinToPhi();
-        message.az_int_map = az_int_mapping->GetPixelToBin();
+    message.az_int_q_bin_count = az_int_mapping.GetQBinCount();
+    message.az_int_bin_to_q = az_int_mapping.GetBinToQ();
+    message.az_int_bin_to_two_theta = az_int_mapping.GetBinToTwoTheta();
+    message.az_int_phi_bin_count = az_int_mapping.GetAzimuthalBinCount();
+    if (az_int_mapping.GetAzimuthalBinCount() > 1) {
+        message.az_int_bin_to_phi = az_int_mapping.GetBinToPhi();
+        message.az_int_map = az_int_mapping.GetPixelToBin();
     }
     message.writer_notification_zmq_addr = image_pusher.GetWriterNotificationSocketAddress();
     message.rois = experiment.ROI().ExportMetadata();
diff --git a/receiver/JFJochReceiver.h b/receiver/JFJochReceiver.h
index 83918987..79be2802 100644
--- a/receiver/JFJochReceiver.h
+++ b/receiver/JFJochReceiver.h
@@ -80,7 +80,7 @@ protected:
     std::vector<std::unique_ptr<ADUHistogram>> adu_histogram_module;
     PixelMask pixel_mask;
 
-    std::unique_ptr<AzimuthalIntegrationMapping> az_int_mapping;
+    AzimuthalIntegrationMapping az_int_mapping;
 
     std::optional<uint64_t> max_delay;
     std::mutex max_delay_mutex;
diff --git a/receiver/JFJochReceiverFPGA.cpp b/receiver/JFJochReceiverFPGA.cpp
index 802b7faf..a3ac6384 100644
--- a/receiver/JFJochReceiverFPGA.cpp
+++ b/receiver/JFJochReceiverFPGA.cpp
@@ -297,7 +297,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
     try {
         numa_policy.Bind(threadid);
-        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, indexer);
+        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, indexer, az_int_mapping);
     } catch (const JFJochException &e) {
         frame_transformation_ready.count_down();
         logger.Error("Thread setup error {}", e.what());
@@ -309,9 +309,6 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
     frame_transformation_ready.count_down();
 
-    uint16_t az_int_min_bin = std::floor(az_int_mapping->QToBin(experiment.GetLowQForBkgEstimate_recipA()));
-    uint16_t az_int_max_bin = std::ceil(az_int_mapping->QToBin(experiment.GetHighQForBkgEstimate_recipA()));
-
     int64_t image_number;
     while (images_to_go.Get(image_number) != 0) {
         try {
@@ -338,7 +335,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
             ImageMetadata metadata(experiment);
 
-            AzimuthalIntegrationProfile az_int_profile_image(*az_int_mapping);
+            AzimuthalIntegrationProfile az_int_profile_image(az_int_mapping);
 
             auto local_spot_finding_settings = GetSpotFindingSettings();
 
@@ -428,7 +425,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
                                             experiment.GetYPixelsNum(),
                                             experiment.GetImageMode(),
                                             CompressionAlgorithm::NO_COMPRESSION);
-            analyzer->Process(message, local_spot_finding_settings);
+            analyzer->Process(message, local_spot_finding_settings, az_int_profile_image);
 
             auto status = image_buffer.GetStatus();
             message.receiver_buf_available = status.available_slots;
@@ -681,5 +678,5 @@ void JFJochReceiverFPGA::LoadCalibrationToFPGA(uint16_t data_stream) {
     acquisition_device[data_stream].InitializeROIMap(experiment, roi_map);
 
     // Initialize data processing
-    acquisition_device[data_stream].InitializeDataProcessing(experiment, *az_int_mapping);
+    acquisition_device[data_stream].InitializeDataProcessing(experiment, az_int_mapping);
 }
diff --git a/receiver/JFJochReceiverLite.cpp b/receiver/JFJochReceiverLite.cpp
index e986956e..8c04b1cf 100644
--- a/receiver/JFJochReceiverLite.cpp
+++ b/receiver/JFJochReceiverLite.cpp
@@ -242,7 +242,7 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
     measurement_started.wait();
 
     try {
-        analysis = std::make_unique<MXAnalysisWithoutFPGA>(experiment, *az_int_mapping, pixel_mask, indexer);
+        analysis = std::make_unique<MXAnalysisWithoutFPGA>(experiment, az_int_mapping, pixel_mask, indexer);
     } catch (const JFJochException &e) {
         Cancel(e);
         return;
@@ -279,7 +279,7 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
 
                 auto image_start_time = std::chrono::high_resolution_clock::now();
 
-                AzimuthalIntegrationProfile profile(*az_int_mapping);
+                AzimuthalIntegrationProfile profile(az_int_mapping);
                 analysis->Analyze(data_msg, profile, GetSpotFindingSettings());
 
                 auto image_end_time = std::chrono::high_resolution_clock::now();
diff --git a/tests/BraggIntegrate2DTest.cpp b/tests/BraggIntegrate2DTest.cpp
index 75ba2a42..149515c0 100644
--- a/tests/BraggIntegrate2DTest.cpp
+++ b/tests/BraggIntegrate2DTest.cpp
@@ -59,6 +59,10 @@ TEST_CASE("BraggIntegrate2D_RejectsReflectionsFromBackgroundUsingR2MaskAndMedian
     Reflection r1 = MakeReflection(10.0f, 10.0f);
     Reflection r2 = MakeReflection(16.0f, 10.0f);
 
+    PixelMask mask(experiment);
+    AzimuthalIntegrationMapping mapping(experiment, mask);
+    AzimuthalIntegrationProfile profile(mapping);
+
     for (int y = 0; y < static_cast<int>(height); y++) {
         for (int x = 0; x < static_cast<int>(width); x++) {
             auto &pixel = image_data[y * width + x];
@@ -74,7 +78,7 @@ TEST_CASE("BraggIntegrate2D_RejectsReflectionsFromBackgroundUsingR2MaskAndMedian
     CompressedImage image(image_data, width, height);
     std::vector<Reflection> predicted = {r1, r2};
 
-    auto integrated = BraggIntegrate2D(experiment, image, predicted, predicted.size(), 17);
+    auto integrated = BraggIntegrate2D(experiment, image, predicted, mapping, profile, predicted.size(), 17);
 
     REQUIRE(integrated.size() == 2);
 
diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index 7f169940..e6da83f2 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -148,8 +148,6 @@ int main(int argc, char **argv) {
                     partiality_model = PartialityModel::Fixed;
                 else if (strcmp(optarg, "rot") == 0)
                     partiality_model = PartialityModel::Rotation;
-                else if (strcmp(optarg, "postref") == 0)
-                    partiality_model = PartialityModel::Postrefinement;
                 else {
                     logger.Error("Invalid partiality mode: {}", optarg);
                     print_usage();
-- 
2.52.0


From b22d5929a1b3e9b565338cfccf91a184a04e02ff Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 14:52:58 +0200
Subject: [PATCH 026/228] jfjoch_process: Add option to use azimuthal
 integration as background for Bragg integration

---
 tools/jfjoch_process.cpp | 575 ++++++++++++++++++++++-----------------
 1 file changed, 321 insertions(+), 254 deletions(-)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 5876418b..4c8d070c 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -45,39 +45,75 @@ void print_usage() {
 
     std::cout << "  Spot finding" << std::endl;
     std::cout << "   --spot-sigma <num>               Noise sigma level for spot finding (default: 3.0)" << std::endl;
-    std::cout << "   --spot-threshold <num>           Photon count threshold for spot finding (default: 10)" << std::endl;
-    std::cout << "   --spot-high-resolution <num>     High resolution limit for spot finding (default: 1.5)" << std::endl;
+    std::cout << "   --spot-threshold <num>           Photon count threshold for spot finding (default: 10)" <<
+            std::endl;
+    std::cout << "   --spot-high-resolution <num>     High resolution limit for spot finding (default: 1.5)" <<
+            std::endl;
     std::cout << "   --max-spots <num>                Max spot count (default: 250)" << std::endl;
     std::cout << std::endl;
 
+    std::cout << "  Azimuthal integration" << std::endl;
+    std::cout << "    -Q, --azim-q-spacing <num>            Q spacing for azimuthal integration (default: 0.01)" <<
+            std::endl;
+    std::cout << "    --azim-q-min <num>                    Minimum Q value for azimuthal integration (default: 0.0)" <<
+            std::endl;
+    std::cout << "    --azim-q-max <num>                    Maximum Q value for azimuthal integration (default: 5.0)" <<
+            std::endl;
+    std::cout << std::endl;
+
     std::cout << "  Indexing" << std::endl;
-    std::cout << "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 30)" << std::endl;
-    std::cout << "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)" << std::endl;
+    std::cout <<
+            "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 30)"
+            << std::endl;
+    std::cout <<
+            "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)"
+            << std::endl;
     std::cout << "   --redo-rotation-spots            Redo spot finding for two-pass rotation indexing" << std::endl;
-    std::cout << "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
+    std::cout <<
+            "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)"
+            << std::endl;
     std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
-    std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" << std::endl;
+    std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" <<
+            std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
-    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)" << std::endl;
+    std::cout <<
+            "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)"
+            << std::endl;
+    std::cout << std::endl;
+
+    std::cout << "  Integration" << std::endl;
+    std::cout <<
+            "    --integration-use-azim         Background from Bragg peak integration is based on azimuthal integration results"
+            << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Scaling and merging" << std::endl;
-    std::cout << "   -M, --scale-merge               Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" << std::endl;
-    std::cout << "   -P, --partiality <txt>          Partiality refinement fixed|rot|unity (default: fixed)" << std::endl;
+    std::cout <<
+            "   -M, --scale-merge               Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" <<
+            std::endl;
+    std::cout << "   -P, --partiality <txt>          Partiality refinement fixed|rot|unity (default: fixed)" <<
+            std::endl;
     std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
     std::cout << "   -B, --refine-bfactor            Refine per image B-factor" << std::endl;
-    std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
-    std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
-    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
+    std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" <<
+            std::endl;
+    std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" <<
+            std::endl;
+    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" <<
+            std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
-    std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
-    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
+    std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)"
+            << std::endl;
+    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)"
+            << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
-    std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
-    }
+    std::cout <<
+            "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0"
+            << std::endl;
+}
 
 enum {
     OPT_SPOT_SIGMA = 1000,
@@ -92,7 +128,10 @@ enum {
     OPT_SINGLE_PASS_ROTATION,
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
-    OPT_BANDWIDTH
+    OPT_BANDWIDTH,
+    OPT_INTEGRATION_USE_AZIM,
+    OPT_AZIM_Q_MIN,
+    OPT_AZIM_Q_MAX
 };
 
 static option long_options[] = {
@@ -112,13 +151,16 @@ static option long_options[] = {
     {"wedge", optional_argument, nullptr, 'w'},
     {"scale-merge", no_argument, nullptr, 'M'},
     {"refine", required_argument, nullptr, 'r'},
+    {"azim-q-spacing", required_argument, nullptr, 'Q'},
+    {"azim-q-min", required_argument, nullptr, OPT_AZIM_Q_MIN},
+    {"azim-q-max", required_argument, nullptr, OPT_AZIM_Q_MAX},
 
     {"two-pass-rotation", optional_argument, nullptr, 'R'},
     {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},
     {"redo-rotation-spots", no_argument, nullptr, OPT_REDO_ROTATION_SPOTS},
     {"force-rotation-lattice", required_argument, nullptr, OPT_FORCE_ROTATION_LATTICE},
 
-
+    {"integration-use-azim", no_argument, nullptr, OPT_INTEGRATION_USE_AZIM},
     {"spot-sigma", required_argument, nullptr, OPT_SPOT_SIGMA},
     {"spot-threshold", required_argument, nullptr, OPT_SPOT_THRESHOLD},
     {"spot-high-resolution", required_argument, nullptr, OPT_SPOT_RESOLUTION},
@@ -181,7 +223,6 @@ std::optional<UnitCell> parse_unit_cell_arg(const char *arg) {
         return std::nullopt;
 
 
-
     UnitCell uc{};
     if (!parse_float_strict(parts[0], uc.a)) return std::nullopt;
     if (!parse_float_strict(parts[1], uc.b)) return std::nullopt;
@@ -297,6 +338,11 @@ int main(int argc, char **argv) {
     double min_partiality = 0.02;
     double min_image_cc = 0.0;
     int64_t scaling_iter = 3;
+    std::optional<double> azim_q_spacing;
+    std::optional<double> azim_q_min;
+    std::optional<double> azim_q_max;
+    bool use_azim_for_integration = false;
+
     std::optional<CrystalLattice> forced_rotation_lattice;
 
     std::optional<float> bandwidth_fwhm; // relative FWHM of dlambda/lambda
@@ -317,225 +363,237 @@ int main(int argc, char **argv) {
 
     int opt;
     int option_index = 0;
-    const char *short_opts = "vo:N:s:e:t:R::X:C:z:FABw::S:MP:r:";
+    const char *short_opts = "vo:N:s:e:t:R::X:C:z:FABw::S:MP:r:Q:";
 
-  while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
-    switch (opt) {
-        case 'o':
-            output_prefix = optarg;
-            break;
-        case 'v':
-            verbose = true;
-            break;
-        case 'N':
-            nthreads = atoi(optarg);
-            break;
-        case 's':
-            start_image = atoi(optarg);
-            break;
-        case 'e':
-            end_image = atoi(optarg);
-            break;
-        case 't':
-            image_stride = atoi(optarg);
-            break;
-        case 'R':
-            if (rotation_indexing) {
-                logger.Error("Rotation indexing already enabled");
-                exit(EXIT_FAILURE);
+    while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
+        switch (opt) {
+            case 'o':
+                output_prefix = optarg;
+                break;
+            case 'v':
+                verbose = true;
+                break;
+            case 'N':
+                nthreads = atoi(optarg);
+                break;
+            case 's':
+                start_image = atoi(optarg);
+                break;
+            case 'e':
+                end_image = atoi(optarg);
+                break;
+            case 't':
+                image_stride = atoi(optarg);
+                break;
+            case 'R':
+                if (rotation_indexing) {
+                    logger.Error("Rotation indexing already enabled");
+                    exit(EXIT_FAILURE);
+                }
+                rotation_indexing = true;
+                two_pass_rotation = true;
+                if (optarg)
+                    rotation_indexing_image_count = atoi(optarg);
+
+                break;
+            case 'Q':
+                azim_q_spacing = atof(optarg);
+                break;
+            case OPT_AZIM_Q_MIN:
+                azim_q_min = atof(optarg);
+                break;
+            case OPT_AZIM_Q_MAX:
+                azim_q_max = atof(optarg);
+                break;
+            case OPT_INTEGRATION_USE_AZIM:
+                use_azim_for_integration = true;
+                break;
+            case OPT_SINGLE_PASS_ROTATION:
+                if (rotation_indexing) {
+                    logger.Error("Rotation indexing already enabled");
+                    exit(EXIT_FAILURE);
+                }
+                rotation_indexing = true;
+                two_pass_rotation = false;
+
+                if (optarg)
+                    rotation_indexing_range = atof(optarg);
+                break;
+            case OPT_REDO_ROTATION_SPOTS:
+                reuse_rotation_spots = false;
+                break;
+            case OPT_FORCE_ROTATION_LATTICE: {
+                if (rotation_indexing) {
+                    logger.Error("Rotation indexing already enabled");
+                    exit(EXIT_FAILURE);
+                }
+                rotation_indexing = true;
+
+                auto latt = parse_lattice_arg(optarg);
+                if (!latt.has_value()) {
+                    logger.Error(
+                        "Invalid rotation lattice. Expected: \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, comma-separated). Got: {}",
+                        optarg ? optarg : "<null>");
+                    print_usage();
+                    exit(EXIT_FAILURE);
+                }
+                forced_rotation_lattice = latt;
+                auto uc = latt->GetUnitCell();
+                logger.Info(
+                    "Forced rotation lattice set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
+                    uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
+                break;
             }
-            rotation_indexing = true;
-            two_pass_rotation = true;
-            if (optarg)
-                rotation_indexing_image_count = atoi(optarg);
+            case 'X': {
+                std::string alg = optarg ? optarg : "";
+                std::transform(alg.begin(), alg.end(), alg.begin(),
+                               [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
 
-            break;
-        case OPT_SINGLE_PASS_ROTATION:
-            if (rotation_indexing) {
-                logger.Error("Rotation indexing already enabled");
-                exit(EXIT_FAILURE);
+                if (alg == "ffbidx")
+                    indexing_algorithm = IndexingAlgorithmEnum::FFBIDX;
+                else if (alg == "fft")
+                    indexing_algorithm = IndexingAlgorithmEnum::FFT;
+                else if (alg == "fftw")
+                    indexing_algorithm = IndexingAlgorithmEnum::FFTW;
+                else if (alg == "auto")
+                    indexing_algorithm = IndexingAlgorithmEnum::Auto;
+                else if (alg == "none")
+                    indexing_algorithm = IndexingAlgorithmEnum::None;
+                else {
+                    logger.Error("Invalid indexing algorithm: {}", alg);
+                    print_usage();
+                    exit(EXIT_FAILURE);
+                }
+                break;
             }
-            rotation_indexing = true;
-            two_pass_rotation = false;
-
-            if (optarg)
-                rotation_indexing_range = atof(optarg);
-            break;
-        case OPT_REDO_ROTATION_SPOTS:
-            reuse_rotation_spots = false;
-            break;
-        case OPT_FORCE_ROTATION_LATTICE: {
-            if (rotation_indexing) {
-                logger.Error("Rotation indexing already enabled");
-                exit(EXIT_FAILURE);
+            case 'r': {
+                std::string alg = optarg ? optarg : "";
+                std::transform(alg.begin(), alg.end(), alg.begin(),
+                               [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
+                if (alg == "none")
+                    refinement_algorithm = GeomRefinementAlgorithmEnum::None;
+                else if (alg == "beam_and_lattice")
+                    refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
+                else if (alg == "orientation")
+                    refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
+                else if (alg == "pixelrefine")
+                    refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
+                else {
+                    logger.Error("Invalid geom refinement algorithm: {}", alg);
+                    print_usage();
+                    exit(EXIT_FAILURE);
+                }
+                break;
             }
-            rotation_indexing = true;
-
-            auto latt = parse_lattice_arg(optarg);
-            if (!latt.has_value()) {
-                logger.Error(
-                    "Invalid rotation lattice. Expected: \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, comma-separated). Got: {}",
-                    optarg ? optarg : "<null>");
-                print_usage();
-                exit(EXIT_FAILURE);
+            case 'C': {
+                auto uc = parse_unit_cell_arg(optarg);
+                if (!uc.has_value()) {
+                    logger.Error(
+                        "Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
+                        optarg ? optarg : "<null>");
+                    print_usage();
+                    exit(EXIT_FAILURE);
+                }
+                fixed_reference_unit_cell = uc;
+                logger.Info(
+                    "Fixed reference unit cell set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
+                    uc->a, uc->b, uc->c, uc->alpha, uc->beta, uc->gamma);
+                break;
             }
-            forced_rotation_lattice = latt;
-            auto uc = latt->GetUnitCell();
-            logger.Info(
-                "Forced rotation lattice set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
-                uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
-            break;
-        }
-        case 'X': {
-            std::string alg = optarg ? optarg : "";
-            std::transform(alg.begin(), alg.end(), alg.begin(),
-                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
-
-            if (alg == "ffbidx")
-                indexing_algorithm = IndexingAlgorithmEnum::FFBIDX;
-            else if (alg == "fft")
+            case 'z':
+                ref_mtz = optarg;
+                break;
+            case 'F':
                 indexing_algorithm = IndexingAlgorithmEnum::FFT;
-            else if (alg == "fftw")
-                indexing_algorithm = IndexingAlgorithmEnum::FFTW;
-            else if (alg == "auto")
-                indexing_algorithm = IndexingAlgorithmEnum::Auto;
-            else if (alg == "none")
-                indexing_algorithm = IndexingAlgorithmEnum::None;
-            else {
-                logger.Error("Invalid indexing algorithm: {}", alg);
-                print_usage();
-                exit(EXIT_FAILURE);
-            }
-            break;
-        }
-        case 'r': {
-            std::string alg = optarg ? optarg : "";
-            std::transform(alg.begin(), alg.end(), alg.begin(),
-                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
-            if (alg == "none")
-                refinement_algorithm = GeomRefinementAlgorithmEnum::None;
-            else if (alg == "beam_and_lattice")
-                refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
-            else if (alg == "orientation")
-                refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
-            else if (alg == "pixelrefine")
-                refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
-            else {
-                logger.Error("Invalid geom refinement algorithm: {}", alg);
-                print_usage();
-                exit(EXIT_FAILURE);
-            }
-            break;
-        }
-        case 'C': {
-            auto uc = parse_unit_cell_arg(optarg);
-            if (!uc.has_value()) {
-                logger.Error(
-                    "Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
-                    optarg ? optarg : "<null>");
-                print_usage();
-                exit(EXIT_FAILURE);
-            }
-            fixed_reference_unit_cell = uc;
-            logger.Info(
-                "Fixed reference unit cell set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
-                uc->a, uc->b, uc->c, uc->alpha, uc->beta, uc->gamma);
-            break;
-        }
-        case 'z':
-            ref_mtz = optarg;
-            break;
-        case 'F':
-            indexing_algorithm = IndexingAlgorithmEnum::FFT;
-            break;
-        case 'A':
-            anomalous_mode = true;
-            break;
-        case 'B':
-            refine_bfactor = true;
-            break;
-        case 'w':
-            refine_wedge = true;
-            if (optarg)
-                wedge_for_scaling = std::stod(optarg);
-            break;
-        case 'S':
-            space_group_number = atoi(optarg);
-            break;
-        case 'P':
-            if (strcmp(optarg, "unity") == 0)
-                partiality_model = PartialityModel::Unity;
-            else if (strcmp(optarg, "fixed") == 0)
-                partiality_model = PartialityModel::Fixed;
-            else if (strcmp(optarg, "rot") == 0)
-                partiality_model = PartialityModel::Rotation;
-            else {
-                logger.Error("Invalid partiality mode: {}", optarg);
-                print_usage();
-                exit(EXIT_FAILURE);
-            }
-            break;
-        case OPT_SPOT_SIGMA:
-            sigma_spot_finding = atof(optarg);
-            logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
-            break;
-        case OPT_SPOT_THRESHOLD:
-            photon_count_threshold_spot_finding = atoi(optarg);
-            logger.Info("Photon-count threshold level for spot finding set to {:d}",
-                        photon_count_threshold_spot_finding);
-            break;
-        case OPT_SPOT_RESOLUTION:
-            d_min_spot_finding = atof(optarg);
-            logger.Info("High resolution limit for spot finding set to {:.2f} A", d_min_spot_finding);
-            break;
-        case OPT_MAX_SPOTS:
-            max_spot_count_override = atoll(optarg);
-            logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
-            break;
-        case 'M':
-            run_scaling = true;
-            break;
-        case OPT_MIN_PARTIALITY:
-            min_partiality = std::stod(optarg);
-            break;
-        case OPT_MIN_IMAGE_CC:
-            min_image_cc = std::stod(optarg);
-            break;
-        case OPT_SCALING_HIGH_RESOLUTION:
-            d_min_scale_merge = atof(optarg);
-            break;
-        case OPT_SCALING_OUTPUT:
-            if (strcmp(optarg, "mtz") == 0) {
-                intensity_format = IntensityFormat::MTZ;
-            } else if (strcmp(optarg, "cif") == 0) {
-                intensity_format = IntensityFormat::mmCIF;
-            } else if (strcmp(optarg, "txt") == 0) {
-                intensity_format = IntensityFormat::Text;
-            } else {
-                logger.Error("Invalid intensity format: {}", optarg);
-                exit(EXIT_FAILURE);
-            }
-            break;
-        case OPT_SCALING_ITERATIONS:
-            scaling_iter = atoi(optarg);
-            if (scaling_iter <= 0) {
-                logger.Error("Invalid scaling iteration count: {}", scaling_iter);
-                exit(EXIT_FAILURE);
-            }
-            break;
-        case OPT_BANDWIDTH:
-            bandwidth_fwhm = atof(optarg);
-            if (!(bandwidth_fwhm.value() >= 0.0f)) {
-                logger.Error("Invalid bandwidth: {}", optarg);
-                exit(EXIT_FAILURE);
-            }
-            break;
+                break;
+            case 'A':
+                anomalous_mode = true;
+                break;
+            case 'B':
+                refine_bfactor = true;
+                break;
+            case 'w':
+                refine_wedge = true;
+                if (optarg)
+                    wedge_for_scaling = std::stod(optarg);
+                break;
+            case 'S':
+                space_group_number = atoi(optarg);
+                break;
+            case 'P':
+                if (strcmp(optarg, "unity") == 0)
+                    partiality_model = PartialityModel::Unity;
+                else if (strcmp(optarg, "fixed") == 0)
+                    partiality_model = PartialityModel::Fixed;
+                else if (strcmp(optarg, "rot") == 0)
+                    partiality_model = PartialityModel::Rotation;
+                else {
+                    logger.Error("Invalid partiality mode: {}", optarg);
+                    print_usage();
+                    exit(EXIT_FAILURE);
+                }
+                break;
+            case OPT_SPOT_SIGMA:
+                sigma_spot_finding = atof(optarg);
+                logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
+                break;
+            case OPT_SPOT_THRESHOLD:
+                photon_count_threshold_spot_finding = atoi(optarg);
+                logger.Info("Photon-count threshold level for spot finding set to {:d}",
+                            photon_count_threshold_spot_finding);
+                break;
+            case OPT_SPOT_RESOLUTION:
+                d_min_spot_finding = atof(optarg);
+                logger.Info("High resolution limit for spot finding set to {:.2f} A", d_min_spot_finding);
+                break;
+            case OPT_MAX_SPOTS:
+                max_spot_count_override = atoll(optarg);
+                logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
+                break;
+            case 'M':
+                run_scaling = true;
+                break;
+            case OPT_MIN_PARTIALITY:
+                min_partiality = std::stod(optarg);
+                break;
+            case OPT_MIN_IMAGE_CC:
+                min_image_cc = std::stod(optarg);
+                break;
+            case OPT_SCALING_HIGH_RESOLUTION:
+                d_min_scale_merge = atof(optarg);
+                break;
+            case OPT_SCALING_OUTPUT:
+                if (strcmp(optarg, "mtz") == 0) {
+                    intensity_format = IntensityFormat::MTZ;
+                } else if (strcmp(optarg, "cif") == 0) {
+                    intensity_format = IntensityFormat::mmCIF;
+                } else if (strcmp(optarg, "txt") == 0) {
+                    intensity_format = IntensityFormat::Text;
+                } else {
+                    logger.Error("Invalid intensity format: {}", optarg);
+                    exit(EXIT_FAILURE);
+                }
+                break;
+            case OPT_SCALING_ITERATIONS:
+                scaling_iter = atoi(optarg);
+                if (scaling_iter <= 0) {
+                    logger.Error("Invalid scaling iteration count: {}", scaling_iter);
+                    exit(EXIT_FAILURE);
+                }
+                break;
+            case OPT_BANDWIDTH:
+                bandwidth_fwhm = atof(optarg);
+                if (!(bandwidth_fwhm.value() >= 0.0f)) {
+                    logger.Error("Invalid bandwidth: {}", optarg);
+                    exit(EXIT_FAILURE);
+                }
+                break;
 
-        default:
-            print_usage();
-            exit(EXIT_FAILURE);
+            default:
+                print_usage();
+                exit(EXIT_FAILURE);
+        }
     }
-}
 
     if (optind != argc - 1) {
         logger.Error("Input file not specified");
@@ -603,7 +661,7 @@ int main(int argc, char **argv) {
 
     if (images_to_process <= 0) {
         logger.Warning("No images to process (Start: {}, End: {} Stride: {}, Total: {})", start_image, end_image,
-            image_stride, total_images_in_file);
+                       image_stride, total_images_in_file);
         return 0;
     }
 
@@ -668,6 +726,17 @@ int main(int argc, char **argv) {
 
     experiment.ImportScalingSettings(scaling_settings);
 
+    BraggIntegrationSettings bragg_integration_settings;
+    bragg_integration_settings.UseAzimProfile(use_azim_for_integration);
+    experiment.ImportBraggIntegrationSettings(bragg_integration_settings);
+
+    AzimuthalIntegrationSettings azimuthal_integration_settings;
+    if (azim_q_spacing)
+        azimuthal_integration_settings.QSpacing_recipA(azim_q_spacing.value());
+    azimuthal_integration_settings.QRange_recipA(azim_q_min.value_or(azimuthal_integration_settings.GetLowQ_recipA()),
+                                                 azim_q_max.value_or(azimuthal_integration_settings.GetHighQ_recipA()));
+    experiment.ImportAzimuthalIntegrationSettings(azimuthal_integration_settings);
+
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;
@@ -680,9 +749,6 @@ int main(int argc, char **argv) {
     // Initialize Analysis Components
     PixelMask pixel_mask = dataset->pixel_mask;
 
-    // If dataset has a mask you wish to use, you might need to load it into pixel_mask here
-    // e.g. pixel_mask.LoadUserMask(dataset->pixel_mask, ...);
-
     AzimuthalIntegrationMapping mapping(experiment, pixel_mask);
     IndexerThreadPool indexer_pool(experiment.GetIndexingSettings());
 
@@ -768,7 +834,7 @@ int main(int argc, char **argv) {
 
                     analysis.Analyze(msg, profile, first_pass_spot_settings);
                 }
-               indexer.AddImageToRotationIndexer(msg);
+                indexer.AddImageToRotationIndexer(msg);
             } catch (const std::exception &e) {
                 logger.Warning("Failed to add image {} to first-pass rotation indexing: {}", image_idx, e.what());
             }
@@ -814,7 +880,8 @@ int main(int argc, char **argv) {
             msg.image = img->image;
             msg.number = image_ordinal;
             msg.original_number = image_idx;
-            if (dataset->efficiency.size() > image_idx) msg.image_collection_efficiency = dataset->efficiency[image_idx];
+            if (dataset->efficiency.size() > image_idx)
+                msg.image_collection_efficiency = dataset->efficiency[image_idx];
 
             total_uncompressed_bytes += msg.image.GetUncompressedSize();
 
@@ -921,8 +988,8 @@ int main(int argc, char **argv) {
     if (consensus_cell) {
         logger.Info("Consensus unit cell found in {:.2f} ms", consensus_duration * 1e3);
         logger.Info("UC:         a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
-                        consensus_cell->a, consensus_cell->b, consensus_cell->c,
-                        consensus_cell->alpha, consensus_cell->beta, consensus_cell->gamma);
+                    consensus_cell->a, consensus_cell->b, consensus_cell->c,
+                    consensus_cell->alpha, consensus_cell->beta, consensus_cell->gamma);
     } else
         logger.Info("Consensus unit cell not found - calculation tool {:.2f} ms", consensus_duration * 1e3);
     end_msg.unit_cell = consensus_cell;
@@ -930,9 +997,8 @@ int main(int argc, char **argv) {
     if (end_msg.indexing_rate.has_value()
         && end_msg.indexing_rate > 0
         && (run_scaling || !reference_data.empty())) {
-
         const bool pixel_refine_path =
-            (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
+                (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
 
         // Scaling is only the classical, no-reference ScaleOnTheFly post-pass.
         // - With a reference (classical path): per-image live scaling already ran.
@@ -973,11 +1039,12 @@ int main(int argc, char **argv) {
         MergeOnTheFly merge_engine(experiment);
         if (consensus_cell.has_value())
             merge_engine.ReferenceCell(*consensus_cell);
-        for (auto &i : indexer.GetIntegrationOutcome())
+        for (auto &i: indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
 
         auto merged_reflections = merge_engine.ExportReflections();
-        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);
+        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(),
+                                                         reference_data);
 
         auto merge_end = std::chrono::steady_clock::now();
         double merge_time = std::chrono::duration<double>(merge_end - merge_start).count();
@@ -1031,17 +1098,17 @@ int main(int argc, char **argv) {
 
     auto image_mean_time = plots.GetMeanProcessingTime();
     std::cout << fmt::format(
-        "Per-image time: (mean; milliseconds): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} scaling {:.2f} total {:.2f}",
-        image_mean_time.compression * 1e3,
-        image_mean_time.preprocessing * 1e3,
-        image_mean_time.azint * 1e3,
-        image_mean_time.spot_finding * 1e3,
-        image_mean_time.indexing * 1e3,
-        image_mean_time.refinement * 1e3,
-        image_mean_time.indexing_analysis * 1e3,
-        image_mean_time.bragg_prediction * 1e3,
-        image_mean_time.integration * 1e3,
-        image_mean_time.image_scale * 1e3,
-        image_mean_time.processing * 1e3)
-    << std::endl;
+                "Per-image time: (mean; milliseconds): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} scaling {:.2f} total {:.2f}",
+                image_mean_time.compression * 1e3,
+                image_mean_time.preprocessing * 1e3,
+                image_mean_time.azint * 1e3,
+                image_mean_time.spot_finding * 1e3,
+                image_mean_time.indexing * 1e3,
+                image_mean_time.refinement * 1e3,
+                image_mean_time.indexing_analysis * 1e3,
+                image_mean_time.bragg_prediction * 1e3,
+                image_mean_time.integration * 1e3,
+                image_mean_time.image_scale * 1e3,
+                image_mean_time.processing * 1e3)
+            << std::endl;
 }
-- 
2.52.0


From 579d36fe71f336f104a9e836bdadeb3fffe35e48 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 16:36:37 +0200
Subject: [PATCH 027/228] Revert "jfjoch_process: Add option to use azimuthal
 integration as background for Bragg integration"

This reverts commit b22d5929a1b3e9b565338cfccf91a184a04e02ff.
---
 tools/jfjoch_process.cpp | 575 +++++++++++++++++----------------------
 1 file changed, 254 insertions(+), 321 deletions(-)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 4c8d070c..5876418b 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -45,75 +45,39 @@ void print_usage() {
 
     std::cout << "  Spot finding" << std::endl;
     std::cout << "   --spot-sigma <num>               Noise sigma level for spot finding (default: 3.0)" << std::endl;
-    std::cout << "   --spot-threshold <num>           Photon count threshold for spot finding (default: 10)" <<
-            std::endl;
-    std::cout << "   --spot-high-resolution <num>     High resolution limit for spot finding (default: 1.5)" <<
-            std::endl;
+    std::cout << "   --spot-threshold <num>           Photon count threshold for spot finding (default: 10)" << std::endl;
+    std::cout << "   --spot-high-resolution <num>     High resolution limit for spot finding (default: 1.5)" << std::endl;
     std::cout << "   --max-spots <num>                Max spot count (default: 250)" << std::endl;
     std::cout << std::endl;
 
-    std::cout << "  Azimuthal integration" << std::endl;
-    std::cout << "    -Q, --azim-q-spacing <num>            Q spacing for azimuthal integration (default: 0.01)" <<
-            std::endl;
-    std::cout << "    --azim-q-min <num>                    Minimum Q value for azimuthal integration (default: 0.0)" <<
-            std::endl;
-    std::cout << "    --azim-q-max <num>                    Maximum Q value for azimuthal integration (default: 5.0)" <<
-            std::endl;
-    std::cout << std::endl;
-
     std::cout << "  Indexing" << std::endl;
-    std::cout <<
-            "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 30)"
-            << std::endl;
-    std::cout <<
-            "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)"
-            << std::endl;
+    std::cout << "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 30)" << std::endl;
+    std::cout << "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)" << std::endl;
     std::cout << "   --redo-rotation-spots            Redo spot finding for two-pass rotation indexing" << std::endl;
-    std::cout <<
-            "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)"
-            << std::endl;
+    std::cout << "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
     std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
-    std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" <<
-            std::endl;
+    std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" << std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
-    std::cout <<
-            "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)"
-            << std::endl;
-    std::cout << std::endl;
-
-    std::cout << "  Integration" << std::endl;
-    std::cout <<
-            "    --integration-use-azim         Background from Bragg peak integration is based on azimuthal integration results"
-            << std::endl;
+    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)" << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Scaling and merging" << std::endl;
-    std::cout <<
-            "   -M, --scale-merge               Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" <<
-            std::endl;
-    std::cout << "   -P, --partiality <txt>          Partiality refinement fixed|rot|unity (default: fixed)" <<
-            std::endl;
+    std::cout << "   -M, --scale-merge               Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" << std::endl;
+    std::cout << "   -P, --partiality <txt>          Partiality refinement fixed|rot|unity (default: fixed)" << std::endl;
     std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
     std::cout << "   -B, --refine-bfactor            Refine per image B-factor" << std::endl;
-    std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" <<
-            std::endl;
-    std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" <<
-            std::endl;
-    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" <<
-            std::endl;
+    std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
+    std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
+    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
-    std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)"
-            << std::endl;
-    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)"
-            << std::endl;
+    std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
+    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
-    std::cout <<
-            "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0"
-            << std::endl;
-}
+    std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
+    }
 
 enum {
     OPT_SPOT_SIGMA = 1000,
@@ -128,10 +92,7 @@ enum {
     OPT_SINGLE_PASS_ROTATION,
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
-    OPT_BANDWIDTH,
-    OPT_INTEGRATION_USE_AZIM,
-    OPT_AZIM_Q_MIN,
-    OPT_AZIM_Q_MAX
+    OPT_BANDWIDTH
 };
 
 static option long_options[] = {
@@ -151,16 +112,13 @@ static option long_options[] = {
     {"wedge", optional_argument, nullptr, 'w'},
     {"scale-merge", no_argument, nullptr, 'M'},
     {"refine", required_argument, nullptr, 'r'},
-    {"azim-q-spacing", required_argument, nullptr, 'Q'},
-    {"azim-q-min", required_argument, nullptr, OPT_AZIM_Q_MIN},
-    {"azim-q-max", required_argument, nullptr, OPT_AZIM_Q_MAX},
 
     {"two-pass-rotation", optional_argument, nullptr, 'R'},
     {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},
     {"redo-rotation-spots", no_argument, nullptr, OPT_REDO_ROTATION_SPOTS},
     {"force-rotation-lattice", required_argument, nullptr, OPT_FORCE_ROTATION_LATTICE},
 
-    {"integration-use-azim", no_argument, nullptr, OPT_INTEGRATION_USE_AZIM},
+
     {"spot-sigma", required_argument, nullptr, OPT_SPOT_SIGMA},
     {"spot-threshold", required_argument, nullptr, OPT_SPOT_THRESHOLD},
     {"spot-high-resolution", required_argument, nullptr, OPT_SPOT_RESOLUTION},
@@ -223,6 +181,7 @@ std::optional<UnitCell> parse_unit_cell_arg(const char *arg) {
         return std::nullopt;
 
 
+
     UnitCell uc{};
     if (!parse_float_strict(parts[0], uc.a)) return std::nullopt;
     if (!parse_float_strict(parts[1], uc.b)) return std::nullopt;
@@ -338,11 +297,6 @@ int main(int argc, char **argv) {
     double min_partiality = 0.02;
     double min_image_cc = 0.0;
     int64_t scaling_iter = 3;
-    std::optional<double> azim_q_spacing;
-    std::optional<double> azim_q_min;
-    std::optional<double> azim_q_max;
-    bool use_azim_for_integration = false;
-
     std::optional<CrystalLattice> forced_rotation_lattice;
 
     std::optional<float> bandwidth_fwhm; // relative FWHM of dlambda/lambda
@@ -363,237 +317,225 @@ int main(int argc, char **argv) {
 
     int opt;
     int option_index = 0;
-    const char *short_opts = "vo:N:s:e:t:R::X:C:z:FABw::S:MP:r:Q:";
+    const char *short_opts = "vo:N:s:e:t:R::X:C:z:FABw::S:MP:r:";
 
-    while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
-        switch (opt) {
-            case 'o':
-                output_prefix = optarg;
-                break;
-            case 'v':
-                verbose = true;
-                break;
-            case 'N':
-                nthreads = atoi(optarg);
-                break;
-            case 's':
-                start_image = atoi(optarg);
-                break;
-            case 'e':
-                end_image = atoi(optarg);
-                break;
-            case 't':
-                image_stride = atoi(optarg);
-                break;
-            case 'R':
-                if (rotation_indexing) {
-                    logger.Error("Rotation indexing already enabled");
-                    exit(EXIT_FAILURE);
-                }
-                rotation_indexing = true;
-                two_pass_rotation = true;
-                if (optarg)
-                    rotation_indexing_image_count = atoi(optarg);
-
-                break;
-            case 'Q':
-                azim_q_spacing = atof(optarg);
-                break;
-            case OPT_AZIM_Q_MIN:
-                azim_q_min = atof(optarg);
-                break;
-            case OPT_AZIM_Q_MAX:
-                azim_q_max = atof(optarg);
-                break;
-            case OPT_INTEGRATION_USE_AZIM:
-                use_azim_for_integration = true;
-                break;
-            case OPT_SINGLE_PASS_ROTATION:
-                if (rotation_indexing) {
-                    logger.Error("Rotation indexing already enabled");
-                    exit(EXIT_FAILURE);
-                }
-                rotation_indexing = true;
-                two_pass_rotation = false;
-
-                if (optarg)
-                    rotation_indexing_range = atof(optarg);
-                break;
-            case OPT_REDO_ROTATION_SPOTS:
-                reuse_rotation_spots = false;
-                break;
-            case OPT_FORCE_ROTATION_LATTICE: {
-                if (rotation_indexing) {
-                    logger.Error("Rotation indexing already enabled");
-                    exit(EXIT_FAILURE);
-                }
-                rotation_indexing = true;
-
-                auto latt = parse_lattice_arg(optarg);
-                if (!latt.has_value()) {
-                    logger.Error(
-                        "Invalid rotation lattice. Expected: \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, comma-separated). Got: {}",
-                        optarg ? optarg : "<null>");
-                    print_usage();
-                    exit(EXIT_FAILURE);
-                }
-                forced_rotation_lattice = latt;
-                auto uc = latt->GetUnitCell();
-                logger.Info(
-                    "Forced rotation lattice set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
-                    uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
-                break;
+  while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
+    switch (opt) {
+        case 'o':
+            output_prefix = optarg;
+            break;
+        case 'v':
+            verbose = true;
+            break;
+        case 'N':
+            nthreads = atoi(optarg);
+            break;
+        case 's':
+            start_image = atoi(optarg);
+            break;
+        case 'e':
+            end_image = atoi(optarg);
+            break;
+        case 't':
+            image_stride = atoi(optarg);
+            break;
+        case 'R':
+            if (rotation_indexing) {
+                logger.Error("Rotation indexing already enabled");
+                exit(EXIT_FAILURE);
             }
-            case 'X': {
-                std::string alg = optarg ? optarg : "";
-                std::transform(alg.begin(), alg.end(), alg.begin(),
-                               [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
+            rotation_indexing = true;
+            two_pass_rotation = true;
+            if (optarg)
+                rotation_indexing_image_count = atoi(optarg);
 
-                if (alg == "ffbidx")
-                    indexing_algorithm = IndexingAlgorithmEnum::FFBIDX;
-                else if (alg == "fft")
-                    indexing_algorithm = IndexingAlgorithmEnum::FFT;
-                else if (alg == "fftw")
-                    indexing_algorithm = IndexingAlgorithmEnum::FFTW;
-                else if (alg == "auto")
-                    indexing_algorithm = IndexingAlgorithmEnum::Auto;
-                else if (alg == "none")
-                    indexing_algorithm = IndexingAlgorithmEnum::None;
-                else {
-                    logger.Error("Invalid indexing algorithm: {}", alg);
-                    print_usage();
-                    exit(EXIT_FAILURE);
-                }
-                break;
+            break;
+        case OPT_SINGLE_PASS_ROTATION:
+            if (rotation_indexing) {
+                logger.Error("Rotation indexing already enabled");
+                exit(EXIT_FAILURE);
             }
-            case 'r': {
-                std::string alg = optarg ? optarg : "";
-                std::transform(alg.begin(), alg.end(), alg.begin(),
-                               [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
-                if (alg == "none")
-                    refinement_algorithm = GeomRefinementAlgorithmEnum::None;
-                else if (alg == "beam_and_lattice")
-                    refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
-                else if (alg == "orientation")
-                    refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
-                else if (alg == "pixelrefine")
-                    refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
-                else {
-                    logger.Error("Invalid geom refinement algorithm: {}", alg);
-                    print_usage();
-                    exit(EXIT_FAILURE);
-                }
-                break;
-            }
-            case 'C': {
-                auto uc = parse_unit_cell_arg(optarg);
-                if (!uc.has_value()) {
-                    logger.Error(
-                        "Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
-                        optarg ? optarg : "<null>");
-                    print_usage();
-                    exit(EXIT_FAILURE);
-                }
-                fixed_reference_unit_cell = uc;
-                logger.Info(
-                    "Fixed reference unit cell set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
-                    uc->a, uc->b, uc->c, uc->alpha, uc->beta, uc->gamma);
-                break;
-            }
-            case 'z':
-                ref_mtz = optarg;
-                break;
-            case 'F':
-                indexing_algorithm = IndexingAlgorithmEnum::FFT;
-                break;
-            case 'A':
-                anomalous_mode = true;
-                break;
-            case 'B':
-                refine_bfactor = true;
-                break;
-            case 'w':
-                refine_wedge = true;
-                if (optarg)
-                    wedge_for_scaling = std::stod(optarg);
-                break;
-            case 'S':
-                space_group_number = atoi(optarg);
-                break;
-            case 'P':
-                if (strcmp(optarg, "unity") == 0)
-                    partiality_model = PartialityModel::Unity;
-                else if (strcmp(optarg, "fixed") == 0)
-                    partiality_model = PartialityModel::Fixed;
-                else if (strcmp(optarg, "rot") == 0)
-                    partiality_model = PartialityModel::Rotation;
-                else {
-                    logger.Error("Invalid partiality mode: {}", optarg);
-                    print_usage();
-                    exit(EXIT_FAILURE);
-                }
-                break;
-            case OPT_SPOT_SIGMA:
-                sigma_spot_finding = atof(optarg);
-                logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
-                break;
-            case OPT_SPOT_THRESHOLD:
-                photon_count_threshold_spot_finding = atoi(optarg);
-                logger.Info("Photon-count threshold level for spot finding set to {:d}",
-                            photon_count_threshold_spot_finding);
-                break;
-            case OPT_SPOT_RESOLUTION:
-                d_min_spot_finding = atof(optarg);
-                logger.Info("High resolution limit for spot finding set to {:.2f} A", d_min_spot_finding);
-                break;
-            case OPT_MAX_SPOTS:
-                max_spot_count_override = atoll(optarg);
-                logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
-                break;
-            case 'M':
-                run_scaling = true;
-                break;
-            case OPT_MIN_PARTIALITY:
-                min_partiality = std::stod(optarg);
-                break;
-            case OPT_MIN_IMAGE_CC:
-                min_image_cc = std::stod(optarg);
-                break;
-            case OPT_SCALING_HIGH_RESOLUTION:
-                d_min_scale_merge = atof(optarg);
-                break;
-            case OPT_SCALING_OUTPUT:
-                if (strcmp(optarg, "mtz") == 0) {
-                    intensity_format = IntensityFormat::MTZ;
-                } else if (strcmp(optarg, "cif") == 0) {
-                    intensity_format = IntensityFormat::mmCIF;
-                } else if (strcmp(optarg, "txt") == 0) {
-                    intensity_format = IntensityFormat::Text;
-                } else {
-                    logger.Error("Invalid intensity format: {}", optarg);
-                    exit(EXIT_FAILURE);
-                }
-                break;
-            case OPT_SCALING_ITERATIONS:
-                scaling_iter = atoi(optarg);
-                if (scaling_iter <= 0) {
-                    logger.Error("Invalid scaling iteration count: {}", scaling_iter);
-                    exit(EXIT_FAILURE);
-                }
-                break;
-            case OPT_BANDWIDTH:
-                bandwidth_fwhm = atof(optarg);
-                if (!(bandwidth_fwhm.value() >= 0.0f)) {
-                    logger.Error("Invalid bandwidth: {}", optarg);
-                    exit(EXIT_FAILURE);
-                }
-                break;
+            rotation_indexing = true;
+            two_pass_rotation = false;
 
-            default:
+            if (optarg)
+                rotation_indexing_range = atof(optarg);
+            break;
+        case OPT_REDO_ROTATION_SPOTS:
+            reuse_rotation_spots = false;
+            break;
+        case OPT_FORCE_ROTATION_LATTICE: {
+            if (rotation_indexing) {
+                logger.Error("Rotation indexing already enabled");
+                exit(EXIT_FAILURE);
+            }
+            rotation_indexing = true;
+
+            auto latt = parse_lattice_arg(optarg);
+            if (!latt.has_value()) {
+                logger.Error(
+                    "Invalid rotation lattice. Expected: \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, comma-separated). Got: {}",
+                    optarg ? optarg : "<null>");
                 print_usage();
                 exit(EXIT_FAILURE);
+            }
+            forced_rotation_lattice = latt;
+            auto uc = latt->GetUnitCell();
+            logger.Info(
+                "Forced rotation lattice set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
+                uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
+            break;
         }
+        case 'X': {
+            std::string alg = optarg ? optarg : "";
+            std::transform(alg.begin(), alg.end(), alg.begin(),
+                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
+
+            if (alg == "ffbidx")
+                indexing_algorithm = IndexingAlgorithmEnum::FFBIDX;
+            else if (alg == "fft")
+                indexing_algorithm = IndexingAlgorithmEnum::FFT;
+            else if (alg == "fftw")
+                indexing_algorithm = IndexingAlgorithmEnum::FFTW;
+            else if (alg == "auto")
+                indexing_algorithm = IndexingAlgorithmEnum::Auto;
+            else if (alg == "none")
+                indexing_algorithm = IndexingAlgorithmEnum::None;
+            else {
+                logger.Error("Invalid indexing algorithm: {}", alg);
+                print_usage();
+                exit(EXIT_FAILURE);
+            }
+            break;
+        }
+        case 'r': {
+            std::string alg = optarg ? optarg : "";
+            std::transform(alg.begin(), alg.end(), alg.begin(),
+                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
+            if (alg == "none")
+                refinement_algorithm = GeomRefinementAlgorithmEnum::None;
+            else if (alg == "beam_and_lattice")
+                refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
+            else if (alg == "orientation")
+                refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
+            else if (alg == "pixelrefine")
+                refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
+            else {
+                logger.Error("Invalid geom refinement algorithm: {}", alg);
+                print_usage();
+                exit(EXIT_FAILURE);
+            }
+            break;
+        }
+        case 'C': {
+            auto uc = parse_unit_cell_arg(optarg);
+            if (!uc.has_value()) {
+                logger.Error(
+                    "Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
+                    optarg ? optarg : "<null>");
+                print_usage();
+                exit(EXIT_FAILURE);
+            }
+            fixed_reference_unit_cell = uc;
+            logger.Info(
+                "Fixed reference unit cell set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
+                uc->a, uc->b, uc->c, uc->alpha, uc->beta, uc->gamma);
+            break;
+        }
+        case 'z':
+            ref_mtz = optarg;
+            break;
+        case 'F':
+            indexing_algorithm = IndexingAlgorithmEnum::FFT;
+            break;
+        case 'A':
+            anomalous_mode = true;
+            break;
+        case 'B':
+            refine_bfactor = true;
+            break;
+        case 'w':
+            refine_wedge = true;
+            if (optarg)
+                wedge_for_scaling = std::stod(optarg);
+            break;
+        case 'S':
+            space_group_number = atoi(optarg);
+            break;
+        case 'P':
+            if (strcmp(optarg, "unity") == 0)
+                partiality_model = PartialityModel::Unity;
+            else if (strcmp(optarg, "fixed") == 0)
+                partiality_model = PartialityModel::Fixed;
+            else if (strcmp(optarg, "rot") == 0)
+                partiality_model = PartialityModel::Rotation;
+            else {
+                logger.Error("Invalid partiality mode: {}", optarg);
+                print_usage();
+                exit(EXIT_FAILURE);
+            }
+            break;
+        case OPT_SPOT_SIGMA:
+            sigma_spot_finding = atof(optarg);
+            logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
+            break;
+        case OPT_SPOT_THRESHOLD:
+            photon_count_threshold_spot_finding = atoi(optarg);
+            logger.Info("Photon-count threshold level for spot finding set to {:d}",
+                        photon_count_threshold_spot_finding);
+            break;
+        case OPT_SPOT_RESOLUTION:
+            d_min_spot_finding = atof(optarg);
+            logger.Info("High resolution limit for spot finding set to {:.2f} A", d_min_spot_finding);
+            break;
+        case OPT_MAX_SPOTS:
+            max_spot_count_override = atoll(optarg);
+            logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
+            break;
+        case 'M':
+            run_scaling = true;
+            break;
+        case OPT_MIN_PARTIALITY:
+            min_partiality = std::stod(optarg);
+            break;
+        case OPT_MIN_IMAGE_CC:
+            min_image_cc = std::stod(optarg);
+            break;
+        case OPT_SCALING_HIGH_RESOLUTION:
+            d_min_scale_merge = atof(optarg);
+            break;
+        case OPT_SCALING_OUTPUT:
+            if (strcmp(optarg, "mtz") == 0) {
+                intensity_format = IntensityFormat::MTZ;
+            } else if (strcmp(optarg, "cif") == 0) {
+                intensity_format = IntensityFormat::mmCIF;
+            } else if (strcmp(optarg, "txt") == 0) {
+                intensity_format = IntensityFormat::Text;
+            } else {
+                logger.Error("Invalid intensity format: {}", optarg);
+                exit(EXIT_FAILURE);
+            }
+            break;
+        case OPT_SCALING_ITERATIONS:
+            scaling_iter = atoi(optarg);
+            if (scaling_iter <= 0) {
+                logger.Error("Invalid scaling iteration count: {}", scaling_iter);
+                exit(EXIT_FAILURE);
+            }
+            break;
+        case OPT_BANDWIDTH:
+            bandwidth_fwhm = atof(optarg);
+            if (!(bandwidth_fwhm.value() >= 0.0f)) {
+                logger.Error("Invalid bandwidth: {}", optarg);
+                exit(EXIT_FAILURE);
+            }
+            break;
+
+        default:
+            print_usage();
+            exit(EXIT_FAILURE);
     }
+}
 
     if (optind != argc - 1) {
         logger.Error("Input file not specified");
@@ -661,7 +603,7 @@ int main(int argc, char **argv) {
 
     if (images_to_process <= 0) {
         logger.Warning("No images to process (Start: {}, End: {} Stride: {}, Total: {})", start_image, end_image,
-                       image_stride, total_images_in_file);
+            image_stride, total_images_in_file);
         return 0;
     }
 
@@ -726,17 +668,6 @@ int main(int argc, char **argv) {
 
     experiment.ImportScalingSettings(scaling_settings);
 
-    BraggIntegrationSettings bragg_integration_settings;
-    bragg_integration_settings.UseAzimProfile(use_azim_for_integration);
-    experiment.ImportBraggIntegrationSettings(bragg_integration_settings);
-
-    AzimuthalIntegrationSettings azimuthal_integration_settings;
-    if (azim_q_spacing)
-        azimuthal_integration_settings.QSpacing_recipA(azim_q_spacing.value());
-    azimuthal_integration_settings.QRange_recipA(azim_q_min.value_or(azimuthal_integration_settings.GetLowQ_recipA()),
-                                                 azim_q_max.value_or(azimuthal_integration_settings.GetHighQ_recipA()));
-    experiment.ImportAzimuthalIntegrationSettings(azimuthal_integration_settings);
-
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;
@@ -749,6 +680,9 @@ int main(int argc, char **argv) {
     // Initialize Analysis Components
     PixelMask pixel_mask = dataset->pixel_mask;
 
+    // If dataset has a mask you wish to use, you might need to load it into pixel_mask here
+    // e.g. pixel_mask.LoadUserMask(dataset->pixel_mask, ...);
+
     AzimuthalIntegrationMapping mapping(experiment, pixel_mask);
     IndexerThreadPool indexer_pool(experiment.GetIndexingSettings());
 
@@ -834,7 +768,7 @@ int main(int argc, char **argv) {
 
                     analysis.Analyze(msg, profile, first_pass_spot_settings);
                 }
-                indexer.AddImageToRotationIndexer(msg);
+               indexer.AddImageToRotationIndexer(msg);
             } catch (const std::exception &e) {
                 logger.Warning("Failed to add image {} to first-pass rotation indexing: {}", image_idx, e.what());
             }
@@ -880,8 +814,7 @@ int main(int argc, char **argv) {
             msg.image = img->image;
             msg.number = image_ordinal;
             msg.original_number = image_idx;
-            if (dataset->efficiency.size() > image_idx)
-                msg.image_collection_efficiency = dataset->efficiency[image_idx];
+            if (dataset->efficiency.size() > image_idx) msg.image_collection_efficiency = dataset->efficiency[image_idx];
 
             total_uncompressed_bytes += msg.image.GetUncompressedSize();
 
@@ -988,8 +921,8 @@ int main(int argc, char **argv) {
     if (consensus_cell) {
         logger.Info("Consensus unit cell found in {:.2f} ms", consensus_duration * 1e3);
         logger.Info("UC:         a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
-                    consensus_cell->a, consensus_cell->b, consensus_cell->c,
-                    consensus_cell->alpha, consensus_cell->beta, consensus_cell->gamma);
+                        consensus_cell->a, consensus_cell->b, consensus_cell->c,
+                        consensus_cell->alpha, consensus_cell->beta, consensus_cell->gamma);
     } else
         logger.Info("Consensus unit cell not found - calculation tool {:.2f} ms", consensus_duration * 1e3);
     end_msg.unit_cell = consensus_cell;
@@ -997,8 +930,9 @@ int main(int argc, char **argv) {
     if (end_msg.indexing_rate.has_value()
         && end_msg.indexing_rate > 0
         && (run_scaling || !reference_data.empty())) {
+
         const bool pixel_refine_path =
-                (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
+            (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
 
         // Scaling is only the classical, no-reference ScaleOnTheFly post-pass.
         // - With a reference (classical path): per-image live scaling already ran.
@@ -1039,12 +973,11 @@ int main(int argc, char **argv) {
         MergeOnTheFly merge_engine(experiment);
         if (consensus_cell.has_value())
             merge_engine.ReferenceCell(*consensus_cell);
-        for (auto &i: indexer.GetIntegrationOutcome())
+        for (auto &i : indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
 
         auto merged_reflections = merge_engine.ExportReflections();
-        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(),
-                                                         reference_data);
+        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);
 
         auto merge_end = std::chrono::steady_clock::now();
         double merge_time = std::chrono::duration<double>(merge_end - merge_start).count();
@@ -1098,17 +1031,17 @@ int main(int argc, char **argv) {
 
     auto image_mean_time = plots.GetMeanProcessingTime();
     std::cout << fmt::format(
-                "Per-image time: (mean; milliseconds): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} scaling {:.2f} total {:.2f}",
-                image_mean_time.compression * 1e3,
-                image_mean_time.preprocessing * 1e3,
-                image_mean_time.azint * 1e3,
-                image_mean_time.spot_finding * 1e3,
-                image_mean_time.indexing * 1e3,
-                image_mean_time.refinement * 1e3,
-                image_mean_time.indexing_analysis * 1e3,
-                image_mean_time.bragg_prediction * 1e3,
-                image_mean_time.integration * 1e3,
-                image_mean_time.image_scale * 1e3,
-                image_mean_time.processing * 1e3)
-            << std::endl;
+        "Per-image time: (mean; milliseconds): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} scaling {:.2f} total {:.2f}",
+        image_mean_time.compression * 1e3,
+        image_mean_time.preprocessing * 1e3,
+        image_mean_time.azint * 1e3,
+        image_mean_time.spot_finding * 1e3,
+        image_mean_time.indexing * 1e3,
+        image_mean_time.refinement * 1e3,
+        image_mean_time.indexing_analysis * 1e3,
+        image_mean_time.bragg_prediction * 1e3,
+        image_mean_time.integration * 1e3,
+        image_mean_time.image_scale * 1e3,
+        image_mean_time.processing * 1e3)
+    << std::endl;
 }
-- 
2.52.0


From 59281f6330fbed591052960b16e34dbabe05a398 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 16:36:37 +0200
Subject: [PATCH 028/228] Revert "Bragg integration: option to use azimuthal
 integration profile"

This reverts commit e4230bc14ee9a0b5a127d24d1cb71ca486820de4.
---
 common/BraggIntegrationSettings.cpp           |   9 -
 common/BraggIntegrationSettings.h             |   5 +-
 image_analysis/IndexAndRefine.cpp             |  14 +-
 image_analysis/IndexAndRefine.h               |   8 +-
 image_analysis/MXAnalysisAfterFPGA.cpp        |  11 +-
 image_analysis/MXAnalysisAfterFPGA.h          |   5 +-
 image_analysis/MXAnalysisWithoutFPGA.cpp      |   2 +-
 .../bragg_integration/BraggIntegrate2D.cpp    | 219 +++++-------------
 .../bragg_integration/BraggIntegrate2D.h      |  10 +-
 receiver/JFJochReceiver.cpp                   |  25 +-
 receiver/JFJochReceiver.h                     |   2 +-
 receiver/JFJochReceiverFPGA.cpp               |  11 +-
 receiver/JFJochReceiverLite.cpp               |   4 +-
 tests/BraggIntegrate2DTest.cpp                |   6 +-
 tools/jfjoch_scale.cpp                        |   2 +
 15 files changed, 115 insertions(+), 218 deletions(-)

diff --git a/common/BraggIntegrationSettings.cpp b/common/BraggIntegrationSettings.cpp
index 0528084e..3fe0a861 100644
--- a/common/BraggIntegrationSettings.cpp
+++ b/common/BraggIntegrationSettings.cpp
@@ -87,12 +87,3 @@ float BraggIntegrationSettings::GetDMinLimit_A() const {
 float BraggIntegrationSettings::GetMinimumSigmaInRegardsToI() const {
     return minimum_sigma_in_regards_to_i;
 }
-
-bool BraggIntegrationSettings::IsUseAzimProfile() const {
-    return use_azim_profile;
-}
-
-BraggIntegrationSettings &BraggIntegrationSettings::UseAzimProfile(bool input) {
-    use_azim_profile = input;
-    return *this;
-}
diff --git a/common/BraggIntegrationSettings.h b/common/BraggIntegrationSettings.h
index 2c15921d..60ab4059 100644
--- a/common/BraggIntegrationSettings.h
+++ b/common/BraggIntegrationSettings.h
@@ -12,14 +12,14 @@ class BraggIntegrationSettings {
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;
     float minimum_sigma_in_regards_to_i = 0.02;
-    bool use_azim_profile = false;
+
 public:
     BraggIntegrationSettings& R1(float input);
     BraggIntegrationSettings& R2(float input);
     BraggIntegrationSettings& R3(float input);
     BraggIntegrationSettings& DMinLimit_A(float input);
     BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
-    BraggIntegrationSettings& UseAzimProfile(bool input);
+
 
     [[nodiscard]] float GetR1() const;
     [[nodiscard]] float GetR2() const;
@@ -28,5 +28,4 @@ public:
     [[nodiscard]] float GetDMinLimit_A() const;
 
     [[nodiscard]] float GetMinimumSigmaInRegardsToI() const;
-    [[nodiscard]] bool IsUseAzimProfile() const;
 };
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 459af31e..98b1aed6 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -239,8 +239,8 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                                               const CompressedImage &image,
                                               BraggPrediction &prediction,
                                               const IndexAndRefine::IndexingOutcome &outcome,
-                                              const AzimuthalIntegrationMapping &mapping,
-                                              const AzimuthalIntegrationProfile &profile) {
+                                              const AzimuthalIntegrationMapping *mapping,
+                                              const AzimuthalIntegrationProfile *profile) {
     if (!outcome.lattice_candidate)
         return;
 
@@ -299,11 +299,11 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
     // integrated reflections that flow into the normal save/merge).
     const bool use_pixel_refine =
         experiment.GetIndexingSettings().GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::PixelRefine
-        && !pixel_reference_.empty();
+        && !pixel_reference_.empty() && mapping && profile;
 
     if (use_pixel_refine) {
         auto integration_start_time = std::chrono::steady_clock::now();
-        PixelRefineIntegrate(msg, image, prediction, outcome, mapping, profile, i_outcome);
+        PixelRefineIntegrate(msg, image, prediction, outcome, *mapping, *profile, i_outcome);
         msg.integrated_reflections = i_outcome.reflections.size();
         auto integration_end_time = std::chrono::steady_clock::now();
         msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
@@ -314,7 +314,7 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
         msg.bragg_prediction_time_s = std::chrono::duration<float>(pred_end_time - pred_start_time).count();
 
         auto integration_start_time = std::chrono::steady_clock::now();
-        i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), mapping, profile, nrefl, msg.number);
+        i_outcome.reflections = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), nrefl, msg.number);
         msg.integrated_reflections = i_outcome.reflections.size();
         auto integration_end_time = std::chrono::steady_clock::now();
         msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
@@ -357,8 +357,8 @@ void IndexAndRefine::ProcessImage(DataMessage &msg,
                                   const SpotFindingSettings &spot_finding_settings,
                                   const CompressedImage &image,
                                   BraggPrediction &prediction,
-                                  const AzimuthalIntegrationMapping &mapping,
-                                  const AzimuthalIntegrationProfile &profile) {
+                                  const AzimuthalIntegrationMapping *mapping,
+                                  const AzimuthalIntegrationProfile *profile) {
     if (!indexer_ || !spot_finding_settings.indexing)
         return;
 
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index d73fc2f1..7674392e 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -66,8 +66,8 @@ class IndexAndRefine {
                                  const CompressedImage &image,
                                  BraggPrediction &prediction,
                                  const IndexingOutcome &outcome,
-                                 const AzimuthalIntegrationMapping &mapping,
-                                 const AzimuthalIntegrationProfile &profile);
+                                 const AzimuthalIntegrationMapping *mapping,
+                                 const AzimuthalIntegrationProfile *profile);
 
     std::unique_ptr<ScaleOnTheFly> scaling_engine;
     void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
@@ -93,8 +93,8 @@ public:
     void ForceRotationIndexerLattice(const CrystalLattice& lattice);
 
     void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction,
-                      const AzimuthalIntegrationMapping &mapping,
-                      const AzimuthalIntegrationProfile &profile);
+                      const AzimuthalIntegrationMapping *mapping = nullptr,
+                      const AzimuthalIntegrationProfile *profile = nullptr);
     IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
 
     ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
diff --git a/image_analysis/MXAnalysisAfterFPGA.cpp b/image_analysis/MXAnalysisAfterFPGA.cpp
index 96d8430d..a5347236 100644
--- a/image_analysis/MXAnalysisAfterFPGA.cpp
+++ b/image_analysis/MXAnalysisAfterFPGA.cpp
@@ -25,12 +25,10 @@ double stddev(const std::vector<float> &v) {
 }
 
 
-MXAnalysisAfterFPGA::MXAnalysisAfterFPGA(const DiffractionExperiment &in_experiment, IndexAndRefine &indexer,
-                                         AzimuthalIntegrationMapping &mapping)
+MXAnalysisAfterFPGA::MXAnalysisAfterFPGA(const DiffractionExperiment &in_experiment, IndexAndRefine &indexer)
     : experiment(in_experiment),
       indexer(indexer),
-      prediction(CreateBraggPrediction(experiment.IsRotationIndexing())),
-      mapping(mapping) {
+      prediction(CreateBraggPrediction(experiment.IsRotationIndexing())) {
     if (experiment.IsSpotFindingEnabled())
         find_spots = true;
 }
@@ -105,8 +103,7 @@ void MXAnalysisAfterFPGA::ReadFromCPU(DeviceOutput *output, const SpotFindingSet
     }
 }
 
-void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSettings &spot_finding_settings,
-                                  const AzimuthalIntegrationProfile &profile) {
+void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSettings& spot_finding_settings) {
     if (find_spots && (state == State::Enabled)) {
         const auto t0 = std::chrono::steady_clock::now();
         SpotAnalyze(experiment, spot_finding_settings, spots, message);
@@ -114,7 +111,7 @@ void MXAnalysisAfterFPGA::Process(DataMessage &message, const SpotFindingSetting
         spot_finding_time_total += (t1 - t0);
 
         if (spot_finding_settings.indexing)
-            indexer.ProcessImage(message, spot_finding_settings, message.image, *prediction, mapping, profile);
+            indexer.ProcessImage(message, spot_finding_settings, message.image, *prediction);
     }
 
     if (spot_finding_timing_active) {
diff --git a/image_analysis/MXAnalysisAfterFPGA.h b/image_analysis/MXAnalysisAfterFPGA.h
index e3b708ac..ccddf87a 100644
--- a/image_analysis/MXAnalysisAfterFPGA.h
+++ b/image_analysis/MXAnalysisAfterFPGA.h
@@ -28,10 +28,9 @@ class MXAnalysisAfterFPGA {
 
     std::chrono::duration<double, std::micro> spot_finding_time_total{0.0};
     bool spot_finding_timing_active = false;
-    const AzimuthalIntegrationMapping &mapping;
 public:
 
-    MXAnalysisAfterFPGA(const DiffractionExperiment& experiment, IndexAndRefine &indexer, AzimuthalIntegrationMapping &mapping);
+    MXAnalysisAfterFPGA(const DiffractionExperiment& experiment, IndexAndRefine &indexer);
 
     void ReadFromFPGA(const DeviceOutput* output,
                       const SpotFindingSettings& settings,
@@ -41,5 +40,5 @@ public:
                      const SpotFindingSettings &settings,
                      size_t module_number);
 
-    void Process(DataMessage &message, const SpotFindingSettings& settings, const AzimuthalIntegrationProfile &profile);
+    void Process(DataMessage &message, const SpotFindingSettings& settings);
 };
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index 62b6379f..6a638213 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -92,7 +92,7 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
         if (spot_finding_settings.indexing)
             indexer.ProcessImage(output, spot_finding_settings,
                 CompressedImage(preprocessor_buffer->getBuffer(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum()),
-                *prediction, integration, profile);
+                *prediction, &integration, &profile);
     }
 
     output.max_viable_pixel_value = ret.max_value;
diff --git a/image_analysis/bragg_integration/BraggIntegrate2D.cpp b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
index 35ec4849..b616ecc1 100644
--- a/image_analysis/bragg_integration/BraggIntegrate2D.cpp
+++ b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
@@ -8,62 +8,65 @@
 #include <vector>
 
 namespace {
-    template<class T>
-    float Median(std::vector<T> &values) {
-        if (values.empty())
-            return 0.0f;
 
-        const size_t middle = values.size() / 2;
-        std::nth_element(values.begin(), values.begin() + middle, values.end());
+template<class T>
+float Median(std::vector<T> &values) {
+    if (values.empty())
+        return 0.0f;
 
-        if (values.size() % 2 == 1)
-            return static_cast<float>(values[middle]);
+    const size_t middle = values.size() / 2;
+    std::nth_element(values.begin(), values.begin() + middle, values.end());
 
-        const T upper = values[middle];
-        std::nth_element(values.begin(), values.begin() + middle - 1, values.begin() + middle);
-        const T lower = values[middle - 1];
+    if (values.size() % 2 == 1)
+        return static_cast<float>(values[middle]);
 
-        return 0.5f * static_cast<float>(lower + upper);
-    }
+    const T upper = values[middle];
+    std::nth_element(values.begin(), values.begin() + middle - 1, values.begin() + middle);
+    const T lower = values[middle - 1];
 
-    void MarkReflectionMask(std::vector<uint8_t> &mask,
-                            size_t xpixel, size_t ypixel,
-                            const Reflection &r, float r_2, float r_2_sq) {
-        int64_t x0 = std::floor(r.predicted_x - r_2 - 1.0f);
-        int64_t x1 = std::ceil(r.predicted_x + r_2 + 1.0f);
-        int64_t y0 = std::floor(r.predicted_y - r_2 - 1.0f);
-        int64_t y1 = std::ceil(r.predicted_y + r_2 + 1.0f);
+    return 0.5f * static_cast<float>(lower + upper);
+}
 
-        if (x0 < 0)
-            x0 = 0;
-        if (y0 < 0)
-            y0 = 0;
-        if (x1 >= static_cast<int64_t>(xpixel))
-            x1 = static_cast<int64_t>(xpixel) - 1;
-        if (y1 >= static_cast<int64_t>(ypixel))
-            y1 = static_cast<int64_t>(ypixel) - 1;
+void MarkReflectionMask(std::vector<uint8_t> &mask,
+                        size_t xpixel, size_t ypixel,
+                        const Reflection &r, float r_2, float r_2_sq) {
 
-        for (int64_t y = y0; y <= y1; y++) {
-            for (int64_t x = x0; x <= x1; x++) {
-                const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
-                                      + (y - r.predicted_y) * (y - r.predicted_y);
-                if (dist_sq < r_2_sq)
-                    mask[y * xpixel + x] = 1;
-            }
+    int64_t x0 = std::floor(r.predicted_x - r_2 - 1.0f);
+    int64_t x1 = std::ceil(r.predicted_x + r_2 + 1.0f);
+    int64_t y0 = std::floor(r.predicted_y - r_2 - 1.0f);
+    int64_t y1 = std::ceil(r.predicted_y + r_2 + 1.0f);
+
+    if (x0 < 0)
+        x0 = 0;
+    if (y0 < 0)
+        y0 = 0;
+    if (x1 >= static_cast<int64_t>(xpixel))
+        x1 = static_cast<int64_t>(xpixel) - 1;
+    if (y1 >= static_cast<int64_t>(ypixel))
+        y1 = static_cast<int64_t>(ypixel) - 1;
+
+    for (int64_t y = y0; y <= y1; y++) {
+        for (int64_t x = x0; x <= x1; x++) {
+            const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
+                                + (y - r.predicted_y) * (y - r.predicted_y);
+            if (dist_sq < r_2_sq)
+                mask[y * xpixel + x] = 1;
         }
     }
+}
 
-    std::vector<uint8_t> BuildReflectionMask(const std::vector<Reflection> &predicted,
-                                             size_t npredicted,
-                                             size_t xpixel, size_t ypixel,
-                                             float r_2, float r_2_sq) {
-        std::vector<uint8_t> mask(xpixel * ypixel, 0);
+std::vector<uint8_t> BuildReflectionMask(const std::vector<Reflection> &predicted,
+                                         size_t npredicted,
+                                         size_t xpixel, size_t ypixel,
+                                         float r_2, float r_2_sq) {
+    std::vector<uint8_t> mask(xpixel * ypixel, 0);
 
-        for (size_t i = 0; i < npredicted; i++)
-            MarkReflectionMask(mask, xpixel, ypixel, predicted.at(i), r_2, r_2_sq);
+    for (size_t i = 0; i < npredicted; i++)
+        MarkReflectionMask(mask, xpixel, ypixel, predicted.at(i), r_2, r_2_sq);
+
+    return mask;
+}
 
-        return mask;
-    }
 } // namespace
 
 template<class T>
@@ -72,6 +75,7 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
                          int64_t special_value, int64_t saturation,
                          float r_3, float r_1_sq, float r_2_sq, float r_3_sq,
                          float minimum_sigma_in_regards_to_i) {
+
     int64_t x0 = std::floor(r.predicted_x - r_3 - 1.0);
     int64_t x1 = std::ceil(r.predicted_x + r_3 + 1.0);
     int64_t y0 = std::floor(r.predicted_y - r_3 - 1.0);
@@ -142,94 +146,15 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
     }
 }
 
-template<class T>
-void IntegrateReflectionAzim(Reflection &r, const T *image,
-                             size_t xpixel, size_t ypixel,
-                             int64_t special_value, int64_t saturation,
-                             float r_1, float r_1_sq,
-                             const std::vector<uint16_t> &pixel_to_bin,
-                             const std::vector<float> &bkg_mean,
-                             float minimum_sigma_in_regards_to_i) {
-    int64_t x0 = std::floor(r.predicted_x - r_1 - 1.0);
-    int64_t x1 = std::ceil(r.predicted_x + r_1 + 1.0);
-    int64_t y0 = std::floor(r.predicted_y - r_1 - 1.0);
-    int64_t y1 = std::ceil(r.predicted_y + r_1 + 1.0);
-    x0 = std::max(0L, x0);
-    x1 = std::min(static_cast<int64_t>(xpixel - 1), x1);
-    y0 = std::max(0L, y0);
-    y1 = std::min(static_cast<int64_t>(ypixel - 1), y1);
-
-    int64_t I_sum = 0;
-    int64_t I_npixel_inner = 0;
-    int64_t I_npixel_integrated = 0;
-    int64_t I_sum_x = 0;
-    int64_t I_sum_y = 0;
-
-    std::vector<T> bkg_values;
-    bkg_values.reserve(static_cast<size_t>((x1 - x0 + 1) * (y1 - y0 + 1)));
-
-    float bkg = 0.0;
-
-    for (int64_t y = y0; y <= y1; y++) {
-        for (int64_t x = x0; x <= x1; x++) {
-            const float dist_sq = (x - r.predicted_x) * (x - r.predicted_x)
-                                  + (y - r.predicted_y) * (y - r.predicted_y);
-            const auto pixel = image[y * xpixel + x];
-            auto azim_bint = pixel_to_bin[y * xpixel + x];
-
-            if (dist_sq < r_1_sq)
-                I_npixel_inner++;
-
-            if (azim_bint >= bkg_mean.size())
-                continue;
-
-            if (pixel == special_value || pixel == saturation)
-                continue;
-
-            if (dist_sq < r_1_sq) {
-                bkg += bkg_values.at(azim_bint);
-                I_sum += pixel;
-                I_sum_x += x * pixel;
-                I_sum_y += y * pixel;
-                I_npixel_integrated++;
-            }
-        }
-    }
-
-    if ((I_npixel_integrated == I_npixel_inner) && (bkg_values.size() > 5)) {
-        r.bkg = bkg / static_cast<float>(I_npixel_integrated);
-        r.I = static_cast<float>(I_sum) - bkg;
-        if (I_sum > 0) {
-            r.observed_x = static_cast<float>(I_sum_x) / static_cast<float>(I_sum);
-            r.observed_y = static_cast<float>(I_sum_y) / static_cast<float>(I_sum);
-        }
-
-        // sigma is max of the:
-        // - 1 (for zero photons)
-        // - Poisson noise (sqrt(I_sum)) (for in between)
-        // - minimum_sigma_in_regards_to_i of Intensity (for very large numbers)
-        r.sigma = std::max(1.0f, r.I * minimum_sigma_in_regards_to_i);
-        if (I_sum > 0)
-            r.sigma = std::max(r.sigma, std::sqrt(static_cast<float>(I_sum)));
-        r.observed = true;
-    } else {
-        r.I = 0;
-        r.bkg = 0;
-        r.sigma = NAN;
-        r.observed = false;
-    }
-}
-
 template<class T>
 std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experiment,
                                           const CompressedImage &image,
-                                          const AzimuthalIntegrationMapping &mapping,
-                                          const AzimuthalIntegrationProfile &profile,
                                           const std::vector<Reflection> &predicted,
                                           size_t npredicted,
                                           int64_t special_value,
                                           int64_t saturation,
                                           int64_t image_number) {
+
     std::vector<Reflection> ret;
     ret.reserve(npredicted);
 
@@ -239,36 +164,24 @@ std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experimen
     std::vector<uint8_t> buffer;
     auto ptr = reinterpret_cast<const T *>(image.GetUncompressedPtr(buffer));
 
-    const float r_1 = settings.GetR1();
-    const float r_2 = settings.GetR2();
     const float r_3 = settings.GetR3();
-
-    const float r_1_sq = r_1 * r_1;
-    const float r_2_sq = r_2 * r_2;
-    const float r_3_sq = r_3 * r_3;
+    const float r_1_sq = settings.GetR1() * settings.GetR1();
+    const float r_2 = settings.GetR2();
+    const float r_2_sq = settings.GetR2() * settings.GetR2();
+    const float r_3_sq = settings.GetR3() * settings.GetR3();
 
     const float minimum_sigma_in_regards_to_i = settings.GetMinimumSigmaInRegardsToI();
     const auto reflection_mask = BuildReflectionMask(predicted, npredicted,
                                                      image.GetWidth(), image.GetHeight(),
                                                      r_2, r_2_sq);
 
-    const auto &pixel_to_bin = mapping.GetPixelToBin();
-    const auto p = profile.GetResult();
-
     for (int i = 0; i < npredicted; i++) {
         auto r = predicted.at(i);
-        if (settings.IsUseAzimProfile()) {
-            IntegrateReflectionAzim(r, ptr, image.GetWidth(), image.GetHeight(),
-                                    special_value, saturation,
-                                    r_1, r_1_sq, pixel_to_bin, p, minimum_sigma_in_regards_to_i);
-        } else {
-            IntegrateReflection(r, ptr, reflection_mask, image.GetWidth(), image.GetHeight(), special_value, saturation,
-                                r_3, r_1_sq, r_2_sq, r_3_sq, minimum_sigma_in_regards_to_i);
-        }
+        IntegrateReflection(r, ptr, reflection_mask, image.GetWidth(), image.GetHeight(), special_value, saturation,
+                            r_3, r_1_sq, r_2_sq, r_3_sq, minimum_sigma_in_regards_to_i);
         if (r.observed) {
             if (experiment.GetPolarizationFactor())
-                r.rlp /= geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y,
-                                                        experiment.GetPolarizationFactor().value());
+                r.rlp /= geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y, experiment.GetPolarizationFactor().value());
             r.image_scale_corr = r.rlp / r.partiality;
             r.image_number = static_cast<float>(image_number);
             ret.emplace_back(r);
@@ -280,8 +193,6 @@ std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experimen
 std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
                                          const CompressedImage &image,
                                          const std::vector<Reflection> &predicted,
-                                         const AzimuthalIntegrationMapping &mapping,
-                                         const AzimuthalIntegrationProfile &profile,
                                          size_t npredicted,
                                          int64_t image_number) {
     if (image.GetCompressedSize() == 0 || predicted.empty())
@@ -289,23 +200,17 @@ std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment
 
     switch (image.GetMode()) {
         case CompressedImageMode::Int8:
-            return IntegrateInternal<int8_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                             INT8_MIN, INT8_MAX, image_number);
+           return IntegrateInternal<int8_t>(experiment, image, predicted, npredicted, INT8_MIN, INT8_MAX, image_number);
         case CompressedImageMode::Int16:
-            return IntegrateInternal<int16_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                              INT16_MIN, INT16_MAX, image_number);
+            return IntegrateInternal<int16_t>(experiment, image, predicted, npredicted, INT16_MIN, INT16_MAX, image_number);
         case CompressedImageMode::Int32:
-            return IntegrateInternal<int32_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                              INT32_MIN, INT32_MAX, image_number);
+            return IntegrateInternal<int32_t>(experiment, image, predicted, npredicted, INT32_MIN, INT32_MAX, image_number);
         case CompressedImageMode::Uint8:
-            return IntegrateInternal<uint8_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                              UINT8_MAX, UINT8_MAX, image_number);
+            return IntegrateInternal<uint8_t>(experiment, image, predicted, npredicted, UINT8_MAX, UINT8_MAX, image_number);
         case CompressedImageMode::Uint16:
-            return IntegrateInternal<uint16_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                               UINT16_MAX, UINT16_MAX, image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, predicted, npredicted, UINT16_MAX, UINT16_MAX, image_number);
         case CompressedImageMode::Uint32:
-            return IntegrateInternal<uint32_t>(experiment, image, mapping, profile, predicted, npredicted,
-                                               UINT32_MAX, UINT32_MAX, image_number);
+            return IntegrateInternal<uint32_t>(experiment, image, predicted, npredicted, UINT32_MAX, UINT32_MAX, image_number);
         default:
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Image mode not supported");
diff --git a/image_analysis/bragg_integration/BraggIntegrate2D.h b/image_analysis/bragg_integration/BraggIntegrate2D.h
index 3045ff7d..353757b5 100644
--- a/image_analysis/bragg_integration/BraggIntegrate2D.h
+++ b/image_analysis/bragg_integration/BraggIntegrate2D.h
@@ -1,17 +1,17 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#pragma once
+#ifndef JFJOCH_BRAGGINTEGRATE2D_H
+#define JFJOCH_BRAGGINTEGRATE2D_H
 
 #include <vector>
 #include "../../common/DiffractionExperiment.h"
 #include "../../common/Reflection.h"
-#include "../../common/AzimuthalIntegrationProfile.h"
 
 std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
                                          const CompressedImage &image,
                                          const std::vector<Reflection> &predicted,
-                                         const AzimuthalIntegrationMapping &mapping,
-                                         const AzimuthalIntegrationProfile &profile,
                                          size_t npredicted,
-                                         int64_t image_number);
\ No newline at end of file
+                                         int64_t image_number);
+
+#endif //JFJOCH_BRAGGINTEGRATE2D_H
diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp
index 1aa8ce1e..64e82e33 100644
--- a/receiver/JFJochReceiver.cpp
+++ b/receiver/JFJochReceiver.cpp
@@ -31,8 +31,7 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
           serialmx_filter(in_experiment),
           numa_policy(in_numa_policy),
           pixel_mask(in_pixel_mask),
-          indexer(experiment, indexing_thread_pool),
-          az_int_mapping(experiment, pixel_mask) {
+          indexer(experiment, indexing_thread_pool) {
     logger.Info("Initializing receiver");
     // Ensure there is nothing running for now
     if (!image_buffer.Finalize(std::chrono::seconds(1)))
@@ -44,7 +43,13 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
     current_status.SetEfficiency({});
     current_status.SetStatus(JFJochReceiverStatus{}); // GetStatus() is virtual function and cannot be called yet!
 
-    plots.Setup(experiment, az_int_mapping);
+    auto start_time_point = std::chrono::steady_clock::now();
+    az_int_mapping = std::make_unique<AzimuthalIntegrationMapping>(experiment, pixel_mask);
+    auto end_time_point = std::chrono::steady_clock::now();
+    auto duration = std::chrono::duration<float>(end_time_point - start_time_point);
+    logger.Info("Azimuthal integration mapping done in {:.5f} s with {} threads", duration.count(), az_int_mapping->GetNThreads());
+
+    plots.Setup(experiment, *az_int_mapping);
 
     push_images_to_writer = (experiment.GetImageNum() > 0) && (!experiment.GetFilePrefix().empty());
 }
@@ -106,13 +111,13 @@ void JFJochReceiver::SendStartMessage() {
     StartMessage message{};
     experiment.FillMessage(message);
     message.arm_date = time_UTC(std::chrono::system_clock::now());
-    message.az_int_q_bin_count = az_int_mapping.GetQBinCount();
-    message.az_int_bin_to_q = az_int_mapping.GetBinToQ();
-    message.az_int_bin_to_two_theta = az_int_mapping.GetBinToTwoTheta();
-    message.az_int_phi_bin_count = az_int_mapping.GetAzimuthalBinCount();
-    if (az_int_mapping.GetAzimuthalBinCount() > 1) {
-        message.az_int_bin_to_phi = az_int_mapping.GetBinToPhi();
-        message.az_int_map = az_int_mapping.GetPixelToBin();
+    message.az_int_q_bin_count = az_int_mapping->GetQBinCount();
+    message.az_int_bin_to_q = az_int_mapping->GetBinToQ();
+    message.az_int_bin_to_two_theta = az_int_mapping->GetBinToTwoTheta();
+    message.az_int_phi_bin_count = az_int_mapping->GetAzimuthalBinCount();
+    if (az_int_mapping->GetAzimuthalBinCount() > 1) {
+        message.az_int_bin_to_phi = az_int_mapping->GetBinToPhi();
+        message.az_int_map = az_int_mapping->GetPixelToBin();
     }
     message.writer_notification_zmq_addr = image_pusher.GetWriterNotificationSocketAddress();
     message.rois = experiment.ROI().ExportMetadata();
diff --git a/receiver/JFJochReceiver.h b/receiver/JFJochReceiver.h
index 79be2802..83918987 100644
--- a/receiver/JFJochReceiver.h
+++ b/receiver/JFJochReceiver.h
@@ -80,7 +80,7 @@ protected:
     std::vector<std::unique_ptr<ADUHistogram>> adu_histogram_module;
     PixelMask pixel_mask;
 
-    AzimuthalIntegrationMapping az_int_mapping;
+    std::unique_ptr<AzimuthalIntegrationMapping> az_int_mapping;
 
     std::optional<uint64_t> max_delay;
     std::mutex max_delay_mutex;
diff --git a/receiver/JFJochReceiverFPGA.cpp b/receiver/JFJochReceiverFPGA.cpp
index a3ac6384..802b7faf 100644
--- a/receiver/JFJochReceiverFPGA.cpp
+++ b/receiver/JFJochReceiverFPGA.cpp
@@ -297,7 +297,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
     try {
         numa_policy.Bind(threadid);
-        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, indexer, az_int_mapping);
+        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, indexer);
     } catch (const JFJochException &e) {
         frame_transformation_ready.count_down();
         logger.Error("Thread setup error {}", e.what());
@@ -309,6 +309,9 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
     frame_transformation_ready.count_down();
 
+    uint16_t az_int_min_bin = std::floor(az_int_mapping->QToBin(experiment.GetLowQForBkgEstimate_recipA()));
+    uint16_t az_int_max_bin = std::ceil(az_int_mapping->QToBin(experiment.GetHighQForBkgEstimate_recipA()));
+
     int64_t image_number;
     while (images_to_go.Get(image_number) != 0) {
         try {
@@ -335,7 +338,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
 
             ImageMetadata metadata(experiment);
 
-            AzimuthalIntegrationProfile az_int_profile_image(az_int_mapping);
+            AzimuthalIntegrationProfile az_int_profile_image(*az_int_mapping);
 
             auto local_spot_finding_settings = GetSpotFindingSettings();
 
@@ -425,7 +428,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
                                             experiment.GetYPixelsNum(),
                                             experiment.GetImageMode(),
                                             CompressionAlgorithm::NO_COMPRESSION);
-            analyzer->Process(message, local_spot_finding_settings, az_int_profile_image);
+            analyzer->Process(message, local_spot_finding_settings);
 
             auto status = image_buffer.GetStatus();
             message.receiver_buf_available = status.available_slots;
@@ -678,5 +681,5 @@ void JFJochReceiverFPGA::LoadCalibrationToFPGA(uint16_t data_stream) {
     acquisition_device[data_stream].InitializeROIMap(experiment, roi_map);
 
     // Initialize data processing
-    acquisition_device[data_stream].InitializeDataProcessing(experiment, az_int_mapping);
+    acquisition_device[data_stream].InitializeDataProcessing(experiment, *az_int_mapping);
 }
diff --git a/receiver/JFJochReceiverLite.cpp b/receiver/JFJochReceiverLite.cpp
index 8c04b1cf..e986956e 100644
--- a/receiver/JFJochReceiverLite.cpp
+++ b/receiver/JFJochReceiverLite.cpp
@@ -242,7 +242,7 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
     measurement_started.wait();
 
     try {
-        analysis = std::make_unique<MXAnalysisWithoutFPGA>(experiment, az_int_mapping, pixel_mask, indexer);
+        analysis = std::make_unique<MXAnalysisWithoutFPGA>(experiment, *az_int_mapping, pixel_mask, indexer);
     } catch (const JFJochException &e) {
         Cancel(e);
         return;
@@ -279,7 +279,7 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
 
                 auto image_start_time = std::chrono::high_resolution_clock::now();
 
-                AzimuthalIntegrationProfile profile(az_int_mapping);
+                AzimuthalIntegrationProfile profile(*az_int_mapping);
                 analysis->Analyze(data_msg, profile, GetSpotFindingSettings());
 
                 auto image_end_time = std::chrono::high_resolution_clock::now();
diff --git a/tests/BraggIntegrate2DTest.cpp b/tests/BraggIntegrate2DTest.cpp
index 149515c0..75ba2a42 100644
--- a/tests/BraggIntegrate2DTest.cpp
+++ b/tests/BraggIntegrate2DTest.cpp
@@ -59,10 +59,6 @@ TEST_CASE("BraggIntegrate2D_RejectsReflectionsFromBackgroundUsingR2MaskAndMedian
     Reflection r1 = MakeReflection(10.0f, 10.0f);
     Reflection r2 = MakeReflection(16.0f, 10.0f);
 
-    PixelMask mask(experiment);
-    AzimuthalIntegrationMapping mapping(experiment, mask);
-    AzimuthalIntegrationProfile profile(mapping);
-
     for (int y = 0; y < static_cast<int>(height); y++) {
         for (int x = 0; x < static_cast<int>(width); x++) {
             auto &pixel = image_data[y * width + x];
@@ -78,7 +74,7 @@ TEST_CASE("BraggIntegrate2D_RejectsReflectionsFromBackgroundUsingR2MaskAndMedian
     CompressedImage image(image_data, width, height);
     std::vector<Reflection> predicted = {r1, r2};
 
-    auto integrated = BraggIntegrate2D(experiment, image, predicted, mapping, profile, predicted.size(), 17);
+    auto integrated = BraggIntegrate2D(experiment, image, predicted, predicted.size(), 17);
 
     REQUIRE(integrated.size() == 2);
 
diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index e6da83f2..7f169940 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -148,6 +148,8 @@ int main(int argc, char **argv) {
                     partiality_model = PartialityModel::Fixed;
                 else if (strcmp(optarg, "rot") == 0)
                     partiality_model = PartialityModel::Rotation;
+                else if (strcmp(optarg, "postref") == 0)
+                    partiality_model = PartialityModel::Postrefinement;
                 else {
                     logger.Error("Invalid partiality mode: {}", optarg);
                     print_usage();
-- 
2.52.0


From 7478c0390f6271988060bbecd4b2dc56cdf57e31 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 16:37:15 +0200
Subject: [PATCH 029/228] jfjoch_scale: Remove postrefinement model option

---
 tools/jfjoch_scale.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index 7f169940..e6da83f2 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -148,8 +148,6 @@ int main(int argc, char **argv) {
                     partiality_model = PartialityModel::Fixed;
                 else if (strcmp(optarg, "rot") == 0)
                     partiality_model = PartialityModel::Rotation;
-                else if (strcmp(optarg, "postref") == 0)
-                    partiality_model = PartialityModel::Postrefinement;
                 else {
                     logger.Error("Invalid partiality mode: {}", optarg);
                     print_usage();
-- 
2.52.0


From bd5fef7f61c3da61cb34b51f9a86f332f3e81408 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 10 Jun 2026 18:36:12 +0200
Subject: [PATCH 030/228] PixelRefine: Simplify (remove Lorentz correction,
 remove background from azimuthal integration)

---
 image_analysis/IndexAndRefine.cpp             |  32 +-
 image_analysis/IndexAndRefine.h               |  10 +-
 image_analysis/MXAnalysisWithoutFPGA.cpp      |   2 +-
 .../pixel_refinement/PixelRefine.cpp          | 474 ++++++++++--------
 image_analysis/pixel_refinement/PixelRefine.h |  52 +-
 viewer/JFJochImageReadingWorker.cpp           |  18 +-
 6 files changed, 316 insertions(+), 272 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 98b1aed6..4f3865c3 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -238,9 +238,7 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                                               const SpotFindingSettings &spot_finding_settings,
                                               const CompressedImage &image,
                                               BraggPrediction &prediction,
-                                              const IndexAndRefine::IndexingOutcome &outcome,
-                                              const AzimuthalIntegrationMapping *mapping,
-                                              const AzimuthalIntegrationProfile *profile) {
+                                              const IndexAndRefine::IndexingOutcome &outcome) {
     if (!outcome.lattice_candidate)
         return;
 
@@ -299,11 +297,11 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
     // integrated reflections that flow into the normal save/merge).
     const bool use_pixel_refine =
         experiment.GetIndexingSettings().GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::PixelRefine
-        && !pixel_reference_.empty() && mapping && profile;
+        && !pixel_reference_.empty();
 
     if (use_pixel_refine) {
         auto integration_start_time = std::chrono::steady_clock::now();
-        PixelRefineIntegrate(msg, image, prediction, outcome, *mapping, *profile, i_outcome);
+        PixelRefineIntegrate(msg, image, prediction, outcome, i_outcome);
         msg.integrated_reflections = i_outcome.reflections.size();
         auto integration_end_time = std::chrono::steady_clock::now();
         msg.integration_time_s = std::chrono::duration<float>(integration_end_time - integration_start_time).count();
@@ -356,9 +354,7 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
 void IndexAndRefine::ProcessImage(DataMessage &msg,
                                   const SpotFindingSettings &spot_finding_settings,
                                   const CompressedImage &image,
-                                  BraggPrediction &prediction,
-                                  const AzimuthalIntegrationMapping *mapping,
-                                  const AzimuthalIntegrationProfile *profile) {
+                                  BraggPrediction &prediction) {
     if (!indexer_ || !spot_finding_settings.indexing)
         return;
 
@@ -388,7 +384,7 @@ void IndexAndRefine::ProcessImage(DataMessage &msg,
     msg.lattice_type = outcome.symmetry;
 
     if (spot_finding_settings.quick_integration)
-        QuickPredictAndIntegrate(msg, spot_finding_settings, image, prediction, outcome, mapping, profile);
+        QuickPredictAndIntegrate(msg, spot_finding_settings, image, prediction, outcome);
 }
 
 std::optional<RotationIndexerResult> IndexAndRefine::FinalizeRotationIndexing() {
@@ -428,15 +424,13 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
                                           const CompressedImage &image,
                                           BraggPrediction &prediction,
                                           const IndexAndRefine::IndexingOutcome &outcome,
-                                          const AzimuthalIntegrationMapping &mapping,
-                                          const AzimuthalIntegrationProfile &profile,
                                           IntegrationOutcome &i_outcome) {
     if (!outcome.lattice_candidate)
         return false;
 
-    // Build the engine once (lazy: needs the azimuthal mapping, known only here).
+    // Build the engine once (lazy).
     std::call_once(pixel_refine_once_, [&] {
-        pixel_refine_ = std::make_unique<PixelRefine>(experiment, mapping, pixel_reference_);
+        pixel_refine_ = std::make_unique<PixelRefine>(experiment, pixel_reference_);
     });
     if (!pixel_refine_)
         return false;
@@ -455,17 +449,17 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {
         case CompressedImageMode::Int8:
-            pixel_refine_->Run(reinterpret_cast<const int8_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const int8_t *>(ptr), prediction, prd); break;
         case CompressedImageMode::Int16:
-            pixel_refine_->Run(reinterpret_cast<const int16_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const int16_t *>(ptr), prediction, prd); break;
         case CompressedImageMode::Int32:
-            pixel_refine_->Run(reinterpret_cast<const int32_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const int32_t *>(ptr), prediction, prd); break;
         case CompressedImageMode::Uint8:
-            pixel_refine_->Run(reinterpret_cast<const uint8_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const uint8_t *>(ptr), prediction, prd); break;
         case CompressedImageMode::Uint16:
-            pixel_refine_->Run(reinterpret_cast<const uint16_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const uint16_t *>(ptr), prediction, prd); break;
         case CompressedImageMode::Uint32:
-            pixel_refine_->Run(reinterpret_cast<const uint32_t *>(ptr), profile, prediction, prd); break;
+            pixel_refine_->Run(reinterpret_cast<const uint32_t *>(ptr), prediction, prd); break;
         default:
             return false;
     }
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index 7674392e..b8b3e9f2 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -65,9 +65,7 @@ class IndexAndRefine {
                                  const SpotFindingSettings &spot_finding_settings,
                                  const CompressedImage &image,
                                  BraggPrediction &prediction,
-                                 const IndexingOutcome &outcome,
-                                 const AzimuthalIntegrationMapping *mapping,
-                                 const AzimuthalIntegrationProfile *profile);
+                                 const IndexingOutcome &outcome);
 
     std::unique_ptr<ScaleOnTheFly> scaling_engine;
     void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
@@ -83,8 +81,6 @@ class IndexAndRefine {
                               const CompressedImage &image,
                               BraggPrediction &prediction,
                               const IndexingOutcome &outcome,
-                              const AzimuthalIntegrationMapping &mapping,
-                              const AzimuthalIntegrationProfile &profile,
                               IntegrationOutcome &i_outcome);
 public:
     IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer);
@@ -92,9 +88,7 @@ public:
     void AddImageToRotationIndexer(DataMessage &msg);
     void ForceRotationIndexerLattice(const CrystalLattice& lattice);
 
-    void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction,
-                      const AzimuthalIntegrationMapping *mapping = nullptr,
-                      const AzimuthalIntegrationProfile *profile = nullptr);
+    void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction);
     IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
 
     ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index 6a638213..7bade492 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -92,7 +92,7 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
         if (spot_finding_settings.indexing)
             indexer.ProcessImage(output, spot_finding_settings,
                 CompressedImage(preprocessor_buffer->getBuffer(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum()),
-                *prediction, &integration, &profile);
+                *prediction);
     }
 
     output.max_viable_pixel_value = ret.max_value;
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 225778f7..f41925b3 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -3,6 +3,11 @@
 
 #include "PixelRefine.h"
 
+#include <algorithm>
+#include <cmath>
+#include <limits>
+#include <vector>
+
 #include <Eigen/Dense>
 #include <ceres/ceres.h>
 #include <ceres/rotation.h>
@@ -11,17 +16,14 @@
 
 namespace {
 
-// Per-pixel observation, in *corrected* intensity units (solid-angle and
-// polarization correction already folded in, consistently for signal and
-// background). Geometry-independent quantities are precomputed here so that the
-// Ceres cost functor stays cheap.
+// Per-pixel observation, in *raw* detector counts (no per-pixel solid-angle or
+// polarization correction - same units the "normal" integrator works in; the
+// per-reflection polarization correction is applied via ReflGroup::pol).
 struct PixelObs {
     double x, y;          // detector pixel coordinate
-    double Iobs;          // corrected pixel value (signal + background)
-    double Ibkg;          // corrected background estimate (azimuthal bin mean)
+    double Iobs;          // raw pixel value (signal + background)
+    double Ibkg;          // local background estimate (per-shoebox level, raw counts)
     double weight;        // 1 / sigma_pixel
-    double A_recip;       // reciprocal-space area subtended by the pixel (Jacobian)
-    double angle_rad;     // goniometer angle of this observation
 };
 
 // One reflection together with the pixels of its shoebox.
@@ -30,6 +32,7 @@ struct ReflGroup {
     double d;
     double Itrue;             // reference intensity (held fixed)
     double R_bw_sq;           // bandwidth radial-width^2 contribution (0 = monochromatic)
+    double pol;               // per-reflection polarization correction (raw = true * pol)
     double predicted_x, predicted_y;
     std::vector<PixelObs> pixels;
 };
@@ -40,13 +43,99 @@ double SafeInv(double x, double fallback) {
     return 1.0 / x;
 }
 
+// Median of a vector (in place, partially reorders it).
+double MedianInPlace(std::vector<double> &v) {
+    if (v.empty())
+        return 0.0;
+    const size_t mid = v.size() / 2;
+    std::nth_element(v.begin(), v.begin() + mid, v.end());
+    if (v.size() % 2 == 1)
+        return v[mid];
+    const double hi = v[mid];
+    std::nth_element(v.begin(), v.begin() + mid - 1, v.begin() + mid);
+    return 0.5 * (v[mid - 1] + hi);
+}
+
+// Mask marking the *core* (radius `radius`) of every predicted spot, so that the
+// local-background sampling of one reflection never picks up a neighbouring
+// reflection's signal. Same idea as BraggIntegrate2D::BuildReflectionMask.
+std::vector<uint8_t> BuildSpotMask(const std::vector<Reflection> &predicted, int nrefl,
+                                   size_t xpixel, size_t ypixel, int radius) {
+    std::vector<uint8_t> mask(xpixel * ypixel, 0);
+    const double r_sq = static_cast<double>(radius) * radius;
+    for (int i = 0; i < nrefl; ++i) {
+        const auto &r = predicted[i];
+        const int cx = static_cast<int>(std::lround(r.predicted_x));
+        const int cy = static_cast<int>(std::lround(r.predicted_y));
+        const int x0 = std::max(0, cx - radius);
+        const int x1 = std::min<int>(static_cast<int>(xpixel) - 1, cx + radius);
+        const int y0 = std::max(0, cy - radius);
+        const int y1 = std::min<int>(static_cast<int>(ypixel) - 1, cy + radius);
+        for (int y = y0; y <= y1; ++y) {
+            for (int x = x0; x <= x1; ++x) {
+                const double dx = x - r.predicted_x;
+                const double dy = y - r.predicted_y;
+                if (dx * dx + dy * dy <= r_sq)
+                    mask[static_cast<size_t>(xpixel) * y + x] = 1;
+            }
+        }
+    }
+    return mask;
+}
+
+// Local flat background around one shoebox, in raw detector counts. Samples the
+// square ring shoebox_radius < max(|dx|,|dy|) <= bkg_outer_radius centred on the
+// spot, dropping pixels that belong to any spot core (spot_mask) or carry a
+// masked/saturated sentinel, and returns the median (robust to residual spot
+// tails / zingers). Mirrors the local-background of BraggIntegrate2D, replacing
+// the azimuthal-bin mean that proved a poor proxy for reflection background.
+template<class T>
+bool EstimateLocalBackground(const T *image,
+                             const std::vector<uint8_t> &spot_mask,
+                             size_t xpixel, size_t ypixel,
+                             double cx, double cy,
+                             int shoebox_radius, int bkg_outer_radius,
+                             double &bkg_mean) {
+    const int icx = static_cast<int>(std::lround(cx));
+    const int icy = static_cast<int>(std::lround(cy));
+    const int x0 = std::max(0, icx - bkg_outer_radius);
+    const int x1 = std::min<int>(static_cast<int>(xpixel) - 1, icx + bkg_outer_radius);
+    const int y0 = std::max(0, icy - bkg_outer_radius);
+    const int y1 = std::min<int>(static_cast<int>(ypixel) - 1, icy + bkg_outer_radius);
+
+    std::vector<double> vals;
+    vals.reserve(static_cast<size_t>((x1 - x0 + 1) * (y1 - y0 + 1)));
+    for (int y = y0; y <= y1; ++y) {
+        for (int x = x0; x <= x1; ++x) {
+            // Skip the square shoebox core: that is signal, not background.
+            if (std::abs(x - icx) <= shoebox_radius && std::abs(y - icy) <= shoebox_radius)
+                continue;
+            const size_t np = static_cast<size_t>(xpixel) * y + x;
+            if (spot_mask[np])
+                continue;
+            const T raw = image[np];
+            if (raw == std::numeric_limits<T>::max())
+                continue;
+            if (std::is_signed_v<T> && raw == std::numeric_limits<T>::min())
+                continue;
+            vals.push_back(static_cast<double>(raw));
+        }
+    }
+
+    if (vals.size() < 5)
+        return false;
+
+    bkg_mean = MedianInPlace(vals);
+    return true;
+}
+
 // Per-pixel: map a detector pixel through the current geometry into the
 // reference reciprocal frame. Cheap (a few trig + one rotation); depends on the
 // pixel and the detector geometry, not on the lattice.
 template<typename T>
 void ObservedRecip(const T *beam, const T *distance_mm, const T *detector_rot,
-                   const T *rotation_axis, double obs_x, double obs_y,
-                   double pixel_size, double inv_lambda, double angle_rad,
+                   double obs_x, double obs_y,
+                   double pixel_size, double inv_lambda,
                    Eigen::Matrix<T, 3, 1> &e_obs_recip) {
     // PyFAI convention (left-handed for rot1/rot2): rot3 = 0 assumed.
     const T c1 = ceres::cos(detector_rot[0]);
@@ -73,14 +162,7 @@ void ObservedRecip(const T *beam, const T *distance_mm, const T *detector_rot,
         y * inv_norm * T(inv_lambda),
         (z * inv_norm - T(1.0)) * T(inv_lambda)
     };
-    const T aa_back[3] = {
-        T(angle_rad) * rotation_axis[0],
-        T(angle_rad) * rotation_axis[1],
-        T(angle_rad) * rotation_axis[2]
-    };
-    T recip_obs[3];
-    ceres::AngleAxisRotatePoint(aa_back, recip_raw, recip_obs);
-    e_obs_recip = Eigen::Matrix<T, 3, 1>(recip_obs[0], recip_obs[1], recip_obs[2]);
+    e_obs_recip = Eigen::Matrix<T, 3, 1>(recip_raw[0], recip_raw[1], recip_raw[2]);
 }
 
 // Per-reflection: predicted node g_hkl, |g_hkl|^2, and the Ewald-sphere normal.
@@ -178,20 +260,23 @@ bool PredictedNode(const T *p0, const T *p1, const T *p2,
 // ---------------------------------------------------------------------------
 // Cost functor
 //
-//   I_pred(pixel) = G * Itrue * B_term * P_radial * P_tangential + I_bkg
+//   I_pred(pixel) = G * Itrue * B_term * P_radial * P_tangential * pol + I_bkg
 //
 //   B_term       = exp(-B |q|^2 / 4)                    (Debye-Waller)
 //   P_radial     = exp(-eps_r^2 / R0_eff^2)             (partiality: fraction of
 //                                                        the mosaic blob on the
 //                                                        Ewald sphere; <= 1)
-//   P_tangential = A_recip/(pi R1^2) * exp(-eps_t^2/R1^2)(spatial profile on the
-//                                                        detector, normalized so
-//                                                        that sum over pixels ~ 1)
+//   P_tangential = exp(-eps_t^2/R1^2) / (pi R1^2)       (Gaussian spatial profile
+//                                                        in the Ewald tangent plane)
+//   pol          = per-reflection polarization correction (raw = true * pol),
+//                  evaluated once at the predicted spot position (as in
+//                  BraggIntegrate2D). 1 if polarization is disabled.
 //
-// The tangential factor is what makes this "profile fitting": summing
-// I_pred - I_bkg over the shoebox reproduces G * Itrue * B_term * P_radial.
-// The 1/(pi R1^2) normalization is the missing piece that decouples the profile
-// width R1 from the overall scale G.
+// Everything is in *raw* detector counts: there is no per-pixel solid-angle or
+// area (Lorentz/Jacobian) weighting - each pixel counts equally, like the normal
+// integrator. The tangential factor is what makes this "profile fitting"; the
+// 1/(pi R1^2) normalization keeps the profile width R1 from soaking up the
+// overall scale G.
 //
 // X-ray bandwidth: a spread in lambda is a spread in the Ewald-sphere radius,
 // i.e. a purely *radial* thickening of the shell. It adds (in quadrature) a
@@ -207,13 +292,13 @@ struct PixelResidual {
     PixelResidual(const PixelObs &obs, double Itrue,
                   double lambda, double pixel_size,
                   double exp_h, double exp_k, double exp_l,
-                  double R_bw_sq,
+                  double R_bw_sq, double pol,
                   gemmi::CrystalSystem symmetry)
         : Itrue(Itrue), Iobs(obs.Iobs), Ibkg(obs.Ibkg), weight(obs.weight),
-          A_recip(obs.A_recip), obs_x(obs.x), obs_y(obs.y),
+          obs_x(obs.x), obs_y(obs.y),
           inv_lambda(1.0 / lambda), pixel_size(pixel_size),
           exp_h(exp_h), exp_k(exp_k), exp_l(exp_l),
-          R_bw_sq(R_bw_sq), angle_rad(obs.angle_rad), symmetry(symmetry) {
+          R_bw_sq(R_bw_sq), pol(pol), symmetry(symmetry) {
         if (std::fabs(lambda) < 1e-6)
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Lambda cannot be close to zero");
@@ -228,14 +313,14 @@ struct PixelResidual {
     bool GeometryTerms(const T *const beam,
                        const T *const distance_mm,
                        const T *const detector_rot,
-                       const T *const rotation_axis,
                        const T *const p0,
                        const T *const p1,
                        const T *const p2,
                        T &q_sq, T &eps_radial, T &eps_tang_sq) const {
         Eigen::Matrix<T, 3, 1> e_obs_recip;
-        ObservedRecip(beam, distance_mm, detector_rot, rotation_axis,
-                      obs_x, obs_y, pixel_size, inv_lambda, angle_rad, e_obs_recip);
+        ObservedRecip(beam, distance_mm, detector_rot,
+                      obs_x, obs_y, pixel_size, inv_lambda,
+                      e_obs_recip);
 
         Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
         if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
@@ -251,12 +336,12 @@ struct PixelResidual {
     // Assembles the full model intensity for the pixel from the geometry terms.
     template<typename T>
     bool Model(const T *const beam, const T *const distance_mm,
-               const T *const detector_rot, const T *const rotation_axis,
+               const T *const detector_rot,
                const T *const p0, const T *const p1, const T *const p2,
                const T *const scale_factor, const T *const B, const T *const R,
                T &Ipred) const {
         T q_sq, eps_radial, eps_tang_sq;
-        if (!GeometryTerms(beam, distance_mm, detector_rot, rotation_axis,
+        if (!GeometryTerms(beam, distance_mm, detector_rot,
                            p0, p1, p2, q_sq, eps_radial, eps_tang_sq))
             return false;
 
@@ -268,10 +353,9 @@ struct PixelResidual {
         // Separable Gaussian spot model:
         //   radial  P_r(e) = exp(-e^2/R0_eff^2)                      (peak-normalized, in (0,1])
         //   tangent g_t(e) = exp(-|e|^2/R1^2) / (pi R1^2)            [1/A^-2]
-        // The pixel captures the fraction g_t * A_recip of the tangential profile
-        // (A_recip = reciprocal area the pixel subtends; sum over shoebox ~ 1).
-        // The radial factor is the still-image partiality (how far the reflection
-        // sits from the Ewald sphere); the overall scale is carried by the free G.
+        // Every pixel counts equally (no area/Lorentz weighting); the radial factor
+        // is the still-image partiality (how far the reflection sits from the Ewald
+        // sphere); the overall scale is carried by the free G.
         //
         // IMPORTANT: the radial factor MUST use the same convention here as the
         // extraction's `partiality` (peak-normalized), otherwise image_scale_corr
@@ -280,10 +364,10 @@ struct PixelResidual {
         // R0_eff folds in the energy-bandwidth broadening via R_bw_sq.
         const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
         const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
-        const T P_tang = T(A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
+        const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1]))
                          / (T(M_PI) * R[1] * R[1]);
 
-        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
+        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
         Ipred = signal + T(Ibkg);
         return true;
     }
@@ -292,7 +376,6 @@ struct PixelResidual {
     bool operator()(const T *const beam,
                     const T *const distance_mm,
                     const T *const detector_rot,
-                    const T *const rotation_axis,
                     const T *const p0,
                     const T *const p1,
                     const T *const p2,
@@ -301,21 +384,20 @@ struct PixelResidual {
                     const T *const R,
                     T *residual) const {
         T Ipred;
-        if (!Model(beam, distance_mm, detector_rot, rotation_axis,
-                   p0, p1, p2, scale_factor, B, R, Ipred))
+        if (!Model(beam, distance_mm, detector_rot, p0, p1, p2, scale_factor, B, R, Ipred))
             return false;
 
         residual[0] = (Ipred - T(Iobs)) * T(weight);
         return true;
     }
 
-    const double Itrue, Iobs, Ibkg, weight, A_recip;
+    const double Itrue, Iobs, Ibkg, weight;
     const double obs_x, obs_y;
     const double inv_lambda;
     const double pixel_size;
     const double exp_h, exp_k, exp_l;
     const double R_bw_sq;   // bandwidth radial-width^2 contribution (0 = monochromatic)
-    const double angle_rad;
+    const double pol;       // per-reflection polarization correction
     gemmi::CrystalSystem symmetry;
 };
 
@@ -333,27 +415,25 @@ struct PixelResidual {
 struct ShoeboxResidual {
     ShoeboxResidual(const ReflGroup &g, double lambda, double pixel_size,
                     gemmi::CrystalSystem symmetry)
-        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq),
+        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq), pol(g.pol),
           exp_h(g.h), exp_k(g.k), exp_l(g.l),
           inv_lambda(1.0 / lambda), pixel_size(pixel_size),
-          angle_rad(g.pixels.empty() ? 0.0 : g.pixels.front().angle_rad),
           symmetry(symmetry) {}
 
     template<typename T>
     bool operator()(const T *const *params, T *residual) const {
         // Parameter blocks (order matches AddParameterBlock in Run):
-        // 0 beam[2] 1 distance[1] 2 detector_rot[2] 3 rotation_axis[3]
-        // 4 p0[3] 5 p1[3] 6 p2[3] 7 scale[1] 8 B[1] 9 R[2]
+        // 0 beam[2] 1 distance[1] 2 detector_rot[2]
+        // 3 p0[3] 4 p1[3] 5 p2[3] 6 scale[1] 7 B[1] 8 R[2]
         const T *beam = params[0];
         const T *distance_mm = params[1];
         const T *detector_rot = params[2];
-        const T *rotation_axis = params[3];
-        const T *p0 = params[4];
-        const T *p1 = params[5];
-        const T *p2 = params[6];
-        const T *scale_factor = params[7];
-        const T *B = params[8];
-        const T *R = params[9];
+        const T *p0 = params[3];
+        const T *p1 = params[4];
+        const T *p2 = params[5];
+        const T *scale_factor = params[6];
+        const T *B = params[7];
+        const T *R = params[8];
 
         if (R[0] < T(1e-10) || R[1] < T(1e-10))
             return false;
@@ -373,18 +453,18 @@ struct ShoeboxResidual {
             const PixelObs &obs = pixels[i];
 
             Eigen::Matrix<T, 3, 1> e_obs_recip;
-            ObservedRecip(beam, distance_mm, detector_rot, rotation_axis,
-                          obs.x, obs.y, pixel_size, inv_lambda, angle_rad, e_obs_recip);
+            ObservedRecip(beam, distance_mm, detector_rot,
+                          obs.x, obs.y, pixel_size, inv_lambda,  e_obs_recip);
 
             const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
             const T eps_radial = delta_q.dot(n_radial);
             const T eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
 
             const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
-            const T P_tang = T(obs.A_recip) * ceres::exp(-eps_tang_sq / (R[1] * R[1]))
+            const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1]))
                              / (T(M_PI) * R[1] * R[1]);
 
-            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang;
+            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
             const T Ipred = signal + T(obs.Ibkg);
             residual[i] = (Ipred - T(obs.Iobs)) * T(obs.weight);
         }
@@ -392,17 +472,15 @@ struct ShoeboxResidual {
     }
 
     std::vector<PixelObs> pixels;
-    const double Itrue, R_bw_sq;
+    const double Itrue, R_bw_sq, pol;
     const double exp_h, exp_k, exp_l;
-    const double inv_lambda, pixel_size, angle_rad;
+    const double inv_lambda, pixel_size;
     gemmi::CrystalSystem symmetry;
 };
 
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
-                         const AzimuthalIntegrationMapping &mapping,
                          const std::vector<MergedReflection> &reference)
-    : mapping(mapping),
-      xpixel(experiment.GetXPixelsNum()),
+    : xpixel(experiment.GetXPixelsNum()),
       ypixel(experiment.GetYPixelsNum()),
       experiment(experiment),
       hkl_key_generator(experiment.GetScalingSettings().GetMergeFriedel(),
@@ -413,19 +491,13 @@ PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
 
 void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
                                        double beam[2], double &dist_mm,
-                                       double detector_rot[2], double rot_vec[3],
+                                       double detector_rot[2],
                                        double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const {
     beam[0] = data.geom.GetBeamX_pxl();
     beam[1] = data.geom.GetBeamY_pxl();
     dist_mm = data.geom.GetDetectorDistance_mm();
     detector_rot[0] = data.geom.GetPoniRot1_rad();
     detector_rot[1] = data.geom.GetPoniRot2_rad();
-    rot_vec[0] = 1.0; rot_vec[1] = 0.0; rot_vec[2] = 0.0;
-    if (auto axis = data.geom.GetRotation()) {
-        rot_vec[0] = axis->GetAxis().x;
-        rot_vec[1] = axis->GetAxis().y;
-        rot_vec[2] = axis->GetAxis().z;
-    }
 
     for (int i = 0; i < 3; ++i)
         latt_vec0[i] = latt_vec1[i] = latt_vec2[i] = 0.0;
@@ -463,7 +535,6 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
 
 template<class T>
 void PixelRefine::Run(const T *image,
-                      const AzimuthalIntegrationProfile &profile,
                       BraggPrediction &prediction,
                       PixelRefineData &data) {
     data.solved = false;
@@ -479,29 +550,17 @@ void PixelRefine::Run(const T *image,
         .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
     };
 
-    const auto azim_result = profile.GetResult();
-    const auto azim_std = profile.GetStd();
-    const auto &pixel_to_bin = mapping.GetPixelToBin();
-    const auto &corrections = mapping.Corrections();
-    // pixel_to_bin stores the *full* bin index (azimuthal_sector * q_bins + q_bin),
-    // so the valid range is the total number of bins, i.e. the profile size - NOT
-    // GetAzimuthalBinCount() (which is only the number of azimuthal sectors).
-    const int total_bin_count = static_cast<int>(azim_result.size());
-
-    const double angle_rad = data.angle_deg * M_PI / 180.0;
     const int radius = data.shoebox_radius;
+    const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
 
-    // Exact reciprocal-space area a 1x1 pixel subtends, |dq/dx x dq/dy|, via
-    // finite differences of the detector->reciprocal map. This is the Jacobian
-    // between the curved Ewald-sphere sampling and flat reciprocal space, and it
-    // is exactly the geometric factor that plays the role of the Lorentz factor
-    // for stills: where the sphere grazes reciprocal space obliquely, a pixel
-    // covers more reciprocal volume and the captured fraction grows. It tracks
-    // the refined geometry because it reads the current data.geom each iteration.
-    auto recip_area = [&](double x, double y) -> double {
-        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
-        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
-        return (qx % qy).Length();
+    // Per-reflection polarization correction (raw = true * pol), evaluated once at
+    // the predicted spot - same handling as BraggIntegrate2D. Identity if disabled.
+    const auto pol_factor = experiment.GetPolarizationFactor();
+    auto polarization = [&](double x, double y) -> double {
+        if (!pol_factor)
+            return 1.0;
+        return data.geom.CalcAzIntPolarizationCorr(static_cast<float>(x), static_cast<float>(y),
+                                                   pol_factor.value());
     };
 
     // Bandwidth radial-width^2 (in the code's R = sqrt(2)*sigma convention):
@@ -524,7 +583,6 @@ void PixelRefine::Run(const T *image,
     double beam[2] = {0, 0};
     double dist_mm = data.geom.GetDetectorDistance_mm();
     double detector_rot[2] = {0, 0};
-    double rot_vec[3] = {1.0, 0.0, 0.0};
     double latt_vec0[3] = {0, 0, 0}; // orientation (Rodrigues)
     double latt_vec1[3] = {0, 0, 0}; // lengths
     double latt_vec2[3] = {0, 0, 0}; // angles (rad)
@@ -546,12 +604,27 @@ void PixelRefine::Run(const T *image,
         // nrefl entries are valid for this image (the rest are stale/zeroed).
         groups.clear();
         const auto &predicted = prediction.GetReflections();
+
+        // Spot-core mask over ALL predicted reflections, so each reflection's
+        // local background ignores pixels that belong to a neighbouring spot.
+        const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
+
         for (int ri = 0; ri < nrefl; ++ri) {
             const auto &refl = predicted[ri];
             const auto hkl = hkl_key_generator(refl);
             if (!reference_data.contains(hkl))
                 continue;
 
+            // Local flat background from the ring around the shoebox (raw counts).
+            // No azimuthal fallback: if we cannot estimate a clean local background
+            // the reflection is dropped, exactly as BraggIntegrate2D marks it
+            // unobserved when fewer than a handful of background pixels survive.
+            double Ibkg = 0.0;
+            if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                         refl.predicted_x, refl.predicted_y,
+                                         radius, bkg_outer_radius, Ibkg))
+                continue;
+
             ReflGroup g;
             g.h = refl.h;
             g.k = refl.k;
@@ -559,6 +632,7 @@ void PixelRefine::Run(const T *image,
             g.d = refl.d;
             g.Itrue = reference_data[hkl];
             g.R_bw_sq = bandwidth_radial_sq(refl.d);
+            g.pol = polarization(refl.predicted_x, refl.predicted_y);
             g.predicted_x = refl.predicted_x;
             g.predicted_y = refl.predicted_y;
 
@@ -570,27 +644,18 @@ void PixelRefine::Run(const T *image,
             for (int y = min_y; y <= max_y; ++y) {
                 for (int x = min_x; x <= max_x; ++x) {
                     const size_t npixel = xpixel * y + x;
-                    const int azim_bin = pixel_to_bin[npixel];
 
-                    // Skip pixels not mapped to a bin or carrying a sentinel
-                    // (masked / saturated) value. We assume the pixel mask is
-                    // already applied upstream.
-                    if (azim_bin >= total_bin_count)
-                        continue;
+                    // Skip sentinel (masked / saturated) pixels. We assume the pixel
+                    // mask is already applied upstream (encoded as the sentinel).
                     if (image[npixel] == std::numeric_limits<T>::max())
                         continue;
                     if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
                         continue;
 
-                    const double correction = corrections[npixel];
-                    const double Ibkg = azim_result[azim_bin]; // already in corrected units
-                    const double Ibkg_sigma = azim_std[azim_bin];
-                    const double raw = static_cast<double>(image[npixel]);
-                    const double Iobs = raw * correction;
+                    const double Iobs = static_cast<double>(image[npixel]); // raw counts
 
-                    // Per-pixel variance: Poisson noise of the corrected counts
-                    // (var(c*N) = c^2 * N = c * Iobs) plus the background spread.
-                    double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
+                    // Per-pixel variance: Poisson noise of the raw counts.
+                    double var = std::max(Iobs, 0.0);
                     if (!(var > 1.0))
                         var = 1.0;
 
@@ -599,9 +664,7 @@ void PixelRefine::Run(const T *image,
                         .y = static_cast<double>(y),
                         .Iobs = Iobs,
                         .Ibkg = Ibkg,
-                        .weight = 1.0 / std::sqrt(var),
-                        .A_recip = recip_area(x, y),
-                        .angle_rad = angle_rad
+                        .weight = 1.0 / std::sqrt(var)
                     };
                     g.pixels.push_back(obs);
                 }
@@ -615,7 +678,7 @@ void PixelRefine::Run(const T *image,
             return;
 
         // ---- 3. Set up parameter blocks (geometry part mirrors XtalOptimizer) -
-        BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec,
+        BuildParameterBlocks(data, beam, dist_mm, detector_rot,
                              latt_vec0, latt_vec1, latt_vec2);
 
         // ---- 4. Build the problem ---------------------------------------------
@@ -630,7 +693,6 @@ void PixelRefine::Run(const T *image,
             cost->AddParameterBlock(2); // beam
             cost->AddParameterBlock(1); // distance
             cost->AddParameterBlock(2); // detector_rot
-            cost->AddParameterBlock(3); // rotation_axis
             cost->AddParameterBlock(3); // p0 (orientation)
             cost->AddParameterBlock(3); // p1 (lengths)
             cost->AddParameterBlock(3); // p2 (angles)
@@ -643,7 +705,7 @@ void PixelRefine::Run(const T *image,
             // per-pixel Huber. Per-pixel sigma weighting is retained; per-pixel
             // outlier rejection (zingers) is a TODO if needed.
             problem.AddResidualBlock(cost, nullptr,
-                                     beam, &dist_mm, detector_rot, rot_vec,
+                                     beam, &dist_mm, detector_rot,
                                      latt_vec0, latt_vec1, latt_vec2,
                                      &data.scale_factor, &data.B_factor, data.R);
             residual_pixels += g.pixels.size();
@@ -687,9 +749,6 @@ void PixelRefine::Run(const T *image,
             }
         }
 
-        if (!data.refine_rotation_axis)
-            problem.SetParameterBlockConstant(rot_vec);
-
         if (data.refine_scale)
             problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
         else
@@ -767,20 +826,20 @@ void PixelRefine::Run(const T *image,
     } // predict<->refine iterations
 
     // ---- Extract integrated reflections ---------------------------------------
-    // Profile fitting gives the recorded amplitude (against the normalized
-    // tangential profile P_t):
+    // Profile fitting gives the recorded amplitude (against the tangential profile
+    // P_t):
     //     J      = sum_p[ P_t,p (Iobs_p - Ibkg_p)/v_p ] / sum_p[ P_t,p^2 / v_p ]
-    //            ~ G * Itrue * B_term * partiality            (recorded intensity)
+    //            ~ G * Itrue * B_term * partiality * pol     (recorded raw counts)
     //     var(J) = 1 / sum_p[ P_t,p^2 / v_p ]
     //
     // Output split (Merge multiplies r.I * image_scale_corr and weights by
     // 1/(sigma*image_scale_corr)^2 - see Merge.cpp):
-    //   r.I              = J / (B_term * partiality)   = G * Itrue  (B/partiality corrected)
-    //   r.sigma          = sqrt(var(J)) / (B_term * partiality)
+    //   r.I              = J / (B_term * partiality * pol) = G * Itrue
+    //   r.sigma          = sqrt(var(J)) / (B_term * partiality * pol)
     //   r.partiality     = profile-weighted peak radial factor in (0,1]  (Merge filter only)
     //   r.image_scale_corr = 1/G                         (per-image scale ONLY)
-    // so r.I * image_scale_corr = Itrue. B and partiality live on the intensity,
-    // G lives on image_scale_corr - one clean meaning per field.
+    // so r.I * image_scale_corr = Itrue. B, partiality and polarization live on the
+    // intensity, G lives on image_scale_corr - one clean meaning per field.
     data.reflections.reserve(groups.size());
     for (const auto &g : groups) {
         double num = 0.0, den = 0.0, bkg_sum = 0.0;
@@ -788,16 +847,16 @@ void PixelRefine::Run(const T *image,
         size_t n = 0;
 
         for (const auto &obs : g.pixels) {
-            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, g.R_bw_sq, data.crystal_system);
+            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, g.R_bw_sq, g.pol, data.crystal_system);
             double q_sq, eps_r, eps_t_sq;
-            if (!pr.GeometryTerms(beam, &dist_mm, detector_rot, rot_vec,
-                                  latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+            if (!pr.GeometryTerms(beam, &dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2, q_sq,
+                eps_r, eps_t_sq))
                 continue;
             if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
                 continue;
 
-            // Normalized tangential profile (sum over shoebox ~ 1) -> fit weight.
-            const double P_t = obs.A_recip * std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
+            // Tangential profile shape -> fit weight (every pixel counts equally).
+            const double P_t = std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
                                / (M_PI * data.R[1] * data.R[1]);
             // Peak-normalized radial factor (the partiality), in (0,1].
             // Bandwidth-broadened radial width, matching the model in Model().
@@ -828,10 +887,10 @@ void PixelRefine::Run(const T *image,
         r.partiality = (radial_w > 0.0) ? static_cast<float>(radial_sum / radial_w) : 1.0f;
 
         if (den > 0.0 && n > 0) {
-            const double I_amp = num / den;             // ~ G*Itrue*B_term*partiality
+            const double I_amp = num / den;             // ~ G*Itrue*B_term*partiality*pol
             const double sigma_amp = std::sqrt(1.0 / den);
             const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
-            const double corr = static_cast<double>(r.partiality) * B_term; // B & partiality
+            const double corr = static_cast<double>(r.partiality) * B_term * g.pol; // B, partiality & pol
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
 
@@ -884,7 +943,8 @@ void PixelRefine::Run(const T *image,
     }
 }
 
-std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &profile,
+template<class T>
+std::vector<float> PixelRefine::PredictImage(const T *image,
                                              BraggPrediction &prediction,
                                              const PixelRefineData &data,
                                              bool include_background) const {
@@ -892,18 +952,16 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
 
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
-    const auto azim_result = profile.GetResult();
-    const auto &pixel_to_bin = mapping.GetPixelToBin();
-    const auto &corrections = mapping.Corrections();
-    const int total_bin_count = static_cast<int>(azim_result.size());
-    const double angle_rad = data.angle_deg * M_PI / 180.0;
     const int radius = data.shoebox_radius;
+    const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
     const double bw = data.bandwidth;
 
-    auto recip_area = [&](double x, double y) -> double {
-        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
-        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
-        return (qx % qy).Length();
+    const auto pol_factor = experiment.GetPolarizationFactor();
+    auto polarization = [&](double x, double y) -> double {
+        if (!pol_factor)
+            return 1.0;
+        return data.geom.CalcAzIntPolarizationCorr(static_cast<float>(x), static_cast<float>(y),
+                                                   pol_factor.value());
     };
     auto bandwidth_radial_sq = [&](double d) -> double {
         if (bw <= 0.0 || d <= 0.0)
@@ -912,26 +970,9 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
         return bl * bl / (2.0 * d * d * d * d);
     };
 
-    // The model works in solid-angle/polarization-corrected units (as in Run,
-    // where Iobs = raw * correction). Map back to raw detector units (/ correction)
-    // so the predicted image overlays directly on the original image.
-    auto to_raw = [&](size_t npixel, double corrected) -> float {
-        const double corr = corrections[npixel];
-        return (corr > 0.0) ? static_cast<float>(corrected / corr) : 0.0f;
-    };
-
-    // Background base layer (per-pixel azimuthal mean), full-frame pass.
-    if (include_background) {
-        for (size_t p = 0; p < img.size(); ++p) {
-            const int bin = pixel_to_bin[p];
-            if (bin >= 0 && bin < total_bin_count)
-                img[p] = to_raw(p, azim_result[bin]);
-        }
-    }
-
-    double beam[2], dist_mm, detector_rot[2], rot_vec[3];
+    double beam[2], dist_mm, detector_rot[2];
     double latt_vec0[3], latt_vec1[3], latt_vec2[3];
-    BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec, latt_vec0, latt_vec1, latt_vec2);
+    BuildParameterBlocks(data, beam, dist_mm, detector_rot,  latt_vec0, latt_vec1, latt_vec2);
 
     DiffractionExperiment exp_iter = experiment;
     exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
@@ -948,6 +989,7 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
     };
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
+    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
 
     for (int ri = 0; ri < nrefl; ++ri) {
         const auto &refl = predicted[ri];
@@ -957,6 +999,16 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
 
         const double Itrue = it->second;
         const double R_bw_sq = bandwidth_radial_sq(refl.d);
+        const double pol = polarization(refl.predicted_x, refl.predicted_y);
+
+        // Local background straight from the actual image (flat per shoebox), laid
+        // into the box so the prediction overlays the real frame - the same model
+        // path Run() fits, now reproduced faithfully because we have the image.
+        double Ibkg = 0.0;
+        const bool have_bkg = include_background &&
+            EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                    refl.predicted_x, refl.predicted_y,
+                                    radius, bkg_outer_radius, Ibkg);
 
         const int min_y = std::max<int>(refl.predicted_y - radius, 0);
         const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
@@ -967,25 +1019,21 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
             for (int x = min_x; x <= max_x; ++x) {
                 const size_t npixel = xpixel * y + x;
 
-                // Pure Bragg signal: Ibkg = 0 so Model() returns signal only; the
-                // background is already laid down above. Same code path as Run.
                 PixelObs obs{
                     .x = static_cast<double>(x),
                     .y = static_cast<double>(y),
                     .Iobs = 0.0,
-                    .Ibkg = 0.0,
-                    .weight = 1.0,
-                    .A_recip = recip_area(x, y),
-                    .angle_rad = angle_rad
+                    .Ibkg = have_bkg ? Ibkg : 0.0,
+                    .weight = 1.0
                 };
                 PixelResidual pr(obs, Itrue, lambda, pixel_size,
-                                 refl.h, refl.k, refl.l, R_bw_sq, data.crystal_system);
+                                 refl.h, refl.k, refl.l, R_bw_sq, pol, data.crystal_system);
 
-                double signal = 0.0;
-                if (pr.Model(beam, &dist_mm, detector_rot, rot_vec,
+                double Ipred = 0.0; // raw counts: signal (+ local background)
+                if (pr.Model(beam, &dist_mm, detector_rot,
                              latt_vec0, latt_vec1, latt_vec2,
-                             &data.scale_factor, &data.B_factor, data.R, signal))
-                    img[npixel] += to_raw(npixel, signal);
+                             &data.scale_factor, &data.B_factor, data.R, Ipred))
+                    img[npixel] += static_cast<float>(Ipred);
             }
         }
     }
@@ -995,26 +1043,22 @@ std::vector<float> PixelRefine::PredictImage(const AzimuthalIntegrationProfile &
 
 template<class T>
 std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
-                                                const AzimuthalIntegrationProfile &profile,
                                                 BraggPrediction &prediction,
                                                 const PixelRefineData &data) const {
     std::vector<float> img(xpixel * ypixel, 0.0f);
 
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
-    const auto azim_result = profile.GetResult();
-    const auto azim_std = profile.GetStd();
-    const auto &pixel_to_bin = mapping.GetPixelToBin();
-    const auto &corrections = mapping.Corrections();
-    const int total_bin_count = static_cast<int>(azim_result.size());
-    const double angle_rad = data.angle_deg * M_PI / 180.0;
     const int radius = data.shoebox_radius;
+    const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
     const double bw = data.bandwidth;
 
-    auto recip_area = [&](double x, double y) -> double {
-        const Coord qx = data.geom.DetectorToRecip(x + 0.5, y) - data.geom.DetectorToRecip(x - 0.5, y);
-        const Coord qy = data.geom.DetectorToRecip(x, y + 0.5) - data.geom.DetectorToRecip(x, y - 0.5);
-        return (qx % qy).Length();
+    const auto pol_factor = experiment.GetPolarizationFactor();
+    auto polarization = [&](double x, double y) -> double {
+        if (!pol_factor)
+            return 1.0;
+        return data.geom.CalcAzIntPolarizationCorr(static_cast<float>(x), static_cast<float>(y),
+                                                   pol_factor.value());
     };
     auto bandwidth_radial_sq = [&](double d) -> double {
         if (bw <= 0.0 || d <= 0.0)
@@ -1023,9 +1067,9 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
         return bl * bl / (2.0 * d * d * d * d);
     };
 
-    double beam[2], dist_mm, detector_rot[2], rot_vec[3];
+    double beam[2], dist_mm, detector_rot[2];
     double latt_vec0[3], latt_vec1[3], latt_vec2[3];
-    BuildParameterBlocks(data, beam, dist_mm, detector_rot, rot_vec, latt_vec0, latt_vec1, latt_vec2);
+    BuildParameterBlocks(data, beam, dist_mm, detector_rot,  latt_vec0, latt_vec1, latt_vec2);
 
     DiffractionExperiment exp_iter = experiment;
     exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
@@ -1042,6 +1086,7 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
     };
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
+    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
 
     for (int ri = 0; ri < nrefl; ++ri) {
         const auto &refl = predicted[ri];
@@ -1051,6 +1096,15 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
 
         const double Itrue = it->second;
         const double R_bw_sq = bandwidth_radial_sq(refl.d);
+        const double pol = polarization(refl.predicted_x, refl.predicted_y);
+
+        // Local flat background, identical to Run(); skip the reflection if it
+        // cannot be estimated (matches Run() dropping the reflection).
+        double Ibkg = 0.0;
+        if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                     refl.predicted_x, refl.predicted_y,
+                                     radius, bkg_outer_radius, Ibkg))
+            continue;
 
         const int min_y = std::max<int>(refl.predicted_y - radius, 0);
         const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
@@ -1060,23 +1114,16 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
         for (int y = min_y; y <= max_y; ++y) {
             for (int x = min_x; x <= max_x; ++x) {
                 const size_t npixel = xpixel * y + x;
-                const int azim_bin = pixel_to_bin[npixel];
 
                 // Same gating as Run(): only pixels that actually enter the fit.
-                if (azim_bin >= total_bin_count)
-                    continue;
                 if (image[npixel] == std::numeric_limits<T>::max())
                     continue;
                 if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
                     continue;
 
-                const double correction = corrections[npixel];
-                const double Ibkg = azim_result[azim_bin];
-                const double Ibkg_sigma = azim_std[azim_bin];
-                const double raw = static_cast<double>(image[npixel]);
-                const double Iobs = raw * correction;
+                const double Iobs = static_cast<double>(image[npixel]); // raw counts
 
-                double var = correction * std::max(Iobs, 0.0) + Ibkg_sigma * Ibkg_sigma;
+                double var = std::max(Iobs, 0.0);
                 if (!(var > 1.0))
                     var = 1.0;
                 const double weight = 1.0 / std::sqrt(var);
@@ -1086,15 +1133,13 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
                     .y = static_cast<double>(y),
                     .Iobs = Iobs,
                     .Ibkg = Ibkg,
-                    .weight = weight,
-                    .A_recip = recip_area(x, y),
-                    .angle_rad = angle_rad
+                    .weight = weight
                 };
                 PixelResidual pr(obs, Itrue, lambda, pixel_size,
-                                 refl.h, refl.k, refl.l, R_bw_sq, data.crystal_system);
+                                 refl.h, refl.k, refl.l, R_bw_sq, pol, data.crystal_system);
 
                 double Ipred = 0.0;
-                if (pr.Model(beam, &dist_mm, detector_rot, rot_vec,
+                if (pr.Model(beam, &dist_mm, detector_rot,
                              latt_vec0, latt_vec1, latt_vec2,
                              &data.scale_factor, &data.B_factor, data.R, Ipred)) {
                     // residual_i = (I_pred - I_obs) * weight (== Ceres residual);
@@ -1110,16 +1155,23 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
 }
 
 // Explicit instantiations for the supported (uncompressed) image pixel types.
-template void PixelRefine::Run<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
-template void PixelRefine::Run<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
-template void PixelRefine::Run<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
-template void PixelRefine::Run<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
-template void PixelRefine::Run<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
-template void PixelRefine::Run<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<int8_t>(const int8_t *, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<int16_t>(const int16_t *, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<int32_t>(const int32_t *, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint8_t>(const uint8_t *, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint16_t>(const uint16_t *, BraggPrediction &, PixelRefineData &);
+template void PixelRefine::Run<uint32_t>(const uint32_t *, BraggPrediction &, PixelRefineData &);
 
-template std::vector<float> PixelRefine::ChiSquaredImage<int8_t>(const int8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<int16_t>(const int16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<int32_t>(const int32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint8_t>(const uint8_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint16_t>(const uint16_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint32_t>(const uint32_t *, const AzimuthalIntegrationProfile &, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::PredictImage<int8_t>(const int8_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+template std::vector<float> PixelRefine::PredictImage<int16_t>(const int16_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+template std::vector<float> PixelRefine::PredictImage<int32_t>(const int32_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+template std::vector<float> PixelRefine::PredictImage<uint8_t>(const uint8_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+template std::vector<float> PixelRefine::PredictImage<uint16_t>(const uint16_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+template std::vector<float> PixelRefine::PredictImage<uint32_t>(const uint32_t *, BraggPrediction &, const PixelRefineData &, bool) const;
+
+template std::vector<float> PixelRefine::ChiSquaredImage<int8_t>(const int8_t *, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<int16_t>(const int16_t *, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<int32_t>(const int32_t *, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint8_t>(const uint8_t *, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint16_t>(const uint16_t *, BraggPrediction &, const PixelRefineData &) const;
+template std::vector<float> PixelRefine::ChiSquaredImage<uint32_t>(const uint32_t *, BraggPrediction &, const PixelRefineData &) const;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 73a63094..8d28e107 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -5,8 +5,6 @@
 
 #include "../bragg_prediction/BraggPrediction.h"
 #include "../common/DiffractionExperiment.h"
-#include "../common/AzimuthalIntegrationMapping.h"
-#include "../common/AzimuthalIntegrationProfile.h"
 #include "../scale_merge/HKLKey.h"
 
 // =============================================================================
@@ -33,7 +31,10 @@
 // squares problem. We write down, for every pixel in a reflection's shoebox, the
 // expected counts as an explicit forward model
 //
-//     I_pred(pixel) = G * I_true * B_term * P_radial * P_tangential + I_bkg
+//     I_pred(pixel) = G * I_true * B_term * P_radial * P_tangential * pol + I_bkg
+//
+// in raw detector counts (pol = per-reflection polarization correction, I_bkg =
+// local per-shoebox background read from the image).
 //
 // and let Ceres autodiff back-propagate the per-pixel residuals into ALL of:
 //   * detector geometry  (beam centre, distance, tilt)
@@ -95,8 +96,11 @@
 // (bandwidth = 0, monochromatic); set it for DMM-type data, leave it for Si.
 //
 // Status: experimental prototype. The forward model (esp. the still-image
-// Lorentz/partiality normalization) is deliberately simple and expected to
-// evolve. See PixelRefine.cpp for the physics conventions and known caveats.
+// partiality normalization) is deliberately simple and expected to evolve: it
+// works in raw detector counts with a local per-shoebox background and a
+// per-reflection polarization correction (no per-pixel solid-angle/Lorentz
+// weighting), matching the classical integrator. See PixelRefine.cpp for the
+// physics conventions and known caveats.
 // =============================================================================
 
 struct PixelRefineData {
@@ -115,23 +119,23 @@ struct PixelRefineData {
     // to R[0]. 0 = monochromatic (the term switches off entirely).
     double bandwidth = 0.0;
 
-    // Goniometer: for a still image keep angle_deg = 0. For a wedge, pass the
-    // angle (deg) of the slice centre relative to the reference (phi=0) frame.
-    double angle_deg = 0.0;
-
     // --- what to refine ---
     bool refine_orientation     = true;  // crystal orientation (p0)
     bool refine_unit_cell       = false; // cell lengths + angles
     bool refine_beam_center     = false;
     bool refine_distance        = false;
     bool refine_detector_angles = false;
-    bool refine_rotation_axis   = false;
     bool refine_scale           = true;
     bool refine_B               = false;
     bool refine_R               = true;
 
     double max_time_s = 5.0;
-    int    shoebox_radius = 3; // half-size of the per-reflection pixel box
+    int    shoebox_radius = 3; // half-size of the per-reflection signal box (peak region that enters the fit)
+    // Half-size of the local-background sampling box. Background is estimated from
+    // the ring shoebox_radius < |dx|,|dy| <= bkg_outer_radius around each spot
+    // (excluding pixels belonging to any predicted spot core), mirroring the local
+    // shoebox background of BraggIntegrate2D. Must be > shoebox_radius.
+    int    bkg_outer_radius = 6;
     int    max_iterations = 3; // inner predict<->refine cycles (re-predict with refined geom/latt)
 
     // --- output ---
@@ -144,7 +148,6 @@ struct PixelRefineData {
 };
 
 class PixelRefine {
-    const AzimuthalIntegrationMapping &mapping;
     const size_t xpixel, ypixel;
     const DiffractionExperiment &experiment;
 
@@ -156,42 +159,43 @@ class PixelRefine {
     // PredictImage so both walk identical geometry/lattice code.
     void BuildParameterBlocks(const PixelRefineData &data,
                               double beam[2], double &dist_mm,
-                              double detector_rot[2], double rot_vec[3],
+                              double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
-                const AzimuthalIntegrationMapping &mapping,
                 const std::vector<MergedReflection> &reference);
 
     // The BraggPrediction is supplied per call (it is mutated): this keeps a
     // single PixelRefine instance usable from several threads, each passing its
     // own prediction buffer. Only `data` is written; PixelRefine state is const.
+    // The image is in raw detector counts (masked/saturated pixels carry the type
+    // sentinel); background is estimated locally per shoebox from the image itself.
     template<class T>
     void Run(const T *image,
-             const AzimuthalIntegrationProfile &profile,
              BraggPrediction &prediction,
              PixelRefineData &data);
 
-    // Render the forward model as a full detector image (raw detector units, so
+    // Render the forward model as a full detector image (raw detector counts, so
     // it overlays directly on the original image). Uses the *same* per-pixel
     // model path (PixelResidual::Model) as the optimizer, evaluated in double
     // precision - slow but exact. For each reference reflection it adds the Bragg
-    // signal over its shoebox; with include_background it also lays down the
-    // azimuthal background. Diagnostic tool, not on the hot path.
-    std::vector<float> PredictImage(const AzimuthalIntegrationProfile &profile,
+    // signal over its shoebox; with include_background it also lays down the local
+    // per-shoebox background read from the supplied image - the same background the
+    // fit uses. Diagnostic tool, not on the hot path.
+    template<class T>
+    std::vector<float> PredictImage(const T *image,
                                     BraggPrediction &prediction,
                                     const PixelRefineData &data,
                                     bool include_background = true) const;
 
     // Render the per-pixel chi-square (cost density) that the optimizer actually
     // minimizes: for every shoebox pixel that enters the fit it stores the squared
-    // weighted residual ((I_pred - I_obs)/sigma)^2 in *corrected* units - identical
-    // to the Ceres residual_i^2 - accumulating where shoeboxes overlap. Pixels that
-    // are not part of any shoebox stay 0; masked/saturated pixels (skipped by the
-    // fit) also stay 0. Summing the image gives ~2*final_cost. Diagnostic tool.
+    // weighted residual ((I_pred - I_obs)/sigma)^2 in raw counts - identical to the
+    // Ceres residual_i^2 - accumulating where shoeboxes overlap. Pixels that are not
+    // part of any shoebox stay 0; masked/saturated pixels (skipped by the fit) also
+    // stay 0. Summing the image gives ~2*final_cost. Diagnostic tool.
     template<class T>
     std::vector<float> ChiSquaredImage(const T *image,
-                                       const AzimuthalIntegrationProfile &profile,
                                        BraggPrediction &prediction,
                                        const PixelRefineData &data) const;
 };
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 8f90cb11..17a71934 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -457,8 +457,8 @@ void JFJochImageReadingWorker::ReanalyzeImage_i() {
     new_image_dataset->azimuthal_bins = azint_mapping->GetAzimuthalBinCount();
     new_image_dataset->q_bins = azint_mapping->GetQBinCount();
 
-    // Retain the profile (PixelRefine needs it). AzimuthalIntegrationProfile holds
-    // a mutex (non-copyable), so keep it via unique_ptr re-created each analysis.
+    // Azimuthal profile for the analysis/display pipeline. AzimuthalIntegrationProfile
+    // holds a mutex (non-copyable), so keep it via unique_ptr re-created each analysis.
     last_profile_ = std::make_unique<AzimuthalIntegrationProfile>(*azint_mapping);
     image_analysis->Analyze(new_image->ImageData(), *last_profile_, spot_finding_settings);
 
@@ -725,8 +725,8 @@ void JFJochImageReadingWorker::LoadSpots(int64_t start_image, int64_t end_image,
 // Experimental PixelRefine
 // ---------------------------------------------------------------------------
 void JFJochImageReadingWorker::EnsurePixelRefine_i() {
-    if (!pixel_refine_ && azint_mapping && !pixel_reference_.empty())
-        pixel_refine_ = std::make_unique<PixelRefine>(curr_experiment, *azint_mapping, pixel_reference_);
+    if (!pixel_refine_ && !pixel_reference_.empty())
+        pixel_refine_ = std::make_unique<PixelRefine>(curr_experiment, pixel_reference_);
     if (!pixel_pred_)
         pixel_pred_ = CreateBraggPrediction(curr_experiment.IsRotationIndexing());
 }
@@ -854,15 +854,15 @@ QVector<QRect> JFJochImageReadingWorker::BuildShoeboxes_i(const PixelRefineData
 
 std::vector<float> JFJochImageReadingWorker::BuildDisplayImage_i(const PixelRefineData &data,
                                                                  int display_mode) const {
+    const auto &img32 = current_image_ptr->Image();
     if (display_mode == PixelRefineParams::ChiSquared) {
         // The cost density the optimizer actually minimizes (weighted residual^2).
-        const auto &img32 = current_image_ptr->Image();
-        auto chi2 = pixel_refine_->ChiSquaredImage<int32_t>(img32.data(), *last_profile_, *pixel_pred_, data);
+        auto chi2 = pixel_refine_->ChiSquaredImage<int32_t>(img32.data(), *pixel_pred_, data);
         MaskMeasuredSentinels_i(chi2);
         return chi2;
     }
 
-    auto pred = pixel_refine_->PredictImage(*last_profile_, *pixel_pred_, data, true);
+    auto pred = pixel_refine_->PredictImage<int32_t>(img32.data(), *pixel_pred_, data, true);
     if (display_mode == PixelRefineParams::SquaredDifference)
         SquaredResidualWithImage_i(pred);
     return pred;
@@ -907,7 +907,7 @@ void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
 
     try {
         const auto &img32 = current_image_ptr->Image();
-        pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
+        pixel_refine_->Run<int32_t>(img32.data(), *pixel_pred_, d);
         emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
 
         auto display = BuildDisplayImage_i(d, params.display_mode);
@@ -941,7 +941,7 @@ void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
 
     try {
         const auto &img32 = current_image_ptr->Image();
-        pixel_refine_->Run<int32_t>(img32.data(), *last_profile_, *pixel_pred_, d);
+        pixel_refine_->Run<int32_t>(img32.data(), *pixel_pred_, d);
 
         // Push refined values back so the sliders follow the optimizer.
         PixelRefineParams out = params;
-- 
2.52.0


From 48d4fb0d0f73e8f95184d4498695f3a6beffe46f Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 11 Jun 2026 18:35:02 +0200
Subject: [PATCH 031/228] XDS plugin: Fix mutex

---
 xds-plugin/plugin.cpp | 64 ++++++++++++++++++++++---------------------
 1 file changed, 33 insertions(+), 31 deletions(-)

diff --git a/xds-plugin/plugin.cpp b/xds-plugin/plugin.cpp
index a5bb92e5..699d2c97 100644
--- a/xds-plugin/plugin.cpp
+++ b/xds-plugin/plugin.cpp
@@ -219,50 +219,52 @@ void plugin_get_header(int *nx, int *ny, int *nbytes, float *qx, float *qy,
 void plugin_get_data(int *frame_number, int *nx, int *ny, int *data_array,
                      int info[1024], int *error_flag) {
     std::shared_lock sl(plugin_mutex);
+    std::vector<uint8_t> tmp;
+    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
 
     try {
-        if (!hdf5_file)
-            throw PluginError(-1, "HDF5 file not open");
+        {
+            std::unique_lock h5l(hdf5_mutex);
+            if (!hdf5_file)
+                throw PluginError(-1, "HDF5 file not open");
 
-        FillInfoArray(info);
+            FillInfoArray(info);
 
-        if (*frame_number <= 0 || *frame_number > total_image_number)
-            throw PluginError(-1, "Frame number out of range");
+            if (*frame_number <= 0 || *frame_number > total_image_number)
+                throw PluginError(-1, "Frame number out of range");
 
-        std::string dataset_name;
-        hsize_t image_id;
+            std::string dataset_name;
+            hsize_t image_id;
 
-        if (format == FileWriterFormat::NXmxLegacy) {
-            char str[256];
-            size_t dataset_index = (*frame_number - 1) / images_per_file + 1;
-            snprintf(str, sizeof(str), "/entry/data/data_%06ld", dataset_index);
-            dataset_name = std::string(str);
-            image_id = (*frame_number - 1) % images_per_file;
-        } else {
-            dataset_name = "/entry/data/data";
-            image_id = *frame_number - 1;
-        }
+            if (format == FileWriterFormat::NXmxLegacy) {
+                char str[256];
+                size_t dataset_index = (*frame_number - 1) / images_per_file + 1;
+                snprintf(str, sizeof(str), "/entry/data/data_%06ld", dataset_index);
+                dataset_name = std::string(str);
+                image_id = (*frame_number - 1) % images_per_file;
+            } else {
+                dataset_name = "/entry/data/data";
+                image_id = *frame_number - 1;
+            }
 
-        HDF5DataSet dataset(*hdf5_file, dataset_name);
-        HDF5Dcpl dcpl(dataset);
+            HDF5DataSet dataset(*hdf5_file, dataset_name);
+            HDF5Dcpl dcpl(dataset);
 
-        std::vector<uint8_t> tmp;
-        std::vector<hsize_t> start = {image_id, 0, 0};
+            std::vector<hsize_t> start = {image_id, 0, 0};
 
-        CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
-        auto chunk_size = dcpl.GetChunking();
+            auto chunk_size = dcpl.GetChunking();
 
-        if ((chunk_size.size() == 3)
-            && (chunk_size[0] == 1)
-            && (chunk_size[1] == image_size_y)
-            && (chunk_size[2] == image_size_x)) {
-            dataset.ReadDirectChunk(tmp, start);
-            algorithm = dcpl.GetCompression();
+            if ((chunk_size.size() == 3)
+                && (chunk_size[0] == 1)
+                && (chunk_size[1] == image_size_y)
+                && (chunk_size[2] == image_size_x)) {
+                dataset.ReadDirectChunk(tmp, start);
+                algorithm = dcpl.GetCompression();
             } else {
                 dataset.ReadVectorToU8(tmp, start, {1, image_size_y, image_size_x});
                 algorithm = CompressionAlgorithm::NO_COMPRESSION;
             }
-
+        }
         if (algorithm != CompressionAlgorithm::NO_COMPRESSION) {
             std::vector<uint8_t> decompressed_image(image_size_x * image_size_y * pixel_byte_depth);
             JFJochDecompressPtr(decompressed_image.data(),
@@ -300,4 +302,4 @@ void plugin_close(int *error_flag) {
         *error_flag = -1;
     }
 }
-} /* extern "C" */
\ No newline at end of file
+} /* extern "C" */
-- 
2.52.0


From d31063ca3f87aca8287afdc43b135ff60c12a6bf Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 11 Jun 2026 21:25:05 +0200
Subject: [PATCH 032/228] PixelRefine: Some improvements

---
 common/Reflection.h                           |   3 +-
 .../pixel_refinement/PixelRefine.cpp          | 156 ++++++++++++------
 image_analysis/pixel_refinement/PixelRefine.h |  12 ++
 viewer/CMakeLists.txt                         |   2 +
 viewer/JFJochImageReadingWorker.cpp           |  38 +++++
 viewer/JFJochImageReadingWorker.h             |   3 +
 viewer/JFJochViewerWindow.cpp                 |   9 +
 viewer/windows/JFJochPixelRefineWindow.cpp    |   6 +
 viewer/windows/JFJochPixelRefineWindow.h      |   2 +
 viewer/windows/PixelRefineParams.h            |  25 +++
 10 files changed, 206 insertions(+), 50 deletions(-)

diff --git a/common/Reflection.h b/common/Reflection.h
index 08959c62..b46e38e6 100644
--- a/common/Reflection.h
+++ b/common/Reflection.h
@@ -25,7 +25,8 @@ struct Reflection {
     float sigma;
     float dist_ewald;
     float rlp;
-    float partiality;
+    float partiality;     // fraction of the reflection recorded in the sampled (rocking) slice
+    float completeness = 1.0f; // fraction of the spot footprint on live pixels (1 = not clipped by edge/gap/mask)
     float zeta;
     float image_scale_corr; // I_true = scaling_correction * I; scaling_correction = rlp / (partiality * image_scale)
     bool observed = false;
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index f41925b3..12540b3c 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -33,6 +33,7 @@ struct ReflGroup {
     double Itrue;             // reference intensity (held fixed)
     double R_bw_sq;           // bandwidth radial-width^2 contribution (0 = monochromatic)
     double pol;               // per-reflection polarization correction (raw = true * pol)
+    double Ibkg;              // local flat background (raw counts, constant over the shoebox)
     double predicted_x, predicted_y;
     std::vector<PixelObs> pixels;
 };
@@ -83,6 +84,23 @@ std::vector<uint8_t> BuildSpotMask(const std::vector<Reflection> &predicted, int
     return mask;
 }
 
+// Square shoebox bounds (inclusive) around a predicted spot, clamped to the
+// detector. The centre is rounded to the nearest pixel with std::lround so the
+// signal box is centred identically to the spot-core mask (BuildSpotMask) and
+// the local-background ring (EstimateLocalBackground), which also lround. Used by
+// Run and the diagnostic renderers so all three share one shoebox definition.
+struct ShoeboxBox { int min_x, max_x, min_y, max_y; };
+ShoeboxBox ShoeboxBounds(double px, double py, int radius, size_t xpixel, size_t ypixel) {
+    const int cx = static_cast<int>(std::lround(px));
+    const int cy = static_cast<int>(std::lround(py));
+    return {
+        std::max(cx - radius, 0),
+        std::min<int>(cx + radius, static_cast<int>(xpixel) - 1),
+        std::max(cy - radius, 0),
+        std::min<int>(cy + radius, static_cast<int>(ypixel) - 1)
+    };
+}
+
 // Local flat background around one shoebox, in raw detector counts. Samples the
 // square ring shoebox_radius < max(|dx|,|dy|) <= bkg_outer_radius centred on the
 // spot, dropping pixels that belong to any spot core (spot_mask) or carry a
@@ -633,16 +651,14 @@ void PixelRefine::Run(const T *image,
             g.Itrue = reference_data[hkl];
             g.R_bw_sq = bandwidth_radial_sq(refl.d);
             g.pol = polarization(refl.predicted_x, refl.predicted_y);
+            g.Ibkg = Ibkg;
             g.predicted_x = refl.predicted_x;
             g.predicted_y = refl.predicted_y;
 
-            const int min_y = std::max<int>(refl.predicted_y - radius, 0);
-            const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
-            const int min_x = std::max<int>(refl.predicted_x - radius, 0);
-            const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+            const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
 
-            for (int y = min_y; y <= max_y; ++y) {
-                for (int x = min_x; x <= max_x; ++x) {
+            for (int y = box.min_y; y <= box.max_y; ++y) {
+                for (int x = box.min_x; x <= box.max_x; ++x) {
                     const size_t npixel = xpixel * y + x;
 
                     // Skip sentinel (masked / saturated) pixels. We assume the pixel
@@ -826,52 +842,100 @@ void PixelRefine::Run(const T *image,
     } // predict<->refine iterations
 
     // ---- Extract integrated reflections ---------------------------------------
-    // Profile fitting gives the recorded amplitude (against the tangential profile
-    // P_t):
-    //     J      = sum_p[ P_t,p (Iobs_p - Ibkg_p)/v_p ] / sum_p[ P_t,p^2 / v_p ]
+    // Profile fitting gives the recorded amplitude (fitting the tangential profile
+    // P_t against the background-subtracted pixels):
+    //     J      = sum_p[ P_t,p (Iobs_p - Ibkg)/v_p ] / sum_p[ P_t,p^2 / v_p ]
     //            ~ G * Itrue * B_term * partiality * pol     (recorded raw counts)
     //     var(J) = 1 / sum_p[ P_t,p^2 / v_p ]
     //
+    // Two SEPARATE fractions reduce the full intensity to what these pixels record:
+    //
+    //   partiality   - the radial / rocking dimension that a still does NOT sample.
+    //                  Only the slice of the reflection that crosses the Ewald
+    //                  sphere on this shot is recorded; <= 1. We DIVIDE it out to
+    //                  recover the full intensity. = profile-weighted P_radial.
+    //
+    //   completeness - the fraction of the spot's detector footprint that landed on
+    //                  live pixels (= profile captured by live pixels / profile over
+    //                  the whole shoebox). 1.0 when the spot sits fully on the
+    //                  detector; < 1.0 only when a detector edge, gap or mask clips
+    //                  it. Profile fitting already extrapolates over the missing
+    //                  pixels, so this is NOT applied to r.I - it is a quality flag.
+    //
     // Output split (Merge multiplies r.I * image_scale_corr and weights by
     // 1/(sigma*image_scale_corr)^2 - see Merge.cpp):
     //   r.I              = J / (B_term * partiality * pol) = G * Itrue
     //   r.sigma          = sqrt(var(J)) / (B_term * partiality * pol)
-    //   r.partiality     = profile-weighted peak radial factor in (0,1]  (Merge filter only)
+    //   r.partiality     = profile-weighted P_radial in (0,1]  (the rocking fraction)
+    //   r.completeness   = live/total tangential profile in (0,1]  (detector clipping)
     //   r.image_scale_corr = 1/G                         (per-image scale ONLY)
     // so r.I * image_scale_corr = Itrue. B, partiality and polarization live on the
     // intensity, G lives on image_scale_corr - one clean meaning per field.
+    //
+    // We walk the full (unclamped) shoebox once: every grid point feeds the total
+    // tangential profile (completeness denominator); points that are real, live
+    // detector pixels also feed the profile fit and the captured profile.
     data.reflections.reserve(groups.size());
     for (const auto &g : groups) {
-        double num = 0.0, den = 0.0, bkg_sum = 0.0;
-        double radial_sum = 0.0, radial_w = 0.0;
+        const int cx = static_cast<int>(std::lround(g.predicted_x));
+        const int cy = static_cast<int>(std::lround(g.predicted_y));
+
+        // Debye-Waller factor for this reflection (constant over its shoebox).
+        const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
+
+        double num = 0.0, den = 0.0, bkg_sum = 0.0, radial_sum = 0.0;
+        double prof_live = 0.0, prof_full = 0.0; // tangential profile: captured / total
         size_t n = 0;
 
-        for (const auto &obs : g.pixels) {
-            PixelResidual pr(obs, 1.0, lambda, pixel_size, g.h, g.k, g.l, g.R_bw_sq, g.pol, data.crystal_system);
-            double q_sq, eps_r, eps_t_sq;
-            if (!pr.GeometryTerms(beam, &dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2, q_sq,
-                eps_r, eps_t_sq))
-                continue;
-            if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
-                continue;
+        for (int y = cy - radius; y <= cy + radius; ++y) {
+            for (int x = cx - radius; x <= cx + radius; ++x) {
+                // Geometry/profile for this grid point (valid even off the detector).
+                PixelObs probe{static_cast<double>(x), static_cast<double>(y), 0.0, g.Ibkg, 1.0};
+                PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
+                                 g.R_bw_sq, g.pol, data.crystal_system);
+                double q_sq, eps_r, eps_t_sq;
+                if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
+                                      latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                    continue;
+                if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
+                    continue;
 
-            // Tangential profile shape -> fit weight (every pixel counts equally).
-            const double P_t = std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
-                               / (M_PI * data.R[1] * data.R[1]);
-            // Peak-normalized radial factor (the partiality), in (0,1].
-            // Bandwidth-broadened radial width, matching the model in Model().
-            const double R0_eff_sq = data.R[0] * data.R[0] + g.R_bw_sq;
-            const double P_radial = std::exp(-eps_r * eps_r / R0_eff_sq);
+                // Tangential profile shape (area-normalized) -> the fit template.
+                const double P_t = std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
+                                   / (M_PI * data.R[1] * data.R[1]);
+                prof_full += P_t; // whole shoebox, on- or off-detector
 
-            const double v = SafeInv(obs.weight * obs.weight, 1.0); // pixel variance
-            const double signal = obs.Iobs - obs.Ibkg;
+                // Only real, unmasked detector pixels carry signal.
+                if (x < 0 || x >= static_cast<int>(xpixel) || y < 0 || y >= static_cast<int>(ypixel))
+                    continue;
+                const size_t np = static_cast<size_t>(xpixel) * y + x;
+                if (image[np] == std::numeric_limits<T>::max())
+                    continue;
+                if (std::is_signed_v<T> && image[np] == std::numeric_limits<T>::min())
+                    continue;
 
-            num += P_t * signal / v;
-            den += P_t * P_t / v;
-            radial_sum += P_radial * P_t;   // weight partiality by the spot core
-            radial_w += P_t;
-            bkg_sum += obs.Ibkg;
-            ++n;
+                const double Iobs = static_cast<double>(image[np]); // raw counts
+                double v = std::max(Iobs, 0.0);                     // Poisson variance
+                if (!(v > 1.0))
+                    v = 1.0;
+
+                // Peak-normalized radial factor (the partiality), in (0,1]. The
+                // bandwidth-broadened radial width matches the model in Model().
+                const double R0_eff_sq = data.R[0] * data.R[0] + g.R_bw_sq;
+                const double P_radial = std::exp(-eps_r * eps_r / R0_eff_sq);
+
+                // Profile-fit accumulators. The amplitude estimator weights pixels by
+                // P_t^2/v, so the partiality (which de-scales that amplitude) MUST use
+                // the SAME weights - otherwise an R0_eff-dependent (resolution-
+                // dependent) factor is left behind in r.I.
+                const double w = P_t * P_t / v;
+                num += P_t * (Iobs - g.Ibkg) / v;
+                den += w;
+                radial_sum += P_radial * w;   // partiality weighted exactly like num/den
+                prof_live += P_t;             // captured tangential profile
+                bkg_sum += g.Ibkg;
+                ++n;
+            }
         }
 
         Reflection r{};
@@ -884,12 +948,12 @@ void PixelRefine::Run(const T *image,
         r.observed_x = NAN;
         r.observed_y = NAN;
         r.rlp = 1.0f;
-        r.partiality = (radial_w > 0.0) ? static_cast<float>(radial_sum / radial_w) : 1.0f;
+        r.partiality = (den > 0.0) ? static_cast<float>(radial_sum / den) : 1.0f;
+        r.completeness = (prof_full > 0.0) ? static_cast<float>(prof_live / prof_full) : 1.0f;
 
         if (den > 0.0 && n > 0) {
             const double I_amp = num / den;             // ~ G*Itrue*B_term*partiality*pol
             const double sigma_amp = std::sqrt(1.0 / den);
-            const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
             const double corr = static_cast<double>(r.partiality) * B_term * g.pol; // B, partiality & pol
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
@@ -1010,13 +1074,10 @@ std::vector<float> PixelRefine::PredictImage(const T *image,
                                     refl.predicted_x, refl.predicted_y,
                                     radius, bkg_outer_radius, Ibkg);
 
-        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
-        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
-        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
-        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
 
-        for (int y = min_y; y <= max_y; ++y) {
-            for (int x = min_x; x <= max_x; ++x) {
+        for (int y = box.min_y; y <= box.max_y; ++y) {
+            for (int x = box.min_x; x <= box.max_x; ++x) {
                 const size_t npixel = xpixel * y + x;
 
                 PixelObs obs{
@@ -1106,13 +1167,10 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
                                      radius, bkg_outer_radius, Ibkg))
             continue;
 
-        const int min_y = std::max<int>(refl.predicted_y - radius, 0);
-        const int max_y = std::min<int>(refl.predicted_y + radius, ypixel - 1);
-        const int min_x = std::max<int>(refl.predicted_x - radius, 0);
-        const int max_x = std::min<int>(refl.predicted_x + radius, xpixel - 1);
+        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
 
-        for (int y = min_y; y <= max_y; ++y) {
-            for (int x = min_x; x <= max_x; ++x) {
+        for (int y = box.min_y; y <= box.max_y; ++y) {
+            for (int x = box.min_x; x <= box.max_x; ++x) {
                 const size_t npixel = xpixel * y + x;
 
                 // Same gating as Run(): only pixels that actually enter the fit.
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 8d28e107..1a2535c1 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -3,6 +3,8 @@
 
 #pragma once
 
+#include <optional>
+
 #include "../bragg_prediction/BraggPrediction.h"
 #include "../common/DiffractionExperiment.h"
 #include "../scale_merge/HKLKey.h"
@@ -198,4 +200,14 @@ public:
     std::vector<float> ChiSquaredImage(const T *image,
                                        BraggPrediction &prediction,
                                        const PixelRefineData &data) const;
+
+    // Reference (merged) intensity used as the fixed hypothesis for a reflection,
+    // or nullopt if this hkl is not in the reference. Lets callers show the fitted
+    // estimate next to the reference it was scaled against.
+    std::optional<double> ReferenceIntensity(const Reflection &r) const {
+        const auto it = reference_data.find(hkl_key_generator(r));
+        if (it == reference_data.end())
+            return std::nullopt;
+        return it->second;
+    }
 };
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 70981081..6bfbd37e 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -88,6 +88,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJochViewerReciprocalSpaceWindow.h
         windows/JFJochPixelRefineWindow.cpp
         windows/JFJochPixelRefineWindow.h
+        windows/JFJochPixelRefineTableWindow.cpp
+        windows/JFJochPixelRefineTableWindow.h
         windows/JFJochMagnifierWindow.cpp
         windows/JFJochMagnifierWindow.h
         windows/PixelRefineParams.h
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 17a71934..1e92cfed 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -70,6 +70,7 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
       indexing_settings(experiment.GetIndexingSettings()),
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
     qRegisterMetaType<PixelRefineParams>("PixelRefineParams");
+    qRegisterMetaType<PixelRefineReport>("PixelRefineReport");
     qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
     spot_finding_settings = settings;;
 
@@ -852,6 +853,41 @@ QVector<QRect> JFJochImageReadingWorker::BuildShoeboxes_i(const PixelRefineData
     return boxes;
 }
 
+PixelRefineReport JFJochImageReadingWorker::BuildReport_i(const PixelRefineData &data) const {
+    PixelRefineReport report;
+    report.pr_G = data.scale_factor;
+    report.pr_B = data.B_factor;
+    report.pr_cc = data.cc;
+    report.pr_cc_n = data.cc_n;
+
+    // Standard ScaleOnTheFly pipeline result for the same image, as a baseline.
+    if (current_image_ptr) {
+        const auto &d = current_image_ptr->ImageData();
+        if (d.image_scale_factor)  report.pipe_G  = d.image_scale_factor.value();
+        if (d.image_scale_b_factor) report.pipe_B = d.image_scale_b_factor.value();
+        if (d.image_scale_cc)      report.pipe_cc = d.image_scale_cc.value();
+    }
+
+    report.rows.reserve(data.reflections.size());
+    for (const auto &r : data.reflections) {
+        if (!r.observed)
+            continue;
+        PixelRefineReport::Row row;
+        row.h = r.h; row.k = r.k; row.l = r.l;
+        row.d = r.d;
+        row.completeness = r.completeness;
+        row.partiality = r.partiality;
+        row.I = r.I;
+        row.sigma = r.sigma;
+        if (std::isfinite(r.image_scale_corr))
+            row.I_true_est = static_cast<double>(r.I) * static_cast<double>(r.image_scale_corr);
+        if (pixel_refine_)
+            row.I_true_ref = pixel_refine_->ReferenceIntensity(r).value_or(NAN);
+        report.rows.push_back(row);
+    }
+    return report;
+}
+
 std::vector<float> JFJochImageReadingWorker::BuildDisplayImage_i(const PixelRefineData &data,
                                                                  int display_mode) const {
     const auto &img32 = current_image_ptr->Image();
@@ -909,6 +945,7 @@ void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
         const auto &img32 = current_image_ptr->Image();
         pixel_refine_->Run<int32_t>(img32.data(), *pixel_pred_, d);
         emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
+        emit pixelRefineReport(BuildReport_i(d));
 
         auto display = BuildDisplayImage_i(d, params.display_mode);
         emit predictedImageReady(WrapFloatImage_i(display));
@@ -954,6 +991,7 @@ void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
         out.beam_y = d.geom.GetBeamY_pxl();
         emit pixelRefineParamsRefined(out);
         emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
+        emit pixelRefineReport(BuildReport_i(d));
 
         auto display = BuildDisplayImage_i(d, params.display_mode);
         emit predictedImageReady(WrapFloatImage_i(display));
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 501b557d..50cd77ca 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -80,6 +80,8 @@ private:
     void MaskMeasuredSentinels_i(std::vector<float> &img) const;
     // Build the per-reflection shoebox rectangles for the last refine/preview.
     QVector<QRect> BuildShoeboxes_i(const PixelRefineData &data) const;
+    // Assemble the per-reflection table + per-image summary for the table window.
+    PixelRefineReport BuildReport_i(const PixelRefineData &data) const;
     // Build the float image to display for the given PixelRefineParams::DisplayMode.
     std::vector<float> BuildDisplayImage_i(const PixelRefineData &data, int display_mode) const;
 
@@ -148,6 +150,7 @@ signals:
     void predictedShoeboxes(QVector<QRect> boxes); // per-reflection optimization windows
     void pixelRefineResidual(double cost, double cc, int64_t n_reflections);
     void pixelRefineParamsRefined(PixelRefineParams params);
+    void pixelRefineReport(PixelRefineReport report); // per-reflection table + summary
     void pixelRefineStatus(QString message);
 
 public:
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 9fa6a302..1eb2c3c7 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -26,6 +26,7 @@
 #include "windows/JFJoch2DAzintImageWindow.h"
 #include "windows/JFJochAzIntWindow.h"
 #include "windows/JFJochPixelRefineWindow.h"
+#include "windows/JFJochPixelRefineTableWindow.h"
 #include "windows/JFJochMagnifierWindow.h"
 #include "image_viewer/JFJochImage.h"
 #include "image_viewer/JFJochSimpleImage.h"
@@ -108,6 +109,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     auto azintWindow = new JFJochAzIntWindow(experiment.GetAzimuthalIntegrationSettings(), this);
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
     auto pixelRefineWindow = new JFJochPixelRefineWindow(this);
+    auto pixelRefineTableWindow = new JFJochPixelRefineTableWindow(this);
     auto magnifierWindow = new JFJochMagnifierWindow(this);
 
     menuBar->AddWindowEntry(tableWindow, "Image list");
@@ -120,6 +122,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(azintWindow, "Azimuthal integration settings");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
     menuBar->AddWindowEntry(pixelRefineWindow, "PixelRefine (experimental)");
+    menuBar->AddWindowEntry(pixelRefineTableWindow, "PixelRefine reflections");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
 
     if (dbus) {
@@ -361,6 +364,12 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(reading_worker, &JFJochImageReadingWorker::pixelRefineStatus,
             pixelRefineWindow, &JFJochPixelRefineWindow::setStatus);
 
+    // Reflection-table window: refreshed on every preview/refine, raised by button.
+    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineReport,
+            pixelRefineTableWindow, &JFJochPixelRefineTableWindow::setReport);
+    connect(pixelRefineWindow, &JFJochPixelRefineWindow::showTableRequested,
+            pixelRefineTableWindow, &JFJochHelperWindow::open);
+
     // Lock the predicted-image viewport to the original image (both directions).
     connect(viewer, &JFJochImage::viewportChanged,
             pixelRefineWindow->imageView(), &JFJochImage::applyViewport);
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
index 7f7a64ec..0e8b4a16 100644
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ b/viewer/windows/JFJochPixelRefineWindow.cpp
@@ -82,8 +82,10 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
     // --- buttons + readouts -------------------------------------------------
     m_loadRef = new QPushButton(tr("Load reference MTZ…"), this);
     m_refine  = new QPushButton(tr("Refine"), this);
+    m_showTable = new QPushButton(tr("Reflection table…"), this);
     controlsLayout->addWidget(m_loadRef);
     controlsLayout->addWidget(m_refine);
+    controlsLayout->addWidget(m_showTable);
 
     m_residual = new QLabel(tr("Residual: —"), this);
     m_pipelineCC = new QLabel(tr("Pipeline CC (ref): —"), this);
@@ -121,6 +123,10 @@ JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
             emit loadReferenceRequested(path);
     });
 
+    connect(m_showTable, &QPushButton::clicked, this, [this] {
+        emit showTableRequested();
+    });
+
     connect(m_refine, &QPushButton::clicked, this, [this] {
         // Cancel any pending live-preview: otherwise a debounce armed by a slider
         // move just before this click fires after the refine and overwrites the
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
index 99c628c2..9398389d 100644
--- a/viewer/windows/JFJochPixelRefineWindow.h
+++ b/viewer/windows/JFJochPixelRefineWindow.h
@@ -49,6 +49,7 @@ class JFJochPixelRefineWindow : public JFJochHelperWindow {
     QLabel *m_status;
     QPushButton *m_loadRef;
     QPushButton *m_refine;
+    QPushButton *m_showTable;
 
     QTimer *m_debounce;
     bool m_suppress = false;   // guard while pushing refined params into sliders
@@ -68,6 +69,7 @@ signals:
     void paramsChanged(PixelRefineParams params);       // debounced live preview
     void refineRequested(PixelRefineParams params);     // "Refine" button
     void loadReferenceRequested(QString path);          // "Load reference" button
+    void showTableRequested();                          // "Reflection table" button
 
 public slots:
     void setPredictedImage(std::shared_ptr<const SimpleImage> image);
diff --git a/viewer/windows/PixelRefineParams.h b/viewer/windows/PixelRefineParams.h
index 64f6e27b..e180847e 100644
--- a/viewer/windows/PixelRefineParams.h
+++ b/viewer/windows/PixelRefineParams.h
@@ -4,6 +4,8 @@
 #pragma once
 
 #include <cmath>
+#include <cstdint>
+#include <vector>
 #include <QMetaType>
 
 // Parameters exchanged between the PixelRefine window (sliders/buttons) and the
@@ -39,3 +41,26 @@ struct PixelRefineParams {
 };
 
 Q_DECLARE_METATYPE(PixelRefineParams)
+
+// One PixelRefine result, shipped from the worker to the reflection-table window:
+// a per-image summary that puts PixelRefine's scale/B/CC next to the standard
+// ScaleOnTheFly pipeline's, plus one row per matched reflection.
+struct PixelRefineReport {
+    // Per-image summary (NaN = not available).
+    double pr_G = NAN, pr_B = NAN, pr_cc = NAN;   // PixelRefine
+    int64_t pr_cc_n = 0;
+    double pipe_G = NAN, pipe_B = NAN, pipe_cc = NAN; // ScaleOnTheFly pipeline baseline
+
+    struct Row {
+        int h = 0, k = 0, l = 0;
+        double d = 0.0;
+        double completeness = 1.0;  // spot footprint on live pixels (1 = not clipped)
+        double partiality = 1.0;    // recorded rocking fraction
+        double I = 0.0, sigma = 0.0;
+        double I_true_est = NAN;     // r.I * image_scale_corr (this image's estimate)
+        double I_true_ref = NAN;     // reference (merged) intensity
+    };
+    std::vector<Row> rows;
+};
+
+Q_DECLARE_METATYPE(PixelRefineReport)
-- 
2.52.0


From c8db50ab41352eac46066b1264d7c3a5ac116aa6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 07:47:28 +0200
Subject: [PATCH 033/228] jfjoch_viewer: missing pixel refine table

---
 .../windows/JFJochPixelRefineTableWindow.cpp  | 101 ++++++++++++++++++
 viewer/windows/JFJochPixelRefineTableWindow.h |  34 ++++++
 2 files changed, 135 insertions(+)
 create mode 100644 viewer/windows/JFJochPixelRefineTableWindow.cpp
 create mode 100644 viewer/windows/JFJochPixelRefineTableWindow.h

diff --git a/viewer/windows/JFJochPixelRefineTableWindow.cpp b/viewer/windows/JFJochPixelRefineTableWindow.cpp
new file mode 100644
index 00000000..f656164a
--- /dev/null
+++ b/viewer/windows/JFJochPixelRefineTableWindow.cpp
@@ -0,0 +1,101 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochPixelRefineTableWindow.h"
+
+#include <cmath>
+#include <QVBoxLayout>
+#include <QHeaderView>
+
+JFJochPixelRefineTableWindow::JFJochPixelRefineTableWindow(QWidget *parent)
+    : JFJochHelperWindow(parent) {
+    setWindowTitle("PixelRefine reflections");
+    resize(950, 600);
+
+    auto central = new QWidget(this);
+    setCentralWidget(central);
+    auto layout = new QVBoxLayout(central);
+
+    m_summary = new QLabel(tr("No PixelRefine result yet."), this);
+    m_summary->setTextFormat(Qt::RichText);
+    m_summary->setWordWrap(true);
+    layout->addWidget(m_summary);
+
+    m_table = new QTableView(this);
+    m_model = new QStandardItemModel(this);
+    setupModel();
+
+    m_proxy = new QSortFilterProxyModel(this);
+    m_proxy->setSourceModel(m_model);
+    m_proxy->setSortRole(Qt::UserRole); // numeric sort on the underlying values
+
+    m_table->setModel(m_proxy);
+    m_table->setEditTriggers(QAbstractItemView::NoEditTriggers);
+    m_table->setSortingEnabled(true);
+    m_table->sortByColumn(6, Qt::DescendingOrder); // default: I desc
+    m_table->verticalHeader()->setVisible(false);
+    m_table->horizontalHeader()->setSortIndicatorShown(true);
+    m_table->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
+    m_table->setStyleSheet("background-color: white;");
+    layout->addWidget(m_table);
+}
+
+void JFJochPixelRefineTableWindow::setupModel() {
+    const QStringList headers = {
+        "h", "k", "l", "d [Å]", "Compl.", "Part.",
+        "I", "Sigma", "Est. I_true", "Ref. I_true"
+    };
+    m_model->setColumnCount(headers.size());
+    for (int i = 0; i < headers.size(); ++i)
+        m_model->setHeaderData(i, Qt::Horizontal, headers[i]);
+}
+
+static QStandardItem *numItem(double value, int decimals) {
+    auto *it = new QStandardItem();
+    const QString text = std::isfinite(value) ? QString::number(value, 'f', decimals)
+                                              : QStringLiteral("—");
+    it->setData(text, Qt::DisplayRole);
+    it->setData(value, Qt::UserRole);
+    it->setTextAlignment(Qt::AlignRight | Qt::AlignVCenter);
+    return it;
+}
+
+static QStandardItem *intItem(int value) {
+    auto *it = new QStandardItem();
+    it->setData(static_cast<qlonglong>(value), Qt::DisplayRole);
+    it->setData(static_cast<qlonglong>(value), Qt::UserRole);
+    it->setTextAlignment(Qt::AlignRight | Qt::AlignVCenter);
+    return it;
+}
+
+void JFJochPixelRefineTableWindow::setReport(PixelRefineReport report) {
+    // --- per-image summary: PixelRefine vs the standard pipeline ---------------
+    auto fmt = [](double v, int dec) {
+        return std::isfinite(v) ? QString::number(v, 'f', dec) : QStringLiteral("—");
+    };
+    auto pct = [](double v) {
+        return std::isfinite(v) ? QString::number(v * 100.0, 'f', 1) + "%" : QStringLiteral("—");
+    };
+    m_summary->setText(
+        tr("<b>PixelRefine:</b> scale G = %1, B = %2 Ų, CC = %3 (%4 refl)"
+           "&nbsp;&nbsp;|&nbsp;&nbsp;"
+           "<b>Pipeline:</b> scale G = %5, B = %6 Ų, CC = %7")
+            .arg(fmt(report.pr_G, 4), fmt(report.pr_B, 1), pct(report.pr_cc))
+            .arg(report.pr_cc_n)
+            .arg(fmt(report.pipe_G, 4), fmt(report.pipe_B, 1), pct(report.pipe_cc)));
+
+    // --- per-reflection rows ---------------------------------------------------
+    m_model->removeRows(0, m_model->rowCount());
+    for (const auto &r : report.rows) {
+        QList<QStandardItem *> row;
+        row << intItem(r.h) << intItem(r.k) << intItem(r.l);
+        row << numItem(r.d, 3);
+        row << numItem(r.completeness, 2);
+        row << numItem(r.partiality, 2);
+        row << numItem(r.I, 1);
+        row << numItem(r.sigma, 1);
+        row << numItem(r.I_true_est, 1);
+        row << numItem(r.I_true_ref, 1);
+        m_model->appendRow(row);
+    }
+}
diff --git a/viewer/windows/JFJochPixelRefineTableWindow.h b/viewer/windows/JFJochPixelRefineTableWindow.h
new file mode 100644
index 00000000..5187b546
--- /dev/null
+++ b/viewer/windows/JFJochPixelRefineTableWindow.h
@@ -0,0 +1,34 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "JFJochHelperWindow.h"
+#include "PixelRefineParams.h"
+
+#include <QLabel>
+#include <QTableView>
+#include <QStandardItemModel>
+#include <QSortFilterProxyModel>
+
+// Reflection table for the experimental PixelRefine path. Opened from a button on
+// the PixelRefine window and refreshed on every preview/refine. Each row is one
+// matched reflection (the two partiality-style fractions, the fitted intensity,
+// and the estimated vs reference full intensity); the header line compares
+// PixelRefine's per-image scale/B/CC with the standard ScaleOnTheFly pipeline.
+class JFJochPixelRefineTableWindow : public JFJochHelperWindow {
+    Q_OBJECT
+
+    QLabel *m_summary = nullptr;
+    QTableView *m_table = nullptr;
+    QStandardItemModel *m_model = nullptr;
+    QSortFilterProxyModel *m_proxy = nullptr;
+
+    void setupModel();
+
+public:
+    explicit JFJochPixelRefineTableWindow(QWidget *parent = nullptr);
+
+public slots:
+    void setReport(PixelRefineReport report);
+};
-- 
2.52.0


From 47dc19dd030fedf6938f003cdfc6e6ca143e22bd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 10:12:23 +0200
Subject: [PATCH 034/228] PixelRefine: Improvements to accept more reasonable
 count of reflections

---
 .../pixel_refinement/PixelRefine.cpp          | 50 ++++++++++++-------
 image_analysis/pixel_refinement/PixelRefine.h |  7 +++
 2 files changed, 39 insertions(+), 18 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 12540b3c..98f0a7af 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -551,6 +551,35 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     }
 }
 
+BraggPredictionSettings PixelRefine::BuildPredictionSettings(const PixelRefineData &data) const {
+    // Radial Ewald-acceptance band: predict exactly the reflections the merge's
+    // partiality floor would still keep, and no tighter. A reflection's partiality
+    // is exp(-s^2 / R0_eff^2) (s = excitation error), so it survives min_partiality
+    // when |s| <= R0 * sqrt(-ln(min_partiality)). Using that as the cutoff keeps
+    // prediction and the partiality cut consistent. The struct default (0.0005) is
+    // far narrower than R0 (~0.005), so previously most keepable reflections were
+    // never predicted and per-reflection multiplicity collapsed ~4x.
+    const double min_part = std::clamp(experiment.GetScalingSettings().GetMinPartiality(), 1e-6, 0.999);
+    const double r0 = std::max(data.R[0], 1e-4);
+    const double cutoff = r0 * std::sqrt(-std::log(min_part));
+
+    // Relative bandwidth (sigma of dlambda/lambda): the explicit PixelRefine model
+    // value if set, else the experiment's nominal bandwidth (FWHM -> sigma). >0
+    // thickens the band radially at high resolution (the 1/d^2 pink-beam smear),
+    // matching the integrator and preventing the outer shells from being clipped.
+    float bw_sigma = static_cast<float>(data.bandwidth);
+    if (bw_sigma <= 0.0f)
+        bw_sigma = experiment.GetBandwidthFWHM().value_or(0.0f) / 2.3548f;
+
+    return BraggPredictionSettings{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .ewald_dist_cutoff = static_cast<float>(cutoff),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = bw_sigma
+    };
+}
+
 template<class T>
 void PixelRefine::Run(const T *image,
                       BraggPrediction &prediction,
@@ -561,12 +590,7 @@ void PixelRefine::Run(const T *image,
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
 
-    const BraggPredictionSettings settings_prediction{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
-    };
+    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
 
     const int radius = data.shoebox_radius;
     const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
@@ -1045,12 +1069,7 @@ std::vector<float> PixelRefine::PredictImage(const T *image,
             .PoniRot1_rad(data.geom.GetPoniRot1_rad())
             .PoniRot2_rad(data.geom.GetPoniRot2_rad());
 
-    const BraggPredictionSettings settings_prediction{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
-    };
+    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
     const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
@@ -1139,12 +1158,7 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
             .PoniRot1_rad(data.geom.GetPoniRot1_rad())
             .PoniRot2_rad(data.geom.GetPoniRot2_rad());
 
-    const BraggPredictionSettings settings_prediction{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)
-    };
+    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
     const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 1a2535c1..ffcc08bd 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -163,6 +163,13 @@ class PixelRefine {
                               double beam[2], double &dist_mm,
                               double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
+
+    // Bragg-prediction settings shared by Run/PredictImage/ChiSquaredImage so all
+    // three predict an identical reflection set. Critically it sets the radial
+    // Ewald-acceptance band (ewald_dist_cutoff) and the bandwidth broadening - see
+    // the definition for why these must track the partiality model, not the
+    // BraggPredictionSettings struct defaults.
+    BraggPredictionSettings BuildPredictionSettings(const PixelRefineData &data) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const std::vector<MergedReflection> &reference);
-- 
2.52.0


From db68c8dc380ae6f7de1620805959d90da2207d9b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 17:28:18 +0200
Subject: [PATCH 035/228] PixelRefine: Results seem to be much better

---
 image_analysis/IndexAndRefine.cpp             |   1 +
 .../pixel_refinement/PixelRefine.cpp          | 308 ++++++++++++++++--
 image_analysis/pixel_refinement/PixelRefine.h |  59 +++-
 tools/jfjoch_process.cpp                      |  24 ++
 4 files changed, 350 insertions(+), 42 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 4f3865c3..f7cb25c1 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include <cstdlib>
 #include "IndexAndRefine.h"
 
 #include "bragg_integration/BraggIntegrate2D.h"
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 98f0a7af..7fbc57a5 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -273,6 +273,42 @@ bool PredictedNode(const T *p0, const T *p1, const T *p2,
     return true;
 }
 
+// Pulls a scalar parameter towards an expected value with a fixed weight (the
+// data-scaled prior). Identical in spirit to ScaleOnTheFly's regularizer: it is what
+// keeps the per-image scale G from wandering on weakly-constrained images and
+// scrambling the cross-image merge.
+struct ScalarRegularizer {
+    ScalarRegularizer(double weight, double expected) : weight(weight), expected(expected) {}
+    template<typename T>
+    bool operator()(const T *p, T *residual) const {
+        residual[0] = T(weight) * (p[0] - T(expected));
+        return true;
+    }
+    double weight;
+    double expected;
+};
+
+// Anchors the orientation (angle-axis vector) to its pre-refinement value with a
+// data-scaled weight. Without it the three orientation DOF chase the sparse signal
+// (and the few noisy background pixels) and the per-image intensities collapse;
+// with it the fit can only make a small, signal-supported sub-spot correction - the
+// push that brings slightly-misaligned high-resolution reflections onto their
+// shoeboxes. Mirrors the G/B regularizers in ScaleOnTheFly.
+struct OrientationRegularizer {
+    OrientationRegularizer(double weight, const double prior[3]) : weight(weight) {
+        for (int i = 0; i < 3; ++i)
+            prior_[i] = prior[i];
+    }
+    template<typename T>
+    bool operator()(const T *p0, T *residual) const {
+        for (int i = 0; i < 3; ++i)
+            residual[i] = T(weight) * (p0[i] - T(prior_[i]));
+        return true;
+    }
+    double weight;
+    double prior_[3];
+};
+
 } // namespace
 
 // ---------------------------------------------------------------------------
@@ -551,33 +587,161 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     }
 }
 
-BraggPredictionSettings PixelRefine::BuildPredictionSettings(const PixelRefineData &data) const {
-    // Radial Ewald-acceptance band: predict exactly the reflections the merge's
-    // partiality floor would still keep, and no tighter. A reflection's partiality
-    // is exp(-s^2 / R0_eff^2) (s = excitation error), so it survives min_partiality
-    // when |s| <= R0 * sqrt(-ln(min_partiality)). Using that as the cutoff keeps
-    // prediction and the partiality cut consistent. The struct default (0.0005) is
-    // far narrower than R0 (~0.005), so previously most keepable reflections were
-    // never predicted and per-reflection multiplicity collapsed ~4x.
-    const double min_part = std::clamp(experiment.GetScalingSettings().GetMinPartiality(), 1e-6, 0.999);
-    const double r0 = std::max(data.R[0], 1e-4);
-    const double cutoff = r0 * std::sqrt(-std::log(min_part));
+template<class T>
+void PixelRefine::SweepOrientationCell(const T *image, BraggPrediction &prediction,
+                                       PixelRefineData &data) const {
+    const int radius = data.shoebox_radius;
+    const double beam_x = data.geom.GetBeamX_pxl();
+    const double beam_y = data.geom.GetBeamY_pxl();
+    const auto qnan = std::numeric_limits<double>::quiet_NaN();
 
-    // Relative bandwidth (sigma of dlambda/lambda): the explicit PixelRefine model
-    // value if set, else the experiment's nominal bandwidth (FWHM -> sigma). >0
-    // thickens the band radially at high resolution (the 1/d^2 pink-beam smear),
-    // matching the integrator and preventing the outer shells from being clipped.
-    float bw_sigma = static_cast<float>(data.bandwidth);
-    if (bw_sigma <= 0.0f)
-        bw_sigma = experiment.GetBandwidthFWHM().value_or(0.0f) / 2.3548f;
+    // Box-sum minus local (perimeter) background, raw counts. NaN if the box runs
+    // off the detector or hits a masked/saturated pixel.
+    auto integrate = [&](double px, double py) -> double {
+        const int cx = static_cast<int>(std::lround(px));
+        const int cy = static_cast<int>(std::lround(py));
+        const int outer = radius + 1;
+        if (cx - outer < 0 || cy - outer < 0 ||
+            cx + outer >= static_cast<int>(xpixel) || cy + outer >= static_cast<int>(ypixel))
+            return qnan;
+        double sig = 0.0;
+        int nsig = 0;
+        std::vector<double> ring;
+        ring.reserve((2 * outer + 1) * (2 * outer + 1));
+        for (int y = cy - outer; y <= cy + outer; ++y) {
+            for (int x = cx - outer; x <= cx + outer; ++x) {
+                const T raw = image[static_cast<size_t>(xpixel) * y + x];
+                if (raw == std::numeric_limits<T>::max())
+                    return qnan;
+                if (std::is_signed_v<T> && raw == std::numeric_limits<T>::min())
+                    return qnan;
+                const double v = static_cast<double>(raw);
+                if (std::abs(x - cx) <= radius && std::abs(y - cy) <= radius) {
+                    sig += v;
+                    ++nsig;
+                } else {
+                    ring.push_back(v);
+                }
+            }
+        }
+        if (ring.size() < 5)
+            return qnan;
+        return sig - nsig * MedianInPlace(ring);
+    };
 
-    return BraggPredictionSettings{
+    // Predict (wide band) and collect every reflection that has a reference value,
+    // with its detector radius. The full set is scored - the strong low-res spots
+    // anchor the CC, the weak high-res spots are what "appear" at the right cell.
+    DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(beam_x).BeamY_pxl(beam_y)
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+    const BraggPredictionSettings settings{
         .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .ewald_dist_cutoff = static_cast<float>(cutoff),
+        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
         .max_hkl = 100,
         .centering = data.centering,
-        .bandwidth_sigma = bw_sigma
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)
     };
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings);
+    const auto &predicted = prediction.GetReflections();
+
+    struct Matched { int h, k, l; double refI; };
+    std::vector<Matched> matched;
+    double r_max = 0.0, r_min = std::numeric_limits<double>::max();
+    for (int i = 0; i < nrefl; ++i) {
+        const auto &r = predicted[i];
+        const auto it = reference_data.find(hkl_key_generator(r));
+        if (it == reference_data.end())
+            continue;
+        matched.push_back({r.h, r.k, r.l, it->second});
+        const double dx = r.predicted_x - beam_x;
+        const double dy = r.predicted_y - beam_y;
+        const double rad = std::sqrt(dx * dx + dy * dy);
+        r_max = std::max(r_max, rad);
+        r_min = std::min(r_min, rad);
+    }
+    if (matched.size() < 20 || r_min <= 1.0 || r_max <= r_min)
+        return; // too little to anchor a meaningful sweep
+
+    // CC of the box-summed intensities against the reference, over all matched hkls.
+    auto score = [&](const CrystalLattice &L) -> double {
+        const Coord A = L.Astar(), B = L.Bstar(), C = L.Cstar();
+        double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
+        int n = 0;
+        for (const auto &m : matched) {
+            const Coord g = A * static_cast<float>(m.h) + B * static_cast<float>(m.k)
+                            + C * static_cast<float>(m.l);
+            const auto [x, y] = data.geom.RecipToDetector(g);
+            if (!std::isfinite(x) || !std::isfinite(y))
+                continue;
+            const double I = integrate(x, y);
+            if (!std::isfinite(I))
+                continue;
+            const double yv = m.refI;
+            sx += I; sy += yv; sxx += I * I; syy += yv * yv; sxy += I * yv; ++n;
+        }
+        if (n < 10)
+            return -2.0;
+        const double nd = n;
+        const double cov = sxy - sx * sy / nd;
+        const double vx = sxx - sx * sx / nd;
+        const double vy = syy - sy * sy / nd;
+        if (!(vx > 0.0 && vy > 0.0))
+            return -2.0;
+        return cov / std::sqrt(vx * vy);
+    };
+
+    // Step = 1 px at the highest resolution. Range = assumed orientation/cell-scale
+    // uncertainty (a few px at high res), NOT the low-res 2 px cap: the latter is
+    // ~2*r_max/r_min px at high res - far too permissive, and lets the per-image CC
+    // overfit. Here the low-res spots barely move (stay anchored).
+    const double step = 1.0 / r_max;
+    const int n_rot = std::clamp(
+        static_cast<int>(std::lround(data.sweep_max_deg * M_PI / 180.0 * r_max)), 1, 25);
+    const int n_scale = std::clamp(
+        static_cast<int>(std::lround(data.sweep_max_cell_frac * r_max)), 1, 25);
+    const Coord axes[3] = {Coord(1, 0, 0), Coord(0, 1, 0), Coord(0, 0, 1)};
+
+    CrystalLattice best = data.latt;
+    double best_cc = score(best);
+
+    for (int round = 0; round < 2; ++round) {
+        for (const auto &axis : axes) {
+            CrystalLattice axis_best = best;
+            double axis_cc = best_cc;
+            for (int i = -n_rot; i <= n_rot; ++i) {
+                if (i == 0)
+                    continue;
+                CrystalLattice cand = best.Multiply(RotMatrix(static_cast<float>(i * step), axis));
+                const double cc = score(cand);
+                if (cc > axis_cc) {
+                    axis_cc = cc;
+                    axis_best = cand;
+                }
+            }
+            best = axis_best;
+            best_cc = axis_cc;
+        }
+        CrystalLattice scale_best = best;
+        double scale_cc = best_cc;
+        for (int i = -n_scale; i <= n_scale; ++i) {
+            if (i == 0)
+                continue;
+            const double s = 1.0 / (1.0 + i * step); // cell scale (1+eps) -> recip * 1/(1+eps)
+            CrystalLattice cand = best.Multiply(gemmi::Mat33(s, 0, 0, 0, s, 0, 0, 0, s));
+            const double cc = score(cand);
+            if (cc > scale_cc) {
+                scale_cc = cc;
+                scale_best = cand;
+            }
+        }
+        best = scale_best;
+        best_cc = scale_cc;
+    }
+
+    data.latt = best;
 }
 
 template<class T>
@@ -587,10 +751,21 @@ void PixelRefine::Run(const T *image,
     data.solved = false;
     data.reflections.clear();
 
+    // Global orientation + cell-scale sweep before the local LSQ, to recentre the
+    // high-resolution shoeboxes onto signal that small misalignments hide.
+    if (data.sweep_orientation)
+        SweepOrientationCell(image, prediction, data);
+
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
 
-    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
+    };
 
     const int radius = data.shoebox_radius;
     const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
@@ -628,6 +803,7 @@ void PixelRefine::Run(const T *image,
     double latt_vec0[3] = {0, 0, 0}; // orientation (Rodrigues)
     double latt_vec1[3] = {0, 0, 0}; // lengths
     double latt_vec2[3] = {0, 0, 0}; // angles (rad)
+    double orient_prior[3] = {0, 0, 0}; // pre-refinement orientation (regularization anchor)
 
     const bool eval_only = (data.max_iterations <= 0);
     const int n_iter = std::max(1, data.max_iterations);
@@ -694,17 +870,32 @@ void PixelRefine::Run(const T *image,
 
                     const double Iobs = static_cast<double>(image[npixel]); // raw counts
 
-                    // Per-pixel variance: Poisson noise of the raw counts.
-                    double var = std::max(Iobs, 0.0);
-                    if (!(var > 1.0))
-                        var = 1.0;
+                    // Variance for the fit weight. Weighting by the observed count
+                    // (var = Iobs) lets down-fluctuated background pixels carry the
+                    // largest 1/sqrt(var) weight, which biases the fit towards "no
+                    // signal" and drove the per-image scale G to 0 on weak images
+                    // (collapsing the merge). Use the local background as the
+                    // (background-limited) variance, constant over the shoebox - the
+                    // same de-biasing applied to the extraction.
+                    double var = std::max(Ibkg, 1.0);
+                    double weight = 1.0 / std::sqrt(var);
+
+                    // Signal-weighting: down-weight pixels far from the predicted spot
+                    // centre so the empty shoebox corners cannot dilute or destabilise
+                    // the fit; the signal-bearing core drives the refined parameters.
+                    if (data.fit_signal_sigma_pix > 0.0) {
+                        const double dx = x - g.predicted_x;
+                        const double dy = y - g.predicted_y;
+                        const double s2 = data.fit_signal_sigma_pix * data.fit_signal_sigma_pix;
+                        weight *= std::exp(-0.5 * (dx * dx + dy * dy) / s2);
+                    }
 
                     PixelObs obs{
                         .x = static_cast<double>(x),
                         .y = static_cast<double>(y),
                         .Iobs = Iobs,
                         .Ibkg = Ibkg,
-                        .weight = 1.0 / std::sqrt(var)
+                        .weight = weight
                     };
                     g.pixels.push_back(obs);
                 }
@@ -721,6 +912,12 @@ void PixelRefine::Run(const T *image,
         BuildParameterBlocks(data, beam, dist_mm, detector_rot,
                              latt_vec0, latt_vec1, latt_vec2);
 
+        // Anchor for orientation regularization = the spot-centroid orientation we
+        // started from (captured before any pixel-level refinement moved it).
+        if (iter == 0)
+            for (int i = 0; i < 3; ++i)
+                orient_prior[i] = latt_vec0[i];
+
         // ---- 4. Build the problem ---------------------------------------------
         // One residual block per shoebox (N residuals), so the expensive
         // per-reflection node geometry is evaluated once per reflection instead
@@ -753,8 +950,21 @@ void PixelRefine::Run(const T *image,
         data.residual_count = residual_pixels;
 
         // ---- 5. Constrain / bound parameter blocks ----------------------------
-        if (!data.refine_orientation)
+        if (!data.refine_orientation) {
             problem.SetParameterBlockConstant(latt_vec0);
+        } else if (data.orient_reg_sigma_deg > 0.0) {
+            // Anchor orientation to its spot-centroid prior. The weight is scaled to
+            // the *pixel* data term (sqrt(n_pixels)/sigma_rad), not the reflection
+            // count - the data has one residual per shoebox pixel, so a reflection-
+            // scaled prior (~50x too weak) was simply not felt. At a misorientation of
+            // orient_reg_sigma_deg the prior matches the data, so the fit only moves
+            // further when the pixels strongly agree it should.
+            const double sigma_rad = std::max(data.orient_reg_sigma_deg * M_PI / 180.0, 1e-9);
+            const double w = std::sqrt(static_cast<double>(residual_pixels)) / sigma_rad;
+            auto *reg = new ceres::AutoDiffCostFunction<OrientationRegularizer, 3, 3>(
+                new OrientationRegularizer(w, orient_prior));
+            problem.AddResidualBlock(reg, nullptr, latt_vec0);
+        }
 
         if (!data.refine_unit_cell) {
             problem.SetParameterBlockConstant(latt_vec1);
@@ -789,10 +999,20 @@ void PixelRefine::Run(const T *image,
             }
         }
 
-        if (data.refine_scale)
+        if (data.refine_scale) {
             problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
-        else
+            // Regularize G towards 1 so weakly-constrained images cannot wander
+            // (an unconstrained 1/G is what collapsed the cross-image merge). Weight
+            // scaled to the pixel data term (n_pixels), not the reflection count.
+            if (data.scale_reg_sigma > 0.0) {
+                const double w = std::sqrt(static_cast<double>(residual_pixels) / data.scale_reg_sigma);
+                auto *reg = new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
+                    new ScalarRegularizer(w, 1.0));
+                problem.AddResidualBlock(reg, nullptr, &data.scale_factor);
+            }
+        } else {
             problem.SetParameterBlockConstant(&data.scale_factor);
+        }
 
         if (!data.refine_B)
             problem.SetParameterBlockConstant(&data.B_factor);
@@ -939,9 +1159,15 @@ void PixelRefine::Run(const T *image,
                     continue;
 
                 const double Iobs = static_cast<double>(image[np]); // raw counts
-                double v = std::max(Iobs, 0.0);                     // Poisson variance
-                if (!(v > 1.0))
-                    v = 1.0;
+                // Variance for the profile-fit weights. Weighting by the *observed*
+                // per-pixel count (v = Iobs) biases the amplitude negative: a
+                // down-fluctuated background pixel gets the smallest v and hence the
+                // largest 1/v weight, so num = sum P_t (Iobs - Ibkg)/v is pulled below
+                // zero - worst where the signal is weakest, i.e. the high-resolution
+                // shells (the negative <I/sig> we see there). For background-limited
+                // reflections the variance is the local background, constant over the
+                // shoebox, so use that instead of the observed count.
+                double v = std::max(g.Ibkg, 1.0);
 
                 // Peak-normalized radial factor (the partiality), in (0,1]. The
                 // bandwidth-broadened radial width matches the model in Model().
@@ -1069,7 +1295,13 @@ std::vector<float> PixelRefine::PredictImage(const T *image,
             .PoniRot1_rad(data.geom.GetPoniRot1_rad())
             .PoniRot2_rad(data.geom.GetPoniRot2_rad());
 
-    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
+    };
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
     const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
@@ -1158,7 +1390,13 @@ std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
             .PoniRot1_rad(data.geom.GetPoniRot1_rad())
             .PoniRot2_rad(data.geom.GetPoniRot2_rad());
 
-    const BraggPredictionSettings settings_prediction = BuildPredictionSettings(data);
+    const BraggPredictionSettings settings_prediction{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)
+    };
     const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
     const auto &predicted = prediction.GetReflections();
     const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index ffcc08bd..fc4acabd 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -129,7 +129,50 @@ struct PixelRefineData {
     bool refine_detector_angles = false;
     bool refine_scale           = true;
     bool refine_B               = false;
-    bool refine_R               = true;
+    bool refine_R               = false; // per-image R refinement is unstable on sparse
+                                         // stills; R is held at its nominal value
+
+    // Orientation refinement is anchored to the pre-refinement (spot-centroid)
+    // orientation with weight sqrt(n_refl)/sigma, so the pixel fit can only nudge
+    // the orientation by ~this many degrees before the prior pushes back. This is
+    // what turns the (otherwise overfitting) 3-DOF orientation refinement into a
+    // small, signal-supported sub-spot correction. Larger => freer; very large
+    // approaches the unregularized (collapsing) fit. ~1 deg gives the best CCref here;
+    // beyond ~2 deg the per-image fit overfits and the merge collapses.
+    double orient_reg_sigma_deg = 1.0;
+
+    // Signal-weighting of the *fit* residuals: each pixel's weight is multiplied by
+    // a detector-space Gaussian exp(-r^2/2 sigma^2) centred on the predicted spot, so
+    // the many empty shoebox-corner pixels stop diluting (and destabilising) the fit
+    // and the signal-bearing core drives the refined scale/R. <= 0 disables (uniform).
+    double fit_signal_sigma_pix = 1.5;
+
+    // Per-image scale G is regularized towards 1 with weight sqrt(n_refl/scale_reg_sigma)
+    // (mirrors ScaleOnTheFly). Without this the unconstrained G wanders on weakly
+    // measured images and 1/G scrambles the cross-image merge. <= 0 disables.
+    double scale_reg_sigma = 2.0;
+
+    // Radial Ewald-sphere acceptance band for prediction (A^-1): a reflection is
+    // given a shoebox when ||S|-1/lambda| <= this. The narrow default predicts only
+    // reflections already on the Ewald sphere; widening it (towards the integrator's
+    // ~2-3x profile radius) lets in the slightly-misaligned high-resolution
+    // reflections - more multiplicity, and something for orientation refinement to
+    // actually centre. Safe to widen only with the per-image fit kept well-behaved
+    // (de-biased variance + signal-weighting + regularization, all default here).
+    double ewald_dist_cutoff = 0.0020;
+
+    // Pre-LSQ global orientation+cell sweep (maximises CC vs reference over the
+    // strongest reflections). Bounds are derived from the detector geometry: the
+    // step moves the highest-resolution spot by 1 px, the range moves the lowest-
+    // resolution spot by ~2 px (rotation) / ~1 px (cell scale), so the low-res
+    // XtalOptimizer solution is preserved while high-res spots are recentred.
+    bool   sweep_orientation = false;
+    // Sweep half-range as the *orientation uncertainty* (degrees) and cell-scale
+    // uncertainty (fraction). These set how far the highest-resolution spot may move
+    // (a few px); low-res spots barely move and stay anchored. Keep small - a large
+    // range lets the per-image CC overfit and degrades the merge.
+    double sweep_max_deg = 0.15;
+    double sweep_max_cell_frac = 0.003;
 
     double max_time_s = 5.0;
     int    shoebox_radius = 3; // half-size of the per-reflection signal box (peak region that enters the fit)
@@ -164,12 +207,14 @@ class PixelRefine {
                               double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
 
-    // Bragg-prediction settings shared by Run/PredictImage/ChiSquaredImage so all
-    // three predict an identical reflection set. Critically it sets the radial
-    // Ewald-acceptance band (ewald_dist_cutoff) and the bandwidth broadening - see
-    // the definition for why these must track the partiality model, not the
-    // BraggPredictionSettings struct defaults.
-    BraggPredictionSettings BuildPredictionSettings(const PixelRefineData &data) const;
+    // Global orientation + uniform cell-scale sweep run before the LSQ. Re-projects
+    // the strongest reference reflections through candidate lattices and keeps the
+    // one maximising CC vs the reference intensities (coordinate descent over the 3
+    // Rodrigues axes + cell scale, within geometry-derived pixel bounds). Writes the
+    // refined orientation/cell back into data.latt. See PixelRefineData::sweep_*.
+    template<class T>
+    void SweepOrientationCell(const T *image, BraggPrediction &prediction,
+                              PixelRefineData &data) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const std::vector<MergedReflection> &reference);
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 5876418b..61ea164d 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -12,6 +12,9 @@
 #include <fstream>
 #include <sstream>
 #include <getopt.h>
+#include <algorithm>
+#include <numeric>
+#include <cmath>
 
 #include "../reader/JFJochHDF5Reader.h"
 #include "../common/Logger.h"
@@ -968,6 +971,27 @@ int main(int argc, char **argv) {
             logger.Info("Reference provided: per-image live scaling already applied; merging directly");
         }
 
+        // --- Phase 1 diagnostic: distribution of the per-image scale CC vs the
+        // reference. High per-image CC with low merged CC1/2 => each image is fine
+        // and the cross-image merge is the problem; low per-image CC => the
+        // per-image extraction itself is noise. Logged for any reference run.
+        {
+            std::vector<float> ccs;
+            for (const auto &i : indexer.GetIntegrationOutcome())
+                if (i.image_scale_cc && std::isfinite(*i.image_scale_cc))
+                    ccs.push_back(*i.image_scale_cc);
+            if (!ccs.empty()) {
+                std::sort(ccs.begin(), ccs.end());
+                const double mean = std::accumulate(ccs.begin(), ccs.end(), 0.0) / ccs.size();
+                auto q = [&](double f) { return ccs[std::min(ccs.size() - 1, static_cast<size_t>(f * ccs.size()))]; };
+                logger.Info("Per-image scale CC vs reference: n={} mean={:.3f} median={:.3f} "
+                            "p10={:.3f} p90={:.3f} min={:.3f} max={:.3f}",
+                            ccs.size(), mean, q(0.5), q(0.1), q(0.9), ccs.front(), ccs.back());
+            } else {
+                logger.Info("Per-image scale CC vs reference: none available");
+            }
+        }
+
         auto merge_start = std::chrono::steady_clock::now();
 
         MergeOnTheFly merge_engine(experiment);
-- 
2.52.0


From 3cdf26232cd2b121677a76af49b13f24ff8eb1de Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 17:29:28 +0200
Subject: [PATCH 036/228] PixelRefine: Document on local changes

---
 image_analysis/pixel_refinement/METHODS.md | 253 +++++++++++++++++++++
 1 file changed, 253 insertions(+)
 create mode 100644 image_analysis/pixel_refinement/METHODS.md

diff --git a/image_analysis/pixel_refinement/METHODS.md b/image_analysis/pixel_refinement/METHODS.md
new file mode 100644
index 00000000..f585ffe5
--- /dev/null
+++ b/image_analysis/pixel_refinement/METHODS.md
@@ -0,0 +1,253 @@
+# PixelRefine — methods and improvements
+
+This note documents the changes made to the still-image *pixel-refinement* integrator
+(`PixelRefine`) and, more importantly, **why** each one was needed. It is written from a
+methods point of view; the equations are the load-bearing part.
+
+`PixelRefine` integrates Bragg reflections on a **still** image by fitting a per-pixel
+forward model against a known *reference* intensity set (e.g. `F_calc` from a deposited
+model). Unlike a rotation experiment, a still samples only a thin slice of each
+reflection, so the integrator must (a) model the partiality of that slice, (b) refine the
+per-image geometry well enough that the high-resolution shoeboxes land on signal, and
+(c) scale each image onto the reference. Each of those three is where the original code
+went wrong.
+
+Throughout, a reflection's shoebox is a small box of raw detector pixels $I_p$ with a
+local flat background $B$; the (area-normalised) model spot profile at pixel $p$ is
+$P_p$, and $v_p$ is the variance used to weight pixel $p$.
+
+---
+
+## 0. The forward model
+
+The recorded amplitude of a still reflection is estimated by profile fitting:
+
+$$
+J \;=\; \frac{\sum_p w_p\,P_p\,(I_p - B)}{\sum_p w_p\,P_p^{2}},
+\qquad w_p = \frac{1}{v_p},
+\qquad \operatorname{var}(J) = \frac{1}{\sum_p P_p^{2}/v_p}.
+$$
+
+The full (rotation-equivalent) intensity is recovered by dividing out the factors a still
+does not record,
+
+$$
+I \;=\; \frac{J}{p\,B_\mathrm{DW}\,\mathrm{pol}},\qquad
+p = \exp\!\left(-\frac{\epsilon_r^{2}}{R_0^{2}}\right),\quad
+B_\mathrm{DW}=\exp\!\left(-\frac{B_\mathrm{fac}}{4 d^{2}}\right),
+$$
+
+where the **partiality** $p$ is the fraction of the mosaic block crossing the Ewald
+sphere, $\epsilon_r = 1/\lambda - |S_{hkl}|$ is the excitation error, $R_0$ the radial
+(rocking) width, and $\mathrm{pol}$ the polarisation correction. The per-image model
+intensity for a pixel is
+
+$$
+I_p^\mathrm{model} = G\,I^\mathrm{ref}\,B_\mathrm{DW}\,p\,P^\mathrm{tang}_p\,\mathrm{pol} + B,
+$$
+
+with $G$ the per-image scale. The per-image least squares minimises
+$\chi^2 = \sum_p w_p\,(I_p^\mathrm{model}-I_p)^2$ over geometry, orientation, $G$, $R$.
+
+---
+
+## 1. De-biased variance (the load-bearing fix)
+
+**Symptom.** Mean intensities went **negative** in the high-resolution shells
+($\langle I/\sigma\rangle$ down to $-12$), which a box-sum integrator never does. The
+per-image scale $G$ also collapsed to $0$ on most images, dropping ~80 % of observations.
+
+**Cause.** Both the extraction and the fit weighted each pixel by its **observed** count,
+$v_p = I_p$. For a background pixel that fluctuated *down* ($I_p < B$), $v_p$ is small, so
+$w_p = 1/v_p$ is *large*, and its contribution $P_p (I_p-B)/v_p < 0$ is large in
+magnitude. Summed over the many (mostly empty) shoebox pixels, this drags $J$ below zero —
+the classic *inverse-observed-count* (Poisson-on-data) bias. It bites hardest where the
+true signal is weakest, i.e. at high resolution. In the fit it manifests differently but
+identically in origin: the weighted empty pixels make "no signal" ($G=0$) the cheapest
+solution, so $G\to 0$.
+
+**Fix.** For background-limited (weak) reflections the correct variance is the local
+background, **constant over the shoebox**:
+
+$$
+v_p = \max(B,\,1)\quad\Longrightarrow\quad
+J = \frac{\sum_p P_p\,(I_p-B)}{\sum_p P_p^{2}},
+$$
+
+the unbiased uniform-variance estimator. This single change turned $\langle I/\sigma\rangle$
+positive at all resolutions and stopped the scale collapse. It is applied to both the
+extraction weight and the fit weight.
+
+---
+
+## 2. Prediction band and multiplicity
+
+**Symptom.** PixelRefine recorded ~4× fewer observations per unique reflection than the
+classical integrator — completeness was fine, *redundancy* was not.
+
+**Cause.** A reflection is given a shoebox only when it lies within a radial band of the
+Ewald sphere,
+
+$$
+\bigl|\,|S_{hkl}| - 1/\lambda\,\bigr| \le \delta .
+$$
+
+For randomly oriented stills the number of images on which a given $hkl$ satisfies this is
+$\propto \delta$. The default $\delta = 5\times10^{-4}\,\text{Å}^{-1}$ was 4–6× tighter
+than the classical integrator's $\delta = 2\text{–}3\times r_\mathrm{profile}$, so each
+reflection was recorded on 4–6× fewer images.
+
+**Fix.** Widen to $\delta = 2\times10^{-3}\,\text{Å}^{-1}$. Multiplicity rose from
+~240 k to ~950 k observations and CC$_\mathrm{ref}$ from 49.7 % to 55.9 %. Widening is
+only safe once the fit is well-behaved (Sections 1, 3, 4); with the original
+unconstrained fit it caused divergence.
+
+---
+
+## 3. Regularising the per-image fit
+
+**Symptom.** Freeing *any* per-image parameter (orientation, $R$, even the scalar scale
+$G$) collapsed the merged data (CC$_{1/2}$ from 90 % to a few %). The predict↔refine loop
+with all parameters frozen was, by contrast, byte-identical to extraction-only — proving
+the *fit*, not the loop, was at fault.
+
+**Cause.** The per-image problem regularised **nothing**: orientation had no prior, $R$
+and $G$ only a lower bound. Three orientation DOF (plus $R$, $G$) against a handful of
+signal pixels per still overfit the noise, and an unconstrained $1/G$ then scrambled the
+cross-image merge.
+
+**Fix.** Anchor each refined parameter to its prior with a *data-scaled* weight, as
+`ScaleOnTheFly` already does for rotation data. The data term has one residual **per
+pixel**, so the prior weight must scale with the pixel count:
+
+$$
+w_\theta = \sqrt{\frac{N_\mathrm{pix}}{\sigma_\theta^{2}}}\,,
+\qquad \chi^2_\mathrm{reg} = w_\theta^{2}\,(\theta-\theta_0)^2 .
+$$
+
+Using $\sqrt{N_\mathrm{refl}}$ instead (as in the rotation scaler) is a factor
+$\sqrt{N_\mathrm{pix}/N_\mathrm{refl}}\approx\sqrt{49}\approx 7$ too weak and is simply not
+felt. Applied to:
+
+* **Scale**: $\theta=G,\ \theta_0=1$. Prevents $1/G$ from wandering; restored CC$_{1/2}$
+  from 4 % back to 87 %.
+* **Orientation**: $\theta$ = Rodrigues vector, $\theta_0$ = spot-centroid orientation,
+  $\sigma_\theta$ in radians. At $\sigma_\theta\!\sim\!1^\circ$ this gives the best
+  CC$_\mathrm{ref}$; beyond $\sim 2^\circ$ the fit overfits and the merge collapses, so
+  $\sigma_\theta$ is the safety knob.
+
+---
+
+## 4. Signal-weighting the fit
+
+**Cause.** Even de-biased, a shoebox is ~80 % empty pixels (≈ 40 of 49 for a radius-3
+box). They carry no information on $G$, $R$ or orientation but add noise and, near the
+overfitting edge, destabilise the fit.
+
+**Fix.** Multiply the fit weight by a detector-space Gaussian centred on the predicted
+spot,
+
+$$
+w_p \;\to\; w_p \cdot \exp\!\left(-\frac{r_p^{2}}{2\sigma_s^{2}}\right),
+\qquad r_p = \lVert (x_p,y_p) - (x_\mathrm{pred},y_\mathrm{pred})\rVert,
+$$
+
+so the signal-bearing core drives the refined parameters ($\sigma_s\approx 1.5$ px). With
+the regularised orientation this lifted CC$_\mathrm{ref}$ from 60.5 % to **62.6 %**.
+
+---
+
+## 5. Global orientation + cell-scale sweep
+
+**Motivation.** The classical refinement (`XtalOptimizer`) works on spot *centroids* from
+spot-finding, which are poor value at high resolution; the local LSQ above is a heavy
+gradient step that cannot make the ~degree-scale global moves needed to pull a
+mis-indexed crystal's high-resolution reflections onto their shoeboxes. A small,
+**global** sweep that simply asks *"at which orientation does the most high-resolution
+signal appear where the reference says it should?"* is structurally better suited.
+
+**Score.** Pearson CC of the box-summed intensities against the reference, over **all**
+matched reflections (not just the strong ones):
+
+$$
+\mathrm{CC}_\mathrm{ref}(L) = \operatorname{corr}_{hkl}\bigl(\,I^\mathrm{box}_{hkl}(L),\ I^\mathrm{ref}_{hkl}\,\bigr).
+$$
+
+The strong low-resolution reflections **anchor** the CC (moving them off their boxes
+collapses it), so the *change* in CC across the sweep is driven almost entirely by weak
+high-resolution reflections falling onto — or off — real signal. This is the "appearing
+out of the void" behaviour.
+
+**Geometry-derived bounds (parameter-free).** A spot at resolution $d$ sits at detector
+radius
+
+$$
+r(d) = \frac{L}{p}\,\frac{\lambda}{d}\quad[\text{px}],
+$$
+
+($L$ = detector distance, $p$ = pixel size). Both a crystal rotation $\delta\theta$ and a
+fractional cell-scale $\epsilon$ displace that spot by an amount proportional to its
+radius:
+
+$$
+\Delta_\mathrm{px} = r(d)\,\delta\theta \quad(\text{rotation}),\qquad
+\Delta_\mathrm{px} = r(d)\,\epsilon \quad(\text{cell scale}).
+$$
+
+So high-resolution spots (large $r$) move most. The two natural constraints fix the grid:
+
+* **Step** = 1 px at the highest resolution: $\;\delta\theta_\mathrm{step} = 1/r_\mathrm{max}$
+  (finer is below the detector's resolving power).
+* **Range** = the orientation uncertainty $\Delta\theta_u$ (a few px at high res). The
+  number of steps per axis is then
+
+$$
+n = \frac{\Delta\theta_u}{\delta\theta_\mathrm{step}} = \Delta\theta_u\, r_\mathrm{max},
+$$
+
+a handful of steps, and the lowest-resolution spots move only
+$n\,\delta\theta_\mathrm{step}\,r_\mathrm{min} = \Delta\theta_u\, r_\mathrm{min} \ll 2$ px
+— i.e. the strong anchors stay put by construction.
+
+> **Lesson learned.** Setting the range from "2 px at low resolution" instead gives
+> $n = 2\,r_\mathrm{max}/r_\mathrm{min} = 2\,d_\mathrm{low}/d_\mathrm{high}$ steps — tens
+> of pixels of high-resolution freedom — which lets the per-image CC overfit and *degrades*
+> the merge. The range must be tied to the (small) orientation uncertainty, not the
+> low-resolution cap.
+
+The sweep is a coordinate descent over the three Rodrigues axes and the cell scale, run
+**before** the LSQ. It improves the high-resolution shells (CC$_\mathrm{ref}$ +1 to +5
+per shell) while preserving CC$_{1/2}\approx 90$ %. It is an *alternative* to the
+loose-$\sigma$ orientation LSQ, not a complement — stacking the two double-moves the
+orientation and overfits. It is therefore available but **off by default**.
+
+---
+
+## Results (lysozyme jet, 1.8 Å, identical input)
+
+| Configuration | N_obs | Compl. | CC$_{1/2}$ | CC$_\mathrm{ref}$ |
+|---|---:|---:|---:|---:|
+| Classical integrator (box-sum) | 421 k | 100 % | 81.4 % | 60.9 % |
+| PixelRefine — original | 61 k | 95 % | 0.0 % | −0.4 % |
+| PixelRefine — consolidated (this work) | 951 k | 100 % | 80.0 % | **62.6 %** |
+
+The consolidated integrator beats the classical one on the accuracy metric
+(CC$_\mathrm{ref}$) with > 2× the multiplicity, and turns a previously unusable result
+(CC$_{1/2}=0$) into a competitive one.
+
+---
+
+## Default recipe (`PixelRefineData`)
+
+| Field | Default | Section |
+|---|---|---|
+| variance | local background $B$ | 1 |
+| `ewald_dist_cutoff` | $2\times10^{-3}\,\text{Å}^{-1}$ | 2 |
+| `scale_reg_sigma` | 2.0 | 3 |
+| `orient_reg_sigma_deg` | 1.0 | 3 |
+| `refine_R` | `false` | 3 |
+| `fit_signal_sigma_pix` | 1.5 | 4 |
+| `sweep_orientation` | `false` (available) | 5 |
+
+`orient_reg_sigma_deg` (accuracy vs. precision) and `ewald_dist_cutoff` (multiplicity vs.
+cost) are the two knobs worth tuning per dataset.
-- 
2.52.0


From e6a50b45c7c8546ad471370f434f5c3ce99636ad Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 18:39:32 +0200
Subject: [PATCH 037/228] Integration: mean background + global error model
 (trustworthy sigmas)

Background estimate: use the mean of the local ring, not the median. For a
right-skewed (Poisson) background the median sits below the mean, so subtracting
it under-subtracts and biases every weak intensity positive; over multiplicity
this becomes fake <I/sig> of a few in no-signal high-resolution shells. Fixed in
both PixelRefine and BraggIntegrate2D (the classical route had the same bug).
<I/sig> now tracks CC honestly and the true resolution limit is visible.

Error model: fit a global a, b (XDS form sigma'^2 = a*sigma^2 + (b*I)^2) from the
scatter of symmetry equivalents at the merge level (so both integrators benefit),
and print it with ISa = 1/b in jfjoch_process. The (b*I)^2 term uses the
reflection mean (not the per-observation I_i, which biases the weights and
collapses CC); a,b come from a relative-weighted bin regression. Replaces the
earlier per-resolution-shell variant, which was partly masking the background bias.

METHODS.md: document both (Sections 6-7), integrator-agnostic.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../bragg_integration/BraggIntegrate2D.cpp    |  26 +---
 image_analysis/pixel_refinement/METHODS.md    |  81 +++++++++++-
 .../pixel_refinement/PixelRefine.cpp          |  16 ++-
 image_analysis/scale_merge/Merge.cpp          | 124 +++++++++++++++++-
 image_analysis/scale_merge/Merge.h            |  22 ++++
 tools/jfjoch_process.cpp                      |  10 ++
 6 files changed, 251 insertions(+), 28 deletions(-)

diff --git a/image_analysis/bragg_integration/BraggIntegrate2D.cpp b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
index b616ecc1..22339929 100644
--- a/image_analysis/bragg_integration/BraggIntegrate2D.cpp
+++ b/image_analysis/bragg_integration/BraggIntegrate2D.cpp
@@ -9,24 +9,6 @@
 
 namespace {
 
-template<class T>
-float Median(std::vector<T> &values) {
-    if (values.empty())
-        return 0.0f;
-
-    const size_t middle = values.size() / 2;
-    std::nth_element(values.begin(), values.begin() + middle, values.end());
-
-    if (values.size() % 2 == 1)
-        return static_cast<float>(values[middle]);
-
-    const T upper = values[middle];
-    std::nth_element(values.begin(), values.begin() + middle - 1, values.begin() + middle);
-    const T lower = values[middle - 1];
-
-    return 0.5f * static_cast<float>(lower + upper);
-}
-
 void MarkReflectionMask(std::vector<uint8_t> &mask,
                         size_t xpixel, size_t ypixel,
                         const Reflection &r, float r_2, float r_2_sq) {
@@ -123,7 +105,13 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
     }
 
     if ((I_npixel_integrated == I_npixel_inner) && (bkg_values.size() > 5)) {
-        r.bkg = Median(bkg_values);
+        // Mean, not median: the median of a right-skewed (Poisson) background sits below
+        // the mean, so subtracting it under-subtracts and biases weak intensities
+        // positive (fake <I/sig> in no-signal high-resolution shells).
+        double bkg_sum = 0.0;
+        for (const T v : bkg_values)
+            bkg_sum += static_cast<double>(v);
+        r.bkg = static_cast<float>(bkg_sum / static_cast<double>(bkg_values.size()));
         r.I = static_cast<float>(I_sum) - static_cast<float>(I_npixel_integrated) * r.bkg;
         if (I_sum > 0) {
             r.observed_x = static_cast<float>(I_sum_x) / static_cast<float>(I_sum);
diff --git a/image_analysis/pixel_refinement/METHODS.md b/image_analysis/pixel_refinement/METHODS.md
index f585ffe5..8604ffc7 100644
--- a/image_analysis/pixel_refinement/METHODS.md
+++ b/image_analysis/pixel_refinement/METHODS.md
@@ -223,6 +223,76 @@ orientation and overfits. It is therefore available but **off by default**.
 
 ---
 
+## 6. Background-estimator bias (the largest σ error; both integrators)
+
+**Symptom.** Pushed past the true resolution limit (e.g. a 1.8 Å crystal merged to 1.3 Å),
+the no-signal shells still reported $\langle I/\sigma\rangle \approx 4\text{–}6$ with
+$\mathrm{CC}_{1/2}\approx 0$ — i.e. confident "data" where there is none. Present in *both*
+`PixelRefine` and the classical `BraggIntegrate2D`.
+
+**Cause.** Both estimated the local background as the **median** of the surrounding ring.
+For a Poisson / right-skewed background the median sits *below* the mean,
+
+$$
+\operatorname{median}(B) < \mathbb{E}[B],
+$$
+
+so subtracting it under-subtracts on every pixel. The leftover positive offset is tiny per
+pixel but coherent, so over an $n_\mathrm{pix}$-pixel peak and a multiplicity-$m$ merge it
+grows to a fake signal
+
+$$
+\langle I\rangle_\mathrm{bias} \;\approx\; n_\mathrm{pix}\,\bigl(\mathbb{E}[B]-\operatorname{median}(B)\bigr),
+\qquad
+\Bigl(\tfrac{I}{\sigma}\Bigr)_\mathrm{merged,\,bias} \propto \sqrt{m}.
+$$
+
+It is worst where the real signal is weakest (high resolution), because there the offset is
+all that remains — which is exactly the observed signature. *Nothing leaks into the
+high-resolution shells; the background is simply under-estimated.*
+
+**Fix.** Use the **mean** of the ring (outliers excluded by the existing spot-core mask and
+saturation sentinels). $\langle I/\sigma\rangle$ then collapses to ~0 wherever
+$\mathrm{CC}\approx0$, tracks CC down the shells, and the honest resolution limit becomes
+visible. This was the single largest contributor to untrustworthy σ — a one-line change in
+each integrator, *not* a variance-model problem.
+
+---
+
+## 7. Error model (global $a, b$; XDS form)
+
+Counting statistics under-estimate the variance of strong reflections, which carry
+systematic errors (scaling, partiality, detector) proportional to intensity, not to
+$\sqrt{I}$. After merging, this leaves CC$_{1/2}$ and $\langle I/\sigma\rangle$
+inconsistent. The standard correction (XDS / DIALS / AIMLESS) inflates the variance with a
+**global** two-parameter model:
+
+$$
+\sigma'^{\,2} \;=\; a\,\sigma^{2} + \bigl(b\,\langle I\rangle\bigr)^{2},
+\qquad
+\mathrm{ISa} \;=\; \frac{1}{b}\;=\;\lim_{I\to\infty}\frac{I}{\sigma'} .
+$$
+
+Two points matter for an unbiased fit:
+
+* The $I^2$ term uses the reflection **mean** $\langle I\rangle$ (constant over its
+  observations), **not** the per-observation $I_i$. Using $I_i$ gives a down-fluctuated
+  point a small $\sigma'$ and hence a large $1/\sigma'^2$ weight, biasing the merged mean —
+  which collapses CC. (This was the decisive bug in the first attempt.)
+* $a$ and $b$ are fit from the spread of symmetry equivalents: for an observation in a
+  group of $n$, $\mathbb{E}[(I_i-\langle I\rangle)^2] = \sigma_i^2(1-h_i)$ with leverage
+  $h_i = w_i/\sum w$. Binning by intensity and regressing the bin medians of
+  $(I_i-\langle I\rangle)^2/(1-h_i)$ on $(\sigma^2, \langle I\rangle^2)$ — *weighted by
+  $1/\mathrm{dev}^4$ so the fit is relative* — gives $(a, b^2)$; the relative weight stops
+  the strong bins (which fix $b$) from swamping the weak bins (which fix $a$).
+
+It is applied at the merge level (`MergeOnTheFly`), so **both** integrators benefit, and
+`jfjoch_process` prints the model and ISa. Earlier per-resolution-shell variants were
+dropped: the standard tools use a single global $a, b$, and the per-shell version was
+partly masking the background bias of Section 6.
+
+---
+
 ## Results (lysozyme jet, 1.8 Å, identical input)
 
 | Configuration | N_obs | Compl. | CC$_{1/2}$ | CC$_\mathrm{ref}$ |
@@ -237,17 +307,22 @@ The consolidated integrator beats the classical one on the accuracy metric
 
 ---
 
-## Default recipe (`PixelRefineData`)
+## Default recipe
 
-| Field | Default | Section |
+Sections 1–5 are `PixelRefine`-specific; Sections 6–7 act at the integration/merge level
+and apply to the classical route too.
+
+| Field / behaviour | Default | Section |
 |---|---|---|
-| variance | local background $B$ | 1 |
+| fit/extraction variance | local background $B$ | 1 |
 | `ewald_dist_cutoff` | $2\times10^{-3}\,\text{Å}^{-1}$ | 2 |
 | `scale_reg_sigma` | 2.0 | 3 |
 | `orient_reg_sigma_deg` | 1.0 | 3 |
 | `refine_R` | `false` | 3 |
 | `fit_signal_sigma_pix` | 1.5 | 4 |
 | `sweep_orientation` | `false` (available) | 5 |
+| local background estimator | **mean** of the ring | 6 |
+| merge error model | global $a,b$ (ISa printed) | 7 |
 
 `orient_reg_sigma_deg` (accuracy vs. precision) and `ewald_dist_cutoff` (multiplicity vs.
 cost) are the two knobs worth tuning per dataset.
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 7fbc57a5..c398b9d3 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -104,9 +104,9 @@ ShoeboxBox ShoeboxBounds(double px, double py, int radius, size_t xpixel, size_t
 // Local flat background around one shoebox, in raw detector counts. Samples the
 // square ring shoebox_radius < max(|dx|,|dy|) <= bkg_outer_radius centred on the
 // spot, dropping pixels that belong to any spot core (spot_mask) or carry a
-// masked/saturated sentinel, and returns the median (robust to residual spot
-// tails / zingers). Mirrors the local-background of BraggIntegrate2D, replacing
-// the azimuthal-bin mean that proved a poor proxy for reflection background.
+// masked/saturated sentinel, and returns their MEAN. (The median, used previously,
+// sits below the mean for a skewed background and so biases the subtracted intensity
+// positive.) Mirrors the local-background region of BraggIntegrate2D.
 template<class T>
 bool EstimateLocalBackground(const T *image,
                              const std::vector<uint8_t> &spot_mask,
@@ -143,7 +143,15 @@ bool EstimateLocalBackground(const T *image,
     if (vals.size() < 5)
         return false;
 
-    bkg_mean = MedianInPlace(vals);
+    // Mean background, NOT median. The median of a right-skewed (Poisson) background sits
+    // below the mean, so subtracting it under-subtracts and biases every weak integrated
+    // intensity positive - which averages up over multiplicity into fake <I/sig> in the
+    // no-signal high-resolution shells. The mean is unbiased; modern fast detectors put
+    // few zingers in the ring, so it is not robustified here.
+    double sum = 0.0;
+    for (const double v : vals)
+        sum += v;
+    bkg_mean = sum / static_cast<double>(vals.size());
     return true;
 }
 
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 4f4fd8ee..3acf2ba4 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -58,12 +58,12 @@ void MergeOnTheFly::AddImage(const IntegrationOutcome &outcome, bool cc_mask) {
             continue;
 
         const float I_corr = r.I * r.image_scale_corr;
-        const float sigma_corr = r.sigma * r.image_scale_corr;
+        float sigma_corr = r.sigma * r.image_scale_corr;
         if (!std::isfinite(I_corr) || !std::isfinite(sigma_corr) || sigma_corr <= 0.0)
             continue;
-
         auto hkl = generator(r);
         auto hkl_key = hkl.pack();
+        sigma_corr = CorrectedSigma(I_corr, sigma_corr, hkl_key);
 
         auto it = accumulator.find(hkl_key);
         if (it == accumulator.end())
@@ -88,6 +88,126 @@ void MergeOnTheFly::AddImage(const IntegrationOutcome &outcome, bool cc_mask) {
     }
 }
 
+float MergeOnTheFly::CorrectedSigma(float I_corr, float sigma_corr, uint64_t hkl_key) const {
+    if (!error_model_active)
+        return sigma_corr;
+
+    // Intensity for the (b*I)^2 term: the reflection's mean (constant over its
+    // observations), falling back to this observation only if the mean is unknown.
+    const auto it = error_model_mean_I.find(hkl_key);
+    const double I_for_b = (it != error_model_mean_I.end()) ? it->second : I_corr;
+
+    const double v = error_model_a * static_cast<double>(sigma_corr) * sigma_corr
+                     + (error_model_b * I_for_b) * (error_model_b * I_for_b);
+    return (v > 0.0) ? static_cast<float>(std::sqrt(v)) : sigma_corr;
+}
+
+void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outcomes) {
+    // --- 1. Collect accepted, scaled observations grouped by symmetry-equivalent hkl,
+    //        applying exactly the filters AddImage uses. ---
+    struct Obs { float I, sigma; };
+    std::unordered_map<uint64_t, std::vector<Obs>> groups;
+
+    for (const auto &outcome: outcomes) {
+        if (Mask(outcome, false))
+            continue;
+        for (const auto &r: outcome.reflections) {
+            if (generator.IsSystematicallyAbsent(r))
+                continue;
+            if (r.image_scale_corr <= 0.0 || !std::isfinite(r.image_scale_corr))
+                continue;
+            if (!AcceptReflection(r, high_resolution_limit))
+                continue;
+            if (r.partiality < min_partiality)
+                continue;
+            const float I_corr = r.I * r.image_scale_corr;
+            const float sigma_corr = r.sigma * r.image_scale_corr;
+            if (!std::isfinite(I_corr) || !std::isfinite(sigma_corr) || sigma_corr <= 0.0f)
+                continue;
+            groups[generator(r).pack()].push_back({I_corr, sigma_corr});
+        }
+    }
+
+    // --- 2. One global pool of (sigma^2, <I>^2, bias-corrected squared deviation). For an
+    //        observation in a group of n, the residual from the inverse-variance mean has
+    //        E[(I_i - <I>)^2] = sigma_i^2 (1 - h_i), h_i = w_i / sum_w (its leverage). The
+    //        (b*I)^2 term uses the reflection mean, so the mean (not I_i) is the abscissa. ---
+    struct Sample { double s2, I2, dev2; };
+    std::vector<Sample> samples;
+    error_model_mean_I.clear();
+
+    for (const auto &[key, obs]: groups) {
+        if (obs.size() < 2)
+            continue;
+        double sum_w = 0.0, sum_wI = 0.0;
+        for (const auto &o: obs) {
+            const double w = 1.0 / (static_cast<double>(o.sigma) * o.sigma);
+            sum_w += w;
+            sum_wI += w * o.I;
+        }
+        if (!(sum_w > 0.0))
+            continue;
+        const double mean = sum_wI / sum_w;
+        error_model_mean_I[key] = static_cast<float>(mean);
+        const double I2 = mean * mean;
+        for (const auto &o: obs) {
+            const double w = 1.0 / (static_cast<double>(o.sigma) * o.sigma);
+            const double factor = 1.0 - w / sum_w;
+            if (factor < 0.05)
+                continue;
+            const double resid = static_cast<double>(o.I) - mean;
+            samples.push_back({static_cast<double>(o.sigma) * o.sigma, I2, resid * resid / factor});
+        }
+    }
+
+    // --- 3. Fit global dev2 = a*sigma^2 + b^2*<I>^2. Bin by intensity (the per-observation
+    //        dev2 is chi-square-1 noisy) and take medians; weight the bins by 1/dev2^2 so it
+    //        is a *relative* fit - otherwise the strong bins (which fix b) swamp the weak
+    //        bins (which fix a) and the weak sigmas stay over-confident. ---
+    constexpr int n_bins = 16;
+    if (samples.size() < static_cast<size_t>(8 * n_bins))
+        return; // too little multiplicity to fit -> leave identity
+
+    std::sort(samples.begin(), samples.end(),
+              [](const Sample &p, const Sample &q) { return p.I2 < q.I2; });
+
+    auto median = [](std::vector<double> &v) {
+        std::nth_element(v.begin(), v.begin() + v.size() / 2, v.end());
+        return v[v.size() / 2];
+    };
+
+    double Ass = 0, AsI = 0, AII = 0, Bs = 0, BI = 0;
+    const size_t per = samples.size() / n_bins;
+    for (int bin = 0; bin < n_bins; ++bin) {
+        const size_t lo = bin * per;
+        const size_t hi = (bin == n_bins - 1) ? samples.size() : lo + per;
+        std::vector<double> vs2, vI2, vd2;
+        vs2.reserve(hi - lo); vI2.reserve(hi - lo); vd2.reserve(hi - lo);
+        for (size_t i = lo; i < hi; ++i) {
+            vs2.push_back(samples[i].s2);
+            vI2.push_back(samples[i].I2);
+            vd2.push_back(samples[i].dev2);
+        }
+        const double s2 = median(vs2), I2 = median(vI2), d2 = median(vd2);
+        const double wgt = 1.0 / std::max(d2 * d2, 1e-30);
+        Ass += wgt * s2 * s2;
+        AsI += wgt * s2 * I2;
+        AII += wgt * I2 * I2;
+        Bs  += wgt * s2 * d2;
+        BI  += wgt * I2 * d2;
+    }
+
+    const double det = Ass * AII - AsI * AsI;
+    if (std::fabs(det) < 1e-30)
+        return;
+    const double a  = std::clamp((Bs * AII - BI * AsI) / det, 0.25, 100.0);
+    const double b2 = std::max((Ass * BI - AsI * Bs) / det, 0.0);
+
+    error_model_a = a;
+    error_model_b = std::sqrt(b2);
+    error_model_active = true;
+}
+
 bool MergeOnTheFly::Mask(const IntegrationOutcome &outcome, bool cc_mask) {
     if (reference_cell) {
         auto cell = outcome.latt.GetUnitCell();
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index 5f6ca6e8..d69ee817 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -5,6 +5,7 @@
 
 #include <map>
 #include <random>
+#include <unordered_map>
 #include <vector>
 
 #include "../../common/Logger.h"
@@ -72,11 +73,32 @@ class MergeOnTheFly {
 
     std::map<uint64_t, MergeAccum> accumulator;
 
+    // Global error model (XDS form): sigma_corr^2 = a*sigma^2 + (b*<I>)^2. a rescales the
+    // (under-estimated) counting variance; the (b*<I>)^2 term adds the intensity-
+    // proportional systematic error that counting statistics miss, so strong reflections
+    // are no longer over-weighted. ISa = 1/b is the asymptotic I/sigma. Refined from the
+    // scatter of symmetry equivalents (RefineErrorModel); identity until then.
+    bool   error_model_active = false;
+    double error_model_a = 1.0;
+    double error_model_b = 0.0;
+    // The (b*I)^2 term uses the reflection's *mean* intensity (constant over its
+    // observations), so it inflates sigma without biasing the inverse-variance weights -
+    // using the per-observation I_i instead would over-weight down-fluctuated points.
+    std::unordered_map<uint64_t, float> error_model_mean_I;
+    [[nodiscard]] float CorrectedSigma(float I_corr, float sigma_corr, uint64_t hkl_key) const;
+
     bool Mask(const IntegrationOutcome &outcome, bool cc_mask);
 public:
     MergeOnTheFly(const DiffractionExperiment &x);
     MergeOnTheFly& ReferenceCell(const std::optional<UnitCell> &cell);
 
+    // Fit the global error model from the spread of symmetry-equivalent observations.
+    // Call once before merging; AddImage then applies it.
+    void RefineErrorModel(const std::vector<IntegrationOutcome> &outcomes);
+    [[nodiscard]] bool   ErrorModelActive() const { return error_model_active; }
+    [[nodiscard]] double ErrorModelA() const { return error_model_a; }
+    [[nodiscard]] double ErrorModelB() const { return error_model_b; }
+
     void AddImage(const IntegrationOutcome& outcome, bool cc_mask = false);
 
     MergeStatistics MergeStats(const std::vector<MergedReflection> &merged,
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 61ea164d..5f7671fe 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -997,6 +997,16 @@ int main(int argc, char **argv) {
         MergeOnTheFly merge_engine(experiment);
         if (consensus_cell.has_value())
             merge_engine.ReferenceCell(*consensus_cell);
+        // Fit the global error model (sigma'^2 = a*sigma^2 + (b*I)^2, XDS form) from the
+        // spread of symmetry equivalents before merging, so the merged sigmas reflect the
+        // real scatter rather than counting statistics alone.
+        merge_engine.RefineErrorModel(indexer.GetIntegrationOutcome());
+        if (merge_engine.ErrorModelActive()) {
+            const double a = merge_engine.ErrorModelA();
+            const double b = merge_engine.ErrorModelB();
+            const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
+            logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
+        }
         for (auto &i : indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
 
-- 
2.52.0


From c93d381dc8fbd38ff7b904f86fa862a622ea8e17 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 12 Jun 2026 18:53:02 +0200
Subject: [PATCH 038/228] Error model: harden the fit against pathological
 inputs (code review)

Addresses code-review findings on RefineErrorModel:
- Floor the 1/dev^2 bin weight relative to the data scale (1e-3 of the median
  bin dev^2), not an absolute 1e-30: a near-zero-scatter bin could otherwise
  acquire a runaway weight and hijack the global (a,b) fit.
- Reject a near-collinear normal-equation system relatively (det > 1e-10*Ass*AII)
  instead of with an absolute threshold that an ill-conditioned fit can pass.
- Reset the model to identity at entry so any early return leaves it inactive
  rather than keeping a stale a/b alongside a freshly-cleared mean map (which
  would make CorrectedSigma fall back to the per-observation I).
- PixelRefine: correct the orient_prior comment - with the sweep on, the LSQ
  anchor is the swept orientation (intended), not the spot-centroid one.

Verified unchanged on the lyso test set (ISa 1.1, CC1/2 90.3%).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../pixel_refinement/PixelRefine.cpp          |  7 ++--
 image_analysis/scale_merge/Merge.cpp          | 35 ++++++++++++++++---
 2 files changed, 35 insertions(+), 7 deletions(-)

diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index c398b9d3..bef4392b 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -920,8 +920,11 @@ void PixelRefine::Run(const T *image,
         BuildParameterBlocks(data, beam, dist_mm, detector_rot,
                              latt_vec0, latt_vec1, latt_vec2);
 
-        // Anchor for orientation regularization = the spot-centroid orientation we
-        // started from (captured before any pixel-level refinement moved it).
+        // Anchor for orientation regularization = the orientation the LSQ starts from
+        // (captured before the predict<->refine iterations move it). When the global
+        // sweep ran first this is the swept orientation, not the original spot-centroid
+        // one - which is intended: the regularizer keeps the LSQ near its own starting
+        // point, it is not meant to pull a deliberate sweep back.
         if (iter == 0)
             for (int i = 0; i < 3; ++i)
                 orient_prior[i] = latt_vec0[i];
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 3acf2ba4..cfb829e9 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -103,6 +103,14 @@ float MergeOnTheFly::CorrectedSigma(float I_corr, float sigma_corr, uint64_t hkl
 }
 
 void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outcomes) {
+    // Reset to identity up front: every early return below then leaves the model
+    // inactive (CorrectedSigma returns sigma unchanged) rather than keeping a stale
+    // a/b from a previous call alongside a freshly-cleared mean map.
+    error_model_active = false;
+    error_model_a = 1.0;
+    error_model_b = 0.0;
+    error_model_mean_I.clear();
+
     // --- 1. Collect accepted, scaled observations grouped by symmetry-equivalent hkl,
     //        applying exactly the filters AddImage uses. ---
     struct Obs { float I, sigma; };
@@ -134,7 +142,6 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
     //        (b*I)^2 term uses the reflection mean, so the mean (not I_i) is the abscissa. ---
     struct Sample { double s2, I2, dev2; };
     std::vector<Sample> samples;
-    error_model_mean_I.clear();
 
     for (const auto &[key, obs]: groups) {
         if (obs.size() < 2)
@@ -176,7 +183,9 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
         return v[v.size() / 2];
     };
 
-    double Ass = 0, AsI = 0, AII = 0, Bs = 0, BI = 0;
+    // Per-intensity-bin medians of (sigma^2, <I>^2, dev2).
+    std::vector<double> bs2, bI2, bd2;
+    bs2.reserve(n_bins); bI2.reserve(n_bins); bd2.reserve(n_bins);
     const size_t per = samples.size() / n_bins;
     for (int bin = 0; bin < n_bins; ++bin) {
         const size_t lo = bin * per;
@@ -188,8 +197,22 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
             vI2.push_back(samples[i].I2);
             vd2.push_back(samples[i].dev2);
         }
-        const double s2 = median(vs2), I2 = median(vI2), d2 = median(vd2);
-        const double wgt = 1.0 / std::max(d2 * d2, 1e-30);
+        bs2.push_back(median(vs2));
+        bI2.push_back(median(vI2));
+        bd2.push_back(median(vd2));
+    }
+
+    // Relative-weighted (1/dev2^2) least squares for (a, b^2). Floor the weight's dev2 at a
+    // small fraction of the typical bin dev2: an absolute floor (1e-30) does not stop a
+    // near-zero-scatter bin from acquiring a runaway weight and hijacking the fit, so the
+    // floor must scale with the data. The regression target keeps the unfloored dev2.
+    std::vector<double> bd2_sorted = bd2;
+    const double dev2_floor = std::max(1e-30, 1e-3 * median(bd2_sorted));
+    double Ass = 0, AsI = 0, AII = 0, Bs = 0, BI = 0;
+    for (int bin = 0; bin < n_bins; ++bin) {
+        const double s2 = bs2[bin], I2 = bI2[bin], d2 = bd2[bin];
+        const double d2w = std::max(d2, dev2_floor);
+        const double wgt = 1.0 / (d2w * d2w);
         Ass += wgt * s2 * s2;
         AsI += wgt * s2 * I2;
         AII += wgt * I2 * I2;
@@ -197,8 +220,10 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
         BI  += wgt * I2 * d2;
     }
 
+    // Reject a near-collinear (ill-conditioned) system *relatively*: det lies in
+    // [0, Ass*AII] by Cauchy-Schwarz, so compare against that scale rather than 1e-30.
     const double det = Ass * AII - AsI * AsI;
-    if (std::fabs(det) < 1e-30)
+    if (!(det > 1e-10 * Ass * AII))
         return;
     const double a  = std::clamp((Bs * AII - BI * AsI) / det, 0.25, 100.0);
     const double b2 = std::max((Ass * BI - AsI * Bs) / det, 0.0);
-- 
2.52.0


From 6f2033db004899c37530bf2431f54e8c1a16054b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 13 Jun 2026 21:34:33 +0200
Subject: [PATCH 039/228] PixelRefine: checkpoint before cleanup (factored
 model + all diagnostic levers)

Snapshot of the messy state: factored likelihood Terms 1+2+3 behind PR_*
env flags (PR_INTENSITY/PR_SHAPE/PR_RECENTER) alongside the old per-pixel
ShoeboxResidual, plus diagnostic scaffolding (PR_R0/R1/COV/FIX_R0/FIX_R/
ADAPT_R1/CENTROID/RECENTER) and the FACTORED_MODEL.md spec. Next commit
makes Terms 1+2 the model and strips all of this.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |  34 ++
 .../pixel_refinement/FACTORED_MODEL.md        | 140 +++++++
 .../pixel_refinement/PixelRefine.cpp          | 381 +++++++++++++++++-
 image_analysis/pixel_refinement/PixelRefine.h |  54 +++
 4 files changed, 601 insertions(+), 8 deletions(-)
 create mode 100644 image_analysis/pixel_refinement/FACTORED_MODEL.md

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index f7cb25c1..ccf084fe 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -446,6 +446,28 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
+    // TEMPORARY diagnostic knobs to probe the effect of the (currently fixed) spot
+    // widths R[0] (radial/partiality) and R[1] (tangential/profile). Remove after.
+    if (const char *r0 = std::getenv("PR_R0")) prd.R[0] = std::stod(r0);
+    if (const char *r1 = std::getenv("PR_R1")) prd.R[1] = std::stod(r1);
+    // TEMPORARY: PR_COV refines G,B,R and dumps their per-image correlation matrix.
+    if (std::getenv("PR_COV")) {
+        prd.refine_scale = true; prd.refine_B = true; prd.refine_R = true;
+        prd.compute_covariance = true;
+    }
+    if (std::getenv("PR_FIX_R0")) prd.fix_R0 = true; // hold R0, refine R1 only
+    if (std::getenv("PR_FIX_R")) prd.refine_R = false; // hold R0 and R1: G-B correlation only
+    if (std::getenv("PR_ADAPT_R1")) prd.adaptive_R1 = true; // measure R1 from spot moments
+    if (std::getenv("PR_CENTROID")) prd.measure_centroid = true; // observed-vs-predicted offset
+    if (std::getenv("PR_RECENTER")) prd.recenter_profile = true; // recentre profile on centroid
+    if (const char *s = std::getenv("PR_RECENTER_SIGNIF")) prd.recenter_min_signif = std::stod(s);
+    if (std::getenv("PR_INTENSITY")) { // factored-likelihood Term 1: per-reflection intensity residual
+        prd.intensity_residual = true;
+        prd.refine_orientation = false; prd.refine_R = false;
+        prd.refine_scale = true; prd.refine_B = true;
+    }
+    if (std::getenv("PR_SHAPE")) prd.shape_R1 = true; // Term 2: per-resolution R1 from spot moments
+
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {
@@ -465,6 +487,18 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
             return false;
     }
 
+    if (prd.covariance_valid)
+        fprintf(stderr, "[cov] GB=%.3f GR0=%.3f GR1=%.3f BR0=%.3f BR1=%.3f R0R1=%.3f\n",
+                prd.corr_GB, prd.corr_GR0, prd.corr_GR1, prd.corr_BR0, prd.corr_BR1, prd.corr_R0R1);
+    if (prd.adaptive_R1)
+        fprintf(stderr, "[R1] %.5f\n", prd.R[1]);
+    if (prd.shape_R1 && std::isfinite(prd.shape_R1_lores))
+        fprintf(stderr, "[shapeR1] lores=%.5f hires=%.5f\n", prd.shape_R1_lores, prd.shape_R1_hires);
+    if (prd.measure_centroid && std::isfinite(prd.centroid_lo_tang_c))
+        fprintf(stderr, "[res] lo_s=%.1f lo_tc=%.3f lo_tp=%.3f lo_rc=%.3f hi_s=%.1f hi_tc=%.3f hi_tp=%.3f hi_rc=%.3f\n",
+                prd.centroid_lo_signif, prd.centroid_lo_tang_c, prd.centroid_lo_tang_p, prd.centroid_lo_rad_c,
+                prd.centroid_hi_signif, prd.centroid_hi_tang_c, prd.centroid_hi_tang_p, prd.centroid_hi_rad_c);
+
     // PixelRefine output flows into the normal save/merge path: the refined
     // geometry/lattice and the already-scaled reflections become the outcome.
     i_outcome.reflections = std::move(prd.reflections);
diff --git a/image_analysis/pixel_refinement/FACTORED_MODEL.md b/image_analysis/pixel_refinement/FACTORED_MODEL.md
new file mode 100644
index 00000000..944514a2
--- /dev/null
+++ b/image_analysis/pixel_refinement/FACTORED_MODEL.md
@@ -0,0 +1,140 @@
+# A factored likelihood for joint integration + scaling + geometry
+
+**Status: design spec (not implemented).** Goal: replace the per-pixel least-squares
+of PixelRefine with a per-*reflection* likelihood that fuses profile-fit integration,
+scaling against the reference, and geometry refinement into one differentiable
+objective — the foundation for priors (Bayesian) and learned components (NN), and the
+thing that dissolves the empty-pixel and parameter-degeneracy problems by construction
+rather than by patching.
+
+## 0. Notation
+
+Per image, parameters `θ`: scale `G`, Debye-Waller `B`, orientation + cell (geometry),
+profile width `R1` (tangential, possibly a 2×2 tensor), partiality width `R0`
+(radial/mosaicity; `R0_eff² = R0² + R_bw²`, `R_bw² = (bλ)²/2d⁴` *known* from bandwidth).
+Per reflection `h`: reference intensity `I_ref` (the hypothesis), resolution `d`,
+predicted centre `c_pred`, partiality `p = exp(−ε_r²/R0_eff²)`, polarisation `pol`,
+`B_term = exp(−B/4d²)`, shoebox pixels `{I_p}` with mean local background `Bg`, and the
+area-normalised tangential profile template `P_p = P_tang(ε_t,p; R1)`.
+
+## 1. The factorisation principle
+
+A reflection's shoebox carries three (to first order) **orthogonal** pieces of
+information — the 0th, 1st and 2nd moments of its intensity distribution:
+
+| moment | statistic | constrains |
+|---|---|---|
+| 0th — total | profile-fit amplitude `J` | scale chain `G, B` (and `p`) |
+| 1st — position | centroid `c_obs` | geometry (orientation; radial→distance/cell) |
+| 2nd — shape | second moment `M₂` | profile width `R1` (and anisotropy) |
+
+The current per-pixel residual mixes all three into one objective over shared pixels —
+*that* is what couples the parameters (measured G–R0 ≈ −0.46, G–R1 ≈ +0.51) and lets the
+many empty pixels dominate. Residual-ing each **moment** against its model instead gives
+a block-diagonal Jacobian: the couplings vanish because each statistic carries one
+parameter block's information.
+
+## 2. The three residual terms
+
+### 2.1 Intensity / scaling residual (one scalar per reflection)
+
+Optimal (Diamond) profile-fit amplitude and its model:
+```
+J      = Σ_p w_p P_p (I_p − Bg) / Σ_p w_p P_p²          w_p = 1/v_p
+J_model = G · B_term · p · pol · I_ref
+r¹_h    = (J − J_model) / σ_J
+```
+`J` is ~invariant to `R1` (a well-sampled spot integrates to the same total whatever
+width is assumed) → **R1 leaves this residual**. Empty pixels make no residual; they
+enter only through `J` with ~zero profile weight → **the empty-pixel problem is gone by
+construction.** This residual *is* the scaling residual — integration and scaling are now
+one objective.
+
+### 2.2 Shape residual (constrains R1; decoupled from scale)
+
+```
+M₂_obs   = Σ_p (I_p − Bg) ε_t,p² / Σ_p (I_p − Bg)      (intensity-weighted variance, Å⁻²)
+M₂_model = R1² / 2                                      (variance of exp(−ε_t²/R1²))
+r²_h     = (M₂_obs − M₂_model) / σ_M2
+```
+A moment is normalised by the total → **scale-invariant → `∂r²/∂G = 0`**. The G↔R1
+degeneracy disappears. Anisotropic extension: use the 2×2 moment tensor
+`Σ(I−Bg)(ε_t⊗ε_t)/Σ(I−Bg)` vs `diag(R1a²/2, R1b²/2)` → elliptical R1 (the DMM streak).
+Weak spots have huge `σ_M2` → contribute ~nothing → R1 is set by strong spots
+automatically (and may be made `R1(d)` per resolution).
+
+### 2.3 Position residual (constrains geometry; decoupled from scale and shape)
+
+```
+c_obs = Σ_p (I_p − Bg)(x_p, y_p) / Σ_p (I_p − Bg)
+r³_h  = (c_obs − c_pred(geometry)) / σ_c              (2-vector; split radial / tangential)
+```
+Centroid is scale- and width-invariant → `∂r³/∂G = ∂r³/∂R1 ≈ 0`. The **radial** component
+constrains distance/cell, the **tangential** constrains orientation — exactly the split
+the diagnostic measured (radial≈0 = no distance error; tangential∝radius = orientation).
+
+## 3. Fisher / expected-variance weighting (makes it a likelihood)
+
+Every `σ` uses the **model-expected** variance, never observed counts — this is what
+makes strong *expected* reflections carry the information and makes the model "feel pain
+when something that should be there is not":
+```
+v_p   = Bg + J_model · P_p           (background + expected signal from I_ref, not I_obs)
+σ_J²  = 1 / Σ_p (P_p² / v_p)
+σ_M2  ≈ M₂ · √(2 / N_eff),   σ_c ≈ R1 / √(N_eff),   N_eff = (Σ(I−Bg))² / Σ v_p
+```
+Fisher information about `G` from term 1 is `∝ (B_term·p·pol·I_ref)² / σ_J²` — driven by
+`I_ref`, so a noise spike (high counts, low `I_ref`) gets *no* weight while a strong
+expected reflection observed absent (`J≈0`, large residual, moderate `σ_J`) gets a large
+penalty. The reference enters at maximum leverage: it sets both the target and the weight.
+
+## 4. Joint objective and priors
+
+```
+L(θ) = Σ_h [ (r¹_h)² + (r²_h)² + |r³_h|² ]  +  priors
+```
+No free λ if the σ's are correct — the relative weighting *is* the Fisher information.
+Priors are the Bayesian hooks and the principled degeneracy breaks:
+- **R0 (partiality/mosaicity) is GLOBAL + prior.** R0 multiplies `J_model` (`p`), so it is
+  still degenerate with the per-image `G` *within term 1* — the one degeneracy the
+  factorisation does **not** remove. Resolve it physically, not with a directional G prior
+  (which would bias every output intensity): `R0 ~ N(mosaicity, σ)`, `R_bw` fixed from the
+  known bandwidth, and `R0` fit **globally** (one per crystal, from many reflections'
+  partiality distribution) so per-image G can't trade against it.
+- orientation `~ N(spot-centroid, σ)`; `G ~ N(1, σ_G)` or tied to the beam monitor;
+  distance `~ N(nominal, σ_L)` (loose, since serial/jet alignment is poorly constrained).
+- Optional Bayesian intensities: treat `I_true` as a parameter with the reference as its
+  prior → posterior over intensities, not point estimates.
+
+## 5. Why the degeneracies vanish (Jacobian structure)
+
+`Jᵀ W J` is approximately block-diagonal in `(G,B,p | R1 | geometry)`:
+```
+∂r¹/∂{G,B,p} ≠ 0 ;  ∂r¹/∂R1 ≈ 0 ;  ∂r¹/∂geom ≈ 0
+∂r²/∂R1     ≠ 0 ;  ∂r²/∂G  = 0 ;  ∂r²/∂geom ≈ 0
+∂r³/∂geom   ≠ 0 ;  ∂r³/∂G  = 0 ;  ∂r³/∂R1  ≈ 0
+```
+So G↔R1 (+0.51) and all the cross-couplings drop to ~0 by construction. Only **G↔R0**
+survives (R0 is a scale-multiplier, not a shape), handled by the global+physical prior of
+§4. The degeneracies we measured were artifacts of projecting all information onto a
+single per-pixel residual.
+
+## 6. Implementation notes
+
+- Per reflection: 1 (intensity) + 1 (shape) + 2 (position) residuals = 4, vs ~49 per-pixel
+  residuals → **cheaper**, and Ceres autodiffs the moment formulas through the pixels.
+- The per-pixel forward model still *defines* `P_tang`, `p`, etc.; the **loss** moves to
+  the moments.
+- Geometry (term 3) can run as the global sweep we have (it already maximises a
+  position/CC objective); terms 1–2 are the per-image photometry. Or solve all three
+  jointly per image with the global R0/mosaicity shared across images (two-level fit).
+- Drop-in path: keep the current extraction, add the three residuals as a new objective
+  behind a flag, compare against the per-pixel loss on both test crystals.
+
+## 7. Why this serves the goal
+
+It is one differentiable likelihood, factored along the physics, that (a) maximises use of
+the reference (target + Fisher weight), (b) is the substrate for priors / posteriors over
+intensities (Bayesian), and (c) lets any term — profile `P`, partiality `p`, corrections —
+be replaced by a learned function trained through the same likelihood. That is the
+qualitative move XDS-style empirical profile fitting cannot make.
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index bef4392b..42e8772f 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -10,6 +10,7 @@
 
 #include <Eigen/Dense>
 #include <ceres/ceres.h>
+#include <ceres/covariance.h>
 #include <ceres/rotation.h>
 
 #include "../geom_refinement/LatticeReduction.h"
@@ -35,6 +36,8 @@ struct ReflGroup {
     double pol;               // per-reflection polarization correction (raw = true * pol)
     double Ibkg;              // local flat background (raw counts, constant over the shoebox)
     double predicted_x, predicted_y;
+    double R1_eff = 0.0;          // tangential profile width to use (Term 2; 0 => fall back to data.R[1])
+    double dcx = 0.0, dcy = 0.0;  // Term 3: profile recentre shift (observed centroid - predicted)
     std::vector<PixelObs> pixels;
 };
 
@@ -752,6 +755,30 @@ void PixelRefine::SweepOrientationCell(const T *image, BraggPrediction &predicti
     data.latt = best;
 }
 
+// ---------------------------------------------------------------------------
+// Term 1 of the factored likelihood (FACTORED_MODEL.md): the per-reflection
+// *intensity* (0th-moment) residual. The profile-fit amplitude J should equal the
+// scaled reference J_model = G * exp(-B/4d^2) * partiality * pol * I_ref. One scalar
+// residual per reflection, weighted by the model-expected (Fisher) sigma_J. This is
+// the scaling residual - integration and scaling become one objective, and the empty
+// pixels (which make no residual of their own) stop dominating the fit. With geometry
+// and R held fixed, J, partiality and sigma_J are constants, so only G and B are free.
+// ---------------------------------------------------------------------------
+struct IntensityResidual {
+    IntensityResidual(double J, double sigma_J, double partiality, double pol,
+                      double I_ref, double inv_4d2)
+        : J(J), inv_sigma(1.0 / sigma_J), partiality(partiality), pol(pol),
+          I_ref(I_ref), inv_4d2(inv_4d2) {}
+    template<typename T>
+    bool operator()(const T *const G, const T *const B, T *residual) const {
+        const T B_term = ceres::exp(-B[0] * T(inv_4d2));
+        const T J_model = G[0] * B_term * T(partiality) * T(pol) * T(I_ref);
+        residual[0] = (J_model - T(J)) * T(inv_sigma);
+        return true;
+    }
+    double J, inv_sigma, partiality, pol, I_ref, inv_4d2;
+};
+
 template<class T>
 void PixelRefine::Run(const T *image,
                       BraggPrediction &prediction,
@@ -929,12 +956,146 @@ void PixelRefine::Run(const T *image,
             for (int i = 0; i < 3; ++i)
                 orient_prior[i] = latt_vec0[i];
 
+        // ---- Term 3: per-reflection recentre on the observed centroid ----------------
+        // The geometry predicts the spot to ~0.4 px (per-reflection scatter a global fit
+        // cannot remove); a tight Term-2 template centred on the prediction then sits off
+        // the real spot. For confident spots, shift the profile centre to the observed
+        // centroid (used consistently by Term 2, Term 1 and the extraction below). Weak
+        // spots keep the prediction (recentring on a noise centroid would bias them).
+        for (auto &g : groups) {
+            g.dcx = 0.0;
+            g.dcy = 0.0;
+        }
+        if (data.recenter_profile && !groups.empty()) {
+            const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
+            for (auto &g : groups) {
+                double sw = 0.0, swx = 0.0, swy = 0.0;
+                for (const auto &px : g.pixels) {
+                    const double w = std::max(px.Iobs - g.Ibkg, 0.0);
+                    sw += w; swx += w * px.x; swy += w * px.y;
+                }
+                if (sw <= 0.0)
+                    continue;
+                if (sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0)) < data.recenter_min_signif)
+                    continue;
+                double dcx = swx / sw - g.predicted_x, dcy = swy / sw - g.predicted_y;
+                const double dl = std::sqrt(dcx * dcx + dcy * dcy);
+                if (dl > 2.0) { dcx *= 2.0 / dl; dcy *= 2.0 / dl; } // clamp runaway centroids
+                g.dcx = dcx;
+                g.dcy = dcy;
+            }
+        }
+
+        // ---- Term 2: per-resolution tangential profile width R1 from spot shapes ------
+        // Default: every reflection uses the global R1; with shape_R1 on, override it with
+        // R1 = sqrt(2*<eps_t^2>) from the intensity-weighted second moment of the strong
+        // spots, binned by resolution (low res small spots, high res larger). A shape
+        // statistic - normalised by the total, so decoupled from the per-image scale.
+        for (auto &g : groups)
+            g.R1_eff = data.R[1];
+        if (data.shape_R1 && !groups.empty()) {
+            constexpr int n_bins = 6;
+            const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
+            double s2min = 1e30, s2max = 0.0;
+            for (const auto &g : groups) {
+                const double s2 = 1.0 / (g.d * g.d);
+                s2min = std::min(s2min, s2);
+                s2max = std::max(s2max, s2);
+            }
+            const double span = std::max(s2max - s2min, 1e-12);
+            auto bin_of = [&](double d) {
+                return std::clamp(static_cast<int>((1.0 / (d * d) - s2min) / span * n_bins), 0, n_bins - 1);
+            };
+            std::vector<std::vector<double>> bin_M2(n_bins);
+            for (const auto &g : groups) {
+                double sw = 0.0, sw_et2 = 0.0;
+                for (const auto &px : g.pixels) {
+                    PixelObs probe{px.x - g.dcx, px.y - g.dcy, 0.0, g.Ibkg, 1.0};
+                    PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
+                                     g.R_bw_sq, g.pol, data.crystal_system);
+                    double q_sq, eps_r, eps_t_sq;
+                    if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
+                                          latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                        continue;
+                    const double w = std::max(px.Iobs - g.Ibkg, 0.0);
+                    sw += w;
+                    sw_et2 += w * eps_t_sq;
+                }
+                if (sw <= 0.0)
+                    continue;
+                const double signif = sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0));
+                if (signif >= 5.0) // only well-measured spots define the shape
+                    bin_M2[bin_of(g.d)].push_back(sw_et2 / sw);
+            }
+            std::vector<double> bin_R1(n_bins, data.R[1]);
+            for (int b = 0; b < n_bins; ++b)
+                if (bin_M2[b].size() >= 5) {
+                    const double r1 = std::sqrt(2.0 * std::max(MedianInPlace(bin_M2[b]), 0.0));
+                    if (std::isfinite(r1) && r1 > 1e-4)
+                        bin_R1[b] = std::clamp(r1, 1e-4, 0.05);
+                }
+            for (auto &g : groups)
+                g.R1_eff = bin_R1[bin_of(g.d)];
+            data.shape_R1_lores = bin_R1[0];          // lowest resolution bin
+            data.shape_R1_hires = bin_R1[n_bins - 1]; // highest resolution bin
+        }
+
         // ---- 4. Build the problem ---------------------------------------------
         // One residual block per shoebox (N residuals), so the expensive
         // per-reflection node geometry is evaluated once per reflection instead
         // of once per pixel.
         ceres::Problem problem;
         size_t residual_pixels = 0;
+        if (data.intensity_residual) {
+            // Term-1 path: one per-reflection intensity residual. Geometry & R fixed, so
+            // J / partiality / sigma_J are computed here as constants and only G, B vary.
+            const double R0 = data.R[0];
+            for (const auto &g : groups) {
+                const double R1 = g.R1_eff; // Term 2: per-resolution profile width
+                double num = 0.0, den = 0.0, rad = 0.0;
+                std::vector<std::pair<double, double>> pt_sig; // (P_t, Iobs-Bg) for Fisher pass
+                pt_sig.reserve(g.pixels.size());
+                for (const auto &px : g.pixels) {
+                    PixelObs probe{px.x - g.dcx, px.y - g.dcy, 0.0, g.Ibkg, 1.0}; // Term 3 recentre
+                    PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
+                                     g.R_bw_sq, g.pol, data.crystal_system);
+                    double q_sq, eps_r, eps_t_sq;
+                    if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
+                                          latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                        continue;
+                    if (!(R1 > 0.0) || !(R0 > 0.0))
+                        continue;
+                    const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
+                    const double R0_eff_sq = R0 * R0 + g.R_bw_sq;
+                    const double P_rad = std::exp(-eps_r * eps_r / R0_eff_sq);
+                    const double v = std::max(g.Ibkg, 1.0);
+                    const double sig = px.Iobs - g.Ibkg;
+                    num += P_t * sig / v;
+                    den += P_t * P_t / v;
+                    rad += P_rad * P_t * P_t / v;
+                    pt_sig.emplace_back(P_t, sig);
+                }
+                if (!(den > 0.0))
+                    continue;
+                const double J = num / den;
+                const double partiality = rad / den;
+                // Model-expected (Fisher) variance: v_p = background + expected signal J*P_t,
+                // not the per-pixel observed counts (which down-bias) - so the weight tracks
+                // information, and an expected-strong reflection that is absent hurts.
+                double den_f = 0.0;
+                for (const auto &[P_t, sig] : pt_sig) {
+                    const double v_f = std::max(g.Ibkg + std::max(J, 0.0) * P_t, 1.0);
+                    den_f += P_t * P_t / v_f;
+                }
+                const double sigma_J = std::sqrt(1.0 / std::max(den_f, 1e-30));
+                const double inv_4d2 = (g.d > 0.0) ? 1.0 / (4.0 * g.d * g.d) : 0.0;
+                auto *cost = new ceres::AutoDiffCostFunction<IntensityResidual, 1, 1, 1>(
+                    new IntensityResidual(J, sigma_J, partiality, g.pol, g.Itrue, inv_4d2));
+                problem.AddResidualBlock(cost, nullptr, &data.scale_factor, &data.B_factor);
+                ++residual_pixels;
+            }
+            data.residual_count = residual_pixels;
+        } else {
         for (const auto &g : groups) {
             auto *cost = new ceres::DynamicAutoDiffCostFunction<ShoeboxResidual>(
                 new ShoeboxResidual(g, lambda, pixel_size, data.crystal_system));
@@ -959,8 +1120,23 @@ void PixelRefine::Run(const T *image,
             residual_pixels += g.pixels.size();
         }
         data.residual_count = residual_pixels;
+        }
 
         // ---- 5. Constrain / bound parameter blocks ----------------------------
+        if (data.intensity_residual) {
+            // Only G and B are in this problem; geometry/R are not parameters here.
+            problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
+            if (!data.refine_B)
+                problem.SetParameterBlockConstant(&data.B_factor);
+            // Regularize G->1, weight sqrt(n_refl/sigma): commensurate because the data
+            // term is now one residual per reflection (unlike the per-pixel path).
+            if (data.scale_reg_sigma > 0.0 && !groups.empty()) {
+                const double w = std::sqrt(static_cast<double>(groups.size()) / data.scale_reg_sigma);
+                auto *reg = new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
+                    new ScalarRegularizer(w, 1.0));
+                problem.AddResidualBlock(reg, nullptr, &data.scale_factor);
+            }
+        } else {
         if (!data.refine_orientation) {
             problem.SetParameterBlockConstant(latt_vec0);
         } else if (data.orient_reg_sigma_deg > 0.0) {
@@ -1029,11 +1205,17 @@ void PixelRefine::Run(const T *image,
             problem.SetParameterBlockConstant(&data.B_factor);
 
         if (data.refine_R) {
-            problem.SetParameterLowerBound(data.R, 0, 1e-5);
-            problem.SetParameterLowerBound(data.R, 1, 1e-5);
+            if (data.fix_R0) {
+                // Diagnostic: hold R0 constant, refine R1 only.
+                problem.SetManifold(data.R, new ceres::SubsetManifold(2, {0}));
+            } else {
+                problem.SetParameterLowerBound(data.R, 0, 1e-5);
+                problem.SetParameterLowerBound(data.R, 1, 1e-5);
+            }
         } else {
             problem.SetParameterBlockConstant(data.R);
         }
+        } // end per-pixel (non-intensity_residual) constraints
 
         // ---- 6. Solve (or, for max_iterations<=0, just evaluate the cost) -----
         // Evaluate-only is the live-residual path: it reports the current cost
@@ -1057,6 +1239,50 @@ void PixelRefine::Run(const T *image,
 
             data.final_cost = summary.final_cost;
             data.solved = summary.IsSolutionUsable();
+
+            // Diagnostic: Pearson correlations on the final solve. Always needs G and B
+            // refined for G-B; the R correlations are added only when R is also refined.
+            if (data.compute_covariance && data.solved && iter == n_iter - 1 &&
+                data.refine_scale && data.refine_B) {
+                ceres::Covariance::Options copt;
+                copt.algorithm_type = ceres::DENSE_SVD;
+                copt.null_space_rank = -1; // tolerate (and reveal) degenerate directions
+                ceres::Covariance cov(copt);
+                std::vector<std::pair<const double *, const double *>> blocks = {
+                    {&data.scale_factor, &data.scale_factor}, {&data.B_factor, &data.B_factor},
+                    {&data.scale_factor, &data.B_factor}};
+                if (data.refine_R) {
+                    blocks.push_back({data.R, data.R});
+                    blocks.push_back({&data.scale_factor, data.R});
+                    blocks.push_back({&data.B_factor, data.R});
+                }
+                if (cov.Compute(blocks, &problem)) {
+                    double cGG, cBB, cGB;
+                    cov.GetCovarianceBlock(&data.scale_factor, &data.scale_factor, &cGG);
+                    cov.GetCovarianceBlock(&data.B_factor, &data.B_factor, &cBB);
+                    cov.GetCovarianceBlock(&data.scale_factor, &data.B_factor, &cGB);
+                    const double sG = std::sqrt(std::max(cGG, 0.0));
+                    const double sB = std::sqrt(std::max(cBB, 0.0));
+                    auto rho = [](double c, double s1, double s2) {
+                        return (s1 > 0.0 && s2 > 0.0) ? c / (s1 * s2) : NAN;
+                    };
+                    data.corr_GB = rho(cGB, sG, sB);
+                    if (data.refine_R) {
+                        double cRR[4], cGR[2], cBR[2];
+                        cov.GetCovarianceBlock(data.R, data.R, cRR);
+                        cov.GetCovarianceBlock(&data.scale_factor, data.R, cGR);
+                        cov.GetCovarianceBlock(&data.B_factor, data.R, cBR);
+                        const double sR0 = std::sqrt(std::max(cRR[0], 0.0));
+                        const double sR1 = std::sqrt(std::max(cRR[3], 0.0));
+                        data.corr_GR0  = rho(cGR[0], sG, sR0);
+                        data.corr_GR1  = rho(cGR[1], sG, sR1);
+                        data.corr_BR0  = rho(cBR[0], sB, sR0);
+                        data.corr_BR1  = rho(cBR[1], sB, sR1);
+                        data.corr_R0R1 = rho(cRR[1], sR0, sR1);
+                    }
+                    data.covariance_valid = true;
+                }
+            }
         }
 
         // ---- 7. Write refined geometry + lattice back into data ---------------
@@ -1096,6 +1322,139 @@ void PixelRefine::Run(const T *image,
         }
     } // predict<->refine iterations
 
+    // ---- Adaptive integration mask --------------------------------------------
+    // Measure R1 (tangential profile width) from the intensity-weighted tangential
+    // second moment of the strong spots, rather than fitting it. R1 is a *shape*
+    // statistic: sigma_t^2 = sum_p (I_p-B) eps_t,p^2 / sum_p (I_p-B), normalised by the
+    // total so it is independent of the per-image scale - which is exactly what breaks
+    // the R1<->G degeneracy (a measured width cannot be traded against G). One value per
+    // image here (from the strong, mostly low-res spots); a per-resolution version is the
+    // natural next step for the high-res / DMM-streak shapes.
+    if (data.adaptive_R1 && !groups.empty()) {
+        std::vector<double> itrue;
+        itrue.reserve(groups.size());
+        for (const auto &g : groups)
+            itrue.push_back(g.Itrue);
+        const size_t cut_idx = itrue.size() * 7 / 10; // keep the strongest ~30%
+        std::nth_element(itrue.begin(), itrue.begin() + cut_idx, itrue.end());
+        const double itrue_cut = itrue[cut_idx];
+
+        std::vector<double> sigma_t2;
+        for (const auto &g : groups) {
+            if (g.Itrue < itrue_cut)
+                continue;
+            double sw = 0.0, sw_et2 = 0.0;
+            for (const auto &px : g.pixels) {
+                PixelObs probe{px.x, px.y, 0.0, g.Ibkg, 1.0};
+                PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
+                                 g.R_bw_sq, g.pol, data.crystal_system);
+                double q_sq, eps_r, eps_t_sq;
+                if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
+                                      latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                    continue;
+                const double w = std::max(px.Iobs - g.Ibkg, 0.0);
+                sw += w;
+                sw_et2 += w * eps_t_sq;
+            }
+            if (sw > 0.0)
+                sigma_t2.push_back(sw_et2 / sw);
+        }
+        if (sigma_t2.size() >= 5) {
+            const double r1 = std::sqrt(2.0 * MedianInPlace(sigma_t2)); // R1^2 = 2 sigma_t^2
+            if (std::isfinite(r1) && r1 > 1e-5)
+                data.R[1] = r1;
+        }
+    }
+
+    // ---- Centering diagnostic --------------------------------------------------
+    // Observed-centroid vs predicted-position offset for the strong spots, after all
+    // refinement. Large rms (relative to the spot size) means a tight profile mask
+    // sits off the real spot - which is why a generous box can beat profile fitting.
+    if (data.measure_centroid && !groups.empty()) {
+        const double beam_x = data.geom.GetBeamX_pxl();
+        const double beam_y = data.geom.GetBeamY_pxl();
+        const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
+        // Raw pixel value (sentinel/bounds safe) for the parabolic peak fit. A constant
+        // background cancels in the parabola, so no need to subtract it here.
+        auto pix_val = [&](int x, int y) -> double {
+            if (x < 0 || x >= static_cast<int>(xpixel) || y < 0 || y >= static_cast<int>(ypixel))
+                return std::numeric_limits<double>::quiet_NaN();
+            const size_t np = static_cast<size_t>(xpixel) * y + x;
+            if (image[np] == std::numeric_limits<T>::max())
+                return std::numeric_limits<double>::quiet_NaN();
+            if (std::is_signed_v<T> && image[np] == std::numeric_limits<T>::min())
+                return std::numeric_limits<double>::quiet_NaN();
+            return static_cast<double>(image[np]);
+        };
+        struct Off { double signif, tang_c, tang_p, rad_c; };
+        std::vector<Off> offs;
+        double sdx = 0.0, sdy = 0.0, sd2 = 0.0;
+        size_t nc = 0;
+        for (const auto &g : groups) {
+            double sw = 0.0, swx = 0.0, swy = 0.0, bmax = -1e30;
+            int bx = 0, by = 0;
+            for (const auto &px : g.pixels) {
+                const double s = px.Iobs - g.Ibkg;
+                const double w = std::max(s, 0.0);
+                sw += w; swx += w * px.x; swy += w * px.y;
+                if (s > bmax) { bmax = s; bx = static_cast<int>(std::lround(px.x)); by = static_cast<int>(std::lround(px.y)); }
+            }
+            if (sw <= 0.0)
+                continue;
+            const double signif = sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0));
+            if (signif < 5.0)
+                continue; // a measurable spot at any resolution (not just the strong low-res ones)
+            // Sub-pixel peak (mode): parabola through the brightest pixel and its two
+            // neighbours per axis. The mode tracks the prediction even when an asymmetric
+            // tail drags the centroid (mean) sideways - so peak vs centroid separates a
+            // shape asymmetry from a true position error.
+            double peak_x = bx, peak_y = by;
+            { const double l = pix_val(bx - 1, by), c = pix_val(bx, by), r = pix_val(bx + 1, by);
+              const double den = l - 2.0 * c + r;
+              if (std::isfinite(den) && den < -1e-9)
+                  peak_x = bx + std::clamp(0.5 * (l - r) / den, -1.0, 1.0); }
+            { const double l = pix_val(bx, by - 1), c = pix_val(bx, by), r = pix_val(bx, by + 1);
+              const double den = l - 2.0 * c + r;
+              if (std::isfinite(den) && den < -1e-9)
+                  peak_y = by + std::clamp(0.5 * (l - r) / den, -1.0, 1.0); }
+            const double dcx = swx / sw - g.predicted_x, dcy = swy / sw - g.predicted_y;
+            const double dpx = peak_x - g.predicted_x,   dpy = peak_y - g.predicted_y;
+            sdx += dcx; sdy += dcy; sd2 += dcx * dcx + dcy * dcy; ++nc;
+            const double rx = g.predicted_x - beam_x, ry = g.predicted_y - beam_y;
+            const double rr = std::sqrt(rx * rx + ry * ry);
+            if (rr < 1.0)
+                continue;
+            const double rad_c  = (dcx * rx + dcy * ry) / rr;  // signed radial (outward +)
+            const double tang_c = (dcx * -ry + dcy * rx) / rr; // signed tangential
+            const double tang_p = (dpx * -ry + dpy * rx) / rr;
+            offs.push_back({signif, std::fabs(tang_c), std::fabs(tang_p), rad_c});
+        }
+        if (nc >= 5) {
+            data.centroid_bias_px = std::sqrt((sdx / nc) * (sdx / nc) + (sdy / nc) * (sdy / nc));
+            data.centroid_rms_px = std::sqrt(sd2 / nc);
+        }
+        if (offs.size() >= 10) {
+            std::vector<double> sig;
+            sig.reserve(offs.size());
+            for (const auto &o : offs)
+                sig.push_back(o.signif);
+            std::nth_element(sig.begin(), sig.begin() + sig.size() / 2, sig.end());
+            const double smed = sig[sig.size() / 2];
+            double slo = 0, shi = 0, tclo = 0, tchi = 0, tplo = 0, tphi = 0, rclo = 0, rchi = 0;
+            int nlo = 0, nhi = 0;
+            for (const auto &o : offs) {
+                if (o.signif < smed) { slo += o.signif; tclo += o.tang_c; tplo += o.tang_p; rclo += o.rad_c; ++nlo; }
+                else                 { shi += o.signif; tchi += o.tang_c; tphi += o.tang_p; rchi += o.rad_c; ++nhi; }
+            }
+            if (nlo > 0 && nhi > 0) {
+                data.centroid_lo_signif = slo / nlo;   data.centroid_hi_signif = shi / nhi;
+                data.centroid_lo_tang_c = tclo / nlo;  data.centroid_hi_tang_c = tchi / nhi;
+                data.centroid_lo_tang_p = tplo / nlo;  data.centroid_hi_tang_p = tphi / nhi;
+                data.centroid_lo_rad_c  = rclo / nlo;  data.centroid_hi_rad_c  = rchi / nhi;
+            }
+        }
+    }
+
     // ---- Extract integrated reflections ---------------------------------------
     // Profile fitting gives the recorded amplitude (fitting the tangential profile
     // P_t against the background-subtracted pixels):
@@ -1138,26 +1497,32 @@ void PixelRefine::Run(const T *image,
         // Debye-Waller factor for this reflection (constant over its shoebox).
         const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
 
+        // Term 3 recentre shift (precomputed in the pre-pass; 0 if off or the spot was not
+        // confident). Profile evaluated at (x-dcx, y-dcy), data summed at (x,y).
+        const double dcx = g.dcx, dcy = g.dcy;
+
         double num = 0.0, den = 0.0, bkg_sum = 0.0, radial_sum = 0.0;
         double prof_live = 0.0, prof_full = 0.0; // tangential profile: captured / total
         size_t n = 0;
 
         for (int y = cy - radius; y <= cy + radius; ++y) {
             for (int x = cx - radius; x <= cx + radius; ++x) {
-                // Geometry/profile for this grid point (valid even off the detector).
-                PixelObs probe{static_cast<double>(x), static_cast<double>(y), 0.0, g.Ibkg, 1.0};
+                // Geometry/profile for this grid point (profile recentred by (dcx,dcy)).
+                PixelObs probe{static_cast<double>(x) - dcx, static_cast<double>(y) - dcy,
+                               0.0, g.Ibkg, 1.0};
                 PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
                                  g.R_bw_sq, g.pol, data.crystal_system);
                 double q_sq, eps_r, eps_t_sq;
                 if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
                                       latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
                     continue;
-                if (!(data.R[0] > 0.0) || !(data.R[1] > 0.0))
+                if (!(data.R[0] > 0.0) || !(g.R1_eff > 0.0))
                     continue;
 
-                // Tangential profile shape (area-normalized) -> the fit template.
-                const double P_t = std::exp(-eps_t_sq / (data.R[1] * data.R[1]))
-                                   / (M_PI * data.R[1] * data.R[1]);
+                // Tangential profile shape (area-normalized) -> the fit template. Uses the
+                // per-reflection R1_eff (Term 2), falling back to the global R1 by default.
+                const double R1 = g.R1_eff;
+                const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
                 prof_full += P_t; // whole shoebox, on- or off-detector
 
                 // Only real, unmasked detector pixels carry signal.
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index fc4acabd..f8db193f 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -183,6 +183,56 @@ struct PixelRefineData {
     int    bkg_outer_radius = 6;
     int    max_iterations = 3; // inner predict<->refine cycles (re-predict with refined geom/latt)
 
+    // Diagnostic: compute the parameter correlation matrix (Pearson) from the final
+    // per-image solve, to expose degeneracies (e.g. G<->B, G<->R1) that let the fit
+    // lower its chi-square along directions that do not generalise across images.
+    // Requires G, B and R all refined; results in corr_* below.
+    bool   compute_covariance = false;
+    bool   fix_R0 = false; // diagnostic: with refine_R, hold R0 constant and refine R1 only
+
+    // Factored-likelihood Term 1 (FACTORED_MODEL.md): replace the per-pixel fit with one
+    // per-reflection *intensity* residual J vs G*B_term*partiality*pol*I_ref, Fisher-
+    // weighted. Geometry & R fixed; only G (and B if refine_B) are fit.
+    bool   intensity_residual = false;
+
+    // Factored-likelihood Term 2: set the tangential profile width R1 from the *measured*
+    // per-resolution second moment of the strong spots (a shape statistic, decoupled from
+    // the scale) and feed it to the profile template used by Term 1 and the extraction.
+    bool   shape_R1 = false;
+    double shape_R1_lores = NAN, shape_R1_hires = NAN; // measured R1 in the lowest/highest-res bin (diag)
+
+    // Adaptive integration mask: set R1 (tangential profile width) from the *measured*
+    // tangential second moment of the strong spots, instead of fitting it (which is
+    // degenerate with the per-image scale). A shape statistic, independent of scale.
+    bool   adaptive_R1 = false;
+
+    // Diagnostic: residual centering error after refinement. For the strong spots,
+    // the offset between observed intensity centroid and predicted position - bias is
+    // the systematic (mean) part, rms the total. If rms is comparable to the spot size,
+    // a tight profile mask lands off the spot and box-summing wins.
+    bool   measure_centroid = false;
+    double centroid_bias_px = NAN;
+    double centroid_rms_px = NAN;
+    // Offset split by spot significance (lo/hi about the median) and measured two ways:
+    // the intensity *centroid* (mean) and the sub-pixel *peak* (mode, parabolic fit).
+    //  - centroid offset shrinking lo->hi  => noise floor (offset ~ 1/sqrt(counts));
+    //    flat with significance            => a systematic position error to model.
+    //  - peak offset << centroid offset    => the spot is asymmetric (non-Gaussian /
+    //    parallax): the prediction sits on the peak, only the centroid is pulled, so
+    //    recentring on the centroid would be wrong - the shape is what to model.
+    //  - radial centroid offset ~ 0        => no distance/parallax error (parallax is radial).
+    double centroid_lo_signif = NAN, centroid_hi_signif = NAN; // mean significance per bin
+    double centroid_lo_tang_c = NAN, centroid_hi_tang_c = NAN; // mean |tangential centroid offset|
+    double centroid_lo_tang_p = NAN, centroid_hi_tang_p = NAN; // mean |tangential peak offset|
+    double centroid_lo_rad_c  = NAN, centroid_hi_rad_c  = NAN; // mean signed radial centroid offset
+
+    // Test: recentre the extraction profile on each spot's observed centroid (instead of
+    // the predicted position) so a tight mask lands on the real spot - but only for spots
+    // whose in-shoebox significance exceeds recenter_min_signif (recentring on a noise
+    // centroid would bias weak reflections positive).
+    bool   recenter_profile = false;
+    double recenter_min_signif = 5.0;
+
     // --- output ---
     std::vector<Reflection> reflections; // profile-fitted integration result
     bool   solved = false;
@@ -190,6 +240,10 @@ struct PixelRefineData {
     size_t residual_count = 0;
     double cc = NAN;        // per-image CC of scaled intensities vs reference
     int64_t cc_n = 0;       // number of reflections in the CC
+
+    bool   covariance_valid = false;
+    double corr_GB = NAN, corr_GR0 = NAN, corr_GR1 = NAN;
+    double corr_BR0 = NAN, corr_BR1 = NAN, corr_R0R1 = NAN;
 };
 
 class PixelRefine {
-- 
2.52.0


From 100fe7b7e7f56153f0d508f8bdfc7303077f5612 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 13 Jun 2026 22:02:18 +0200
Subject: [PATCH 040/228] PixelRefine: make factored Terms 1+2 the model,
 remove old wiring

PixelRefine is now an intensity-only operation: geometry is fixed (refined
upstream by XtalOptimizer) and the only objective is the factored per-reflection
likelihood (FACTORED_MODEL.md Terms 1+2) - measured per-resolution profile width
R1 plus one Fisher-weighted intensity/scaling residual per reflection, fitting
the per-image scale G and B. Validated on crystal 2 (fixed_master.h5 as stills,
1.7 A): CC1/2 84-92%, CCref 77-92%, flat - reproduces the env-flag prototype and
matches the rotation path from the stills path.

Removed:
- the per-pixel ShoeboxResidual loss and PixelResidual cost functor;
- all in-PixelRefine geometry refinement (orientation/cell/beam/distance/R),
  the regularised-orientation LSQ, signal-weighting, and the global sweep;
- Term 3 (per-spot recentring) - a confirmed no-op on both crystals;
- the diagnostic scaffolding (covariance, centroid, adaptive_R1) and the
  PR_* env knobs + stderr dumps in IndexAndRefine;
- the PredictImage/ChiSquaredImage renderers and the entire viewer
  PixelRefine window/table/params + worker bindings + shoebox overlay.

The sweep box-integrator background median became mean (consistency) by virtue
of removing the sweep. METHODS.md rewritten for the current model; findings
recorded in FINDINGS-2026-06.md. Net -2200 lines.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |   34 -
 .../pixel_refinement/FACTORED_MODEL.md        |    4 +-
 .../pixel_refinement/FINDINGS-2026-06.md      |  122 ++
 image_analysis/pixel_refinement/METHODS.md    |  392 ++---
 .../pixel_refinement/PixelRefine.cpp          | 1557 +++--------------
 image_analysis/pixel_refinement/PixelRefine.h |  316 +---
 viewer/CMakeLists.txt                         |    5 -
 viewer/JFJochImageReadingWorker.cpp           |  294 ----
 viewer/JFJochImageReadingWorker.h             |   39 +-
 viewer/JFJochViewerWindow.cpp                 |   38 -
 viewer/image_viewer/JFJochImage.h             |    5 +-
 viewer/image_viewer/JFJochSimpleImage.cpp     |   24 -
 viewer/image_viewer/JFJochSimpleImage.h       |    6 -
 .../windows/JFJochPixelRefineTableWindow.cpp  |  101 --
 viewer/windows/JFJochPixelRefineTableWindow.h |   34 -
 viewer/windows/JFJochPixelRefineWindow.cpp    |  233 ---
 viewer/windows/JFJochPixelRefineWindow.h      |   79 -
 viewer/windows/PixelRefineParams.h            |   66 -
 18 files changed, 569 insertions(+), 2780 deletions(-)
 create mode 100644 image_analysis/pixel_refinement/FINDINGS-2026-06.md
 delete mode 100644 viewer/windows/JFJochPixelRefineTableWindow.cpp
 delete mode 100644 viewer/windows/JFJochPixelRefineTableWindow.h
 delete mode 100644 viewer/windows/JFJochPixelRefineWindow.cpp
 delete mode 100644 viewer/windows/JFJochPixelRefineWindow.h
 delete mode 100644 viewer/windows/PixelRefineParams.h

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index ccf084fe..f7cb25c1 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -446,28 +446,6 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
-    // TEMPORARY diagnostic knobs to probe the effect of the (currently fixed) spot
-    // widths R[0] (radial/partiality) and R[1] (tangential/profile). Remove after.
-    if (const char *r0 = std::getenv("PR_R0")) prd.R[0] = std::stod(r0);
-    if (const char *r1 = std::getenv("PR_R1")) prd.R[1] = std::stod(r1);
-    // TEMPORARY: PR_COV refines G,B,R and dumps their per-image correlation matrix.
-    if (std::getenv("PR_COV")) {
-        prd.refine_scale = true; prd.refine_B = true; prd.refine_R = true;
-        prd.compute_covariance = true;
-    }
-    if (std::getenv("PR_FIX_R0")) prd.fix_R0 = true; // hold R0, refine R1 only
-    if (std::getenv("PR_FIX_R")) prd.refine_R = false; // hold R0 and R1: G-B correlation only
-    if (std::getenv("PR_ADAPT_R1")) prd.adaptive_R1 = true; // measure R1 from spot moments
-    if (std::getenv("PR_CENTROID")) prd.measure_centroid = true; // observed-vs-predicted offset
-    if (std::getenv("PR_RECENTER")) prd.recenter_profile = true; // recentre profile on centroid
-    if (const char *s = std::getenv("PR_RECENTER_SIGNIF")) prd.recenter_min_signif = std::stod(s);
-    if (std::getenv("PR_INTENSITY")) { // factored-likelihood Term 1: per-reflection intensity residual
-        prd.intensity_residual = true;
-        prd.refine_orientation = false; prd.refine_R = false;
-        prd.refine_scale = true; prd.refine_B = true;
-    }
-    if (std::getenv("PR_SHAPE")) prd.shape_R1 = true; // Term 2: per-resolution R1 from spot moments
-
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {
@@ -487,18 +465,6 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
             return false;
     }
 
-    if (prd.covariance_valid)
-        fprintf(stderr, "[cov] GB=%.3f GR0=%.3f GR1=%.3f BR0=%.3f BR1=%.3f R0R1=%.3f\n",
-                prd.corr_GB, prd.corr_GR0, prd.corr_GR1, prd.corr_BR0, prd.corr_BR1, prd.corr_R0R1);
-    if (prd.adaptive_R1)
-        fprintf(stderr, "[R1] %.5f\n", prd.R[1]);
-    if (prd.shape_R1 && std::isfinite(prd.shape_R1_lores))
-        fprintf(stderr, "[shapeR1] lores=%.5f hires=%.5f\n", prd.shape_R1_lores, prd.shape_R1_hires);
-    if (prd.measure_centroid && std::isfinite(prd.centroid_lo_tang_c))
-        fprintf(stderr, "[res] lo_s=%.1f lo_tc=%.3f lo_tp=%.3f lo_rc=%.3f hi_s=%.1f hi_tc=%.3f hi_tp=%.3f hi_rc=%.3f\n",
-                prd.centroid_lo_signif, prd.centroid_lo_tang_c, prd.centroid_lo_tang_p, prd.centroid_lo_rad_c,
-                prd.centroid_hi_signif, prd.centroid_hi_tang_c, prd.centroid_hi_tang_p, prd.centroid_hi_rad_c);
-
     // PixelRefine output flows into the normal save/merge path: the refined
     // geometry/lattice and the already-scaled reflections become the outcome.
     i_outcome.reflections = std::move(prd.reflections);
diff --git a/image_analysis/pixel_refinement/FACTORED_MODEL.md b/image_analysis/pixel_refinement/FACTORED_MODEL.md
index 944514a2..cb398977 100644
--- a/image_analysis/pixel_refinement/FACTORED_MODEL.md
+++ b/image_analysis/pixel_refinement/FACTORED_MODEL.md
@@ -1,6 +1,8 @@
 # A factored likelihood for joint integration + scaling + geometry
 
-**Status: design spec (not implemented).** Goal: replace the per-pixel least-squares
+**Status: Terms 1+2 implemented and shipping as the PixelRefine default** (see
+`PixelRefine.cpp`, `METHODS.md`, `FINDINGS-2026-06.md`); Term 3 (geometry) and the
+priors/NN extensions of §4 remain future work. Goal: replace the per-pixel least-squares
 of PixelRefine with a per-*reflection* likelihood that fuses profile-fit integration,
 scaling against the reference, and geometry refinement into one differentiable
 objective — the foundation for priors (Bayesian) and learned components (NN), and the
diff --git a/image_analysis/pixel_refinement/FINDINGS-2026-06.md b/image_analysis/pixel_refinement/FINDINGS-2026-06.md
new file mode 100644
index 00000000..a7345de4
--- /dev/null
+++ b/image_analysis/pixel_refinement/FINDINGS-2026-06.md
@@ -0,0 +1,122 @@
+# PixelRefine — findings, June 2026
+
+A record of the main results from the still-integration investigation, validated on two
+lysozyme P4₃2₁2 datasets indexed against the same reference (`6G8A_refine_001.mtz`):
+
+* **Crystal 1 — serial jet stills** (`LysozymeJet5-…`, MicroMAX DMM ~1 % bandwidth).
+* **Crystal 2 — rotation crystal** (`fixed_master.h5`, 1800 × 0.2°, Si mono), run *as
+  stills* as a stress test, and as rotation for reference. XDS output of this crystal
+  (`CORRECT.LP`, `XDS_ASCII.HKL`) is the external ground truth.
+
+---
+
+## 1. The factored model is a qualitative win (crystal 2, stills, 1.7 Å)
+
+Replacing the per-pixel least squares with the factored Terms 1+2 (intensity residual +
+measured per-resolution $R_1$) turns an erratic, high-res-collapsing result into a flat one:
+
+| | N_obs | ⟨I/σ⟩ | CC₁/₂ (per shell) | CCref (per shell) |
+|---|---:|---:|---|---|
+| baseline per-pixel loss | 799 k | 7.2 | 75→81→56→32→…→0 % | erratic, →0 |
+| **factored Terms 1+2** | 1.22 M | 10.7 | **84–92 %, flat to 1.7 Å** | **77–92 %, flat** |
+
+This *reaches the proper rotation (`-R -P rot`) path's quality from the stills path.* The
+mechanism is clean and on-thesis: **Term 1 lifts the per-image scale CC vs the reference
+from 0.09 → 0.40** (median 0.01 → 0.39) — the per-pixel loss produced near-random per-image
+scales; the factored objective makes each image's scale agree with the reference, so the
+merge coheres. The reference enters at maximum leverage (it sets both the target and the
+Fisher weight).
+
+**Term 3 (per-spot recentring) is a no-op** on both crystals (93.5 vs 93.6 % CC₁/₂): the
+generous integration aperture already contains the spot, so shifting the spotlight by the
+sub-pixel prediction offset does not change the integrated total. It was removed; the
+position residual's value can only come as a *geometry* term (refine orientation/distance
+from the centroid), which is XtalOptimizer's job, not a per-spot mask shift.
+
+---
+
+## 2. The residual centroid offset is a sampling floor, not a recoverable error
+
+On the jet, predictions land on the spot to within a ~0.4 px tangential scatter. Three
+independent cuts show this is the **centroid undersampling floor of the ~2×2 spots**, not a
+geometry error or a shape effect:
+
+* **Flat with intensity.** Binned by significance (≈6σ vs ≈39σ, a 6× span) the tangential
+  centroid offset is 0.41 → 0.36 px (median). A background-limited centroid would shrink
+  ∝ 1/significance (≈6×); it does not, so it is a real ~0.35 px floor, not counting noise.
+* **Peak is a *worse* predictor than the centroid** (sub-pixel parabolic mode: 0.52 vs 0.36
+  px at high signif). If an asymmetric tail were dragging the centroid off a correct peak,
+  the peak would be *better* — it is not. So there is **no coherent shape asymmetry** to
+  model; the offset is a zero-mean per-spot scatter from sub-pixel phase aliasing of a spot
+  only ~2 px wide.
+* **Radial centroid offset ≈ 0.01–0.02 px, flat** → no distance/parallax error (parallax is
+  radial and grows outward).
+
+Consequences: recentring cannot rescue weak reflections (their prediction is already
+centred; the 0.4 px is irreducible sampling scatter), which is *why* a generous box beats a
+tight profile mask. A *symmetric* non-Gaussian shape would not move the centroid at all — it
+would show up only in Term 2 ($R_1$), not in a position term.
+
+---
+
+## 3. The σ gap to XDS is fulls-vs-partials, not intensities
+
+XDS reports **ISa = 28.3** (asymptotic relative error 3.5 %); our stills path reports
+**ISa ≈ 1.1** and the rotation path **≈ 1.6**. The decisive clue is in `XDS_ASCII.HKL`: the
+`PEAK` column (fraction of each reflection captured) is **≈ 100 % for 97 % of reflections**,
+and the header gives mosaicity 0.091° < 0.2° oscillation. So **these are full reflections**,
+recorded over the 1–3 frames each rocking curve spans — not partials.
+
+* **XDS** profile-fits in 3D (the third axis is the rotation/rocking direction) and *sums*
+  the rocking curve with profile weights → one full per reflection, counting-limited σ.
+* **jfjoch `-P rot`** integrates a 2D shoebox *per frame* and recovers each full by
+  *dividing* by the rocking-curve fraction $R_j$ — a cheap approximation of 3D integration.
+  That division injects per-observation noise (it amplifies each frame's background noise,
+  pays N independent backgrounds, and carries a random per-observation partiality error).
+
+Crucially, **ISa and merged-intensity accuracy are different axes, decoupled by
+multiplicity.** Our merged intensities are correct (§4), because ~60–240× multiplicity
+averages the per-observation noise down; ISa measures the per-*observation* precision, which
+multiplicity cannot improve. So "right intensities, wrong σ" is not a contradiction.
+
+**A cheap probe confirms it.** Raising `--min-partiality` from 0.02 → 0.5 on crystal 2
+(rotation) lifts ISa **1.6 → 3.8** at *zero* completeness cost (high multiplicity) and with
+CCref flat — and the high-res shells *improve*. The default 0.02 keeps deep-tail partials
+(2 % of a reflection, scaled back ×50) that were over-weighted and polluting the merge. So
+of the ~17× rotation gap, **~2.8× is tunable tail-weighting** and **~6× is structural** (the
+2D-divide vs 3D-sum difference) — the structural part needs a real rocking-curve sum, not a
+knob.
+
+---
+
+## 4. Our intensities are XDS-grade — the limit is σ, not I
+
+Direct CC of merged intensities (both reduced to the 4/mmm asymmetric unit; 98.8 % of
+reflections matched, no manual reindex):
+
+| vs XDS (CC on merged I, to 1.2 Å) | overall | at 1.2 Å |
+|---|---|---|
+| **PixelRefine stills** (factored) | **95.9 %** | 96.9 % |
+| rotation `-P rot` (min_partiality 0.3) | 98.8 % | 98.5 % |
+
+PixelRefine-stills intensities track XDS at **95–98 %, flat to the 1.2 Å diffraction
+limit**, only ~3 % behind full rotation integration. This is exactly what the CC₁/₂→CC_true
+relation predicts (stills CC₁/₂≈0.88 ⇒ 0.967), so it is real, carried by the huge stills
+multiplicity averaging per-observation noise down. **Conclusion: the intensity estimation is
+right; the remaining gap to XDS is entirely the per-observation σ / partiality axis** — the
+3D rocking-curve integration frontier (`FACTORED_MODEL.md` §4), deliberately parked.
+
+---
+
+## What is fixed vs. parked
+
+**Landed (and now the default model):** mean (not median) background in both integrators;
+de-biased (background-limited) variance; widened Ewald prediction band; the factored
+Terms 1+2 as the only PixelRefine objective; the global XDS-form merge error model with ISa.
+
+**Diagnosed dead-ends (do not re-litigate):** per-image $R$ refinement (degenerate with
+scale); per-spot recentring (no-op); chasing the 0.4 px centroid floor (sampling, not
+recoverable). **Parked (rotation-side):** the 3D rocking-curve sum / one-shot
+post-refinement, a `min_partiality` default for high-multiplicity data, and
+partiality-aware variance weighting — the path to XDS-grade ISa, but a separate axis from
+the intensity work.
diff --git a/image_analysis/pixel_refinement/METHODS.md b/image_analysis/pixel_refinement/METHODS.md
index 8604ffc7..1c1fd9e1 100644
--- a/image_analysis/pixel_refinement/METHODS.md
+++ b/image_analysis/pixel_refinement/METHODS.md
@@ -1,31 +1,30 @@
-# PixelRefine — methods and improvements
+# PixelRefine — methods
 
-This note documents the changes made to the still-image *pixel-refinement* integrator
-(`PixelRefine`) and, more importantly, **why** each one was needed. It is written from a
-methods point of view; the equations are the load-bearing part.
+`PixelRefine` is the still-image integrator. It integrates the Bragg reflections of one
+image by **profile fitting against a reference intensity set** $I^\mathrm{ref}$ (e.g.
+`F_calc` from a deposited model, or the current merged estimate in an EM-style outer loop)
+and returns already-scaled intensities. It is an **intensity-wise** operation: the
+detector geometry (orientation, cell, beam, distance) is taken as fixed — it was refined
+upstream by `XtalOptimizer` (`IndexAndRefine::RefineGeometryIfNeeded`) — and PixelRefine
+only measures the spot shape and fits the per-image scale.
 
-`PixelRefine` integrates Bragg reflections on a **still** image by fitting a per-pixel
-forward model against a known *reference* intensity set (e.g. `F_calc` from a deposited
-model). Unlike a rotation experiment, a still samples only a thin slice of each
-reflection, so the integrator must (a) model the partiality of that slice, (b) refine the
-per-image geometry well enough that the high-resolution shoeboxes land on signal, and
-(c) scale each image onto the reference. Each of those three is where the original code
-went wrong.
+The objective is the factored per-reflection likelihood of `FACTORED_MODEL.md`, **Terms 1
+and 2**. This note records the equations and the reasons behind each design choice.
 
 Throughout, a reflection's shoebox is a small box of raw detector pixels $I_p$ with a
-local flat background $B$; the (area-normalised) model spot profile at pixel $p$ is
-$P_p$, and $v_p$ is the variance used to weight pixel $p$.
+local flat background $B$; the area-normalised tangential profile at pixel $p$ is $P_p$,
+and $v_p$ is the variance used to weight pixel $p$.
 
 ---
 
 ## 0. The forward model
 
-The recorded amplitude of a still reflection is estimated by profile fitting:
+The recorded amplitude of a still reflection is the profile-fit amplitude
 
 $$
-J \;=\; \frac{\sum_p w_p\,P_p\,(I_p - B)}{\sum_p w_p\,P_p^{2}},
-\qquad w_p = \frac{1}{v_p},
-\qquad \operatorname{var}(J) = \frac{1}{\sum_p P_p^{2}/v_p}.
+J \;=\; \frac{\sum_p P_p\,(I_p - B)/v_p}{\sum_p P_p^{2}/v_p},
+\qquad
+\operatorname{var}(J) = \frac{1}{\sum_p P_p^{2}/v_p}.
 $$
 
 The full (rotation-equivalent) intensity is recovered by dividing out the factors a still
@@ -33,296 +32,183 @@ does not record,
 
 $$
 I \;=\; \frac{J}{p\,B_\mathrm{DW}\,\mathrm{pol}},\qquad
-p = \exp\!\left(-\frac{\epsilon_r^{2}}{R_0^{2}}\right),\quad
+p = \exp\!\left(-\frac{\epsilon_r^{2}}{R_{0,\mathrm{eff}}^{2}}\right),\quad
 B_\mathrm{DW}=\exp\!\left(-\frac{B_\mathrm{fac}}{4 d^{2}}\right),
 $$
 
 where the **partiality** $p$ is the fraction of the mosaic block crossing the Ewald
-sphere, $\epsilon_r = 1/\lambda - |S_{hkl}|$ is the excitation error, $R_0$ the radial
-(rocking) width, and $\mathrm{pol}$ the polarisation correction. The per-image model
-intensity for a pixel is
+sphere, $\epsilon_r$ is the radial excitation error, $R_0$ the radial (rocking) width, and
+$\mathrm{pol}$ the polarisation correction. The tangential profile is a separable,
+area-normalised Gaussian of width $R_1$:
 
 $$
-I_p^\mathrm{model} = G\,I^\mathrm{ref}\,B_\mathrm{DW}\,p\,P^\mathrm{tang}_p\,\mathrm{pol} + B,
+P_p = \frac{1}{\pi R_1^{2}}\exp\!\left(-\frac{\epsilon_{t,p}^{2}}{R_1^{2}}\right).
 $$
 
-with $G$ the per-image scale. The per-image least squares minimises
-$\chi^2 = \sum_p w_p\,(I_p^\mathrm{model}-I_p)^2$ over geometry, orientation, $G$, $R$.
+A finite **X-ray bandwidth** thickens the Ewald shell radially, adding a fixed,
+resolution-dependent term to the radial width, $R_{0,\mathrm{eff}}^2 = R_0^2 +
+(b\lambda)^2/(2d^4)$ ($b$ = relative bandwidth; the pink-beam / DMM signature). $b=0$ is a
+monochromatic no-op.
 
 ---
 
 ## 1. De-biased variance (the load-bearing fix)
 
 **Symptom.** Mean intensities went **negative** in the high-resolution shells
-($\langle I/\sigma\rangle$ down to $-12$), which a box-sum integrator never does. The
-per-image scale $G$ also collapsed to $0$ on most images, dropping ~80 % of observations.
+($\langle I/\sigma\rangle$ down to $-12$), and the per-image scale $G$ collapsed to $0$ on
+most images, dropping ~80 % of observations.
 
-**Cause.** Both the extraction and the fit weighted each pixel by its **observed** count,
-$v_p = I_p$. For a background pixel that fluctuated *down* ($I_p < B$), $v_p$ is small, so
-$w_p = 1/v_p$ is *large*, and its contribution $P_p (I_p-B)/v_p < 0$ is large in
-magnitude. Summed over the many (mostly empty) shoebox pixels, this drags $J$ below zero —
-the classic *inverse-observed-count* (Poisson-on-data) bias. It bites hardest where the
-true signal is weakest, i.e. at high resolution. In the fit it manifests differently but
-identically in origin: the weighted empty pixels make "no signal" ($G=0$) the cheapest
-solution, so $G\to 0$.
+**Cause.** The extraction weighted each pixel by its **observed** count, $v_p = I_p$. A
+down-fluctuated background pixel ($I_p < B$) then gets a small $v_p$, hence a large
+$w_p=1/v_p$, and its contribution $P_p(I_p-B)/v_p < 0$ is large in magnitude. Summed over
+the many empty shoebox pixels this drags $J$ below zero — the *inverse-observed-count*
+(Poisson-on-data) bias, worst where the true signal is weakest (high resolution).
 
-**Fix.** For background-limited (weak) reflections the correct variance is the local
-background, **constant over the shoebox**:
-
-$$
-v_p = \max(B,\,1)\quad\Longrightarrow\quad
-J = \frac{\sum_p P_p\,(I_p-B)}{\sum_p P_p^{2}},
-$$
-
-the unbiased uniform-variance estimator. This single change turned $\langle I/\sigma\rangle$
-positive at all resolutions and stopped the scale collapse. It is applied to both the
-extraction weight and the fit weight.
+**Fix.** For background-limited reflections the correct variance is the local background,
+**constant over the shoebox**, $v_p = \max(B,1)$, giving the unbiased uniform-variance
+estimator $J = \sum_p P_p (I_p-B)/\sum_p P_p^2$. This turned $\langle I/\sigma\rangle$
+positive at all resolutions and stopped the scale collapse.
 
 ---
 
 ## 2. Prediction band and multiplicity
 
-**Symptom.** PixelRefine recorded ~4× fewer observations per unique reflection than the
-classical integrator — completeness was fine, *redundancy* was not.
-
-**Cause.** A reflection is given a shoebox only when it lies within a radial band of the
-Ewald sphere,
-
-$$
-\bigl|\,|S_{hkl}| - 1/\lambda\,\bigr| \le \delta .
-$$
-
-For randomly oriented stills the number of images on which a given $hkl$ satisfies this is
-$\propto \delta$. The default $\delta = 5\times10^{-4}\,\text{Å}^{-1}$ was 4–6× tighter
-than the classical integrator's $\delta = 2\text{–}3\times r_\mathrm{profile}$, so each
-reflection was recorded on 4–6× fewer images.
-
-**Fix.** Widen to $\delta = 2\times10^{-3}\,\text{Å}^{-1}$. Multiplicity rose from
-~240 k to ~950 k observations and CC$_\mathrm{ref}$ from 49.7 % to 55.9 %. Widening is
-only safe once the fit is well-behaved (Sections 1, 3, 4); with the original
-unconstrained fit it caused divergence.
+A reflection is given a shoebox only when it lies within a radial band of the Ewald
+sphere, $\bigl|\,|S_{hkl}| - 1/\lambda\,\bigr| \le \delta$. For randomly oriented stills
+the number of images on which a given $hkl$ qualifies is $\propto \delta$. The original
+$\delta = 5\times10^{-4}\,\text{Å}^{-1}$ was 4–6× tighter than a box integrator, giving 4×
+fewer observations per reflection. Widening to $\delta = 2\times10^{-3}\,\text{Å}^{-1}$
+(`ewald_dist_cutoff`) restores the multiplicity; the partiality $p$ downweights the
+slightly-off-Ewald tails it admits. (Widening is only safe with the de-biased variance of
+§1 and the factored objective of §§3–4 — with a per-pixel geometry fit it diverged.)
 
 ---
 
-## 3. Regularising the per-image fit
+## 3. Term 2 — measured per-resolution profile width $R_1$
 
-**Symptom.** Freeing *any* per-image parameter (orientation, $R$, even the scalar scale
-$G$) collapsed the merged data (CC$_{1/2}$ from 90 % to a few %). The predict↔refine loop
-with all parameters frozen was, by contrast, byte-identical to extraction-only — proving
-the *fit*, not the loop, was at fault.
-
-**Cause.** The per-image problem regularised **nothing**: orientation had no prior, $R$
-and $G$ only a lower bound. Three orientation DOF (plus $R$, $G$) against a handful of
-signal pixels per still overfit the noise, and an unconstrained $1/G$ then scrambled the
-cross-image merge.
-
-**Fix.** Anchor each refined parameter to its prior with a *data-scaled* weight, as
-`ScaleOnTheFly` already does for rotation data. The data term has one residual **per
-pixel**, so the prior weight must scale with the pixel count:
+$R_1$ is **measured, not fitted**. Fitting $R_1$ inside a per-image least squares is
+degenerate with the scale $G$ (a narrower profile and a larger scale trade off), and that
+degeneracy slides the per-image scale and wrecks the merge. But a **second moment** is
+normalised by the total intensity, so it carries shape information *decoupled from scale*:
 
 $$
-w_\theta = \sqrt{\frac{N_\mathrm{pix}}{\sigma_\theta^{2}}}\,,
-\qquad \chi^2_\mathrm{reg} = w_\theta^{2}\,(\theta-\theta_0)^2 .
-$$
-
-Using $\sqrt{N_\mathrm{refl}}$ instead (as in the rotation scaler) is a factor
-$\sqrt{N_\mathrm{pix}/N_\mathrm{refl}}\approx\sqrt{49}\approx 7$ too weak and is simply not
-felt. Applied to:
-
-* **Scale**: $\theta=G,\ \theta_0=1$. Prevents $1/G$ from wandering; restored CC$_{1/2}$
-  from 4 % back to 87 %.
-* **Orientation**: $\theta$ = Rodrigues vector, $\theta_0$ = spot-centroid orientation,
-  $\sigma_\theta$ in radians. At $\sigma_\theta\!\sim\!1^\circ$ this gives the best
-  CC$_\mathrm{ref}$; beyond $\sim 2^\circ$ the fit overfits and the merge collapses, so
-  $\sigma_\theta$ is the safety knob.
-
----
-
-## 4. Signal-weighting the fit
-
-**Cause.** Even de-biased, a shoebox is ~80 % empty pixels (≈ 40 of 49 for a radius-3
-box). They carry no information on $G$, $R$ or orientation but add noise and, near the
-overfitting edge, destabilise the fit.
-
-**Fix.** Multiply the fit weight by a detector-space Gaussian centred on the predicted
-spot,
-
-$$
-w_p \;\to\; w_p \cdot \exp\!\left(-\frac{r_p^{2}}{2\sigma_s^{2}}\right),
-\qquad r_p = \lVert (x_p,y_p) - (x_\mathrm{pred},y_\mathrm{pred})\rVert,
-$$
-
-so the signal-bearing core drives the refined parameters ($\sigma_s\approx 1.5$ px). With
-the regularised orientation this lifted CC$_\mathrm{ref}$ from 60.5 % to **62.6 %**.
-
----
-
-## 5. Global orientation + cell-scale sweep
-
-**Motivation.** The classical refinement (`XtalOptimizer`) works on spot *centroids* from
-spot-finding, which are poor value at high resolution; the local LSQ above is a heavy
-gradient step that cannot make the ~degree-scale global moves needed to pull a
-mis-indexed crystal's high-resolution reflections onto their shoeboxes. A small,
-**global** sweep that simply asks *"at which orientation does the most high-resolution
-signal appear where the reference says it should?"* is structurally better suited.
-
-**Score.** Pearson CC of the box-summed intensities against the reference, over **all**
-matched reflections (not just the strong ones):
-
-$$
-\mathrm{CC}_\mathrm{ref}(L) = \operatorname{corr}_{hkl}\bigl(\,I^\mathrm{box}_{hkl}(L),\ I^\mathrm{ref}_{hkl}\,\bigr).
-$$
-
-The strong low-resolution reflections **anchor** the CC (moving them off their boxes
-collapses it), so the *change* in CC across the sweep is driven almost entirely by weak
-high-resolution reflections falling onto — or off — real signal. This is the "appearing
-out of the void" behaviour.
-
-**Geometry-derived bounds (parameter-free).** A spot at resolution $d$ sits at detector
-radius
-
-$$
-r(d) = \frac{L}{p}\,\frac{\lambda}{d}\quad[\text{px}],
-$$
-
-($L$ = detector distance, $p$ = pixel size). Both a crystal rotation $\delta\theta$ and a
-fractional cell-scale $\epsilon$ displace that spot by an amount proportional to its
-radius:
-
-$$
-\Delta_\mathrm{px} = r(d)\,\delta\theta \quad(\text{rotation}),\qquad
-\Delta_\mathrm{px} = r(d)\,\epsilon \quad(\text{cell scale}).
-$$
-
-So high-resolution spots (large $r$) move most. The two natural constraints fix the grid:
-
-* **Step** = 1 px at the highest resolution: $\;\delta\theta_\mathrm{step} = 1/r_\mathrm{max}$
-  (finer is below the detector's resolving power).
-* **Range** = the orientation uncertainty $\Delta\theta_u$ (a few px at high res). The
-  number of steps per axis is then
-
-$$
-n = \frac{\Delta\theta_u}{\delta\theta_\mathrm{step}} = \Delta\theta_u\, r_\mathrm{max},
-$$
-
-a handful of steps, and the lowest-resolution spots move only
-$n\,\delta\theta_\mathrm{step}\,r_\mathrm{min} = \Delta\theta_u\, r_\mathrm{min} \ll 2$ px
-— i.e. the strong anchors stay put by construction.
-
-> **Lesson learned.** Setting the range from "2 px at low resolution" instead gives
-> $n = 2\,r_\mathrm{max}/r_\mathrm{min} = 2\,d_\mathrm{low}/d_\mathrm{high}$ steps — tens
-> of pixels of high-resolution freedom — which lets the per-image CC overfit and *degrades*
-> the merge. The range must be tied to the (small) orientation uncertainty, not the
-> low-resolution cap.
-
-The sweep is a coordinate descent over the three Rodrigues axes and the cell scale, run
-**before** the LSQ. It improves the high-resolution shells (CC$_\mathrm{ref}$ +1 to +5
-per shell) while preserving CC$_{1/2}\approx 90$ %. It is an *alternative* to the
-loose-$\sigma$ orientation LSQ, not a complement — stacking the two double-moves the
-orientation and overfits. It is therefore available but **off by default**.
-
----
-
-## 6. Background-estimator bias (the largest σ error; both integrators)
-
-**Symptom.** Pushed past the true resolution limit (e.g. a 1.8 Å crystal merged to 1.3 Å),
-the no-signal shells still reported $\langle I/\sigma\rangle \approx 4\text{–}6$ with
-$\mathrm{CC}_{1/2}\approx 0$ — i.e. confident "data" where there is none. Present in *both*
-`PixelRefine` and the classical `BraggIntegrate2D`.
-
-**Cause.** Both estimated the local background as the **median** of the surrounding ring.
-For a Poisson / right-skewed background the median sits *below* the mean,
-
-$$
-\operatorname{median}(B) < \mathbb{E}[B],
-$$
-
-so subtracting it under-subtracts on every pixel. The leftover positive offset is tiny per
-pixel but coherent, so over an $n_\mathrm{pix}$-pixel peak and a multiplicity-$m$ merge it
-grows to a fake signal
-
-$$
-\langle I\rangle_\mathrm{bias} \;\approx\; n_\mathrm{pix}\,\bigl(\mathbb{E}[B]-\operatorname{median}(B)\bigr),
+R_1^2 = 2\,\langle \epsilon_t^2\rangle,
 \qquad
-\Bigl(\tfrac{I}{\sigma}\Bigr)_\mathrm{merged,\,bias} \propto \sqrt{m}.
+\langle \epsilon_t^2\rangle = \frac{\sum_p (I_p-B)\,\epsilon_{t,p}^2}{\sum_p (I_p-B)} .
 $$
 
-It is worst where the real signal is weakest (high resolution), because there the offset is
-all that remains — which is exactly the observed signature. *Nothing leaks into the
-high-resolution shells; the background is simply under-estimated.*
-
-**Fix.** Use the **mean** of the ring (outliers excluded by the existing spot-core mask and
-saturation sentinels). $\langle I/\sigma\rangle$ then collapses to ~0 wherever
-$\mathrm{CC}\approx0$, tracks CC down the shells, and the honest resolution limit becomes
-visible. This was the single largest contributor to untrustworthy σ — a one-line change in
-each integrator, *not* a variance-model problem.
+We bin the strong spots ($\mathrm{signif}\ge 5$) by resolution ($1/d^2$, 6 bins) and take
+the **median** $\langle\epsilon_t^2\rangle$ per bin, so each reflection integrates with the
+$R_1$ of its resolution shell (low-res spots are tight; high-res anisotropic streaks are
+wider). Weak spots fall back to the global $R_1$. Measuring the width rather than fitting
+it is what makes profile-width refinement stable — and it is a selling point: the mask
+adapts to the data per shell.
 
 ---
 
-## 7. Error model (global $a, b$; XDS form)
+## 4. Term 1 — the intensity / scaling residual
+
+The per-pixel least squares is replaced by **one residual per reflection**: the profile-fit
+amplitude $J$ (using the Term-2 $R_1$) should equal the scaled reference,
+
+$$
+r_h = \frac{J_h - G\,B_\mathrm{DW}\,p_h\,\mathrm{pol}_h\,I^\mathrm{ref}_h}{\sigma_{J,h}},
+\qquad
+L = \sum_h r_h^2 + \text{(scale prior)} .
+$$
+
+Only the per-image scale $G$ and Debye–Waller $B$ are optimised; geometry and $R$ are
+fixed. Three consequences:
+
+* **Integration and scaling become one objective.** $J$ *is* the integrated intensity and
+  the residual *is* the scaling residual.
+* **The empty-pixel problem disappears by construction.** Empty pixels enter only through
+  $J$ (with ~zero profile weight); they make no residual of their own and cannot dominate.
+* **Fisher weighting puts the reference at maximum leverage.** $\sigma_J$ uses the
+  *model-expected* variance $v_p = B + \max(J,0)\,P_p$ (background plus expected signal from
+  $I^\mathrm{ref}$), not the observed counts — so a strong *expected* reflection observed
+  absent is penalised, and a noise spike with low $I^\mathrm{ref}$ gets no weight.
+
+The scale is regularised towards 1 with a data-scaled weight $w_G=\sqrt{N_\mathrm{refl}/
+\sigma_G}$ (mirrors `ScaleOnTheFly`) so weakly-measured images cannot drift and scramble
+the merge.
+
+**Geometry is not refined here.** PixelRefine's earlier per-image geometry refinement
+(regularised orientation LSQ, signal-weighting, a global orientation/cell sweep) was
+removed: on true stills the predictions are already good (radial centroid error ≈ 0,
+tangential ≈ a 0.4 px sampling floor that is *not* a recoverable misprediction), and per-image
+geometry refinement only overfit the sparse signal. Geometry is the job of `XtalOptimizer`.
+
+---
+
+## 5. Background estimator — mean, not median (both integrators)
+
+**Symptom.** Pushed past the true resolution limit, the no-signal shells reported
+$\langle I/\sigma\rangle\approx4\text{–}6$ at $\mathrm{CC}_{1/2}\approx0$ — confident "data"
+where there is none. Present in *both* PixelRefine and the classical `BraggIntegrate2D`.
+
+**Cause.** Both used the **median** of the background ring. For a right-skewed (Poisson)
+background $\operatorname{median}(B) < \mathbb{E}[B]$, so subtraction under-subtracts by a
+tiny but *coherent* per-pixel offset that grows over an $n_\mathrm{pix}$ peak and a
+multiplicity-$m$ merge into a fake $\langle I/\sigma\rangle\propto\sqrt{m}$, worst where the
+real signal is weakest.
+
+**Fix.** Use the **mean** of the ring (spot cores and saturation sentinels already
+excluded). $\langle I/\sigma\rangle$ then collapses to ~0 wherever $\mathrm{CC}\approx0$ and
+the honest resolution limit becomes visible. This was the single largest contributor to
+untrustworthy σ — a one-line change in each integrator.
+
+---
+
+## 6. Error model (global $a,b$; XDS form)
 
 Counting statistics under-estimate the variance of strong reflections, which carry
-systematic errors (scaling, partiality, detector) proportional to intensity, not to
-$\sqrt{I}$. After merging, this leaves CC$_{1/2}$ and $\langle I/\sigma\rangle$
-inconsistent. The standard correction (XDS / DIALS / AIMLESS) inflates the variance with a
-**global** two-parameter model:
+systematic errors proportional to $I$, not $\sqrt{I}$. The standard correction inflates the
+variance with a **global** two-parameter model, applied at the merge level so both
+integrators benefit:
 
 $$
-\sigma'^{\,2} \;=\; a\,\sigma^{2} + \bigl(b\,\langle I\rangle\bigr)^{2},
+\sigma'^{\,2} = a\,\sigma^{2} + (b\,\langle I\rangle)^{2},
 \qquad
-\mathrm{ISa} \;=\; \frac{1}{b}\;=\;\lim_{I\to\infty}\frac{I}{\sigma'} .
+\mathrm{ISa} = \frac{1}{b} = \lim_{I\to\infty}\frac{I}{\sigma'} .
 $$
 
-Two points matter for an unbiased fit:
-
-* The $I^2$ term uses the reflection **mean** $\langle I\rangle$ (constant over its
-  observations), **not** the per-observation $I_i$. Using $I_i$ gives a down-fluctuated
-  point a small $\sigma'$ and hence a large $1/\sigma'^2$ weight, biasing the merged mean —
-  which collapses CC. (This was the decisive bug in the first attempt.)
-* $a$ and $b$ are fit from the spread of symmetry equivalents: for an observation in a
-  group of $n$, $\mathbb{E}[(I_i-\langle I\rangle)^2] = \sigma_i^2(1-h_i)$ with leverage
-  $h_i = w_i/\sum w$. Binning by intensity and regressing the bin medians of
-  $(I_i-\langle I\rangle)^2/(1-h_i)$ on $(\sigma^2, \langle I\rangle^2)$ — *weighted by
-  $1/\mathrm{dev}^4$ so the fit is relative* — gives $(a, b^2)$; the relative weight stops
-  the strong bins (which fix $b$) from swamping the weak bins (which fix $a$).
-
-It is applied at the merge level (`MergeOnTheFly`), so **both** integrators benefit, and
-`jfjoch_process` prints the model and ISa. Earlier per-resolution-shell variants were
-dropped: the standard tools use a single global $a, b$, and the per-shell version was
-partly masking the background bias of Section 6.
+The $I^2$ term uses the reflection **mean** $\langle I\rangle$ (not the per-observation
+$I_i$, which would bias the merged mean and collapse CC); $a,b$ are fit from the spread of
+symmetry equivalents with a relative ($1/\mathrm{dev}^4$) weight so the strong bins (which
+fix $b$) do not swamp the weak bins (which fix $a$). `jfjoch_process` prints the model and
+ISa.
 
 ---
 
-## Results (lysozyme jet, 1.8 Å, identical input)
+## Results (lysozyme rotation crystal `fixed_master.h5`, treated as stills, 1.7 Å)
 
-| Configuration | N_obs | Compl. | CC$_{1/2}$ | CC$_\mathrm{ref}$ |
+| Configuration | N_obs | $\langle I/\sigma\rangle$ | CC$_{1/2}$ | CC$_\mathrm{ref}$ |
 |---|---:|---:|---:|---:|
-| Classical integrator (box-sum) | 421 k | 100 % | 81.4 % | 60.9 % |
-| PixelRefine — original | 61 k | 95 % | 0.0 % | −0.4 % |
-| PixelRefine — consolidated (this work) | 951 k | 100 % | 80.0 % | **62.6 %** |
+| Baseline per-pixel loss | 799 k | 7.2 | erratic, →0 at 1.7 Å | erratic |
+| **Factored Terms 1+2 (this model)** | 1.22 M | 10.7 | **84–92 % flat** | **77–92 % flat** |
 
-The consolidated integrator beats the classical one on the accuracy metric
-(CC$_\mathrm{ref}$) with > 2× the multiplicity, and turns a previously unusable result
-(CC$_{1/2}=0$) into a competitive one.
+The factored objective turns the erratic, high-res-collapsing per-pixel result into flat
+~90 % CC$_{1/2}$/CC$_\mathrm{ref}$ to 1.7 Å — matching the proper rotation integration path
+from the *stills* path. (See `FINDINGS-2026-06.md`.)
 
 ---
 
 ## Default recipe
 
-Sections 1–5 are `PixelRefine`-specific; Sections 6–7 act at the integration/merge level
-and apply to the classical route too.
+§§1–4 are PixelRefine-specific; §§5–6 act at the integration/merge level and apply to the
+classical route too.
 
 | Field / behaviour | Default | Section |
 |---|---|---|
 | fit/extraction variance | local background $B$ | 1 |
 | `ewald_dist_cutoff` | $2\times10^{-3}\,\text{Å}^{-1}$ | 2 |
-| `scale_reg_sigma` | 2.0 | 3 |
-| `orient_reg_sigma_deg` | 1.0 | 3 |
-| `refine_R` | `false` | 3 |
-| `fit_signal_sigma_pix` | 1.5 | 4 |
-| `sweep_orientation` | `false` (available) | 5 |
-| local background estimator | **mean** of the ring | 6 |
-| merge error model | global $a,b$ (ISa printed) | 7 |
+| tangential width $R_1$ | measured per resolution shell | 3 |
+| objective | per-reflection intensity residual, Fisher-weighted | 4 |
+| refined parameters | per-image $G$ (and $B$); geometry fixed | 4 |
+| `scale_reg_sigma` | 2.0 | 4 |
+| local background estimator | **mean** of the ring | 5 |
+| merge error model | global $a,b$ (ISa printed) | 6 |
 
-`orient_reg_sigma_deg` (accuracy vs. precision) and `ewald_dist_cutoff` (multiplicity vs.
-cost) are the two knobs worth tuning per dataset.
+`ewald_dist_cutoff` (multiplicity vs. cost) and `bandwidth` (Si vs. DMM) are the two knobs
+worth setting per dataset.
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 42e8772f..75facde4 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -6,11 +6,11 @@
 #include <algorithm>
 #include <cmath>
 #include <limits>
+#include <utility>
 #include <vector>
 
 #include <Eigen/Dense>
 #include <ceres/ceres.h>
-#include <ceres/covariance.h>
 #include <ceres/rotation.h>
 
 #include "../geom_refinement/LatticeReduction.h"
@@ -24,7 +24,6 @@ struct PixelObs {
     double x, y;          // detector pixel coordinate
     double Iobs;          // raw pixel value (signal + background)
     double Ibkg;          // local background estimate (per-shoebox level, raw counts)
-    double weight;        // 1 / sigma_pixel
 };
 
 // One reflection together with the pixels of its shoebox.
@@ -36,17 +35,10 @@ struct ReflGroup {
     double pol;               // per-reflection polarization correction (raw = true * pol)
     double Ibkg;              // local flat background (raw counts, constant over the shoebox)
     double predicted_x, predicted_y;
-    double R1_eff = 0.0;          // tangential profile width to use (Term 2; 0 => fall back to data.R[1])
-    double dcx = 0.0, dcy = 0.0;  // Term 3: profile recentre shift (observed centroid - predicted)
+    double R1_eff = 0.0;      // tangential profile width to use (Term 2)
     std::vector<PixelObs> pixels;
 };
 
-double SafeInv(double x, double fallback) {
-    if (!std::isfinite(x) || std::fabs(x) < 1e-30)
-        return fallback;
-    return 1.0 / x;
-}
-
 // Median of a vector (in place, partially reorders it).
 double MedianInPlace(std::vector<double> &v) {
     if (v.empty())
@@ -90,8 +82,7 @@ std::vector<uint8_t> BuildSpotMask(const std::vector<Reflection> &predicted, int
 // Square shoebox bounds (inclusive) around a predicted spot, clamped to the
 // detector. The centre is rounded to the nearest pixel with std::lround so the
 // signal box is centred identically to the spot-core mask (BuildSpotMask) and
-// the local-background ring (EstimateLocalBackground), which also lround. Used by
-// Run and the diagnostic renderers so all three share one shoebox definition.
+// the local-background ring (EstimateLocalBackground), which also lround.
 struct ShoeboxBox { int min_x, max_x, min_y, max_y; };
 ShoeboxBox ShoeboxBounds(double px, double py, int radius, size_t xpixel, size_t ypixel) {
     const int cx = static_cast<int>(std::lround(px));
@@ -284,6 +275,30 @@ bool PredictedNode(const T *p0, const T *p1, const T *p2,
     return true;
 }
 
+// Geometry terms for one shoebox pixel under a FIXED geometry (PixelRefine no
+// longer refines geometry, so this is a plain double evaluation, not a Ceres cost):
+//   q_sq        = |g_hkl|^2                 (predicted node, for the B-factor)
+//   eps_radial  = deviation along the Ewald normal (the partiality direction)
+//   eps_tang_sq = squared deviation in the tangent plane (the profile direction)
+bool GeometryProbe(double obs_x, double obs_y, double lambda, double pixel_size,
+                   int h, int k, int l, gemmi::CrystalSystem symmetry,
+                   const double beam[2], double dist_mm, const double detector_rot[2],
+                   const double p0[3], const double p1[3], const double p2[3],
+                   double &q_sq, double &eps_radial, double &eps_tang_sq) {
+    const double inv_lambda = 1.0 / lambda;
+    Eigen::Vector3d e_obs;
+    ObservedRecip<double>(beam, &dist_mm, detector_rot, obs_x, obs_y, pixel_size, inv_lambda, e_obs);
+
+    Eigen::Vector3d e_pred, n_radial;
+    if (!PredictedNode<double>(p0, p1, p2, h, k, l, symmetry, inv_lambda, e_pred, n_radial, q_sq))
+        return false;
+
+    const Eigen::Vector3d delta_q = e_obs - e_pred;
+    eps_radial = delta_q.dot(n_radial);
+    eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
+    return true;
+}
+
 // Pulls a scalar parameter towards an expected value with a fixed weight (the
 // data-scaled prior). Identical in spirit to ScaleOnTheFly's regularizer: it is what
 // keeps the per-image scale G from wandering on weakly-constrained images and
@@ -299,250 +314,30 @@ struct ScalarRegularizer {
     double expected;
 };
 
-// Anchors the orientation (angle-axis vector) to its pre-refinement value with a
-// data-scaled weight. Without it the three orientation DOF chase the sparse signal
-// (and the few noisy background pixels) and the per-image intensities collapse;
-// with it the fit can only make a small, signal-supported sub-spot correction - the
-// push that brings slightly-misaligned high-resolution reflections onto their
-// shoeboxes. Mirrors the G/B regularizers in ScaleOnTheFly.
-struct OrientationRegularizer {
-    OrientationRegularizer(double weight, const double prior[3]) : weight(weight) {
-        for (int i = 0; i < 3; ++i)
-            prior_[i] = prior[i];
-    }
+// Term 1 of the factored likelihood (FACTORED_MODEL.md): the per-reflection
+// *intensity* (0th-moment) residual. The profile-fit amplitude J should equal the
+// scaled reference J_model = G * exp(-B/4d^2) * partiality * pol * I_ref. One scalar
+// residual per reflection, weighted by the model-expected (Fisher) sigma_J. This is
+// the scaling residual - integration and scaling become one objective, and the empty
+// pixels (which make no residual of their own) stop dominating the fit. Geometry is
+// fixed, so J, partiality and sigma_J are constants and only G and B are free.
+struct IntensityResidual {
+    IntensityResidual(double J, double sigma_J, double partiality, double pol,
+                      double I_ref, double inv_4d2)
+        : J(J), inv_sigma(1.0 / sigma_J), partiality(partiality), pol(pol),
+          I_ref(I_ref), inv_4d2(inv_4d2) {}
     template<typename T>
-    bool operator()(const T *p0, T *residual) const {
-        for (int i = 0; i < 3; ++i)
-            residual[i] = T(weight) * (p0[i] - T(prior_[i]));
+    bool operator()(const T *const G, const T *const B, T *residual) const {
+        const T B_term = ceres::exp(-B[0] * T(inv_4d2));
+        const T J_model = G[0] * B_term * T(partiality) * T(pol) * T(I_ref);
+        residual[0] = (J_model - T(J)) * T(inv_sigma);
         return true;
     }
-    double weight;
-    double prior_[3];
+    double J, inv_sigma, partiality, pol, I_ref, inv_4d2;
 };
 
 } // namespace
 
-// ---------------------------------------------------------------------------
-// Cost functor
-//
-//   I_pred(pixel) = G * Itrue * B_term * P_radial * P_tangential * pol + I_bkg
-//
-//   B_term       = exp(-B |q|^2 / 4)                    (Debye-Waller)
-//   P_radial     = exp(-eps_r^2 / R0_eff^2)             (partiality: fraction of
-//                                                        the mosaic blob on the
-//                                                        Ewald sphere; <= 1)
-//   P_tangential = exp(-eps_t^2/R1^2) / (pi R1^2)       (Gaussian spatial profile
-//                                                        in the Ewald tangent plane)
-//   pol          = per-reflection polarization correction (raw = true * pol),
-//                  evaluated once at the predicted spot position (as in
-//                  BraggIntegrate2D). 1 if polarization is disabled.
-//
-// Everything is in *raw* detector counts: there is no per-pixel solid-angle or
-// area (Lorentz/Jacobian) weighting - each pixel counts equally, like the normal
-// integrator. The tangential factor is what makes this "profile fitting"; the
-// 1/(pi R1^2) normalization keeps the profile width R1 from soaking up the
-// overall scale G.
-//
-// X-ray bandwidth: a spread in lambda is a spread in the Ewald-sphere radius,
-// i.e. a purely *radial* thickening of the shell. It adds (in quadrature) a
-// resolution-dependent term to the radial width:
-//     R0_eff^2 = R0^2 + R_bw^2 ,   R_bw^2 = (b*lambda)^2 / (2 d^4)
-// where b = relative bandwidth (sigma of dlambda/lambda). R_bw grows like 1/d^2,
-// so bandwidth leaves low-resolution spots sharp and smears high-resolution ones
-// radially - the pink-beam/DMM signature. R_bw_sq is a fixed per-reflection
-// constant (b is known), so R0 keeps meaning "intrinsic" width (mosaic +
-// divergence + beam). b = 0 makes R_bw = 0: a monochromatic no-op.
-// ---------------------------------------------------------------------------
-struct PixelResidual {
-    PixelResidual(const PixelObs &obs, double Itrue,
-                  double lambda, double pixel_size,
-                  double exp_h, double exp_k, double exp_l,
-                  double R_bw_sq, double pol,
-                  gemmi::CrystalSystem symmetry)
-        : Itrue(Itrue), Iobs(obs.Iobs), Ibkg(obs.Ibkg), weight(obs.weight),
-          obs_x(obs.x), obs_y(obs.y),
-          inv_lambda(1.0 / lambda), pixel_size(pixel_size),
-          exp_h(exp_h), exp_k(exp_k), exp_l(exp_l),
-          R_bw_sq(R_bw_sq), pol(pol), symmetry(symmetry) {
-        if (std::fabs(lambda) < 1e-6)
-            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                                  "Lambda cannot be close to zero");
-    }
-
-    // Maps a detector pixel through the current geometry + lattice into the
-    // reference reciprocal frame and returns:
-    //   q_sq        = |g_hkl|^2                 (predicted node, for B-factor)
-    //   eps_radial  = deviation along Ewald normal (partiality direction)
-    //   eps_tang_sq = squared deviation in the detector-tangential plane (profile)
-    template<typename T>
-    bool GeometryTerms(const T *const beam,
-                       const T *const distance_mm,
-                       const T *const detector_rot,
-                       const T *const p0,
-                       const T *const p1,
-                       const T *const p2,
-                       T &q_sq, T &eps_radial, T &eps_tang_sq) const {
-        Eigen::Matrix<T, 3, 1> e_obs_recip;
-        ObservedRecip(beam, distance_mm, detector_rot,
-                      obs_x, obs_y, pixel_size, inv_lambda,
-                      e_obs_recip);
-
-        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
-        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
-                           e_pred_recip, n_radial, q_sq))
-            return false;
-
-        const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-        eps_radial = delta_q.dot(n_radial);
-        eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
-        return true;
-    }
-
-    // Assembles the full model intensity for the pixel from the geometry terms.
-    template<typename T>
-    bool Model(const T *const beam, const T *const distance_mm,
-               const T *const detector_rot,
-               const T *const p0, const T *const p1, const T *const p2,
-               const T *const scale_factor, const T *const B, const T *const R,
-               T &Ipred) const {
-        T q_sq, eps_radial, eps_tang_sq;
-        if (!GeometryTerms(beam, distance_mm, detector_rot,
-                           p0, p1, p2, q_sq, eps_radial, eps_tang_sq))
-            return false;
-
-        if (R[0] < T(1e-10) || R[1] < T(1e-10))
-            return false;
-
-        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
-
-        // Separable Gaussian spot model:
-        //   radial  P_r(e) = exp(-e^2/R0_eff^2)                      (peak-normalized, in (0,1])
-        //   tangent g_t(e) = exp(-|e|^2/R1^2) / (pi R1^2)            [1/A^-2]
-        // Every pixel counts equally (no area/Lorentz weighting); the radial factor
-        // is the still-image partiality (how far the reflection sits from the Ewald
-        // sphere); the overall scale is carried by the free G.
-        //
-        // IMPORTANT: the radial factor MUST use the same convention here as the
-        // extraction's `partiality` (peak-normalized), otherwise image_scale_corr
-        // = 1/(partiality*G*B) does not invert the model and a leftover, R0_eff-
-        // dependent (hence resolution-dependent) factor biases the intensities.
-        // R0_eff folds in the energy-bandwidth broadening via R_bw_sq.
-        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
-        const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
-        const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1]))
-                         / (T(M_PI) * R[1] * R[1]);
-
-        const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
-        Ipred = signal + T(Ibkg);
-        return true;
-    }
-
-    template<typename T>
-    bool operator()(const T *const beam,
-                    const T *const distance_mm,
-                    const T *const detector_rot,
-                    const T *const p0,
-                    const T *const p1,
-                    const T *const p2,
-                    const T *const scale_factor,
-                    const T *const B,
-                    const T *const R,
-                    T *residual) const {
-        T Ipred;
-        if (!Model(beam, distance_mm, detector_rot, p0, p1, p2, scale_factor, B, R, Ipred))
-            return false;
-
-        residual[0] = (Ipred - T(Iobs)) * T(weight);
-        return true;
-    }
-
-    const double Itrue, Iobs, Ibkg, weight;
-    const double obs_x, obs_y;
-    const double inv_lambda;
-    const double pixel_size;
-    const double exp_h, exp_k, exp_l;
-    const double R_bw_sq;   // bandwidth radial-width^2 contribution (0 = monochromatic)
-    const double pol;       // per-reflection polarization correction
-    gemmi::CrystalSystem symmetry;
-};
-
-// ---------------------------------------------------------------------------
-// Per-shoebox cost functor
-//
-// One residual block per reflection emitting N residuals (one per shoebox pixel).
-// The expensive per-reflection geometry (PredictedNode: symmetry-aware B matrix,
-// three rotations, cross products) is computed ONCE; only the cheap per-pixel
-// ObservedRecip + Gaussian profile run in the pixel loop. This is identical in
-// value to the old one-block-per-pixel formulation but ~(pixels-per-shoebox)x
-// fewer evaluations of the costly node computation. Uses the same shared helpers
-// (and hence the same conventions) as PixelResidual.
-// ---------------------------------------------------------------------------
-struct ShoeboxResidual {
-    ShoeboxResidual(const ReflGroup &g, double lambda, double pixel_size,
-                    gemmi::CrystalSystem symmetry)
-        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq), pol(g.pol),
-          exp_h(g.h), exp_k(g.k), exp_l(g.l),
-          inv_lambda(1.0 / lambda), pixel_size(pixel_size),
-          symmetry(symmetry) {}
-
-    template<typename T>
-    bool operator()(const T *const *params, T *residual) const {
-        // Parameter blocks (order matches AddParameterBlock in Run):
-        // 0 beam[2] 1 distance[1] 2 detector_rot[2]
-        // 3 p0[3] 4 p1[3] 5 p2[3] 6 scale[1] 7 B[1] 8 R[2]
-        const T *beam = params[0];
-        const T *distance_mm = params[1];
-        const T *detector_rot = params[2];
-        const T *p0 = params[3];
-        const T *p1 = params[4];
-        const T *p2 = params[5];
-        const T *scale_factor = params[6];
-        const T *B = params[7];
-        const T *R = params[8];
-
-        if (R[0] < T(1e-10) || R[1] < T(1e-10))
-            return false;
-
-        // --- per-reflection: computed once ---------------------------------
-        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
-        T q_sq;
-        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
-                           e_pred_recip, n_radial, q_sq))
-            return false;
-
-        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
-        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
-
-        // --- per-pixel loop -------------------------------------------------
-        for (size_t i = 0; i < pixels.size(); ++i) {
-            const PixelObs &obs = pixels[i];
-
-            Eigen::Matrix<T, 3, 1> e_obs_recip;
-            ObservedRecip(beam, distance_mm, detector_rot,
-                          obs.x, obs.y, pixel_size, inv_lambda,  e_obs_recip);
-
-            const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-            const T eps_radial = delta_q.dot(n_radial);
-            const T eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
-
-            const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
-            const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1]))
-                             / (T(M_PI) * R[1] * R[1]);
-
-            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
-            const T Ipred = signal + T(obs.Ibkg);
-            residual[i] = (Ipred - T(obs.Iobs)) * T(obs.weight);
-        }
-        return true;
-    }
-
-    std::vector<PixelObs> pixels;
-    const double Itrue, R_bw_sq, pol;
-    const double exp_h, exp_k, exp_l;
-    const double inv_lambda, pixel_size;
-    gemmi::CrystalSystem symmetry;
-};
-
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
                          const std::vector<MergedReflection> &reference)
     : xpixel(experiment.GetXPixelsNum()),
@@ -598,187 +393,6 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     }
 }
 
-template<class T>
-void PixelRefine::SweepOrientationCell(const T *image, BraggPrediction &prediction,
-                                       PixelRefineData &data) const {
-    const int radius = data.shoebox_radius;
-    const double beam_x = data.geom.GetBeamX_pxl();
-    const double beam_y = data.geom.GetBeamY_pxl();
-    const auto qnan = std::numeric_limits<double>::quiet_NaN();
-
-    // Box-sum minus local (perimeter) background, raw counts. NaN if the box runs
-    // off the detector or hits a masked/saturated pixel.
-    auto integrate = [&](double px, double py) -> double {
-        const int cx = static_cast<int>(std::lround(px));
-        const int cy = static_cast<int>(std::lround(py));
-        const int outer = radius + 1;
-        if (cx - outer < 0 || cy - outer < 0 ||
-            cx + outer >= static_cast<int>(xpixel) || cy + outer >= static_cast<int>(ypixel))
-            return qnan;
-        double sig = 0.0;
-        int nsig = 0;
-        std::vector<double> ring;
-        ring.reserve((2 * outer + 1) * (2 * outer + 1));
-        for (int y = cy - outer; y <= cy + outer; ++y) {
-            for (int x = cx - outer; x <= cx + outer; ++x) {
-                const T raw = image[static_cast<size_t>(xpixel) * y + x];
-                if (raw == std::numeric_limits<T>::max())
-                    return qnan;
-                if (std::is_signed_v<T> && raw == std::numeric_limits<T>::min())
-                    return qnan;
-                const double v = static_cast<double>(raw);
-                if (std::abs(x - cx) <= radius && std::abs(y - cy) <= radius) {
-                    sig += v;
-                    ++nsig;
-                } else {
-                    ring.push_back(v);
-                }
-            }
-        }
-        if (ring.size() < 5)
-            return qnan;
-        return sig - nsig * MedianInPlace(ring);
-    };
-
-    // Predict (wide band) and collect every reflection that has a reference value,
-    // with its detector radius. The full set is scored - the strong low-res spots
-    // anchor the CC, the weak high-res spots are what "appear" at the right cell.
-    DiffractionExperiment exp_iter = experiment;
-    exp_iter.BeamX_pxl(beam_x).BeamY_pxl(beam_y)
-            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-    const BraggPredictionSettings settings{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)
-    };
-    const int nrefl = prediction.Calc(exp_iter, data.latt, settings);
-    const auto &predicted = prediction.GetReflections();
-
-    struct Matched { int h, k, l; double refI; };
-    std::vector<Matched> matched;
-    double r_max = 0.0, r_min = std::numeric_limits<double>::max();
-    for (int i = 0; i < nrefl; ++i) {
-        const auto &r = predicted[i];
-        const auto it = reference_data.find(hkl_key_generator(r));
-        if (it == reference_data.end())
-            continue;
-        matched.push_back({r.h, r.k, r.l, it->second});
-        const double dx = r.predicted_x - beam_x;
-        const double dy = r.predicted_y - beam_y;
-        const double rad = std::sqrt(dx * dx + dy * dy);
-        r_max = std::max(r_max, rad);
-        r_min = std::min(r_min, rad);
-    }
-    if (matched.size() < 20 || r_min <= 1.0 || r_max <= r_min)
-        return; // too little to anchor a meaningful sweep
-
-    // CC of the box-summed intensities against the reference, over all matched hkls.
-    auto score = [&](const CrystalLattice &L) -> double {
-        const Coord A = L.Astar(), B = L.Bstar(), C = L.Cstar();
-        double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
-        int n = 0;
-        for (const auto &m : matched) {
-            const Coord g = A * static_cast<float>(m.h) + B * static_cast<float>(m.k)
-                            + C * static_cast<float>(m.l);
-            const auto [x, y] = data.geom.RecipToDetector(g);
-            if (!std::isfinite(x) || !std::isfinite(y))
-                continue;
-            const double I = integrate(x, y);
-            if (!std::isfinite(I))
-                continue;
-            const double yv = m.refI;
-            sx += I; sy += yv; sxx += I * I; syy += yv * yv; sxy += I * yv; ++n;
-        }
-        if (n < 10)
-            return -2.0;
-        const double nd = n;
-        const double cov = sxy - sx * sy / nd;
-        const double vx = sxx - sx * sx / nd;
-        const double vy = syy - sy * sy / nd;
-        if (!(vx > 0.0 && vy > 0.0))
-            return -2.0;
-        return cov / std::sqrt(vx * vy);
-    };
-
-    // Step = 1 px at the highest resolution. Range = assumed orientation/cell-scale
-    // uncertainty (a few px at high res), NOT the low-res 2 px cap: the latter is
-    // ~2*r_max/r_min px at high res - far too permissive, and lets the per-image CC
-    // overfit. Here the low-res spots barely move (stay anchored).
-    const double step = 1.0 / r_max;
-    const int n_rot = std::clamp(
-        static_cast<int>(std::lround(data.sweep_max_deg * M_PI / 180.0 * r_max)), 1, 25);
-    const int n_scale = std::clamp(
-        static_cast<int>(std::lround(data.sweep_max_cell_frac * r_max)), 1, 25);
-    const Coord axes[3] = {Coord(1, 0, 0), Coord(0, 1, 0), Coord(0, 0, 1)};
-
-    CrystalLattice best = data.latt;
-    double best_cc = score(best);
-
-    for (int round = 0; round < 2; ++round) {
-        for (const auto &axis : axes) {
-            CrystalLattice axis_best = best;
-            double axis_cc = best_cc;
-            for (int i = -n_rot; i <= n_rot; ++i) {
-                if (i == 0)
-                    continue;
-                CrystalLattice cand = best.Multiply(RotMatrix(static_cast<float>(i * step), axis));
-                const double cc = score(cand);
-                if (cc > axis_cc) {
-                    axis_cc = cc;
-                    axis_best = cand;
-                }
-            }
-            best = axis_best;
-            best_cc = axis_cc;
-        }
-        CrystalLattice scale_best = best;
-        double scale_cc = best_cc;
-        for (int i = -n_scale; i <= n_scale; ++i) {
-            if (i == 0)
-                continue;
-            const double s = 1.0 / (1.0 + i * step); // cell scale (1+eps) -> recip * 1/(1+eps)
-            CrystalLattice cand = best.Multiply(gemmi::Mat33(s, 0, 0, 0, s, 0, 0, 0, s));
-            const double cc = score(cand);
-            if (cc > scale_cc) {
-                scale_cc = cc;
-                scale_best = cand;
-            }
-        }
-        best = scale_best;
-        best_cc = scale_cc;
-    }
-
-    data.latt = best;
-}
-
-// ---------------------------------------------------------------------------
-// Term 1 of the factored likelihood (FACTORED_MODEL.md): the per-reflection
-// *intensity* (0th-moment) residual. The profile-fit amplitude J should equal the
-// scaled reference J_model = G * exp(-B/4d^2) * partiality * pol * I_ref. One scalar
-// residual per reflection, weighted by the model-expected (Fisher) sigma_J. This is
-// the scaling residual - integration and scaling become one objective, and the empty
-// pixels (which make no residual of their own) stop dominating the fit. With geometry
-// and R held fixed, J, partiality and sigma_J are constants, so only G and B are free.
-// ---------------------------------------------------------------------------
-struct IntensityResidual {
-    IntensityResidual(double J, double sigma_J, double partiality, double pol,
-                      double I_ref, double inv_4d2)
-        : J(J), inv_sigma(1.0 / sigma_J), partiality(partiality), pol(pol),
-          I_ref(I_ref), inv_4d2(inv_4d2) {}
-    template<typename T>
-    bool operator()(const T *const G, const T *const B, T *residual) const {
-        const T B_term = ceres::exp(-B[0] * T(inv_4d2));
-        const T J_model = G[0] * B_term * T(partiality) * T(pol) * T(I_ref);
-        residual[0] = (J_model - T(J)) * T(inv_sigma);
-        return true;
-    }
-    double J, inv_sigma, partiality, pol, I_ref, inv_4d2;
-};
-
 template<class T>
 void PixelRefine::Run(const T *image,
                       BraggPrediction &prediction,
@@ -786,11 +400,6 @@ void PixelRefine::Run(const T *image,
     data.solved = false;
     data.reflections.clear();
 
-    // Global orientation + cell-scale sweep before the local LSQ, to recentre the
-    // high-resolution shoeboxes onto signal that small misalignments hide.
-    if (data.sweep_orientation)
-        SweepOrientationCell(image, prediction, data);
-
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
 
@@ -826,701 +435,244 @@ void PixelRefine::Run(const T *image,
         return bl * bl / (2.0 * d * d * d * d);
     };
 
-    // Mutable experiment whose geometry is re-synced from the refined data.geom
-    // before each prediction, so shoeboxes track the refined geometry/cell.
+    // Geometry is FIXED here: orientation/cell/detector were already refined upstream
+    // by XtalOptimizer (IndexAndRefine::RefineGeometryIfNeeded). PixelRefine is an
+    // intensity-only operation - it predicts shoeboxes with this geometry, measures the
+    // tangential profile width, and fits the per-image scale G (and B) to the reference.
+    double beam[2], dist_mm, detector_rot[2];
+    double latt_vec0[3], latt_vec1[3], latt_vec2[3];
+    BuildParameterBlocks(data, beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2);
+
+    // ---- 1. Predict shoeboxes for the current geometry ------------------------
     DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+            .BeamY_pxl(data.geom.GetBeamY_pxl())
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+
+    // ---- 2. Collect per-reflection shoebox pixels + local background ----------
+    // GetReflections() returns the full pre-sized buffer; only the first nrefl
+    // entries are valid for this image. A spot-core mask over ALL predictions keeps
+    // each reflection's background ring from picking up a neighbour's signal.
+    const auto &predicted = prediction.GetReflections();
+    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
 
-    // State retained after the loop for the final reflection extraction.
     std::vector<ReflGroup> groups;
-    double beam[2] = {0, 0};
-    double dist_mm = data.geom.GetDetectorDistance_mm();
-    double detector_rot[2] = {0, 0};
-    double latt_vec0[3] = {0, 0, 0}; // orientation (Rodrigues)
-    double latt_vec1[3] = {0, 0, 0}; // lengths
-    double latt_vec2[3] = {0, 0, 0}; // angles (rad)
-    double orient_prior[3] = {0, 0, 0}; // pre-refinement orientation (regularization anchor)
+    for (int ri = 0; ri < nrefl; ++ri) {
+        const auto &refl = predicted[ri];
+        const auto hkl = hkl_key_generator(refl);
+        if (!reference_data.contains(hkl))
+            continue;
 
-    const bool eval_only = (data.max_iterations <= 0);
-    const int n_iter = std::max(1, data.max_iterations);
-    for (int iter = 0; iter < n_iter; ++iter) {
-        // ---- 1. Re-sync prediction geometry from the (refined) model ----------
-        exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
-                .BeamY_pxl(data.geom.GetBeamY_pxl())
-                .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-                .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-                .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+        // Local flat background from the ring around the shoebox (raw counts). If we
+        // cannot estimate a clean local background the reflection is dropped, exactly
+        // as BraggIntegrate2D marks it unobserved when too few background pixels survive.
+        double Ibkg = 0.0;
+        if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                     refl.predicted_x, refl.predicted_y,
+                                     radius, bkg_outer_radius, Ibkg))
+            continue;
 
-        const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+        ReflGroup g;
+        g.h = refl.h;
+        g.k = refl.k;
+        g.l = refl.l;
+        g.d = refl.d;
+        g.Itrue = reference_data[hkl];
+        g.R_bw_sq = bandwidth_radial_sq(refl.d);
+        g.pol = polarization(refl.predicted_x, refl.predicted_y);
+        g.Ibkg = Ibkg;
+        g.predicted_x = refl.predicted_x;
+        g.predicted_y = refl.predicted_y;
 
-        // ---- 2. Collect per-reflection shoebox pixels -------------------------
-        // GetReflections() returns the full pre-sized buffer; only the first
-        // nrefl entries are valid for this image (the rest are stale/zeroed).
-        groups.clear();
-        const auto &predicted = prediction.GetReflections();
-
-        // Spot-core mask over ALL predicted reflections, so each reflection's
-        // local background ignores pixels that belong to a neighbouring spot.
-        const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
-
-        for (int ri = 0; ri < nrefl; ++ri) {
-            const auto &refl = predicted[ri];
-            const auto hkl = hkl_key_generator(refl);
-            if (!reference_data.contains(hkl))
-                continue;
-
-            // Local flat background from the ring around the shoebox (raw counts).
-            // No azimuthal fallback: if we cannot estimate a clean local background
-            // the reflection is dropped, exactly as BraggIntegrate2D marks it
-            // unobserved when fewer than a handful of background pixels survive.
-            double Ibkg = 0.0;
-            if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
-                                         refl.predicted_x, refl.predicted_y,
-                                         radius, bkg_outer_radius, Ibkg))
-                continue;
-
-            ReflGroup g;
-            g.h = refl.h;
-            g.k = refl.k;
-            g.l = refl.l;
-            g.d = refl.d;
-            g.Itrue = reference_data[hkl];
-            g.R_bw_sq = bandwidth_radial_sq(refl.d);
-            g.pol = polarization(refl.predicted_x, refl.predicted_y);
-            g.Ibkg = Ibkg;
-            g.predicted_x = refl.predicted_x;
-            g.predicted_y = refl.predicted_y;
-
-            const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
-
-            for (int y = box.min_y; y <= box.max_y; ++y) {
-                for (int x = box.min_x; x <= box.max_x; ++x) {
-                    const size_t npixel = xpixel * y + x;
-
-                    // Skip sentinel (masked / saturated) pixels. We assume the pixel
-                    // mask is already applied upstream (encoded as the sentinel).
-                    if (image[npixel] == std::numeric_limits<T>::max())
-                        continue;
-                    if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
-                        continue;
-
-                    const double Iobs = static_cast<double>(image[npixel]); // raw counts
-
-                    // Variance for the fit weight. Weighting by the observed count
-                    // (var = Iobs) lets down-fluctuated background pixels carry the
-                    // largest 1/sqrt(var) weight, which biases the fit towards "no
-                    // signal" and drove the per-image scale G to 0 on weak images
-                    // (collapsing the merge). Use the local background as the
-                    // (background-limited) variance, constant over the shoebox - the
-                    // same de-biasing applied to the extraction.
-                    double var = std::max(Ibkg, 1.0);
-                    double weight = 1.0 / std::sqrt(var);
-
-                    // Signal-weighting: down-weight pixels far from the predicted spot
-                    // centre so the empty shoebox corners cannot dilute or destabilise
-                    // the fit; the signal-bearing core drives the refined parameters.
-                    if (data.fit_signal_sigma_pix > 0.0) {
-                        const double dx = x - g.predicted_x;
-                        const double dy = y - g.predicted_y;
-                        const double s2 = data.fit_signal_sigma_pix * data.fit_signal_sigma_pix;
-                        weight *= std::exp(-0.5 * (dx * dx + dy * dy) / s2);
-                    }
-
-                    PixelObs obs{
-                        .x = static_cast<double>(x),
-                        .y = static_cast<double>(y),
-                        .Iobs = Iobs,
-                        .Ibkg = Ibkg,
-                        .weight = weight
-                    };
-                    g.pixels.push_back(obs);
-                }
-            }
-
-            if (!g.pixels.empty())
-                groups.push_back(std::move(g));
-        }
-
-        if (groups.empty())
-            return;
-
-        // ---- 3. Set up parameter blocks (geometry part mirrors XtalOptimizer) -
-        BuildParameterBlocks(data, beam, dist_mm, detector_rot,
-                             latt_vec0, latt_vec1, latt_vec2);
-
-        // Anchor for orientation regularization = the orientation the LSQ starts from
-        // (captured before the predict<->refine iterations move it). When the global
-        // sweep ran first this is the swept orientation, not the original spot-centroid
-        // one - which is intended: the regularizer keeps the LSQ near its own starting
-        // point, it is not meant to pull a deliberate sweep back.
-        if (iter == 0)
-            for (int i = 0; i < 3; ++i)
-                orient_prior[i] = latt_vec0[i];
-
-        // ---- Term 3: per-reflection recentre on the observed centroid ----------------
-        // The geometry predicts the spot to ~0.4 px (per-reflection scatter a global fit
-        // cannot remove); a tight Term-2 template centred on the prediction then sits off
-        // the real spot. For confident spots, shift the profile centre to the observed
-        // centroid (used consistently by Term 2, Term 1 and the extraction below). Weak
-        // spots keep the prediction (recentring on a noise centroid would bias them).
-        for (auto &g : groups) {
-            g.dcx = 0.0;
-            g.dcy = 0.0;
-        }
-        if (data.recenter_profile && !groups.empty()) {
-            const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
-            for (auto &g : groups) {
-                double sw = 0.0, swx = 0.0, swy = 0.0;
-                for (const auto &px : g.pixels) {
-                    const double w = std::max(px.Iobs - g.Ibkg, 0.0);
-                    sw += w; swx += w * px.x; swy += w * px.y;
-                }
-                if (sw <= 0.0)
+        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
+        for (int y = box.min_y; y <= box.max_y; ++y) {
+            for (int x = box.min_x; x <= box.max_x; ++x) {
+                const size_t npixel = xpixel * y + x;
+                // Skip sentinel (masked / saturated) pixels.
+                if (image[npixel] == std::numeric_limits<T>::max())
                     continue;
-                if (sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0)) < data.recenter_min_signif)
+                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
                     continue;
-                double dcx = swx / sw - g.predicted_x, dcy = swy / sw - g.predicted_y;
-                const double dl = std::sqrt(dcx * dcx + dcy * dcy);
-                if (dl > 2.0) { dcx *= 2.0 / dl; dcy *= 2.0 / dl; } // clamp runaway centroids
-                g.dcx = dcx;
-                g.dcy = dcy;
+                g.pixels.push_back({static_cast<double>(x), static_cast<double>(y),
+                                    static_cast<double>(image[npixel]), Ibkg});
             }
         }
+        if (!g.pixels.empty())
+            groups.push_back(std::move(g));
+    }
+    if (groups.empty())
+        return;
 
-        // ---- Term 2: per-resolution tangential profile width R1 from spot shapes ------
-        // Default: every reflection uses the global R1; with shape_R1 on, override it with
-        // R1 = sqrt(2*<eps_t^2>) from the intensity-weighted second moment of the strong
-        // spots, binned by resolution (low res small spots, high res larger). A shape
-        // statistic - normalised by the total, so decoupled from the per-image scale.
-        for (auto &g : groups)
-            g.R1_eff = data.R[1];
-        if (data.shape_R1 && !groups.empty()) {
-            constexpr int n_bins = 6;
-            const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
-            double s2min = 1e30, s2max = 0.0;
-            for (const auto &g : groups) {
-                const double s2 = 1.0 / (g.d * g.d);
-                s2min = std::min(s2min, s2);
-                s2max = std::max(s2max, s2);
-            }
-            const double span = std::max(s2max - s2min, 1e-12);
-            auto bin_of = [&](double d) {
-                return std::clamp(static_cast<int>((1.0 / (d * d) - s2min) / span * n_bins), 0, n_bins - 1);
-            };
-            std::vector<std::vector<double>> bin_M2(n_bins);
-            for (const auto &g : groups) {
-                double sw = 0.0, sw_et2 = 0.0;
-                for (const auto &px : g.pixels) {
-                    PixelObs probe{px.x - g.dcx, px.y - g.dcy, 0.0, g.Ibkg, 1.0};
-                    PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
-                                     g.R_bw_sq, g.pol, data.crystal_system);
-                    double q_sq, eps_r, eps_t_sq;
-                    if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
-                                          latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
-                        continue;
-                    const double w = std::max(px.Iobs - g.Ibkg, 0.0);
-                    sw += w;
-                    sw_et2 += w * eps_t_sq;
-                }
-                if (sw <= 0.0)
-                    continue;
-                const double signif = sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0));
-                if (signif >= 5.0) // only well-measured spots define the shape
-                    bin_M2[bin_of(g.d)].push_back(sw_et2 / sw);
-            }
-            std::vector<double> bin_R1(n_bins, data.R[1]);
-            for (int b = 0; b < n_bins; ++b)
-                if (bin_M2[b].size() >= 5) {
-                    const double r1 = std::sqrt(2.0 * std::max(MedianInPlace(bin_M2[b]), 0.0));
-                    if (std::isfinite(r1) && r1 > 1e-4)
-                        bin_R1[b] = std::clamp(r1, 1e-4, 0.05);
-                }
-            for (auto &g : groups)
-                g.R1_eff = bin_R1[bin_of(g.d)];
-            data.shape_R1_lores = bin_R1[0];          // lowest resolution bin
-            data.shape_R1_hires = bin_R1[n_bins - 1]; // highest resolution bin
-        }
-
-        // ---- 4. Build the problem ---------------------------------------------
-        // One residual block per shoebox (N residuals), so the expensive
-        // per-reflection node geometry is evaluated once per reflection instead
-        // of once per pixel.
-        ceres::Problem problem;
-        size_t residual_pixels = 0;
-        if (data.intensity_residual) {
-            // Term-1 path: one per-reflection intensity residual. Geometry & R fixed, so
-            // J / partiality / sigma_J are computed here as constants and only G, B vary.
-            const double R0 = data.R[0];
-            for (const auto &g : groups) {
-                const double R1 = g.R1_eff; // Term 2: per-resolution profile width
-                double num = 0.0, den = 0.0, rad = 0.0;
-                std::vector<std::pair<double, double>> pt_sig; // (P_t, Iobs-Bg) for Fisher pass
-                pt_sig.reserve(g.pixels.size());
-                for (const auto &px : g.pixels) {
-                    PixelObs probe{px.x - g.dcx, px.y - g.dcy, 0.0, g.Ibkg, 1.0}; // Term 3 recentre
-                    PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
-                                     g.R_bw_sq, g.pol, data.crystal_system);
-                    double q_sq, eps_r, eps_t_sq;
-                    if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
-                                          latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
-                        continue;
-                    if (!(R1 > 0.0) || !(R0 > 0.0))
-                        continue;
-                    const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
-                    const double R0_eff_sq = R0 * R0 + g.R_bw_sq;
-                    const double P_rad = std::exp(-eps_r * eps_r / R0_eff_sq);
-                    const double v = std::max(g.Ibkg, 1.0);
-                    const double sig = px.Iobs - g.Ibkg;
-                    num += P_t * sig / v;
-                    den += P_t * P_t / v;
-                    rad += P_rad * P_t * P_t / v;
-                    pt_sig.emplace_back(P_t, sig);
-                }
-                if (!(den > 0.0))
-                    continue;
-                const double J = num / den;
-                const double partiality = rad / den;
-                // Model-expected (Fisher) variance: v_p = background + expected signal J*P_t,
-                // not the per-pixel observed counts (which down-bias) - so the weight tracks
-                // information, and an expected-strong reflection that is absent hurts.
-                double den_f = 0.0;
-                for (const auto &[P_t, sig] : pt_sig) {
-                    const double v_f = std::max(g.Ibkg + std::max(J, 0.0) * P_t, 1.0);
-                    den_f += P_t * P_t / v_f;
-                }
-                const double sigma_J = std::sqrt(1.0 / std::max(den_f, 1e-30));
-                const double inv_4d2 = (g.d > 0.0) ? 1.0 / (4.0 * g.d * g.d) : 0.0;
-                auto *cost = new ceres::AutoDiffCostFunction<IntensityResidual, 1, 1, 1>(
-                    new IntensityResidual(J, sigma_J, partiality, g.pol, g.Itrue, inv_4d2));
-                problem.AddResidualBlock(cost, nullptr, &data.scale_factor, &data.B_factor);
-                ++residual_pixels;
-            }
-            data.residual_count = residual_pixels;
-        } else {
+    // ---- 3. Term 2: per-resolution tangential profile width R1 ----------------
+    // R1 = sqrt(2*<eps_t^2>) from the intensity-weighted tangential second moment of
+    // the strong spots, binned by resolution (low res small spots, high res larger).
+    // A *shape* statistic, normalised by the total intensity, so it is decoupled from
+    // the per-image scale - which is what makes measuring it (rather than fitting it,
+    // where it is degenerate with G) stable. Weak spots fall back to the global R[1].
+    for (auto &g : groups)
+        g.R1_eff = data.R[1];
+    {
+        constexpr int n_bins = 6;
+        const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
+        double s2min = 1e30, s2max = 0.0;
         for (const auto &g : groups) {
-            auto *cost = new ceres::DynamicAutoDiffCostFunction<ShoeboxResidual>(
-                new ShoeboxResidual(g, lambda, pixel_size, data.crystal_system));
-            cost->AddParameterBlock(2); // beam
-            cost->AddParameterBlock(1); // distance
-            cost->AddParameterBlock(2); // detector_rot
-            cost->AddParameterBlock(3); // p0 (orientation)
-            cost->AddParameterBlock(3); // p1 (lengths)
-            cost->AddParameterBlock(3); // p2 (angles)
-            cost->AddParameterBlock(1); // scale G
-            cost->AddParameterBlock(1); // B
-            cost->AddParameterBlock(2); // R
-            cost->SetNumResiduals(static_cast<int>(g.pixels.size()));
-            // No robust loss here: a per-block (whole-shoebox) Huber would act on
-            // the sum of ~N squared residuals and mis-scale, unlike the previous
-            // per-pixel Huber. Per-pixel sigma weighting is retained; per-pixel
-            // outlier rejection (zingers) is a TODO if needed.
-            problem.AddResidualBlock(cost, nullptr,
-                                     beam, &dist_mm, detector_rot,
-                                     latt_vec0, latt_vec1, latt_vec2,
-                                     &data.scale_factor, &data.B_factor, data.R);
-            residual_pixels += g.pixels.size();
+            const double s2 = 1.0 / (g.d * g.d);
+            s2min = std::min(s2min, s2);
+            s2max = std::max(s2max, s2);
         }
-        data.residual_count = residual_pixels;
-        }
-
-        // ---- 5. Constrain / bound parameter blocks ----------------------------
-        if (data.intensity_residual) {
-            // Only G and B are in this problem; geometry/R are not parameters here.
-            problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
-            if (!data.refine_B)
-                problem.SetParameterBlockConstant(&data.B_factor);
-            // Regularize G->1, weight sqrt(n_refl/sigma): commensurate because the data
-            // term is now one residual per reflection (unlike the per-pixel path).
-            if (data.scale_reg_sigma > 0.0 && !groups.empty()) {
-                const double w = std::sqrt(static_cast<double>(groups.size()) / data.scale_reg_sigma);
-                auto *reg = new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
-                    new ScalarRegularizer(w, 1.0));
-                problem.AddResidualBlock(reg, nullptr, &data.scale_factor);
-            }
-        } else {
-        if (!data.refine_orientation) {
-            problem.SetParameterBlockConstant(latt_vec0);
-        } else if (data.orient_reg_sigma_deg > 0.0) {
-            // Anchor orientation to its spot-centroid prior. The weight is scaled to
-            // the *pixel* data term (sqrt(n_pixels)/sigma_rad), not the reflection
-            // count - the data has one residual per shoebox pixel, so a reflection-
-            // scaled prior (~50x too weak) was simply not felt. At a misorientation of
-            // orient_reg_sigma_deg the prior matches the data, so the fit only moves
-            // further when the pixels strongly agree it should.
-            const double sigma_rad = std::max(data.orient_reg_sigma_deg * M_PI / 180.0, 1e-9);
-            const double w = std::sqrt(static_cast<double>(residual_pixels)) / sigma_rad;
-            auto *reg = new ceres::AutoDiffCostFunction<OrientationRegularizer, 3, 3>(
-                new OrientationRegularizer(w, orient_prior));
-            problem.AddResidualBlock(reg, nullptr, latt_vec0);
-        }
-
-        if (!data.refine_unit_cell) {
-            problem.SetParameterBlockConstant(latt_vec1);
-            problem.SetParameterBlockConstant(latt_vec2);
-        } else {
-            for (int i = 0; i < 3; ++i) {
-                problem.SetParameterLowerBound(latt_vec1, i, 5.0);
-                problem.SetParameterUpperBound(latt_vec1, i, 1000.0);
-            }
-            if (data.crystal_system != gemmi::CrystalSystem::Monoclinic &&
-                data.crystal_system != gemmi::CrystalSystem::Triclinic)
-                problem.SetParameterBlockConstant(latt_vec2);
-        }
-
-        if (!data.refine_beam_center)
-            problem.SetParameterBlockConstant(beam);
-
-        if (!data.refine_distance) {
-            problem.SetParameterBlockConstant(&dist_mm);
-        } else {
-            problem.SetParameterLowerBound(&dist_mm, 0, dist_mm * 0.9);
-            problem.SetParameterUpperBound(&dist_mm, 0, dist_mm * 1.1);
-        }
-
-        if (!data.refine_detector_angles) {
-            problem.SetParameterBlockConstant(detector_rot);
-        } else {
-            const double rng = 3.0 / 180.0 * M_PI;
-            for (int i = 0; i < 2; ++i) {
-                problem.SetParameterLowerBound(detector_rot, i, detector_rot[i] - rng);
-                problem.SetParameterUpperBound(detector_rot, i, detector_rot[i] + rng);
-            }
-        }
-
-        if (data.refine_scale) {
-            problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
-            // Regularize G towards 1 so weakly-constrained images cannot wander
-            // (an unconstrained 1/G is what collapsed the cross-image merge). Weight
-            // scaled to the pixel data term (n_pixels), not the reflection count.
-            if (data.scale_reg_sigma > 0.0) {
-                const double w = std::sqrt(static_cast<double>(residual_pixels) / data.scale_reg_sigma);
-                auto *reg = new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
-                    new ScalarRegularizer(w, 1.0));
-                problem.AddResidualBlock(reg, nullptr, &data.scale_factor);
-            }
-        } else {
-            problem.SetParameterBlockConstant(&data.scale_factor);
-        }
-
-        if (!data.refine_B)
-            problem.SetParameterBlockConstant(&data.B_factor);
-
-        if (data.refine_R) {
-            if (data.fix_R0) {
-                // Diagnostic: hold R0 constant, refine R1 only.
-                problem.SetManifold(data.R, new ceres::SubsetManifold(2, {0}));
-            } else {
-                problem.SetParameterLowerBound(data.R, 0, 1e-5);
-                problem.SetParameterLowerBound(data.R, 1, 1e-5);
-            }
-        } else {
-            problem.SetParameterBlockConstant(data.R);
-        }
-        } // end per-pixel (non-intensity_residual) constraints
-
-        // ---- 6. Solve (or, for max_iterations<=0, just evaluate the cost) -----
-        // Evaluate-only is the live-residual path: it reports the current cost
-        // without moving any parameter, so a UI can show how good the present
-        // R0/R1/bandwidth/geometry are as the user drags sliders.
-        if (eval_only) {
-            double cost = 0.0;
-            problem.Evaluate(ceres::Problem::EvaluateOptions(), &cost, nullptr, nullptr, nullptr);
-            data.final_cost = cost;
-            data.solved = true;
-        } else {
-            ceres::Solver::Options options;
-            options.linear_solver_type = ceres::DENSE_QR;
-            options.minimizer_progress_to_stdout = false;
-            options.logging_type = ceres::LoggingType::SILENT;
-            options.max_solver_time_in_seconds = data.max_time_s;
-            options.num_threads = 1;
-
-            ceres::Solver::Summary summary;
-            ceres::Solve(options, &problem, &summary);
-
-            data.final_cost = summary.final_cost;
-            data.solved = summary.IsSolutionUsable();
-
-            // Diagnostic: Pearson correlations on the final solve. Always needs G and B
-            // refined for G-B; the R correlations are added only when R is also refined.
-            if (data.compute_covariance && data.solved && iter == n_iter - 1 &&
-                data.refine_scale && data.refine_B) {
-                ceres::Covariance::Options copt;
-                copt.algorithm_type = ceres::DENSE_SVD;
-                copt.null_space_rank = -1; // tolerate (and reveal) degenerate directions
-                ceres::Covariance cov(copt);
-                std::vector<std::pair<const double *, const double *>> blocks = {
-                    {&data.scale_factor, &data.scale_factor}, {&data.B_factor, &data.B_factor},
-                    {&data.scale_factor, &data.B_factor}};
-                if (data.refine_R) {
-                    blocks.push_back({data.R, data.R});
-                    blocks.push_back({&data.scale_factor, data.R});
-                    blocks.push_back({&data.B_factor, data.R});
-                }
-                if (cov.Compute(blocks, &problem)) {
-                    double cGG, cBB, cGB;
-                    cov.GetCovarianceBlock(&data.scale_factor, &data.scale_factor, &cGG);
-                    cov.GetCovarianceBlock(&data.B_factor, &data.B_factor, &cBB);
-                    cov.GetCovarianceBlock(&data.scale_factor, &data.B_factor, &cGB);
-                    const double sG = std::sqrt(std::max(cGG, 0.0));
-                    const double sB = std::sqrt(std::max(cBB, 0.0));
-                    auto rho = [](double c, double s1, double s2) {
-                        return (s1 > 0.0 && s2 > 0.0) ? c / (s1 * s2) : NAN;
-                    };
-                    data.corr_GB = rho(cGB, sG, sB);
-                    if (data.refine_R) {
-                        double cRR[4], cGR[2], cBR[2];
-                        cov.GetCovarianceBlock(data.R, data.R, cRR);
-                        cov.GetCovarianceBlock(&data.scale_factor, data.R, cGR);
-                        cov.GetCovarianceBlock(&data.B_factor, data.R, cBR);
-                        const double sR0 = std::sqrt(std::max(cRR[0], 0.0));
-                        const double sR1 = std::sqrt(std::max(cRR[3], 0.0));
-                        data.corr_GR0  = rho(cGR[0], sG, sR0);
-                        data.corr_GR1  = rho(cGR[1], sG, sR1);
-                        data.corr_BR0  = rho(cBR[0], sB, sR0);
-                        data.corr_BR1  = rho(cBR[1], sB, sR1);
-                        data.corr_R0R1 = rho(cRR[1], sR0, sR1);
-                    }
-                    data.covariance_valid = true;
-                }
-            }
-        }
-
-        // ---- 7. Write refined geometry + lattice back into data ---------------
-        if (data.refine_beam_center)
-            data.geom.BeamX_pxl(beam[0]).BeamY_pxl(beam[1]);
-        if (data.refine_distance)
-            data.geom.DetectorDistance_mm(dist_mm);
-        if (data.refine_detector_angles)
-            data.geom.PoniRot1_rad(detector_rot[0]).PoniRot2_rad(detector_rot[1]);
-
-        if (data.refine_orientation || data.refine_unit_cell) {
-            switch (data.crystal_system) {
-                case gemmi::CrystalSystem::Orthorhombic:
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                    break;
-                case gemmi::CrystalSystem::Tetragonal:
-                    latt_vec1[1] = latt_vec1[0];
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                    break;
-                case gemmi::CrystalSystem::Cubic:
-                    latt_vec1[1] = latt_vec1[0];
-                    latt_vec1[2] = latt_vec1[0];
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                    break;
-                case gemmi::CrystalSystem::Hexagonal:
-                    latt_vec1[1] = latt_vec1[0];
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
-                    break;
-                case gemmi::CrystalSystem::Monoclinic:
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
-                    break;
-                default:
-                    data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
-                                                          latt_vec2[0], latt_vec2[1], latt_vec2[2]);
-                    break;
-            }
-        }
-    } // predict<->refine iterations
-
-    // ---- Adaptive integration mask --------------------------------------------
-    // Measure R1 (tangential profile width) from the intensity-weighted tangential
-    // second moment of the strong spots, rather than fitting it. R1 is a *shape*
-    // statistic: sigma_t^2 = sum_p (I_p-B) eps_t,p^2 / sum_p (I_p-B), normalised by the
-    // total so it is independent of the per-image scale - which is exactly what breaks
-    // the R1<->G degeneracy (a measured width cannot be traded against G). One value per
-    // image here (from the strong, mostly low-res spots); a per-resolution version is the
-    // natural next step for the high-res / DMM-streak shapes.
-    if (data.adaptive_R1 && !groups.empty()) {
-        std::vector<double> itrue;
-        itrue.reserve(groups.size());
-        for (const auto &g : groups)
-            itrue.push_back(g.Itrue);
-        const size_t cut_idx = itrue.size() * 7 / 10; // keep the strongest ~30%
-        std::nth_element(itrue.begin(), itrue.begin() + cut_idx, itrue.end());
-        const double itrue_cut = itrue[cut_idx];
-
-        std::vector<double> sigma_t2;
+        const double span = std::max(s2max - s2min, 1e-12);
+        auto bin_of = [&](double d) {
+            return std::clamp(static_cast<int>((1.0 / (d * d) - s2min) / span * n_bins), 0, n_bins - 1);
+        };
+        std::vector<std::vector<double>> bin_M2(n_bins);
         for (const auto &g : groups) {
-            if (g.Itrue < itrue_cut)
-                continue;
             double sw = 0.0, sw_et2 = 0.0;
             for (const auto &px : g.pixels) {
-                PixelObs probe{px.x, px.y, 0.0, g.Ibkg, 1.0};
-                PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
-                                 g.R_bw_sq, g.pol, data.crystal_system);
                 double q_sq, eps_r, eps_t_sq;
-                if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
-                                      latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+                                   beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
+                                   q_sq, eps_r, eps_t_sq))
                     continue;
                 const double w = std::max(px.Iobs - g.Ibkg, 0.0);
                 sw += w;
                 sw_et2 += w * eps_t_sq;
             }
-            if (sw > 0.0)
-                sigma_t2.push_back(sw_et2 / sw);
-        }
-        if (sigma_t2.size() >= 5) {
-            const double r1 = std::sqrt(2.0 * MedianInPlace(sigma_t2)); // R1^2 = 2 sigma_t^2
-            if (std::isfinite(r1) && r1 > 1e-5)
-                data.R[1] = r1;
-        }
-    }
-
-    // ---- Centering diagnostic --------------------------------------------------
-    // Observed-centroid vs predicted-position offset for the strong spots, after all
-    // refinement. Large rms (relative to the spot size) means a tight profile mask
-    // sits off the real spot - which is why a generous box can beat profile fitting.
-    if (data.measure_centroid && !groups.empty()) {
-        const double beam_x = data.geom.GetBeamX_pxl();
-        const double beam_y = data.geom.GetBeamY_pxl();
-        const double box_px = (2.0 * radius + 1.0) * (2.0 * radius + 1.0);
-        // Raw pixel value (sentinel/bounds safe) for the parabolic peak fit. A constant
-        // background cancels in the parabola, so no need to subtract it here.
-        auto pix_val = [&](int x, int y) -> double {
-            if (x < 0 || x >= static_cast<int>(xpixel) || y < 0 || y >= static_cast<int>(ypixel))
-                return std::numeric_limits<double>::quiet_NaN();
-            const size_t np = static_cast<size_t>(xpixel) * y + x;
-            if (image[np] == std::numeric_limits<T>::max())
-                return std::numeric_limits<double>::quiet_NaN();
-            if (std::is_signed_v<T> && image[np] == std::numeric_limits<T>::min())
-                return std::numeric_limits<double>::quiet_NaN();
-            return static_cast<double>(image[np]);
-        };
-        struct Off { double signif, tang_c, tang_p, rad_c; };
-        std::vector<Off> offs;
-        double sdx = 0.0, sdy = 0.0, sd2 = 0.0;
-        size_t nc = 0;
-        for (const auto &g : groups) {
-            double sw = 0.0, swx = 0.0, swy = 0.0, bmax = -1e30;
-            int bx = 0, by = 0;
-            for (const auto &px : g.pixels) {
-                const double s = px.Iobs - g.Ibkg;
-                const double w = std::max(s, 0.0);
-                sw += w; swx += w * px.x; swy += w * px.y;
-                if (s > bmax) { bmax = s; bx = static_cast<int>(std::lround(px.x)); by = static_cast<int>(std::lround(px.y)); }
-            }
             if (sw <= 0.0)
                 continue;
             const double signif = sw / std::sqrt(std::max(box_px * g.Ibkg, 1.0));
-            if (signif < 5.0)
-                continue; // a measurable spot at any resolution (not just the strong low-res ones)
-            // Sub-pixel peak (mode): parabola through the brightest pixel and its two
-            // neighbours per axis. The mode tracks the prediction even when an asymmetric
-            // tail drags the centroid (mean) sideways - so peak vs centroid separates a
-            // shape asymmetry from a true position error.
-            double peak_x = bx, peak_y = by;
-            { const double l = pix_val(bx - 1, by), c = pix_val(bx, by), r = pix_val(bx + 1, by);
-              const double den = l - 2.0 * c + r;
-              if (std::isfinite(den) && den < -1e-9)
-                  peak_x = bx + std::clamp(0.5 * (l - r) / den, -1.0, 1.0); }
-            { const double l = pix_val(bx, by - 1), c = pix_val(bx, by), r = pix_val(bx, by + 1);
-              const double den = l - 2.0 * c + r;
-              if (std::isfinite(den) && den < -1e-9)
-                  peak_y = by + std::clamp(0.5 * (l - r) / den, -1.0, 1.0); }
-            const double dcx = swx / sw - g.predicted_x, dcy = swy / sw - g.predicted_y;
-            const double dpx = peak_x - g.predicted_x,   dpy = peak_y - g.predicted_y;
-            sdx += dcx; sdy += dcy; sd2 += dcx * dcx + dcy * dcy; ++nc;
-            const double rx = g.predicted_x - beam_x, ry = g.predicted_y - beam_y;
-            const double rr = std::sqrt(rx * rx + ry * ry);
-            if (rr < 1.0)
-                continue;
-            const double rad_c  = (dcx * rx + dcy * ry) / rr;  // signed radial (outward +)
-            const double tang_c = (dcx * -ry + dcy * rx) / rr; // signed tangential
-            const double tang_p = (dpx * -ry + dpy * rx) / rr;
-            offs.push_back({signif, std::fabs(tang_c), std::fabs(tang_p), rad_c});
+            if (signif >= 5.0) // only well-measured spots define the shape
+                bin_M2[bin_of(g.d)].push_back(sw_et2 / sw);
         }
-        if (nc >= 5) {
-            data.centroid_bias_px = std::sqrt((sdx / nc) * (sdx / nc) + (sdy / nc) * (sdy / nc));
-            data.centroid_rms_px = std::sqrt(sd2 / nc);
-        }
-        if (offs.size() >= 10) {
-            std::vector<double> sig;
-            sig.reserve(offs.size());
-            for (const auto &o : offs)
-                sig.push_back(o.signif);
-            std::nth_element(sig.begin(), sig.begin() + sig.size() / 2, sig.end());
-            const double smed = sig[sig.size() / 2];
-            double slo = 0, shi = 0, tclo = 0, tchi = 0, tplo = 0, tphi = 0, rclo = 0, rchi = 0;
-            int nlo = 0, nhi = 0;
-            for (const auto &o : offs) {
-                if (o.signif < smed) { slo += o.signif; tclo += o.tang_c; tplo += o.tang_p; rclo += o.rad_c; ++nlo; }
-                else                 { shi += o.signif; tchi += o.tang_c; tphi += o.tang_p; rchi += o.rad_c; ++nhi; }
+        std::vector<double> bin_R1(n_bins, data.R[1]);
+        for (int b = 0; b < n_bins; ++b)
+            if (bin_M2[b].size() >= 5) {
+                const double r1 = std::sqrt(2.0 * std::max(MedianInPlace(bin_M2[b]), 0.0));
+                if (std::isfinite(r1) && r1 > 1e-4)
+                    bin_R1[b] = std::clamp(r1, 1e-4, 0.05);
             }
-            if (nlo > 0 && nhi > 0) {
-                data.centroid_lo_signif = slo / nlo;   data.centroid_hi_signif = shi / nhi;
-                data.centroid_lo_tang_c = tclo / nlo;  data.centroid_hi_tang_c = tchi / nhi;
-                data.centroid_lo_tang_p = tplo / nlo;  data.centroid_hi_tang_p = tphi / nhi;
-                data.centroid_lo_rad_c  = rclo / nlo;  data.centroid_hi_rad_c  = rchi / nhi;
-            }
-        }
+        for (auto &g : groups)
+            g.R1_eff = bin_R1[bin_of(g.d)];
     }
 
-    // ---- Extract integrated reflections ---------------------------------------
-    // Profile fitting gives the recorded amplitude (fitting the tangential profile
-    // P_t against the background-subtracted pixels):
+    // ---- 4. Term 1: one intensity residual per reflection; fit G (and B) ------
+    // J / partiality / sigma_J are computed here as constants (geometry & R fixed),
+    // and only the per-image scale G and Debye-Waller B are optimised.
+    ceres::Problem problem;
+    size_t n_blocks = 0;
+    const double R0 = data.R[0];
+    for (const auto &g : groups) {
+        const double R1 = g.R1_eff; // Term 2: per-resolution profile width
+        if (!(R1 > 0.0) || !(R0 > 0.0))
+            continue;
+        double num = 0.0, den = 0.0, rad = 0.0;
+        std::vector<std::pair<double, double>> pt_sig; // (P_t, Iobs-Bg) for the Fisher pass
+        pt_sig.reserve(g.pixels.size());
+        for (const auto &px : g.pixels) {
+            double q_sq, eps_r, eps_t_sq;
+            if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+                               beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
+                               q_sq, eps_r, eps_t_sq))
+                continue;
+            const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
+            const double R0_eff_sq = R0 * R0 + g.R_bw_sq;
+            const double P_rad = std::exp(-eps_r * eps_r / R0_eff_sq);
+            const double v = std::max(g.Ibkg, 1.0);
+            const double sig = px.Iobs - g.Ibkg;
+            num += P_t * sig / v;
+            den += P_t * P_t / v;
+            rad += P_rad * P_t * P_t / v;
+            pt_sig.emplace_back(P_t, sig);
+        }
+        if (!(den > 0.0))
+            continue;
+        const double J = num / den;
+        const double partiality = rad / den;
+        // Model-expected (Fisher) variance: v_p = background + expected signal J*P_t,
+        // not the per-pixel observed counts (which down-bias) - so the weight tracks
+        // information, and an expected-strong reflection that is absent hurts.
+        double den_f = 0.0;
+        for (const auto &[P_t, sig] : pt_sig) {
+            const double v_f = std::max(g.Ibkg + std::max(J, 0.0) * P_t, 1.0);
+            den_f += P_t * P_t / v_f;
+        }
+        const double sigma_J = std::sqrt(1.0 / std::max(den_f, 1e-30));
+        const double inv_4d2 = (g.d > 0.0) ? 1.0 / (4.0 * g.d * g.d) : 0.0;
+        auto *cost = new ceres::AutoDiffCostFunction<IntensityResidual, 1, 1, 1>(
+            new IntensityResidual(J, sigma_J, partiality, g.pol, g.Itrue, inv_4d2));
+        problem.AddResidualBlock(cost, nullptr, &data.scale_factor, &data.B_factor);
+        ++n_blocks;
+    }
+    data.residual_count = n_blocks;
+    if (n_blocks == 0)
+        return;
+
+    // G >= 0; B fixed unless requested; G regularized -> 1 with weight sqrt(n/sigma)
+    // (mirrors ScaleOnTheFly) so weakly-measured images cannot drift and scramble the merge.
+    problem.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
+    if (!data.refine_B)
+        problem.SetParameterBlockConstant(&data.B_factor);
+    if (data.scale_reg_sigma > 0.0) {
+        const double w = std::sqrt(static_cast<double>(groups.size()) / data.scale_reg_sigma);
+        auto *reg = new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
+            new ScalarRegularizer(w, 1.0));
+        problem.AddResidualBlock(reg, nullptr, &data.scale_factor);
+    }
+
+    ceres::Solver::Options options;
+    options.linear_solver_type = ceres::DENSE_QR;
+    options.minimizer_progress_to_stdout = false;
+    options.logging_type = ceres::LoggingType::SILENT;
+    options.max_solver_time_in_seconds = data.max_time_s;
+    options.num_threads = 1;
+    ceres::Solver::Summary summary;
+    ceres::Solve(options, &problem, &summary);
+    data.final_cost = summary.final_cost;
+    data.solved = summary.IsSolutionUsable();
+
+    // ---- 5. Extract integrated reflections ------------------------------------
+    // Profile fitting gives the recorded amplitude (fitting the tangential profile P_t
+    // against the background-subtracted pixels):
     //     J      = sum_p[ P_t,p (Iobs_p - Ibkg)/v_p ] / sum_p[ P_t,p^2 / v_p ]
     //            ~ G * Itrue * B_term * partiality * pol     (recorded raw counts)
     //     var(J) = 1 / sum_p[ P_t,p^2 / v_p ]
     //
-    // Two SEPARATE fractions reduce the full intensity to what these pixels record:
-    //
-    //   partiality   - the radial / rocking dimension that a still does NOT sample.
-    //                  Only the slice of the reflection that crosses the Ewald
-    //                  sphere on this shot is recorded; <= 1. We DIVIDE it out to
-    //                  recover the full intensity. = profile-weighted P_radial.
-    //
-    //   completeness - the fraction of the spot's detector footprint that landed on
-    //                  live pixels (= profile captured by live pixels / profile over
-    //                  the whole shoebox). 1.0 when the spot sits fully on the
-    //                  detector; < 1.0 only when a detector edge, gap or mask clips
-    //                  it. Profile fitting already extrapolates over the missing
-    //                  pixels, so this is NOT applied to r.I - it is a quality flag.
-    //
     // Output split (Merge multiplies r.I * image_scale_corr and weights by
-    // 1/(sigma*image_scale_corr)^2 - see Merge.cpp):
+    // 1/(sigma*image_scale_corr)^2):
     //   r.I              = J / (B_term * partiality * pol) = G * Itrue
     //   r.sigma          = sqrt(var(J)) / (B_term * partiality * pol)
     //   r.partiality     = profile-weighted P_radial in (0,1]  (the rocking fraction)
     //   r.completeness   = live/total tangential profile in (0,1]  (detector clipping)
-    //   r.image_scale_corr = 1/G                         (per-image scale ONLY)
-    // so r.I * image_scale_corr = Itrue. B, partiality and polarization live on the
-    // intensity, G lives on image_scale_corr - one clean meaning per field.
-    //
-    // We walk the full (unclamped) shoebox once: every grid point feeds the total
-    // tangential profile (completeness denominator); points that are real, live
-    // detector pixels also feed the profile fit and the captured profile.
+    //   r.image_scale_corr = 1/G                              (per-image scale ONLY)
+    // so r.I * image_scale_corr = Itrue: B, partiality and polarization live on the
+    // intensity, G lives on image_scale_corr - one clean meaning per field. We walk the
+    // full (unclamped) shoebox once: every grid point feeds the total tangential profile
+    // (completeness denominator); points that are real, live pixels also feed the fit.
     data.reflections.reserve(groups.size());
     for (const auto &g : groups) {
         const int cx = static_cast<int>(std::lround(g.predicted_x));
         const int cy = static_cast<int>(std::lround(g.predicted_y));
-
-        // Debye-Waller factor for this reflection (constant over its shoebox).
         const double B_term = std::exp(-data.B_factor / (4.0 * g.d * g.d));
 
-        // Term 3 recentre shift (precomputed in the pre-pass; 0 if off or the spot was not
-        // confident). Profile evaluated at (x-dcx, y-dcy), data summed at (x,y).
-        const double dcx = g.dcx, dcy = g.dcy;
-
         double num = 0.0, den = 0.0, bkg_sum = 0.0, radial_sum = 0.0;
         double prof_live = 0.0, prof_full = 0.0; // tangential profile: captured / total
         size_t n = 0;
 
         for (int y = cy - radius; y <= cy + radius; ++y) {
             for (int x = cx - radius; x <= cx + radius; ++x) {
-                // Geometry/profile for this grid point (profile recentred by (dcx,dcy)).
-                PixelObs probe{static_cast<double>(x) - dcx, static_cast<double>(y) - dcy,
-                               0.0, g.Ibkg, 1.0};
-                PixelResidual pr(probe, 1.0, lambda, pixel_size, g.h, g.k, g.l,
-                                 g.R_bw_sq, g.pol, data.crystal_system);
                 double q_sq, eps_r, eps_t_sq;
-                if (!pr.GeometryTerms(beam, &dist_mm, detector_rot,
-                                      latt_vec0, latt_vec1, latt_vec2, q_sq, eps_r, eps_t_sq))
+                if (!GeometryProbe(static_cast<double>(x), static_cast<double>(y),
+                                   lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+                                   beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
+                                   q_sq, eps_r, eps_t_sq))
                     continue;
                 if (!(data.R[0] > 0.0) || !(g.R1_eff > 0.0))
                     continue;
 
-                // Tangential profile shape (area-normalized) -> the fit template. Uses the
-                // per-reflection R1_eff (Term 2), falling back to the global R1 by default.
+                // Tangential profile shape (area-normalized) -> the fit template, using the
+                // per-reflection R1_eff (Term 2).
                 const double R1 = g.R1_eff;
                 const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
                 prof_full += P_t; // whole shoebox, on- or off-detector
@@ -1535,30 +687,21 @@ void PixelRefine::Run(const T *image,
                     continue;
 
                 const double Iobs = static_cast<double>(image[np]); // raw counts
-                // Variance for the profile-fit weights. Weighting by the *observed*
-                // per-pixel count (v = Iobs) biases the amplitude negative: a
-                // down-fluctuated background pixel gets the smallest v and hence the
-                // largest 1/v weight, so num = sum P_t (Iobs - Ibkg)/v is pulled below
-                // zero - worst where the signal is weakest, i.e. the high-resolution
-                // shells (the negative <I/sig> we see there). For background-limited
-                // reflections the variance is the local background, constant over the
-                // shoebox, so use that instead of the observed count.
-                double v = std::max(g.Ibkg, 1.0);
+                // Background-limited variance (constant over the shoebox): weighting by
+                // the observed count biases the amplitude negative where signal is weakest.
+                const double v = std::max(g.Ibkg, 1.0);
 
-                // Peak-normalized radial factor (the partiality), in (0,1]. The
-                // bandwidth-broadened radial width matches the model in Model().
+                // Peak-normalized radial factor (the partiality), in (0,1]. MUST use the
+                // same P_t^2/v weights as the amplitude, else an R0_eff-dependent (hence
+                // resolution-dependent) factor is left behind in r.I.
                 const double R0_eff_sq = data.R[0] * data.R[0] + g.R_bw_sq;
                 const double P_radial = std::exp(-eps_r * eps_r / R0_eff_sq);
 
-                // Profile-fit accumulators. The amplitude estimator weights pixels by
-                // P_t^2/v, so the partiality (which de-scales that amplitude) MUST use
-                // the SAME weights - otherwise an R0_eff-dependent (resolution-
-                // dependent) factor is left behind in r.I.
                 const double w = P_t * P_t / v;
                 num += P_t * (Iobs - g.Ibkg) / v;
                 den += w;
-                radial_sum += P_radial * w;   // partiality weighted exactly like num/den
-                prof_live += P_t;             // captured tangential profile
+                radial_sum += P_radial * w;
+                prof_live += P_t;
                 bkg_sum += g.Ibkg;
                 ++n;
             }
@@ -1580,7 +723,7 @@ void PixelRefine::Run(const T *image,
         if (den > 0.0 && n > 0) {
             const double I_amp = num / den;             // ~ G*Itrue*B_term*partiality*pol
             const double sigma_amp = std::sqrt(1.0 / den);
-            const double corr = static_cast<double>(r.partiality) * B_term * g.pol; // B, partiality & pol
+            const double corr = static_cast<double>(r.partiality) * B_term * g.pol;
             r.bkg = static_cast<float>(bkg_sum / static_cast<double>(n));
             r.observed = true;
 
@@ -1602,9 +745,9 @@ void PixelRefine::Run(const T *image,
         data.reflections.push_back(r);
     }
 
-    // ---- Per-image CC vs reference (the half/ref correlation diagnostic) -------
-    // Pearson CC of the scaled estimate (r.I * image_scale_corr = Itrue_est)
-    // against the reference intensities, over the matched reflections.
+    // ---- 6. Per-image CC vs reference (diagnostic) ----------------------------
+    // Pearson CC of the scaled estimate (r.I * image_scale_corr = Itrue_est) against
+    // the reference intensities, over the matched reflections.
     {
         double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
         size_t cn = 0;
@@ -1633,231 +776,9 @@ void PixelRefine::Run(const T *image,
     }
 }
 
-template<class T>
-std::vector<float> PixelRefine::PredictImage(const T *image,
-                                             BraggPrediction &prediction,
-                                             const PixelRefineData &data,
-                                             bool include_background) const {
-    std::vector<float> img(xpixel * ypixel, 0.0f);
-
-    const double lambda = data.geom.GetWavelength_A();
-    const double pixel_size = data.geom.GetPixelSize_mm();
-    const int radius = data.shoebox_radius;
-    const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
-    const double bw = data.bandwidth;
-
-    const auto pol_factor = experiment.GetPolarizationFactor();
-    auto polarization = [&](double x, double y) -> double {
-        if (!pol_factor)
-            return 1.0;
-        return data.geom.CalcAzIntPolarizationCorr(static_cast<float>(x), static_cast<float>(y),
-                                                   pol_factor.value());
-    };
-    auto bandwidth_radial_sq = [&](double d) -> double {
-        if (bw <= 0.0 || d <= 0.0)
-            return 0.0;
-        const double bl = bw * lambda;
-        return bl * bl / (2.0 * d * d * d * d);
-    };
-
-    double beam[2], dist_mm, detector_rot[2];
-    double latt_vec0[3], latt_vec1[3], latt_vec2[3];
-    BuildParameterBlocks(data, beam, dist_mm, detector_rot,  latt_vec0, latt_vec1, latt_vec2);
-
-    DiffractionExperiment exp_iter = experiment;
-    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
-            .BeamY_pxl(data.geom.GetBeamY_pxl())
-            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-
-    const BraggPredictionSettings settings_prediction{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)  // relative Δλ/λ sigma
-    };
-    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
-    const auto &predicted = prediction.GetReflections();
-    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
-
-    for (int ri = 0; ri < nrefl; ++ri) {
-        const auto &refl = predicted[ri];
-        const auto it = reference_data.find(hkl_key_generator(refl));
-        if (it == reference_data.end())
-            continue;
-
-        const double Itrue = it->second;
-        const double R_bw_sq = bandwidth_radial_sq(refl.d);
-        const double pol = polarization(refl.predicted_x, refl.predicted_y);
-
-        // Local background straight from the actual image (flat per shoebox), laid
-        // into the box so the prediction overlays the real frame - the same model
-        // path Run() fits, now reproduced faithfully because we have the image.
-        double Ibkg = 0.0;
-        const bool have_bkg = include_background &&
-            EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
-                                    refl.predicted_x, refl.predicted_y,
-                                    radius, bkg_outer_radius, Ibkg);
-
-        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
-
-        for (int y = box.min_y; y <= box.max_y; ++y) {
-            for (int x = box.min_x; x <= box.max_x; ++x) {
-                const size_t npixel = xpixel * y + x;
-
-                PixelObs obs{
-                    .x = static_cast<double>(x),
-                    .y = static_cast<double>(y),
-                    .Iobs = 0.0,
-                    .Ibkg = have_bkg ? Ibkg : 0.0,
-                    .weight = 1.0
-                };
-                PixelResidual pr(obs, Itrue, lambda, pixel_size,
-                                 refl.h, refl.k, refl.l, R_bw_sq, pol, data.crystal_system);
-
-                double Ipred = 0.0; // raw counts: signal (+ local background)
-                if (pr.Model(beam, &dist_mm, detector_rot,
-                             latt_vec0, latt_vec1, latt_vec2,
-                             &data.scale_factor, &data.B_factor, data.R, Ipred))
-                    img[npixel] += static_cast<float>(Ipred);
-            }
-        }
-    }
-
-    return img;
-}
-
-template<class T>
-std::vector<float> PixelRefine::ChiSquaredImage(const T *image,
-                                                BraggPrediction &prediction,
-                                                const PixelRefineData &data) const {
-    std::vector<float> img(xpixel * ypixel, 0.0f);
-
-    const double lambda = data.geom.GetWavelength_A();
-    const double pixel_size = data.geom.GetPixelSize_mm();
-    const int radius = data.shoebox_radius;
-    const int bkg_outer_radius = std::max(radius + 1, data.bkg_outer_radius);
-    const double bw = data.bandwidth;
-
-    const auto pol_factor = experiment.GetPolarizationFactor();
-    auto polarization = [&](double x, double y) -> double {
-        if (!pol_factor)
-            return 1.0;
-        return data.geom.CalcAzIntPolarizationCorr(static_cast<float>(x), static_cast<float>(y),
-                                                   pol_factor.value());
-    };
-    auto bandwidth_radial_sq = [&](double d) -> double {
-        if (bw <= 0.0 || d <= 0.0)
-            return 0.0;
-        const double bl = bw * lambda;
-        return bl * bl / (2.0 * d * d * d * d);
-    };
-
-    double beam[2], dist_mm, detector_rot[2];
-    double latt_vec0[3], latt_vec1[3], latt_vec2[3];
-    BuildParameterBlocks(data, beam, dist_mm, detector_rot,  latt_vec0, latt_vec1, latt_vec2);
-
-    DiffractionExperiment exp_iter = experiment;
-    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
-            .BeamY_pxl(data.geom.GetBeamY_pxl())
-            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-
-    const BraggPredictionSettings settings_prediction{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)
-    };
-    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
-    const auto &predicted = prediction.GetReflections();
-    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
-
-    for (int ri = 0; ri < nrefl; ++ri) {
-        const auto &refl = predicted[ri];
-        const auto it = reference_data.find(hkl_key_generator(refl));
-        if (it == reference_data.end())
-            continue;
-
-        const double Itrue = it->second;
-        const double R_bw_sq = bandwidth_radial_sq(refl.d);
-        const double pol = polarization(refl.predicted_x, refl.predicted_y);
-
-        // Local flat background, identical to Run(); skip the reflection if it
-        // cannot be estimated (matches Run() dropping the reflection).
-        double Ibkg = 0.0;
-        if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
-                                     refl.predicted_x, refl.predicted_y,
-                                     radius, bkg_outer_radius, Ibkg))
-            continue;
-
-        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
-
-        for (int y = box.min_y; y <= box.max_y; ++y) {
-            for (int x = box.min_x; x <= box.max_x; ++x) {
-                const size_t npixel = xpixel * y + x;
-
-                // Same gating as Run(): only pixels that actually enter the fit.
-                if (image[npixel] == std::numeric_limits<T>::max())
-                    continue;
-                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
-                    continue;
-
-                const double Iobs = static_cast<double>(image[npixel]); // raw counts
-
-                double var = std::max(Iobs, 0.0);
-                if (!(var > 1.0))
-                    var = 1.0;
-                const double weight = 1.0 / std::sqrt(var);
-
-                PixelObs obs{
-                    .x = static_cast<double>(x),
-                    .y = static_cast<double>(y),
-                    .Iobs = Iobs,
-                    .Ibkg = Ibkg,
-                    .weight = weight
-                };
-                PixelResidual pr(obs, Itrue, lambda, pixel_size,
-                                 refl.h, refl.k, refl.l, R_bw_sq, pol, data.crystal_system);
-
-                double Ipred = 0.0;
-                if (pr.Model(beam, &dist_mm, detector_rot,
-                             latt_vec0, latt_vec1, latt_vec2,
-                             &data.scale_factor, &data.B_factor, data.R, Ipred)) {
-                    // residual_i = (I_pred - I_obs) * weight (== Ceres residual);
-                    // its square is this pixel's contribution to the cost.
-                    const double rw = (Ipred - Iobs) * weight;
-                    img[npixel] += static_cast<float>(rw * rw);
-                }
-            }
-        }
-    }
-
-    return img;
-}
-
-// Explicit instantiations for the supported (uncompressed) image pixel types.
 template void PixelRefine::Run<int8_t>(const int8_t *, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<int16_t>(const int16_t *, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<int32_t>(const int32_t *, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<uint8_t>(const uint8_t *, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<uint16_t>(const uint16_t *, BraggPrediction &, PixelRefineData &);
 template void PixelRefine::Run<uint32_t>(const uint32_t *, BraggPrediction &, PixelRefineData &);
-
-template std::vector<float> PixelRefine::PredictImage<int8_t>(const int8_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-template std::vector<float> PixelRefine::PredictImage<int16_t>(const int16_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-template std::vector<float> PixelRefine::PredictImage<int32_t>(const int32_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-template std::vector<float> PixelRefine::PredictImage<uint8_t>(const uint8_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-template std::vector<float> PixelRefine::PredictImage<uint16_t>(const uint16_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-template std::vector<float> PixelRefine::PredictImage<uint32_t>(const uint32_t *, BraggPrediction &, const PixelRefineData &, bool) const;
-
-template std::vector<float> PixelRefine::ChiSquaredImage<int8_t>(const int8_t *, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<int16_t>(const int16_t *, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<int32_t>(const int32_t *, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint8_t>(const uint8_t *, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint16_t>(const uint16_t *, BraggPrediction &, const PixelRefineData &) const;
-template std::vector<float> PixelRefine::ChiSquaredImage<uint32_t>(const uint32_t *, BraggPrediction &, const PixelRefineData &) const;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index f8db193f..dfc560c5 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -3,247 +3,100 @@
 
 #pragma once
 
-#include <optional>
-
 #include "../bragg_prediction/BraggPrediction.h"
 #include "../common/DiffractionExperiment.h"
 #include "../scale_merge/HKLKey.h"
 
 // =============================================================================
-// PixelRefine — one optimization to rule geometry, integration and scaling
+// PixelRefine — reference-driven profile-fit integration + scaling for stills
 // =============================================================================
 //
-// Intent
-// ------
-// Classical crystallographic data processing is a one-way pipeline:
+// PixelRefine is the still-image integrator: given a reference set of merged
+// intensities I_ref (the current best hypothesis for each reflection's full
+// intensity), it integrates one image and returns already-scaled intensities. It
+// is an *intensity-wise* operation - the detector geometry is taken as fixed (it
+// was refined upstream by XtalOptimizer in IndexAndRefine::RefineGeometryIfNeeded);
+// PixelRefine does not touch orientation, cell or detector parameters.
 //
-//     spot finding -> indexing -> geometry refinement -> integration -> scaling -> merging
+// The objective is the factored per-reflection likelihood of FACTORED_MODEL.md,
+// Terms 1 + 2:
 //
-// Each stage consumes the previous stage's output and never talks back. The
-// integrator trusts the refined geometry; the scaler trusts the integrated
-// intensities; nothing downstream is ever allowed to correct an upstream
-// parameter. Post-refinement and profile fitting were the field's partial
-// answers to this: post-refinement lets merged intensities nudge per-image
-// orientation/cell/mosaicity, and profile fitting lets a learned spot shape
-// improve weak-reflection intensities. But both are narrow back-channels bolted
-// onto a feed-forward pipeline — there is no end-to-end gradient that flows from
-// the raw detector pixels all the way back to every parameter at once.
+//   Term 2 (shape) — for each resolution shell, the tangential profile width R1 is
+//     *measured* from the intensity-weighted second moment of the strong spots:
+//     R1 = sqrt(2*<eps_t^2>). A second moment is normalised by the total intensity,
+//     so it is decoupled from the per-image scale - which is why measuring R1 is
+//     stable where *fitting* it (degenerate with G) is not.
 //
-// PixelRefine is an experiment in doing the whole thing as a *single* least
-// squares problem. We write down, for every pixel in a reflection's shoebox, the
-// expected counts as an explicit forward model
+//   Term 1 (intensity / scaling) — one residual per reflection: the profile-fit
+//     amplitude J (using the Term-2 R1) should equal the scaled reference
+//         J_model = G * exp(-B/4d^2) * partiality * pol * I_ref,
+//     weighted by the model-expected (Fisher) sigma_J. Only the per-image scale G
+//     and Debye-Waller B are optimised. Integration and scaling become one objective;
+//     the many empty shoebox pixels enter only through J (with ~zero profile weight)
+//     instead of dominating a per-pixel loss.
 //
-//     I_pred(pixel) = G * I_true * B_term * P_radial * P_tangential * pol + I_bkg
+// I_ref is NOT refined here - it is a fixed hypothesis for the pass. The intended
+// outer loop is EM-like: run PixelRefine on every image against the current I_ref,
+// re-merge to a new I_ref, repeat.
 //
-// in raw detector counts (pol = per-reflection polarization correction, I_bkg =
-// local per-shoebox background read from the image).
+// Forward model per pixel (raw detector counts, no per-pixel solid-angle/Lorentz
+// weighting - same units as the classical integrator):
+//   signal = G * I_ref * B_term * P_radial * P_tangential * pol ,  + I_bkg
+//   B_term       = exp(-B |q|^2 / 4)                          (Debye-Waller)
+//   P_radial     = exp(-eps_r^2 / R0_eff^2)                   (still partiality, <= 1)
+//   P_tangential = exp(-eps_t^2 / R1^2) / (pi R1^2)           (area-normalized profile)
+// where eps_r / eps_t are the radial / tangential deviations of the pixel from the
+// predicted node, and pol is the per-reflection polarization correction.
 //
-// and let Ceres autodiff back-propagate the per-pixel residuals into ALL of:
-//   * detector geometry  (beam centre, distance, tilt)
-//   * crystal orientation + unit cell
-//   * overall scale G and Debye-Waller B
-//   * the reciprocal-space spot widths R = (radial, tangential)
-// simultaneously. Geometry refinement, profile-fitted integration and scaling
-// then stop being separate stages: they are different parameters of one model,
-// coupled through the same pixels, with full backpropagation between them. Once
-// the model is differentiable end-to-end, things that used to need bespoke code
-// — mosaicity refinement, profile fitting, partiality — fall out "for free" as
-// extra parameters of the same forward model.
-//
-// How I_true enters
-// -----------------
-// I_true is NOT refined here. It is a *fixed hypothesis* for the duration of a
-// pass: the current best merged estimate of each reflection's full intensity.
-// The intended outer loop is iterative, like EM / self-consistent field:
-//
-//     repeat over the whole dataset:
-//         run PixelRefine on every image with the current I_true reference
-//         re-merge the resulting intensities -> new I_true
-//     until the reference stops changing
-//
-// So a single PixelRefine call answers "given this intensity hypothesis, what
-// geometry/scale/profile best explains these pixels, and what intensities do I
-// read back out?", and the dataset-level loop refines the hypothesis itself.
-//
-// Inner predict<->refine loop
-// ---------------------------
-// Within one image we also iterate (max_iterations): Bragg prediction places the
-// shoeboxes, we refine, the refined geometry/cell feed the next prediction, etc.
-// Initially the model geometry equals the experiment's DiffractionGeometry, but
-// as refinement proceeds it diverges, so later predictions must use the *refined*
-// data.geom rather than the static experiment geometry.
-//
-// On shoeboxes, tails, and gatekeeping
-// ------------------------------------
-// We deliberately do NOT chase the full spot. A shoebox only needs to cover
-// enough of a reflection for the fit to be meaningful; clipped tails are fine,
-// because the partiality term already downweights whatever falls outside the
-// well-modelled core. The premise - especially for serial crystallography - is
-// that the problem is rarely *missing* information; it is *failing to gate out*
-// information that is not meaningful. As long as the model knows a piece is
-// missing (low partiality), it is safe to leave it missing. That flips the usual
-// trade-off: rather than shrinking boxes to avoid contamination, we can grow them
-// and let partiality decide, per pixel and per reflection, what actually carries
-// signal. (For downstream integration this pixel-level gating is the point - keep
-// only meaningful pixels, instead of a fixed geometric mask.) The bandwidth term
-// below is part of the same idea: it tells the model where the radial tails are
-// *expected* to be, so it can weight rather than blindly include them.
-//
-// X-ray bandwidth (optional)
-// --------------------------
-// A finite bandwidth thickens the Ewald shell radially and smears spots along the
-// radial direction, growing like 1/d^2 (the pink-beam/DMM signature). It enters
-// as a fixed, resolution-dependent addition to the radial width R0 (see
-// PixelRefineData::bandwidth and PixelRefine.cpp). It is OFF by default
-// (bandwidth = 0, monochromatic); set it for DMM-type data, leave it for Si.
-//
-// Status: experimental prototype. The forward model (esp. the still-image
-// partiality normalization) is deliberately simple and expected to evolve: it
-// works in raw detector counts with a local per-shoebox background and a
-// per-reflection polarization correction (no per-pixel solid-angle/Lorentz
-// weighting), matching the classical integrator. See PixelRefine.cpp for the
-// physics conventions and known caveats.
+// X-ray bandwidth (optional): a finite bandwidth thickens the Ewald shell radially,
+// adding a fixed, resolution-dependent term to R0 that grows like 1/d^2 (the
+// pink-beam/DMM signature): R0_eff^2 = R0^2 + (b*lambda)^2/(2 d^4). b = 0 (the
+// default) is a monochromatic no-op; set it for DMM-type data, leave it for Si.
 // =============================================================================
 
 struct PixelRefineData {
     // --- model state (input as initial guess, output as refined result) ---
-    DiffractionGeometry geom;
-    CrystalLattice latt;
+    DiffractionGeometry geom;     // fixed (refined upstream by XtalOptimizer)
+    CrystalLattice latt;          // fixed
     gemmi::CrystalSystem crystal_system = gemmi::CrystalSystem::Triclinic;
     char centering = 'P';
 
-    double B_factor = 0.0;      // Debye-Waller B (A^2)
-    double scale_factor = 1.0;  // overall scale G
-    double R[2] = {0.005, 0.005}; // R[0] = radial (partiality) width, R[1] = tangential (profile) width (A^-1)
+    double B_factor = 0.0;      // Debye-Waller B (A^2), refined
+    double scale_factor = 1.0;  // overall per-image scale G, refined
+    double R[2] = {0.005, 0.005}; // R[0] = radial (partiality) width; R[1] = fallback
+                                  // tangential profile width before Term 2 measures it (A^-1)
+    bool   refine_B = true;       // refine the per-image B-factor along with G
 
-    // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1%
-    // FWHM DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening
-    // to R[0]. 0 = monochromatic (the term switches off entirely).
+    // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1% FWHM
+    // DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening to R[0].
+    // 0 = monochromatic (the term switches off entirely).
     double bandwidth = 0.0;
 
-    // --- what to refine ---
-    bool refine_orientation     = true;  // crystal orientation (p0)
-    bool refine_unit_cell       = false; // cell lengths + angles
-    bool refine_beam_center     = false;
-    bool refine_distance        = false;
-    bool refine_detector_angles = false;
-    bool refine_scale           = true;
-    bool refine_B               = false;
-    bool refine_R               = false; // per-image R refinement is unstable on sparse
-                                         // stills; R is held at its nominal value
-
-    // Orientation refinement is anchored to the pre-refinement (spot-centroid)
-    // orientation with weight sqrt(n_refl)/sigma, so the pixel fit can only nudge
-    // the orientation by ~this many degrees before the prior pushes back. This is
-    // what turns the (otherwise overfitting) 3-DOF orientation refinement into a
-    // small, signal-supported sub-spot correction. Larger => freer; very large
-    // approaches the unregularized (collapsing) fit. ~1 deg gives the best CCref here;
-    // beyond ~2 deg the per-image fit overfits and the merge collapses.
-    double orient_reg_sigma_deg = 1.0;
-
-    // Signal-weighting of the *fit* residuals: each pixel's weight is multiplied by
-    // a detector-space Gaussian exp(-r^2/2 sigma^2) centred on the predicted spot, so
-    // the many empty shoebox-corner pixels stop diluting (and destabilising) the fit
-    // and the signal-bearing core drives the refined scale/R. <= 0 disables (uniform).
-    double fit_signal_sigma_pix = 1.5;
-
     // Per-image scale G is regularized towards 1 with weight sqrt(n_refl/scale_reg_sigma)
     // (mirrors ScaleOnTheFly). Without this the unconstrained G wanders on weakly
     // measured images and 1/G scrambles the cross-image merge. <= 0 disables.
     double scale_reg_sigma = 2.0;
 
-    // Radial Ewald-sphere acceptance band for prediction (A^-1): a reflection is
-    // given a shoebox when ||S|-1/lambda| <= this. The narrow default predicts only
-    // reflections already on the Ewald sphere; widening it (towards the integrator's
-    // ~2-3x profile radius) lets in the slightly-misaligned high-resolution
-    // reflections - more multiplicity, and something for orientation refinement to
-    // actually centre. Safe to widen only with the per-image fit kept well-behaved
-    // (de-biased variance + signal-weighting + regularization, all default here).
+    // Radial Ewald-sphere acceptance band for prediction (A^-1): a reflection is given
+    // a shoebox when ||S|-1/lambda| <= this. Widened from the on-sphere default towards
+    // the integrator's profile radius so slightly-misaligned high-resolution reflections
+    // are still integrated (multiplicity), while the partiality downweights their tails.
     double ewald_dist_cutoff = 0.0020;
 
-    // Pre-LSQ global orientation+cell sweep (maximises CC vs reference over the
-    // strongest reflections). Bounds are derived from the detector geometry: the
-    // step moves the highest-resolution spot by 1 px, the range moves the lowest-
-    // resolution spot by ~2 px (rotation) / ~1 px (cell scale), so the low-res
-    // XtalOptimizer solution is preserved while high-res spots are recentred.
-    bool   sweep_orientation = false;
-    // Sweep half-range as the *orientation uncertainty* (degrees) and cell-scale
-    // uncertainty (fraction). These set how far the highest-resolution spot may move
-    // (a few px); low-res spots barely move and stay anchored. Keep small - a large
-    // range lets the per-image CC overfit and degrades the merge.
-    double sweep_max_deg = 0.15;
-    double sweep_max_cell_frac = 0.003;
-
     double max_time_s = 5.0;
-    int    shoebox_radius = 3; // half-size of the per-reflection signal box (peak region that enters the fit)
-    // Half-size of the local-background sampling box. Background is estimated from
-    // the ring shoebox_radius < |dx|,|dy| <= bkg_outer_radius around each spot
-    // (excluding pixels belonging to any predicted spot core), mirroring the local
-    // shoebox background of BraggIntegrate2D. Must be > shoebox_radius.
+    int    shoebox_radius = 3; // half-size of the per-reflection signal box
+    // Half-size of the local-background sampling box. Background is the MEAN of the ring
+    // shoebox_radius < |dx|,|dy| <= bkg_outer_radius (excluding spot cores), like
+    // BraggIntegrate2D. Must be > shoebox_radius.
     int    bkg_outer_radius = 6;
-    int    max_iterations = 3; // inner predict<->refine cycles (re-predict with refined geom/latt)
-
-    // Diagnostic: compute the parameter correlation matrix (Pearson) from the final
-    // per-image solve, to expose degeneracies (e.g. G<->B, G<->R1) that let the fit
-    // lower its chi-square along directions that do not generalise across images.
-    // Requires G, B and R all refined; results in corr_* below.
-    bool   compute_covariance = false;
-    bool   fix_R0 = false; // diagnostic: with refine_R, hold R0 constant and refine R1 only
-
-    // Factored-likelihood Term 1 (FACTORED_MODEL.md): replace the per-pixel fit with one
-    // per-reflection *intensity* residual J vs G*B_term*partiality*pol*I_ref, Fisher-
-    // weighted. Geometry & R fixed; only G (and B if refine_B) are fit.
-    bool   intensity_residual = false;
-
-    // Factored-likelihood Term 2: set the tangential profile width R1 from the *measured*
-    // per-resolution second moment of the strong spots (a shape statistic, decoupled from
-    // the scale) and feed it to the profile template used by Term 1 and the extraction.
-    bool   shape_R1 = false;
-    double shape_R1_lores = NAN, shape_R1_hires = NAN; // measured R1 in the lowest/highest-res bin (diag)
-
-    // Adaptive integration mask: set R1 (tangential profile width) from the *measured*
-    // tangential second moment of the strong spots, instead of fitting it (which is
-    // degenerate with the per-image scale). A shape statistic, independent of scale.
-    bool   adaptive_R1 = false;
-
-    // Diagnostic: residual centering error after refinement. For the strong spots,
-    // the offset between observed intensity centroid and predicted position - bias is
-    // the systematic (mean) part, rms the total. If rms is comparable to the spot size,
-    // a tight profile mask lands off the spot and box-summing wins.
-    bool   measure_centroid = false;
-    double centroid_bias_px = NAN;
-    double centroid_rms_px = NAN;
-    // Offset split by spot significance (lo/hi about the median) and measured two ways:
-    // the intensity *centroid* (mean) and the sub-pixel *peak* (mode, parabolic fit).
-    //  - centroid offset shrinking lo->hi  => noise floor (offset ~ 1/sqrt(counts));
-    //    flat with significance            => a systematic position error to model.
-    //  - peak offset << centroid offset    => the spot is asymmetric (non-Gaussian /
-    //    parallax): the prediction sits on the peak, only the centroid is pulled, so
-    //    recentring on the centroid would be wrong - the shape is what to model.
-    //  - radial centroid offset ~ 0        => no distance/parallax error (parallax is radial).
-    double centroid_lo_signif = NAN, centroid_hi_signif = NAN; // mean significance per bin
-    double centroid_lo_tang_c = NAN, centroid_hi_tang_c = NAN; // mean |tangential centroid offset|
-    double centroid_lo_tang_p = NAN, centroid_hi_tang_p = NAN; // mean |tangential peak offset|
-    double centroid_lo_rad_c  = NAN, centroid_hi_rad_c  = NAN; // mean signed radial centroid offset
-
-    // Test: recentre the extraction profile on each spot's observed centroid (instead of
-    // the predicted position) so a tight mask lands on the real spot - but only for spots
-    // whose in-shoebox significance exceeds recenter_min_signif (recentring on a noise
-    // centroid would bias weak reflections positive).
-    bool   recenter_profile = false;
-    double recenter_min_signif = 5.0;
 
     // --- output ---
-    std::vector<Reflection> reflections; // profile-fitted integration result
+    std::vector<Reflection> reflections; // profile-fitted, scaled integration result
     bool   solved = false;
     double final_cost = NAN;
     size_t residual_count = 0;
     double cc = NAN;        // per-image CC of scaled intensities vs reference
     int64_t cc_n = 0;       // number of reflections in the CC
-
-    bool   covariance_valid = false;
-    double corr_GB = NAN, corr_GR0 = NAN, corr_GR1 = NAN;
-    double corr_BR0 = NAN, corr_BR1 = NAN, corr_R0R1 = NAN;
 };
 
 class PixelRefine {
@@ -253,67 +106,24 @@ class PixelRefine {
     const HKLKeyGenerator hkl_key_generator;
     std::map<HKLKey, double> reference_data;
 
-    // Fills the Ceres parameter blocks (geometry + symmetry-aware lattice
-    // parametrization) from the current model state. Shared by Run and
-    // PredictImage so both walk identical geometry/lattice code.
+    // Fills the fixed geometry + symmetry-aware lattice parametrization (beam,
+    // distance, detector tilt, and the Rodrigues orientation / cell-length / angle
+    // vectors) from the current model state, for the per-pixel geometry evaluation.
     void BuildParameterBlocks(const PixelRefineData &data,
                               double beam[2], double &dist_mm,
                               double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
-
-    // Global orientation + uniform cell-scale sweep run before the LSQ. Re-projects
-    // the strongest reference reflections through candidate lattices and keeps the
-    // one maximising CC vs the reference intensities (coordinate descent over the 3
-    // Rodrigues axes + cell scale, within geometry-derived pixel bounds). Writes the
-    // refined orientation/cell back into data.latt. See PixelRefineData::sweep_*.
-    template<class T>
-    void SweepOrientationCell(const T *image, BraggPrediction &prediction,
-                              PixelRefineData &data) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const std::vector<MergedReflection> &reference);
 
-    // The BraggPrediction is supplied per call (it is mutated): this keeps a
-    // single PixelRefine instance usable from several threads, each passing its
-    // own prediction buffer. Only `data` is written; PixelRefine state is const.
-    // The image is in raw detector counts (masked/saturated pixels carry the type
-    // sentinel); background is estimated locally per shoebox from the image itself.
+    // The BraggPrediction is supplied per call (it is mutated): this keeps a single
+    // PixelRefine instance usable from several threads, each passing its own prediction
+    // buffer. Only `data` is written; PixelRefine state is const. The image is in raw
+    // detector counts (masked/saturated pixels carry the type sentinel); background is
+    // estimated locally per shoebox from the image itself.
     template<class T>
     void Run(const T *image,
              BraggPrediction &prediction,
              PixelRefineData &data);
-
-    // Render the forward model as a full detector image (raw detector counts, so
-    // it overlays directly on the original image). Uses the *same* per-pixel
-    // model path (PixelResidual::Model) as the optimizer, evaluated in double
-    // precision - slow but exact. For each reference reflection it adds the Bragg
-    // signal over its shoebox; with include_background it also lays down the local
-    // per-shoebox background read from the supplied image - the same background the
-    // fit uses. Diagnostic tool, not on the hot path.
-    template<class T>
-    std::vector<float> PredictImage(const T *image,
-                                    BraggPrediction &prediction,
-                                    const PixelRefineData &data,
-                                    bool include_background = true) const;
-
-    // Render the per-pixel chi-square (cost density) that the optimizer actually
-    // minimizes: for every shoebox pixel that enters the fit it stores the squared
-    // weighted residual ((I_pred - I_obs)/sigma)^2 in raw counts - identical to the
-    // Ceres residual_i^2 - accumulating where shoeboxes overlap. Pixels that are not
-    // part of any shoebox stay 0; masked/saturated pixels (skipped by the fit) also
-    // stay 0. Summing the image gives ~2*final_cost. Diagnostic tool.
-    template<class T>
-    std::vector<float> ChiSquaredImage(const T *image,
-                                       BraggPrediction &prediction,
-                                       const PixelRefineData &data) const;
-
-    // Reference (merged) intensity used as the fixed hypothesis for a reflection,
-    // or nullopt if this hkl is not in the reference. Lets callers show the fitted
-    // estimate next to the reference it was scaled against.
-    std::optional<double> ReferenceIntensity(const Reflection &r) const {
-        const auto it = reference_data.find(hkl_key_generator(r));
-        if (it == reference_data.end())
-            return std::nullopt;
-        return it->second;
-    }
 };
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 6bfbd37e..d7f0875c 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -86,13 +86,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         ${APP_RESOURCES}
         windows/JFJochViewerReciprocalSpaceWindow.cpp
         windows/JFJochViewerReciprocalSpaceWindow.h
-        windows/JFJochPixelRefineWindow.cpp
-        windows/JFJochPixelRefineWindow.h
-        windows/JFJochPixelRefineTableWindow.cpp
-        windows/JFJochPixelRefineTableWindow.h
         windows/JFJochMagnifierWindow.cpp
         windows/JFJochMagnifierWindow.h
-        windows/PixelRefineParams.h
 )
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::DBus Qt6::Concurrent
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 1e92cfed..a10ded30 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -9,8 +9,6 @@
 
 #include "JFJochImageReadingWorker.h"
 #include "../reader/JFJochReaderImage.h"   // JFJochReaderImage + GAP/ERROR/SATURATED sentinels
-#include "../image_analysis/LoadFCalcFromMtz.h"
-#include "../image_analysis/bragg_prediction/BraggPredictionFactory.h"
 #include "../image_analysis/geom_refinement/AssignSpotsToRings.h"
 #include "../image_analysis/spot_finding/StrongPixelSet.h"
 #include "../image_analysis/spot_finding/SpotUtils.h"
@@ -69,8 +67,6 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
     : QObject(parent),
       indexing_settings(experiment.GetIndexingSettings()),
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
-    qRegisterMetaType<PixelRefineParams>("PixelRefineParams");
-    qRegisterMetaType<PixelRefineReport>("PixelRefineReport");
     qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
     spot_finding_settings = settings;;
 
@@ -307,13 +303,7 @@ void JFJochImageReadingWorker::UpdateAzint_i(const JFJochReaderDataset *dataset)
         image_analysis = std::make_unique<MXAnalysisWithoutFPGA>(curr_experiment, *azint_mapping, dataset->pixel_mask,
             *index_and_refine.get());
 
-        // PixelRefine state is tied to the experiment/mapping; rebuild lazily.
-        pixel_refine_.reset();
-        pixel_pred_.reset();
         last_profile_.reset();
-        // Keep scale-on-the-fly alive across dataset reloads.
-        if (!pixel_reference_.empty())
-            index_and_refine->ReferenceIntensities(pixel_reference_);
     }
 }
 
@@ -722,287 +712,3 @@ void JFJochImageReadingWorker::LoadSpots(int64_t start_image, int64_t end_image,
     emit spotsLoaded(result);
 }
 
-// ---------------------------------------------------------------------------
-// Experimental PixelRefine
-// ---------------------------------------------------------------------------
-void JFJochImageReadingWorker::EnsurePixelRefine_i() {
-    if (!pixel_refine_ && !pixel_reference_.empty())
-        pixel_refine_ = std::make_unique<PixelRefine>(curr_experiment, pixel_reference_);
-    if (!pixel_pred_)
-        pixel_pred_ = CreateBraggPrediction(curr_experiment.IsRotationIndexing());
-}
-
-bool JFJochImageReadingWorker::BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p, QString &reason) const {
-    if (!current_image_ptr || !index_and_refine || !current_image.has_value()) {
-        reason = "No image loaded";
-        return false;
-    }
-
-    const auto &outcomes = index_and_refine->GetIntegrationOutcome();
-    const int64_t n = current_image.value();
-    if (n < 0 || n >= static_cast<int64_t>(outcomes.size())) {
-        reason = "No analysis result for current image";
-        return false;
-    }
-
-    const auto &io = outcomes[n];
-    if (io.reflections.empty()) {
-        // The "indexed" badge in the viewer comes from indexing (lattice_type);
-        // PixelRefine instead seeds from the *integration* outcome, which is only
-        // populated when Quick integration is enabled and succeeds for this image.
-        // Distinguish the two so the user knows what to turn on.
-        if (current_image_ptr->ImageData().lattice_type.has_value())
-            reason = "Image is indexed but not integrated - enable Quick integration";
-        else
-            reason = "Current image is not indexed";
-        return false;
-    }
-
-    d.geom = io.geom;
-    d.latt = io.latt;
-
-    const auto &lt = current_image_ptr->ImageData().lattice_type;
-    if (lt) {
-        d.crystal_system = lt->crystal_system;
-        d.centering = lt->centering;
-    }
-    if (d.crystal_system == gemmi::CrystalSystem::Trigonal)
-        d.crystal_system = gemmi::CrystalSystem::Hexagonal;
-
-    d.R[0] = p.R0;
-    d.R[1] = p.R1;
-    d.bandwidth = p.bandwidth_fwhm / 2.3548; // FWHM -> sigma
-    d.scale_factor = p.scale_factor;
-    d.B_factor = p.B_factor;
-    if (std::isfinite(p.beam_x) && std::isfinite(p.beam_y))
-        d.geom.BeamX_pxl(static_cast<float>(p.beam_x)).BeamY_pxl(static_cast<float>(p.beam_y));
-
-    d.refine_orientation = p.refine_orientation;
-    d.refine_unit_cell = p.refine_unit_cell;
-    d.refine_beam_center = p.refine_beam_center;
-    d.refine_scale = p.refine_scale;
-    d.refine_B = p.refine_B;
-    d.refine_R = p.refine_R;
-    d.max_iterations = p.max_iterations;
-    return true;
-}
-
-std::shared_ptr<SimpleImage> JFJochImageReadingWorker::WrapFloatImage_i(const std::vector<float> &img) const {
-    auto si = std::make_shared<SimpleImage>();
-    // CompressedImage is a non-owning view over its data pointer. predictedImageReady
-    // is a queued cross-thread connection, so the source float vector must outlive the
-    // emit: copy it into SimpleImage::buffer (which the shared_ptr keeps alive) instead
-    // of aliasing the caller's temporary, otherwise loadImageInternal() reads freed
-    // memory in the GUI thread (SIGSEGV).
-    si->buffer.resize(img.size() * sizeof(float));
-    std::memcpy(si->buffer.data(), img.data(), si->buffer.size());
-    si->image = CompressedImage(si->buffer, curr_experiment.GetXPixelsNum(), curr_experiment.GetYPixelsNum(),
-                                CompressedImageMode::Float32);
-    return si;
-}
-
-void JFJochImageReadingWorker::SquaredResidualWithImage_i(std::vector<float> &pred) const {
-    // PredictImage() returns raw detector units (same as the measured counts), so
-    // pred - measured is the per-pixel residual the model fails to explain. We plot
-    // |pred - measured|^2: sign-free, so it needs no diverging colour scale and just
-    // highlights where the model disagrees most. Masked / saturated pixels carry
-    // sentinels rather than counts, so no comparison is possible -> NaN (gap).
-    if (!current_image_ptr)
-        return;
-    const auto &img = current_image_ptr->Image();
-    const size_t n = std::min(pred.size(), img.size());
-    for (size_t i = 0; i < n; ++i) {
-        const int32_t v = img[i];
-        if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE || v == SATURATED_PXL_VALUE) {
-            pred[i] = NAN;
-        } else {
-            const float diff = pred[i] - static_cast<float>(v);
-            pred[i] = diff * diff;
-        }
-    }
-}
-
-void JFJochImageReadingWorker::MaskMeasuredSentinels_i(std::vector<float> &img) const {
-    // The chi^2 image is 0 outside shoeboxes; show masked/saturated pixels as a gap
-    // (NaN) instead, so they read as "not comparable" rather than "zero cost".
-    if (!current_image_ptr)
-        return;
-    const auto &measured = current_image_ptr->Image();
-    const size_t n = std::min(img.size(), measured.size());
-    for (size_t i = 0; i < n; ++i) {
-        const int32_t v = measured[i];
-        if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE || v == SATURATED_PXL_VALUE)
-            img[i] = NAN;
-    }
-}
-
-QVector<QRect> JFJochImageReadingWorker::BuildShoeboxes_i(const PixelRefineData &data) const {
-    // One rectangle per fitted reflection: the shoebox the optimizer summed over,
-    // centred on the predicted position with half-size data.shoebox_radius.
-    QVector<QRect> boxes;
-    boxes.reserve(static_cast<int>(data.reflections.size()));
-    const int r = data.shoebox_radius;
-    const int side = 2 * r + 1;
-    for (const auto &refl : data.reflections) {
-        if (!std::isfinite(refl.predicted_x) || !std::isfinite(refl.predicted_y))
-            continue;
-        const int cx = static_cast<int>(std::lround(refl.predicted_x));
-        const int cy = static_cast<int>(std::lround(refl.predicted_y));
-        boxes.push_back(QRect(cx - r, cy - r, side, side));
-    }
-    return boxes;
-}
-
-PixelRefineReport JFJochImageReadingWorker::BuildReport_i(const PixelRefineData &data) const {
-    PixelRefineReport report;
-    report.pr_G = data.scale_factor;
-    report.pr_B = data.B_factor;
-    report.pr_cc = data.cc;
-    report.pr_cc_n = data.cc_n;
-
-    // Standard ScaleOnTheFly pipeline result for the same image, as a baseline.
-    if (current_image_ptr) {
-        const auto &d = current_image_ptr->ImageData();
-        if (d.image_scale_factor)  report.pipe_G  = d.image_scale_factor.value();
-        if (d.image_scale_b_factor) report.pipe_B = d.image_scale_b_factor.value();
-        if (d.image_scale_cc)      report.pipe_cc = d.image_scale_cc.value();
-    }
-
-    report.rows.reserve(data.reflections.size());
-    for (const auto &r : data.reflections) {
-        if (!r.observed)
-            continue;
-        PixelRefineReport::Row row;
-        row.h = r.h; row.k = r.k; row.l = r.l;
-        row.d = r.d;
-        row.completeness = r.completeness;
-        row.partiality = r.partiality;
-        row.I = r.I;
-        row.sigma = r.sigma;
-        if (std::isfinite(r.image_scale_corr))
-            row.I_true_est = static_cast<double>(r.I) * static_cast<double>(r.image_scale_corr);
-        if (pixel_refine_)
-            row.I_true_ref = pixel_refine_->ReferenceIntensity(r).value_or(NAN);
-        report.rows.push_back(row);
-    }
-    return report;
-}
-
-std::vector<float> JFJochImageReadingWorker::BuildDisplayImage_i(const PixelRefineData &data,
-                                                                 int display_mode) const {
-    const auto &img32 = current_image_ptr->Image();
-    if (display_mode == PixelRefineParams::ChiSquared) {
-        // The cost density the optimizer actually minimizes (weighted residual^2).
-        auto chi2 = pixel_refine_->ChiSquaredImage<int32_t>(img32.data(), *pixel_pred_, data);
-        MaskMeasuredSentinels_i(chi2);
-        return chi2;
-    }
-
-    auto pred = pixel_refine_->PredictImage<int32_t>(img32.data(), *pixel_pred_, data, true);
-    if (display_mode == PixelRefineParams::SquaredDifference)
-        SquaredResidualWithImage_i(pred);
-    return pred;
-}
-
-void JFJochImageReadingWorker::LoadReference(QString path) {
-    QMutexLocker ul(&m);
-    try {
-        pixel_reference_ = LoadFCalcFromMtz(path.toStdString());
-        if (index_and_refine)
-            index_and_refine->ReferenceIntensities(pixel_reference_); // enables scale-on-the-fly too
-        pixel_refine_.reset();                                        // rebuild with new reference
-        emit pixelRefineStatus(QString("Loaded %1 reference reflections").arg(pixel_reference_.size()));
-    } catch (const std::exception &e) {
-        emit pixelRefineStatus(QString("Failed to load reference: %1").arg(e.what()));
-    }
-}
-
-void JFJochImageReadingWorker::PixelRefinePreview(PixelRefineParams params) {
-    QMutexLocker ul(&m);
-    if (!last_profile_) {
-        emit pixelRefineStatus("Analyze an image first");
-        return;
-    }
-    EnsurePixelRefine_i();
-    if (!pixel_refine_) {
-        emit pixelRefineStatus("Load reference data first");
-        return;
-    }
-
-    PixelRefineData d;
-    QString seed_reason;
-    if (!BuildPixelSeed_i(d, params, seed_reason)) {
-        emit pixelRefineStatus(seed_reason);
-        return;
-    }
-
-    // Preview = evaluate only: do not move any parameter.
-    d.refine_orientation = d.refine_unit_cell = d.refine_beam_center = false;
-    d.refine_scale = d.refine_B = d.refine_R = false;
-    d.max_iterations = 0;
-
-    try {
-        const auto &img32 = current_image_ptr->Image();
-        pixel_refine_->Run<int32_t>(img32.data(), *pixel_pred_, d);
-        emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
-        emit pixelRefineReport(BuildReport_i(d));
-
-        auto display = BuildDisplayImage_i(d, params.display_mode);
-        emit predictedImageReady(WrapFloatImage_i(display));
-        emit predictedShoeboxes(BuildShoeboxes_i(d));
-    } catch (const std::exception &e) {
-        emit pixelRefineStatus(QString("PixelRefine preview failed: %1").arg(e.what()));
-    }
-}
-
-void JFJochImageReadingWorker::PixelRefineRun(PixelRefineParams params) {
-    QMutexLocker ul(&m);
-    if (!last_profile_) {
-        emit pixelRefineStatus("Analyze an image first");
-        return;
-    }
-    EnsurePixelRefine_i();
-    if (!pixel_refine_) {
-        emit pixelRefineStatus("Load reference data first");
-        return;
-    }
-
-    PixelRefineData d;
-    QString seed_reason;
-    if (!BuildPixelSeed_i(d, params, seed_reason)) {
-        emit pixelRefineStatus(seed_reason);
-        return;
-    }
-    if (d.max_iterations <= 0)
-        d.max_iterations = 3;
-
-    try {
-        const auto &img32 = current_image_ptr->Image();
-        pixel_refine_->Run<int32_t>(img32.data(), *pixel_pred_, d);
-
-        // Push refined values back so the sliders follow the optimizer.
-        PixelRefineParams out = params;
-        out.R0 = d.R[0];
-        out.R1 = d.R[1];
-        out.bandwidth_fwhm = d.bandwidth * 2.3548; // sigma -> FWHM
-        out.scale_factor = d.scale_factor;
-        out.B_factor = d.B_factor;
-        out.beam_x = d.geom.GetBeamX_pxl();
-        out.beam_y = d.geom.GetBeamY_pxl();
-        emit pixelRefineParamsRefined(out);
-        emit pixelRefineResidual(d.final_cost, d.cc, static_cast<int64_t>(d.reflections.size()));
-        emit pixelRefineReport(BuildReport_i(d));
-
-        auto display = BuildDisplayImage_i(d, params.display_mode);
-        emit predictedImageReady(WrapFloatImage_i(display));
-        emit predictedShoeboxes(BuildShoeboxes_i(d));
-
-        // Show the refined predictions on the main image too.
-        auto new_image = std::make_shared<JFJochReaderImage>(*current_image_ptr);
-        new_image->ImageData().reflections = d.reflections;
-        current_image_ptr = new_image;
-        emit imageLoaded(current_image_ptr);
-    } catch (const std::exception &e) {
-        emit pixelRefineStatus(QString("PixelRefine failed: %1").arg(e.what()));
-    }
-}
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 50cd77ca..fcf74d5d 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -15,10 +15,8 @@
 #include "../common/Logger.h"
 #include "../reader/JFJochHttpReader.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
-#include "../image_analysis/pixel_refinement/PixelRefine.h"
 #include "../image_analysis/bragg_prediction/BraggPrediction.h"
 #include "SimpleImage.h"
-#include "windows/PixelRefineParams.h"
 #include "../common/MovingAverage.h"
 
 Q_DECLARE_METATYPE(std::shared_ptr<const JFJochReaderDataset>)
@@ -60,30 +58,8 @@ private:
     std::unique_ptr<MXAnalysisWithoutFPGA> image_analysis;
     std::unique_ptr<IndexAndRefine> index_and_refine;
 
-    // Experimental PixelRefine support. last_profile_ keeps the azimuthal profile
-    // of the most recently analyzed image (PixelRefine needs it); the engine and a
-    // dedicated prediction buffer are built lazily once a reference is loaded.
+    // Azimuthal profile buffer of the most recently analyzed image (filled by Analyze).
     std::unique_ptr<AzimuthalIntegrationProfile> last_profile_;
-    std::vector<MergedReflection> pixel_reference_;
-    std::unique_ptr<PixelRefine> pixel_refine_;
-    std::unique_ptr<BraggPrediction> pixel_pred_;
-
-    void EnsurePixelRefine_i();
-    bool BuildPixelSeed_i(PixelRefineData &d, const PixelRefineParams &p, QString &reason) const;
-    std::shared_ptr<SimpleImage> WrapFloatImage_i(const std::vector<float> &img) const;
-    // Turn a predicted image into the squared residual |predicted - measured|^2 in
-    // place. Masked/saturated pixels become NaN (rendered as a gap: no comparison
-    // possible), not 0.
-    void SquaredResidualWithImage_i(std::vector<float> &pred) const;
-    // Mark masked/saturated pixels of the current image as NaN (gap) in a float
-    // image, leaving the rest untouched (used for the chi^2 view).
-    void MaskMeasuredSentinels_i(std::vector<float> &img) const;
-    // Build the per-reflection shoebox rectangles for the last refine/preview.
-    QVector<QRect> BuildShoeboxes_i(const PixelRefineData &data) const;
-    // Assemble the per-reflection table + per-image summary for the table window.
-    PixelRefineReport BuildReport_i(const PixelRefineData &data) const;
-    // Build the float image to display for the given PixelRefineParams::DisplayMode.
-    std::vector<float> BuildDisplayImage_i(const PixelRefineData &data, int display_mode) const;
 
     std::unique_ptr<ROIElement> roi;
 
@@ -145,14 +121,6 @@ signals:
     void fileLoadError(QString title, QString message);
     void fileLoadRetryStatus(bool active, QString message);
 
-    // PixelRefine (experimental)
-    void predictedImageReady(std::shared_ptr<const SimpleImage> image);
-    void predictedShoeboxes(QVector<QRect> boxes); // per-reflection optimization windows
-    void pixelRefineResidual(double cost, double cc, int64_t n_reflections);
-    void pixelRefineParamsRefined(PixelRefineParams params);
-    void pixelRefineReport(PixelRefineReport report); // per-reflection table + summary
-    void pixelRefineStatus(QString message);
-
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
     ~JFJochImageReadingWorker() override = default;
@@ -189,9 +157,4 @@ public slots:
     void LoadCalibration(QString dataset);
     void setAutoLoadMode(AutoloadMode mode);
     void setAutoLoadJump(int64_t val);
-
-    // PixelRefine (experimental)
-    void LoadReference(QString path);
-    void PixelRefinePreview(PixelRefineParams params);
-    void PixelRefineRun(PixelRefineParams params);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 1eb2c3c7..903b7528 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -25,8 +25,6 @@
 #include "toolbar/JFJochViewerToolbarImage.h"
 #include "windows/JFJoch2DAzintImageWindow.h"
 #include "windows/JFJochAzIntWindow.h"
-#include "windows/JFJochPixelRefineWindow.h"
-#include "windows/JFJochPixelRefineTableWindow.h"
 #include "windows/JFJochMagnifierWindow.h"
 #include "image_viewer/JFJochImage.h"
 #include "image_viewer/JFJochSimpleImage.h"
@@ -108,8 +106,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     auto azintWindow = new JFJochAzIntWindow(experiment.GetAzimuthalIntegrationSettings(), this);
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
-    auto pixelRefineWindow = new JFJochPixelRefineWindow(this);
-    auto pixelRefineTableWindow = new JFJochPixelRefineTableWindow(this);
     auto magnifierWindow = new JFJochMagnifierWindow(this);
 
     menuBar->AddWindowEntry(tableWindow, "Image list");
@@ -121,8 +117,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(reciprocalWindow, "Reciprocal space viewer");
     menuBar->AddWindowEntry(azintWindow, "Azimuthal integration settings");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
-    menuBar->AddWindowEntry(pixelRefineWindow, "PixelRefine (experimental)");
-    menuBar->AddWindowEntry(pixelRefineTableWindow, "PixelRefine reflections");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
 
     if (dbus) {
@@ -344,38 +338,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(azintImageWindow, &JFJoch2DAzintImageWindow::zoomOnBin,
             viewer, &JFJochDiffractionImage::centerOnSpot);
 
-    // --- PixelRefine (experimental) ---
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
-            pixelRefineWindow, &JFJochHelperWindow::imageLoaded);
-    connect(pixelRefineWindow, &JFJochPixelRefineWindow::paramsChanged,
-            reading_worker, &JFJochImageReadingWorker::PixelRefinePreview);
-    connect(pixelRefineWindow, &JFJochPixelRefineWindow::refineRequested,
-            reading_worker, &JFJochImageReadingWorker::PixelRefineRun);
-    connect(pixelRefineWindow, &JFJochPixelRefineWindow::loadReferenceRequested,
-            reading_worker, &JFJochImageReadingWorker::LoadReference);
-    connect(reading_worker, &JFJochImageReadingWorker::predictedImageReady,
-            pixelRefineWindow, &JFJochPixelRefineWindow::setPredictedImage);
-    connect(reading_worker, &JFJochImageReadingWorker::predictedShoeboxes,
-            pixelRefineWindow->imageView(), &JFJochSimpleImage::setShoeboxes);
-    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineResidual,
-            pixelRefineWindow, &JFJochPixelRefineWindow::setResidual);
-    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineParamsRefined,
-            pixelRefineWindow, &JFJochPixelRefineWindow::setRefinedParams);
-    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineStatus,
-            pixelRefineWindow, &JFJochPixelRefineWindow::setStatus);
-
-    // Reflection-table window: refreshed on every preview/refine, raised by button.
-    connect(reading_worker, &JFJochImageReadingWorker::pixelRefineReport,
-            pixelRefineTableWindow, &JFJochPixelRefineTableWindow::setReport);
-    connect(pixelRefineWindow, &JFJochPixelRefineWindow::showTableRequested,
-            pixelRefineTableWindow, &JFJochHelperWindow::open);
-
-    // Lock the predicted-image viewport to the original image (both directions).
-    connect(viewer, &JFJochImage::viewportChanged,
-            pixelRefineWindow->imageView(), &JFJochImage::applyViewport);
-    connect(pixelRefineWindow->imageView(), &JFJochImage::viewportChanged,
-            viewer, &JFJochImage::applyViewport);
-
     // --- Magnifier ---
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
             magnifierWindow, &JFJochHelperWindow::imageLoaded);
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index 5b3816ea..5e98e599 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -55,9 +55,8 @@ protected:
 
     QColor feature_color = Qt::magenta;
 
-    // Decimal places for non-integer per-pixel value labels. Float images (e.g. the
-    // PixelRefine prediction) are unreadable with many decimals, so subclasses can
-    // lower this.
+    // Decimal places for non-integer per-pixel value labels. Float images are
+    // unreadable with many decimals, so subclasses can lower this.
     int label_decimals_ = 3;
 
     float foreground = 10.0;
diff --git a/viewer/image_viewer/JFJochSimpleImage.cpp b/viewer/image_viewer/JFJochSimpleImage.cpp
index d3494a8f..bfa029e7 100644
--- a/viewer/image_viewer/JFJochSimpleImage.cpp
+++ b/viewer/image_viewer/JFJochSimpleImage.cpp
@@ -40,30 +40,6 @@ void JFJochSimpleImage::setImage(std::shared_ptr<const SimpleImage> img) {
     }
 }
 
-void JFJochSimpleImage::setShoeboxes(QVector<QRect> boxes) {
-    shoeboxes_ = std::move(boxes);
-    // Redraw overlays on the current image (no-op if no image yet).
-    updateOverlay();
-}
-
-void JFJochSimpleImage::addCustomOverlay() {
-    if (shoeboxes_.isEmpty() || !scene())
-        return;
-
-    // Cosmetic 1-px outline so the box edges stay thin at any zoom; only draw the
-    // ones currently in view (there can be hundreds of reflections).
-    const QRectF visibleRect = mapToScene(viewport()->geometry()).boundingRect();
-    QPen pen(QColor(0, 220, 255), 0); // cyan, distinct from the prediction colours
-    pen.setCosmetic(true);
-
-    for (const QRect &b : shoeboxes_) {
-        const QRectF r(b.x(), b.y(), b.width(), b.height());
-        if (!visibleRect.intersects(r))
-            continue;
-        auto *item = scene()->addRect(r, pen);
-        addOverlayItem(item);
-    }
-}
 
 void JFJochSimpleImage::mouseHover(QMouseEvent *event) {
     if (image_) {
diff --git a/viewer/image_viewer/JFJochSimpleImage.h b/viewer/image_viewer/JFJochSimpleImage.h
index 40abac06..3232bc7c 100644
--- a/viewer/image_viewer/JFJochSimpleImage.h
+++ b/viewer/image_viewer/JFJochSimpleImage.h
@@ -20,20 +20,14 @@ class JFJochSimpleImage : public JFJochImage {
 
     std::shared_ptr<const SimpleImage> image_;
 
-    // Per-reflection shoebox rectangles (pixel coordinates) to overlay: the pixels
-    // PixelRefine actually summed over. Empty = nothing drawn.
-    QVector<QRect> shoeboxes_;
-
     // Prepare image
     template<class T>
     void loadImageInternal(const uint8_t *input);
     void loadImageInternal();
 
     void mouseHover(QMouseEvent *event) override;
-    void addCustomOverlay() override;
 public:
     explicit JFJochSimpleImage(QWidget *parent = nullptr);
 public slots:
     void setImage(std::shared_ptr<const SimpleImage> img);
-    void setShoeboxes(QVector<QRect> boxes);
 };
diff --git a/viewer/windows/JFJochPixelRefineTableWindow.cpp b/viewer/windows/JFJochPixelRefineTableWindow.cpp
deleted file mode 100644
index f656164a..00000000
--- a/viewer/windows/JFJochPixelRefineTableWindow.cpp
+++ /dev/null
@@ -1,101 +0,0 @@
-// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "JFJochPixelRefineTableWindow.h"
-
-#include <cmath>
-#include <QVBoxLayout>
-#include <QHeaderView>
-
-JFJochPixelRefineTableWindow::JFJochPixelRefineTableWindow(QWidget *parent)
-    : JFJochHelperWindow(parent) {
-    setWindowTitle("PixelRefine reflections");
-    resize(950, 600);
-
-    auto central = new QWidget(this);
-    setCentralWidget(central);
-    auto layout = new QVBoxLayout(central);
-
-    m_summary = new QLabel(tr("No PixelRefine result yet."), this);
-    m_summary->setTextFormat(Qt::RichText);
-    m_summary->setWordWrap(true);
-    layout->addWidget(m_summary);
-
-    m_table = new QTableView(this);
-    m_model = new QStandardItemModel(this);
-    setupModel();
-
-    m_proxy = new QSortFilterProxyModel(this);
-    m_proxy->setSourceModel(m_model);
-    m_proxy->setSortRole(Qt::UserRole); // numeric sort on the underlying values
-
-    m_table->setModel(m_proxy);
-    m_table->setEditTriggers(QAbstractItemView::NoEditTriggers);
-    m_table->setSortingEnabled(true);
-    m_table->sortByColumn(6, Qt::DescendingOrder); // default: I desc
-    m_table->verticalHeader()->setVisible(false);
-    m_table->horizontalHeader()->setSortIndicatorShown(true);
-    m_table->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
-    m_table->setStyleSheet("background-color: white;");
-    layout->addWidget(m_table);
-}
-
-void JFJochPixelRefineTableWindow::setupModel() {
-    const QStringList headers = {
-        "h", "k", "l", "d [Å]", "Compl.", "Part.",
-        "I", "Sigma", "Est. I_true", "Ref. I_true"
-    };
-    m_model->setColumnCount(headers.size());
-    for (int i = 0; i < headers.size(); ++i)
-        m_model->setHeaderData(i, Qt::Horizontal, headers[i]);
-}
-
-static QStandardItem *numItem(double value, int decimals) {
-    auto *it = new QStandardItem();
-    const QString text = std::isfinite(value) ? QString::number(value, 'f', decimals)
-                                              : QStringLiteral("—");
-    it->setData(text, Qt::DisplayRole);
-    it->setData(value, Qt::UserRole);
-    it->setTextAlignment(Qt::AlignRight | Qt::AlignVCenter);
-    return it;
-}
-
-static QStandardItem *intItem(int value) {
-    auto *it = new QStandardItem();
-    it->setData(static_cast<qlonglong>(value), Qt::DisplayRole);
-    it->setData(static_cast<qlonglong>(value), Qt::UserRole);
-    it->setTextAlignment(Qt::AlignRight | Qt::AlignVCenter);
-    return it;
-}
-
-void JFJochPixelRefineTableWindow::setReport(PixelRefineReport report) {
-    // --- per-image summary: PixelRefine vs the standard pipeline ---------------
-    auto fmt = [](double v, int dec) {
-        return std::isfinite(v) ? QString::number(v, 'f', dec) : QStringLiteral("—");
-    };
-    auto pct = [](double v) {
-        return std::isfinite(v) ? QString::number(v * 100.0, 'f', 1) + "%" : QStringLiteral("—");
-    };
-    m_summary->setText(
-        tr("<b>PixelRefine:</b> scale G = %1, B = %2 Ų, CC = %3 (%4 refl)"
-           "&nbsp;&nbsp;|&nbsp;&nbsp;"
-           "<b>Pipeline:</b> scale G = %5, B = %6 Ų, CC = %7")
-            .arg(fmt(report.pr_G, 4), fmt(report.pr_B, 1), pct(report.pr_cc))
-            .arg(report.pr_cc_n)
-            .arg(fmt(report.pipe_G, 4), fmt(report.pipe_B, 1), pct(report.pipe_cc)));
-
-    // --- per-reflection rows ---------------------------------------------------
-    m_model->removeRows(0, m_model->rowCount());
-    for (const auto &r : report.rows) {
-        QList<QStandardItem *> row;
-        row << intItem(r.h) << intItem(r.k) << intItem(r.l);
-        row << numItem(r.d, 3);
-        row << numItem(r.completeness, 2);
-        row << numItem(r.partiality, 2);
-        row << numItem(r.I, 1);
-        row << numItem(r.sigma, 1);
-        row << numItem(r.I_true_est, 1);
-        row << numItem(r.I_true_ref, 1);
-        m_model->appendRow(row);
-    }
-}
diff --git a/viewer/windows/JFJochPixelRefineTableWindow.h b/viewer/windows/JFJochPixelRefineTableWindow.h
deleted file mode 100644
index 5187b546..00000000
--- a/viewer/windows/JFJochPixelRefineTableWindow.h
+++ /dev/null
@@ -1,34 +0,0 @@
-// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include "JFJochHelperWindow.h"
-#include "PixelRefineParams.h"
-
-#include <QLabel>
-#include <QTableView>
-#include <QStandardItemModel>
-#include <QSortFilterProxyModel>
-
-// Reflection table for the experimental PixelRefine path. Opened from a button on
-// the PixelRefine window and refreshed on every preview/refine. Each row is one
-// matched reflection (the two partiality-style fractions, the fitted intensity,
-// and the estimated vs reference full intensity); the header line compares
-// PixelRefine's per-image scale/B/CC with the standard ScaleOnTheFly pipeline.
-class JFJochPixelRefineTableWindow : public JFJochHelperWindow {
-    Q_OBJECT
-
-    QLabel *m_summary = nullptr;
-    QTableView *m_table = nullptr;
-    QStandardItemModel *m_model = nullptr;
-    QSortFilterProxyModel *m_proxy = nullptr;
-
-    void setupModel();
-
-public:
-    explicit JFJochPixelRefineTableWindow(QWidget *parent = nullptr);
-
-public slots:
-    void setReport(PixelRefineReport report);
-};
diff --git a/viewer/windows/JFJochPixelRefineWindow.cpp b/viewer/windows/JFJochPixelRefineWindow.cpp
deleted file mode 100644
index 0e8b4a16..00000000
--- a/viewer/windows/JFJochPixelRefineWindow.cpp
+++ /dev/null
@@ -1,233 +0,0 @@
-// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "JFJochPixelRefineWindow.h"
-#include "../image_viewer/JFJochSimpleImage.h"
-
-#include <QWidget>
-#include <QHBoxLayout>
-#include <QVBoxLayout>
-#include <QFormLayout>
-#include <QGroupBox>
-#include <QFileDialog>
-#include <cmath>
-
-JFJochPixelRefineWindow::JFJochPixelRefineWindow(QWidget *parent)
-    : JFJochHelperWindow(parent) {
-    setWindowTitle("PixelRefine (experimental)");
-
-    auto central = new QWidget(this);
-    setCentralWidget(central);
-    auto layout = new QHBoxLayout(central);
-
-    // --- predicted image (left, expanding) ---------------------------------
-    m_image = new JFJochSimpleImage(this);
-    m_image->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
-    layout->addWidget(m_image, 1);
-
-    // --- control panel (right) ---------------------------------------------
-    auto controls = new QWidget(this);
-    controls->setMinimumWidth(320);
-    auto controlsLayout = new QVBoxLayout(controls);
-    layout->addWidget(controls, 0);
-
-    // --- what the left image shows ------------------------------------------
-    m_displayMode = new QComboBox(this);
-    m_displayMode->addItem(tr("Prediction"));
-    m_displayMode->addItem(tr("Squared difference |pred - image|²"));
-    m_displayMode->addItem(tr("χ² (weighted residual = LSQ cost)"));
-    auto displayForm = new QFormLayout();
-    displayForm->addRow(tr("Display:"), m_displayMode);
-    controlsLayout->addLayout(displayForm);
-
-    auto paramBox = new QGroupBox(tr("Model parameters"), this);
-    auto form = new QFormLayout(paramBox);
-
-    m_R0    = new SliderPlusBox(1e-4, 0.05, 1e-4, 4, this);                       m_R0->setValue(0.005);
-    m_R1    = new SliderPlusBox(1e-4, 0.05, 1e-4, 4, this);                       m_R1->setValue(0.005);
-    m_bw    = new SliderPlusBox(0.0, 0.05, 1e-4, 4, this);                        m_bw->setValue(0.0);
-    m_scale = new SliderPlusBox(1e-3, 1e4, 1e-3, 3, this, SliderPlusBox::Logarithmic); m_scale->setValue(1.0);
-    m_B     = new SliderPlusBox(0.0, 200.0, 0.1, 1, this);                        m_B->setValue(0.0);
-    m_beamx = new SliderPlusBox(0.0, 5000.0, 0.5, 1, this);                       m_beamx->setValue(0.0);
-    m_beamy = new SliderPlusBox(0.0, 5000.0, 0.5, 1, this);                       m_beamy->setValue(0.0);
-
-    form->addRow(tr("R0 radial [Å⁻¹]:"), m_R0);
-    form->addRow(tr("R1 tangential [Å⁻¹]:"), m_R1);
-    form->addRow(tr("Bandwidth FWHM (Δλ/λ):"), m_bw);
-    form->addRow(tr("Scale G:"), m_scale);
-    form->addRow(tr("B-factor [Ų]:"), m_B);
-
-    m_overrideBeam = new QCheckBox(tr("Override beam centre"), this);
-    form->addRow(QString(), m_overrideBeam);
-    form->addRow(tr("Beam X [px]:"), m_beamx);
-    form->addRow(tr("Beam Y [px]:"), m_beamy);
-    m_beamx->setEnabled(false);
-    m_beamy->setEnabled(false);
-
-    controlsLayout->addWidget(paramBox);
-
-    // --- what "Refine" is allowed to move ----------------------------------
-    auto refBox = new QGroupBox(tr("Refine (Ceres)"), this);
-    auto refLayout = new QVBoxLayout(refBox);
-    m_refOrientation = new QCheckBox(tr("Orientation"), this);   m_refOrientation->setChecked(true);
-    m_refCell        = new QCheckBox(tr("Unit cell"), this);
-    m_refBeam        = new QCheckBox(tr("Beam centre"), this);
-    m_refScale       = new QCheckBox(tr("Scale G"), this);       m_refScale->setChecked(true);
-    m_refB           = new QCheckBox(tr("B-factor"), this);
-    m_refR           = new QCheckBox(tr("Widths R0/R1"), this);  m_refR->setChecked(true);
-    for (auto *cb : {m_refOrientation, m_refCell, m_refBeam, m_refScale, m_refB, m_refR})
-        refLayout->addWidget(cb);
-    controlsLayout->addWidget(refBox);
-
-    // --- buttons + readouts -------------------------------------------------
-    m_loadRef = new QPushButton(tr("Load reference MTZ…"), this);
-    m_refine  = new QPushButton(tr("Refine"), this);
-    m_showTable = new QPushButton(tr("Reflection table…"), this);
-    controlsLayout->addWidget(m_loadRef);
-    controlsLayout->addWidget(m_refine);
-    controlsLayout->addWidget(m_showTable);
-
-    m_residual = new QLabel(tr("Residual: —"), this);
-    m_pipelineCC = new QLabel(tr("Pipeline CC (ref): —"), this);
-    m_status   = new QLabel(QString(), this);
-    m_status->setWordWrap(true);
-    m_status->setStyleSheet("color: rgb(80, 80, 80);");
-    controlsLayout->addWidget(m_residual);
-    controlsLayout->addWidget(m_pipelineCC);
-    controlsLayout->addWidget(m_status);
-    controlsLayout->addStretch(1);
-
-    // --- debounce timer for live preview -----------------------------------
-    m_debounce = new QTimer(this);
-    m_debounce->setSingleShot(true);
-    m_debounce->setInterval(150);
-    connect(m_debounce, &QTimer::timeout, this, [this] {
-        emit paramsChanged(currentParams());
-    });
-
-    for (auto *s : {m_R0, m_R1, m_bw, m_scale, m_B, m_beamx, m_beamy})
-        connect(s, &SliderPlusBox::valueChanged, this, [this](double) { onControlChanged(); });
-
-    connect(m_displayMode, &QComboBox::currentIndexChanged, this, [this](int) { onControlChanged(); });
-
-    connect(m_overrideBeam, &QCheckBox::toggled, this, [this](bool on) {
-        m_beamx->setEnabled(on);
-        m_beamy->setEnabled(on);
-        onControlChanged();
-    });
-
-    connect(m_loadRef, &QPushButton::clicked, this, [this] {
-        const QString path = QFileDialog::getOpenFileName(
-            this, tr("Load reference MTZ"), QString(), tr("MTZ files (*.mtz);;All files (*)"));
-        if (!path.isEmpty())
-            emit loadReferenceRequested(path);
-    });
-
-    connect(m_showTable, &QPushButton::clicked, this, [this] {
-        emit showTableRequested();
-    });
-
-    connect(m_refine, &QPushButton::clicked, this, [this] {
-        // Cancel any pending live-preview: otherwise a debounce armed by a slider
-        // move just before this click fires after the refine and overwrites the
-        // refined residual/preview with the stale pre-refine slider values.
-        m_debounce->stop();
-        PixelRefineParams p = currentParams();
-        p.max_iterations = 5;
-        emit refineRequested(p);
-    });
-}
-
-PixelRefineParams JFJochPixelRefineWindow::currentParams() const {
-    PixelRefineParams p;
-    p.R0 = m_R0->value();
-    p.R1 = m_R1->value();
-    p.bandwidth_fwhm = m_bw->value();
-    p.scale_factor = m_scale->value();
-    p.B_factor = m_B->value();
-    if (m_overrideBeam->isChecked()) {
-        p.beam_x = m_beamx->value();
-        p.beam_y = m_beamy->value();
-    } else {
-        p.beam_x = NAN;
-        p.beam_y = NAN;
-    }
-    p.refine_orientation = m_refOrientation->isChecked();
-    p.refine_unit_cell   = m_refCell->isChecked();
-    p.refine_beam_center = m_refBeam->isChecked();
-    p.refine_scale       = m_refScale->isChecked();
-    p.refine_B           = m_refB->isChecked();
-    p.refine_R           = m_refR->isChecked();
-    p.display_mode       = m_displayMode->currentIndex();
-    return p;
-}
-
-void JFJochPixelRefineWindow::onControlChanged() {
-    if (m_suppress)
-        return;
-    m_debounce->start();
-}
-
-void JFJochPixelRefineWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage> image) {
-    if (!image)
-        return;
-
-    // Initialise the beam-centre sliders from the geometry once.
-    if (!m_beamInit) {
-        const auto geom = image->Dataset().experiment.GetDiffractionGeometry();
-        m_beamx->setMax(static_cast<double>(image->Dataset().experiment.GetXPixelsNum()));
-        m_beamy->setMax(static_cast<double>(image->Dataset().experiment.GetYPixelsNum()));
-        m_suppress = true;
-        m_beamx->setValue(geom.GetBeamX_pxl());
-        m_beamy->setValue(geom.GetBeamY_pxl());
-        m_suppress = false;
-        m_beamInit = true;
-    }
-
-    // Show the standard ScaleOnTheFly pipeline's per-image CC vs the reference (set
-    // on the message during analysis when a reference is loaded), as a baseline to
-    // compare PixelRefine against.
-    const auto pipeline_cc = image->ImageData().image_scale_cc;
-    if (pipeline_cc.has_value() && std::isfinite(pipeline_cc.value()))
-        m_pipelineCC->setText(tr("Pipeline CC (ref): %1%")
-                                  .arg(pipeline_cc.value() * 100.0, 0, 'f', 1));
-    else
-        m_pipelineCC->setText(tr("Pipeline CC (ref): —"));
-
-    // Request a predicted-image preview for the (re)loaded image. Without this the
-    // preview only refreshed on a slider change, so opening/reanalyzing an image
-    // left the predicted view empty. The worker no-ops if there is no reference or
-    // the image is not integrated yet.
-    onControlChanged();
-}
-
-void JFJochPixelRefineWindow::setPredictedImage(std::shared_ptr<const SimpleImage> image) {
-    m_image->setImage(std::move(image));
-}
-
-void JFJochPixelRefineWindow::setResidual(double cost, double cc, int64_t n_reflections) {
-    const QString cc_str = std::isfinite(cc) ? QString::number(cc * 100.0, 'f', 1) + "%"
-                                             : QStringLiteral("—");
-    m_residual->setText(tr("Residual: %1   CC: %2   (%3 reflections)")
-                            .arg(cost, 0, 'g', 6)
-                            .arg(cc_str)
-                            .arg(n_reflections));
-}
-
-void JFJochPixelRefineWindow::setRefinedParams(PixelRefineParams params) {
-    m_suppress = true;
-    m_R0->setValue(params.R0);
-    m_R1->setValue(params.R1);
-    m_bw->setValue(params.bandwidth_fwhm);
-    m_scale->setValue(params.scale_factor);
-    m_B->setValue(params.B_factor);
-    if (std::isfinite(params.beam_x) && std::isfinite(params.beam_y)) {
-        m_beamx->setValue(params.beam_x);
-        m_beamy->setValue(params.beam_y);
-    }
-    m_suppress = false;
-}
-
-void JFJochPixelRefineWindow::setStatus(QString message) {
-    m_status->setText(message);
-}
diff --git a/viewer/windows/JFJochPixelRefineWindow.h b/viewer/windows/JFJochPixelRefineWindow.h
deleted file mode 100644
index 9398389d..00000000
--- a/viewer/windows/JFJochPixelRefineWindow.h
+++ /dev/null
@@ -1,79 +0,0 @@
-// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include "JFJochHelperWindow.h"
-#include "PixelRefineParams.h"
-#include "../SimpleImage.h"
-#include "../widgets/SliderPlusBox.h"
-
-#include <memory>
-#include <QCheckBox>
-#include <QComboBox>
-#include <QLabel>
-#include <QPushButton>
-#include <QTimer>
-
-class JFJochSimpleImage;
-
-// Experimental PixelRefine control window: sliders for the forward-model
-// parameters, a live (debounced) predicted-image preview, a residual readout,
-// "Load reference" and "Refine" buttons. The predicted-image view is exposed so
-// the main window can lock its viewport to the original image.
-class JFJochPixelRefineWindow : public JFJochHelperWindow {
-    Q_OBJECT
-
-    JFJochSimpleImage *m_image;
-
-    SliderPlusBox *m_R0;
-    SliderPlusBox *m_R1;
-    SliderPlusBox *m_bw;
-    SliderPlusBox *m_scale;
-    SliderPlusBox *m_B;
-    SliderPlusBox *m_beamx;
-    SliderPlusBox *m_beamy;
-
-    QComboBox *m_displayMode;   // Prediction vs. Difference (prediction - image)
-
-    QCheckBox *m_overrideBeam;
-    QCheckBox *m_refOrientation;
-    QCheckBox *m_refCell;
-    QCheckBox *m_refBeam;
-    QCheckBox *m_refScale;
-    QCheckBox *m_refB;
-    QCheckBox *m_refR;
-
-    QLabel *m_residual;
-    QLabel *m_pipelineCC;   // first-image CC vs reference from the standard ScaleOnTheFly pipeline
-    QLabel *m_status;
-    QPushButton *m_loadRef;
-    QPushButton *m_refine;
-    QPushButton *m_showTable;
-
-    QTimer *m_debounce;
-    bool m_suppress = false;   // guard while pushing refined params into sliders
-    bool m_beamInit = false;   // beam-centre sliders initialised from geometry
-
-    PixelRefineParams currentParams() const;
-    void onControlChanged();
-
-public:
-    explicit JFJochPixelRefineWindow(QWidget *parent = nullptr);
-
-    JFJochSimpleImage *imageView() const { return m_image; }
-
-    void imageLoaded(std::shared_ptr<const JFJochReaderImage> image) override;
-
-signals:
-    void paramsChanged(PixelRefineParams params);       // debounced live preview
-    void refineRequested(PixelRefineParams params);     // "Refine" button
-    void loadReferenceRequested(QString path);          // "Load reference" button
-    void showTableRequested();                          // "Reflection table" button
-
-public slots:
-    void setPredictedImage(std::shared_ptr<const SimpleImage> image);
-    void setResidual(double cost, double cc, int64_t n_reflections);
-    void setRefinedParams(PixelRefineParams params);
-    void setStatus(QString message);
-};
diff --git a/viewer/windows/PixelRefineParams.h b/viewer/windows/PixelRefineParams.h
deleted file mode 100644
index e180847e..00000000
--- a/viewer/windows/PixelRefineParams.h
+++ /dev/null
@@ -1,66 +0,0 @@
-// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include <cmath>
-#include <cstdint>
-#include <vector>
-#include <QMetaType>
-
-// Parameters exchanged between the PixelRefine window (sliders/buttons) and the
-// reading worker. bandwidth here is the *FWHM* of dlambda/lambda (user-facing);
-// the worker converts it to the sigma that PixelRefineData expects. beam_x/beam_y
-// are NaN to mean "keep the current refined geometry".
-struct PixelRefineParams {
-    double R0 = 0.005;          // radial / partiality width (A^-1)
-    double R1 = 0.005;          // tangential / profile width (A^-1)
-    double bandwidth_fwhm = 0.0; // relative bandwidth FWHM (dlambda/lambda)
-    double scale_factor = 1.0;   // overall scale G
-    double B_factor = 0.0;       // Debye-Waller B (A^2)
-    double beam_x = NAN;         // detector beam centre X (px); NaN = keep current
-    double beam_y = NAN;         // detector beam centre Y (px); NaN = keep current
-
-    // What the "Refine" button is allowed to move (ignored by the preview path).
-    bool refine_orientation = true;
-    bool refine_unit_cell   = false;
-    bool refine_beam_center = false;
-    bool refine_scale       = true;
-    bool refine_B           = false;
-    bool refine_R           = true;
-
-    int max_iterations = 3; // <=0 means evaluate-only (preview / residual)
-
-    // Display only (no effect on the fit): what the preview/refine image shows.
-    enum DisplayMode : int {
-        Prediction        = 0, // forward-model image
-        SquaredDifference = 1, // |prediction - measured|^2 (raw, unweighted)
-        ChiSquared        = 2  // ((prediction - measured)/sigma)^2 = the LSQ cost density
-    };
-    int display_mode = Prediction;
-};
-
-Q_DECLARE_METATYPE(PixelRefineParams)
-
-// One PixelRefine result, shipped from the worker to the reflection-table window:
-// a per-image summary that puts PixelRefine's scale/B/CC next to the standard
-// ScaleOnTheFly pipeline's, plus one row per matched reflection.
-struct PixelRefineReport {
-    // Per-image summary (NaN = not available).
-    double pr_G = NAN, pr_B = NAN, pr_cc = NAN;   // PixelRefine
-    int64_t pr_cc_n = 0;
-    double pipe_G = NAN, pipe_B = NAN, pipe_cc = NAN; // ScaleOnTheFly pipeline baseline
-
-    struct Row {
-        int h = 0, k = 0, l = 0;
-        double d = 0.0;
-        double completeness = 1.0;  // spot footprint on live pixels (1 = not clipped)
-        double partiality = 1.0;    // recorded rocking fraction
-        double I = 0.0, sigma = 0.0;
-        double I_true_est = NAN;     // r.I * image_scale_corr (this image's estimate)
-        double I_true_ref = NAN;     // reference (merged) intensity
-    };
-    std::vector<Row> rows;
-};
-
-Q_DECLARE_METATYPE(PixelRefineReport)
-- 
2.52.0


From bf6efc7fe9d72d8773e51083bef2ca6d935a2b13 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 13 Jun 2026 23:27:36 +0200
Subject: [PATCH 041/228] Integration radius: default r1=4, CLI flag,
 PixelRefine shares the knob

Bumped the default signal-box radius to r1=4 (r2=6, r3=8): on the lysozyme jet
(1% DMM) it lifts CCref 50.1->52.2% and CC1/2 90.8->92.5% (its broadened spots
spill past a radius-3 box), is neutral on the mono crystal and on the classical
integrator. Added 'jfjoch_process --integration-radius <r1|r1,r2,r3>' (a single
value derives r2=r1+2, r3=r1+4) and wired PixelRefine's shoebox radius to
BraggIntegrationSettings::GetR1() so it shares the classical integrator's knob.

(Explored but rejected: an elliptical/anisotropic Term-2 profile. The jet's
tangential spots are mildly anisotropic - axis ratio 1.15->1.44 low->high res,
azimuthal mosaic, separate from the radial DMM bandwidth - but using the measured
2x2 covariance as the profile DEGRADED the jet, CC1/2 92.5->83.5: the tight
measured width loses to a generous aperture, same lesson as the radius bump.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/BraggIntegrationSettings.h |  4 ++--
 image_analysis/IndexAndRefine.cpp |  3 +++
 tools/jfjoch_process.cpp          | 29 ++++++++++++++++++++++++++++-
 3 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/common/BraggIntegrationSettings.h b/common/BraggIntegrationSettings.h
index 60ab4059..dbe75ae6 100644
--- a/common/BraggIntegrationSettings.h
+++ b/common/BraggIntegrationSettings.h
@@ -6,8 +6,8 @@
 #include <optional>
 
 class BraggIntegrationSettings {
-    float r_1 = 3;
-    float r_2 = 5;
+    float r_1 = 4;
+    float r_2 = 6;
     float r_3 = 8;
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index f7cb25c1..479d5ac1 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -446,6 +446,9 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
+    // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
+    prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
+
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 5f7671fe..01ed1bf6 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -80,6 +80,7 @@ void print_usage() {
 
     std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
     std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
+    std::cout << "   --integration-radius <r>        Signal-box radius r1, or r1,r2,r3 (px). One value => r2=r1+2, r3=r1+4" << std::endl;
     }
 
 enum {
@@ -95,7 +96,8 @@ enum {
     OPT_SINGLE_PASS_ROTATION,
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
-    OPT_BANDWIDTH
+    OPT_BANDWIDTH,
+    OPT_INTEGRATION_RADIUS
 };
 
 static option long_options[] = {
@@ -132,6 +134,7 @@ static option long_options[] = {
     {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
     {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
+    {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -312,6 +315,7 @@ int main(int argc, char **argv) {
 
     float d_min_spot_finding = 1.5;
     std::optional<float> d_min_scale_merge;
+    std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
 
     if (argc == 1) {
         print_usage();
@@ -501,6 +505,9 @@ int main(int argc, char **argv) {
         case OPT_MIN_PARTIALITY:
             min_partiality = std::stod(optarg);
             break;
+        case OPT_INTEGRATION_RADIUS:
+            integration_radius_arg = optarg;
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -671,6 +678,26 @@ int main(int argc, char **argv) {
 
     experiment.ImportScalingSettings(scaling_settings);
 
+    // Integration radii: r1 (signal box), r2/r3 (background annulus). PixelRefine reads
+    // r1 as its shoebox radius; the classical integrator uses all three.
+    if (integration_radius_arg) {
+        std::vector<float> rr;
+        std::stringstream ss(*integration_radius_arg);
+        std::string tok;
+        while (std::getline(ss, tok, ',')) {
+            trim_in_place(tok);
+            if (!tok.empty()) rr.push_back(std::stof(tok));
+        }
+        float r1, r2, r3;
+        if (rr.size() == 1) { r1 = rr[0]; r2 = r1 + 2.0f; r3 = r1 + 4.0f; }
+        else if (rr.size() == 3) { r1 = rr[0]; r2 = rr[1]; r3 = rr[2]; }
+        else { logger.Error("--integration-radius expects r1 or r1,r2,r3"); return 1; }
+        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
+        bis.R1(r1).R2(r2).R3(r3);
+        experiment.ImportBraggIntegrationSettings(bis);
+        logger.Info("Integration radii set to r1={:.1f} r2={:.1f} r3={:.1f}", r1, r2, r3);
+    }
+
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;
-- 
2.52.0


From cfcd4c9e56491a38848e902eef1e545d7420cddd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 14 Jun 2026 09:18:09 +0200
Subject: [PATCH 042/228] PixelRefine: R1 multiplier (fix tight-Term2
 regression) + env-gated orientation refine

Full-jet R-free showed the factored model regressed vs the traditional pipeline
(R-free 0.34 vs 0.26, CCref 58 vs 76), traced to Term 2 using the raw measured
profile width: it is too tight (~0.002 A^-1), so the template sits off the ~0.4 px
centroid-floor scatter and underestimates the intensity (box-sum is immune). Fix,
XDS-style (integrate over ~6 sigma): multiply the measured R1 by r1_multiplier
(default 6) before use. On the jet at 1.3 A this recovers CCref 55.2 -> 59.3
(~ traditional's 60.5); crystal 2 -0.7. Tunable via env PR_RMULT for R-free.

Also reinstates the pre-factored per-image orientation refinement (per-pixel
ShoeboxResidual against the shoebox, regularised to the spot-centroid orientation,
re-predict), behind env PR_ORIENT (off by default), to A/B its effect on serial-data
R-free. On the jet CCref it is a no-op (XtalOptimizer orientation already at the
optimum), but CCref is a weak R-free proxy here, so it is left for R-free validation.

NOTE: PR_RMULT / PR_ORIENT are temporary diagnostic env knobs; the final multiplier
value and the orientation-refine decision are to be fixed against R-free, then baked.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |   2 +
 .../pixel_refinement/PixelRefine.cpp          | 265 ++++++++++++++----
 image_analysis/pixel_refinement/PixelRefine.h |  16 ++
 3 files changed, 225 insertions(+), 58 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 479d5ac1..34244a4a 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -448,6 +448,8 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
 
     // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
     prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
+    if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // TEMP: Term-2 R1 multiplier sweep
+    if (std::getenv("PR_ORIENT")) prd.refine_orientation = true; // A/B: per-image orientation refinement
 
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 75facde4..843d6360 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -24,6 +24,7 @@ struct PixelObs {
     double x, y;          // detector pixel coordinate
     double Iobs;          // raw pixel value (signal + background)
     double Ibkg;          // local background estimate (per-shoebox level, raw counts)
+    double weight;        // 1/sigma_pixel (used only by the optional orientation refinement)
 };
 
 // One reflection together with the pixels of its shoebox.
@@ -336,6 +337,69 @@ struct IntensityResidual {
     double J, inv_sigma, partiality, pol, I_ref, inv_4d2;
 };
 
+// Per-shoebox per-pixel forward-model cost (raw counts), used ONLY by the optional
+// orientation refinement: I_pred = G*Itrue*B_term*P_radial*P_tang*pol + Ibkg. The
+// expensive node geometry is computed once per reflection; the cheap ObservedRecip +
+// Gaussian profile run per pixel. Shares ObservedRecip/PredictedNode with GeometryProbe.
+struct ShoeboxResidual {
+    ShoeboxResidual(const ReflGroup &g, double lambda, double pixel_size,
+                    gemmi::CrystalSystem symmetry)
+        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq), pol(g.pol),
+          exp_h(g.h), exp_k(g.k), exp_l(g.l),
+          inv_lambda(1.0 / lambda), pixel_size(pixel_size), symmetry(symmetry) {}
+    template<typename T>
+    bool operator()(const T *const *params, T *residual) const {
+        // 0 beam 1 dist 2 detector_rot 3 p0 4 p1 5 p2 6 scale 7 B 8 R
+        const T *beam = params[0]; const T *distance_mm = params[1]; const T *detector_rot = params[2];
+        const T *p0 = params[3]; const T *p1 = params[4]; const T *p2 = params[5];
+        const T *scale_factor = params[6]; const T *B = params[7]; const T *R = params[8];
+        if (R[0] < T(1e-10) || R[1] < T(1e-10))
+            return false;
+        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
+        T q_sq;
+        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
+                           e_pred_recip, n_radial, q_sq))
+            return false;
+        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
+        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
+        for (size_t i = 0; i < pixels.size(); ++i) {
+            const PixelObs &obs = pixels[i];
+            Eigen::Matrix<T, 3, 1> e_obs_recip;
+            ObservedRecip(beam, distance_mm, detector_rot, obs.x, obs.y, pixel_size, inv_lambda, e_obs_recip);
+            const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
+            const T eps_radial = delta_q.dot(n_radial);
+            const T eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
+            const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
+            const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1])) / (T(M_PI) * R[1] * R[1]);
+            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
+            residual[i] = (signal + T(obs.Ibkg) - T(obs.Iobs)) * T(obs.weight);
+        }
+        return true;
+    }
+    std::vector<PixelObs> pixels;
+    const double Itrue, R_bw_sq, pol;
+    const double exp_h, exp_k, exp_l;
+    const double inv_lambda, pixel_size;
+    gemmi::CrystalSystem symmetry;
+};
+
+// Anchors the orientation (angle-axis vector) to its prior with a data-scaled weight, so
+// the per-image fit can only make a small, signal-supported sub-spot correction.
+struct OrientationRegularizer {
+    OrientationRegularizer(double weight, const double prior[3]) : weight(weight) {
+        for (int i = 0; i < 3; ++i)
+            prior_[i] = prior[i];
+    }
+    template<typename T>
+    bool operator()(const T *p0, T *residual) const {
+        for (int i = 0; i < 3; ++i)
+            residual[i] = T(weight) * (p0[i] - T(prior_[i]));
+        return true;
+    }
+    double weight;
+    double prior_[3];
+};
+
 } // namespace
 
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
@@ -443,69 +507,154 @@ void PixelRefine::Run(const T *image,
     double latt_vec0[3], latt_vec1[3], latt_vec2[3];
     BuildParameterBlocks(data, beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2);
 
-    // ---- 1. Predict shoeboxes for the current geometry ------------------------
-    DiffractionExperiment exp_iter = experiment;
-    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
-            .BeamY_pxl(data.geom.GetBeamY_pxl())
-            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
-
-    // ---- 2. Collect per-reflection shoebox pixels + local background ----------
-    // GetReflections() returns the full pre-sized buffer; only the first nrefl
-    // entries are valid for this image. A spot-core mask over ALL predictions keeps
-    // each reflection's background ring from picking up a neighbour's signal.
-    const auto &predicted = prediction.GetReflections();
-    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
-
+    // ---- 1-2. Predict shoeboxes + collect pixels (a lambda so it can be re-run after
+    //           an orientation refinement moves the predicted positions). ----------
+    // A spot-core mask over ALL predictions keeps each reflection's background ring from
+    // picking up a neighbour's signal. Pixels carry a fit weight (background-limited
+    // variance, signal-weighted toward the predicted centre) used only by the optional
+    // orientation refinement - the factored integration weights by v = Ibkg directly.
     std::vector<ReflGroup> groups;
-    for (int ri = 0; ri < nrefl; ++ri) {
-        const auto &refl = predicted[ri];
-        const auto hkl = hkl_key_generator(refl);
-        if (!reference_data.contains(hkl))
-            continue;
-
-        // Local flat background from the ring around the shoebox (raw counts). If we
-        // cannot estimate a clean local background the reflection is dropped, exactly
-        // as BraggIntegrate2D marks it unobserved when too few background pixels survive.
-        double Ibkg = 0.0;
-        if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
-                                     refl.predicted_x, refl.predicted_y,
-                                     radius, bkg_outer_radius, Ibkg))
-            continue;
-
-        ReflGroup g;
-        g.h = refl.h;
-        g.k = refl.k;
-        g.l = refl.l;
-        g.d = refl.d;
-        g.Itrue = reference_data[hkl];
-        g.R_bw_sq = bandwidth_radial_sq(refl.d);
-        g.pol = polarization(refl.predicted_x, refl.predicted_y);
-        g.Ibkg = Ibkg;
-        g.predicted_x = refl.predicted_x;
-        g.predicted_y = refl.predicted_y;
-
-        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
-        for (int y = box.min_y; y <= box.max_y; ++y) {
-            for (int x = box.min_x; x <= box.max_x; ++x) {
-                const size_t npixel = xpixel * y + x;
-                // Skip sentinel (masked / saturated) pixels.
-                if (image[npixel] == std::numeric_limits<T>::max())
-                    continue;
-                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
-                    continue;
-                g.pixels.push_back({static_cast<double>(x), static_cast<double>(y),
-                                    static_cast<double>(image[npixel]), Ibkg});
+    auto build_groups = [&]() {
+        groups.clear();
+        DiffractionExperiment exp_iter = experiment;
+        exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+                .BeamY_pxl(data.geom.GetBeamY_pxl())
+                .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+                .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+                .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+        const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+        const auto &predicted = prediction.GetReflections();
+        const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
+        for (int ri = 0; ri < nrefl; ++ri) {
+            const auto &refl = predicted[ri];
+            const auto hkl = hkl_key_generator(refl);
+            if (!reference_data.contains(hkl))
+                continue;
+            double Ibkg = 0.0;
+            if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                         refl.predicted_x, refl.predicted_y,
+                                         radius, bkg_outer_radius, Ibkg))
+                continue;
+            ReflGroup g;
+            g.h = refl.h;
+            g.k = refl.k;
+            g.l = refl.l;
+            g.d = refl.d;
+            g.Itrue = reference_data[hkl];
+            g.R_bw_sq = bandwidth_radial_sq(refl.d);
+            g.pol = polarization(refl.predicted_x, refl.predicted_y);
+            g.Ibkg = Ibkg;
+            g.predicted_x = refl.predicted_x;
+            g.predicted_y = refl.predicted_y;
+            const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
+            for (int y = box.min_y; y <= box.max_y; ++y) {
+                for (int x = box.min_x; x <= box.max_x; ++x) {
+                    const size_t npixel = xpixel * y + x;
+                    if (image[npixel] == std::numeric_limits<T>::max())
+                        continue;
+                    if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
+                        continue;
+                    double weight = 1.0 / std::sqrt(std::max(Ibkg, 1.0));
+                    if (data.fit_signal_sigma_pix > 0.0) {
+                        const double dx = x - refl.predicted_x, dy = y - refl.predicted_y;
+                        const double s2 = data.fit_signal_sigma_pix * data.fit_signal_sigma_pix;
+                        weight *= std::exp(-0.5 * (dx * dx + dy * dy) / s2);
+                    }
+                    g.pixels.push_back({static_cast<double>(x), static_cast<double>(y),
+                                        static_cast<double>(image[npixel]), Ibkg, weight});
+                }
             }
+            if (!g.pixels.empty())
+                groups.push_back(std::move(g));
         }
-        if (!g.pixels.empty())
-            groups.push_back(std::move(g));
-    }
+    };
+    build_groups();
     if (groups.empty())
         return;
 
+    // ---- Optional per-image orientation refinement (off by default) -----------------
+    // The pre-factored per-pixel step: refine the orientation (and a nuisance scale)
+    // against the shoebox pixels via ShoeboxResidual, regularised to the spot-centroid
+    // orientation, then re-predict. Dropped from the factored model (geometry fixed to
+    // XtalOptimizer); behind PixelRefineData::refine_orientation to A/B its R-free effect.
+    if (data.refine_orientation) {
+        const double orient_prior[3] = {latt_vec0[0], latt_vec0[1], latt_vec0[2]};
+        ceres::Problem oprob;
+        size_t npix = 0;
+        for (const auto &g : groups) {
+            auto *cost = new ceres::DynamicAutoDiffCostFunction<ShoeboxResidual>(
+                new ShoeboxResidual(g, lambda, pixel_size, data.crystal_system));
+            for (int b : {2, 1, 2, 3, 3, 3, 1, 1, 2})
+                cost->AddParameterBlock(b);
+            cost->SetNumResiduals(static_cast<int>(g.pixels.size()));
+            oprob.AddResidualBlock(cost, nullptr, beam, &dist_mm, detector_rot,
+                                   latt_vec0, latt_vec1, latt_vec2,
+                                   &data.scale_factor, &data.B_factor, data.R);
+            npix += g.pixels.size();
+        }
+        // Refine only orientation (latt_vec0) + the nuisance scale G; everything else fixed.
+        oprob.SetParameterBlockConstant(beam);
+        oprob.SetParameterBlockConstant(&dist_mm);
+        oprob.SetParameterBlockConstant(detector_rot);
+        oprob.SetParameterBlockConstant(latt_vec1);
+        oprob.SetParameterBlockConstant(latt_vec2);
+        oprob.SetParameterBlockConstant(&data.B_factor);
+        oprob.SetParameterBlockConstant(data.R);
+        oprob.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
+        if (data.orient_reg_sigma_deg > 0.0 && npix > 0) {
+            const double sigma_rad = std::max(data.orient_reg_sigma_deg * M_PI / 180.0, 1e-9);
+            const double w = std::sqrt(static_cast<double>(npix)) / sigma_rad;
+            oprob.AddResidualBlock(new ceres::AutoDiffCostFunction<OrientationRegularizer, 3, 3>(
+                new OrientationRegularizer(w, orient_prior)), nullptr, latt_vec0);
+        }
+        if (data.scale_reg_sigma > 0.0) {
+            const double w = std::sqrt(static_cast<double>(groups.size()) / data.scale_reg_sigma);
+            oprob.AddResidualBlock(new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
+                new ScalarRegularizer(w, 1.0)), nullptr, &data.scale_factor);
+        }
+        ceres::Solver::Options oopt;
+        oopt.linear_solver_type = ceres::DENSE_QR;
+        oopt.logging_type = ceres::LoggingType::SILENT;
+        oopt.minimizer_progress_to_stdout = false;
+        oopt.max_solver_time_in_seconds = data.max_time_s;
+        oopt.num_threads = 1;
+        ceres::Solver::Summary osum;
+        ceres::Solve(oopt, &oprob, &osum);
+
+        // Write the refined orientation back into data.latt (cell held at latt_vec1/2),
+        // then re-predict + rebuild groups at the new orientation. Scale is reset; Term 1
+        // re-fits it properly below.
+        switch (data.crystal_system) {
+            case gemmi::CrystalSystem::Tetragonal:
+                latt_vec1[1] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Cubic:
+                latt_vec1[1] = latt_vec1[0];
+                latt_vec1[2] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Hexagonal:
+                latt_vec1[1] = latt_vec1[0];
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
+                break;
+            case gemmi::CrystalSystem::Monoclinic:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
+                break;
+            case gemmi::CrystalSystem::Orthorhombic:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
+                break;
+            default:
+                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
+                                                      latt_vec2[0], latt_vec2[1], latt_vec2[2]);
+                break;
+        }
+        data.scale_factor = 1.0;
+        build_groups();
+        if (groups.empty())
+            return;
+    }
+
     // ---- 3. Term 2: per-resolution tangential profile width R1 ----------------
     // R1 = sqrt(2*<eps_t^2>) from the intensity-weighted tangential second moment of
     // the strong spots, binned by resolution (low res small spots, high res larger).
@@ -549,7 +698,7 @@ void PixelRefine::Run(const T *image,
         std::vector<double> bin_R1(n_bins, data.R[1]);
         for (int b = 0; b < n_bins; ++b)
             if (bin_M2[b].size() >= 5) {
-                const double r1 = std::sqrt(2.0 * std::max(MedianInPlace(bin_M2[b]), 0.0));
+                const double r1 = data.r1_multiplier * std::sqrt(2.0 * std::max(MedianInPlace(bin_M2[b]), 0.0));
                 if (std::isfinite(r1) && r1 > 1e-4)
                     bin_R1[b] = std::clamp(r1, 1e-4, 0.05);
             }
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index dfc560c5..1e7a2dac 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -67,6 +67,22 @@ struct PixelRefineData {
                                   // tangential profile width before Term 2 measures it (A^-1)
     bool   refine_B = true;       // refine the per-image B-factor along with G
 
+    // Term 2 measures the physical tangential width R1, but the *integration* profile must
+    // be generous (XDS-style: integrate over ~6-10 sigma), or a tight template centred on
+    // the prediction sits off the ~0.4 px centroid-floor scatter and underestimates the
+    // intensity. The measured R1 is multiplied by this before use. 1.0 = the raw physical
+    // width (too tight - regressed R-free on the serial jet); ~6 recovers it (closes the
+    // CCref gap to box-sum). Tune the final value against R-free.
+    double r1_multiplier = 6.0;
+
+    // Optional per-image orientation refinement (env-gated, off by default): the
+    // pre-factored per-pixel step that refines the crystal orientation against the
+    // shoebox pixels, regularised to the spot-centroid orientation, before integration.
+    // Reinstated to A/B its effect on serial-data R-free vs the fixed-geometry default.
+    bool   refine_orientation = false;
+    double orient_reg_sigma_deg = 1.0;  // orientation-prior strength (deg)
+    double fit_signal_sigma_pix = 1.5;  // signal-weighting sigma for the orientation fit (px)
+
     // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1% FWHM
     // DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening to R[0].
     // 0 = monochromatic (the term switches off entirely).
-- 
2.52.0


From 45ee8c2b40204ceaa4126f004e5024830b17e01b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 14 Jun 2026 19:59:50 +0200
Subject: [PATCH 043/228] PixelRefine: env-gated orientation + cell-scale sweep
 (PR_SWEEP) for R-free A/B

R-free validation (full jet, 1.5 A) confirmed the r1_multiplier fix: PR x6 beats
traditional (R-free 0.2625 vs 0.2802), the multiplier optimum is ~6 (x6==x9 on
R-free; x9 only buys CC1/2 internal consistency), and per-image orientation
*refinement* is a no-op (0.2618 vs 0.2625).

Re-adds the reference-driven orientation + uniform cell-scale SWEEP behind PR_SWEEP
(off by default) to test whether the cell-scale degree of freedom - which the
gradient orientation refinement lacks, and which moves the high-res shells radially
- helps R-free at 1.5 A on serial data. CCref is a near-no-op on the jet (as for
the gradient path), but that does not certify R-free, so it is left for validation.

NOTE: PR_RMULT / PR_ORIENT / PR_SWEEP remain temporary diagnostic env knobs; once
the sweep R-free is in, bake r1_multiplier=6, drop the no-op paths, strip the knobs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |   1 +
 .../pixel_refinement/PixelRefine.cpp          | 142 ++++++++++++++++++
 image_analysis/pixel_refinement/PixelRefine.h |  12 ++
 3 files changed, 155 insertions(+)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 34244a4a..a37a6962 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -450,6 +450,7 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
     if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // TEMP: Term-2 R1 multiplier sweep
     if (std::getenv("PR_ORIENT")) prd.refine_orientation = true; // A/B: per-image orientation refinement
+    if (std::getenv("PR_SWEEP")) prd.sweep_orientation = true; // A/B: orientation + cell-scale sweep
 
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 843d6360..b2f2161f 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -457,6 +457,144 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     }
 }
 
+// Optional pre-pass (env-gated): a small GLOBAL orientation + uniform cell-scale sweep that
+// maximises CC of the box-summed intensities against the reference. Unlike the per-pixel
+// orientation refinement it also adjusts a per-image cell scale (a radial degree of freedom),
+// and makes coarse global moves the local gradient cannot. Coordinate descent over the three
+// Rodrigues axes + cell scale within geometry-derived pixel bounds (highest-resolution spot
+// moves ~1 px/step, lowest barely moves). Writes the best orientation/cell into data.latt.
+template<class T>
+void PixelRefine::SweepOrientationCell(const T *image, BraggPrediction &prediction,
+                                       PixelRefineData &data) const {
+    const int radius = data.shoebox_radius;
+    const double beam_x = data.geom.GetBeamX_pxl();
+    const double beam_y = data.geom.GetBeamY_pxl();
+    const auto qnan = std::numeric_limits<double>::quiet_NaN();
+
+    // Box-sum minus local (perimeter) background MEAN, raw counts; NaN off-detector/masked.
+    auto integrate = [&](double px, double py) -> double {
+        const int cx = static_cast<int>(std::lround(px));
+        const int cy = static_cast<int>(std::lround(py));
+        const int outer = radius + 1;
+        if (cx - outer < 0 || cy - outer < 0 ||
+            cx + outer >= static_cast<int>(xpixel) || cy + outer >= static_cast<int>(ypixel))
+            return qnan;
+        double sig = 0.0;
+        int nsig = 0;
+        std::vector<double> ring;
+        ring.reserve((2 * outer + 1) * (2 * outer + 1));
+        for (int y = cy - outer; y <= cy + outer; ++y) {
+            for (int x = cx - outer; x <= cx + outer; ++x) {
+                const T raw = image[static_cast<size_t>(xpixel) * y + x];
+                if (raw == std::numeric_limits<T>::max())
+                    return qnan;
+                if (std::is_signed_v<T> && raw == std::numeric_limits<T>::min())
+                    return qnan;
+                const double v = static_cast<double>(raw);
+                if (std::abs(x - cx) <= radius && std::abs(y - cy) <= radius) {
+                    sig += v; ++nsig;
+                } else {
+                    ring.push_back(v);
+                }
+            }
+        }
+        if (ring.size() < 5)
+            return qnan;
+        double rsum = 0.0;
+        for (const double v : ring)
+            rsum += v;
+        return sig - nsig * (rsum / static_cast<double>(ring.size()));
+    };
+
+    DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(beam_x).BeamY_pxl(beam_y)
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+    const BraggPredictionSettings settings{
+        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
+        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
+        .max_hkl = 100,
+        .centering = data.centering,
+        .bandwidth_sigma = static_cast<float>(data.bandwidth)
+    };
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings);
+    const auto &predicted = prediction.GetReflections();
+
+    struct Matched { int h, k, l; double refI; };
+    std::vector<Matched> matched;
+    double r_max = 0.0, r_min = std::numeric_limits<double>::max();
+    for (int i = 0; i < nrefl; ++i) {
+        const auto &r = predicted[i];
+        const auto it = reference_data.find(hkl_key_generator(r));
+        if (it == reference_data.end())
+            continue;
+        matched.push_back({r.h, r.k, r.l, it->second});
+        const double dx = r.predicted_x - beam_x, dy = r.predicted_y - beam_y;
+        const double rad = std::sqrt(dx * dx + dy * dy);
+        r_max = std::max(r_max, rad);
+        r_min = std::min(r_min, rad);
+    }
+    if (matched.size() < 20 || r_min <= 1.0 || r_max <= r_min)
+        return; // too little to anchor a meaningful sweep
+
+    auto score = [&](const CrystalLattice &L) -> double {
+        const Coord A = L.Astar(), B = L.Bstar(), C = L.Cstar();
+        double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
+        int n = 0;
+        for (const auto &m : matched) {
+            const Coord g = A * static_cast<float>(m.h) + B * static_cast<float>(m.k)
+                            + C * static_cast<float>(m.l);
+            const auto [x, y] = data.geom.RecipToDetector(g);
+            if (!std::isfinite(x) || !std::isfinite(y))
+                continue;
+            const double I = integrate(x, y);
+            if (!std::isfinite(I))
+                continue;
+            sx += I; sy += m.refI; sxx += I * I; syy += m.refI * m.refI; sxy += I * m.refI; ++n;
+        }
+        if (n < 10)
+            return -2.0;
+        const double nd = n;
+        const double cov = sxy - sx * sy / nd, vx = sxx - sx * sx / nd, vy = syy - sy * sy / nd;
+        return (vx > 0.0 && vy > 0.0) ? cov / std::sqrt(vx * vy) : -2.0;
+    };
+
+    const double step = 1.0 / r_max;
+    const int n_rot = std::clamp(
+        static_cast<int>(std::lround(data.sweep_max_deg * M_PI / 180.0 * r_max)), 1, 25);
+    const int n_scale = std::clamp(
+        static_cast<int>(std::lround(data.sweep_max_cell_frac * r_max)), 1, 25);
+    const Coord axes[3] = {Coord(1, 0, 0), Coord(0, 1, 0), Coord(0, 0, 1)};
+
+    CrystalLattice best = data.latt;
+    double best_cc = score(best);
+    for (int round = 0; round < 2; ++round) {
+        for (const auto &axis : axes) {
+            CrystalLattice axis_best = best;
+            double axis_cc = best_cc;
+            for (int i = -n_rot; i <= n_rot; ++i) {
+                if (i == 0) continue;
+                CrystalLattice cand = best.Multiply(RotMatrix(static_cast<float>(i * step), axis));
+                const double cc = score(cand);
+                if (cc > axis_cc) { axis_cc = cc; axis_best = cand; }
+            }
+            best = axis_best; best_cc = axis_cc;
+        }
+        CrystalLattice scale_best = best;
+        double scale_cc = best_cc;
+        for (int i = -n_scale; i <= n_scale; ++i) {
+            if (i == 0) continue;
+            const double s = 1.0 / (1.0 + i * step);
+            CrystalLattice cand = best.Multiply(gemmi::Mat33(s, 0, 0, 0, s, 0, 0, 0, s));
+            const double cc = score(cand);
+            if (cc > scale_cc) { scale_cc = cc; scale_best = cand; }
+        }
+        best = scale_best; best_cc = scale_cc;
+    }
+    data.latt = best;
+}
+
 template<class T>
 void PixelRefine::Run(const T *image,
                       BraggPrediction &prediction,
@@ -464,6 +602,10 @@ void PixelRefine::Run(const T *image,
     data.solved = false;
     data.reflections.clear();
 
+    // Optional reference-driven orientation + cell-scale sweep before prediction (env-gated).
+    if (data.sweep_orientation)
+        SweepOrientationCell(image, prediction, data);
+
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
 
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 1e7a2dac..40dba239 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -83,6 +83,13 @@ struct PixelRefineData {
     double orient_reg_sigma_deg = 1.0;  // orientation-prior strength (deg)
     double fit_signal_sigma_pix = 1.5;  // signal-weighting sigma for the orientation fit (px)
 
+    // Optional reference-driven orientation + per-image cell-scale sweep before prediction
+    // (env-gated, off by default). Coarse global moves the gradient refinement cannot make,
+    // plus a radial (cell-scale) DOF the gradient path lacks. See SweepOrientationCell.
+    bool   sweep_orientation = false;
+    double sweep_max_deg = 0.15;
+    double sweep_max_cell_frac = 0.003;
+
     // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1% FWHM
     // DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening to R[0].
     // 0 = monochromatic (the term switches off entirely).
@@ -129,6 +136,11 @@ class PixelRefine {
                               double beam[2], double &dist_mm,
                               double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
+
+    // Reference-driven global orientation + cell-scale sweep (see PixelRefineData::sweep_*).
+    template<class T>
+    void SweepOrientationCell(const T *image, BraggPrediction &prediction,
+                              PixelRefineData &data) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const std::vector<MergedReflection> &reference);
-- 
2.52.0


From a47b376dc39f77d0ca4581e0a47fc7197b872952 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 14 Jun 2026 20:56:53 +0200
Subject: [PATCH 044/228] Merge: per-observation outlier rejection (env-gated
 PR_REJECT)

At the jet's ~1000x multiplicity R-free is bias-limited, and the merge had NO
outlier rejection - serial data zingers/overlaps/mis-indexed frames bias every
merged mean. Add a robust per-observation cut: drop observations whose corrected
intensity lies > reject_nsigma error-model sigmas from the reflection's MEDIAN.
The error-model sigma already captures the genuine (partiality) scatter, and the
median is a robust centre, so only the tail beyond the real spread is removed -
not good partials. The median is computed in RefineErrorModel (which already pools
the observations per reflection); AddImage applies the cut.

Env-gated via PR_REJECT=<nsigma> (off by default); logs the count removed. On the
jet (CC proxy) it lifts CCref +8 (nsigma 6, 0.6% cut) to +11 (nsigma 3, 7.4% cut)
- the cut is vs the data's own median, not the reference, so the gain is real
cleaner means. R-free validation + the nsigma sweet spot (over-rejection risk at
low nsigma) are for Filip's full-jet R-free.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/scale_merge/Merge.cpp | 25 +++++++++++++++++++++++++
 image_analysis/scale_merge/Merge.h   | 14 ++++++++++++++
 tools/jfjoch_process.cpp             |  7 +++++++
 3 files changed, 46 insertions(+)

diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index cfb829e9..08f875ba 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -65,6 +65,19 @@ void MergeOnTheFly::AddImage(const IntegrationOutcome &outcome, bool cc_mask) {
         auto hkl_key = hkl.pack();
         sigma_corr = CorrectedSigma(I_corr, sigma_corr, hkl_key);
 
+        // Robust outlier rejection: drop this observation if it sits more than
+        // reject_nsigma error-model sigmas from the reflection's median. Needs the active
+        // error model so sigma_corr reflects the real scatter (else the threshold is the
+        // bare counting sigma and would cull good partials).
+        if (reject_outliers && error_model_active) {
+            const auto mit = reject_median_I.find(hkl_key);
+            if (mit != reject_median_I.end() &&
+                std::fabs(I_corr - mit->second) > reject_nsigma * sigma_corr) {
+                ++reject_count;
+                continue;
+            }
+        }
+
         auto it = accumulator.find(hkl_key);
         if (it == accumulator.end())
             it = accumulator.emplace(hkl_key, MergeAccum{
@@ -110,6 +123,8 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
     error_model_a = 1.0;
     error_model_b = 0.0;
     error_model_mean_I.clear();
+    reject_median_I.clear();
+    reject_count = 0;
 
     // --- 1. Collect accepted, scaled observations grouped by symmetry-equivalent hkl,
     //        applying exactly the filters AddImage uses. ---
@@ -156,6 +171,16 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
             continue;
         const double mean = sum_wI / sum_w;
         error_model_mean_I[key] = static_cast<float>(mean);
+        // Robust centre for outlier rejection: the median intensity (resists the very
+        // outliers the inverse-variance mean is being protected from).
+        {
+            std::vector<float> iv;
+            iv.reserve(obs.size());
+            for (const auto &o: obs)
+                iv.push_back(o.I);
+            std::nth_element(iv.begin(), iv.begin() + iv.size() / 2, iv.end());
+            reject_median_I[key] = iv[iv.size() / 2];
+        }
         const double I2 = mean * mean;
         for (const auto &o: obs) {
             const double w = 1.0 / (static_cast<double>(o.sigma) * o.sigma);
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index d69ee817..a1ea2776 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -87,6 +87,16 @@ class MergeOnTheFly {
     std::unordered_map<uint64_t, float> error_model_mean_I;
     [[nodiscard]] float CorrectedSigma(float I_corr, float sigma_corr, uint64_t hkl_key) const;
 
+    // Optional per-observation outlier rejection: drop observations whose corrected
+    // intensity lies more than reject_nsigma error-model sigmas from the reflection's
+    // *median* (a robust centre). The error-model sigma already captures the genuine
+    // (e.g. partiality) scatter, so this removes only the tail beyond it - zingers,
+    // overlaps, mis-indexed frames - not good partials. Populated by RefineErrorModel.
+    bool   reject_outliers = false;
+    double reject_nsigma = 6.0;
+    std::unordered_map<uint64_t, float> reject_median_I;
+    size_t reject_count = 0;
+
     bool Mask(const IntegrationOutcome &outcome, bool cc_mask);
 public:
     MergeOnTheFly(const DiffractionExperiment &x);
@@ -99,6 +109,10 @@ public:
     [[nodiscard]] double ErrorModelA() const { return error_model_a; }
     [[nodiscard]] double ErrorModelB() const { return error_model_b; }
 
+    // Enable per-observation outlier rejection (call after RefineErrorModel, before AddImage).
+    void SetRejectOutliers(double nsigma) { reject_outliers = true; reject_nsigma = nsigma; }
+    [[nodiscard]] size_t RejectedCount() const { return reject_count; }
+
     void AddImage(const IntegrationOutcome& outcome, bool cc_mask = false);
 
     MergeStatistics MergeStats(const std::vector<MergedReflection> &merged,
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 01ed1bf6..ef847d86 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -1034,8 +1034,15 @@ int main(int argc, char **argv) {
             const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
             logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
         }
+        if (const char *rj = std::getenv("PR_REJECT")) { // TEMP A/B: per-observation outlier rejection
+            const double nsig = std::atof(rj);
+            merge_engine.SetRejectOutliers(nsig);
+            logger.Info("Outlier rejection enabled: dropping observations > {:.1f} sigma from the per-reflection median", nsig);
+        }
         for (auto &i : indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
+        if (merge_engine.RejectedCount() > 0)
+            logger.Info("Outlier rejection removed {} observations", merge_engine.RejectedCount());
 
         auto merged_reflections = merge_engine.ExportReflections();
         auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);
-- 
2.52.0


From 6f733d74c2555d6243ebb6767b989282e379b3ce Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 12:42:25 +0200
Subject: [PATCH 045/228] Merge: make outlier rejection a ScalingSettings
 parameter + CLI flag, default 6

Promote the per-observation merge outlier rejection from the temporary PR_REJECT
env knob to a real setting: ScalingSettings::OutlierRejectNsigma (default 6, <=0
disables), driven into MergeOnTheFly via the constructor, with a --reject-outliers
CLI flag in jfjoch_process. Default-on at 6 sigma matches XDS (MISFITS/REJECT) and
DIALS (normalised-deviation test); it validated on the full-jet R-free (0.2625 ->
0.2585). Applies to both the PixelRefine and classical merge paths.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/ScalingSettings.cpp           |  9 +++++++++
 common/ScalingSettings.h             |  3 +++
 image_analysis/scale_merge/Merge.cpp |  8 +++++---
 image_analysis/scale_merge/Merge.h   |  3 +--
 tools/jfjoch_process.cpp             | 19 ++++++++++++-------
 5 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/common/ScalingSettings.cpp b/common/ScalingSettings.cpp
index a91aa1ff..866d48a4 100644
--- a/common/ScalingSettings.cpp
+++ b/common/ScalingSettings.cpp
@@ -115,6 +115,15 @@ ScalingSettings &ScalingSettings::MinCCForImage(double input) {
     return *this;
 }
 
+double ScalingSettings::GetOutlierRejectNsigma() const {
+    return outlier_reject_nsigma;
+}
+
+ScalingSettings &ScalingSettings::OutlierRejectNsigma(double input) {
+    outlier_reject_nsigma = input; // <= 0 disables; no upper bound (large = effectively off)
+    return *this;
+}
+
 double ScalingSettings::GetMinPartiality() const {
     return min_partiality;
 }
diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index f7c724f8..6d548cfc 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -23,6 +23,7 @@ class ScalingSettings {
     std::optional<double> wedge_for_scaling;
     double min_partiality = 0.02;
     double min_cc_for_image = 0.0;
+    double outlier_reject_nsigma = 6.0; // per-observation merge outlier rejection (XDS/DIALS-style); <= 0 disables
 
     double rfree_fraction = 0.05;
     IntensityFormat intensity_format = IntensityFormat::MTZ;
@@ -37,6 +38,7 @@ public:
     ScalingSettings& HighResolutionLimit_A(double limit);
     ScalingSettings& MinPartiality(double min_partiality);
     ScalingSettings& MinCCForImage(double min_cc_for_image);
+    ScalingSettings& OutlierRejectNsigma(double input);
 
     ScalingSettings& RfreeFraction(double input);
     ScalingSettings& FileFormat(IntensityFormat input);
@@ -63,6 +65,7 @@ public:
 
     [[nodiscard]] double GetMinPartiality() const;
     [[nodiscard]] double GetMinCCForImage() const;
+    [[nodiscard]] double GetOutlierRejectNsigma() const;
 
     [[nodiscard]] double GetRfreeFraction() const;
     [[nodiscard]] IntensityFormat GetFileFormat() const;
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 08f875ba..d604e092 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -31,7 +31,9 @@ MergeOnTheFly::MergeOnTheFly(const DiffractionExperiment &x)
                          ? std::optional<double>(scaling_settings.GetMinCCForImage())
                          : std::nullopt),
       min_partiality(scaling_settings.GetMinPartiality()),
-      generator(scaling_settings.GetMergeFriedel(), space_group_number) {
+      generator(scaling_settings.GetMergeFriedel(), space_group_number),
+      reject_outliers(scaling_settings.GetOutlierRejectNsigma() > 0.0),
+      reject_nsigma(scaling_settings.GetOutlierRejectNsigma()) {
 }
 
 MergeOnTheFly &MergeOnTheFly::ReferenceCell(const std::optional<UnitCell> &cell) {
@@ -172,8 +174,8 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
         const double mean = sum_wI / sum_w;
         error_model_mean_I[key] = static_cast<float>(mean);
         // Robust centre for outlier rejection: the median intensity (resists the very
-        // outliers the inverse-variance mean is being protected from).
-        {
+        // outliers the inverse-variance mean is being protected from). Only when active.
+        if (reject_outliers) {
             std::vector<float> iv;
             iv.reserve(obs.size());
             for (const auto &o: obs)
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index a1ea2776..ab9877f4 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -109,8 +109,7 @@ public:
     [[nodiscard]] double ErrorModelA() const { return error_model_a; }
     [[nodiscard]] double ErrorModelB() const { return error_model_b; }
 
-    // Enable per-observation outlier rejection (call after RefineErrorModel, before AddImage).
-    void SetRejectOutliers(double nsigma) { reject_outliers = true; reject_nsigma = nsigma; }
+    // Outlier rejection (driven by ScalingSettings::GetOutlierRejectNsigma) reports its count.
     [[nodiscard]] size_t RejectedCount() const { return reject_count; }
 
     void AddImage(const IntegrationOutcome& outcome, bool cc_mask = false);
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index ef847d86..93ade850 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -72,6 +72,7 @@ void print_usage() {
     std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
     std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
+    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: 6; 0 disables)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
@@ -97,7 +98,8 @@ enum {
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
     OPT_BANDWIDTH,
-    OPT_INTEGRATION_RADIUS
+    OPT_INTEGRATION_RADIUS,
+    OPT_REJECT_OUTLIERS
 };
 
 static option long_options[] = {
@@ -135,6 +137,7 @@ static option long_options[] = {
     {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
+    {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -316,6 +319,7 @@ int main(int argc, char **argv) {
     float d_min_spot_finding = 1.5;
     std::optional<float> d_min_scale_merge;
     std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
+    std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
 
     if (argc == 1) {
         print_usage();
@@ -508,6 +512,9 @@ int main(int argc, char **argv) {
         case OPT_INTEGRATION_RADIUS:
             integration_radius_arg = optarg;
             break;
+        case OPT_REJECT_OUTLIERS:
+            outlier_reject_nsigma = std::stod(optarg);
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -674,6 +681,8 @@ int main(int argc, char **argv) {
         scaling_settings.RotationWedgeForScaling(wedge_for_scaling);
     scaling_settings.MinPartiality(min_partiality);
     scaling_settings.MinCCForImage(min_image_cc);
+    if (outlier_reject_nsigma)
+        scaling_settings.OutlierRejectNsigma(*outlier_reject_nsigma);
     scaling_settings.FileFormat(intensity_format);
 
     experiment.ImportScalingSettings(scaling_settings);
@@ -1034,15 +1043,11 @@ int main(int argc, char **argv) {
             const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
             logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
         }
-        if (const char *rj = std::getenv("PR_REJECT")) { // TEMP A/B: per-observation outlier rejection
-            const double nsig = std::atof(rj);
-            merge_engine.SetRejectOutliers(nsig);
-            logger.Info("Outlier rejection enabled: dropping observations > {:.1f} sigma from the per-reflection median", nsig);
-        }
         for (auto &i : indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
         if (merge_engine.RejectedCount() > 0)
-            logger.Info("Outlier rejection removed {} observations", merge_engine.RejectedCount());
+            logger.Info("Outlier rejection (>{:.1f} sigma from the per-reflection median) removed {} observations",
+                        experiment.GetScalingSettings().GetOutlierRejectNsigma(), merge_engine.RejectedCount());
 
         auto merged_reflections = merge_engine.ExportReflections();
         auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);
-- 
2.52.0


From 102a2a7c814c8a54a14c95d888e3ed4220ef7095 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 13:34:54 +0200
Subject: [PATCH 046/228] PixelRefine: strip experimental env knobs
 (orientation, sweep, Lorentz, ML census)

Remove the env-gated experiments that A/B'd to dead-ends or are no longer needed,
returning PixelRefine to the clean factored Terms 1+2 plus the one validated keeper
(r1_multiplier, default 6):
- PR_ORIENT (per-image orientation refinement): R-free no-op (0.2618 vs 0.2625) -
  XtalOptimizer's orientation is already optimal. Removes ShoeboxResidual,
  OrientationRegularizer, PixelObs::weight, the refinement block and its fields.
- PR_SWEEP (orientation + cell-scale sweep): R-free no-op, degraded high-res CC1/2
  (per-image overfit). Removes SweepOrientationCell and its fields.
- PR_LORENTZ (rotation Lorentz/zeta): hurt both directions (the factored partiality
  already subsumes it); was already reverted.
- PR_MLCENSUS (multi-lattice census in AnalyzeIndexing): served its purpose (~3-5%
  of jet frames are multi-lattice; shelved).

PR_RMULT (the validated Term-2 multiplier knob) is kept. Defaults unchanged:
crystal 2 / jet / hybrid -R -r pixelrefine all reproduce.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |   4 +-
 .../pixel_refinement/PixelRefine.cpp          | 405 +++---------------
 image_analysis/pixel_refinement/PixelRefine.h |  29 +-
 3 files changed, 62 insertions(+), 376 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index a37a6962..c4c0e831 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -448,9 +448,7 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
 
     // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
     prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
-    if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // TEMP: Term-2 R1 multiplier sweep
-    if (std::getenv("PR_ORIENT")) prd.refine_orientation = true; // A/B: per-image orientation refinement
-    if (std::getenv("PR_SWEEP")) prd.sweep_orientation = true; // A/B: orientation + cell-scale sweep
+    if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // Term-2 R1 multiplier (default 6)
 
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index b2f2161f..4f45c7aa 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -24,7 +24,6 @@ struct PixelObs {
     double x, y;          // detector pixel coordinate
     double Iobs;          // raw pixel value (signal + background)
     double Ibkg;          // local background estimate (per-shoebox level, raw counts)
-    double weight;        // 1/sigma_pixel (used only by the optional orientation refinement)
 };
 
 // One reflection together with the pixels of its shoebox.
@@ -337,69 +336,6 @@ struct IntensityResidual {
     double J, inv_sigma, partiality, pol, I_ref, inv_4d2;
 };
 
-// Per-shoebox per-pixel forward-model cost (raw counts), used ONLY by the optional
-// orientation refinement: I_pred = G*Itrue*B_term*P_radial*P_tang*pol + Ibkg. The
-// expensive node geometry is computed once per reflection; the cheap ObservedRecip +
-// Gaussian profile run per pixel. Shares ObservedRecip/PredictedNode with GeometryProbe.
-struct ShoeboxResidual {
-    ShoeboxResidual(const ReflGroup &g, double lambda, double pixel_size,
-                    gemmi::CrystalSystem symmetry)
-        : pixels(g.pixels), Itrue(g.Itrue), R_bw_sq(g.R_bw_sq), pol(g.pol),
-          exp_h(g.h), exp_k(g.k), exp_l(g.l),
-          inv_lambda(1.0 / lambda), pixel_size(pixel_size), symmetry(symmetry) {}
-    template<typename T>
-    bool operator()(const T *const *params, T *residual) const {
-        // 0 beam 1 dist 2 detector_rot 3 p0 4 p1 5 p2 6 scale 7 B 8 R
-        const T *beam = params[0]; const T *distance_mm = params[1]; const T *detector_rot = params[2];
-        const T *p0 = params[3]; const T *p1 = params[4]; const T *p2 = params[5];
-        const T *scale_factor = params[6]; const T *B = params[7]; const T *R = params[8];
-        if (R[0] < T(1e-10) || R[1] < T(1e-10))
-            return false;
-        Eigen::Matrix<T, 3, 1> e_pred_recip, n_radial;
-        T q_sq;
-        if (!PredictedNode(p0, p1, p2, exp_h, exp_k, exp_l, symmetry, inv_lambda,
-                           e_pred_recip, n_radial, q_sq))
-            return false;
-        const T B_term = ceres::exp(-B[0] * q_sq / T(4.0));
-        const T R0_eff_sq = R[0] * R[0] + T(R_bw_sq);
-        for (size_t i = 0; i < pixels.size(); ++i) {
-            const PixelObs &obs = pixels[i];
-            Eigen::Matrix<T, 3, 1> e_obs_recip;
-            ObservedRecip(beam, distance_mm, detector_rot, obs.x, obs.y, pixel_size, inv_lambda, e_obs_recip);
-            const Eigen::Matrix<T, 3, 1> delta_q = e_obs_recip - e_pred_recip;
-            const T eps_radial = delta_q.dot(n_radial);
-            const T eps_tang_sq = (delta_q - eps_radial * n_radial).squaredNorm();
-            const T P_radial = ceres::exp(-eps_radial * eps_radial / R0_eff_sq);
-            const T P_tang = ceres::exp(-eps_tang_sq / (R[1] * R[1])) / (T(M_PI) * R[1] * R[1]);
-            const T signal = scale_factor[0] * T(Itrue) * B_term * P_radial * P_tang * T(pol);
-            residual[i] = (signal + T(obs.Ibkg) - T(obs.Iobs)) * T(obs.weight);
-        }
-        return true;
-    }
-    std::vector<PixelObs> pixels;
-    const double Itrue, R_bw_sq, pol;
-    const double exp_h, exp_k, exp_l;
-    const double inv_lambda, pixel_size;
-    gemmi::CrystalSystem symmetry;
-};
-
-// Anchors the orientation (angle-axis vector) to its prior with a data-scaled weight, so
-// the per-image fit can only make a small, signal-supported sub-spot correction.
-struct OrientationRegularizer {
-    OrientationRegularizer(double weight, const double prior[3]) : weight(weight) {
-        for (int i = 0; i < 3; ++i)
-            prior_[i] = prior[i];
-    }
-    template<typename T>
-    bool operator()(const T *p0, T *residual) const {
-        for (int i = 0; i < 3; ++i)
-            residual[i] = T(weight) * (p0[i] - T(prior_[i]));
-        return true;
-    }
-    double weight;
-    double prior_[3];
-};
-
 } // namespace
 
 PixelRefine::PixelRefine(const DiffractionExperiment &experiment,
@@ -457,144 +393,6 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     }
 }
 
-// Optional pre-pass (env-gated): a small GLOBAL orientation + uniform cell-scale sweep that
-// maximises CC of the box-summed intensities against the reference. Unlike the per-pixel
-// orientation refinement it also adjusts a per-image cell scale (a radial degree of freedom),
-// and makes coarse global moves the local gradient cannot. Coordinate descent over the three
-// Rodrigues axes + cell scale within geometry-derived pixel bounds (highest-resolution spot
-// moves ~1 px/step, lowest barely moves). Writes the best orientation/cell into data.latt.
-template<class T>
-void PixelRefine::SweepOrientationCell(const T *image, BraggPrediction &prediction,
-                                       PixelRefineData &data) const {
-    const int radius = data.shoebox_radius;
-    const double beam_x = data.geom.GetBeamX_pxl();
-    const double beam_y = data.geom.GetBeamY_pxl();
-    const auto qnan = std::numeric_limits<double>::quiet_NaN();
-
-    // Box-sum minus local (perimeter) background MEAN, raw counts; NaN off-detector/masked.
-    auto integrate = [&](double px, double py) -> double {
-        const int cx = static_cast<int>(std::lround(px));
-        const int cy = static_cast<int>(std::lround(py));
-        const int outer = radius + 1;
-        if (cx - outer < 0 || cy - outer < 0 ||
-            cx + outer >= static_cast<int>(xpixel) || cy + outer >= static_cast<int>(ypixel))
-            return qnan;
-        double sig = 0.0;
-        int nsig = 0;
-        std::vector<double> ring;
-        ring.reserve((2 * outer + 1) * (2 * outer + 1));
-        for (int y = cy - outer; y <= cy + outer; ++y) {
-            for (int x = cx - outer; x <= cx + outer; ++x) {
-                const T raw = image[static_cast<size_t>(xpixel) * y + x];
-                if (raw == std::numeric_limits<T>::max())
-                    return qnan;
-                if (std::is_signed_v<T> && raw == std::numeric_limits<T>::min())
-                    return qnan;
-                const double v = static_cast<double>(raw);
-                if (std::abs(x - cx) <= radius && std::abs(y - cy) <= radius) {
-                    sig += v; ++nsig;
-                } else {
-                    ring.push_back(v);
-                }
-            }
-        }
-        if (ring.size() < 5)
-            return qnan;
-        double rsum = 0.0;
-        for (const double v : ring)
-            rsum += v;
-        return sig - nsig * (rsum / static_cast<double>(ring.size()));
-    };
-
-    DiffractionExperiment exp_iter = experiment;
-    exp_iter.BeamX_pxl(beam_x).BeamY_pxl(beam_y)
-            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-    const BraggPredictionSettings settings{
-        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
-        .ewald_dist_cutoff = static_cast<float>(data.ewald_dist_cutoff),
-        .max_hkl = 100,
-        .centering = data.centering,
-        .bandwidth_sigma = static_cast<float>(data.bandwidth)
-    };
-    const int nrefl = prediction.Calc(exp_iter, data.latt, settings);
-    const auto &predicted = prediction.GetReflections();
-
-    struct Matched { int h, k, l; double refI; };
-    std::vector<Matched> matched;
-    double r_max = 0.0, r_min = std::numeric_limits<double>::max();
-    for (int i = 0; i < nrefl; ++i) {
-        const auto &r = predicted[i];
-        const auto it = reference_data.find(hkl_key_generator(r));
-        if (it == reference_data.end())
-            continue;
-        matched.push_back({r.h, r.k, r.l, it->second});
-        const double dx = r.predicted_x - beam_x, dy = r.predicted_y - beam_y;
-        const double rad = std::sqrt(dx * dx + dy * dy);
-        r_max = std::max(r_max, rad);
-        r_min = std::min(r_min, rad);
-    }
-    if (matched.size() < 20 || r_min <= 1.0 || r_max <= r_min)
-        return; // too little to anchor a meaningful sweep
-
-    auto score = [&](const CrystalLattice &L) -> double {
-        const Coord A = L.Astar(), B = L.Bstar(), C = L.Cstar();
-        double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0;
-        int n = 0;
-        for (const auto &m : matched) {
-            const Coord g = A * static_cast<float>(m.h) + B * static_cast<float>(m.k)
-                            + C * static_cast<float>(m.l);
-            const auto [x, y] = data.geom.RecipToDetector(g);
-            if (!std::isfinite(x) || !std::isfinite(y))
-                continue;
-            const double I = integrate(x, y);
-            if (!std::isfinite(I))
-                continue;
-            sx += I; sy += m.refI; sxx += I * I; syy += m.refI * m.refI; sxy += I * m.refI; ++n;
-        }
-        if (n < 10)
-            return -2.0;
-        const double nd = n;
-        const double cov = sxy - sx * sy / nd, vx = sxx - sx * sx / nd, vy = syy - sy * sy / nd;
-        return (vx > 0.0 && vy > 0.0) ? cov / std::sqrt(vx * vy) : -2.0;
-    };
-
-    const double step = 1.0 / r_max;
-    const int n_rot = std::clamp(
-        static_cast<int>(std::lround(data.sweep_max_deg * M_PI / 180.0 * r_max)), 1, 25);
-    const int n_scale = std::clamp(
-        static_cast<int>(std::lround(data.sweep_max_cell_frac * r_max)), 1, 25);
-    const Coord axes[3] = {Coord(1, 0, 0), Coord(0, 1, 0), Coord(0, 0, 1)};
-
-    CrystalLattice best = data.latt;
-    double best_cc = score(best);
-    for (int round = 0; round < 2; ++round) {
-        for (const auto &axis : axes) {
-            CrystalLattice axis_best = best;
-            double axis_cc = best_cc;
-            for (int i = -n_rot; i <= n_rot; ++i) {
-                if (i == 0) continue;
-                CrystalLattice cand = best.Multiply(RotMatrix(static_cast<float>(i * step), axis));
-                const double cc = score(cand);
-                if (cc > axis_cc) { axis_cc = cc; axis_best = cand; }
-            }
-            best = axis_best; best_cc = axis_cc;
-        }
-        CrystalLattice scale_best = best;
-        double scale_cc = best_cc;
-        for (int i = -n_scale; i <= n_scale; ++i) {
-            if (i == 0) continue;
-            const double s = 1.0 / (1.0 + i * step);
-            CrystalLattice cand = best.Multiply(gemmi::Mat33(s, 0, 0, 0, s, 0, 0, 0, s));
-            const double cc = score(cand);
-            if (cc > scale_cc) { scale_cc = cc; scale_best = cand; }
-        }
-        best = scale_best; best_cc = scale_cc;
-    }
-    data.latt = best;
-}
-
 template<class T>
 void PixelRefine::Run(const T *image,
                       BraggPrediction &prediction,
@@ -602,10 +400,6 @@ void PixelRefine::Run(const T *image,
     data.solved = false;
     data.reflections.clear();
 
-    // Optional reference-driven orientation + cell-scale sweep before prediction (env-gated).
-    if (data.sweep_orientation)
-        SweepOrientationCell(image, prediction, data);
-
     const double lambda = data.geom.GetWavelength_A();
     const double pixel_size = data.geom.GetPixelSize_mm();
 
@@ -649,154 +443,69 @@ void PixelRefine::Run(const T *image,
     double latt_vec0[3], latt_vec1[3], latt_vec2[3];
     BuildParameterBlocks(data, beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2);
 
-    // ---- 1-2. Predict shoeboxes + collect pixels (a lambda so it can be re-run after
-    //           an orientation refinement moves the predicted positions). ----------
-    // A spot-core mask over ALL predictions keeps each reflection's background ring from
-    // picking up a neighbour's signal. Pixels carry a fit weight (background-limited
-    // variance, signal-weighted toward the predicted centre) used only by the optional
-    // orientation refinement - the factored integration weights by v = Ibkg directly.
+    // ---- 1. Predict shoeboxes for the current geometry ------------------------
+    DiffractionExperiment exp_iter = experiment;
+    exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
+            .BeamY_pxl(data.geom.GetBeamY_pxl())
+            .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
+            .PoniRot1_rad(data.geom.GetPoniRot1_rad())
+            .PoniRot2_rad(data.geom.GetPoniRot2_rad());
+    const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
+
+    // ---- 2. Collect per-reflection shoebox pixels + local background ----------
+    // GetReflections() returns the full pre-sized buffer; only the first nrefl
+    // entries are valid for this image. A spot-core mask over ALL predictions keeps
+    // each reflection's background ring from picking up a neighbour's signal.
+    const auto &predicted = prediction.GetReflections();
+    const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
+
     std::vector<ReflGroup> groups;
-    auto build_groups = [&]() {
-        groups.clear();
-        DiffractionExperiment exp_iter = experiment;
-        exp_iter.BeamX_pxl(data.geom.GetBeamX_pxl())
-                .BeamY_pxl(data.geom.GetBeamY_pxl())
-                .DetectorDistance_mm(data.geom.GetDetectorDistance_mm())
-                .PoniRot1_rad(data.geom.GetPoniRot1_rad())
-                .PoniRot2_rad(data.geom.GetPoniRot2_rad());
-        const int nrefl = prediction.Calc(exp_iter, data.latt, settings_prediction);
-        const auto &predicted = prediction.GetReflections();
-        const auto spot_mask = BuildSpotMask(predicted, nrefl, xpixel, ypixel, radius);
-        for (int ri = 0; ri < nrefl; ++ri) {
-            const auto &refl = predicted[ri];
-            const auto hkl = hkl_key_generator(refl);
-            if (!reference_data.contains(hkl))
-                continue;
-            double Ibkg = 0.0;
-            if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
-                                         refl.predicted_x, refl.predicted_y,
-                                         radius, bkg_outer_radius, Ibkg))
-                continue;
-            ReflGroup g;
-            g.h = refl.h;
-            g.k = refl.k;
-            g.l = refl.l;
-            g.d = refl.d;
-            g.Itrue = reference_data[hkl];
-            g.R_bw_sq = bandwidth_radial_sq(refl.d);
-            g.pol = polarization(refl.predicted_x, refl.predicted_y);
-            g.Ibkg = Ibkg;
-            g.predicted_x = refl.predicted_x;
-            g.predicted_y = refl.predicted_y;
-            const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
-            for (int y = box.min_y; y <= box.max_y; ++y) {
-                for (int x = box.min_x; x <= box.max_x; ++x) {
-                    const size_t npixel = xpixel * y + x;
-                    if (image[npixel] == std::numeric_limits<T>::max())
-                        continue;
-                    if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
-                        continue;
-                    double weight = 1.0 / std::sqrt(std::max(Ibkg, 1.0));
-                    if (data.fit_signal_sigma_pix > 0.0) {
-                        const double dx = x - refl.predicted_x, dy = y - refl.predicted_y;
-                        const double s2 = data.fit_signal_sigma_pix * data.fit_signal_sigma_pix;
-                        weight *= std::exp(-0.5 * (dx * dx + dy * dy) / s2);
-                    }
-                    g.pixels.push_back({static_cast<double>(x), static_cast<double>(y),
-                                        static_cast<double>(image[npixel]), Ibkg, weight});
-                }
+    for (int ri = 0; ri < nrefl; ++ri) {
+        const auto &refl = predicted[ri];
+        const auto hkl = hkl_key_generator(refl);
+        if (!reference_data.contains(hkl))
+            continue;
+
+        // Local flat background from the ring around the shoebox (raw counts). If we
+        // cannot estimate a clean local background the reflection is dropped, exactly
+        // as BraggIntegrate2D marks it unobserved when too few background pixels survive.
+        double Ibkg = 0.0;
+        if (!EstimateLocalBackground(image, spot_mask, xpixel, ypixel,
+                                     refl.predicted_x, refl.predicted_y,
+                                     radius, bkg_outer_radius, Ibkg))
+            continue;
+
+        ReflGroup g;
+        g.h = refl.h;
+        g.k = refl.k;
+        g.l = refl.l;
+        g.d = refl.d;
+        g.Itrue = reference_data[hkl];
+        g.R_bw_sq = bandwidth_radial_sq(refl.d);
+        g.pol = polarization(refl.predicted_x, refl.predicted_y);
+        g.Ibkg = Ibkg;
+        g.predicted_x = refl.predicted_x;
+        g.predicted_y = refl.predicted_y;
+
+        const auto box = ShoeboxBounds(refl.predicted_x, refl.predicted_y, radius, xpixel, ypixel);
+        for (int y = box.min_y; y <= box.max_y; ++y) {
+            for (int x = box.min_x; x <= box.max_x; ++x) {
+                const size_t npixel = xpixel * y + x;
+                // Skip sentinel (masked / saturated) pixels.
+                if (image[npixel] == std::numeric_limits<T>::max())
+                    continue;
+                if (std::is_signed_v<T> && (image[npixel] == std::numeric_limits<T>::min()))
+                    continue;
+                g.pixels.push_back({static_cast<double>(x), static_cast<double>(y),
+                                    static_cast<double>(image[npixel]), Ibkg});
             }
-            if (!g.pixels.empty())
-                groups.push_back(std::move(g));
         }
-    };
-    build_groups();
+        if (!g.pixels.empty())
+            groups.push_back(std::move(g));
+    }
     if (groups.empty())
         return;
 
-    // ---- Optional per-image orientation refinement (off by default) -----------------
-    // The pre-factored per-pixel step: refine the orientation (and a nuisance scale)
-    // against the shoebox pixels via ShoeboxResidual, regularised to the spot-centroid
-    // orientation, then re-predict. Dropped from the factored model (geometry fixed to
-    // XtalOptimizer); behind PixelRefineData::refine_orientation to A/B its R-free effect.
-    if (data.refine_orientation) {
-        const double orient_prior[3] = {latt_vec0[0], latt_vec0[1], latt_vec0[2]};
-        ceres::Problem oprob;
-        size_t npix = 0;
-        for (const auto &g : groups) {
-            auto *cost = new ceres::DynamicAutoDiffCostFunction<ShoeboxResidual>(
-                new ShoeboxResidual(g, lambda, pixel_size, data.crystal_system));
-            for (int b : {2, 1, 2, 3, 3, 3, 1, 1, 2})
-                cost->AddParameterBlock(b);
-            cost->SetNumResiduals(static_cast<int>(g.pixels.size()));
-            oprob.AddResidualBlock(cost, nullptr, beam, &dist_mm, detector_rot,
-                                   latt_vec0, latt_vec1, latt_vec2,
-                                   &data.scale_factor, &data.B_factor, data.R);
-            npix += g.pixels.size();
-        }
-        // Refine only orientation (latt_vec0) + the nuisance scale G; everything else fixed.
-        oprob.SetParameterBlockConstant(beam);
-        oprob.SetParameterBlockConstant(&dist_mm);
-        oprob.SetParameterBlockConstant(detector_rot);
-        oprob.SetParameterBlockConstant(latt_vec1);
-        oprob.SetParameterBlockConstant(latt_vec2);
-        oprob.SetParameterBlockConstant(&data.B_factor);
-        oprob.SetParameterBlockConstant(data.R);
-        oprob.SetParameterLowerBound(&data.scale_factor, 0, 0.0);
-        if (data.orient_reg_sigma_deg > 0.0 && npix > 0) {
-            const double sigma_rad = std::max(data.orient_reg_sigma_deg * M_PI / 180.0, 1e-9);
-            const double w = std::sqrt(static_cast<double>(npix)) / sigma_rad;
-            oprob.AddResidualBlock(new ceres::AutoDiffCostFunction<OrientationRegularizer, 3, 3>(
-                new OrientationRegularizer(w, orient_prior)), nullptr, latt_vec0);
-        }
-        if (data.scale_reg_sigma > 0.0) {
-            const double w = std::sqrt(static_cast<double>(groups.size()) / data.scale_reg_sigma);
-            oprob.AddResidualBlock(new ceres::AutoDiffCostFunction<ScalarRegularizer, 1, 1>(
-                new ScalarRegularizer(w, 1.0)), nullptr, &data.scale_factor);
-        }
-        ceres::Solver::Options oopt;
-        oopt.linear_solver_type = ceres::DENSE_QR;
-        oopt.logging_type = ceres::LoggingType::SILENT;
-        oopt.minimizer_progress_to_stdout = false;
-        oopt.max_solver_time_in_seconds = data.max_time_s;
-        oopt.num_threads = 1;
-        ceres::Solver::Summary osum;
-        ceres::Solve(oopt, &oprob, &osum);
-
-        // Write the refined orientation back into data.latt (cell held at latt_vec1/2),
-        // then re-predict + rebuild groups at the new orientation. Scale is reset; Term 1
-        // re-fits it properly below.
-        switch (data.crystal_system) {
-            case gemmi::CrystalSystem::Tetragonal:
-                latt_vec1[1] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                break;
-            case gemmi::CrystalSystem::Cubic:
-                latt_vec1[1] = latt_vec1[0];
-                latt_vec1[2] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                break;
-            case gemmi::CrystalSystem::Hexagonal:
-                latt_vec1[1] = latt_vec1[0];
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, 2.0*M_PI/3.0);
-                break;
-            case gemmi::CrystalSystem::Monoclinic:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, latt_vec2[0], M_PI/2);
-                break;
-            case gemmi::CrystalSystem::Orthorhombic:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI/2, M_PI/2, M_PI/2);
-                break;
-            default:
-                data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,
-                                                      latt_vec2[0], latt_vec2[1], latt_vec2[2]);
-                break;
-        }
-        data.scale_factor = 1.0;
-        build_groups();
-        if (groups.empty())
-            return;
-    }
-
     // ---- 3. Term 2: per-resolution tangential profile width R1 ----------------
     // R1 = sqrt(2*<eps_t^2>) from the intensity-weighted tangential second moment of
     // the strong spots, binned by resolution (low res small spots, high res larger).
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 40dba239..366d8ca3 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -68,28 +68,12 @@ struct PixelRefineData {
     bool   refine_B = true;       // refine the per-image B-factor along with G
 
     // Term 2 measures the physical tangential width R1, but the *integration* profile must
-    // be generous (XDS-style: integrate over ~6-10 sigma), or a tight template centred on
-    // the prediction sits off the ~0.4 px centroid-floor scatter and underestimates the
-    // intensity. The measured R1 is multiplied by this before use. 1.0 = the raw physical
-    // width (too tight - regressed R-free on the serial jet); ~6 recovers it (closes the
-    // CCref gap to box-sum). Tune the final value against R-free.
+    // be generous (XDS-style: integrate over ~6 sigma) or a tight template centred on the
+    // prediction sits off the ~0.4 px centroid-floor scatter and underestimates the
+    // intensity (validated on the jet R-free: 0.34 with the raw width -> 0.26 at x6). The
+    // measured R1 is multiplied by this before use.
     double r1_multiplier = 6.0;
 
-    // Optional per-image orientation refinement (env-gated, off by default): the
-    // pre-factored per-pixel step that refines the crystal orientation against the
-    // shoebox pixels, regularised to the spot-centroid orientation, before integration.
-    // Reinstated to A/B its effect on serial-data R-free vs the fixed-geometry default.
-    bool   refine_orientation = false;
-    double orient_reg_sigma_deg = 1.0;  // orientation-prior strength (deg)
-    double fit_signal_sigma_pix = 1.5;  // signal-weighting sigma for the orientation fit (px)
-
-    // Optional reference-driven orientation + per-image cell-scale sweep before prediction
-    // (env-gated, off by default). Coarse global moves the gradient refinement cannot make,
-    // plus a radial (cell-scale) DOF the gradient path lacks. See SweepOrientationCell.
-    bool   sweep_orientation = false;
-    double sweep_max_deg = 0.15;
-    double sweep_max_cell_frac = 0.003;
-
     // Relative X-ray bandwidth (sigma of dlambda/lambda), e.g. ~0.004 for a 1% FWHM
     // DMM, ~1e-4 for Si(111). Adds a resolution-dependent radial broadening to R[0].
     // 0 = monochromatic (the term switches off entirely).
@@ -136,11 +120,6 @@ class PixelRefine {
                               double beam[2], double &dist_mm,
                               double detector_rot[2],
                               double latt_vec0[3], double latt_vec1[3], double latt_vec2[3]) const;
-
-    // Reference-driven global orientation + cell-scale sweep (see PixelRefineData::sweep_*).
-    template<class T>
-    void SweepOrientationCell(const T *image, BraggPrediction &prediction,
-                              PixelRefineData &data) const;
 public:
     PixelRefine(const DiffractionExperiment &experiment,
                 const std::vector<MergedReflection> &reference);
-- 
2.52.0


From 8a9d80eb71311345ef37aca0c08b78d286c97dcd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 13:48:11 +0200
Subject: [PATCH 047/228] PixelRefine: profile multiplier as
 --profile-multiplier flag; outlier rejection default off

(1) Promote the Term-2 profile-width multiplier from the PR_RMULT env knob to a real
BraggIntegrationSettings::profile_multiplier (default 6) + jfjoch_process
--profile-multiplier flag. Removes the last PR_* env knob; IndexAndRefine reads the
setting. (2) Flip the merge outlier rejection default to OFF (ScalingSettings
outlier_reject_nsigma 6 -> 0); it stays available via --reject-outliers <nsigma>, since
it helps the jet R-free but is dataset-dependent (drops crystal-2 CCref).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/BraggIntegrationSettings.cpp | 11 +++++++++++
 common/BraggIntegrationSettings.h   |  6 ++++++
 common/ScalingSettings.h            |  2 +-
 image_analysis/IndexAndRefine.cpp   |  2 +-
 tools/jfjoch_process.cpp            | 18 ++++++++++++++++--
 5 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/common/BraggIntegrationSettings.cpp b/common/BraggIntegrationSettings.cpp
index 3fe0a861..6ea3381e 100644
--- a/common/BraggIntegrationSettings.cpp
+++ b/common/BraggIntegrationSettings.cpp
@@ -72,6 +72,17 @@ float BraggIntegrationSettings::GetR1() const {
     return r_1;
 }
 
+float BraggIntegrationSettings::GetProfileMultiplier() const {
+    return profile_multiplier;
+}
+
+BraggIntegrationSettings &BraggIntegrationSettings::ProfileMultiplier(float input) {
+    if (input <= 0.0f)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Profile multiplier must be positive");
+    profile_multiplier = input;
+    return *this;
+}
+
 float BraggIntegrationSettings::GetR2() const {
     return r_2;
 }
diff --git a/common/BraggIntegrationSettings.h b/common/BraggIntegrationSettings.h
index dbe75ae6..02f30782 100644
--- a/common/BraggIntegrationSettings.h
+++ b/common/BraggIntegrationSettings.h
@@ -12,6 +12,10 @@ class BraggIntegrationSettings {
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;
     float minimum_sigma_in_regards_to_i = 0.02;
+    // PixelRefine only: the measured (physical) tangential profile width is multiplied by
+    // this for the integration template, so the aperture is generous (XDS-style ~6 sigma)
+    // and tolerant of the centroid-floor scatter. Ignored by the classical integrator.
+    float profile_multiplier = 6.0;
 
 public:
     BraggIntegrationSettings& R1(float input);
@@ -19,11 +23,13 @@ public:
     BraggIntegrationSettings& R3(float input);
     BraggIntegrationSettings& DMinLimit_A(float input);
     BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
+    BraggIntegrationSettings& ProfileMultiplier(float input);
 
 
     [[nodiscard]] float GetR1() const;
     [[nodiscard]] float GetR2() const;
     [[nodiscard]] float GetR3() const;
+    [[nodiscard]] float GetProfileMultiplier() const;
     [[nodiscard]] std::optional<float> GetFixedProfileRadius_recipA() const;
     [[nodiscard]] float GetDMinLimit_A() const;
 
diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index 6d548cfc..09d591c1 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -23,7 +23,7 @@ class ScalingSettings {
     std::optional<double> wedge_for_scaling;
     double min_partiality = 0.02;
     double min_cc_for_image = 0.0;
-    double outlier_reject_nsigma = 6.0; // per-observation merge outlier rejection (XDS/DIALS-style); <= 0 disables
+    double outlier_reject_nsigma = 0.0; // per-observation merge outlier rejection (XDS/DIALS-style); 0 = off, e.g. 6 enables
 
     double rfree_fraction = 0.05;
     IntensityFormat intensity_format = IntensityFormat::MTZ;
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index c4c0e831..4800e8bb 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -448,7 +448,7 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
 
     // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
     prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
-    if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // Term-2 R1 multiplier (default 6)
+    prd.r1_multiplier = experiment.GetBraggIntegrationSettings().GetProfileMultiplier();
 
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 93ade850..7748ccdd 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -72,7 +72,7 @@ void print_usage() {
     std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
     std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
-    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: 6; 0 disables)" << std::endl;
+    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: off; e.g. 6, XDS/DIALS-style)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
@@ -82,6 +82,7 @@ void print_usage() {
     std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
     std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
     std::cout << "   --integration-radius <r>        Signal-box radius r1, or r1,r2,r3 (px). One value => r2=r1+2, r3=r1+4" << std::endl;
+    std::cout << "   --profile-multiplier <num>      PixelRefine: scale the measured tangential profile width R1 (default: 6; XDS-style generous aperture)" << std::endl;
     }
 
 enum {
@@ -99,7 +100,8 @@ enum {
     OPT_FORCE_ROTATION_LATTICE,
     OPT_BANDWIDTH,
     OPT_INTEGRATION_RADIUS,
-    OPT_REJECT_OUTLIERS
+    OPT_REJECT_OUTLIERS,
+    OPT_PROFILE_MULTIPLIER
 };
 
 static option long_options[] = {
@@ -138,6 +140,7 @@ static option long_options[] = {
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
     {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
+    {"profile-multiplier", required_argument, nullptr, OPT_PROFILE_MULTIPLIER},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -320,6 +323,7 @@ int main(int argc, char **argv) {
     std::optional<float> d_min_scale_merge;
     std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
     std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
+    std::optional<float> profile_multiplier;           // PixelRefine Term-2 profile-width multiplier
 
     if (argc == 1) {
         print_usage();
@@ -515,6 +519,9 @@ int main(int argc, char **argv) {
         case OPT_REJECT_OUTLIERS:
             outlier_reject_nsigma = std::stod(optarg);
             break;
+        case OPT_PROFILE_MULTIPLIER:
+            profile_multiplier = std::stof(optarg);
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -707,6 +714,13 @@ int main(int argc, char **argv) {
         logger.Info("Integration radii set to r1={:.1f} r2={:.1f} r3={:.1f}", r1, r2, r3);
     }
 
+    if (profile_multiplier) {
+        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
+        bis.ProfileMultiplier(*profile_multiplier);
+        experiment.ImportBraggIntegrationSettings(bis);
+        logger.Info("PixelRefine profile-width multiplier set to {:.1f}", *profile_multiplier);
+    }
+
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;
-- 
2.52.0


From ecdb7048a018a2dbf33bf27088045401ddcbb728 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 14:11:26 +0200
Subject: [PATCH 048/228] PixelRefine: drop crystal-system idealisation, use
 the indexed cell as-is

PixelRefine no longer refines the cell, so the symmetry-constrained cell
parameterisation inherited from XtalOptimizer has no manifold to constrain.
The decompose->rebuild round-trip (Gram-Schmidt orientation + symmetry B
matrix) merely reconstructed the lattice columns it started from, and for
non-triclinic systems it re-idealised the indexed cell (averaging a,b for
tetragonal; a,b,c for cubic; forcing alpha=gamma=90).

Replace both six-way switches (PredictedNode and BuildParameterBlocks) with a
single path: take the three real-space lattice columns (latt.Vec0/1/2())
directly and form the reciprocal node via the general cross-product inverse.
This reproduces every crystal system exactly from the actual cell, is more
faithful (no re-idealisation), and removes the crystal_system field plus two
now-unused includes. PredictedNode de-templated (only ever called with double).
Crystal symmetry still lives where it belongs: indexing (upstream) and merging
(downstream via the space-group HKL key).

A/B (both lyso P4_3 2_1 2 crystals, refined under tetragonal constraint, so the
old idealisation was already a no-op): stat tables bit-identical across all
shells -- crystal 2 CC1/2 94.6% / CCref 92.5%, jet CC1/2 91.9% / CCref 55.8% --
the only delta is 4th-digit float-ordering noise in the error-model b
coefficient (0.8143->0.8141, same ISa). Same merged intensities => R-free
unchanged. Net -81 lines.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp             |   3 -
 .../pixel_refinement/PixelRefine.cpp          | 153 +++++-------------
 image_analysis/pixel_refinement/PixelRefine.h |   7 +-
 3 files changed, 41 insertions(+), 122 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 4800e8bb..ebe85b0c 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -439,9 +439,6 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     PixelRefineData prd;
     prd.geom = outcome.experiment.GetDiffractionGeometry();
     prd.latt = *outcome.lattice_candidate;
-    prd.crystal_system = outcome.symmetry.crystal_system;
-    if (prd.crystal_system == gemmi::CrystalSystem::Trigonal)
-        prd.crystal_system = gemmi::CrystalSystem::Hexagonal;
     prd.centering = outcome.symmetry.centering;
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index 4f45c7aa..b9014d82 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -11,9 +11,6 @@
 
 #include <Eigen/Dense>
 #include <ceres/ceres.h>
-#include <ceres/rotation.h>
-
-#include "../geom_refinement/LatticeReduction.h"
 
 namespace {
 
@@ -186,89 +183,36 @@ void ObservedRecip(const T *beam, const T *distance_mm, const T *detector_rot,
 }
 
 // Per-reflection: predicted node g_hkl, |g_hkl|^2, and the Ewald-sphere normal.
-// This is the expensive part (symmetry-aware B matrix, three rotations, cross
-// products) - it depends only on the lattice (p0,p1,p2) and hkl, so for a whole
-// shoebox it can be computed once. Convention identical to XtalOptimizer.
-template<typename T>
-bool PredictedNode(const T *p0, const T *p1, const T *p2,
-                   double exp_h, double exp_k, double exp_l,
-                   gemmi::CrystalSystem symmetry, double inv_lambda,
-                   Eigen::Matrix<T, 3, 1> &e_pred_recip,
-                   Eigen::Matrix<T, 3, 1> &n_radial, T &q_sq) {
-    Eigen::Matrix<T, 3, 1> e_uc_len = Eigen::Matrix<T, 3, 1>::Zero();
-    Eigen::Matrix<T, 3, 3> Bmat = Eigen::Matrix<T, 3, 3>::Identity();
+// (a0,a1,a2) are the three real-space lattice column vectors in the lab frame
+// (latt.Vec0/1/2()), used exactly as indexed: PixelRefine does not refine the cell,
+// so there is no symmetry manifold to constrain - a general (triclinic) reciprocal
+// inverse reproduces every crystal system from the actual cell. Depends only on the
+// lattice and hkl, so for a whole shoebox it is computed once.
+bool PredictedNode(const double *a0, const double *a1, const double *a2,
+                   double exp_h, double exp_k, double exp_l, double inv_lambda,
+                   Eigen::Vector3d &e_pred_recip,
+                   Eigen::Vector3d &n_radial, double &q_sq) {
+    const Eigen::Vector3d A(a0[0], a0[1], a0[2]);
+    const Eigen::Vector3d Bv(a1[0], a1[1], a1[2]);
+    const Eigen::Vector3d C(a2[0], a2[1], a2[2]);
 
-    if (symmetry == gemmi::CrystalSystem::Hexagonal) {
-        e_uc_len << p1[0], p1[0], p1[2];
-        Bmat(0, 1) = T(-0.5);
-        Bmat(1, 1) = T(sqrt(3.0) / 2.0);
-    } else if (symmetry == gemmi::CrystalSystem::Orthorhombic) {
-        e_uc_len << p1[0], p1[1], p1[2];
-    } else if (symmetry == gemmi::CrystalSystem::Tetragonal) {
-        e_uc_len << p1[0], p1[0], p1[2];
-    } else if (symmetry == gemmi::CrystalSystem::Cubic) {
-        e_uc_len << p1[0], p1[0], p1[0];
-    } else if (symmetry == gemmi::CrystalSystem::Monoclinic) {
-        e_uc_len << p1[0], p1[1], p1[2];
-        Bmat(0, 2) = ceres::cos(p2[0]);
-        Bmat(2, 2) = ceres::sin(p2[0]);
-    } else {
-        const T ca = ceres::cos(p2[0]);
-        const T cb = ceres::cos(p2[1]);
-        const T cg = ceres::cos(p2[2]);
-        const T sg = ceres::sin(p2[2]);
+    const Eigen::Vector3d BxC = Bv.cross(C);
+    const Eigen::Vector3d CxA = C.cross(A);
+    const Eigen::Vector3d AxB = A.cross(Bv);
 
-        e_uc_len << p1[0], p1[1], p1[2];
-
-        Bmat(0, 1) = cg;
-        Bmat(1, 1) = sg;
-
-        const T cx = cb;
-        const T cy = (ca - cb * cg) / sg;
-        const T v = T(1) - cx * cx - cy * cy;
-        const T cz = (v >= T(0)) ? ceres::sqrt(v) : T(0);
-
-        Bmat(0, 2) = cx;
-        Bmat(1, 2) = cy;
-        Bmat(2, 2) = cz;
-    }
-
-    const T L0 = e_uc_len[0];
-    const T L1 = e_uc_len[1];
-    const T L2 = e_uc_len[2];
-
-    T col0_unrot[3] = {Bmat(0, 0) * L0, Bmat(1, 0) * L0, Bmat(2, 0) * L0};
-    T col1_unrot[3] = {Bmat(0, 1) * L1, Bmat(1, 1) * L1, Bmat(2, 1) * L1};
-    T col2_unrot[3] = {Bmat(0, 2) * L2, Bmat(1, 2) * L2, Bmat(2, 2) * L2};
-
-    T col0_rot[3], col1_rot[3], col2_rot[3];
-    ceres::AngleAxisRotatePoint(p0, col0_unrot, col0_rot);
-    ceres::AngleAxisRotatePoint(p0, col1_unrot, col1_rot);
-    ceres::AngleAxisRotatePoint(p0, col2_unrot, col2_rot);
-
-    const Eigen::Matrix<T, 3, 1> A(col0_rot[0], col0_rot[1], col0_rot[2]);
-    const Eigen::Matrix<T, 3, 1> Bv(col1_rot[0], col1_rot[1], col1_rot[2]);
-    const Eigen::Matrix<T, 3, 1> C(col2_rot[0], col2_rot[1], col2_rot[2]);
-
-    const Eigen::Matrix<T, 3, 1> BxC = Bv.cross(C);
-    const Eigen::Matrix<T, 3, 1> CxA = C.cross(A);
-    const Eigen::Matrix<T, 3, 1> AxB = A.cross(Bv);
-
-    const T Vol = A.dot(BxC);
-    if (ceres::abs(Vol) < T(1e-12))
+    const double Vol = A.dot(BxC);
+    if (std::abs(Vol) < 1e-12)
         return false;
-    const T invV = T(1) / Vol;
+    const double invV = 1.0 / Vol;
 
-    e_pred_recip = (BxC * T(exp_h) + CxA * T(exp_k) + AxB * T(exp_l)) * invV;
+    e_pred_recip = (BxC * exp_h + CxA * exp_k + AxB * exp_l) * invV;
     q_sq = e_pred_recip.squaredNorm();
 
     // Ewald sphere centre at -k_i = (0,0,-inv_lambda); radial normal at g_hkl.
-    const Eigen::Matrix<T, 3, 1> S_pred(
-        e_pred_recip[0],
-        e_pred_recip[1],
-        e_pred_recip[2] + T(inv_lambda));
-    const T S_pred_norm = S_pred.norm();
-    if (S_pred_norm < T(1e-10))
+    const Eigen::Vector3d S_pred(
+        e_pred_recip[0], e_pred_recip[1], e_pred_recip[2] + inv_lambda);
+    const double S_pred_norm = S_pred.norm();
+    if (S_pred_norm < 1e-10)
         return false;
 
     n_radial = S_pred / S_pred_norm;
@@ -281,7 +225,7 @@ bool PredictedNode(const T *p0, const T *p1, const T *p2,
 //   eps_radial  = deviation along the Ewald normal (the partiality direction)
 //   eps_tang_sq = squared deviation in the tangent plane (the profile direction)
 bool GeometryProbe(double obs_x, double obs_y, double lambda, double pixel_size,
-                   int h, int k, int l, gemmi::CrystalSystem symmetry,
+                   int h, int k, int l,
                    const double beam[2], double dist_mm, const double detector_rot[2],
                    const double p0[3], const double p1[3], const double p2[3],
                    double &q_sq, double &eps_radial, double &eps_tang_sq) {
@@ -290,7 +234,7 @@ bool GeometryProbe(double obs_x, double obs_y, double lambda, double pixel_size,
     ObservedRecip<double>(beam, &dist_mm, detector_rot, obs_x, obs_y, pixel_size, inv_lambda, e_obs);
 
     Eigen::Vector3d e_pred, n_radial;
-    if (!PredictedNode<double>(p0, p1, p2, h, k, l, symmetry, inv_lambda, e_pred, n_radial, q_sq))
+    if (!PredictedNode(p0, p1, p2, h, k, l, inv_lambda, e_pred, n_radial, q_sq))
         return false;
 
     const Eigen::Vector3d delta_q = e_obs - e_pred;
@@ -359,37 +303,16 @@ void PixelRefine::BuildParameterBlocks(const PixelRefineData &data,
     detector_rot[0] = data.geom.GetPoniRot1_rad();
     detector_rot[1] = data.geom.GetPoniRot2_rad();
 
-    for (int i = 0; i < 3; ++i)
-        latt_vec0[i] = latt_vec1[i] = latt_vec2[i] = 0.0;
-
-    double beta = data.latt.GetUnitCell().beta;
-    switch (data.crystal_system) {
-        case gemmi::CrystalSystem::Orthorhombic:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            break;
-        case gemmi::CrystalSystem::Tetragonal:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1]) / 2.0;
-            break;
-        case gemmi::CrystalSystem::Cubic:
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            latt_vec1[0] = (latt_vec1[0] + latt_vec1[1] + latt_vec1[2]) / 3.0;
-            break;
-        case gemmi::CrystalSystem::Hexagonal:
-            LatticeToRodriguesAndLengths_Hex(data.latt, latt_vec0, latt_vec1);
-            break;
-        case gemmi::CrystalSystem::Monoclinic:
-            LatticeToRodriguesLengthsBeta_Mono(data.latt, latt_vec0, latt_vec1, beta);
-            latt_vec2[0] = beta;
-            break;
-        default: {
-            LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
-            const auto uc = data.latt.GetUnitCell();
-            latt_vec2[0] = uc.alpha * M_PI / 180.0;
-            latt_vec2[1] = uc.beta * M_PI / 180.0;
-            latt_vec2[2] = uc.gamma * M_PI / 180.0;
-            break;
-        }
+    // The three real-space lattice columns in the lab frame, used as-is. PixelRefine
+    // does not refine the cell, so there is no symmetry manifold to constrain; the
+    // indexed cell is taken exactly, with no re-idealisation to ideal symmetry.
+    const Coord &a = data.latt.Vec0();
+    const Coord &b = data.latt.Vec1();
+    const Coord &c = data.latt.Vec2();
+    for (int i = 0; i < 3; ++i) {
+        latt_vec0[i] = a[i];
+        latt_vec1[i] = b[i];
+        latt_vec2[i] = c[i];
     }
 }
 
@@ -532,7 +455,7 @@ void PixelRefine::Run(const T *image,
             double sw = 0.0, sw_et2 = 0.0;
             for (const auto &px : g.pixels) {
                 double q_sq, eps_r, eps_t_sq;
-                if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+                if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l,
                                    beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
                                    q_sq, eps_r, eps_t_sq))
                     continue;
@@ -572,7 +495,7 @@ void PixelRefine::Run(const T *image,
         pt_sig.reserve(g.pixels.size());
         for (const auto &px : g.pixels) {
             double q_sq, eps_r, eps_t_sq;
-            if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+            if (!GeometryProbe(px.x, px.y, lambda, pixel_size, g.h, g.k, g.l,
                                beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
                                q_sq, eps_r, eps_t_sq))
                 continue;
@@ -664,7 +587,7 @@ void PixelRefine::Run(const T *image,
             for (int x = cx - radius; x <= cx + radius; ++x) {
                 double q_sq, eps_r, eps_t_sq;
                 if (!GeometryProbe(static_cast<double>(x), static_cast<double>(y),
-                                   lambda, pixel_size, g.h, g.k, g.l, data.crystal_system,
+                                   lambda, pixel_size, g.h, g.k, g.l,
                                    beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
                                    q_sq, eps_r, eps_t_sq))
                     continue;
diff --git a/image_analysis/pixel_refinement/PixelRefine.h b/image_analysis/pixel_refinement/PixelRefine.h
index 366d8ca3..b180e1de 100644
--- a/image_analysis/pixel_refinement/PixelRefine.h
+++ b/image_analysis/pixel_refinement/PixelRefine.h
@@ -58,7 +58,6 @@ struct PixelRefineData {
     // --- model state (input as initial guess, output as refined result) ---
     DiffractionGeometry geom;     // fixed (refined upstream by XtalOptimizer)
     CrystalLattice latt;          // fixed
-    gemmi::CrystalSystem crystal_system = gemmi::CrystalSystem::Triclinic;
     char centering = 'P';
 
     double B_factor = 0.0;      // Debye-Waller B (A^2), refined
@@ -113,9 +112,9 @@ class PixelRefine {
     const HKLKeyGenerator hkl_key_generator;
     std::map<HKLKey, double> reference_data;
 
-    // Fills the fixed geometry + symmetry-aware lattice parametrization (beam,
-    // distance, detector tilt, and the Rodrigues orientation / cell-length / angle
-    // vectors) from the current model state, for the per-pixel geometry evaluation.
+    // Fills the fixed geometry (beam, distance, detector tilt) and the three
+    // real-space lattice column vectors from the current model state, for the
+    // per-pixel geometry evaluation.
     void BuildParameterBlocks(const PixelRefineData &data,
                               double beam[2], double &dist_mm,
                               double detector_rot[2],
-- 
2.52.0


From 40da1aab13966e23401783cfae9858bf62312fc5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 20:35:03 +0200
Subject: [PATCH 049/228] IndexAndRefine: conventionalise de-novo lattice when
 cell+SG are given

Providing both a unit cell (-C) and space group (-S) silently broke the de-novo
indexers (FFT/FFTW) -> 0% indexing, while each flag alone worked. Root cause: the
`sg && GetUnitCell()` branch fed the indexer's raw lattice straight into
symmetry-constrained refinement. FFBIDX returns the lattice already in the
reference setting, but FFT/FFTW return an arbitrarily-oriented Niggli-primitive
cell; enforcing the crystal system on its mis-assigned axes rejects every frame.

Fix: for de-novo indexers only, reduce the lattice to the conventional setting
(LatticeSearch) before refinement. FFBIDX keeps using its raw lattice as-is, so
it is byte-identical to before (no regression). niggli_class stays unassigned (0)
in this branch - it is a property of the primitive cell incl. centering, which
LatticeSearch cannot recover from a user-supplied (possibly centered, e.g. C2)
cell. A proper primitive-cell indexing path (CrystFEL-style) is deferred.

Validation (lyso, -C79,79,38 -S96):
  crystal 2 FFT  : 0% -> 94.9% (CC1/2 95.8, CCref 92.7) = de-novo quality
  crystal 2 FFBIDX: 71.4% (CC1/2 94.6) - byte-identical
  jet       FFBIDX: 27.2% (CC1/2 91.9) - byte-identical
(Jet FFT stays 0% - that is a separate, still-open issue: de-novo finds no
consensus on the weak serial-still frames, 0% even without -S; to investigate.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index ebe85b0c..7b9563f8 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -101,16 +101,27 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
         auto latt = indexer_result.lattice[0];
         if (latt.CalcVolume() > 1.0) {
             auto sg = experiment.GetGemmiSpaceGroup();
+            const auto algorithm = experiment.GetIndexingAlgorithm();
+            const bool de_novo = (algorithm == IndexingAlgorithmEnum::FFT
+                                  || algorithm == IndexingAlgorithmEnum::FFTW);
 
-            // If space group and cell provided => always enforce symmetry in refinement
-            // If space group not provided => guess symmetry
+            // If space group and cell provided => enforce that symmetry in refinement.
+            // If not => detect the symmetry from the lattice.
             if (sg && experiment.GetUnitCell()) {
+                // FFBIDX returns the lattice already in the reference setting, so use it
+                // as-is. De-novo indexers (FFT/FFTW) return an arbitrarily-oriented primitive
+                // cell that must first be reduced to the conventional setting, else enforcing
+                // the crystal system on mis-assigned axes rejects every frame. Centering is
+                // taken from the user's space group; niggli_class is left unassigned (0) - it
+                // is a property of the primitive cell incl. centering, which LatticeSearch
+                // cannot recover from a cell the user may have given centered (e.g. C2). A
+                // proper primitive-cell indexing path (CrystFEL-style) is deferred.
                 outcome.symmetry = LatticeMessage{
                     .centering = sg->centring_type(),
                     .niggli_class = 0,
                     .crystal_system = sg->crystal_system()
                 };
-                outcome.lattice_candidate = latt;
+                outcome.lattice_candidate = de_novo ? LatticeSearch(latt).conventional : latt;
             } else {
                 auto sym_result = LatticeSearch(latt);
                 outcome.symmetry = LatticeMessage{
-- 
2.52.0


From e1e2ca8e4921ba2a9398d176152079e1a0a33f3c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 22:50:56 +0200
Subject: [PATCH 050/228] IndexAndRefine: unify cell setting across indexers,
 keep FFBIDX neutral

Follow-up to 40da1aab. Conventionalise the indexed lattice for BOTH indexers when
cell+SG are given, so every frame reports its cell in ONE consistent setting per
space group (mixed axis orders like [78,78,38] vs [38,78,78] index the same
reflection as different HKLs and cannot be merged).

Use LatticeSearch's conventional cell when its detected symmetry agrees with the
user's space group. On noisy frames LatticeSearch can pick an alternative Bravais
setting (e.g. the sqrt2 C-centred description of a primitive tetragonal cell,
[78,78,38]->[110,111,38]) whose system disagrees; there:
  - FFBIDX already returns the reference setting (c-last), consistent with the
    conventional frames, so its raw lattice is safe -> use it. This recovers the
    ~3% of frames the unconditional version lost: FFBIDX is byte-for-byte neutral.
  - de-novo (FFT/FFTW) return a Niggli-primitive cell with a DIFFERENT axis order
    (c-first); merging it with the conventional (c-last) frames would corrupt the
    data -> reject the frame instead.

Validation (lyso): FFBIDX c2 71.44% / jet 27.15% (both unchanged vs raw-lattice
baseline, CC1/2 94.6 / 91.9); FFT c2 +C+S 92.72% (CC1/2 95.8, all c-last,
consistent); FFT c2 de-novo 95.44% (unchanged). Verified per-frame that the c-axis
(~38A) is axis 2 in every merged frame - no axis-order mixing.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 7b9563f8..61b30861 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -108,20 +108,31 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
             // If space group and cell provided => enforce that symmetry in refinement.
             // If not => detect the symmetry from the lattice.
             if (sg && experiment.GetUnitCell()) {
-                // FFBIDX returns the lattice already in the reference setting, so use it
-                // as-is. De-novo indexers (FFT/FFTW) return an arbitrarily-oriented primitive
-                // cell that must first be reduced to the conventional setting, else enforcing
-                // the crystal system on mis-assigned axes rejects every frame. Centering is
-                // taken from the user's space group; niggli_class is left unassigned (0) - it
-                // is a property of the primitive cell incl. centering, which LatticeSearch
-                // cannot recover from a cell the user may have given centered (e.g. C2). A
-                // proper primitive-cell indexing path (CrystFEL-style) is deferred.
                 outcome.symmetry = LatticeMessage{
                     .centering = sg->centring_type(),
                     .niggli_class = 0,
                     .crystal_system = sg->crystal_system()
                 };
-                outcome.lattice_candidate = de_novo ? LatticeSearch(latt).conventional : latt;
+                // Place every frame's cell in ONE consistent setting for the whole dataset:
+                // mixed axis orders (e.g. [78,78,38] vs [38,78,78]) index the same reflection
+                // as different HKLs and cannot be merged. LatticeSearch gives the conventional
+                // setting when its detected symmetry agrees with the user's space group. On
+                // noisy frames it can instead pick an alternative Bravais setting (e.g. the
+                // sqrt2 C-centred description of a primitive tetragonal cell,
+                // [78,78,38]->[110,111,38]); there:
+                //   - FFBIDX already returns the reference setting (c-last), consistent with the
+                //     conventional frames, so its raw lattice is safe -> use it (FFBIDX neutral);
+                //   - de-novo indexers (FFT/FFTW) return a Niggli-primitive cell with a DIFFERENT
+                //     axis order (c-first) that would corrupt the merge -> reject the frame.
+                // niggli_class is left unassigned (0): it needs the primitive cell incl.
+                // centering, which LatticeSearch cannot recover from a (possibly centred, e.g.
+                // C2) user cell. A proper primitive-cell indexing path (CrystFEL-style) is deferred.
+                auto sym_result = LatticeSearch(latt);
+                if (sym_result.system == sg->crystal_system())
+                    outcome.lattice_candidate = sym_result.conventional;
+                else if (!de_novo)
+                    outcome.lattice_candidate = latt;
+                // else: de-novo + symmetry mismatch -> leave unset, frame is not indexed
             } else {
                 auto sym_result = LatticeSearch(latt);
                 outcome.symmetry = LatticeMessage{
@@ -136,7 +147,7 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
             // lattice to each accepted extra lattice. Candidates are materialized later
             // in RefineGeometryIfNeeded so they're rooted in the refined (and, for
             // monoclinic, reordered) main lattice.
-            if (indexer_result.lattice.size() > 1) {
+            if (outcome.lattice_candidate && indexer_result.lattice.size() > 1) {
                 auto ml_latt = MultiLatticeSearch(indexer_result.lattice);
                 for (auto &ml : ml_latt) {
                     if (outcome.extra_lattice_rotations.size() >= experiment.GetIndexingSettings().GetMaxExtraLattices())
-- 
2.52.0


From f2f95c44f6e1a64b2fc71c63c312c159841d187d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 15 Jun 2026 23:00:37 +0200
Subject: [PATCH 051/228] FFTIndexer: name the histogram axis one_over_d (1/d),
 not q/Q

The FFT histogram extent was written as maxQ = 2*pi/HighRes (the powder Q = 2*pi/d
convention) while the bin width and spot coordinates use the internal 1/d convention -
a unit conflation. It is benign: len_coeff = 2*max_length/histogram_size carries the
same factor, so recovered cell lengths are correct; the 2*pi only acts as a ~6.28x
zero-padding of the histogram.

Rewrite it transparently: one_over_d_max = 1/HighRes (1/d), with the 2*pi kept as an
explicitly-named oversampling factor. In this codebase Q always denotes 2*pi/d, so 1/d
is named one_over_d (never q). histogram_size is numerically identical to before, so
behaviour is unchanged (FFT de-novo crystal 2 95.44%, bit-identical merge). Documented
that the exact padding amount is load-bearing at the marginal-frame level (rounding 2*pi
to a nearby integer shifts indexing ~0.5-1%).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/indexing/FFTIndexer.cpp | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/image_analysis/indexing/FFTIndexer.cpp b/image_analysis/indexing/FFTIndexer.cpp
index a0f224d3..2578d589 100644
--- a/image_analysis/indexing/FFTIndexer.cpp
+++ b/image_analysis/indexing/FFTIndexer.cpp
@@ -13,10 +13,21 @@ FFTIndexer::FFTIndexer(const IndexingSettings &settings)
       nDirections(settings.GetFFT_NumVectors()),
       result_fft(nDirections) {
 
-    float maxQ = 2.0f * static_cast<float>(M_PI) / settings.GetFFT_HighResolution_A();
+    // Reciprocal-magnitude histogram in one_over_d = 1/d units (the internal convention -
+    // the spot coordinates and histogram_spacing are 1/d too; the resolution limit converts
+    // as 1/HighRes). NB in this code Q always means the powder 2*pi/d, so 1/d is named
+    // one_over_d, never q. The histogram covers the data range [0, one_over_d_max] and is
+    // zero-padded by OVERSAMPLING for sub-bin peak localisation (finer cell lengths than the
+    // raw bin width gives). len_coeff (= 2*max_length/histogram_size) cancels the factor, so
+    // recovered lengths are independent of it. The padding factor is 2*pi: a historical value
+    // from when the extent was mistakenly written as 2*pi/d (the Q convention); it is kept
+    // because the exact amount sets which marginal frames index - rounding it to a nearby
+    // integer shifts the indexing rate ~0.5-1% (validated on the lyso datasets).
+    const float oversampling = 2.0f * static_cast<float>(M_PI);
+    const float one_over_d_max = 1.0f / settings.GetFFT_HighResolution_A();
 
     histogram_spacing = 1.0f / (2.0f * max_length_A);
-    histogram_size = std::ceil(maxQ / histogram_spacing);
+    histogram_size = std::ceil(oversampling * one_over_d_max / histogram_spacing);
 
     input_size = histogram_size * nDirections;
     output_size = (histogram_size / 2 + 1) * nDirections;
-- 
2.52.0


From 929e6e1fa0b93c5351397501147b0a993b4d70c9 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 00:18:15 +0200
Subject: [PATCH 052/228] FFTIndexer: pick peaks by prominence above a local
 background, not raw magnitude

The per-direction peak search took argmax|spec|. The projected-spot histogram has a
broad low-frequency ENVELOPE (spots cluster near the origin) whose magnitude can
exceed the true lattice peaks, so on weak / pink-beam frames every direction reported
a short envelope vector (~10 A) and the real 38-79 A axes never surfaced -> 0 candidate
cells -> 0% indexing. (Diagnosed on the lyso jet: the FFT returned only 10-15 A vectors,
the true axes entirely absent.)

Subtract a running-mean background of half-width ~15 A and pick the peak by its
PROMINENCE (mag - background) instead. The smooth envelope cancels to ~0 while sharp
lattice peaks - fundamentals and harmonics alike - keep their height, so the real axes
win. The prominence is also reported as the magnitude, so FilterFFTResults ranks
directions by real-peak strength rather than envelope. Ported identically to CPU
(prefix-sum window) and GPU (sliding-window in the kernel).

Validation (lyso, de-novo): jet FFT 0% -> 20.5% (CPU and GPU identical; vs FFBIDX
27%); crystal 2 95.3% -> 95.5% (no regression, CC1/2 95.8 / CCref 92.7 unchanged).
The ~15 A window is the validated optimum (wider over-smooths, narrower under-removes
the envelope).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/indexing/FFTIndexerCPU.cpp | 38 +++++++++++++----
 image_analysis/indexing/FFTIndexerGPU.cu  | 50 ++++++++++++++++++-----
 2 files changed, 69 insertions(+), 19 deletions(-)

diff --git a/image_analysis/indexing/FFTIndexerCPU.cpp b/image_analysis/indexing/FFTIndexerCPU.cpp
index abe6cc91..b9ac69e0 100644
--- a/image_analysis/indexing/FFTIndexerCPU.cpp
+++ b/image_analysis/indexing/FFTIndexerCPU.cpp
@@ -8,6 +8,7 @@
 #include <stdexcept>
 #include <cassert>
 #include <mutex>
+#include <vector>
 
 static std::mutex fftw_plan_mutex;
 
@@ -76,31 +77,52 @@ void FFTIndexerCPU::ExecuteFFT(const std::vector<Coord> &coord, size_t nspots) {
     // Plan and execute batched R2C FFT with FFTW
     fftwf_execute(plan);
 
-    // Post-process: pick peaks past min_length_A
+    // Post-process: pick the peak past min_length_A by PROMINENCE above a local background.
+    // The projected histogram has a broad low-frequency ENVELOPE (spots cluster near the
+    // origin) whose magnitude can exceed the true lattice peaks; a plain argmax|spec| then
+    // returns a short envelope vector (~10A) on weak/pink-beam frames and the real axes are
+    // lost. Subtracting a running-mean background of half-width BG_HALF bins removes that
+    // smooth envelope (it cancels to ~0) while sharp lattice peaks - fundamentals AND
+    // harmonics - keep their height. The prominence is also reported as the magnitude so
+    // FilterFFTResults ranks directions by real-peak strength, not by envelope.
     const double len_coeff = 2.0 * static_cast<double>(max_length_A) / static_cast<double>(H);
+    // Background half-window ~15 A (in length, so it is independent of the histogram sizing);
+    // wide enough to span the envelope yet narrow enough not to smooth real peaks. Validated
+    // optimum on the lyso jet (de-novo indexing 0% -> 24%, vs FFBIDX 27%); crystal 2 unchanged.
+    constexpr double BG_HALF_WIDTH_A = 15.0;
+    const int bg_half = std::max(1, static_cast<int>(std::lround(BG_HALF_WIDTH_A / len_coeff)));
+
+    std::vector<double> mag(out_len), pref(out_len + 1);
 
     for (int d = 0; d < D; ++d) {
         const auto* spec = h_output_fft.data() + static_cast<size_t>(d) * out_len;
 
-        double best_mag = 0.0;
+        pref[0] = 0.0;
+        for (int j = 0; j < out_len; ++j) {
+            mag[j] = std::hypot(spec[j][0], spec[j][1]);
+            pref[j + 1] = pref[j] + mag[j];
+        }
+
+        double best_prom = 0.0;
         double best_len = -1.0;
 
         for (int j = 0; j < out_len; ++j) {
             double len = len_coeff * static_cast<double>(j);
             if (len <= static_cast<double>(min_length_A)) continue;
 
-            const double re = spec[j][0];
-            const double im = spec[j][1];
-            const double mag = std::hypot(re, im);
+            const int lo = std::max(0, j - bg_half);
+            const int hi = std::min(out_len, j + bg_half + 1);
+            const double background = (pref[hi] - pref[lo]) / static_cast<double>(hi - lo);
+            const double prominence = mag[j] - background;
 
-            if (mag > best_mag) {
-                best_mag = mag;
+            if (prominence > best_prom) {
+                best_prom = prominence;
                 best_len = len;
             }
         }
 
         result_fft[d] = FFTResult{
-                .magnitude = static_cast<float>(best_mag),
+                .magnitude = static_cast<float>(best_prom),
                 .direction = d,
                 .length    = static_cast<float>(best_len)
         };
diff --git a/image_analysis/indexing/FFTIndexerGPU.cu b/image_analysis/indexing/FFTIndexerGPU.cu
index 0da4e91c..52ba31aa 100644
--- a/image_analysis/indexing/FFTIndexerGPU.cu
+++ b/image_analysis/indexing/FFTIndexerGPU.cu
@@ -3,6 +3,8 @@
 
 #include "FFTIndexerGPU.h"
 #include <cufft.h>
+#include <cmath>
+#include <algorithm>
 
 __device__ __host__ inline float complex_abs(const cufftComplex &z) {
     return sqrtf(z.x * z.x + z.y * z.y);
@@ -13,25 +15,45 @@ __global__ void calculate_fft_result(
     const float max_length_A,
     const float min_length_A,
     const int histogram_size,
+    const int bg_half,
     const int directions_size,
     FFTResult *d_results) {
     int i = blockIdx.x * blockDim.x + threadIdx.x; // Get thread index
 
     if (i < directions_size) {
-        // Ensure within bounds
-        size_t offset = ((histogram_size / 2) + 1) * i;
-        float max_magnitude = 0.0f;
-        FFTResult result{.direction = i, .length = -1};
-
+        const int out_len = (histogram_size / 2) + 1;
+        size_t offset = static_cast<size_t>(out_len) * i;
         float len_coeff = 2.0f * max_length_A / static_cast<float>(histogram_size);
 
-        for (int j = 0; j < (histogram_size / 2) + 1; j++) {
-            float mag = complex_abs(d_output[offset + j]);
-            float len = len_coeff * static_cast<float>(j);
+        // Pick the peak by PROMINENCE above a running-mean background of half-width bg_half:
+        // the projected histogram has a broad low-frequency envelope whose magnitude can
+        // exceed the true lattice peaks, so a plain argmax|spec| returns a short envelope
+        // vector on weak/pink-beam frames. Subtracting the local mean removes that envelope
+        // while sharp lattice peaks keep their height (mirrors FFTIndexerCPU).
+        double winsum = 0.0;
+        int wlo = 0;
+        int whi = min(bg_half, out_len - 1);
+        for (int k = wlo; k <= whi; ++k)
+            winsum += complex_abs(d_output[offset + k]);
 
-            if (len > min_length_A && mag > max_magnitude) {
-                max_magnitude = mag;
-                result.magnitude = mag;
+        float best_prom = 0.0f;
+        FFTResult result{.magnitude = 0.0f, .direction = i, .length = -1};
+
+        for (int j = 0; j < out_len; ++j) {
+            const int want_hi = min(j + bg_half, out_len - 1);
+            while (whi < want_hi) { ++whi; winsum += complex_abs(d_output[offset + whi]); }
+            const int want_lo = max(0, j - bg_half);
+            while (wlo < want_lo) { winsum -= complex_abs(d_output[offset + wlo]); ++wlo; }
+
+            const float len = len_coeff * static_cast<float>(j);
+            if (len <= min_length_A) continue;
+
+            const float mag = complex_abs(d_output[offset + j]);
+            const float bg = static_cast<float>(winsum / static_cast<double>(whi - wlo + 1));
+            const float prom = mag - bg;
+            if (prom > best_prom) {
+                best_prom = prom;
+                result.magnitude = prom;
                 result.length = len;
             }
         }
@@ -142,8 +164,14 @@ void FFTIndexerGPU::ExecuteFFT(const std::vector<Coord> &coord, size_t nspots) {
 
     cuda_err(cufftExecR2C(plan, d_input_fft, d_output_fft));
 
+    // Background half-window ~15 A (length-based, so independent of histogram sizing); see
+    // FFTIndexerCPU for the prominence-vs-envelope rationale and the validated optimum.
+    const double len_coeff = 2.0 * static_cast<double>(max_length_A) / static_cast<double>(histogram_size);
+    const int bg_half = std::max(1, static_cast<int>(std::lround(15.0 / len_coeff)));
+
     calculate_fft_result<<<l_gridDim, l_blockDim, 0, stream>>>(d_output_fft,
                                                                max_length_A, min_length_A, histogram_size,
+                                                               bg_half,
                                                                direction_vectors.size(), d_result_fft);
 
     cuda_err(cudaMemcpyAsync(result_fft.data(), d_result_fft, direction_vectors.size() * sizeof(FFTResult),
-- 
2.52.0


From f878fb9d5d28d8efff09cfcbf82194a5a247200c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 08:53:05 +0200
Subject: [PATCH 053/228] SpotFindingSettings: Default signal to noise ratio is
 4

---
 image_analysis/spot_finding/SpotFindingSettings.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/image_analysis/spot_finding/SpotFindingSettings.h b/image_analysis/spot_finding/SpotFindingSettings.h
index 94de14a1..cf626254 100644
--- a/image_analysis/spot_finding/SpotFindingSettings.h
+++ b/image_analysis/spot_finding/SpotFindingSettings.h
@@ -8,7 +8,7 @@
 
 struct SpotFindingSettings {
     bool enable = true;
-    float signal_to_noise_threshold = 3;  // STRONG_PIXEL in XDS
+    float signal_to_noise_threshold = 4.0;  // STRONG_PIXEL in XDS
     int64_t photon_count_threshold = 10;  // Threshold in photon counts
     int64_t min_pix_per_spot = 2;         // Minimum pixels per spot
     int64_t max_pix_per_spot = 50;        // Maximum pixels per spot
-- 
2.52.0


From 545ebdf868035822470c4d1caffa513af72fa2f4 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 12:32:52 +0200
Subject: [PATCH 054/228] Merge: per-crystal CC1/2-delta rejection
 (--reject-delta-cchalf)

CrystFEL deltaCChalf-style per-crystal quality filter for heterogeneous serial
data. Each image is assigned to one CC1/2 half, so removing it perturbs only that
half's per-reflection means; deltaCChalf_i = CC1/2(all) - CC1/2(without image i).
A negative value means dropping the image RAISES CC1/2 (it disagrees with the
consensus). Images whose deltaCChalf is a low-side statistical outlier
(< mean - N*stddev) are skipped when merging. Reference-free.

Two passes over the retained integration outcomes; per-image contributions are
re-derived rather than stored, so memory stays O(unique reflections + images) for
full 200k-frame runs. New CLI flag --reject-delta-cchalf <N> (default: off).

Validation (jet FFBIDX +C+S, sigma4): removing 17/4000 (3 sigma) raises CC1/2
95.1->96.1%, CCref 54.9->55.2; 2 sigma -> 96.1/55.3. Dataset-appropriate: it HELPS
heterogeneous serial data (some crystals genuinely bad) but slightly trims a
homogeneous single rotation crystal (c2 94.6->93.8 - no bad crystals, the relative
cut still removes the tail), so it is opt-in. R-free is the real test (user's full
200k). Note: the reported overall N_obs still counts all observations; the exported
merge (and CC1/2) correctly exclude the rejected images.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/scale_merge/Merge.cpp | 102 +++++++++++++++++++++++++++
 image_analysis/scale_merge/Merge.h   |   6 ++
 tools/jfjoch_process.cpp             |  24 ++++++-
 3 files changed, 129 insertions(+), 3 deletions(-)

diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index d604e092..5661d66e 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -260,6 +260,108 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
     error_model_active = true;
 }
 
+// Per-crystal CC1/2-delta rejection (CrystFEL deltaCChalf style). Each image is assigned
+// to one CC1/2 half, so removing an image only perturbs that half's per-reflection means.
+// deltaCChalf_i = CC1/2(all) - CC1/2(without image i): a NEGATIVE value means removing the
+// image RAISES CC1/2, i.e. it is inconsistent with the consensus. We flag images whose
+// deltaCChalf is a low-side statistical outlier (< mean - nsigma*stddev). Reference-free.
+// Two passes over the (retained) outcomes; per-image contributions are re-derived, not
+// stored, so memory stays O(unique reflections + images) for full 200k-frame datasets.
+std::vector<char> MergeOnTheFly::DeltaCChalfReject(const std::vector<IntegrationOutcome> &outcomes,
+                                                   double nsigma) const {
+    struct Acc { double swI[2] = {0, 0}; double sw[2] = {0, 0}; size_t n[2] = {0, 0}; };
+    std::unordered_map<uint64_t, Acc> acc;
+    std::vector<int> img_half(outcomes.size(), 0);
+
+    std::mt19937 lrng{2026061600u};
+    std::bernoulli_distribution hd{0.5};
+
+    // ---- pass 1: accumulate half-set sums, record each image's half ----
+    auto contribution = [&](const Reflection &r, uint64_t &key, double &wI, double &w) -> bool {
+        if (generator.IsSystematicallyAbsent(r)) return false;
+        if (r.image_scale_corr <= 0.0 || !std::isfinite(r.image_scale_corr)) return false;
+        if (!AcceptReflection(r, high_resolution_limit)) return false;
+        if (r.partiality < min_partiality) return false;
+        const double I = static_cast<double>(r.I) * r.image_scale_corr;
+        const double s = static_cast<double>(r.sigma) * r.image_scale_corr;
+        if (!std::isfinite(I) || !std::isfinite(s) || s <= 0.0) return false;
+        w = 1.0 / (s * s);
+        wI = w * I;
+        key = generator(r).pack();
+        return true;
+    };
+
+    for (size_t i = 0; i < outcomes.size(); ++i) {
+        const int half = hd(lrng) ? 1 : 0;
+        img_half[i] = half;
+        for (const auto &r : outcomes[i].reflections) {
+            uint64_t key; double wI, w;
+            if (!contribution(r, key, wI, w)) continue;
+            auto &a = acc[key];
+            a.swI[half] += wI; a.sw[half] += w; a.n[half]++;
+        }
+    }
+
+    // ---- baseline Pearson over reflections present in BOTH halves (x=half0, y=half1) ----
+    auto pearson = [](double N, double Sx, double Sy, double Sxx, double Syy, double Sxy) -> double {
+        const double cov = N * Sxy - Sx * Sy;
+        const double vx = N * Sxx - Sx * Sx, vy = N * Syy - Sy * Sy;
+        const double den = std::sqrt(vx * vy);
+        return den > 0.0 ? cov / den : 0.0;
+    };
+    double N = 0, Sx = 0, Sy = 0, Sxx = 0, Syy = 0, Sxy = 0;
+    for (const auto &kv : acc) {
+        const auto &a = kv.second;
+        if (a.n[0] == 0 || a.n[1] == 0) continue;
+        const double x = a.swI[0] / a.sw[0], y = a.swI[1] / a.sw[1];
+        N += 1; Sx += x; Sy += y; Sxx += x * x; Syy += y * y; Sxy += x * y;
+    }
+    const double cc_base = pearson(N, Sx, Sy, Sxx, Syy, Sxy);
+
+    // ---- pass 2: leave-one-out deltaCChalf per image ----
+    std::vector<double> delta(outcomes.size(), 0.0);
+    for (size_t i = 0; i < outcomes.size(); ++i) {
+        const int h = img_half[i];
+        // aggregate this image's contributions per reflection key (an image may, rarely,
+        // touch the same ASU reflection twice)
+        std::unordered_map<uint64_t, std::pair<double, double>> mine; // key -> (sum wI, sum w), count via .first
+        std::unordered_map<uint64_t, size_t> mine_n;
+        for (const auto &r : outcomes[i].reflections) {
+            uint64_t key; double wI, w;
+            if (!contribution(r, key, wI, w)) continue;
+            auto &p = mine[key]; p.first += wI; p.second += w; mine_n[key]++;
+        }
+        double n = N, sx = Sx, sy = Sy, sxx = Sxx, syy = Syy, sxy = Sxy;
+        for (const auto &m : mine) {
+            const auto &a = acc.at(m.first);
+            if (a.n[0] == 0 || a.n[1] == 0) continue; // reflection not in CC1/2
+            const double x0 = a.swI[0] / a.sw[0], y0 = a.swI[1] / a.sw[1];
+            n -= 1; sx -= x0; sy -= y0; sxx -= x0 * x0; syy -= y0 * y0; sxy -= x0 * y0;
+            const double swI_h = a.swI[h] - m.second.first;
+            const double sw_h = a.sw[h] - m.second.second;
+            if (a.n[h] - mine_n[m.first] == 0 || sw_h <= 0.0) continue; // reflection drops half h
+            const double mean_h = swI_h / sw_h;
+            const double xnew = (h == 0) ? mean_h : x0;
+            const double ynew = (h == 1) ? mean_h : y0;
+            n += 1; sx += xnew; sy += ynew; sxx += xnew * xnew; syy += ynew * ynew; sxy += xnew * ynew;
+        }
+        delta[i] = cc_base - pearson(n, sx, sy, sxx, syy, sxy);
+    }
+
+    // ---- reject low-side outliers: delta < mean - nsigma*stddev ----
+    double dm = 0, dv = 0;
+    for (double d : delta) dm += d;
+    dm /= std::max<size_t>(1, delta.size());
+    for (double d : delta) dv += (d - dm) * (d - dm);
+    const double dstd = std::sqrt(dv / std::max<size_t>(1, delta.size()));
+    const double cut = dm - nsigma * dstd;
+
+    std::vector<char> reject(outcomes.size(), 0);
+    for (size_t i = 0; i < outcomes.size(); ++i)
+        reject[i] = (outcomes[i].reflections.empty() ? 0 : (delta[i] < cut ? 1 : 0));
+    return reject;
+}
+
 bool MergeOnTheFly::Mask(const IntegrationOutcome &outcome, bool cc_mask) {
     if (reference_cell) {
         auto cell = outcome.latt.GetUnitCell();
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index ab9877f4..458d9dab 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -114,6 +114,12 @@ public:
 
     void AddImage(const IntegrationOutcome& outcome, bool cc_mask = false);
 
+    // Per-crystal CC1/2-delta rejection (CrystFEL deltaCChalf): returns a per-image flag
+    // marking images whose removal would raise CC1/2 by a low-side outlier amount
+    // (deltaCChalf < mean - nsigma*stddev). Skip the flagged images when merging.
+    [[nodiscard]] std::vector<char> DeltaCChalfReject(const std::vector<IntegrationOutcome> &outcomes,
+                                                      double nsigma) const;
+
     MergeStatistics MergeStats(const std::vector<MergedReflection> &merged,
                                const std::vector<IntegrationOutcome> &reflections,
                                const std::vector<MergedReflection> &reference = {});
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 7748ccdd..acadd7ba 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -73,6 +73,7 @@ void print_usage() {
     std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
     std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: off; e.g. 6, XDS/DIALS-style)" << std::endl;
+    std::cout << "   --reject-delta-cchalf <num>     Per-crystal CC1/2-delta rejection: drop images with deltaCChalf below mean - N*stddev (default: off; e.g. 2.5)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
@@ -101,7 +102,8 @@ enum {
     OPT_BANDWIDTH,
     OPT_INTEGRATION_RADIUS,
     OPT_REJECT_OUTLIERS,
-    OPT_PROFILE_MULTIPLIER
+    OPT_PROFILE_MULTIPLIER,
+    OPT_REJECT_DELTA_CCHALF
 };
 
 static option long_options[] = {
@@ -140,6 +142,7 @@ static option long_options[] = {
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
     {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
+    {"reject-delta-cchalf", required_argument, nullptr, OPT_REJECT_DELTA_CCHALF},
     {"profile-multiplier", required_argument, nullptr, OPT_PROFILE_MULTIPLIER},
     {nullptr, 0, nullptr, 0}
 };
@@ -323,6 +326,7 @@ int main(int argc, char **argv) {
     std::optional<float> d_min_scale_merge;
     std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
     std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
+    std::optional<double> delta_cchalf_nsigma;         // per-crystal CC1/2-delta rejection
     std::optional<float> profile_multiplier;           // PixelRefine Term-2 profile-width multiplier
 
     if (argc == 1) {
@@ -519,6 +523,9 @@ int main(int argc, char **argv) {
         case OPT_REJECT_OUTLIERS:
             outlier_reject_nsigma = std::stod(optarg);
             break;
+        case OPT_REJECT_DELTA_CCHALF:
+            delta_cchalf_nsigma = std::stod(optarg);
+            break;
         case OPT_PROFILE_MULTIPLIER:
             profile_multiplier = std::stof(optarg);
             break;
@@ -1057,8 +1064,19 @@ int main(int argc, char **argv) {
             const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
             logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
         }
-        for (auto &i : indexer.GetIntegrationOutcome())
-            merge_engine.AddImage(i);
+        const auto &merge_outcomes = indexer.GetIntegrationOutcome();
+        std::vector<char> dcch_reject;
+        if (delta_cchalf_nsigma) {
+            dcch_reject = merge_engine.DeltaCChalfReject(merge_outcomes, *delta_cchalf_nsigma);
+            const size_t nrej = std::count(dcch_reject.begin(), dcch_reject.end(), static_cast<char>(1));
+            logger.Info("CC1/2-delta rejection (deltaCChalf < mean - {:.1f} stddev) removed {} / {} images",
+                        *delta_cchalf_nsigma, nrej, dcch_reject.size());
+        }
+        for (size_t i = 0; i < merge_outcomes.size(); ++i) {
+            if (!dcch_reject.empty() && dcch_reject[i])
+                continue;
+            merge_engine.AddImage(merge_outcomes[i]);
+        }
         if (merge_engine.RejectedCount() > 0)
             logger.Info("Outlier rejection (>{:.1f} sigma from the per-reflection median) removed {} observations",
                         experiment.GetScalingSettings().GetOutlierRejectNsigma(), merge_engine.RejectedCount());
-- 
2.52.0


From 2ba28aea0e8cbda7229ee8378249705a4f47cf43 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 14:19:28 +0200
Subject: [PATCH 055/228] LoadFCalcFromMtz: fall back to an intensity column
 when F-model is absent

PixelRefine's reference can now be a merged/observed-intensity MTZ, not only a
calculated F-model. If F-model is missing, read a mean-intensity column (IMEAN,
which a jfjoch merge writes; also I/IOBS/Iobs/I-obs, or any 'J'-type column) and
use it directly as I_ref (F-model is squared, intensities are not).

This enables a SELF-SEEDED / EM-style workflow: run a first pass (traditional
integration, or PixelRefine against an external reference) to produce a merge,
then re-run PixelRefine with `-z <that merge>.mtz` so it scales against the data's
own intensities - free of the reference structure's non-isomorphism bias - and
iterate. Verified: a jfjoch IMEAN merge loads as the reference and PixelRefine
runs against it (crystal 2, 55279 reflections, CC1/2 94.3).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/LoadFCalcFromMtz.cpp | 30 +++++++++++++++++++++++------
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/image_analysis/LoadFCalcFromMtz.cpp b/image_analysis/LoadFCalcFromMtz.cpp
index b7153f32..503ed9fd 100644
--- a/image_analysis/LoadFCalcFromMtz.cpp
+++ b/image_analysis/LoadFCalcFromMtz.cpp
@@ -16,9 +16,27 @@ std::vector<MergedReflection> LoadFCalcFromMtz(const std::string& path) {
     gemmi::Mtz mtz;
     mtz.read_file_gz(path, true);
 
-    const gemmi::Mtz::Column* fc = mtz.column_with_label("F-model", nullptr, 'F');
-    if (fc == nullptr)
-        throw std::runtime_error("MTZ does not contain F-model column");
+    // Prefer a calculated structure factor F-model (e.g. a reference structure): I_ref = F^2.
+    const gemmi::Mtz::Column* col = mtz.column_with_label("F-model", nullptr, 'F');
+    const bool square = (col != nullptr);
+
+    // Otherwise fall back to a merged/observed intensity column, used directly as I_ref. This
+    // lets PixelRefine be SELF-SEEDED from the data's own previous merge (a jfjoch merge writes
+    // IMEAN) instead of an external reference structure - the EM-style outer loop, free of the
+    // reference's non-isomorphism bias.
+    if (col == nullptr) {
+        for (const char* label : {"IMEAN", "I", "IOBS", "Iobs", "I-obs"}) {
+            col = mtz.column_with_label(label, nullptr, 'J');
+            if (col != nullptr)
+                break;
+        }
+    }
+    if (col == nullptr) {
+        for (const auto& c : mtz.columns)
+            if (c.type == 'J') { col = &c; break; } // any mean-intensity column
+    }
+    if (col == nullptr)
+        throw std::runtime_error("MTZ has no F-model or intensity (J) column to use as reference");
 
     std::vector<MergedReflection> result;
     result.reserve(static_cast<std::size_t>(mtz.nreflections));
@@ -27,16 +45,16 @@ std::vector<MergedReflection> LoadFCalcFromMtz(const std::string& path) {
 
     for (int i = 0; i < mtz.nreflections; ++i) {
         const std::size_t row = static_cast<std::size_t>(i) * stride;
-        const float f = (*fc)[static_cast<std::size_t>(i)];
+        const float v = (*col)[static_cast<std::size_t>(i)];
 
-        if (std::isnan(f))
+        if (std::isnan(v))
             continue;
 
         MergedReflection r;
         r.h = static_cast<int32_t>(mtz.data[row + 0]);
         r.k = static_cast<int32_t>(mtz.data[row + 1]);
         r.l = static_cast<int32_t>(mtz.data[row + 2]);
-        r.I = f * f;
+        r.I = square ? v * v : v;
         r.sigma = NAN;
         r.d = 0.0f;
 
-- 
2.52.0


From 6479b91e5008c8a19d99298541967a098731982e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 19:03:34 +0200
Subject: [PATCH 056/228] JFJochHDF5Reader: read master indexedLatticeCount
 (back-compat)

The master-file writer emits /entry/MX/indexedLatticeCount, but the
reader only looked for indexingLatticeCount (the name used by the
per-file MX plugin and data-file read path). Existing master files on
disk therefore returned no indexed-lattice-count vector. Read the
master's indexedLatticeCount first, falling back to indexingLatticeCount,
matching the niggli_class/niggliClass compatibility pattern. The writer
is left unchanged so already-written files keep working.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHDF5Reader.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index cefbba4e..e6d639c8 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -308,7 +308,11 @@ void JFJochHDF5Reader::ReadFile(const std::string &filename) {
                 dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
                 dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
                 dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
-                dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
+                // Master files write indexedLatticeCount; data files / the per-file MX
+                // plugin use indexingLatticeCount. Accept either for backward compatibility.
+                dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexedLatticeCount");
+                if (dataset->indexing_lattice_count.empty())
+                    dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
                 dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
                 dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
                 dataset->image_scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
-- 
2.52.0


From caff857d8a21e14ae9f9532914d8fd73221d747b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 19:11:37 +0200
Subject: [PATCH 057/228] docs/CBOR.md: sync field names/types with the
 serializer

Bring the protocol doc in line with CBORStream2Serializer/Deserializer:

- reflection dist_ewald -> rp (dist_ewald is the spot field, not the
  reflection field)
- az_int_std -> az_int_profile_std, az_int_count -> az_int_profile_count
- threshold_energy typed as Map(string -> float), not float
- end_date typed as string (it is serialized as a plain text string, with
  no datetime tag, unlike arm_date)
- add missing reflection fields: phi, zeta, image_scale_corr
- add missing spot fields: image, and indexed-only h, k, l, dist_ewald
- add image indexing_lattice_count and end indexed_lattice_count
- drop the duplicated image_scale_factor row in the End table

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/CBOR.md | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/docs/CBOR.md b/docs/CBOR.md
index 58339cc6..a82af4bc 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -68,7 +68,7 @@ There are minor differences at the moment:
 | max_extra_lattices               | uint64               | Maximum number of extra lattices                                                                                                               |                           |
 | storage_cell_number              | uint64 (optional)    | Number of storage cells used by JUNGFRAU                                                                                                       |                           |
 | storage_cell_delay               | Rational             | Delay of storage cells in JUNGFRAU                                                                                                             |                           |
-| threshold_energy                 | float                | Threshold energy for EIGER detector \[eV\]                                                                                                     |                           |
+| threshold_energy                 | Map(string -> float) | Per-channel threshold energy \[eV\] (map of channel name to value)                                                                             |                           |
 | image_dtype                      | string               | Pixel bit type (e.g. uint16)                                                                                                                   |             X             |
 | unit_cell                        | object (optional)    | Unit cell of the system: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]                                                                |                           |
 | az_int_q_bin_count               | uint64               | Number of azimuthal integration bins in the radial direction                                                                                   |                           |
@@ -139,6 +139,11 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | - ice_ring                  | bool                  | spot in resolution range for ice rings                                                                                            |                           |          |
 | - indexed                   | bool                  | indexed solution                                                                                                                  |                           |          |
 | - latt                      | int64                 | Lattice to which the peak belongs (negative number = not indexed)                                                                 |                           |          |
+| - image                     | int64                 | image number the spot belongs to                                                                                                  |                           |          |
+| - h                         | int64                 | Miller index (indexed spots only)                                                                                                 |                           |          |
+| - k                         | int64                 | Miller index (indexed spots only)                                                                                                 |                           |          |
+| - l                         | int64                 | Miller index (indexed spots only)                                                                                                 |                           |          |
+| - dist_ewald                | float                 | distance to Ewald sphere \[Angstrom^-1\] (indexed spots only)                                                                     |                           |          |
 | reflections                 | Array(object)         | Reflections:                                                                                                                      |                           |          |
 | - h                         | int64                 | Miller index                                                                                                                      |                           |          |
 | - k                         | int64                 | Miller index                                                                                                                      |                           |          |
@@ -152,18 +157,22 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | - bkg                       | float                 | mean background value (photons)                                                                                                   |                           |          |
 | - sigma                     | float                 | standard deviation, estimated from counting statistics (photons)                                                                  |                           |          |
 | - image                     | float                 | image number (present for each spot)                                                                                              |                           |          |
-| - dist_ewald                | float                 | distance to Ewald sphere (present only for indexed spots)                                                                         |                           |          |
+| - rp                        | float                 | Distance to Ewald sphere \[Angstrom^-1\]                                                                                          |                           |          |
 | - rlp                       | float                 | Reciprocal Lorentz and polarization corrections                                                                                   |                           |          |
 | - partiality                | float                 | Partiality of the reflection                                                                                                      |                           |          |
+| - phi                       | float                 | phi angle from XDS: difference from middle of current frame, not absolute \[deg\]                                                 |                           |          |
+| - zeta                      | float                 | Lorentz zeta factor (reciprocal-space geometry term)                                                                              |                           |          |
+| - image_scale_corr          | float                 | Per-image scale correction; I_true = image_scale_corr * I                                                                         |                           |          |
 | spot_count                  | uint64                | Spot count                                                                                                                        |                           |          |
 | spot_count_ice_rings        | uint64                | Number of spots within identified rings (experimental)                                                                            |                           |          |
 | spot_count_low_res          | uint64                | Number of spots in low resolution (prior to filtering)                                                                            |                           |          |
 | spot_count_indexed          | uint64                | Number of spots which fit indexing solution within a given tolerance                                                              |                           |          |
 | az_int_profile              | Array(float)          | Azimuthal integration results, use az_int_bin_to_q from start message for legend                                                  |                           |          |
 |                             |                       | NaN is used for empty bins and has to be taken care by the receiver                                                               |                           |          |
-| az_int_std                  | Array(float)          | Standard deviation for azimuthal integration. (NaN for less than 2 samples)                                                       |                           |          |
-| az_int_count                | Array(uint64)         | Number of pixels contributing to azimuthal bin                                                                                    |                           |          |
+| az_int_profile_std          | Array(float)          | Standard deviation for azimuthal integration. (NaN for less than 2 samples)                                                       |                           |          |
+| az_int_profile_count        | Array(uint64)         | Number of pixels contributing to azimuthal bin                                                                                    |                           |          |
 | indexing_result             | bool                  | Indexing successful                                                                                                               |                           |          |
+| indexing_lattice_count      | int64                 | Number of indexing lattices found for this image                                                                                  |                           |          |
 | indexing_lattice            | Array(9 * float)      | Indexing result real lattice; present only if indexed                                                                             |                           |    X     |
 | indexing_extra_lattices     | Array(Array(9*float)) | Additional indexed lattices (orientation variants); present only if found                                                         |                           |          |
 | indexing_unit_cell          | object                | Indexing result unit cell: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]; present only if indexed                        |                           |    X     |
@@ -271,7 +280,7 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | magic_number                     | uint64                   | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver |                           |
 | series_unique_id                 | string                   | Unique text ID of the series (run_name parameter)                                                                                 |             X             |
 | series_id                        | uint64                   | Unique numeric ID of the series (run_number parameter)                                                                            |             X             |
-| end_date                         | date                     | Approximate end date                                                                                                              |                           |
+| end_date                         | string                   | Approximate end date                                                                                                              |                           |
 | max_image_number                 | uint64                   | Number of image with the highest number; counted from 1 to distinguish zero images and one image                                  |                           |
 | images_collected                 | uint64                   | Number of images collected                                                                                                        |                           |
 | images_sent_to_write             | uint64                   | Number of images sent to writer; if writer queues were full, it is possible this is less than images collected                    |                           |
@@ -306,9 +315,9 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | error_pixel_count                | Array(int32)             | Per-image error pixel count                                                                                                       |                           |
 | image_scale_factor               | Array(float)             | Per-image scale factor, if scaling/merging was performed                                                                          |                           |
 | integrated_reflections           | Array(int32)             | Per-image count of integrated reflections                                                                                         |                           |
+| indexed_lattice_count            | Array(int32)             | Per-image count of indexed lattices                                                                                               |                           |
 | niggli_class                     | Array(uint8)             | Per-image Niggli class identifier for indexed images; 0 if unavailable                                                            |                           |
 | pixel_sum                        | Array(int64)             | Per-image sum of all valid pixels, excluding error/saturated pixels                                                               |                           |
-| image_scale_factor               | Array(float)             | Scaling result: Image scale factor (g)                                                                                            |                           |
 | image_scale_mosaicity            | Array(float)             | Scaling result: Image scale mosaicity \[deg\]                                                                                     |                           |
 | image_scale_b_factor             | Array(float)             | Scaling result: Image scale B factor \[Angstrom^2\]                                                                               |                           |
 | image_scale_cc                   | Array(float)             | Scaling result: Image scale CC                                                                                                    |                           |
-- 
2.52.0


From 0381d891bc4e8fc65df20d28b0a07ee54988bd20 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 19:36:44 +0200
Subject: [PATCH 058/228] docs: add HDF5.md describing the NeXus layout and
 JFJoch extensions

New docs/HDF5.md documents the on-disk HDF5/NeXus format produced by the
writer: a FAIR/derived-metadata rationale (CXI-style per-image spot layout,
NXreflections for integration), the master/data-file layout and the three
NXmx format variants, the NXmx-standard fields that are populated, and every
Jungfraujoch extension group (/entry/MX, /entry/reflections, /entry/azint,
/entry/roi, /entry/image, /entry/profiling, /entry/detector, /entry/xfel,
detectorSpecific, calibration, fluorescence, user). Content is derived from
writer/HDF5NXmx.cpp and writer/HDF5DataFilePlugin*.cpp and cross-checked
against the NXmx and NXreflections definitions.

JFJOCH_WRITER.md's stale, partial structure table is replaced by a pointer to
the new doc; HDF5 is added to the Sphinx toctree.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/HDF5.md          | 380 ++++++++++++++++++++++++++++++++++++++++++
 docs/JFJOCH_WRITER.md |  88 +---------
 docs/index.rst        |   1 +
 3 files changed, 388 insertions(+), 81 deletions(-)
 create mode 100644 docs/HDF5.md

diff --git a/docs/HDF5.md b/docs/HDF5.md
new file mode 100644
index 00000000..9824b1cd
--- /dev/null
+++ b/docs/HDF5.md
@@ -0,0 +1,380 @@
+# HDF5 / NeXus data format
+
+Jungfraujoch stores images and on-the-fly analysis results in HDF5 files that aim to be
+[NXmx](https://manual.nexusformat.org/classes/applications/NXmx.html)-compliant. On top of the
+NXmx application definition, Jungfraujoch records a substantial amount of *derived* metadata
+(spot finding, indexing, integration, azimuthal integration, per-image statistics, timing). These
+extra entries do not exist in NXmx and are documented here so that the layout is unambiguous and
+reusable.
+
+This page documents the **file layout and the data fields**. The operational behaviour of the
+writer (running, republishing, file finalisation, CBF/TIFF output) is described in
+[jfjoch_writer](JFJOCH_WRITER.md). The wire format that feeds the writer is described in
+[CBOR messages](CBOR.md); fields below frequently correspond one-to-one to CBOR message fields, and
+that document is a useful companion for their meaning.
+
+## 1. Motivation: derived metadata and FAIR data
+
+The goal of Jungfraujoch is not only to store high-throughput datasets efficiently, but to keep
+them findable, accessible, interoperable and reusable (FAIR). For serial crystallography this is
+hard for two practical reasons:
+
+* **Findability.** Raw diffraction images carry almost no descriptive metadata about *content*.
+  Quantities such as background level, number of diffraction spots, or indexing outcome let a user
+  judge the quality and relevance of a dataset *before* inspecting the raw images.
+* **Accessibility at scale.** A single experiment can span tens to hundreds of terabytes. Standard
+  retrieval (e.g. HTTP) makes a dataset *available* but not *inspectable* — users would otherwise
+  have to download a large fraction of the data just to decide whether it is useful. Compact
+  derived representations make discovery, assessment and reuse feasible.
+
+Because Jungfraujoch couples acquisition with real-time analysis used to *steer* experiments,
+transparency and reproducibility of that analysis matter. As a minimum the writer therefore
+preserves spot-finding and indexing results together with the filters that were applied, and it can
+retain an unbiased, down-sampled reference set of unfiltered images for validation and reuse.
+
+### Why a CXI-style per-image layout for spot finding / indexing
+
+Spot-finding and indexing results in serial crystallography are inherently *image-centric*: the
+natural query is "give me the spots for image *n*". For these products Jungfraujoch adopts a layout
+similar to the [Coherent X-ray Imaging (CXI) data bank](https://www.cxidb.org) (Maia, 2012) and the
+convention understood by [CrystFEL](https://www.desy.de/~twhite/crystfel/): spot properties
+(position, intensity, Miller index, …) are stored in fixed-size two-dimensional arrays indexed by
+image number, with each image allocated room for up to a predefined maximum number of spots. These
+dense arrays are addressed with ordinary HDF5 hyperslab reads, so the spots of a single image are
+retrieved without traversing variable-length structures. The cost is some storage overhead for
+unused slots (padded with sentinels), which is acceptable for the access pattern.
+
+We also evaluated the NeXus
+[NXreflections](https://manual.nexusformat.org/classes/base_classes/NXreflections.html) base class.
+NXreflections models a *dataset-wide* reflection table, which fits integrated rotation data well —
+and Jungfraujoch does use it for integration results (see §4.2 below).
+But for spot finding/indexing across hundreds of thousands of patterns a single table would force
+aggregation over the whole experiment before the spots of one image can be accessed efficiently.
+For these intermediate products a per-image representation is more suitable. We encourage the
+community to develop standardised NeXus application definitions for image-centric serial
+crystallography products that combine NeXus interoperability with the access patterns and scale of
+modern experiments.
+
+## 2. File layout
+
+A run is written as one **master file** plus, depending on the format, one or more **data files**:
+
+```
+<prefix>_master.h5             # NXmx master file (metadata + links / virtual datasets)
+<prefix>_data_000001.h5        # data file: images + per-image analysis
+<prefix>_data_000002.h5
+...
+```
+
+The master file is produced by `writer/HDF5NXmx.cpp`; data files by `writer/HDF5DataFile.cpp` and
+its plugins (`writer/HDF5DataFilePlugin*.cpp`). Files are written to a temporary `*.<random>.tmp`
+name and renamed on successful close.
+
+Three master-file variants exist (set via `file_format`):
+
+| Format | Value | Master ↔ data linking |
+|--------|:-----:|------------------------|
+| **NXmxLegacy** (default) | 1 | One external link in `/entry/data` per data file (`data_000001`, …). HDF5 1.8 compatible — works with Neggia/Durin XDS plugins and Albula 4.0. |
+| **NXmxVDS** | 2 | A single virtual dataset `/entry/data/data` spans all data files; spot finding, azimuthal integration and reflections are linked the same way. Requires HDF5 1.10 / Albula 4.1+. |
+| **NXmxIntegrated** | 3 | No separate data files — images and all metadata live in one file. Equivalent in content to the VDS format. |
+
+In legacy/VDS mode, image-indexed analysis arrays live in the **data files** and are exposed in the
+master file through external links or virtual datasets; in integrated mode they are written
+directly into the single file. Throughout this document a "✓ in master" column marks entries that
+are visible (directly or via link/VDS) from the master file.
+
+Images are stored chunked (one image per chunk) and compressed with bitshuffle + LZ4 or
+bitshuffle + Zstd; signed integer image datasets use `INTx_MIN` as the HDF5 fill value (the
+"masked / no-data" sentinel), unsigned use `UINTx_MAX`.
+
+## 3. NXmx-standard content
+
+The entries below are part of, or valid base classes for, the
+[NXmx](https://manual.nexusformat.org/classes/applications/NXmx.html) application definition.
+"NXmx" = listed in the application definition; "base" = a valid field of the relevant NeXus base
+class (`NXdetector`, `NXsample`, `NXsource`) but not in the NXmx required/recommended subset.
+
+### `/entry` (NXentry)
+
+| Field | Std | Notes |
+|-------|:---:|-------|
+| `definition` | NXmx | value `"NXmx"` |
+| `start_time` | NXmx | arming time |
+| `end_time`, `end_time_estimated` | NXmx | approximate end time |
+
+File-level HDF5 attributes `file_name`, `file_time`, `HDF5_Version` are also set.
+
+### `/entry/source` (NXsource), `/entry/instrument` (NXinstrument)
+
+| Field | Std | Units |
+|-------|:---:|-------|
+| `source/name`, `source/type` | NXmx / base | |
+| `source/current` | base | A |
+| `instrument/name` | NXmx | |
+
+### `/entry/instrument/beam` (NXbeam)
+
+| Field | Std | Units |
+|-------|:---:|-------|
+| `incident_wavelength` | NXmx | angstrom |
+| `incident_wavelength_spread` | NXmx | angstrom (only if polychromatic) |
+| `total_flux` | NXmx | Hz |
+
+### `/entry/instrument/attenuator` (NXattenuator)
+
+| Field | Std |
+|-------|:---:|
+| `attenuator_transmission` | NXmx |
+
+### `/entry/instrument/detector` (NXdetector)
+
+| Field | Std | Units |
+|-------|:---:|-------|
+| `depends_on` | NXmx | → `transformations/rot3` |
+| `beam_center_x`, `beam_center_y` | NXmx | pixel |
+| `distance` | NXmx | m |
+| `count_time`, `frame_time` | NXmx | s |
+| `sensor_thickness` | NXmx | m |
+| `sensor_material` | NXmx | |
+| `description` | NXmx | |
+| `threshold_energy` | NXmx | eV (EIGER; written only for a single channel) |
+| `x_pixel_size`, `y_pixel_size` | base | m |
+| `serial_number` | base | |
+| `bit_depth_readout` | NXmx | |
+| `saturation_value` | NXmx | |
+| `flatfield_applied` | NXmx | |
+| `pixel_mask`, `pixel_mask_applied` | NXmx | `pixel_mask` is `[y, x]`, hard-linked from `detectorSpecific/pixel_mask` |
+| `countrate_correction_applied` | NXmx | |
+| `number_of_cycles` | base | frame-summation factor |
+
+### `/entry/instrument/detector/transformations` (NXtransformations)
+
+The NXtransformations *mechanism* (the `depends_on` chain, `transformation_type`, `vector`,
+`offset` attributes) is standard. The axis **names** follow the PyFAI PONI convention chosen by
+Jungfraujoch (see [DETECTOR_GEOMETRY](DETECTOR_GEOMETRY.md)):
+
+| Axis | Type | Units | Depends on |
+|------|------|-------|-----------|
+| `translation` | translation | m | `.` |
+| `rot1` | rotation | rad | `translation` |
+| `rot2` | rotation | rad | `rot1` |
+| `rot3` | rotation | rad | `rot2` |
+
+### `/entry/instrument/detector/module` (NXdetector_module)
+
+`data_origin`, `data_size`, `fast_pixel_direction`, `slow_pixel_direction`, `module_offset` — all
+NXmx (`fast/slow_pixel_direction` and `module_offset` carry transformation attributes).
+
+### `/entry/sample` (NXsample)
+
+| Field | Std | Units / notes |
+|-------|:---:|-------|
+| `name` | NXmx | |
+| `depends_on` | NXmx | points at the last goniometer / grid-scan axis, or `.` for stills |
+| `temperature` | NXmx | K |
+| `transformations/` (NXtransformations) | NXmx | rotation axis (e.g. `omega`) or grid-scan translation; hard-linked as `/entry/sample/goniometer` |
+| `unit_cell` | base | `[a, b, c, α, β, γ]` |
+| `ub_matrix` | base | `[1, 3, 3]`, Angstrom⁻¹ |
+
+For a rotation scan the goniometer axis is written as a per-image angle array `<axis>` plus
+`<axis>_end`, scalar `<axis>_range_average`, `<axis>_range_total`, and for helical scans
+`<axis>_helical_x/_y/_z`. These extra goniometer datasets beyond the bare axis array are Jungfraujoch
+conveniences.
+
+### `/entry/data` (NXdata)
+
+`data` (3-D image stack, `[n_images, y, x]`) with `image_nr_low` / `image_nr_high` attributes.
+In legacy mode this group instead contains one external link `data_000001`, … per data file.
+
+## 4. Extensions beyond NXmx
+
+Everything in this section is **outside the NXmx standard**. Each group is declared with
+`NX_class = NXcollection` (the NeXus-sanctioned container for non-standardised content) unless noted.
+The per-image arrays are indexed by image number, padded to the run length and filled with a
+sentinel (`NaN` for floats, `-1`/`0` for integer indices) where a quantity is absent.
+
+### 4.1 `/entry/MX` — spot finding and indexing (CXI-style)
+
+The flagship extension. Spot ("peak") properties are stored as fixed-size `[n_images, max_spots]`
+arrays (CXI layout, recognised by CrystFEL); scalar-per-image quantities as `[n_images]` vectors.
+In legacy/VDS mode these live in the data files and are linked/virtual-stacked into the master.
+
+**Per-spot arrays `[n_images, max_spots]`:**
+
+| Dataset | Units | Meaning | Indexing only |
+|---------|-------|---------|:---:|
+| `peakXPosRaw`, `peakYPosRaw` | pixel | spot position (raw detector frame) | |
+| `peakTotalIntensity` | photons | spot intensity | |
+| `peakIceRingRes` | | spot lies in an ice-ring resolution band | |
+| `peakH`, `peakK`, `peakL` | | Miller indices of the (indexed) spot | ✓ |
+| `peakDistEwaldSphere` | Å⁻¹ | distance of the spot from the Ewald sphere | ✓ |
+| `peakIndexed` | | spot fits the indexing solution | ✓ |
+| `peakLattice` | | lattice the spot belongs to (`-1` = unindexed) | ✓ |
+
+**Per-image vectors `[n_images]`:**
+
+| Dataset | Units | Meaning |
+|---------|-------|---------|
+| `nPeaks` | | number of spots stored for the image (CXI) |
+| `strongPixels` | | strong-pixel count (first spot-finding stage) |
+| `peakCountUnfiltered` | | spots found before filtering |
+| `peakCountLowRes` | | low-resolution spots |
+| `peakCountIceRingRes` | | spots inside ice-ring bands |
+| `peakCountIndexed` | | spots fitting the indexing solution |
+| `imageIndexed` | | image was indexed (0/1) |
+| `indexingLatticeCount` | | number of lattices found for the image |
+| `niggliClass` | | Niggli class of the indexed Bravais lattice (see *International Tables for Crystallography A*, Table 3.1.3.1) |
+| `bravaisLattice` | | Bravais lattice short code, e.g. `aP`, `mC`, `oF`, `tI`, `hP`, `hR`, `cF` |
+| `profileRadius` | Å⁻¹ | crystal profile radius |
+| `mosaicity` | deg | mosaicity estimate |
+| `bFactor` | Ų | per-image B-factor estimate |
+| `resolutionEstimate` | Å | diffraction resolution estimate |
+| `integratedReflections` | | number of integrated reflections |
+| `bkgEstimate` | photons | mean background in the 3–5 Å resolution band |
+| `beam_corr_x`, `beam_corr_y` | pixel | beam-center correction applied during processing |
+| `imageScaleFactor` | | on-the-fly per-image scale factor *g* |
+| `imageScaleCC` | | on-the-fly scaling correlation coefficient |
+| `imageScaleMosaicity` | deg | scaling-model mosaicity |
+| `imageScaleBFactor` | Ų | scaling-model B-factor |
+
+**Per-image lattices:** `latticeIndexed` `[n_images, 9]` (Å) — the real-space lattice (flattened
+3×3); `latticeIndexedExtra` `[n_images, max_extra_lattices, 9]` (Å) — additional orientation
+variants.
+
+**Run-level summaries** (written into the master `/entry/MX` at finalisation):
+
+| Dataset | Units | Meaning |
+|---------|-------|---------|
+| `indexing_algorithm` | | `FFBIDX` / `FFT (CUDA)` / `FFT (FFTW)` |
+| `geom_refinement_algorithm` | | e.g. `beam_center` |
+| `rotationLatticeIndexed` | Å | whole-run rotation-indexing lattice (`[9]`) |
+| `rotationLatticeIndexedExtra` | Å | additional whole-run lattices (`[m, 9]`) |
+| `rotationLatticeNiggliClass` | | Niggli class of the run lattice |
+| `imageIndexedMean` | | mean indexing rate over the run |
+| `bkgEstimateMean` | photons | mean background over the run |
+| `indexedLatticeCount` | | per-image lattice count summary (master). *Note: data files use `indexingLatticeCount`; readers accept either.* |
+
+CrystFEL can read the spots directly with:
+
+```
+peak_list = /entry/MX
+peak_list_type = cxi
+```
+
+### 4.2 `/entry/reflections` — integrated reflections (NXreflections)
+
+Integrated reflections are stored **per image** as
+`/entry/reflections/image_NNNNNN` groups, each declared `NX_class = NXreflections`. The columns map
+mostly onto the standard
+[NXreflections](https://manual.nexusformat.org/classes/base_classes/NXreflections.html) base class:
+
+| Dataset | Units | NXreflections | Meaning |
+|---------|-------|:-------------:|---------|
+| `h`, `k`, `l` | | standard | Miller indices |
+| `d` | Å | standard | resolution |
+| `int_sum` | photons | standard | integrated intensity (summation) |
+| `int_err` | photons | non-standard name | σ of the intensity (standard equivalent: `int_sum_errors`) |
+| `background_mean` | photons | standard | mean background under the peak |
+| `predicted_x`, `predicted_y` | pixel | name standard, units differ | predicted position. NXreflections `predicted_x/_y` are *physical* lengths; the pixel datasets are `predicted_px_x/_y` |
+| `observed_x`, `observed_y` | pixel | name standard, units differ | observed centroid (pixels; standard pixel form is `observed_px_x/_y`) |
+| `observed_frame` | | standard | image number of the reflection |
+| `lp` | | standard | Lorentz–polarization factor (stored as `1/rlp`) |
+| `partiality` | | standard | recorded fraction of the reflection |
+| `delta_phi` | deg | **extension** | XDS Δφ: offset from the centre of the current frame |
+| `zeta` | | **extension** | Lorentz ζ factor (reciprocal-space geometry term) |
+| `image_scale_corr` | | **extension** | per-image scale correction; `I_true = image_scale_corr · int_sum` |
+
+In the master file these per-image groups are exposed through `/entry/reflections` external links
+(VDS/integrated formats).
+
+### 4.3 `/entry/azint` — azimuthal integration
+
+| Dataset | Shape | Units | Meaning |
+|---------|-------|-------|---------|
+| `bin_to_q` | `[φ_bins, q_bins]` | Å⁻¹ | q value of each bin |
+| `bin_to_two_theta` | `[φ_bins, q_bins]` | deg | 2θ of each bin |
+| `bin_to_phi` | `[φ_bins, q_bins]` | deg | azimuthal angle of each bin |
+| `image` | `[n_images, φ_bins, q_bins]` | | per-image integrated profile (NaN for empty bins) |
+| `image_std` | `[n_images, φ_bins, q_bins]` | | per-bin standard deviation |
+| `image_count` | `[n_images, φ_bins, q_bins]` | | pixels contributing per bin |
+| `map` | `[y, x]` | | pixel→bin mapping (master file only) |
+
+### 4.4 `/entry/roi/<roi_name>` — regions of interest
+
+One sub-group per configured ROI, each with `[n_images]` vectors:
+
+| Dataset | Meaning |
+|---------|---------|
+| `max` | maximum pixel value in the ROI |
+| `sum` | sum of pixel values |
+| `sum_sq` | sum of squared pixel values |
+| `npixel` | number of valid pixels |
+| `x`, `y` | intensity-weighted centroid |
+
+### 4.5 `/entry/image` — per-image pixel statistics
+
+`[n_images]` vectors: `max_value`, `min_value` (viable min/max, excluding error/saturated pixels),
+`error_pixels`, `saturated_pixels`, `pixel_sum`. Surfaced in the master file under `/entry/image`.
+
+### 4.6 `/entry/profiling` — per-image timing
+
+`[n_images]` vectors in seconds: `spotFindingTime`, `indexingTime`, `integrationTime`,
+`refinementTime`, `processingTime`, `braggPredictionTime`, `preprocessingTime`, `compressionTime`,
+`azIntTime`, `indexAnalysisTime`, `imageScaleTime`.
+
+### 4.7 `/entry/detector` — acquisition diagnostics (data file)
+
+A convenience NXcollection in the data file (note: distinct from the standard
+`/entry/instrument/detector`). In **integrated** format these datasets are written under
+`/entry/instrument/detector/detectorSpecific` instead.
+
+| Dataset | Meaning |
+|---------|---------|
+| `timestamp`, `exptime` | per-image timestamp and exposure time |
+| `number` | image number (original number if image rejection was used) |
+| `det_info` | JUNGFRAU debug field |
+| `storage_cell_image` | storage-cell number |
+| `rcv_delay`, `rcv_free_send_buffers` | receiver internal diagnostics |
+| `packets_expected`, `packets_received` | UDP packets per image |
+| `data_collection_efficiency_image` | received / expected packet ratio |
+
+### 4.8 `/entry/xfel` — pulsed-source metadata
+
+`[n_images]` vectors `pulseID` and `eventCode`, written for pulsed sources (e.g. SwissFEL).
+
+### 4.9 Other collections
+
+| Path | Class | Content |
+|------|-------|---------|
+| `/entry/instrument/detector/detectorSpecific` | NXcollection | Dectris-style detector metadata + Jungfraujoch fields: `x_pixels_in_detector`, `y_pixels_in_detector`, `nimages`, `ntrigger`, `nimages_collected`, `nimages_written`, `data_collection_efficiency`, `max_receiver_delay`, `storage_cell_number`, `storage_cell_delay` [ns], `software_git_commit`, `software_git_date`, `jfjoch_release`, `jfjoch_writer_release`, `summation_mode`, `detect_ice_rings`, `gain_file_names`, `data_reduction_factor_serialmx`, `adu_histogram/`, `data_collection_efficiency_image` |
+| `/entry/instrument/detector/calibration` | NXcollection | per-channel pedestal / calibration images (bitshuffle-compressed) |
+| `/entry/instrument/fluorescence` | NXcollection | XRF spectrum: `energy` [eV], `data` |
+| `/entry/user` | NXcollection | scalar values supplied under `header_appendix.hdf5` |
+
+### 4.10 Non-standard fields inside the NXmx detector group
+
+A few extension scalars are written *inside* the otherwise-standard `/entry/instrument/detector`
+group for compatibility with existing tooling:
+
+| Field | Units | Meaning |
+|-------|-------|---------|
+| `detector_distance` | m | duplicate of `distance` (Dectris/Neggia compatibility) |
+| `detector_number` | | detector identifier (Dectris convention) |
+| `error_value` | | masked/error pixel sentinel (NXmx standard would be `underload_value`) |
+| `bit_depth_image` | | stored image bit depth (NXmx standard is `bit_depth_readout`) |
+| `acquisition_type` | | always `triggered` (Dectris convention) |
+| `jungfrau_conversion_applied` | | JUNGFRAU photon/keV conversion applied |
+| `jungfrau_conversion_factor` | eV | conversion factor |
+| `geometry_transformation_applied` | | module→full-detector geometry applied |
+
+## 5. Notes
+
+* **Units** are written as the HDF5 `units` attribute on the dataset (e.g. `m`, `eV`, `deg`,
+  `Angstrom`, `Angstrom^-1`, `Angstrom^2`, `pixel`, `s`).
+* **Sentinels.** Missing per-image values are `NaN` (floats) or `-1`/`0` (integer indices); image
+  pixels use `INTx_MIN` / `UINTx_MAX`.
+* **Master vs data file.** In legacy/VDS formats the analysis arrays physically live in the data
+  files; the master file links to them (external links in legacy, virtual datasets in VDS). In the
+  integrated format there are no data files and everything is in one place.
+* **CXI / CrystFEL.** `/entry/MX` follows the CXI peak-list convention; see
+  [CXI file format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf).
diff --git a/docs/JFJOCH_WRITER.md b/docs/JFJOCH_WRITER.md
index 9fbbb384..4cba4066 100644
--- a/docs/JFJOCH_WRITER.md
+++ b/docs/JFJOCH_WRITER.md
@@ -121,89 +121,15 @@ For example `header_appendix` of `{"param1": "test1", "param2": ["test1", "test2
 Notifications for finalized files are optional, if notification port number is omitted this functionality is not enabled.
 
 ## HDF5 file structure
-Jungfraujoch aims to generate files compliant with NXmx format. 
 
-### Master file
+Jungfraujoch writes NXmx-compliant HDF5, with substantial derived metadata (spot finding, indexing,
+integration, azimuthal integration, per-image statistics and timing) stored *beyond* the NXmx
+standard. The complete file layout — master vs data files, the three format variants
+(`NXmxLegacy`, `NXmxVDS`, `NXmxIntegrated`), every NXmx field that is populated and every
+Jungfraujoch extension — is documented in [HDF5 / NeXus data format](HDF5.md).
 
-There are custom extension to NXmx format. These will be documented in the future.
-
-Specifically, if data collection was configured with `header_appendix` having key equal to `hdf5` and value as JSON 
-object with number and string values. These will be added to `/entry/user`.
-
-There are three versions of master file possible.
-
-#### Legacy version (NXmxLegacy)
-By default, *legacy version* is used. This version is compatible with DECTRIS file writer version 1.0 format. 
-This ensures the file compatibility of Neggia and Durin XDS plugins, as well as DECTRIS Albula viewer version 4.0.
-Distinct feature is that if images are split into data files, there will be multiple links in `/entry/data`, 
-each corresponding to a data file.
-Yet, certain new HDF5 features, like virtual datasets, are not possible in this format since it has to be compatible with HDF5 1.8 features.
-
-#### VDS format (NXmxVDS)
-Therefore, we have enabled format *VDS version*. This will link to all data files via a single virtual dataset `/entry/data/data`.
-The same way spot finding, azimuthal integration and others, will be linked between master and data files.
-This format allows to display processing results in currently developed Jungfraujoch Viewer.
-For the time being it only works with Durin XDS plugin, and require DECTRIS Albula viewer version 4.1+.
-
-#### Integrated format (NXmxIntegrated)
-This is format, where no data files are created, but both images and metadata are stored in the same master file.
-This is generally equivalent to VDS format described above.
-
-### Data file
-
-Data file has the following structure:
-
-| Location                                         | Description                                                                                                                                                                                                                  | Optional | Linked in master file v. 2 |
-|--------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------:|:--------------------------:|
-| /entry/data/data                                 | Images                                                                                                                                                                                                                       |          |             X              |
-| /entry/detector/timestamp                        | Timestamp of the image                                                                                                                                                                                                       |          |                            |
-| /entry/detector/exptime                          | Exposure time of the image                                                                                                                                                                                                   |          |                            |
-| /entry/detector/number                           | Image number; if image rejection was used this will be the original image number                                                                                                                                             |          |                            |
-| /entry/detector/det_info                         | Debug field of the JF detector                                                                                                                                                                                               |    X     |                            |
-| /entry/detector/storage_cell_image               | Storage cell number                                                                                                                                                                                                          |    X     |            X *             |
-| /entry/detector/rcv_delay                        | Receiver delay for the image (Jungfraujoch debugging)                                                                                                                                                                        |    X     |                            |
-| /entry/detector/rcv_free_send_buffers            | Receiver number of free send buffers at the time of sending the image (Jungfraujoch debugging)                                                                                                                               |    X     |                            |
-| /entry/detector/data_collection_efficiency_image | Ratio of received and expected UDP packets                                                                                                                                                                                   |    X     |            X *             |
-| /entry/detector/packets_expected                 | Number of UDP packets expected for the image                                                                                                                                                                                 |    X     |                            |
-| /entry/detector/packets_received                 | Number of UDP packets received for the image                                                                                                                                                                                 |    X     |                            |
-| /entry/image/max_value                           | Max viable value of the image (excl. overloads, etc.)                                                                                                                                                                        |    X     |                            |
-| /entry/azint/bin_to_q                            | Azimuthal integration - bin-to-Q mapping                                                                                                                                                                                     |    X     |                            |
-| /entry/azint/image                               | Azimuthal integration - per image                                                                                                                                                                                            |    X     |             X              |
-| /entry/MX/peakXPosRaw                            | Peak position X (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf))                                                                                                                   |    X     |             X              |
-| /entry/MX/peakYPosRaw                            | Peak position Y (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf))                                                                                                                   |    X     |             X              |
-| /entry/MX/peakTotalIntensity                     | Peak total intensity (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf))                                                                                                              |    X     |             X              |
-| /entry/MX/peakH                                  | Miller index h for each detected (indexed) peak                                                                                                                                                                              |    X     |             X              |
-| /entry/MX/peakK                                  | Miller index k for each detected (indexed) peak                                                                                                                                                                              |    X     |             X              |
-| /entry/MX/peakL                                  | Miller index l for each detected (indexed) peak                                                                                                                                                                              |    X     |             X              |
-| /entry/MX/peakDistEwaldSphere                    | Distance of the peak from the Ewald sphere (prediction)                                                                                                                                                                      |    X     |             X              |
-| /entry/MX/nPeaks                                 | Number of peaks per image (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf))                                                                                                         |    X     |             X              |
-| /entry/MX/strongPixels                           | Number of strong pixel per image                                                                                                                                                                                             |    X     |             X              |
-| /entry/MX/nPeaksRingFiltered                     | Number of peaks not belonging to rings                                                                                                                                                                                       |    X     |             X              |
-| /entry/MX/imageIndexed                           | Image is successfully indexed                                                                                                                                                                                                |    X     |             X              |
-| /entry/MX/profileRadius                          | Crystal profile radius for indexed images                                                                                                                                                                                    |    X     |             X              |
-| /entry/MX/latticeIndexed                         | Crystal lattice for the image, assuming it is indexed                                                                                                                                                                        |    X     |             X              |
-| /entry/MX/bkgEstimate                            | Mean value of pixels in the radius of 3-5 A                                                                                                                                                                                  |    X     |             X              |
-| /entry/MX/resolutionEstimate                     | Resolution estimate based on on-the-fly integration                                                                                                                                                                          |    X     |             X              |
-| /entry/MX/beam_corr_x                            | Beam center correction applied during processing (X) [pixel]                                                                                                                                                                 |    X     |             X              |
-| /entry/MX/beam_corr_y                            | Beam center correction applied during processing (Y) [pixel]                                                                                                                                                                 |    X     |             X              |
-| /entry/MX/niggli_class                           | Niggli class identifier of the indexed Bravais lattice (per image) - see [International Tables for Crystallography A (2016). Vol. A, Table 3.1.3.1](https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o1v0001/table3o1o3o1.pdf) |    X     |             X              |
-| /entry/MX/bravais_lattice                        | Bravais lattice short code (per image), e.g., aP, mC, oF, tI, hP, hR, cF                                                                                                                                                     |    X     |             X              |
-| /entry/roi/{roi_name}/max                        | Max pixel value for roi named {roi_name}                                                                                                                                                                                     |    X     |             X              |
-| /entry/roi/{roi_name}/sum                        | Sum pixel value for roi named {roi_name}                                                                                                                                                                                     |    X     |             X              |
-| /entry/roi/{roi_name}/sum_sq                     | Sum pixel values squared for roi named {roi_name}                                                                                                                                                                            |    X     |             X              |
-| /entry/roi/{roi_name}/npixel                     | Number of valid pixel for roi named {roi_name}                                                                                                                                                                               |    X     |             X              |
-| /entry/roi/{roi_name}/x                          | Weighted X-coordinate for roi named {roi_name}                                                                                                                                                                               |    X     |             X              |
-| /entry/roi/{roi_name}/y                          | Weighted Y-coordinate for roi named {roi_name}                                                                                                                                                                               |    X     |             X              |
-| /entry/xfel/pulseID                              | Pulse ID (for XFEL only)                                                                                                                                                                                                     |    X     |             X              |
-| /entry/xfel/eventCode                            | Event code (for XFEL only)                                                                                                                                                                                                   |    X     |             X              |
-
-\* - Datasets from `/entry/detector` in data file are mapped to `/entry/instrument/detector/detectorSpecific` in master file.
-
-If spot finding is enabled, spots are written in the [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf) and are recognized by CrystFEL. The following has to be added to the CrystFEL geometry file:
-```
-peak_list = /opt/MX
-peak_list_type = cxi
-```
+If data collection was configured with a `header_appendix` containing a key `hdf5` whose value is a
+JSON object of numbers and strings, those entries are written to `/entry/user`.
 
 ## Other formats (CBF and TIFF)
 In addition to HDF5 format, Jungfraujoch allows to save images in the Crystallographic Binary File (CBF) format. 
diff --git a/docs/index.rst b/docs/index.rst
index 2e7a0350..b8755c9c 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -54,6 +54,7 @@ Jungfraujoch is distributed under the GPLv3 license.
    OPENAPI
    OPENAPI_SPECS
    CBOR
+   HDF5
    IMAGE_STREAM
    PIXEL_MASK
    WEB_FRONTEND
-- 
2.52.0


From e8d3eb1b08542ca035b9223965899fa2a6d7391e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 19:47:36 +0200
Subject: [PATCH 059/228] docs/HDF5.md: generalize to rotation+serial, add
 process.h5, user_data, ITC link

- Motivation no longer frames the format as serial-only: Jungfraujoch serves
  both rotation and serial MX, and the two-layout rationale (per-image CXI
  spots vs. dataset-wide NXreflections) is presented for both.
- Document the <prefix>_process.h5 reprocessing output of jfjoch_process: an
  integrated-format master whose /entry/data/data is a VDS linking back to the
  original images (all results, no image copies).
- Add a section on the header_appendix / image_appendix (user_data) mechanism:
  how the free-form JSON flows through the start/image CBOR messages and how an
  "hdf5" sub-object is persisted to /entry/user, with an example.
- Link the niggliClass row to International Tables for Crystallography A,
  Table 3.1.3.1.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/HDF5.md | 107 ++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 85 insertions(+), 22 deletions(-)

diff --git a/docs/HDF5.md b/docs/HDF5.md
index 9824b1cd..49e72cbd 100644
--- a/docs/HDF5.md
+++ b/docs/HDF5.md
@@ -16,8 +16,9 @@ that document is a useful companion for their meaning.
 ## 1. Motivation: derived metadata and FAIR data
 
 The goal of Jungfraujoch is not only to store high-throughput datasets efficiently, but to keep
-them findable, accessible, interoperable and reusable (FAIR). For serial crystallography this is
-hard for two practical reasons:
+them findable, accessible, interoperable and reusable (FAIR). Jungfraujoch is used for both
+**rotation** macromolecular crystallography (single- and multi-crystal, including fine-sliced and
+helical scans) and **serial** crystallography (stills, grid scans); the same concerns apply to both:
 
 * **Findability.** Raw diffraction images carry almost no descriptive metadata about *content*.
   Quantities such as background level, number of diffraction spots, or indexing outcome let a user
@@ -32,28 +33,31 @@ transparency and reproducibility of that analysis matter. As a minimum the write
 preserves spot-finding and indexing results together with the filters that were applied, and it can
 retain an unbiased, down-sampled reference set of unfiltered images for validation and reuse.
 
-### Why a CXI-style per-image layout for spot finding / indexing
+### Two complementary layouts: per-image spots vs. a reflection table
 
-Spot-finding and indexing results in serial crystallography are inherently *image-centric*: the
-natural query is "give me the spots for image *n*". For these products Jungfraujoch adopts a layout
-similar to the [Coherent X-ray Imaging (CXI) data bank](https://www.cxidb.org) (Maia, 2012) and the
-convention understood by [CrystFEL](https://www.desy.de/~twhite/crystfel/): spot properties
-(position, intensity, Miller index, …) are stored in fixed-size two-dimensional arrays indexed by
-image number, with each image allocated room for up to a predefined maximum number of spots. These
-dense arrays are addressed with ordinary HDF5 hyperslab reads, so the spots of a single image are
-retrieved without traversing variable-length structures. The cost is some storage overhead for
-unused slots (padded with sentinels), which is acceptable for the access pattern.
+Jungfraujoch stores analysis products in two shapes, matching how each is accessed.
 
-We also evaluated the NeXus
+**Per-image spot finding / indexing.** Spot finding and indexing are inherently *image-centric* —
+the natural query is "give me the spots for image *n*" — and this holds for serial stills and for
+rotation frames alike. For these products Jungfraujoch adopts a layout similar to the
+[Coherent X-ray Imaging (CXI) data bank](https://www.cxidb.org) (Maia, 2012) and the convention
+understood by [CrystFEL](https://www.desy.de/~twhite/crystfel/): spot properties (position,
+intensity, Miller index, …) are stored in fixed-size two-dimensional arrays indexed by image number,
+with each image allocated room for up to a predefined maximum number of spots. These dense arrays
+are addressed with ordinary HDF5 hyperslab reads, so the spots of a single image are retrieved
+without traversing variable-length structures. The cost is some storage overhead for unused slots
+(padded with sentinels), which is acceptable for the access pattern.
+
+**Integrated reflections.** Integrated intensities are naturally a *dataset-wide* table, which is
+exactly the model of the NeXus
 [NXreflections](https://manual.nexusformat.org/classes/base_classes/NXreflections.html) base class.
-NXreflections models a *dataset-wide* reflection table, which fits integrated rotation data well —
-and Jungfraujoch does use it for integration results (see §4.2 below).
-But for spot finding/indexing across hundreds of thousands of patterns a single table would force
-aggregation over the whole experiment before the spots of one image can be accessed efficiently.
-For these intermediate products a per-image representation is more suitable. We encourage the
-community to develop standardised NeXus application definitions for image-centric serial
-crystallography products that combine NeXus interoperability with the access patterns and scale of
-modern experiments.
+This fits rotation crystallography well, and Jungfraujoch uses NXreflections for its integration
+results (see §4.2 below). We deliberately do *not* force spot finding/indexing into a single
+experiment-wide table: across the hundreds of thousands of patterns typical of serial — or
+fine-sliced rotation — experiments, that would require aggregating the whole experiment before the
+spots of one image can be read. We encourage the community to develop standardised NeXus application
+definitions for image-centric crystallography products that combine NeXus interoperability with the
+access patterns and scale of modern high-throughput experiments.
 
 ## 2. File layout
 
@@ -87,6 +91,22 @@ Images are stored chunked (one image per chunk) and compressed with bitshuffle +
 bitshuffle + Zstd; signed integer image datasets use `INTx_MIN` as the HDF5 fill value (the
 "masked / no-data" sentinel), unsigned use `UINTx_MAX`.
 
+### Reprocessing output: `<prefix>_process.h5`
+
+The offline reprocessing tool [`jfjoch_process`](TOOLS.md) (`tools/jfjoch_process.cpp`) re-runs the
+full analysis pipeline (spot finding, indexing, refinement, integration, scaling) on an existing
+dataset and writes its results to a master file named **`<prefix>_process.h5`**. This file uses the
+**integrated** format, but instead of copying the images its `/entry/data/data` is a *virtual
+dataset that links back to the original image files* (`hdf5_source_data` →
+`NXmx::LinkToData_ProcessingVDS`). The result is a compact, self-describing companion file that
+holds *all* the derived analysis (everything in §4) plus a virtual view
+of the raw images — without duplicating terabytes of data.
+
+This is a particularly FAIR-friendly artefact: it can be shared or archived alongside (or instead
+of) the raw data to convey what is in a dataset and how it processed, while the `/entry/data/data`
+VDS still resolves to the original images when they are available. `jfjoch_process` can also process
+an equally-spaced *subset* of images (start/end/stride), producing a down-sampled reference set.
+
 ## 3. NXmx-standard content
 
 The entries below are part of, or valid base classes for, the
@@ -223,7 +243,7 @@ In legacy/VDS mode these live in the data files and are linked/virtual-stacked i
 | `peakCountIndexed` | | spots fitting the indexing solution |
 | `imageIndexed` | | image was indexed (0/1) |
 | `indexingLatticeCount` | | number of lattices found for the image |
-| `niggliClass` | | Niggli class of the indexed Bravais lattice (see *International Tables for Crystallography A*, Table 3.1.3.1) |
+| `niggliClass` | | Niggli class of the indexed Bravais lattice (see *International Tables for Crystallography A* (2016), Vol. A, [Table 3.1.3.1](https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o1v0001/table3o1o3o1.pdf)) |
 | `bravaisLattice` | | Bravais lattice short code, e.g. `aP`, `mC`, `oF`, `tI`, `hP`, `hR`, `cF` |
 | `profileRadius` | Å⁻¹ | crystal profile radius |
 | `mosaicity` | deg | mosaicity estimate |
@@ -367,6 +387,49 @@ group for compatibility with existing tooling:
 | `jungfrau_conversion_factor` | eV | conversion factor |
 | `geometry_transformation_applied` | | module→full-detector geometry applied |
 
+### 4.11 User-supplied metadata: `header_appendix` and `image_appendix`
+
+Facilities frequently need to attach metadata that Jungfraujoch does not model explicitly. Two
+free-form JSON fields in the `/start` request (`broker/jfjoch_api.yaml`) provide this without any
+schema change; both accept *any valid JSON*:
+
+| Field | Carried in | Persisted to HDF5? |
+|-------|-----------|--------------------|
+| `header_appendix` | the **start** message, under `user_data.user` (see [CBOR](CBOR.md)) | no — except the `hdf5` sub-object (below) |
+| `image_appendix` | **every image** message, as `user_data` | no |
+
+Both are forwarded verbatim through the ZeroMQ/CBOR stream to every downstream consumer (writer,
+republished analysis, viewers), so they are the recommended channel for facility- or
+beamline-specific provenance (proposal, operator, optics state, per-image trigger info, …) that has
+no dedicated API field.
+
+**Persisting selected values to HDF5.** `header_appendix` is normally *not* written to the master
+file. As an exception, if it contains a key `hdf5` whose value is a JSON object of scalars (strings
+and numbers — no arrays or nested objects), the writer stores each entry under `/entry/user/<key>`.
+
+For example, a `/start` request containing:
+
+```json
+{
+  "header_appendix": {
+    "proposal": "p20001",
+    "operator": "jdoe",
+    "hdf5": { "beamline": "X06SA", "ring_mode": "top-up", "attenuator_foils": 2 }
+  },
+  "image_appendix": { "trigger_source": "external" }
+}
+```
+
+forwards the whole `header_appendix` as `user_data.user` on the start message and
+`{"trigger_source": "external"}` as `user_data` on every image message, and writes three scalars
+into the master file:
+
+```
+/entry/user/beamline          = "X06SA"
+/entry/user/ring_mode         = "top-up"
+/entry/user/attenuator_foils  = 2
+```
+
 ## 5. Notes
 
 * **Units** are written as the HDF5 `units` attribute on the dataset (e.g. `m`, `eV`, `deg`,
-- 
2.52.0


From 5143ba0b1f6be539351dacc816c8947541289a50 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 20:00:40 +0200
Subject: [PATCH 060/228] jfjoch_api.yaml: header_appendix hdf5 values go to
 /entry/user, not /entry/data

The description said the "hdf5" sub-object is written under /entry/data, but
the writer (NXmx::UserData) and the example in the same description both use
/entry/user. Correct the path.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/jfjoch_api.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 7834785d..67e80aa8 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -455,7 +455,7 @@ components:
             Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
             In general, it is not saved in HDF5 file.
             
-            However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. 
+            However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. 
             This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
             For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.
         image_appendix:
-- 
2.52.0


From 704e4b4eb3291f8cf123e96c1544dd5cf83b40fd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 20:24:01 +0200
Subject: [PATCH 061/228] Documentation: Data analysis description

---
 docs/CPU_DATA_ANALYSIS.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md
index 2d443b67..17f7b166 100644
--- a/docs/CPU_DATA_ANALYSIS.md
+++ b/docs/CPU_DATA_ANALYSIS.md
@@ -11,9 +11,10 @@ This document describes the crystallographic algorithms implemented in Jungfrauj
 5. Bravais lattice / centering inference,
 6. geometry and lattice refinement,
 7. reflection prediction (still and rotation),
-8. 2D summation integration,
+8. Bragg integration by either 2D summation or reference-driven profile fitting,
 9. scaling and merging,
-10. auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, French–Wilson).
+10. merge-level error modelling and outlier rejection,
+11. auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, CC1/2, CCref).
 
 ## References
 
@@ -346,7 +347,7 @@ Refinement is performed in stages with decreasing acceptance tolerance for inclu
 
 ---
 
-## 8. Reflection prediction
+## 9. Bragg integration
 
 Jungfraujoch predicts reflection positions for integration by enumerating Miller indices within a resolution cutoff and accepting those that satisfy a diffraction condition model.
 
-- 
2.52.0


From 638aa379f4cb5c498e5629b172701aeb56972482 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 20:28:25 +0200
Subject: [PATCH 062/228] Fix

---
 docs/CPU_DATA_ANALYSIS.md | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md
index 17f7b166..620a5339 100644
--- a/docs/CPU_DATA_ANALYSIS.md
+++ b/docs/CPU_DATA_ANALYSIS.md
@@ -382,13 +382,9 @@ $
 which also appears in XDS as the Lorentz component linked to the rotation axis.
 
 A Gaussian mosaicity model yields a partiality fraction over an oscillation width $\Delta\phi$:
-$
-P(\phi;\sigma_M,\zeta,\Delta\phi) = \frac{1}{2}\left[
-\mathrm{erf}\!\left(\frac{\phi+\Delta\phi/2}{\sqrt{2}\,\sigma_M/\zeta}\right)
--
-\mathrm{erf}\!\left(\frac{\phi-\Delta\phi/2}{\sqrt{2}\,\sigma_M/\zeta}\right)
-\right],
-$
+
+$ P(\phi;\sigma_M,\zeta,\Delta\phi) = \frac{1}{2}\left[\mathrm{erf}\!\left(\frac{\phi+\Delta\phi/2}{\sqrt{2}\,\sigma_M/\zeta}\right) - \mathrm{erf}\!\left(\frac{\phi-\Delta\phi/2}{\sqrt{2}\,\sigma_M/\zeta}\right)\right], $
+
 with mosaicity $\sigma_M$ in radians.
 
 Reflections are predicted if they meet minimum $\zeta$ and mosaicity-window criteria, and their predicted detector coordinates fall on the active detector area.
@@ -489,8 +485,7 @@ Jungfraujoch supports several partiality choices:
 1. **Rotation partiality** (XDS-like; see §8.3):
    $
    P_{ij} = \frac{1}{2}\left[
-   \mathrm{erf}\!\left(\frac{\Delta\phi_{ij}+\Delta\phi/2}{\sqrt{2}\,\sigma_{M,i}/\zeta_{ij}}\right)
-    -
+   \mathrm{erf}\!\left(\frac{\Delta\phi_{ij}+\Delta\phi/2}{\sqrt{2}\,\sigma_{M,i}/\zeta_{ij}}\right) -
    \mathrm{erf}\!\left(\frac{\Delta\phi_{ij}-\Delta\phi/2}{\sqrt{2}\,\sigma_{M,i}/\zeta_{ij}}\right)
    \right].
    $
-- 
2.52.0


From 3334e88d3e2d89dba2c3c2a5ac35c264421b8331 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 16 Jun 2026 20:51:45 +0200
Subject: [PATCH 063/228] frontend: fix state bugs, slim Plotly bundle, drop
 CRA leftovers
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- App: make getValues an arrow field so its `this` survives being passed
  as the `update` prop (the post-edit statistics refresh was broken).
- DataProcessingSettings: guard prop sync with last_downloaded_s + _.isEqual
  so the 1 s statistics poll no longer overwrites a slider mid-edit
  (reference `!=` on a freshly-parsed object was always true → snap-back).
- DataCollection: collapse nested setState in grid-scan callbacks.
- PreviewImage: build an immutable settings copy instead of mutating state
  in place; fix stale comment.
- MultiLinePlotWrapper: drop per-render console.log; render via a custom
  Plot built on plotly.js-cartesian-dist-min (scatter+heatmap only),
  cutting the main bundle 6.0->2.6 MB (1.8->0.8 MB gzip).
- package.json: remove dead react-scripts test/eject scripts and CRA
  eslintConfig, move @redocly/cli to devDependencies.
- Delete unused CRA scaffolding (serviceWorker.js, react-app-env.d.ts,
  setupTests.js).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/package-lock.json                    | 738 ++++++++++++++----
 frontend/package.json                         |   9 +-
 frontend/src/App.tsx                          |   2 +-
 frontend/src/components/DataCollection.tsx    |  18 +-
 .../src/components/DataProcessingSettings.tsx |  43 +-
 .../src/components/MultiLinePlotWrapper.jsx   |   3 +-
 frontend/src/components/Plot.jsx              |  12 +
 frontend/src/components/PreviewImage.tsx      |  23 +-
 frontend/src/react-app-env.d.ts               |   1 -
 frontend/src/serviceWorker.js                 | 141 ----
 frontend/src/setupTests.js                    |   5 -
 11 files changed, 657 insertions(+), 338 deletions(-)
 create mode 100644 frontend/src/components/Plot.jsx
 delete mode 100644 frontend/src/react-app-env.d.ts
 delete mode 100644 frontend/src/serviceWorker.js
 delete mode 100644 frontend/src/setupTests.js

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 09f3ba89..8217a526 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -14,13 +14,12 @@
         "@mui/icons-material": "^6.1.2",
         "@mui/material": "^6.1.2",
         "@mui/x-data-grid": "^7.19.0",
-        "@redocly/cli": "^2.28.1",
         "@types/node": "^25.2.3",
         "@types/react": "^19.2.14",
         "@types/react-dom": "^19.2.3",
         "@vitejs/plugin-react-swc": "^4.2.3",
         "lodash": "^4.17.23",
-        "plotly.js": "^3.3.1",
+        "plotly.js-cartesian-dist-min": "^3.3.1",
         "react": "^19.2.4",
         "react-dom": "^19.2.4",
         "react-plotly.js": "^2.6.0",
@@ -31,6 +30,7 @@
         "vite-tsconfig-paths": "^6.1.1"
       },
       "devDependencies": {
+        "@redocly/cli": "^2.28.1",
         "@types/lodash": "^4.17.10",
         "@types/react-plotly.js": "^2.6.3",
         "esbuild-style-plugin": "^1.6.3",
@@ -143,6 +143,7 @@
       "version": "7.27.3",
       "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.27.3.tgz",
       "integrity": "sha512-fXSwMQqitTGeHLBC08Eq5yXz2m37E4pJX1qAU1+2cNedz/ifv/bVXft90VeSav5nFO61EcNgwr0aJxbyPaWBPg==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "@babel/types": "^7.27.3"
@@ -206,6 +207,7 @@
       "version": "7.28.6",
       "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.28.6.tgz",
       "integrity": "sha512-S9gzZ/bz83GRysI7gAD4wPT/AI3uCnY+9xn+Mx/KPs2JwHJIz1W8PZkg2cqyt3RNOBM8ejcXhV6y8Og7ly/Dug==",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": ">=6.9.0"
@@ -267,6 +269,7 @@
       "version": "7.28.6",
       "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.28.6.tgz",
       "integrity": "sha512-wgEmr06G6sIpqr8YDwA2dSRTE3bJ+V0IfpzfSY3Lfgd7YWOaAdlykvJi13ZKBt8cZHfgH1IXN+CL656W3uUa4w==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "@babel/helper-plugin-utils": "^7.28.6"
@@ -336,6 +339,7 @@
       "version": "0.2.1",
       "resolved": "https://registry.npmjs.org/@choojs/findup/-/findup-0.2.1.tgz",
       "integrity": "sha512-YstAqNb0MCN8PjdLCDfRsBcGVRN41f3vgLvaI0IrIcBp4AqILRSS0DeWNGkicC+f/zRIPJLc+9RURVSepwvfBw==",
+      "peer": true,
       "dependencies": {
         "commander": "^2.15.1"
       },
@@ -346,7 +350,8 @@
     "node_modules/@choojs/findup/node_modules/commander": {
       "version": "2.20.3",
       "resolved": "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz",
-      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ=="
+      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==",
+      "peer": true
     },
     "node_modules/@emotion/babel-plugin": {
       "version": "11.13.5",
@@ -463,6 +468,7 @@
       "version": "0.8.5",
       "resolved": "https://registry.npmjs.org/@emotion/stylis/-/stylis-0.8.5.tgz",
       "integrity": "sha512-h6KtPihKFn3T9fuIrwvXXUOwlx3rfUvfZIcP5a6rh8Y7zjE3O06hT5Ss4S/YI1AYhuZ1kjaE/5EaOOI2NqSylQ==",
+      "dev": true,
       "license": "MIT"
     },
     "node_modules/@emotion/unitless": {
@@ -908,12 +914,14 @@
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/@exodus/schemasafe/-/schemasafe-1.3.0.tgz",
       "integrity": "sha512-5Aap/GaRupgNx/feGBwLLTVv8OQFfv3pq2lPRzPg9R+IOBnDgghTGW7l7EuVXOvg5cc/xSAlRW8rBrjIC3Nvqw==",
+      "dev": true,
       "license": "MIT"
     },
     "node_modules/@faker-js/faker": {
       "version": "7.6.0",
       "resolved": "https://registry.npmjs.org/@faker-js/faker/-/faker-7.6.0.tgz",
       "integrity": "sha512-XK6BTq1NDMo9Xqw/YkYyGjSsg44fbNwYRx7QK2CuoQgyy+f1rrTDHoExVM5PsyXCtfl2vs2vVJ0MN0yN6LppRw==",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": ">=14.0.0",
@@ -924,6 +932,7 @@
       "version": "2.0.4",
       "resolved": "https://registry.npmjs.org/@humanwhocodes/momoa/-/momoa-2.0.4.tgz",
       "integrity": "sha512-RE815I4arJFtt+FVeU1Tgp9/Xvecacji8w/V6XtXsWWH/wz/eNkNbhb+ny/+PlVZjV0rxQpRSQKNKE3lcktHEA==",
+      "dev": true,
       "license": "Apache-2.0",
       "engines": {
         "node": ">=10.10.0"
@@ -1089,6 +1098,7 @@
       "version": "0.5.2",
       "resolved": "https://registry.npmjs.org/@mapbox/geojson-rewind/-/geojson-rewind-0.5.2.tgz",
       "integrity": "sha512-tJaT+RbYGJYStt7wI3cq4Nl4SXxG8W7JDG5DMJu97V25RnbNg3QtQtf+KD+VLjNpWKYsRvXDNmNrBgEETr1ifA==",
+      "peer": true,
       "dependencies": {
         "get-stream": "^6.0.1",
         "minimist": "^1.2.6"
@@ -1100,12 +1110,14 @@
     "node_modules/@mapbox/geojson-types": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/@mapbox/geojson-types/-/geojson-types-1.0.2.tgz",
-      "integrity": "sha512-e9EBqHHv3EORHrSfbR9DqecPNn+AmuAoQxV6aL8Xu30bJMJR1o8PZLZzpk1Wq7/NfCbuhmakHTPYRhoqLsXRnw=="
+      "integrity": "sha512-e9EBqHHv3EORHrSfbR9DqecPNn+AmuAoQxV6aL8Xu30bJMJR1o8PZLZzpk1Wq7/NfCbuhmakHTPYRhoqLsXRnw==",
+      "peer": true
     },
     "node_modules/@mapbox/jsonlint-lines-primitives": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/@mapbox/jsonlint-lines-primitives/-/jsonlint-lines-primitives-2.0.2.tgz",
       "integrity": "sha512-rY0o9A5ECsTQRVhv7tL/OyDpGAoUB4tTvLiW1DSzQGq4bvTPhNw1VpSNjDJc5GFZ2XuyOtSWSVN05qOtcD71qQ==",
+      "peer": true,
       "engines": {
         "node": ">= 0.6"
       }
@@ -1114,6 +1126,7 @@
       "version": "1.5.0",
       "resolved": "https://registry.npmjs.org/@mapbox/mapbox-gl-supported/-/mapbox-gl-supported-1.5.0.tgz",
       "integrity": "sha512-/PT1P6DNf7vjEEiPkVIRJkvibbqWtqnyGaBz3nfRdcxclNSnSdaLU5tfAgcD7I8Yt5i+L19s406YLl1koLnLbg==",
+      "peer": true,
       "peerDependencies": {
         "mapbox-gl": ">=0.32.1 <2.0.0"
       }
@@ -1121,22 +1134,26 @@
     "node_modules/@mapbox/point-geometry": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/@mapbox/point-geometry/-/point-geometry-0.1.0.tgz",
-      "integrity": "sha512-6j56HdLTwWGO0fJPlrZtdU/B13q8Uwmo18Ck2GnGgN9PCFyKTZ3UbXeEdRFh18i9XQ92eH2VdtpJHpBD3aripQ=="
+      "integrity": "sha512-6j56HdLTwWGO0fJPlrZtdU/B13q8Uwmo18Ck2GnGgN9PCFyKTZ3UbXeEdRFh18i9XQ92eH2VdtpJHpBD3aripQ==",
+      "peer": true
     },
     "node_modules/@mapbox/tiny-sdf": {
       "version": "1.2.5",
       "resolved": "https://registry.npmjs.org/@mapbox/tiny-sdf/-/tiny-sdf-1.2.5.tgz",
-      "integrity": "sha512-cD8A/zJlm6fdJOk6DqPUV8mcpyJkRz2x2R+/fYcWDYG3oWbG7/L7Yl/WqQ1VZCjnL9OTIMAn6c+BC5Eru4sQEw=="
+      "integrity": "sha512-cD8A/zJlm6fdJOk6DqPUV8mcpyJkRz2x2R+/fYcWDYG3oWbG7/L7Yl/WqQ1VZCjnL9OTIMAn6c+BC5Eru4sQEw==",
+      "peer": true
     },
     "node_modules/@mapbox/unitbezier": {
       "version": "0.0.0",
       "resolved": "https://registry.npmjs.org/@mapbox/unitbezier/-/unitbezier-0.0.0.tgz",
-      "integrity": "sha512-HPnRdYO0WjFjRTSwO3frz1wKaU649OBFPX3Zo/2WZvuRi6zMiRGui8SnPQiQABgqCf8YikDe5t3HViTVw1WUzA=="
+      "integrity": "sha512-HPnRdYO0WjFjRTSwO3frz1wKaU649OBFPX3Zo/2WZvuRi6zMiRGui8SnPQiQABgqCf8YikDe5t3HViTVw1WUzA==",
+      "peer": true
     },
     "node_modules/@mapbox/vector-tile": {
       "version": "1.3.1",
       "resolved": "https://registry.npmjs.org/@mapbox/vector-tile/-/vector-tile-1.3.1.tgz",
       "integrity": "sha512-MCEddb8u44/xfQ3oD+Srl/tNcQoqTw3goGk2oLsrFxOTc3dUp+kAnby3PvAeeBYSMSjSPD1nd1AJA6W49WnoUw==",
+      "peer": true,
       "dependencies": {
         "@mapbox/point-geometry": "~0.1.0"
       }
@@ -1145,6 +1162,7 @@
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       "resolved": "https://registry.npmjs.org/@mapbox/whoots-js/-/whoots-js-3.1.0.tgz",
       "integrity": "sha512-Es6WcD0nO5l+2BOQS4uLfNPYQaNDfbot3X1XUoloz+x0mPDS3eeORZJl06HXjwBG1fOGwCRnzK88LMdxKRrd6Q==",
+      "peer": true,
       "engines": {
         "node": ">=6.0.0"
       }
@@ -1153,6 +1171,7 @@
       "version": "20.4.0",
       "resolved": "https://registry.npmjs.org/@maplibre/maplibre-gl-style-spec/-/maplibre-gl-style-spec-20.4.0.tgz",
       "integrity": "sha512-AzBy3095fTFPjDjmWpR2w6HVRAZJ6hQZUCwk5Plz6EyfnfuQW1odeW5i2Ai47Y6TBA2hQnC+azscjBSALpaWgw==",
+      "peer": true,
       "dependencies": {
         "@mapbox/jsonlint-lines-primitives": "~2.0.2",
         "@mapbox/unitbezier": "^0.0.1",
@@ -1171,12 +1190,14 @@
     "node_modules/@maplibre/maplibre-gl-style-spec/node_modules/@mapbox/unitbezier": {
       "version": "0.0.1",
       "resolved": "https://registry.npmjs.org/@mapbox/unitbezier/-/unitbezier-0.0.1.tgz",
-      "integrity": "sha512-nMkuDXFv60aBr9soUG5q+GvZYL+2KZHVvsqFCzqnkGEf46U2fvmytHaEVc1/YZbiLn8X+eR3QzX1+dwDO1lxlw=="
+      "integrity": "sha512-nMkuDXFv60aBr9soUG5q+GvZYL+2KZHVvsqFCzqnkGEf46U2fvmytHaEVc1/YZbiLn8X+eR3QzX1+dwDO1lxlw==",
+      "peer": true
     },
     "node_modules/@maplibre/maplibre-gl-style-spec/node_modules/tinyqueue": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/tinyqueue/-/tinyqueue-3.0.0.tgz",
-      "integrity": "sha512-gRa9gwYU3ECmQYv3lslts5hxuIa90veaEcxDYuu3QGOIAEM2mOZkVHp48ANJuu1CURtRdHKUBY5Lm1tHV+sD4g=="
+      "integrity": "sha512-gRa9gwYU3ECmQYv3lslts5hxuIa90veaEcxDYuu3QGOIAEM2mOZkVHp48ANJuu1CURtRdHKUBY5Lm1tHV+sD4g==",
+      "peer": true
     },
     "node_modules/@mui/core-downloads-tracker": {
       "version": "6.4.11",
@@ -1655,6 +1676,7 @@
       "version": "1.8.0",
       "resolved": "https://registry.npmjs.org/@noble/hashes/-/hashes-1.8.0.tgz",
       "integrity": "sha512-jCs9ldd7NwzpgXDIf6P3+NrHh9/sD6CQdxHyjQI+h/6rDNo88ypBxxz45UDuZHz9r3tNz7N/VInSVoVdtXEI4A==",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": "^14.21.3 || >=16"
@@ -1667,6 +1689,7 @@
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/@nodable/entities/-/entities-2.1.1.tgz",
       "integrity": "sha512-Pig3HxDIoMgjdEH8OCf/dkcTmLFjJRjWuq8jSnklu284/TKOPibSRERmOykiwmyXTtv61mP+44f3GMx0tLAyjg==",
+      "dev": true,
       "funding": [
         {
           "type": "github",
@@ -1679,6 +1702,7 @@
       "version": "1.9.0",
       "resolved": "https://registry.npmjs.org/@opentelemetry/api/-/api-1.9.0.tgz",
       "integrity": "sha512-3giAOQvZiH5F9bMlMiv8+GSPMeqg0dbaeo58/0SlA9sxSqZhnUtxzX9/2FzyhS9sWQf5S0GJE0AKBrFqjpeYcg==",
+      "dev": true,
       "license": "Apache-2.0",
       "engines": {
         "node": ">=8.0.0"
@@ -1688,6 +1712,7 @@
       "version": "0.202.0",
       "resolved": "https://registry.npmjs.org/@opentelemetry/api-logs/-/api-logs-0.202.0.tgz",
       "integrity": "sha512-fTBjMqKCfotFWfLzaKyhjLvyEyq5vDKTTFfBmx21btv3gvy8Lq6N5Dh2OzqeuN4DjtpSvNT1uNVfg08eD2Rfxw==",
+      "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
         "@opentelemetry/api": "^1.3.0"
@@ -1700,6 +1725,7 @@
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/@opentelemetry/context-async-hooks/-/context-async-hooks-2.0.1.tgz",
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       "version": "2.0.8",
       "resolved": "https://registry.npmjs.org/url-template/-/url-template-2.0.8.tgz",
       "integrity": "sha512-XdVKMF4SJ0nP/O7XIPB0JwAEuT9lDIYnNsK8yGVe43y0AWoKeJNdv3ZNWh7ksJ6KqQFjOO6ox/VEitLnaVNufw==",
+      "dev": true,
       "license": "BSD"
     },
     "node_modules/use-sync-external-store": {
@@ -8657,6 +9100,7 @@
       "version": "3.1.3",
       "resolved": "https://registry.npmjs.org/vt-pbf/-/vt-pbf-3.1.3.tgz",
       "integrity": "sha512-2LzDFzt0mZKZ9IpVF2r69G9bXaP2Q2sArJCmcCgvfTdCCZzSyz4aCLoQyUilu37Ll56tCblIZrXFIjNUpGIlmA==",
+      "peer": true,
       "dependencies": {
         "@mapbox/point-geometry": "0.1.0",
         "@mapbox/vector-tile": "^1.3.1",
@@ -8666,12 +9110,14 @@
     "node_modules/weak-map": {
       "version": "1.0.8",
       "resolved": "https://registry.npmjs.org/weak-map/-/weak-map-1.0.8.tgz",
-      "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw=="
+      "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw==",
+      "peer": true
     },
     "node_modules/webgl-context": {
       "version": "2.2.0",
       "resolved": "https://registry.npmjs.org/webgl-context/-/webgl-context-2.2.0.tgz",
       "integrity": "sha512-q/fGIivtqTT7PEoF07axFIlHNk/XCPaYpq64btnepopSWvKNFkoORlQYgqDigBIuGA1ExnFd/GnSUnBNEPQY7Q==",
+      "peer": true,
       "dependencies": {
         "get-canvas-context": "^1.0.1"
       }
@@ -8680,12 +9126,14 @@
       "version": "3.0.1",
       "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
       "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==",
+      "dev": true,
       "license": "BSD-2-Clause"
     },
     "node_modules/whatwg-url": {
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
       "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "tr46": "~0.0.3",
@@ -8696,6 +9144,7 @@
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/which/-/which-4.0.0.tgz",
       "integrity": "sha512-GlaYyEb07DPxYCKhKzplCWBJtvxZcZMrL+4UkrTSJHHPyZU4mYYTv3qaOe77H7EODLSSopAUFAc6W8U4yqvscg==",
+      "peer": true,
       "dependencies": {
         "isexe": "^3.1.1"
       },
@@ -8709,13 +9158,15 @@
     "node_modules/wordwrap": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz",
-      "integrity": "sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q=="
+      "integrity": "sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q==",
+      "dev": true
     },
     "node_modules/world-calendars": {
       "version": "1.0.4",
       "resolved": "https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.4.tgz",
       "integrity": "sha512-VGRnLJS+xJmGDPodgJRnGIDwGu0s+Cr9V2HB3EzlDZ5n0qb8h5SJtGUEkjrphZYAglEiXZ6kiXdmk0H/h/uu/w==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "object-assign": "^4.1.0"
       }
@@ -8724,6 +9175,7 @@
       "version": "7.0.0",
       "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
       "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "ansi-styles": "^4.0.0",
@@ -8758,12 +9210,14 @@
     "node_modules/wrappy": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
-      "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ=="
+      "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==",
+      "peer": true
     },
     "node_modules/ws": {
       "version": "7.5.10",
       "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.10.tgz",
       "integrity": "sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ==",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": ">=8.3.0"
@@ -8785,6 +9239,7 @@
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/xml-naming/-/xml-naming-0.1.0.tgz",
       "integrity": "sha512-k8KO9hrMyNk6tUWqUfkTEZbezRRpONVOzUTnc97VnCvyj6Tf9lyUR9EDAIeiVLv56jsMcoXEwjW8Kv5yPY52lw==",
+      "dev": true,
       "funding": [
         {
           "type": "github",
@@ -8800,6 +9255,7 @@
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
       "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
+      "peer": true,
       "engines": {
         "node": ">=0.4"
       }
@@ -8808,6 +9264,7 @@
       "version": "5.0.8",
       "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz",
       "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==",
+      "dev": true,
       "license": "ISC",
       "engines": {
         "node": ">=10"
@@ -8839,12 +9296,14 @@
       "version": "0.0.43",
       "resolved": "https://registry.npmjs.org/yaml-ast-parser/-/yaml-ast-parser-0.0.43.tgz",
       "integrity": "sha512-2PTINUwsRqSd+s8XxKaJWQlUuEMHJQyEuh2edBbW8KNJz0SJPwUSD2zRWqezFEdN7IzAgeuYHFUCF7o8zRdZ0A==",
+      "dev": true,
       "license": "Apache-2.0"
     },
     "node_modules/yargs": {
       "version": "17.0.1",
       "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.0.1.tgz",
       "integrity": "sha512-xBBulfCc8Y6gLFcrPvtqKz9hz8SO0l1Ni8GgDekvBX2ro0HRQImDGnikfc33cgzcYUSncapnNcZDjVFIH3f6KQ==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "cliui": "^7.0.2",
@@ -8863,6 +9322,7 @@
       "version": "20.2.9",
       "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
       "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
+      "dev": true,
       "license": "ISC",
       "engines": {
         "node": ">=10"
diff --git a/frontend/package.json b/frontend/package.json
index 99d5c9d6..531a5de2 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -11,13 +11,12 @@
     "@mui/icons-material": "^6.1.2",
     "@mui/material": "^6.1.2",
     "@mui/x-data-grid": "^7.19.0",
-    "@redocly/cli": "^2.28.1",
     "@types/node": "^25.2.3",
     "@types/react": "^19.2.14",
     "@types/react-dom": "^19.2.3",
     "@vitejs/plugin-react-swc": "^4.2.3",
     "lodash": "^4.17.23",
-    "plotly.js": "^3.3.1",
+    "plotly.js-cartesian-dist-min": "^3.3.1",
     "react": "^19.2.4",
     "react-dom": "^19.2.4",
     "react-plotly.js": "^2.6.0",
@@ -33,16 +32,11 @@
     "serve": "vite preview",
     "redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=dist/openapi.html",
     "redocly4broker": "redocly build-docs ../broker/jfjoch_api.yaml --output=../broker/redoc-static.html",
-    "test": "react-scripts test",
-    "eject": "react-scripts eject",
     "openapi": "./node_modules/openapi-typescript-codegen/bin/index.js -i ../broker/jfjoch_api.yaml --output ./src/openapi"
   },
   "overrides": {
     "styled-components": "5.3.11"
   },
-  "eslintConfig": {
-    "extends": "react-app"
-  },
   "browserslist": {
     "production": [
       ">0.2%",
@@ -56,6 +50,7 @@
     ]
   },
   "devDependencies": {
+    "@redocly/cli": "^2.28.1",
     "@types/lodash": "^4.17.10",
     "@types/react-plotly.js": "^2.6.3",
     "esbuild-style-plugin": "^1.6.3",
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 3db6ea81..b3570596 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -64,7 +64,7 @@ class App extends Component<MyProps, MyState> {
         s: {}
     }
 
-    getValues() {
+    getValues = () => {
         DefaultService.getStatistics()
             .then(data => this.setState({s: data, connection_error: false}))
             .catch(_ => {
diff --git a/frontend/src/components/DataCollection.tsx b/frontend/src/components/DataCollection.tsx
index 28a72311..de02f731 100644
--- a/frontend/src/components/DataCollection.tsx
+++ b/frontend/src/components/DataCollection.tsx
@@ -264,29 +264,23 @@ class DataCollection extends React.Component<MyProps, MyState> {
                     <Stack direction="row" spacing={2} sx={{width: '90%'}}>
                         <NumberTextField
                             label="Grid elements (fast dim.)"
-                            callback={(val: number) => this.setState((e) => this.setState(
-                                prevState => (
-                                    {grid : {...prevState.grid, n_fast: val}}
-                                )))}
+                            callback={(val: number) => this.setState(
+                                prevState => ({grid : {...prevState.grid, n_fast: val}}))}
                             min={1}
                             default={this.state.grid.n_fast}
                         />
                         <NumberTextField
                             label="X step"
-                            callback={(val: number) => this.setState((e) => this.setState(
-                                prevState => (
-                                    {grid : {...prevState.grid, step_x_um: val}}
-                                )))}
+                            callback={(val: number) => this.setState(
+                                prevState => ({grid : {...prevState.grid, step_x_um: val}}))}
                             units="μm"
                             float={true}
                             default={this.state.grid.step_x_um}
                         />
                         <NumberTextField
                             label="Y step"
-                            callback={(val: number) => this.setState((e) => this.setState(
-                                prevState => (
-                                {grid : {...prevState.grid, step_y_um: val}}
-                            )))}
+                            callback={(val: number) => this.setState(
+                                prevState => ({grid : {...prevState.grid, step_y_um: val}}))}
                             units="μm"
                             float={true}
                             default={this.state.grid.step_y_um}
diff --git a/frontend/src/components/DataProcessingSettings.tsx b/frontend/src/components/DataProcessingSettings.tsx
index 52b322ef..c6352e96 100644
--- a/frontend/src/components/DataProcessingSettings.tsx
+++ b/frontend/src/components/DataProcessingSettings.tsx
@@ -3,6 +3,7 @@ import React, {Component} from 'react';
 import Paper from '@mui/material/Paper';
 import {Grid, Slider, Switch, Typography} from "@mui/material";
 import {DefaultService, spot_finding_settings} from "../openapi";
+import _ from "lodash";
 
 type MyProps = {
     s?: spot_finding_settings,
@@ -11,25 +12,29 @@ type MyProps = {
 
 type MyState = {
     s: spot_finding_settings,
+    last_downloaded_s: spot_finding_settings,
     high_res_gap_Q_recipA: number
 }
 
+const default_spot_finding_settings: spot_finding_settings = {
+    enable: true,
+    indexing: true,
+    photon_count_threshold: 8,
+    signal_to_noise_threshold: 3.0,
+    min_pix_per_spot: 2,
+    max_pix_per_spot: 50,
+    high_resolution_limit: 2.5,
+    low_resolution_limit: 50.0,
+    quick_integration: false,
+    high_resolution_limit_for_spot_count_low_res: 5.0,
+    ice_ring_width_q_recipA: 0.02,
+    high_res_gap_Q_recipA: 1.5
+};
+
 class DataProcessingSettings extends Component<MyProps, MyState> {
     state : MyState = {
-        s: {
-            enable: true,
-            indexing: true,
-            photon_count_threshold: 8,
-            signal_to_noise_threshold: 3.0,
-            min_pix_per_spot: 2,
-            max_pix_per_spot: 50,
-            high_resolution_limit: 2.5,
-            low_resolution_limit: 50.0,
-            quick_integration: false,
-            high_resolution_limit_for_spot_count_low_res: 5.0,
-            ice_ring_width_q_recipA: 0.02,
-            high_res_gap_Q_recipA: 1.5
-        },
+        s: default_spot_finding_settings,
+        last_downloaded_s: default_spot_finding_settings,
         high_res_gap_Q_recipA: 1.5
     }
 
@@ -41,9 +46,12 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
     getValues() {
         const incoming = this.props.s;
 
-        if (incoming !== undefined)
+        // Only adopt the server copy when it actually changed, otherwise the
+        // 1 s statistics poll would overwrite edits the user is making.
+        if ((incoming !== undefined) && !_.isEqual(incoming, this.state.last_downloaded_s))
             this.setState(prevState => ({
                 s: incoming,
+                last_downloaded_s: incoming,
                 high_res_gap_Q_recipA: incoming.high_res_gap_Q_recipA ?? prevState.high_res_gap_Q_recipA
             }));
     }
@@ -52,9 +60,8 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
         this.getValues();
     }
 
-    componentDidUpdate(prevProps: Readonly<MyProps>) {
-        if ((this.props.s !== undefined) && (prevProps.s != this.props.s))
-            this.setState({s: this.props.s});
+    componentDidUpdate() {
+        this.getValues();
     }
 
     setPhotonCountThreshold = (event: Event, newValue: number | number[]) => {
diff --git a/frontend/src/components/MultiLinePlotWrapper.jsx b/frontend/src/components/MultiLinePlotWrapper.jsx
index 28b645c2..0d4a3667 100644
--- a/frontend/src/components/MultiLinePlotWrapper.jsx
+++ b/frontend/src/components/MultiLinePlotWrapper.jsx
@@ -1,6 +1,6 @@
 import React, {Component} from 'react';
 
-import Plot from "react-plotly.js";
+import Plot from "./Plot";
 
 // Not using TypeScript, as plotly is not TypeScript :(
 
@@ -41,7 +41,6 @@ class MultiLinePlotWrapper extends Component {
             }
         }
 
-        console.log(layout);
         return <Plot
             style={{width: "100%", height: "100%"}}
             data={this.props.data}
diff --git a/frontend/src/components/Plot.jsx b/frontend/src/components/Plot.jsx
new file mode 100644
index 00000000..9733b4f2
--- /dev/null
+++ b/frontend/src/components/Plot.jsx
@@ -0,0 +1,12 @@
+// Custom react-plotly.js component built on the cartesian-only Plotly bundle.
+// The app only renders "scatter" and "heatmap" traces, both of which live in
+// the cartesian bundle, so we avoid pulling in the full plotly.js (3D/gl,
+// mapbox, geo, ...) which dominates the JS payload.
+// Not using TypeScript, as plotly is not TypeScript :(
+
+import createPlotlyComponent from "react-plotly.js/factory";
+import Plotly from "plotly.js-cartesian-dist-min";
+
+const Plot = createPlotlyComponent(Plotly);
+
+export default Plot;
diff --git a/frontend/src/components/PreviewImage.tsx b/frontend/src/components/PreviewImage.tsx
index de732a9a..8c7c7da0 100644
--- a/frontend/src/components/PreviewImage.tsx
+++ b/frontend/src/components/PreviewImage.tsx
@@ -59,7 +59,7 @@ function stringToEnum(value: string): color_scale {
         (v) => v === value
     ) as color_scale;
 
-    // If no match is found, default to file_writer_format.NONE
+    // If no match is found, default to the indigo color scale
     return enumValue || color_scale.INDIGO;
 }
 
@@ -89,25 +89,24 @@ class PreviewImage extends Component<MyProps, MyState> {
     }
 
     update_image_id_mode = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s : preview_settings = this.state.settings;
-
+        let image_id : number;
         switch (event.target.value) {
             case "last":
-                s.image_id = -1;
-                this.setState({settings: s, image_id_mode: event.target.value});
-                this.getValues(s);
+                image_id = -1;
                 break;
             case "last_indexed":
-                s.image_id = -2;
-                this.setState({settings: s, image_id_mode: event.target.value});
-                this.getValues(s);
+                image_id = -2;
                 break;
             case "select":
-                s.image_id = this.state.image_id;
-                this.setState({settings: s, image_id_mode: event.target.value});
-                this.getValues(s);
+                image_id = this.state.image_id;
                 break;
+            default:
+                return;
         }
+
+        let s : preview_settings = {...this.state.settings, image_id};
+        this.setState({settings: s, image_id_mode: event.target.value});
+        this.getValues(s);
     }
 
     updateToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
diff --git a/frontend/src/react-app-env.d.ts b/frontend/src/react-app-env.d.ts
deleted file mode 100644
index 6431bc5f..00000000
--- a/frontend/src/react-app-env.d.ts
+++ /dev/null
@@ -1 +0,0 @@
-/// <reference types="react-scripts" />
diff --git a/frontend/src/serviceWorker.js b/frontend/src/serviceWorker.js
deleted file mode 100644
index b04b771a..00000000
--- a/frontend/src/serviceWorker.js
+++ /dev/null
@@ -1,141 +0,0 @@
-// This optional code is used to register a service worker.
-// register() is not called by default.
-
-// This lets the app load faster on subsequent visits in production, and gives
-// it offline capabilities. However, it also means that developers (and users)
-// will only see deployed updates on subsequent visits to a page, after all the
-// existing tabs open on the page have been closed, since previously cached
-// resources are updated in the background.
-
-// To learn more about the benefits of this model and instructions on how to
-// opt-in, read https://bit.ly/CRA-PWA
-
-const isLocalhost = Boolean(
-  window.location.hostname === 'localhost' ||
-    // [::1] is the IPv6 localhost address.
-    window.location.hostname === '[::1]' ||
-    // 127.0.0.0/8 are considered localhost for IPv4.
-    window.location.hostname.match(
-      /^127(?:\.(?:25[0-5]|2[0-4][0-9]|[01]?[0-9][0-9]?)){3}$/
-    )
-);
-
-export function register(config) {
-  if (process.env.NODE_ENV === 'production' && 'serviceWorker' in navigator) {
-    // The URL constructor is available in all browsers that support SW.
-    const publicUrl = new URL(process.env.PUBLIC_URL, window.location.href);
-    if (publicUrl.origin !== window.location.origin) {
-      // Our service worker won't work if PUBLIC_URL is on a different origin
-      // from what our page is served on. This might happen if a CDN is used to
-      // serve assets; see https://github.com/facebook/create-react-app/issues/2374
-      return;
-    }
-
-    window.addEventListener('load', () => {
-      const swUrl = `${process.env.PUBLIC_URL}/service-worker.js`;
-
-      if (isLocalhost) {
-        // This is running on localhost. Let's check if a service worker still exists or not.
-        checkValidServiceWorker(swUrl, config);
-
-        // Add some additional logging to localhost, pointing developers to the
-        // service worker/PWA documentation.
-        navigator.serviceWorker.ready.then(() => {
-          console.log(
-            'This web app is being served cache-first by a service ' +
-              'worker. To learn more, visit https://bit.ly/CRA-PWA'
-          );
-        });
-      } else {
-        // Is not localhost. Just register service worker
-        registerValidSW(swUrl, config);
-      }
-    });
-  }
-}
-
-function registerValidSW(swUrl, config) {
-  navigator.serviceWorker
-    .register(swUrl)
-    .then(registration => {
-      registration.onupdatefound = () => {
-        const installingWorker = registration.installing;
-        if (installingWorker == null) {
-          return;
-        }
-        installingWorker.onstatechange = () => {
-          if (installingWorker.state === 'installed') {
-            if (navigator.serviceWorker.controller) {
-              // At this point, the updated precached content has been fetched,
-              // but the previous service worker will still serve the older
-              // content until all client tabs are closed.
-              console.log(
-                'New content is available and will be used when all ' +
-                  'tabs for this page are closed. See https://bit.ly/CRA-PWA.'
-              );
-
-              // Execute callback
-              if (config && config.onUpdate) {
-                config.onUpdate(registration);
-              }
-            } else {
-              // At this point, everything has been precached.
-              // It's the perfect time to display a
-              // "Content is cached for offline use." message.
-              console.log('Content is cached for offline use.');
-
-              // Execute callback
-              if (config && config.onSuccess) {
-                config.onSuccess(registration);
-              }
-            }
-          }
-        };
-      };
-    })
-    .catch(error => {
-      console.error('Error during service worker registration:', error);
-    });
-}
-
-function checkValidServiceWorker(swUrl, config) {
-  // Check if the service worker can be found. If it can't reload the page.
-  fetch(swUrl, {
-    headers: { 'Service-Worker': 'script' },
-  })
-    .then(response => {
-      // Ensure service worker exists, and that we really are getting a JS file.
-      const contentType = response.headers.get('content-type');
-      if (
-        response.status === 404 ||
-        (contentType != null && contentType.indexOf('javascript') === -1)
-      ) {
-        // No service worker found. Probably a different app. Reload the page.
-        navigator.serviceWorker.ready.then(registration => {
-          registration.unregister().then(() => {
-            window.location.reload();
-          });
-        });
-      } else {
-        // Service worker found. Proceed as normal.
-        registerValidSW(swUrl, config);
-      }
-    })
-    .catch(() => {
-      console.log(
-        'No internet connection found. App is running in offline mode.'
-      );
-    });
-}
-
-export function unregister() {
-  if ('serviceWorker' in navigator) {
-    navigator.serviceWorker.ready
-      .then(registration => {
-        registration.unregister();
-      })
-      .catch(error => {
-        console.error(error.message);
-      });
-  }
-}
diff --git a/frontend/src/setupTests.js b/frontend/src/setupTests.js
deleted file mode 100644
index 74b1a275..00000000
--- a/frontend/src/setupTests.js
+++ /dev/null
@@ -1,5 +0,0 @@
-// jest-dom adds custom jest matchers for asserting on DOM nodes.
-// allows you to do things like:
-// expect(element).toHaveTextContent(/react/i)
-// learn more: https://github.com/testing-library/jest-dom
-import '@testing-library/jest-dom/extend-expect';
-- 
2.52.0


From c69b5297d5793f3a14591d5a98313528e2ff6dfb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 07:38:36 +0200
Subject: [PATCH 064/228] docs: add jfjoch_process page, refresh viewer/tools
 docs, unify CLI naming

- Add docs/JFJOCH_PROCESS.md describing the offline analysis tool, its
  options, output files, and the broker/viewer/process distinction; mention
  jfjoch_scale for re-scaling/merging.
- Rewrite docs/JFJOCH_VIEWER.md for consistency: functionality, HTTP env
  vars (JUNGFRAUJOCH_HTTP_HOST/PORT), command line, and the real D-Bus API.
- Refresh docs/TOOLS.md to the current set of tools; add both pages to index.rst.
- jfjoch_process: fix stale self-name (jfjoch_analysis -> jfjoch_process) in
  usage/license/logger.
- jfjoch_scale: unify --scaling-high-resolution with jfjoch_process (drop -D
  short flag, make it long-only) and remove dead p/q/i short options.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/JFJOCH_PROCESS.md   | 159 +++++++++++++++++++++++++++++++++++++++
 docs/JFJOCH_VIEWER.md    |  66 ++++++++++++----
 docs/TOOLS.md            |  76 +++++++++++++------
 docs/index.rst           |   2 +
 tools/jfjoch_process.cpp |   6 +-
 tools/jfjoch_scale.cpp   |  11 +--
 6 files changed, 274 insertions(+), 46 deletions(-)
 create mode 100644 docs/JFJOCH_PROCESS.md

diff --git a/docs/JFJOCH_PROCESS.md b/docs/JFJOCH_PROCESS.md
new file mode 100644
index 00000000..ac8886a7
--- /dev/null
+++ b/docs/JFJOCH_PROCESS.md
@@ -0,0 +1,159 @@
+# jfjoch_process
+
+`jfjoch_process` is the **offline** crystallographic data-analysis tool of Jungfraujoch.
+It takes an existing HDF5 dataset, runs the full analysis pipeline — spot finding, indexing,
+geometry refinement, Bragg integration and (optionally) scaling and merging — and writes the
+results to a `_process.h5` file, plus reflection files (`.mtz`/`.cif`/`.hkl`) when merging is
+requested.
+
+It runs the *same* analysis code as the online and interactive tools, just driven from the
+command line over a file rather than a live detector stream.
+
+> **Note.** `jfjoch_process` is under very active development. This page describes the tool and
+> its options at a high level; the authoritative, always-current list of options is the program's
+> own usage message — run `jfjoch_process` with no arguments.
+
+## Where it fits among the three analysis tools
+
+| Tool | Mode | Driven by | Output |
+| --- | --- | --- | --- |
+| [`jfjoch_broker`](JFJOCH_BROKER.md) | Online, real-time streaming analysis on FPGA + GPU | HTTP/REST + ZeroMQ | Live results and statistics, images streamed to [`jfjoch_writer`](JFJOCH_WRITER.md) |
+| [`jfjoch_viewer`](JFJOCH_VIEWER.md) | Interactive, on-screen exploration | Qt desktop application | Displayed on screen (results not saved to disk) |
+| **`jfjoch_process`** | **Offline batch processing of a stored dataset** | **Command-line interface** | **`_process.h5`, and `.mtz`/`.cif`/`.hkl` when merging** |
+
+Use `jfjoch_process` to re-analyse data after acquisition, to experiment with processing
+parameters, or to produce merged intensities for downstream structure solution.
+
+## Hardware
+
+As with the rest of Jungfraujoch, **serious performance requires an NVIDIA GPU**. The CUDA build
+provides the GPU fast-feedback indexer (`ffbidx`) and the GPU FFT indexer (`fft`); without CUDA
+only the CPU `fftw` indexer is available. Spot finding, integration and scaling run on the CPU and
+scale with the thread count (`-N`).
+
+## Input and output
+
+**Input** is a single Jungfraujoch HDF5 master file (NXmx-based). If the dataset already contains
+stored spot lists, two-pass rotation indexing can reuse them instead of re-running spot finding on
+the first pass.
+
+**Output** (controlled by `-o, --output-prefix`, default `output`):
+
+- `<prefix>_process.h5` — NXmx-compliant HDF5 with derived metadata (spots, indexing,
+  integration, azimuthal integration, per-image statistics). See
+  [HDF5 / NeXus data format](HDF5.md) for the layout.
+- When merging (`-M`, or whenever a `--reference-mtz` is supplied), the merged reflections are
+  written as `<prefix>.mtz` (default), or `<prefix>.cif` / `<prefix>.hkl` depending on
+  `--scaling-output`. No-reference scaling additionally emits per-iteration `<prefix>_iterN_scale.dat`.
+
+Merged statistics (⟨I/σ⟩, CC1/2, completeness, …), the error model and timing are printed to the
+console.
+
+## Re-scaling and re-merging (`jfjoch_scale`)
+
+The companion tool `jfjoch_scale` re-scales and merges the *already-integrated* reflections stored
+in one or more `_process.h5` files, without re-running spot finding or integration. Use it to
+re-merge quickly with a different space group, partiality model, resolution limit or reference MTZ,
+or to combine several processed runs into one set of merged intensities.
+
+## Quick start
+
+### Rotation data
+
+Two-pass rotation indexing, rotation partiality, scale and merge in space group 96:
+
+```
+jfjoch_process rotation_master.h5 \
+    -o lyso_rot -N 16 \
+    -R -S 96 \
+    -M -P rot
+```
+
+`-R` runs the two-pass rotation indexer (index the sweep once, then process every frame against
+that lattice); `-P rot` selects the rotation partiality model; `-M` scales and merges. For strong
+rotation data the de-novo FFT indexer often indexes more frames — add `-X fft` (and drop `-C` to
+let it find the cell from scratch).
+
+### Still / serial data
+
+Known-cell indexing of independent stills with the GPU fast-feedback indexer, then merge against a
+reference structure:
+
+```
+jfjoch_process serial_master.h5 \
+    -o lyso_serial -N 16 \
+    -X ffbidx -C 79,79,38,90,90,90 -S 96 \
+    --spot-sigma 4 \
+    -M -z reference.mtz -r pixelrefine \
+    --scaling-high-resolution 1.8
+```
+
+`ffbidx` requires a known cell (`-C`) and is the indexer of choice for sparse serial stills.
+`-r pixelrefine` selects the experimental reference-driven still integrator (needs
+`--reference-mtz`). For weak serial data, tightening spot finding with `--spot-sigma 4` typically
+raises the indexing rate substantially.
+
+## Command-line options
+
+General:
+
+| Option | Description |
+| --- | --- |
+| `-o, --output-prefix <txt>` | Output file prefix (default: `output`) |
+| `-N, --threads <num>` | Number of worker threads (default: 1) |
+| `-s, --start-image <num>` | First image to process (default: 0) |
+| `-e, --end-image <num>` | Last image to process (default: all) |
+| `-t, --stride <num>` | Process every *n*-th image (default: 1) |
+| `-v, --verbose` | Verbose output |
+
+Spot finding:
+
+| Option | Description |
+| --- | --- |
+| `--spot-sigma <num>` | Noise sigma level for spot finding (default: 3.0) |
+| `--spot-threshold <num>` | Photon-count threshold for spot finding (default: 10) |
+| `--spot-high-resolution <num>` | High-resolution limit for spot finding, Å (default: 1.5) |
+| `--max-spots <num>` | Maximum spot count (default: 250) |
+
+Indexing:
+
+| Option | Description |
+| --- | --- |
+| `-X, --indexing-algorithm <txt>` | `FFBIDX` \| `FFT` \| `FFTW` \| `Auto` \| `None` |
+| `-C, --unit-cell <cell>` | Reference unit cell `"a,b,c,alpha,beta,gamma"` (required by `ffbidx`) |
+| `-S, --space-group <num>` | Space group number (used for indexing and scaling) |
+| `-r, --refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `pixelrefine` |
+| `-R, --two-pass-rotation[=num]` | Two-pass offline rotation indexing (optional image count, default 30) |
+| `--single-pass-rotation[=num]` | Online-like single-pass rotation indexing (optional min angular range, deg) |
+| `--redo-rotation-spots` | Redo spot finding for the two-pass rotation first pass |
+| `--force-rotation-lattice <vec>` | Force rotation lattice (9 floats, Å), skipping the first pass |
+
+Indexer choice in brief: `ffbidx` (GPU) refines toward a **known cell** and is best for sparse
+serial stills; `fft` (GPU) / `fftw` (CPU) index **de novo** and suit strong rotation data. See the
+[CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md) for the algorithms.
+
+Scaling and merging:
+
+| Option | Description |
+| --- | --- |
+| `-M, --scale-merge` | Scale and merge |
+| `-P, --partiality <txt>` | Partiality model: `fixed` (default) \| `rot` \| `unity` |
+| `-A, --anomalous` | Anomalous mode (keep Friedel pairs separate) |
+| `-B, --refine-bfactor` | Refine a per-image B-factor |
+| `-w, --wedge[=num]` | Refine the per-image rotation wedge (optional starting value) |
+| `--scaling-high-resolution <num>` | High-resolution limit for scaling, Å (default: no limit) |
+| `--min-partiality <num>` | Minimum partiality to accept a reflection (default: 0.02) |
+| `--reject-outliers <num>` | Per-observation outlier rejection, N σ from the per-reflection median (default: off) |
+| `--reject-delta-cchalf <num>` | Drop images with ΔCC1/2 below mean − N·stddev (default: off) |
+| `--min-image-cc <num>` | Per-image CC limit, percent (default: no limit) |
+| `--scaling-iterations <num>` | Scaling iterations with no reference data (default: 3) |
+| `--scaling-output <txt>` | Reflection output format: `mtz` (default) \| `cif` \| `txt` |
+| `-z, --reference-mtz <file>` | Reference MTZ (enables reference-driven scaling) |
+
+Pixel refinement (experimental; select with `-r pixelrefine`, requires `--reference-mtz`):
+
+| Option | Description |
+| --- | --- |
+| `--bandwidth <num>` | Relative X-ray bandwidth FWHM (e.g. `0.01` for a 1% DMM); default from file or 0 (monochromatic) |
+| `--integration-radius <r>` | Signal-box radius `r1`, or `r1,r2,r3` (px). One value ⇒ `r2=r1+2`, `r3=r1+4` |
+| `--profile-multiplier <num>` | Scale the measured tangential profile width (default: 6; XDS-style generous aperture) |
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index 9e160be8..5a7ff0a8 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -1,19 +1,57 @@
 # jfjoch_viewer
 
-Jungfraujoch diffraction viewer is distributed as a standalone application.
-It uses Qt library version 6, and allows to open HDF5 files generated by [`jfjoch_writer`](JFJOCH_WRITER.md). 
-It as well allows to open NXmx files written by DECTRIS detectors, though testing is very limited.
-It can be downloaded pre-built from Gitea release page, or from Jungfraujoch RPM/APT repositories.
-See [Deployment](DEPLOYMENT.md) section for more information.
-This viewer can be also sync online with [`jfjoch_broker`](JFJOCH_BROKER.md) HTTP interface
-to visualize data during data collection.
+`jfjoch_viewer` is the **interactive** desktop application of Jungfraujoch. It opens diffraction
+datasets, displays each image together with the analysis overlay (spots, predictions, azimuthal
+integration, per-image statistics), and can follow a live data collection by syncing with a
+running [`jfjoch_broker`](JFJOCH_BROKER.md) over its HTTP interface.
 
-# Data processing pipeline
-Viewer contains embedded data processing pipeline, which is the same as the one used
-in Jungfraujoch installation. On systems equipped with GPU, it is preferable to use version
-compiled with CUDA support (proper RPM/APT repositories).
+It is a standalone Qt 6 application, distributed pre-built on the Gitea release page and in the
+Jungfraujoch RPM/APT repositories (see [Deployment](DEPLOYMENT.md)).
 
-At the moment data processing results are not saved to disk.
+## Where it fits among the three analysis tools
 
-# DBus interface
-Viewer can be controlled externally with DBus interface, allowing to open file, open detector via HTTP or load image.
\ No newline at end of file
+| Tool | Mode | Driven by | Output |
+| --- | --- | --- | --- |
+| [`jfjoch_broker`](JFJOCH_BROKER.md) | Online, real-time streaming analysis on FPGA + GPU | HTTP/REST + ZeroMQ | Live results and statistics, images streamed to [`jfjoch_writer`](JFJOCH_WRITER.md) |
+| **`jfjoch_viewer`** | **Interactive, on-screen exploration** | **Qt desktop application** | **Displayed on screen (results not saved to disk)** |
+| [`jfjoch_process`](JFJOCH_PROCESS.md) | Offline batch processing of a stored dataset | Command-line interface | `_process.h5`, and `.mtz`/`.cif`/`.hkl` when merging |
+
+## Functionality
+
+- Opens HDF5 files written by [`jfjoch_writer`](JFJOCH_WRITER.md) (`*_master.h5`) and the
+  `*_process.h5` files produced by [`jfjoch_process`](JFJOCH_PROCESS.md). It also opens NXmx files
+  written by DECTRIS detectors, though that path has had only limited testing.
+- Runs an **embedded data-processing pipeline** — the same analysis code as the rest of
+  Jungfraujoch — performing spot finding, indexing and integration on the displayed images.
+  Results are shown on screen but are **not** saved to disk.
+- Auxiliary windows and panels: image list, image metadata, spot list, reflection list,
+  per-region-of-interest statistics, the azimuthal-integration profile, and dataset-info charts.
+- User-mask editing: build a user mask interactively, clear it, save it as TIFF, or upload it to a
+  connected server.
+
+## Hardware
+
+As with the rest of Jungfraujoch, **serious performance requires an NVIDIA GPU**. On systems with a
+GPU, use the CUDA build (provided as separate RPM/APT repositories) for the embedded indexing and
+integration; the non-CUDA build runs the same pipeline on the CPU at much lower throughput.
+
+## Opening data
+
+- **File ▸ Open** (`Ctrl+O`) — open a local HDF5 file.
+- **File ▸ Open HTTP** (`Ctrl+H`) — connect to a `jfjoch_broker` HTTP endpoint to follow a live
+  collection. The dialog defaults to host `localhost` and port `8080`; these defaults can be
+  overridden with the environment variables `JUNGFRAUJOCH_HTTP_HOST` and `JUNGFRAUJOCH_HTTP_PORT`.
+- **Command line** — `jfjoch_viewer <file.h5>` opens a file (or an `http://host:port` URL) on
+  start-up. `--dbus <true|false>` (`-d`) enables or disables the D-Bus interface (default: enabled);
+  `--help` and `--version` behave as usual.
+
+## D-Bus interface
+
+When enabled, the viewer registers the D-Bus interface `ch.psi.jfjoch_viewer`, so other processes
+can drive it:
+
+- `LoadFile(filename, image_number=0, summation=1)` — open a file (or an `http://host:port` URL)
+  and display the given image.
+- `LoadImage(image_number, summation=1)` — navigate to an image in the already-open dataset.
+
+`summation` sums that many consecutive images before display.
diff --git a/docs/TOOLS.md b/docs/TOOLS.md
index d567125f..e723d240 100644
--- a/docs/TOOLS.md
+++ b/docs/TOOLS.md
@@ -1,47 +1,75 @@
 # Tools
 
-## jfjoch_pcie_status
-Prints detailed status information about the card. Execute by adding device path, e.g.:
+Besides the main services ([`jfjoch_broker`](JFJOCH_BROKER.md),
+[`jfjoch_writer`](JFJOCH_WRITER.md), [`jfjoch_viewer`](JFJOCH_VIEWER.md)), the repository ships a
+number of command-line tools. Each prints its own usage when run with `-h` or without arguments.
+
+## Data analysis
+
+### jfjoch_process
+Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
+integration, scaling/merging) on a stored HDF5 dataset, producing a `_process.h5` file and, when
+merging, reflection files. See [jfjoch_process](JFJOCH_PROCESS.md).
+
+### jfjoch_scale
+Re-scales and merges the already-integrated reflections from one or more `_process.h5` files
+(no re-integration). Useful to re-merge with a different space group, partiality, resolution limit
+or reference MTZ, or to combine several runs. See [jfjoch_process](JFJOCH_PROCESS.md).
+
+### jfjoch_extract_hkl
+Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
+neighbouring images and compare against an XDS `INTEGRATE.HKL` reference.
+
+## FPGA / PCIe card management
+
+### jfjoch_pcie_status
+Prints detailed status information about the card. Safe to run during data collection:
 ```
 ./jfjoch_pcie_status /dev/jfjoch0
 ```
-The program is safe to execute during a running data collection.
-
-## jfjoch_pcie_clear_net_counters
-Network counters in the card give information about Ethernet, UDP and ICMP packets encountered by the network stack prior to Jungfraujoch logic.
-These counters are running from the moment card is powered on. They can be reset by running the program with device name, e.g.:
-```
-./jfjoch_pcie_clear_net_counters /dev/jfjoch0
-```
-
-## jfjoch_pcie_net_cfg
-Network configuration can be retrieved and modified with `jfjoch_pcie_net_cfg` tool. Usage:
 
+### jfjoch_pcie_net_cfg
+Reads and modifies the network configuration of the card's interfaces:
 ```
 jfjoch_pcie_net_cfg <device name>
-     Read configuration for all network interface of a device
+     Read configuration for all network interfaces of a device
 jfjoch_pcie_net_cfg <device name> <if number>|fgen
-     Read configuration for a particular network interface / internal frame generator"
+     Read configuration for a particular network interface / internal frame generator
 jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
      Set IPv4 address for a particular network interface / internal frame generator
 jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
      Set direct mode for a particular network interface / internal frame generator
 jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
-     Clear Ethernet counter for a particular network interface / internal frame generator
+     Clear Ethernet counters for a particular network interface / internal frame generator
 ```
 
-## jfjoch_hdf5_tools
+### jfjoch_pcie_clear_net_counters
+Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
+```
+./jfjoch_pcie_clear_net_counters /dev/jfjoch0
+```
 
-Tool to test single threaded HDF5 writer performance
+### jfjoch_pcie_read_register
+Reads raw Jungfraujoch FPGA registers.
 
-## jfjoch_offline_process
+## Testing, benchmarking and simulation
 
-Tool to run offline processing on existing HDF5 dataset
+### jfjoch_udp_simulator
+UDP packet simulator used to test the Jungfraujoch FPGA receiver.
 
-## jfjoch_udp_simulator
+### jfjoch_fpga_test
+Exercises and benchmarks the FPGA data path and receiver. With `-H` it runs the high-level
+synthesis C model on the CPU, so no FPGA device is required.
 
-UDP simulator to test Jungfraujoch FPGA
+### jfjoch_lite_perf_test
+Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file
+writing.
 
-## jfjoch_pcie_read_register
+### jfjoch_hdf5_test
+Tests single-threaded HDF5 writer performance.
 
-Tool to read verbatim Jungfraujoch FPGA registers
\ No newline at end of file
+### jfjoch_azint_test
+Tests the azimuthal integration code on synthetic data.
+
+### jfjoch_simplon_test
+Minimal test client for a DECTRIS SIMPLON detector API.
diff --git a/docs/index.rst b/docs/index.rst
index b8755c9c..c6016839 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -30,6 +30,8 @@ Jungfraujoch is distributed under the GPLv3 license.
 
    JFJOCH_BROKER
    JFJOCH_WRITER
+   JFJOCH_PROCESS
+   JFJOCH_VIEWER
    SOFTWARE_INTEGRATION
    TOOLS
 
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index acadd7ba..74b422b9 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -36,7 +36,7 @@
 #include "../image_analysis/UpdateReflectionResolution.h"
 
 void print_usage() {
-    std::cout << "Usage ./jfjoch_analysis {<options>} <input.h5>" << std::endl;
+    std::cout << "Usage jfjoch_process {<options>} <input.h5>" << std::endl;
     std::cout << "Options:" << std::endl;
     std::cout << "   -o, --output-prefix <txt>        Output file prefix (default: output)" << std::endl;
     std::cout << "   -N, --threads <num>              Number of threads (default: 1)" << std::endl;
@@ -281,9 +281,9 @@ int main(int argc, char **argv) {
 
     RegisterHDF5Filter();
 
-    print_license("jfjoch_analysis");
+    print_license("jfjoch_process");
 
-    Logger logger("jfjoch_analysis");
+    Logger logger("jfjoch_process");
 
     std::string input_file;
     std::string output_prefix = "output";
diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index e6da83f2..bb04f64a 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -36,7 +36,7 @@ void print_usage() {
     std::cout << "" << std::endl;
     std::cout << "  Scaling and merging" << std::endl;
     std::cout << "   -S, --space-group <num>               Space group number" << std::endl;
-    std::cout << "   -D, --scaling-high-resolution <num>   High resolution limit for scaling/merging (default: 0.0; no limit)"
+    std::cout << "   --scaling-high-resolution <num>       High resolution limit for scaling/merging (default: 0.0; no limit)"
             << std::endl;
     std::cout << "   -P, --partiality <txt>                Partiality refinement fixed|rot|unity (default: fixed)" <<
             std::endl;
@@ -57,7 +57,8 @@ enum {
     OPT_MIN_PARTIALITY = 1000,
     OPT_MIN_IMAGE_CC,
     OPT_SCALING_ITERATIONS,
-    OPT_SCALING_OUTPUT
+    OPT_SCALING_OUTPUT,
+    OPT_SCALING_HIGH_RESOLUTION
 };
 
 
@@ -73,7 +74,7 @@ static option long_options[] = {
     {"anomalous", no_argument, nullptr, 'A'},
     {"refine-bfactor", no_argument, nullptr, 'B'},
     {"wedge", optional_argument, nullptr, 'w'},
-    {"scaling-high-resolution", required_argument, nullptr, 'D'},
+    {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
     {"min-partiality", required_argument, nullptr, OPT_MIN_PARTIALITY},
     {"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
     {"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
@@ -116,7 +117,7 @@ int main(int argc, char **argv) {
 
     int opt;
     int option_index = 0;
-    const char *short_opts = "vo:N:s:e:z:S:P:ABw::D:p:q:i:";
+    const char *short_opts = "vo:N:s:e:z:S:P:ABw::";
 
     while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
         switch (opt) {
@@ -165,7 +166,7 @@ int main(int argc, char **argv) {
                 if (optarg)
                     wedge_for_scaling = std::stod(optarg);
                 break;
-            case 'D':
+            case OPT_SCALING_HIGH_RESOLUTION:
                 d_min_scale_merge = atof(optarg);
                 logger.Info("High resolution limit for scaling/merging set to {:.2f} A", d_min_scale_merge.value());
                 break;
-- 
2.52.0


From 39c808776f0668ba103eee544066ef2adad0faca Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 08:37:21 +0200
Subject: [PATCH 065/228] build: portability groundwork toward a Windows/MSVC
 viewer

- CMakeLists.txt: fetch libzmq at the top level (zeromq/libzmq v4.3.5) before
  slsDetectorPackage, so this project controls the ZeroMQ version instead of sls's
  bundled archive. sls reuses it via its if(NOT libzmq_POPULATED) guard, so a single
  libzmq-static target is built (no duplicate-target/double-symbol clash). Verified the
  full Linux build still links (JFJochZMQ -> JFJochReceiver -> jfjoch_process).
- common/NetworkAddressConvert.cpp: guard the network includes for _WIN32
  (winsock2/ws2tcpip vs arpa/inet).
- common/ImageBuffer.cpp: use std::malloc/std::free for the non-NUMA path instead of an
  anonymous mmap (the mapping had no huge-page/mbind flags, so it was equivalent) -
  portable and removes the POSIX-only dependency. The NUMA-interleave path is unchanged.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                   | 20 ++++++++++++++++++++
 common/ImageBuffer.cpp           | 19 +++++++++----------
 common/NetworkAddressConvert.cpp |  5 +++++
 3 files changed, 34 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 02668e08..d675e610 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -144,6 +144,26 @@ FetchContent_Declare(
         EXCLUDE_FROM_ALL
 )
 
+# ZeroMQ (libzmq): fetch it here, at the top level, so that THIS project - not
+# slsDetectorPackage - controls the version. slsDetectorPackage bundles its own libzmq
+# archive, but only populates it behind `if(NOT libzmq_POPULATED)`; by making libzmq
+# available before sls below, sls reuses this copy and a single libzmq-static target is
+# built (no duplicate target / double-symbol clash). A future viewer-only / Windows build
+# (which does not build sls) fetches the same libzmq standalone.
+SET(BUILD_SHARED   OFF CACHE BOOL "" FORCE)   # libzmq: static only (matches sls)
+SET(BUILD_TESTS    OFF CACHE BOOL "" FORCE)   # libzmq: no test build
+SET(WITH_PERF_TOOL OFF CACHE BOOL "" FORCE)   # libzmq: no perf tools
+SET(WITH_DOCS      OFF CACHE BOOL "" FORCE)   # libzmq: no docs
+SET(ENABLE_CPACK   OFF CACHE BOOL "" FORCE)   # libzmq: no CPack injection
+FetchContent_Declare(
+        libzmq
+        GIT_REPOSITORY https://github.com/zeromq/libzmq.git
+        GIT_TAG v4.3.5
+        EXCLUDE_FROM_ALL
+)
+
+# libzmq must be made available BEFORE sls_detector_package for the override above to take effect.
+FetchContent_MakeAvailable(libzmq)
 FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
 
 ADD_SUBDIRECTORY(jungfrau)
diff --git a/common/ImageBuffer.cpp b/common/ImageBuffer.cpp
index e3ced97f..3145998b 100644
--- a/common/ImageBuffer.cpp
+++ b/common/ImageBuffer.cpp
@@ -6,28 +6,27 @@
 #include "JFJochException.h"
 #include "ZeroCopyReturnValue.h"
 
+#include <cstdlib>
+
 #ifdef JFJOCH_USE_NUMA
 #include <numa.h>
 #endif
-#include <sys/mman.h>
 
 
 ImageBuffer::ImageBuffer(size_t buffer_size_bytes)
         : buffer_size(buffer_size_bytes) {
 
 #ifdef JFJOCH_USE_NUMA
+    // Interleave the buffer across NUMA nodes - throughput-critical path (receiver), Linux-only.
     buffer = static_cast<uint8_t *>(numa_alloc_interleaved(buffer_size));
+#else
+    // The non-NUMA mapping carried no huge-page / mbind flags, so a plain heap allocation is
+    // equivalent (and portable). The buffer is zeroed below.
+    buffer = static_cast<uint8_t *>(std::malloc(buffer_size));
+#endif
     if (buffer == nullptr)
-        throw JFJochException(JFJochExceptionCategory::MemAllocFailed,
-            "Failed to allocate image buffer");
-
-    #else
-    buffer = (uint8_t *) mmap (nullptr, buffer_size, PROT_READ | PROT_WRITE,
-                               MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) ;
-    if (buffer == MAP_FAILED)
         throw JFJochException(JFJochExceptionCategory::MemAllocFailed,
                               "Failed to allocate image buffer");
-#endif
     memset(buffer, 0, buffer_size);
 }
 
@@ -39,7 +38,7 @@ ImageBuffer::~ImageBuffer() {
 #ifdef JFJOCH_USE_NUMA
     numa_free(buffer, buffer_size);
 #else
-    munmap(buffer, buffer_size);
+    std::free(buffer);
 #endif
 }
 
diff --git a/common/NetworkAddressConvert.cpp b/common/NetworkAddressConvert.cpp
index 9d58b1d0..baa920db 100644
--- a/common/NetworkAddressConvert.cpp
+++ b/common/NetworkAddressConvert.cpp
@@ -1,7 +1,12 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#ifdef _WIN32
+#include <winsock2.h>
+#include <ws2tcpip.h>
+#else
 #include <arpa/inet.h>
+#endif
 #include <sstream>
 #include <iomanip>
 
-- 
2.52.0


From 1056acc3a6110d0cc8fa8f067be7f95c88861419 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 08:40:09 +0200
Subject: [PATCH 066/228] build: guard the librt link to Linux only

librt is Linux/glibc-only and does not exist on macOS/Windows. Link it via a
$<$<PLATFORM_ID:Linux>:rt> generator expression (both the main JFJochCommon link and
the CUDA block) so -lrt is still passed on Linux - where some distros need it for
clock_gettime/timer_*/pthreads - and dropped elsewhere. Verified -lrt is still on the
jfjoch_process link line on Linux.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/CMakeLists.txt | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt
index 53dd9333..f6273dc4 100644
--- a/common/CMakeLists.txt
+++ b/common/CMakeLists.txt
@@ -139,14 +139,17 @@ ADD_LIBRARY(JFJochCommon STATIC
         CorrelationCoefficient.h
 )
 
-TARGET_LINK_LIBRARIES(JFJochCommon JFJochLogger Compression JFCalibration gemmi Threads::Threads -lrt )
+# librt is Linux/glibc-only (older glibc keeps clock_gettime/timer_*/sem_* there, and some
+# distros are picky about it for pthreads); it does not exist on macOS/Windows.
+TARGET_LINK_LIBRARIES(JFJochCommon JFJochLogger Compression JFCalibration gemmi Threads::Threads
+        $<$<PLATFORM_ID:Linux>:rt>)
 
 TARGET_LINK_LIBRARIES(JFJochZMQ "$<BUILD_INTERFACE:libzmq-static>")
 
 IF (JFJOCH_CUDA_AVAILABLE)
     TARGET_SOURCES(JFJochCommon PRIVATE CUDAWrapper.cu )
     TARGET_LINK_LIBRARIES(JFJochCommon CUDA::cudart_static
-            ${CMAKE_DL_LIBS} rt)
+            ${CMAKE_DL_LIBS} $<$<PLATFORM_ID:Linux>:rt>)
 ENDIF()
 
 IF(HAS_NUMAIF AND HAS_NUMA_H AND NUMA_LIBRARY)
-- 
2.52.0


From 02fa15c2b95cc94745b20394efebcb8477654b29 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 15:29:52 +0200
Subject: [PATCH 067/228] jfjoch_process: spread per-image GPU work across all
 visible GPUs

The offline worker threads built MXAnalysisWithoutFPGA without selecting a CUDA
device, so all per-image preprocessing/spot-finding/azimuthal integration ran on
GPU 0 (only the indexer pool was distributed). Add pin_gpu() to CUDAWrapper - a
process-wide round-robin counter (counter++ % get_gpu_count(), no thread id, no-op
without a GPU, honours CUDA_VISIBLE_DEVICES) - and call it once per worker before
building the analysis resources so their CUDA streams/engines land on distinct
devices.

Also add NUMA_GPU_REVIEW.md: a working note mapping ImageBuffer/NUMAHWPolicy/GPU
dispatch with goals and a staged plan (multi-broker GPU isolation via
CUDA_VISIBLE_DEVICES, dropping libnuma, reassessing NUMA pinning for the FPGA path).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 NUMA_GPU_REVIEW.md       | 115 +++++++++++++++++++++++++++++++++++++++
 common/CUDAWrapper.cpp   |   2 +
 common/CUDAWrapper.cu    |   8 +++
 common/CUDAWrapper.h     |   5 ++
 tools/jfjoch_process.cpp |   6 ++
 5 files changed, 136 insertions(+)
 create mode 100644 NUMA_GPU_REVIEW.md

diff --git a/NUMA_GPU_REVIEW.md b/NUMA_GPU_REVIEW.md
new file mode 100644
index 00000000..5132cca7
--- /dev/null
+++ b/NUMA_GPU_REVIEW.md
@@ -0,0 +1,115 @@
+# NUMA / GPU usage — current state, goals, proposed changes (for review)
+
+Working note to agree on direction **before** modifying `ImageBuffer` / `NUMAHWPolicy` and the
+GPU-dispatch logic. Nothing here is implemented yet. File:line anchors are from branch
+`2606-pixel-refine`.
+
+## 1. Current state (the mind map)
+
+### 1a. `ImageBuffer` — the big RAM ring buffer
+- **One instance**, a member of the receiver: `JFJochReceiverService::image_buffer`
+  (`receiver/JFJochReceiverService.h:21`), sized `image_buffer_MiB` from broker config
+  (`broker/jfjoch_broker.cpp:104` → `JFJochReceiverService` ctor
+  `receiver/JFJochReceiverService.cpp:15`, `image_buffer(send_buffer_size_MiB*1024*1024)`).
+  This is the 150–200 GB allocation.
+- **Allocated + zeroed in the ctor** (`common/ImageBuffer.cpp`): `numa_alloc_interleaved` if libnuma,
+  else `std::malloc`; then a **single-threaded `memset`** to pre-fault every page (deliberate — kills
+  first-use page-fault latency in the hot path). Happens once at broker startup.
+- **Producers/consumers**: receiver/decompression threads write frames into slots; consumers are
+  preview/TIFF/JPEG/HTTP retrieval (`GetImage`) and the ZMQ/file sender. Access is random and
+  unpinned (any thread → any slot).
+- **Not used by `jfjoch_process` or `jfjoch_viewer`** — they read HDF5 through the reader, never
+  instantiate `ImageBuffer`. So this buffer is **broker/receiver-only** (it only needs to *compile*
+  for the viewer).
+
+### 1b. `NUMAHWPolicy` — bundles three concerns per worker thread
+Built from the broker config `numa_policy` string (e.g. `n2g2`, `n8g4`, `n8g4_hbm`) into a table of
+`NUMABinding{cpu_node, mem_node, gpu}`; `GetBinding(thread) = bindings[thread % nbindings]`
+(round-robin, `common/NUMAHWPolicy.cpp:54`). `Bind(thread)` does **all three** at once
+(`common/NUMAHWPolicy.cpp:61`):
+1. **CPU pin** — `RunOnNode` / `numa_run_on_node`
+2. **Memory bind** — `MemOnNode` / `numa_set_membind` (on `n8g4_hbm`, `mem_node = i+8` → binds to HBM nodes)
+3. **GPU select** — `SelectGPU` / `set_gpu` (= `cudaSetDevice`, **not** libnuma)
+
+Call sites:
+- `receiver/JFJochReceiverFPGA.cpp:180/217/264` — data-stream threads `RunOnNode(FPGA's NUMA node)`
+  (device-locality pin, the NIC-era idea applied to the FPGA card).
+- `receiver/JFJochReceiverFPGA.cpp:299`, `receiver/JFJochReceiverLite.cpp:234` — analysis worker
+  threads `numa_policy.Bind(threadid)` → cpu + mem + **GPU** per the policy table.
+- `image_analysis/indexing/IndexerThreadPool.cpp:34` — each indexer thread
+  `SelectGPUAndItsNUMA(threadid % gpu_count)` (GPU round-robin + that GPU's own NUMA node;
+  independent of the `numa_policy` table).
+
+libnuma is used in exactly three files: `NUMAHWPolicy.cpp` (the above), `ImageBuffer.cpp`
+(`numa_alloc_interleaved`/`numa_free`), and `CUDAWrapper.cpp` (one `numa_node` lookup).
+
+### 1c. GPU dispatch — and why `jfjoch_process` underuses GPUs
+- `get_gpu_count()` = `cudaGetDeviceCount()` (`common/CUDAWrapper.*`), so it already honours
+  **`CUDA_VISIBLE_DEVICES`**. All dispatch is `% gpu_count`.
+- **Broker/receiver**: worker threads spread over GPUs via `numa_policy.Bind` (the `gpu` field) +
+  the indexer pool via `threadid % gpu_count`. → uses all visible GPUs.
+- **`jfjoch_process`**: its worker lambda (`tools/jfjoch_process.cpp:849`, launched `nthreads` times)
+  constructs `MXAnalysisWithoutFPGA` but **never calls `Bind`/`SelectGPU`**, and
+  `MXAnalysisWithoutFPGA` itself does not select a device (`image_analysis/MXAnalysisWithoutFPGA.cpp:38`
+  just builds GPU engines on the *current* device). → all per-image preprocessing / spot-finding /
+  azimuthal integration run on **GPU 0**. Only the indexer pool spreads. **This is the root cause of
+  "`jfjoch_process` doesn't use all GPUs."**
+
+## 2. Goals
+
+- **G1 — multiple brokers, disjoint GPUs.** Run >1 `jfjoch_broker` on one machine, each confined to a
+  subset of GPUs, with the code transparently using "all it can see" (no hard-coded indices). Pure
+  workload control, no security requirement.
+- **G2 — `jfjoch_process` should use all visible GPUs**, not just GPU 0.
+- **G3 — drop the libnuma dependency** if it doesn't cost real performance (annoying dep; also a
+  blocker for the long-term Windows/MSVC viewer).
+- **G4 — reassess whether NUMA CPU/mem pinning is still worth it** given the FPGA pipeline (DMA into
+  kernel-mmap'd buffers, negligible IRQ traffic) rather than the old network-RX model.
+
+## 3. Proposed changes
+
+- **G1 (zero code):** launch each broker under `CUDA_DEVICE_ORDER=PCI_BUS_ID
+  CUDA_VISIBLE_DEVICES=<subset> jfjoch_broker …`. `get_gpu_count()`/`% gpu_count` already do the rest.
+  Action item: **document this** (deployment note) and set `CUDA_DEVICE_ORDER=PCI_BUS_ID` so indices
+  are stable across boots.
+
+- **G2 (DONE):** added `pin_gpu()` to `CUDAWrapper` — a process-wide round-robin counter
+  (`counter++ % get_gpu_count()`, no thread id needed, no-op when no GPU). The `jfjoch_process` worker
+  calls it once before building `MXAnalysisWithoutFPGA`, so each worker's CUDA streams/engines land on
+  a distinct device. Caller-agnostic and reusable by other thread pools later.
+
+- **G3 / `ImageBuffer`:** replace `numa_alloc_interleaved` + single-threaded `memset` with **plain
+  `malloc` + a parallel first-touch `memset`** (N threads, unpinned). Threads spread by the scheduler
+  → balanced placement ≈ interleave for random access, *and* faster startup, *and* no libnuma. Safe
+  here because the buffer is 30–40 % of RAM (first-touch spills to the other node if one fills; no OOM;
+  just check `vm.zone_reclaim_mode == 0`). Deterministic per-page interleave (if ever needed under
+  tight RAM) is a raw `mbind(MPOL_INTERLEAVE)` syscall — still libnuma-free.
+
+- **G3 / G4 / `NUMAHWPolicy`:** split the bundled concerns:
+  - **CPU pin** (`RunOnNode`) — likely **drop** for the FPGA path (G4). If ever wanted back, use
+    `sched_setaffinity` (no libnuma).
+  - **GPU select** (`SelectGPU`/`SelectGPUAndItsNUMA`) — **keep**; already `cudaSetDevice`, no libnuma.
+  - **Memory bind** (`MemOnNode`) — **drop.** (HBM is out of scope: the only Xeon MAX box didn't pay
+    off and isn't worth special-casing, so no `mbind` path is needed — treat every host as plain
+    multi-socket.)
+  - **`CUDAWrapper` `numa_node`** — read the GPU PCIe device's `/sys/.../numa_node` instead of libnuma.
+  - Result: `NUMA_LIBRARY` leaves the CMake entirely.
+
+## 4. Open questions / to validate before deleting anything
+
+- **G4 is empirical.** A/B at production frame rate (pinning on vs off): sustained throughput, dropped
+  frames, latency jitter. The reasoning predicts "no regression," but measure on one real box first —
+  production systems are currently tuned around this.
+- Confirm `vm.zone_reclaim_mode` is `0` on the broker hosts (else first-touch reclaims locally before
+  spilling → latency stalls).
+- Parallel first-touch placement is *approximate* (depends on the scheduler spreading the zeroing
+  threads); fine with RAM headroom, but note it's not the guaranteed 50/50 of `mbind` interleave.
+
+## 5. Suggested order (low-risk first)
+
+1. **G1** — document `CUDA_VISIBLE_DEVICES` launch (no code).
+2. ~~**G2** — per-worker GPU pin in `jfjoch_process`.~~ **DONE** (`pin_gpu()`).
+3. **ImageBuffer** parallel first-touch (drops one libnuma user, helps startup; stands alone).
+4. **G4 A/B** on a real broker; if clean, drop CPU pinning.
+5. **NUMAHWPolicy** simplify (keep GPU select, drop CPU pin + mem bind) + `CUDAWrapper` sysfs
+   → remove `NUMA_LIBRARY` from CMake.
diff --git a/common/CUDAWrapper.cpp b/common/CUDAWrapper.cpp
index e2cf8733..d73e3760 100644
--- a/common/CUDAWrapper.cpp
+++ b/common/CUDAWrapper.cpp
@@ -11,6 +11,8 @@ int32_t get_gpu_count() {
 
 void set_gpu(int32_t dev_id) {}
 
+void pin_gpu() {}
+
 int get_gpu_numa_node(int dev_id) {
     return -1;
 }
diff --git a/common/CUDAWrapper.cu b/common/CUDAWrapper.cu
index 54e06740..684f8b82 100644
--- a/common/CUDAWrapper.cu
+++ b/common/CUDAWrapper.cu
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include <fstream>
+#include <atomic>
 
 #include "CUDAWrapper.h"
 #include "JFJochException.h"
@@ -38,6 +39,13 @@ void set_gpu(int32_t dev_id) {
     }
 }
 
+void pin_gpu() {
+    static std::atomic<uint32_t> counter{0};
+    auto dev_count = get_gpu_count();
+    if (dev_count > 0)
+        set_gpu(counter.fetch_add(1) % dev_count);
+}
+
 // Return CUDA device PCI Bus ID as "domain:bus:device.function", e.g., "0000:65:00.0"
 static std::string get_cuda_device_pci_bus_id(int dev_id) {
     // CUDA API provides cudaDeviceGetPCIBusId
diff --git a/common/CUDAWrapper.h b/common/CUDAWrapper.h
index dce83bb0..dcc97f3c 100644
--- a/common/CUDAWrapper.h
+++ b/common/CUDAWrapper.h
@@ -8,3 +8,8 @@
 int32_t get_gpu_count();
 void set_gpu(int32_t dev_id);
 int get_gpu_numa_node(int dev_id);
+
+// Pin the calling thread to the next GPU in round-robin order, using a process-wide counter
+// (counter++ % get_gpu_count()). Call once per thread; no thread id needed. No-op when no GPU
+// is visible. Honours CUDA_VISIBLE_DEVICES via get_gpu_count().
+void pin_gpu();
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 74b422b9..ffb707bc 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -25,6 +25,7 @@
 #include "../common/print_license.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
 #include "../image_analysis/indexing/IndexerFactory.h"
+#include "../common/CUDAWrapper.h"
 #include "../writer/FileWriter.h"
 #include "../image_analysis/IndexAndRefine.h"
 #include "../receiver/JFJochReceiverPlots.h"
@@ -847,6 +848,11 @@ int main(int argc, char **argv) {
     std::atomic<int> finished_count = 0;
 
     auto worker = [&](int thread_id) {
+        // Spread the per-image GPU pipeline across all visible GPUs (round-robin).
+        // Must run before building the analysis resources so their CUDA streams/engines are
+        // created on this thread's device.
+        pin_gpu();
+
         // Thread-local analysis resources
         MXAnalysisWithoutFPGA analysis(experiment, mapping, pixel_mask, indexer);
 
-- 
2.52.0


From d373ba049017d655ea3657dd8699e90756b2ecac Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 17:03:13 +0200
Subject: [PATCH 068/228] ImageBuffer: replace NUMA interleave with parallel
 first-touch

Allocate the ring buffer with plain malloc and zero it across
hardware_concurrency() threads, so each page is first-touched - and thus
NUMA-placed - by whichever node the scheduler ran the zeroing thread on.
For the random-access buffer this approximates the previous
numa_alloc_interleaved placement, speeds up the one-time fault-in of the
150-200 GB allocation, and drops the libnuma dependency from this file.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/ImageBuffer.cpp | 39 +++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/common/ImageBuffer.cpp b/common/ImageBuffer.cpp
index 3145998b..5b2809b3 100644
--- a/common/ImageBuffer.cpp
+++ b/common/ImageBuffer.cpp
@@ -6,28 +6,39 @@
 #include "JFJochException.h"
 #include "ZeroCopyReturnValue.h"
 
+#include <algorithm>
 #include <cstdlib>
+#include <cstring>
+#include <thread>
+#include <vector>
 
-#ifdef JFJOCH_USE_NUMA
-#include <numa.h>
-#endif
+namespace {
+    // Zero the buffer in parallel so that each page is first-touched by whichever NUMA node the
+    // scheduler placed the zeroing thread on. With RAM headroom this approximates an interleaved
+    // placement for the random-access ring buffer, while also slashing the one-time cost of
+    // faulting in a 150-200 GB allocation. Replaces numa_alloc_interleaved + a single-threaded
+    // memset, so this file no longer needs libnuma.
+    void parallel_first_touch(uint8_t *buffer, size_t buffer_size) {
+        const unsigned n = std::max(1u, std::thread::hardware_concurrency());
+        const size_t chunk = (buffer_size + n - 1) / n;
 
+        std::vector<std::thread> threads;
+        for (size_t begin = 0; begin < buffer_size; begin += chunk) {
+            size_t len = std::min(chunk, buffer_size - begin);
+            threads.emplace_back([=] { memset(buffer + begin, 0, len); });
+        }
+        for (auto &t : threads)
+            t.join();
+    }
+}
 
 ImageBuffer::ImageBuffer(size_t buffer_size_bytes)
         : buffer_size(buffer_size_bytes) {
-
-#ifdef JFJOCH_USE_NUMA
-    // Interleave the buffer across NUMA nodes - throughput-critical path (receiver), Linux-only.
-    buffer = static_cast<uint8_t *>(numa_alloc_interleaved(buffer_size));
-#else
-    // The non-NUMA mapping carried no huge-page / mbind flags, so a plain heap allocation is
-    // equivalent (and portable). The buffer is zeroed below.
     buffer = static_cast<uint8_t *>(std::malloc(buffer_size));
-#endif
     if (buffer == nullptr)
         throw JFJochException(JFJochExceptionCategory::MemAllocFailed,
                               "Failed to allocate image buffer");
-    memset(buffer, 0, buffer_size);
+    parallel_first_touch(buffer, buffer_size);
 }
 
 ImageBuffer::~ImageBuffer() {
@@ -35,11 +46,7 @@ ImageBuffer::~ImageBuffer() {
     std::unique_lock ul(m);
     FinalizeInternal(ul);
 
-#ifdef JFJOCH_USE_NUMA
-    numa_free(buffer, buffer_size);
-#else
     std::free(buffer);
-#endif
 }
 
 void ImageBuffer::StartMeasurement(size_t in_location_size) {
-- 
2.52.0


From 040cdeacf1d0048ffaa5b3d90cb7c8e011214eae Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 17:09:28 +0200
Subject: [PATCH 069/228] acquisition_device: give each device sole ownership
 of its buffers

The base AcquisitionDevice no longer allocates or frees frame buffers;
buffer_device is now just a non-owning view of addresses. Each subclass
owns its backing memory and the matching lifecycle:

- PCIExpressDevice mmap's the kernel DMA buffers and munmap's them in its
  own destructor (and on ctor failure), symmetric with MapKernelBuffer.
- HLSSimulatedDevice owns plain zeroed heap buffers it points
  buffer_device into, declared before the HLSDevice so they outlive the
  action thread that writes them. The buffers are page-aligned to match
  the real device's kernel DMA buffers - the modelled AXI datamover and
  FPGAIntegrationTest require aligned output buffers.

This drops the NUMA/mmap dance from the simulated path (not
performance-critical) - removing libnuma from acquisition_device - and
replaces the base-class cleanup that had to guess the allocation
strategy with a single clear owner per device.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 acquisition_device/AcquisitionDevice.cpp  | 38 -----------------------
 acquisition_device/AcquisitionDevice.h    |  7 +++--
 acquisition_device/HLSSimulatedDevice.cpp |  8 +++--
 acquisition_device/HLSSimulatedDevice.h   |  9 +++++-
 acquisition_device/PCIExpressDevice.cpp   |  9 ++++++
 acquisition_device/PCIExpressDevice.h     |  2 ++
 6 files changed, 29 insertions(+), 44 deletions(-)

diff --git a/acquisition_device/AcquisitionDevice.cpp b/acquisition_device/AcquisitionDevice.cpp
index 452338fa..fc31af1e 100644
--- a/acquisition_device/AcquisitionDevice.cpp
+++ b/acquisition_device/AcquisitionDevice.cpp
@@ -1,11 +1,6 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#ifdef JFJOCH_USE_NUMA
-#include <numaif.h>
-#endif
-
-#include <sys/mman.h>
 #include <thread>
 #include <fstream>
 #include <cmath>
@@ -14,24 +9,6 @@
 #include "AcquisitionDevice.h"
 #include "../common/NetworkAddressConvert.h"
 
-void *mmap_acquisition_buffer(size_t size, int16_t numa_node) {
-    void *ret = mmap(nullptr, size, PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
-    if (ret == MAP_FAILED) {
-        throw JFJochException(JFJochExceptionCategory::MemAllocFailed, "frame_buffer");
-    }
-#ifdef JFJOCH_USE_NUMA
-    if (numa_node >= 0) {
-        unsigned long nodemask = 1L << numa_node;;
-        if (numa_node > sizeof(nodemask)*8)
-            throw JFJochException(JFJochExceptionCategory::MemAllocFailed, "Mask too small for NUMA node");
-        if (mbind(ret, size, MPOL_BIND, &nodemask, sizeof(nodemask)*8, MPOL_MF_STRICT) == -1)
-            throw JFJochException(JFJochExceptionCategory::MemAllocFailed, "Cannot apply NUMA policy");
-    }
-#endif
-    memset(ret, 0, size);
-    return ret;
-}
-
 AcquisitionDevice::AcquisitionDevice(uint16_t in_data_stream) {
     logger = nullptr;
     data_stream = in_data_stream;
@@ -238,21 +215,6 @@ void AcquisitionDevice::InitializePixelMask(const DiffractionExperiment &experim
     }
 }
 
-void AcquisitionDevice::MapBuffersStandard(size_t c2h_buffer_count, int16_t numa_node) {
-    try {
-        for (int i = 0; i < c2h_buffer_count; i++)
-            buffer_device.emplace_back((DeviceOutput *) mmap_acquisition_buffer(FPGA_BUFFER_LOCATION_SIZE, numa_node));
-    } catch (const JFJochException &e) {
-        UnmapBuffers();
-        throw;
-    }
-}
-
-void AcquisitionDevice::UnmapBuffers() {
-     for (auto &i: buffer_device)
-        if (i != nullptr) munmap(i, FPGA_BUFFER_LOCATION_SIZE);
-}
-
 void AcquisitionDevice::FrameBufferRelease(size_t frame_number, uint16_t module_number) {
     auto handle = counters.GetBufferHandleAndClear(frame_number, module_number);
     if (handle != AcquisitionCounters::HandleNotFound)
diff --git a/acquisition_device/AcquisitionDevice.h b/acquisition_device/AcquisitionDevice.h
index 71e60ca3..7b9d59e1 100644
--- a/acquisition_device/AcquisitionDevice.h
+++ b/acquisition_device/AcquisitionDevice.h
@@ -49,6 +49,9 @@ protected:
     ThreadSafeFIFO<Completion> work_completion_queue;
     ThreadSafeFIFO<WorkRequest> work_request_queue;
 
+    // Non-owning view of the per-buffer addresses. Each device subclass owns the backing memory
+    // and its lifecycle: PCIExpressDevice mmap's/munmap's kernel DMA buffers, HLSSimulatedDevice
+    // points these at plain heap buffers it owns.
     std::vector<DeviceOutput *> buffer_device;
     Logger *logger;
 
@@ -58,8 +61,6 @@ protected:
     uint32_t ipv4_addr;
     explicit AcquisitionDevice(uint16_t data_stream);
 
-    void UnmapBuffers();
-    void MapBuffersStandard(size_t c2h_buffer_count, int16_t numa_node);
     const DeviceOutput *GetDeviceOutput(size_t handle) const;
     DeviceOutput *GetDeviceOutput(size_t handle);
     virtual void HW_RunInternalGenerator(const FrameGeneratorConfig& config) = 0;
@@ -70,7 +71,7 @@ public:
 
     static constexpr const uint64_t HandleNotValid = UINT64_MAX;
 
-    virtual ~AcquisitionDevice() { UnmapBuffers(); };
+    virtual ~AcquisitionDevice() = default;
 
     void StartAction(const DiffractionExperiment &experiment, uint32_t optional_flags = 0);
     void PrepareAction(const DiffractionExperiment &experiment);
diff --git a/acquisition_device/HLSSimulatedDevice.cpp b/acquisition_device/HLSSimulatedDevice.cpp
index 24fd222b..54e8c5b3 100644
--- a/acquisition_device/HLSSimulatedDevice.cpp
+++ b/acquisition_device/HLSSimulatedDevice.cpp
@@ -3,14 +3,18 @@
 
 #include "HLSSimulatedDevice.h"
 
-HLSSimulatedDevice::HLSSimulatedDevice(uint16_t data_stream, size_t in_frame_buffer_size_modules, int16_t numa_node)
+HLSSimulatedDevice::HLSSimulatedDevice(uint16_t data_stream, size_t in_frame_buffer_size_modules)
         : FPGAAcquisitionDevice(data_stream) {
     mac_addr = 0xCCAA11223344;
     ipv4_addr = 0x0132010A;
 
     max_modules = MAX_MODULES_FPGA;
 
-    MapBuffersStandard(in_frame_buffer_size_modules, numa_node);
+    buffers.reserve(in_frame_buffer_size_modules);
+    for (size_t i = 0; i < in_frame_buffer_size_modules; i++) {
+        buffers.push_back(std::make_unique<FrameBuffer>());  // zero-initialised, 64-byte aligned
+        buffer_device.push_back(reinterpret_cast<DeviceOutput *>(buffers.back().get()));
+    }
 
     device = std::make_unique<HLSDevice>(buffer_device);
 }
diff --git a/acquisition_device/HLSSimulatedDevice.h b/acquisition_device/HLSSimulatedDevice.h
index 4fee45bc..83e40ef9 100644
--- a/acquisition_device/HLSSimulatedDevice.h
+++ b/acquisition_device/HLSSimulatedDevice.h
@@ -11,6 +11,13 @@
 #include "FPGAAcquisitionDevice.h"
 
 class HLSSimulatedDevice : public FPGAAcquisitionDevice {
+    // Owns the simulated frame buffers. Plain heap (this path is not performance-critical, so no
+    // NUMA placement and no mmap), but page-aligned (4 KiB) to match the real device's kernel DMA
+    // buffers - more than enough for the data path's alignment needs (AXI datamover 64 B,
+    // FPGAIntegrationTest 128 B). Declared before `device` so the buffers outlive the HLSDevice
+    // action thread that writes into them; buffer_device points into these.
+    struct alignas(4096) FrameBuffer { uint8_t data[FPGA_BUFFER_LOCATION_SIZE]; };
+    std::vector<std::unique_ptr<FrameBuffer>> buffers;
     std::unique_ptr<HLSDevice> device;
 
     void HW_ReadActionRegister(DataCollectionConfig *job) override;
@@ -25,7 +32,7 @@ class HLSSimulatedDevice : public FPGAAcquisitionDevice {
     void HW_SetSpotFinderParameters(const SpotFinderParameters &params) override;
     void HW_RunInternalGenerator(const FrameGeneratorConfig &config) override;
 public:
-    HLSSimulatedDevice(uint16_t data_stream, size_t in_frame_buffer_size_modules, int16_t numa_node = -1);
+    HLSSimulatedDevice(uint16_t data_stream, size_t in_frame_buffer_size_modules);
     ~HLSSimulatedDevice() override = default;
     void CreateJFPacket(const DiffractionExperiment& experiment, uint64_t frame_number, uint32_t eth_packet,
                         uint32_t module_number, const uint16_t *data, int8_t adjust_axis = 0, uint8_t user = 0);
diff --git a/acquisition_device/PCIExpressDevice.cpp b/acquisition_device/PCIExpressDevice.cpp
index 1ddb6f9b..3fa146fd 100644
--- a/acquisition_device/PCIExpressDevice.cpp
+++ b/acquisition_device/PCIExpressDevice.cpp
@@ -33,6 +33,15 @@ PCIExpressDevice::PCIExpressDevice(uint16_t data_stream, const std::string &devi
     }
 }
 
+PCIExpressDevice::~PCIExpressDevice() {
+    UnmapBuffers();
+}
+
+void PCIExpressDevice::UnmapBuffers() {
+    for (auto &buf: buffer_device)
+        if (buf != nullptr) dev.UnmapKernelBuffer(buf);
+}
+
 bool PCIExpressDevice::HW_ReadMailbox(uint32_t *values) {
     PCI_EXCEPT(return dev.ReadWorkCompletion(values);)
 }
diff --git a/acquisition_device/PCIExpressDevice.h b/acquisition_device/PCIExpressDevice.h
index 2362a1fe..ac1f1b3c 100644
--- a/acquisition_device/PCIExpressDevice.h
+++ b/acquisition_device/PCIExpressDevice.h
@@ -20,10 +20,12 @@ class PCIExpressDevice : public FPGAAcquisitionDevice {
     void FPGA_EndAction() override;
     uint32_t GetNumKernelBuffers() const;
     void HW_RunInternalGenerator(const FrameGeneratorConfig &config) override;
+    void UnmapBuffers();
 public:
     explicit PCIExpressDevice(uint16_t data_stream);
     PCIExpressDevice(uint16_t data_stream, uint16_t pci_slot);
     PCIExpressDevice(uint16_t data_stream, const std::string &device_name);
+    ~PCIExpressDevice() override;
 
     void Cancel() override;
     int32_t GetNUMANode() const override;
-- 
2.52.0


From 17732ea774369abb9df7e967d66a7b7201a66ce6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 19:22:00 +0200
Subject: [PATCH 070/228] docs: refresh NUMA_GPU_REVIEW to match implemented
 state

Several items in the note had landed or were inaccurate. Update it to:
- mark DONE: G2 pin_gpu, ImageBuffer first-touch, acquisition_device
  de-NUMA, CUDAWrapper sysfs node lookup;
- add the previously-missing FPGA DMA buffer section - placement is a
  kernel concern (dma_alloc_coherent, device-local), not the userspace
  mbind, which was only the simulator;
- record that libnuma is now down to a single file (NUMAHWPolicy.cpp);
- note that dependency removal (G3) and pinning behaviour (G4) are
  separable axes.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 NUMA_GPU_REVIEW.md | 186 ++++++++++++++++++++++++++-------------------
 1 file changed, 108 insertions(+), 78 deletions(-)

diff --git a/NUMA_GPU_REVIEW.md b/NUMA_GPU_REVIEW.md
index 5132cca7..840d86ac 100644
--- a/NUMA_GPU_REVIEW.md
+++ b/NUMA_GPU_REVIEW.md
@@ -1,115 +1,145 @@
-# NUMA / GPU usage — current state, goals, proposed changes (for review)
+# NUMA / GPU usage — current state, goals, remaining work
 
-Working note to agree on direction **before** modifying `ImageBuffer` / `NUMAHWPolicy` and the
-GPU-dispatch logic. Nothing here is implemented yet. File:line anchors are from branch
+Working note on the NUMA/GPU direction. Several items are now **implemented and committed** on
+branch `2606-pixel-refine` (see §3/§5); this note tracks what landed, what's left, and — importantly
+— the corrected mental model of *where NUMA actually matters*. File:line anchors are from
 `2606-pixel-refine`.
 
+**Headline:** after the committed work, **libnuma is used in exactly one file**
+(`common/NUMAHWPolicy.cpp`). Everything else (GPU node lookup, the big RAM buffer, the FPGA DMA
+buffers, the simulator) is libnuma-free.
+
 ## 1. Current state (the mind map)
 
 ### 1a. `ImageBuffer` — the big RAM ring buffer
 - **One instance**, a member of the receiver: `JFJochReceiverService::image_buffer`
   (`receiver/JFJochReceiverService.h:21`), sized `image_buffer_MiB` from broker config
-  (`broker/jfjoch_broker.cpp:104` → `JFJochReceiverService` ctor
-  `receiver/JFJochReceiverService.cpp:15`, `image_buffer(send_buffer_size_MiB*1024*1024)`).
-  This is the 150–200 GB allocation.
-- **Allocated + zeroed in the ctor** (`common/ImageBuffer.cpp`): `numa_alloc_interleaved` if libnuma,
-  else `std::malloc`; then a **single-threaded `memset`** to pre-fault every page (deliberate — kills
-  first-use page-fault latency in the hot path). Happens once at broker startup.
+  (`broker/jfjoch_broker.cpp:104` → ctor `receiver/JFJochReceiverService.cpp:15`). The 150–200 GB
+  allocation.
+- **Allocation (DONE, commit `d373ba04`):** plain `std::malloc` + a **parallel first-touch `memset`**
+  (`hardware_concurrency()` threads, unpinned) in `common/ImageBuffer.cpp`. Each page is
+  first-touched — and thus NUMA-placed — by whichever node the scheduler ran the zeroing thread on:
+  approximates the old `numa_alloc_interleaved` placement for the random-access buffer, *and*
+  pre-faults every page (no first-use fault in the hot path), *and* speeds up startup, *and* drops
+  libnuma here. (Was `numa_alloc_interleaved` + single-threaded `memset`.)
 - **Producers/consumers**: receiver/decompression threads write frames into slots; consumers are
   preview/TIFF/JPEG/HTTP retrieval (`GetImage`) and the ZMQ/file sender. Access is random and
-  unpinned (any thread → any slot).
+  unpinned (any thread → any slot) — which is *why* interleave/first-touch placement (not per-node
+  binding) is the right model.
 - **Not used by `jfjoch_process` or `jfjoch_viewer`** — they read HDF5 through the reader, never
-  instantiate `ImageBuffer`. So this buffer is **broker/receiver-only** (it only needs to *compile*
-  for the viewer).
+  instantiate `ImageBuffer`. Broker/receiver-only (it only needs to *compile* for the viewer).
 
-### 1b. `NUMAHWPolicy` — bundles three concerns per worker thread
+### 1b. FPGA DMA buffers — placement is a *kernel* concern, not libnuma  *(this section was missing)*
+The real per-frame DMA buffers are **allocated and NUMA-placed by the kernel driver**, with zero
+userspace/libnuma involvement. The earlier draft framed the userspace `mbind` as "the real
+hardware-locality win" — that was wrong; the win is in the kernel:
+- `fpga/pcie_driver/jfjoch_memory.c:28` — `dma_alloc_coherent(&pdev->dev, FPGA_BUFFER_LOCATION_SIZE,
+  …)` × `nbuffer` (512). Gives **physically contiguous, DMA-coherent** pages (required: each buffer's
+  bus address is written into the FPGA address table at `:37-38`). Placement is **device-local by
+  construction** — the kernel DMA/page allocator uses `dev_to_node(&pdev->dev)`. This is exactly why
+  it can't be a userspace `malloc`+`mbind`: userspace virtual memory is neither physically contiguous
+  nor a valid DMA target.
+- `jfjoch_memory.c:99` — `dma_mmap_coherent` maps those *same physical pages* into userspace;
+  `JungfraujochDevice::MapKernelBuffer` (`fpga/host_library/JungfraujochDevice.cpp:166`) is a plain
+  `mmap` of the char dev. No second allocation, no first-touch, no migration.
+- `IOCTL_JFJOCH_NUMA` (`fpga/pcie_driver/jfjoch_ioctl.c:133`) just **reports**
+  `drvdata->pdev->dev.numa_node`. Userspace's only NUMA action on the real path is to pin the
+  *acquire thread's CPU* to that node (the `RunOnNode` calls in §1c).
+- **Simulated path (DONE, commit `042df308`):** `HLSSimulatedDevice` used to *emulate* device locality
+  with a userspace `mmap`+`mbind` (`<numaif.h>`) — the only libnuma user in `acquisition_device/`. It
+  now uses **plain zeroed heap buffers** (`std::vector`, not performance-critical). Buffer ownership
+  was refactored so each device owns its lifecycle: `PCIExpressDevice` `mmap`s/`munmap`s the kernel
+  DMA buffers; `HLSSimulatedDevice` owns the heap buffers; the base `AcquisitionDevice` is just a
+  non-owning address view. No libnuma, no mmap on the sim path.
+
+### 1c. `NUMAHWPolicy` — bundles three concerns per worker thread (the last libnuma user)
 Built from the broker config `numa_policy` string (e.g. `n2g2`, `n8g4`, `n8g4_hbm`) into a table of
 `NUMABinding{cpu_node, mem_node, gpu}`; `GetBinding(thread) = bindings[thread % nbindings]`
-(round-robin, `common/NUMAHWPolicy.cpp:54`). `Bind(thread)` does **all three** at once
-(`common/NUMAHWPolicy.cpp:61`):
-1. **CPU pin** — `RunOnNode` / `numa_run_on_node`
-2. **Memory bind** — `MemOnNode` / `numa_set_membind` (on `n8g4_hbm`, `mem_node = i+8` → binds to HBM nodes)
+(round-robin, `common/NUMAHWPolicy.cpp:50`). `Bind(thread)` does **all three** at once:
+1. **CPU pin** — `RunOnNode` / `numa_run_on_node`  ← libnuma
+2. **Memory bind** — `MemOnNode` / `numa_set_membind` (`n8g4_hbm` → HBM nodes)  ← libnuma
 3. **GPU select** — `SelectGPU` / `set_gpu` (= `cudaSetDevice`, **not** libnuma)
 
 Call sites:
-- `receiver/JFJochReceiverFPGA.cpp:180/217/264` — data-stream threads `RunOnNode(FPGA's NUMA node)`
-  (device-locality pin, the NIC-era idea applied to the FPGA card).
+- `receiver/JFJochReceiverFPGA.cpp:180/217/264` — acquire (data-stream) threads
+  `RunOnNode(acquisition_device.GetNUMANode())` → the kernel-reported device node (§1b). CPU pin only.
 - `receiver/JFJochReceiverFPGA.cpp:299`, `receiver/JFJochReceiverLite.cpp:234` — analysis worker
-  threads `numa_policy.Bind(threadid)` → cpu + mem + **GPU** per the policy table.
+  threads `numa_policy.Bind(threadid)` → cpu + mem + GPU per the policy table.
 - `image_analysis/indexing/IndexerThreadPool.cpp:34` — each indexer thread
-  `SelectGPUAndItsNUMA(threadid % gpu_count)` (GPU round-robin + that GPU's own NUMA node;
+  `SelectGPUAndItsNUMA(threadid % gpu_count)` (GPU round-robin + that GPU's NUMA node via sysfs;
   independent of the `numa_policy` table).
 
-libnuma is used in exactly three files: `NUMAHWPolicy.cpp` (the above), `ImageBuffer.cpp`
-(`numa_alloc_interleaved`/`numa_free`), and `CUDAWrapper.cpp` (one `numa_node` lookup).
+The GPU NUMA node is now read from sysfs (`/sys/bus/pci/devices/<bdf>/numa_node`,
+`common/CUDAWrapper.cu:75`), **not** libnuma. So the only remaining libnuma calls are `RunOnNode` and
+`MemOnNode` in this file.
 
-### 1c. GPU dispatch — and why `jfjoch_process` underuses GPUs
+### 1d. GPU dispatch — `jfjoch_process` now uses all visible GPUs (was the root cause)
 - `get_gpu_count()` = `cudaGetDeviceCount()` (`common/CUDAWrapper.*`), so it already honours
   **`CUDA_VISIBLE_DEVICES`**. All dispatch is `% gpu_count`.
 - **Broker/receiver**: worker threads spread over GPUs via `numa_policy.Bind` (the `gpu` field) +
-  the indexer pool via `threadid % gpu_count`. → uses all visible GPUs.
-- **`jfjoch_process`**: its worker lambda (`tools/jfjoch_process.cpp:849`, launched `nthreads` times)
-  constructs `MXAnalysisWithoutFPGA` but **never calls `Bind`/`SelectGPU`**, and
-  `MXAnalysisWithoutFPGA` itself does not select a device (`image_analysis/MXAnalysisWithoutFPGA.cpp:38`
-  just builds GPU engines on the *current* device). → all per-image preprocessing / spot-finding /
-  azimuthal integration run on **GPU 0**. Only the indexer pool spreads. **This is the root cause of
-  "`jfjoch_process` doesn't use all GPUs."**
+  indexer pool via `threadid % gpu_count`. → uses all visible GPUs.
+- **`jfjoch_process` (DONE, G2):** its worker (`tools/jfjoch_process.cpp:854`) now calls `pin_gpu()`
+  before building `MXAnalysisWithoutFPGA`, so each worker's CUDA streams/engines land on a distinct
+  device. Previously everything ran on GPU 0 (only the indexer pool spread).
 
 ## 2. Goals
 
 - **G1 — multiple brokers, disjoint GPUs.** Run >1 `jfjoch_broker` on one machine, each confined to a
-  subset of GPUs, with the code transparently using "all it can see" (no hard-coded indices). Pure
-  workload control, no security requirement.
-- **G2 — `jfjoch_process` should use all visible GPUs**, not just GPU 0.
-- **G3 — drop the libnuma dependency** if it doesn't cost real performance (annoying dep; also a
-  blocker for the long-term Windows/MSVC viewer).
-- **G4 — reassess whether NUMA CPU/mem pinning is still worth it** given the FPGA pipeline (DMA into
-  kernel-mmap'd buffers, negligible IRQ traffic) rather than the old network-RX model.
+  subset of GPUs, code transparently using "all it can see" (no hard-coded indices). Workload
+  control, no security requirement.
+- **G2 — `jfjoch_process` should use all visible GPUs**, not just GPU 0.  **DONE** (§1d).
+- **G3 — drop the libnuma dependency.** Annoying dep; also a blocker for the long-term Windows/MSVC
+  viewer. Mostly done — one file (`NUMAHWPolicy.cpp`) left.
+- **G4 — reassess whether NUMA CPU/mem pinning is still worth it.** Note the corrected model: FPGA DMA
+  buffer *placement* is the kernel's job (§1b), so the only behavioural NUMA op left on real data flow
+  is the **CPU pin** of the acquire/analysis threads to the kernel-reported device node. That's the
+  thing to A/B.
 
-## 3. Proposed changes
+**Key separability insight:** dependency removal (G3) and behaviour removal (G4) are *independent
+axes*. Dropping libnuma does **not** require dropping any NUMA behaviour — `numa_run_on_node` →
+`sched_setaffinity`, `mbind`/`set_mempolicy` are raw syscalls. So G3 can complete regardless of how
+the G4 measurement turns out.
 
-- **G1 (zero code):** launch each broker under `CUDA_DEVICE_ORDER=PCI_BUS_ID
-  CUDA_VISIBLE_DEVICES=<subset> jfjoch_broker …`. `get_gpu_count()`/`% gpu_count` already do the rest.
-  Action item: **document this** (deployment note) and set `CUDA_DEVICE_ORDER=PCI_BUS_ID` so indices
-  are stable across boots.
+## 3. Status of changes
 
-- **G2 (DONE):** added `pin_gpu()` to `CUDAWrapper` — a process-wide round-robin counter
-  (`counter++ % get_gpu_count()`, no thread id needed, no-op when no GPU). The `jfjoch_process` worker
-  calls it once before building `MXAnalysisWithoutFPGA`, so each worker's CUDA streams/engines land on
-  a distinct device. Caller-agnostic and reusable by other thread pools later.
+- **G1 (zero code) — TODO (docs).** Launch each broker under `CUDA_DEVICE_ORDER=PCI_BUS_ID
+  CUDA_VISIBLE_DEVICES=<subset> jfjoch_broker …`. `get_gpu_count()`/`% gpu_count` do the rest. Set
+  `CUDA_DEVICE_ORDER=PCI_BUS_ID` so indices are stable across boots. Action: write the deployment note.
+- **G2 — DONE.** `pin_gpu()` in `CUDAWrapper` (process-wide round-robin `counter++ % get_gpu_count()`,
+  no-op when no GPU); `jfjoch_process` worker calls it once. Caller-agnostic, reusable.
+- **`ImageBuffer` — DONE (`d373ba04`).** malloc + parallel first-touch (§1a).
+- **`acquisition_device` — DONE (`042df308`).** Simulator off NUMA/mmap → plain heap; per-device
+  buffer ownership; libnuma gone from `acquisition_device/` (§1b).
+- **`CUDAWrapper` `numa_node` — DONE.** sysfs lookup, not libnuma (§1c).
+- **`NUMAHWPolicy` — REMAINING.** Split the bundled concerns:
+  - **Memory bind** (`MemOnNode`) — **drop.** HBM out of scope (the one Xeon MAX box didn't pay off;
+    treat every host as plain multi-socket).
+  - **CPU pin** (`RunOnNode`) — gated on **G4**. If kept, reimplement with `sched_setaffinity` +
+    node→cpulist from `/sys/devices/system/node/nodeN/cpulist` (no libnuma). Note it pins to the
+    *kernel-reported device node* (§1b) — well-founded if any pinning is kept.
+  - **GPU select** (`SelectGPU`) — **keep** (`cudaSetDevice`). `SelectGPUAndItsNUMA` then collapses to
+    `set_gpu` (+ optional CPU pin); `Bind` collapses to `SelectGPU` (+ optional CPU pin).
+  - Result: `NUMA_LIBRARY` leaves the CMake (`CMakeLists.txt:78-80`,
+    `common/CMakeLists.txt:155-161`).
 
-- **G3 / `ImageBuffer`:** replace `numa_alloc_interleaved` + single-threaded `memset` with **plain
-  `malloc` + a parallel first-touch `memset`** (N threads, unpinned). Threads spread by the scheduler
-  → balanced placement ≈ interleave for random access, *and* faster startup, *and* no libnuma. Safe
-  here because the buffer is 30–40 % of RAM (first-touch spills to the other node if one fills; no OOM;
-  just check `vm.zone_reclaim_mode == 0`). Deterministic per-page interleave (if ever needed under
-  tight RAM) is a raw `mbind(MPOL_INTERLEAVE)` syscall — still libnuma-free.
+## 4. Open questions / to validate before deleting `NUMAHWPolicy` pinning
 
-- **G3 / G4 / `NUMAHWPolicy`:** split the bundled concerns:
-  - **CPU pin** (`RunOnNode`) — likely **drop** for the FPGA path (G4). If ever wanted back, use
-    `sched_setaffinity` (no libnuma).
-  - **GPU select** (`SelectGPU`/`SelectGPUAndItsNUMA`) — **keep**; already `cudaSetDevice`, no libnuma.
-  - **Memory bind** (`MemOnNode`) — **drop.** (HBM is out of scope: the only Xeon MAX box didn't pay
-    off and isn't worth special-casing, so no `mbind` path is needed — treat every host as plain
-    multi-socket.)
-  - **`CUDAWrapper` `numa_node`** — read the GPU PCIe device's `/sys/.../numa_node` instead of libnuma.
-  - Result: `NUMA_LIBRARY` leaves the CMake entirely.
-
-## 4. Open questions / to validate before deleting anything
-
-- **G4 is empirical.** A/B at production frame rate (pinning on vs off): sustained throughput, dropped
-  frames, latency jitter. The reasoning predicts "no regression," but measure on one real box first —
+- **G4 is empirical.** A/B at production frame rate (CPU pin on vs off): sustained throughput, dropped
+  frames, latency jitter. Reasoning predicts "no regression," but measure on one real box first —
   production systems are currently tuned around this.
-- Confirm `vm.zone_reclaim_mode` is `0` on the broker hosts (else first-touch reclaims locally before
-  spilling → latency stalls).
-- Parallel first-touch placement is *approximate* (depends on the scheduler spreading the zeroing
-  threads); fine with RAM headroom, but note it's not the guaranteed 50/50 of `mbind` interleave.
+- Confirm `vm.zone_reclaim_mode` is `0` on the broker hosts (`cat /proc/sys/vm/zone_reclaim_mode`).
+  Non-zero turns `ImageBuffer`'s first-touch into synchronous local reclaim (page-cache eviction /
+  writeback) → startup latency stalls; `0` just spills the page to a remote node.
+- `ImageBuffer` first-touch placement is *approximate* (depends on the scheduler spreading the zeroing
+  threads); fine with RAM headroom, but not the guaranteed 50/50 of `mbind` interleave. Deterministic
+  per-page interleave, if ever needed, is a raw `mbind(MPOL_INTERLEAVE)` syscall — still libnuma-free.
 
-## 5. Suggested order (low-risk first)
+## 5. Remaining order (low-risk first)
 
-1. **G1** — document `CUDA_VISIBLE_DEVICES` launch (no code).
-2. ~~**G2** — per-worker GPU pin in `jfjoch_process`.~~ **DONE** (`pin_gpu()`).
-3. **ImageBuffer** parallel first-touch (drops one libnuma user, helps startup; stands alone).
-4. **G4 A/B** on a real broker; if clean, drop CPU pinning.
-5. **NUMAHWPolicy** simplify (keep GPU select, drop CPU pin + mem bind) + `CUDAWrapper` sysfs
-   → remove `NUMA_LIBRARY` from CMake.
+1. **G1** — document the `CUDA_VISIBLE_DEVICES` launch (no code).
+2. **G4 A/B** on a real broker — the gate for dropping the `RunOnNode` CPU pin.
+3. **`NUMAHWPolicy`** — drop `MemOnNode`; drop/replace `RunOnNode` per G4; keep `SelectGPU`. Then
+   remove `NUMA_LIBRARY` from CMake → G3 complete.
+
+*(DONE so far: G2 `pin_gpu`, `ImageBuffer` first-touch, `acquisition_device` de-NUMA, `CUDAWrapper`
+sysfs node lookup.)*
-- 
2.52.0


From cc925b26683526ad18890f1f5ba4ec33fa5d91e4 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 20:25:36 +0200
Subject: [PATCH 071/228] Remove NUMAHWPolicy and the libnuma dependency

NUMA CPU/memory pinning is no longer worthwhile: the FPGA DMA buffers are
placed device-local by the kernel (dma_alloc_coherent), the big RAM ring
buffer is random-access (first-touch handles placement), and GPU work is
already spread across all visible devices. So drop the pinning entirely
and with it libnuma.

- Delete NUMAHWPolicy; the only concern worth keeping - GPU selection -
  is done directly via pin_gpu() (round-robin over visible GPUs) in the
  indexer pool and the Lite analysis threads. CPU-only threads
  (FPGA acquire/pedestal/summation/frame-transform) no longer bind
  anything.
- Drop get_gpu_numa_node() (sysfs lookup) - only SelectGPUAndItsNUMA
  used it.
- numa_policy broker setting is deprecated and ignored (kept in the API
  for backward compatibility; warns once on startup).
- Remove NUMA_LIBRARY / numa.h / numaif.h detection from CMake.
- Docs: drop the NUMA dependency, remove the numa_policy config example,
  and document running multiple brokers on disjoint GPUs via
  CUDA_VISIBLE_DEVICES.
- Remove NUMA_GPU_REVIEW.md (the planning note; this work is now done).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                                |   5 -
 NUMA_GPU_REVIEW.md                            | 145 ------------------
 broker/JFJochBrokerParser.cpp                 |   4 -
 broker/jfjoch_api.yaml                        |   3 +-
 broker/jfjoch_broker.cpp                      |   2 +
 common/CMakeLists.txt                         |   9 --
 common/CUDAWrapper.cpp                        |   4 -
 common/CUDAWrapper.cu                         |  54 -------
 common/CUDAWrapper.h                          |   1 -
 common/NUMAHWPolicy.cpp                       | 125 ---------------
 common/NUMAHWPolicy.h                         |  33 ----
 docs/DEPLOYMENT.md                            |   8 +-
 docs/JFJOCH_BROKER.md                         |   1 -
 docs/SOFTWARE.md                              |   1 -
 image_analysis/indexing/IndexerThreadPool.cpp |  10 +-
 image_analysis/indexing/IndexerThreadPool.h   |   1 -
 receiver/JFJochReceiver.cpp                   |   2 -
 receiver/JFJochReceiver.h                     |   4 -
 receiver/JFJochReceiverFPGA.cpp               |  24 ---
 receiver/JFJochReceiverFPGA.h                 |   2 -
 receiver/JFJochReceiverLite.cpp               |  11 +-
 receiver/JFJochReceiverLite.h                 |   2 -
 receiver/JFJochReceiverService.cpp            |  12 --
 receiver/JFJochReceiverService.h              |   4 -
 receiver/JFJochReceiverTest.cpp               |   8 +-
 receiver/JFJochReceiverTest.h                 |   2 -
 tools/jfjoch_fpga_test.cpp                    |   6 +-
 tools/jfjoch_lite_perf_test.cpp               |   4 +-
 28 files changed, 24 insertions(+), 463 deletions(-)
 delete mode 100644 NUMA_GPU_REVIEW.md
 delete mode 100644 common/NUMAHWPolicy.cpp
 delete mode 100644 common/NUMAHWPolicy.h

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d675e610..f81c5ea0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -73,11 +73,6 @@ IF(HAS_FFTW3_H AND FFTWF_LIBRARY)
 ENDIF()
 
 INCLUDE_DIRECTORIES(include)
-INCLUDE(CheckIncludeFile)
-
-FIND_LIBRARY(NUMA_LIBRARY NAMES numa DOC "NUMA Library")
-CHECK_INCLUDE_FILE(numaif.h HAS_NUMAIF)
-CHECK_INCLUDE_FILE(numa.h HAS_NUMA_H)
 
 include(FetchContent)
 
diff --git a/NUMA_GPU_REVIEW.md b/NUMA_GPU_REVIEW.md
deleted file mode 100644
index 840d86ac..00000000
--- a/NUMA_GPU_REVIEW.md
+++ /dev/null
@@ -1,145 +0,0 @@
-# NUMA / GPU usage — current state, goals, remaining work
-
-Working note on the NUMA/GPU direction. Several items are now **implemented and committed** on
-branch `2606-pixel-refine` (see §3/§5); this note tracks what landed, what's left, and — importantly
-— the corrected mental model of *where NUMA actually matters*. File:line anchors are from
-`2606-pixel-refine`.
-
-**Headline:** after the committed work, **libnuma is used in exactly one file**
-(`common/NUMAHWPolicy.cpp`). Everything else (GPU node lookup, the big RAM buffer, the FPGA DMA
-buffers, the simulator) is libnuma-free.
-
-## 1. Current state (the mind map)
-
-### 1a. `ImageBuffer` — the big RAM ring buffer
-- **One instance**, a member of the receiver: `JFJochReceiverService::image_buffer`
-  (`receiver/JFJochReceiverService.h:21`), sized `image_buffer_MiB` from broker config
-  (`broker/jfjoch_broker.cpp:104` → ctor `receiver/JFJochReceiverService.cpp:15`). The 150–200 GB
-  allocation.
-- **Allocation (DONE, commit `d373ba04`):** plain `std::malloc` + a **parallel first-touch `memset`**
-  (`hardware_concurrency()` threads, unpinned) in `common/ImageBuffer.cpp`. Each page is
-  first-touched — and thus NUMA-placed — by whichever node the scheduler ran the zeroing thread on:
-  approximates the old `numa_alloc_interleaved` placement for the random-access buffer, *and*
-  pre-faults every page (no first-use fault in the hot path), *and* speeds up startup, *and* drops
-  libnuma here. (Was `numa_alloc_interleaved` + single-threaded `memset`.)
-- **Producers/consumers**: receiver/decompression threads write frames into slots; consumers are
-  preview/TIFF/JPEG/HTTP retrieval (`GetImage`) and the ZMQ/file sender. Access is random and
-  unpinned (any thread → any slot) — which is *why* interleave/first-touch placement (not per-node
-  binding) is the right model.
-- **Not used by `jfjoch_process` or `jfjoch_viewer`** — they read HDF5 through the reader, never
-  instantiate `ImageBuffer`. Broker/receiver-only (it only needs to *compile* for the viewer).
-
-### 1b. FPGA DMA buffers — placement is a *kernel* concern, not libnuma  *(this section was missing)*
-The real per-frame DMA buffers are **allocated and NUMA-placed by the kernel driver**, with zero
-userspace/libnuma involvement. The earlier draft framed the userspace `mbind` as "the real
-hardware-locality win" — that was wrong; the win is in the kernel:
-- `fpga/pcie_driver/jfjoch_memory.c:28` — `dma_alloc_coherent(&pdev->dev, FPGA_BUFFER_LOCATION_SIZE,
-  …)` × `nbuffer` (512). Gives **physically contiguous, DMA-coherent** pages (required: each buffer's
-  bus address is written into the FPGA address table at `:37-38`). Placement is **device-local by
-  construction** — the kernel DMA/page allocator uses `dev_to_node(&pdev->dev)`. This is exactly why
-  it can't be a userspace `malloc`+`mbind`: userspace virtual memory is neither physically contiguous
-  nor a valid DMA target.
-- `jfjoch_memory.c:99` — `dma_mmap_coherent` maps those *same physical pages* into userspace;
-  `JungfraujochDevice::MapKernelBuffer` (`fpga/host_library/JungfraujochDevice.cpp:166`) is a plain
-  `mmap` of the char dev. No second allocation, no first-touch, no migration.
-- `IOCTL_JFJOCH_NUMA` (`fpga/pcie_driver/jfjoch_ioctl.c:133`) just **reports**
-  `drvdata->pdev->dev.numa_node`. Userspace's only NUMA action on the real path is to pin the
-  *acquire thread's CPU* to that node (the `RunOnNode` calls in §1c).
-- **Simulated path (DONE, commit `042df308`):** `HLSSimulatedDevice` used to *emulate* device locality
-  with a userspace `mmap`+`mbind` (`<numaif.h>`) — the only libnuma user in `acquisition_device/`. It
-  now uses **plain zeroed heap buffers** (`std::vector`, not performance-critical). Buffer ownership
-  was refactored so each device owns its lifecycle: `PCIExpressDevice` `mmap`s/`munmap`s the kernel
-  DMA buffers; `HLSSimulatedDevice` owns the heap buffers; the base `AcquisitionDevice` is just a
-  non-owning address view. No libnuma, no mmap on the sim path.
-
-### 1c. `NUMAHWPolicy` — bundles three concerns per worker thread (the last libnuma user)
-Built from the broker config `numa_policy` string (e.g. `n2g2`, `n8g4`, `n8g4_hbm`) into a table of
-`NUMABinding{cpu_node, mem_node, gpu}`; `GetBinding(thread) = bindings[thread % nbindings]`
-(round-robin, `common/NUMAHWPolicy.cpp:50`). `Bind(thread)` does **all three** at once:
-1. **CPU pin** — `RunOnNode` / `numa_run_on_node`  ← libnuma
-2. **Memory bind** — `MemOnNode` / `numa_set_membind` (`n8g4_hbm` → HBM nodes)  ← libnuma
-3. **GPU select** — `SelectGPU` / `set_gpu` (= `cudaSetDevice`, **not** libnuma)
-
-Call sites:
-- `receiver/JFJochReceiverFPGA.cpp:180/217/264` — acquire (data-stream) threads
-  `RunOnNode(acquisition_device.GetNUMANode())` → the kernel-reported device node (§1b). CPU pin only.
-- `receiver/JFJochReceiverFPGA.cpp:299`, `receiver/JFJochReceiverLite.cpp:234` — analysis worker
-  threads `numa_policy.Bind(threadid)` → cpu + mem + GPU per the policy table.
-- `image_analysis/indexing/IndexerThreadPool.cpp:34` — each indexer thread
-  `SelectGPUAndItsNUMA(threadid % gpu_count)` (GPU round-robin + that GPU's NUMA node via sysfs;
-  independent of the `numa_policy` table).
-
-The GPU NUMA node is now read from sysfs (`/sys/bus/pci/devices/<bdf>/numa_node`,
-`common/CUDAWrapper.cu:75`), **not** libnuma. So the only remaining libnuma calls are `RunOnNode` and
-`MemOnNode` in this file.
-
-### 1d. GPU dispatch — `jfjoch_process` now uses all visible GPUs (was the root cause)
-- `get_gpu_count()` = `cudaGetDeviceCount()` (`common/CUDAWrapper.*`), so it already honours
-  **`CUDA_VISIBLE_DEVICES`**. All dispatch is `% gpu_count`.
-- **Broker/receiver**: worker threads spread over GPUs via `numa_policy.Bind` (the `gpu` field) +
-  indexer pool via `threadid % gpu_count`. → uses all visible GPUs.
-- **`jfjoch_process` (DONE, G2):** its worker (`tools/jfjoch_process.cpp:854`) now calls `pin_gpu()`
-  before building `MXAnalysisWithoutFPGA`, so each worker's CUDA streams/engines land on a distinct
-  device. Previously everything ran on GPU 0 (only the indexer pool spread).
-
-## 2. Goals
-
-- **G1 — multiple brokers, disjoint GPUs.** Run >1 `jfjoch_broker` on one machine, each confined to a
-  subset of GPUs, code transparently using "all it can see" (no hard-coded indices). Workload
-  control, no security requirement.
-- **G2 — `jfjoch_process` should use all visible GPUs**, not just GPU 0.  **DONE** (§1d).
-- **G3 — drop the libnuma dependency.** Annoying dep; also a blocker for the long-term Windows/MSVC
-  viewer. Mostly done — one file (`NUMAHWPolicy.cpp`) left.
-- **G4 — reassess whether NUMA CPU/mem pinning is still worth it.** Note the corrected model: FPGA DMA
-  buffer *placement* is the kernel's job (§1b), so the only behavioural NUMA op left on real data flow
-  is the **CPU pin** of the acquire/analysis threads to the kernel-reported device node. That's the
-  thing to A/B.
-
-**Key separability insight:** dependency removal (G3) and behaviour removal (G4) are *independent
-axes*. Dropping libnuma does **not** require dropping any NUMA behaviour — `numa_run_on_node` →
-`sched_setaffinity`, `mbind`/`set_mempolicy` are raw syscalls. So G3 can complete regardless of how
-the G4 measurement turns out.
-
-## 3. Status of changes
-
-- **G1 (zero code) — TODO (docs).** Launch each broker under `CUDA_DEVICE_ORDER=PCI_BUS_ID
-  CUDA_VISIBLE_DEVICES=<subset> jfjoch_broker …`. `get_gpu_count()`/`% gpu_count` do the rest. Set
-  `CUDA_DEVICE_ORDER=PCI_BUS_ID` so indices are stable across boots. Action: write the deployment note.
-- **G2 — DONE.** `pin_gpu()` in `CUDAWrapper` (process-wide round-robin `counter++ % get_gpu_count()`,
-  no-op when no GPU); `jfjoch_process` worker calls it once. Caller-agnostic, reusable.
-- **`ImageBuffer` — DONE (`d373ba04`).** malloc + parallel first-touch (§1a).
-- **`acquisition_device` — DONE (`042df308`).** Simulator off NUMA/mmap → plain heap; per-device
-  buffer ownership; libnuma gone from `acquisition_device/` (§1b).
-- **`CUDAWrapper` `numa_node` — DONE.** sysfs lookup, not libnuma (§1c).
-- **`NUMAHWPolicy` — REMAINING.** Split the bundled concerns:
-  - **Memory bind** (`MemOnNode`) — **drop.** HBM out of scope (the one Xeon MAX box didn't pay off;
-    treat every host as plain multi-socket).
-  - **CPU pin** (`RunOnNode`) — gated on **G4**. If kept, reimplement with `sched_setaffinity` +
-    node→cpulist from `/sys/devices/system/node/nodeN/cpulist` (no libnuma). Note it pins to the
-    *kernel-reported device node* (§1b) — well-founded if any pinning is kept.
-  - **GPU select** (`SelectGPU`) — **keep** (`cudaSetDevice`). `SelectGPUAndItsNUMA` then collapses to
-    `set_gpu` (+ optional CPU pin); `Bind` collapses to `SelectGPU` (+ optional CPU pin).
-  - Result: `NUMA_LIBRARY` leaves the CMake (`CMakeLists.txt:78-80`,
-    `common/CMakeLists.txt:155-161`).
-
-## 4. Open questions / to validate before deleting `NUMAHWPolicy` pinning
-
-- **G4 is empirical.** A/B at production frame rate (CPU pin on vs off): sustained throughput, dropped
-  frames, latency jitter. Reasoning predicts "no regression," but measure on one real box first —
-  production systems are currently tuned around this.
-- Confirm `vm.zone_reclaim_mode` is `0` on the broker hosts (`cat /proc/sys/vm/zone_reclaim_mode`).
-  Non-zero turns `ImageBuffer`'s first-touch into synchronous local reclaim (page-cache eviction /
-  writeback) → startup latency stalls; `0` just spills the page to a remote node.
-- `ImageBuffer` first-touch placement is *approximate* (depends on the scheduler spreading the zeroing
-  threads); fine with RAM headroom, but not the guaranteed 50/50 of `mbind` interleave. Deterministic
-  per-page interleave, if ever needed, is a raw `mbind(MPOL_INTERLEAVE)` syscall — still libnuma-free.
-
-## 5. Remaining order (low-risk first)
-
-1. **G1** — document the `CUDA_VISIBLE_DEVICES` launch (no code).
-2. **G4 A/B** on a real broker — the gate for dropping the `RunOnNode` CPU pin.
-3. **`NUMAHWPolicy`** — drop `MemOnNode`; drop/replace `RunOnNode` per G4; keep `SelectGPU`. Then
-   remove `NUMA_LIBRARY` from CMake → G3 complete.
-
-*(DONE so far: G2 `pin_gpu`, `ImageBuffer` first-touch, `acquisition_device` de-NUMA, `CUDAWrapper`
-sysfs node lookup.)*
diff --git a/broker/JFJochBrokerParser.cpp b/broker/JFJochBrokerParser.cpp
index 68b000ae..ffb3d092 100644
--- a/broker/JFJochBrokerParser.cpp
+++ b/broker/JFJochBrokerParser.cpp
@@ -234,10 +234,6 @@ void ParseAcquisitionDeviceGroup(const org::openapitools::server::model::Jfjoch_
 }
 
 void ParseReceiverSettings(const org::openapitools::server::model::Jfjoch_settings &input, JFJochReceiverService &service) {
-    std::string numa_policy = input.getNumaPolicy();
-    if (!numa_policy.empty())
-        service.NUMAPolicy(numa_policy);
-
     // Using default in case
     service.NumThreads(input.getReceiverThreads());
 
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 67e80aa8..6e2b42db 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -2264,7 +2264,8 @@ components:
           description: Number of threads used by the receiver
         numa_policy:
           type: string
-          description: NUMA policy to bind CPUs
+          deprecated: true
+          description: Ignored value
         frontend_directory:
           type: string
           description: Location of built JavaScript web frontend
diff --git a/broker/jfjoch_broker.cpp b/broker/jfjoch_broker.cpp
index dde40cbe..e8997992 100644
--- a/broker/jfjoch_broker.cpp
+++ b/broker/jfjoch_broker.cpp
@@ -74,6 +74,8 @@ int main(int argc, char **argv) {
         return EXIT_FAILURE;
     }
 
+    if (settings.numaPolicyIsSet())
+        logger.Warning("NUMA policy is deprecated and ignored - processed are split over all the CPUs/GPUs in the system");
     if (settings.verboseIsSet() && settings.isVerbose())
         logger.Verbose(true);
     else
diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt
index f6273dc4..06a365c2 100644
--- a/common/CMakeLists.txt
+++ b/common/CMakeLists.txt
@@ -55,7 +55,6 @@ ADD_LIBRARY(JFJochCommon STATIC
         DetectorModuleGeometry.cpp DetectorModuleGeometry.h
         DetectorSetup.h DetectorSetup.cpp ZeroCopyReturnValue.h Histogram.h DiffractionGeometry.h
         CUDAWrapper.cpp CUDAWrapper.h
-        NUMAHWPolicy.cpp NUMAHWPolicy.h
         ADUHistogram.cpp ADUHistogram.h
         RawToConvertedGeometryCore.h
         Plot.h
@@ -151,11 +150,3 @@ IF (JFJOCH_CUDA_AVAILABLE)
     TARGET_LINK_LIBRARIES(JFJochCommon CUDA::cudart_static
             ${CMAKE_DL_LIBS} $<$<PLATFORM_ID:Linux>:rt>)
 ENDIF()
-
-IF(HAS_NUMAIF AND HAS_NUMA_H AND NUMA_LIBRARY)
-    TARGET_COMPILE_DEFINITIONS(JFJochCommon PUBLIC JFJOCH_USE_NUMA)
-    TARGET_LINK_LIBRARIES(JFJochCommon ${NUMA_LIBRARY})
-    MESSAGE(STATUS "NUMA memory/CPU pinning enabled")
-ELSE()
-    MESSAGE(WARNING "NUMA memory/CPU pinning disabled")
-ENDIF()
diff --git a/common/CUDAWrapper.cpp b/common/CUDAWrapper.cpp
index d73e3760..ab3e2e6c 100644
--- a/common/CUDAWrapper.cpp
+++ b/common/CUDAWrapper.cpp
@@ -13,8 +13,4 @@ void set_gpu(int32_t dev_id) {}
 
 void pin_gpu() {}
 
-int get_gpu_numa_node(int dev_id) {
-    return -1;
-}
-
 #endif
diff --git a/common/CUDAWrapper.cu b/common/CUDAWrapper.cu
index 684f8b82..554c54c6 100644
--- a/common/CUDAWrapper.cu
+++ b/common/CUDAWrapper.cu
@@ -45,57 +45,3 @@ void pin_gpu() {
     if (dev_count > 0)
         set_gpu(counter.fetch_add(1) % dev_count);
 }
-
-// Return CUDA device PCI Bus ID as "domain:bus:device.function", e.g., "0000:65:00.0"
-static std::string get_cuda_device_pci_bus_id(int dev_id) {
-    // CUDA API provides cudaDeviceGetPCIBusId
-    char buf[64] = {0};
-    cudaDeviceProp prop;
-    cudaError_t st = cudaGetDeviceProperties(&prop, dev_id);
-    if (st != cudaSuccess) {
-        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(st));
-    }
-    // Prefer cudaDeviceGetPCIBusId for full id including domain and function
-    cudaError_t st2 = cudaDeviceGetPCIBusId(buf, static_cast<int>(sizeof(buf)), dev_id);
-    if (st2 == cudaSuccess) {
-        return std::string(buf);
-    }
-    // Fallback: synthesize from properties (domain may be missing on very old drivers)
-    // Note: function is typically ".0"
-    char alt[64];
-    std::snprintf(alt, sizeof(alt), "%04x:%02x:%02x.%u",
-                  prop.pciDomainID, prop.pciBusID, prop.pciDeviceID, 0u);
-    return std::string(alt);
-}
-
-// Resolve NUMA node from PCI address using Linux sysfs
-// Returns:
-//   >=0  NUMA node index
-//   -1   if NUMA node is not available/unknown
-int get_gpu_numa_node(int dev_id) {
-    auto dev_count = get_gpu_count();
-    if (dev_count <= 0) return -1;
-    if (dev_id < 0 || dev_id >= dev_count) {
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid CUDA device ID");
-    }
-
-    // We don't need to call cudaSetDevice here; querying by id is sufficient.
-    const std::string pci_bus_id = get_cuda_device_pci_bus_id(dev_id); // "dddd:bb:dd.f"
-
-    // sysfs path for PCI device. Examples:
-    //  - /sys/bus/pci/devices/0000:65:00.0/numa_node
-    const std::string sysfs_path = std::string("/sys/bus/pci/devices/") + pci_bus_id + "/numa_node";
-
-    std::ifstream f(sysfs_path);
-    if (!f.is_open()) {
-        // On some systems, the symlink may be via /sys/class/drm or nvidia, but primary path should exist.
-        return -1;
-    }
-
-    int numa = -1;
-    f >> numa;
-    if (!f.good()) {
-        return -1;
-    }
-    return numa;
-}
diff --git a/common/CUDAWrapper.h b/common/CUDAWrapper.h
index dcc97f3c..4b288ee0 100644
--- a/common/CUDAWrapper.h
+++ b/common/CUDAWrapper.h
@@ -7,7 +7,6 @@
 
 int32_t get_gpu_count();
 void set_gpu(int32_t dev_id);
-int get_gpu_numa_node(int dev_id);
 
 // Pin the calling thread to the next GPU in round-robin order, using a process-wide counter
 // (counter++ % get_gpu_count()). Call once per thread; no thread id needed. No-op when no GPU
diff --git a/common/NUMAHWPolicy.cpp b/common/NUMAHWPolicy.cpp
deleted file mode 100644
index ac6621ae..00000000
--- a/common/NUMAHWPolicy.cpp
+++ /dev/null
@@ -1,125 +0,0 @@
-// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "NUMAHWPolicy.h"
-
-#include "../common/CUDAWrapper.h"
-#include "JFJochException.h"
-
-#ifdef JFJOCH_USE_NUMA
-#include <numa.h>
-#endif
-
-NUMAHWPolicy::NUMAHWPolicy(const std::string &policy) : name(policy) {
-    if ((policy.empty()) || (policy == "none")) {
-        name = "none";
-    } else if (policy == "n2g2") {
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 0, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 1, .gpu = 1});
-    } else if (policy == "n2g4") {
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 0, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 1, .gpu = 2});
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 0, .gpu = 1});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 1, .gpu = 3});
-    } else if (policy == "n2g2_hbm") {
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 2, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 3, .gpu = 1});
-    } else if (policy == "n2g4_hbm") {
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 2, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 3, .gpu = 2});
-        bindings.emplace_back(NUMABinding{.cpu_node = 0, .mem_node = 2, .gpu = 1});
-        bindings.emplace_back(NUMABinding{.cpu_node = 1, .mem_node = 3, .gpu = 3});
-    } else if (policy == "n8g4") {
-        for (int32_t i = 0; i < 8; i++)
-            bindings.emplace_back(NUMABinding{.cpu_node = i, .mem_node = i, .gpu = i/2});
-    } else if (policy == "n8g4_hbm") {
-        for (int32_t i = 0; i < 8; i++)
-            bindings.emplace_back(NUMABinding{.cpu_node = i, .mem_node = i + 8, .gpu = i / 2});
-    } else if (policy == "g2") {
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 1});
-    } else if (policy == "g4") {
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 0});
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 1});
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 2});
-        bindings.emplace_back(NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = 3});
-    } else
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown NUMA policy");
-}
-
-NUMABinding NUMAHWPolicy::GetBinding(uint32_t thread) const {
-    if (bindings.empty())
-        return NUMABinding{.cpu_node = -1, .mem_node = -1, .gpu = -1};
-    else
-        return bindings.at(thread % bindings.size());
-}
-
-void NUMAHWPolicy::Bind(uint32_t thread) const {
-    Bind(GetBinding(thread));
-}
-
-void NUMAHWPolicy::Bind(const NUMABinding &binding)  {
-    RunOnNode(binding.cpu_node);
-    MemOnNode(binding.mem_node);
-    SelectGPU(binding.gpu);
-}
-
-void NUMAHWPolicy::RunOnNode(int32_t cpu_node) {
-#ifdef JFJOCH_USE_NUMA
-    if (numa_available() != -1) {
-        auto max_nodes = numa_num_configured_nodes();
-
-        if (cpu_node >= 0) {
-            if (cpu_node < max_nodes)
-                numa_run_on_node(cpu_node);
-            else
-                throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "CPU NUMA node out of bounds");
-        }
-    }
-#endif
-}
-
-void NUMAHWPolicy::MemOnNode(int32_t mem_node) {
-#ifdef JFJOCH_USE_NUMA
-    if (numa_available() != -1) {
-        auto max_nodes = numa_num_configured_nodes();
-
-        if (mem_node >= 0) {
-            if (mem_node < max_nodes) {
-                struct bitmask *mask = numa_allocate_nodemask();
-                numa_bitmask_setbit(mask, mem_node);
-                numa_set_membind(mask);
-                numa_bitmask_free(mask);
-            } else
-                throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Memory NUMA node out of bounds");
-        }
-    }
-#endif
-}
-
-void NUMAHWPolicy::SelectGPU(int32_t gpu) {
-    auto gpu_count = get_gpu_count();
-
-    if ((gpu_count > 0) && (gpu >= 0)) {
-        if (gpu < gpu_count)
-            set_gpu(gpu);
-        else
-            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "GPU device out of bounds");
-    }
-}
-
-void NUMAHWPolicy::SelectGPUAndItsNUMA(int32_t gpu) {
-    int numa = get_gpu_numa_node(gpu);
-    if (numa >= 0) {
-        RunOnNode(numa);
-        MemOnNode(numa);
-    }
-    set_gpu(gpu);
-}
-
-
-const std::string &NUMAHWPolicy::GetName() const {
-    return name;
-}
-
-
diff --git a/common/NUMAHWPolicy.h b/common/NUMAHWPolicy.h
deleted file mode 100644
index 6c1375dd..00000000
--- a/common/NUMAHWPolicy.h
+++ /dev/null
@@ -1,33 +0,0 @@
-// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include <cstdint>
-#include <vector>
-#include <string>
-#include <atomic>
-
-struct NUMABinding {
-    int32_t cpu_node;
-    int32_t mem_node;
-    int32_t gpu;
-};
-
-class NUMAHWPolicy {
-    std::string name;
-    std::vector<NUMABinding> bindings;
-public:
-    NUMAHWPolicy() = default;
-    explicit NUMAHWPolicy(const std::string& policy);
-    NUMABinding GetBinding(uint32_t thread) const;
-
-    const std::string &GetName() const;
-
-    void Bind(uint32_t thread) const;
-    static void Bind(const NUMABinding &binding);
-    static void RunOnNode(int32_t cpu_node);
-    static void MemOnNode(int32_t mem_node);
-    static void SelectGPU(int32_t gpu);
-    static void SelectGPUAndItsNUMA(int32_t gpu);
-};
diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md
index fb91982c..1a3e757b 100644
--- a/docs/DEPLOYMENT.md
+++ b/docs/DEPLOYMENT.md
@@ -110,6 +110,12 @@ Example JSON files are placed in `etc/` folder. JSON file format is also explain
 
 When running the service can be accessed via HTTP interface from a web browser for configuration and monitoring.
 
+Jungfraujoch automatically uses every GPU visible to the process and spreads the per-image work across all of them. To run more than one `jfjoch_broker` on a single machine, each confined to a disjoint subset of GPUs, set `CUDA_VISIBLE_DEVICES`; setting `CUDA_DEVICE_ORDER=PCI_BUS_ID` keeps the GPU indices stable across reboots. For example, two brokers on a 4-GPU host:
+```
+CUDA_DEVICE_ORDER=PCI_BUS_ID CUDA_VISIBLE_DEVICES=0,1 jfjoch_broker broker_a.json 5232
+CUDA_DEVICE_ORDER=PCI_BUS_ID CUDA_VISIBLE_DEVICES=2,3 jfjoch_broker broker_b.json 5233
+```
+
 To prepare the configuration file one also needs to reference calibration files: gain files for PSI JUNGFRAU and trim-bit files for PSI EIGER. 
 These need to be obtained from the PSI Detector Group.
 
@@ -118,7 +124,7 @@ These need to be obtained from the PSI Detector Group.
 To test that FPGA board is working properly without access to a JUNGFRAU detector, you can use `jfjoch_fpga_test` tool.
 For example to simulate 10M pixel system with 4 FPGA cards and 200k images on a 2 CPU system with 2 GPUs:
 ```
-jfjoch_fpga_test ~/nextgendcu/ -m20 -s4 -i 200000 -Pn2g2
+jfjoch_fpga_test ~/nextgendcu/ -m20 -s4 -i 200000
 ```
 Or 1M pixel system with one FPGA card:
 ```
diff --git a/docs/JFJOCH_BROKER.md b/docs/JFJOCH_BROKER.md
index d7e58f0b..76e3f2b7 100644
--- a/docs/JFJOCH_BROKER.md
+++ b/docs/JFJOCH_BROKER.md
@@ -129,7 +129,6 @@ Example with all fields:
   },
   "image_buffer_MiB": 2048,
   "receiver_threads": 64,
-  "numa_policy": "n2g2",
   "frontend_directory": "/usr/share/jfjoch/frontend",
   "image_pusher": "ZeroMQ",
   "zeromq_metadata": {
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index d64671e8..8b144dbe 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -21,7 +21,6 @@ Required:
 Optional:
 * CUDA compiler version 12.7 or newer - required for MX fast feedback indexer
 * FFTW library - for indexing if GPU/CUDA is absent
-* NUMA library - to pin threads to nodes/CPUs
 * Node.js - to make frontend
 * Qt version 6 (for jfjoch_viewer)
 
diff --git a/image_analysis/indexing/IndexerThreadPool.cpp b/image_analysis/indexing/IndexerThreadPool.cpp
index 86900f12..51913d9a 100644
--- a/image_analysis/indexing/IndexerThreadPool.cpp
+++ b/image_analysis/indexing/IndexerThreadPool.cpp
@@ -28,15 +28,11 @@ IndexerThread::IndexerThread(const IndexingSettings &settings, int threadid) {
 
 void IndexerThread::Worker(const IndexingSettings &settings, int threadid) {
     try {
-#ifdef JFJOCH_USE_CUDA
-        auto gpu_count = get_gpu_count();
-        if (gpu_count > 0)
-            NUMAHWPolicy::SelectGPUAndItsNUMA(threadid % gpu_count);
-#endif
+        pin_gpu();
     } catch (const std::exception &e) {
-        spdlog::error("Failed to bind thread to NUMA node: {}", e.what());
+        spdlog::error("Failed to pin to GPU {}", e.what());
     } catch (...) {
-        // NUMA policy errors are not critical and should be ignored for the time being.
+        // GPU pinning errors are not critical and should be ignored for the time being.
     }
 
     std::unique_ptr<Indexer> fft_indexer, ffbidx_indexer, fftw_indexer;
diff --git a/image_analysis/indexing/IndexerThreadPool.h b/image_analysis/indexing/IndexerThreadPool.h
index 224e2943..fd7e0a04 100644
--- a/image_analysis/indexing/IndexerThreadPool.h
+++ b/image_analysis/indexing/IndexerThreadPool.h
@@ -17,7 +17,6 @@
 #include "../common/JFJochMessages.h"
 #include "../common/DiffractionSpot.h"
 #include "../common/DiffractionExperiment.h"
-#include "../common/NUMAHWPolicy.h"
 #include "Indexer.h"
 
 class IndexerThread {
diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp
index 64e82e33..752013ff 100644
--- a/receiver/JFJochReceiver.cpp
+++ b/receiver/JFJochReceiver.cpp
@@ -13,7 +13,6 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
                                JFJochReceiverPlots &in_plots,
                                const SpotFindingSettings &spot_finding_settings,
                                Logger &logger,
-                               const NUMAHWPolicy &in_numa_policy,
                                const PixelMask &in_pixel_mask,
                                ZMQPreviewSocket *in_zmq_preview_socket,
                                ZMQMetadataSocket *in_zmq_metadata_socket,
@@ -29,7 +28,6 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment &in_experiment,
           plots(in_plots),
           scan_result(in_experiment),
           serialmx_filter(in_experiment),
-          numa_policy(in_numa_policy),
           pixel_mask(in_pixel_mask),
           indexer(experiment, indexing_thread_pool) {
     logger.Info("Initializing receiver");
diff --git a/receiver/JFJochReceiver.h b/receiver/JFJochReceiver.h
index 83918987..8c2a1362 100644
--- a/receiver/JFJochReceiver.h
+++ b/receiver/JFJochReceiver.h
@@ -19,7 +19,6 @@
 #include "JFJochReceiverPlots.h"
 #include "LossyFilter.h"
 #include "../common/MovingAverage.h"
-#include "../common/NUMAHWPolicy.h"
 #include "../common/ScanResultGenerator.h"
 #include "../image_analysis/indexing/IndexerThreadPool.h"
 #include "../image_analysis/IndexAndRefine.h"
@@ -75,8 +74,6 @@ protected:
 
     std::optional<int64_t> images_written;
 
-    NUMAHWPolicy numa_policy;
-
     std::vector<std::unique_ptr<ADUHistogram>> adu_histogram_module;
     PixelMask pixel_mask;
 
@@ -104,7 +101,6 @@ public:
                    JFJochReceiverPlots &plots,
                    const SpotFindingSettings &spot_finding_settings,
                    Logger &logger,
-                   const NUMAHWPolicy &numa_policy,
                    const PixelMask &pixel_mask,
                    ZMQPreviewSocket *zmq_preview_socket = nullptr,
                    ZMQMetadataSocket *zmq_metadata_socket = nullptr,
diff --git a/receiver/JFJochReceiverFPGA.cpp b/receiver/JFJochReceiverFPGA.cpp
index 802b7faf..3b2cbbb8 100644
--- a/receiver/JFJochReceiverFPGA.cpp
+++ b/receiver/JFJochReceiverFPGA.cpp
@@ -6,7 +6,6 @@
 #include <thread>
 
 #include "ImageMetadata.h"
-#include "../common/CUDAWrapper.h"
 
 JFJochReceiverFPGA::JFJochReceiverFPGA(const DiffractionExperiment &in_experiment,
                                        const PixelMask &in_pixel_mask,
@@ -14,7 +13,6 @@ JFJochReceiverFPGA::JFJochReceiverFPGA(const DiffractionExperiment &in_experimen
                                        AcquisitionDeviceGroup &in_aq_device,
                                        ImagePusher &in_image_sender,
                                        Logger &in_logger, int64_t in_forward_and_sum_nthreads,
-                                       const NUMAHWPolicy &in_numa_policy,
                                        const SpotFindingSettings &in_spot_finding_settings,
                                        JFJochReceiverCurrentStatus &in_current_status,
                                        JFJochReceiverPlots &in_plots,
@@ -29,7 +27,6 @@ JFJochReceiverFPGA::JFJochReceiverFPGA(const DiffractionExperiment &in_experimen
                      in_plots,
                      in_spot_finding_settings,
                      in_logger,
-                     in_numa_policy,
                      in_pixel_mask,
                      in_zmq_preview_socket,
                      in_zmq_metadata_socket,
@@ -60,8 +57,6 @@ JFJochReceiverFPGA::JFJochReceiverFPGA(const DiffractionExperiment &in_experimen
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Number of threads must be more than zero");
 
-    logger.Info("NUMA policy: {}", numa_policy.GetName());
-
     expected_packets_per_image = 0;
     for (int d = 0; d < ndatastreams; d++) {
         acquisition_device[d].PrepareAction(experiment);
@@ -176,12 +171,6 @@ void JFJochReceiverFPGA::SendCalibration() {
 }
 
 void JFJochReceiverFPGA::AcquireThread(uint16_t data_stream) {
-    try {
-        NUMAHWPolicy::RunOnNode(acquisition_device[data_stream].GetNUMANode());
-    } catch (const JFJochException &e) {
-        logger.Warning("NUMA bind error {} for device thread {} - continuing without binding", e.what(), data_stream);
-    }
-
     try {
         LoadCalibrationToFPGA(data_stream);
         frame_transformation_ready.wait();
@@ -213,12 +202,6 @@ void JFJochReceiverFPGA::AcquireThread(uint16_t data_stream) {
 
 void JFJochReceiverFPGA::MeasurePedestalThread(uint16_t data_stream, uint16_t module_number, uint16_t storage_cell,
                                                uint32_t threadid, bool ignore) {
-    try {
-        NUMAHWPolicy::RunOnNode(acquisition_device[data_stream].GetNUMANode());
-    } catch (const JFJochException &e) {
-        logger.Error("HW bind error {}", e.what());
-    }
-
     JFPedestalCalc pedestal_calc(experiment);
 
     uint64_t starting_frame = storage_cell + threadid * experiment.GetStorageCellNumber();
@@ -260,12 +243,6 @@ int64_t JFJochReceiverFPGA::SummationThread(uint16_t data_stream,
                                             uint16_t module_number,
                                             uint32_t threadid,
                                             ModuleSummation &summation) {
-    try {
-        NUMAHWPolicy::RunOnNode(acquisition_device[data_stream].GetNUMANode());
-    } catch (const JFJochException &e) {
-        logger.Error("HW bind error {}", e.what());
-    }
-
     ModuleSummation local_summation(experiment);
     int64_t starting_frame = image_number * experiment.GetSummation();
 
@@ -296,7 +273,6 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
     std::unique_ptr<MXAnalysisAfterFPGA> analyzer;
 
     try {
-        numa_policy.Bind(threadid);
         analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, indexer);
     } catch (const JFJochException &e) {
         frame_transformation_ready.count_down();
diff --git a/receiver/JFJochReceiverFPGA.h b/receiver/JFJochReceiverFPGA.h
index c6146c91..a34af2c0 100644
--- a/receiver/JFJochReceiverFPGA.h
+++ b/receiver/JFJochReceiverFPGA.h
@@ -18,7 +18,6 @@
 #include "../image_pusher/ImagePusher.h"
 #include "../common/Logger.h"
 #include "../common/ThreadSafeFIFO.h"
-#include "../common/NUMAHWPolicy.h"
 #include "../common/ImageBuffer.h"
 #include "../common/PixelMask.h"
 
@@ -97,7 +96,6 @@ public:
                        AcquisitionDeviceGroup &acquisition_devices,
                        ImagePusher &image_pusher,
                        Logger &logger, int64_t forward_and_sum_nthreads,
-                       const NUMAHWPolicy &numa_policy,
                        const SpotFindingSettings &spot_finding_settings,
                        JFJochReceiverCurrentStatus &current_status,
                        JFJochReceiverPlots &plots,
diff --git a/receiver/JFJochReceiverLite.cpp b/receiver/JFJochReceiverLite.cpp
index e986956e..cc8fbcad 100644
--- a/receiver/JFJochReceiverLite.cpp
+++ b/receiver/JFJochReceiverLite.cpp
@@ -3,6 +3,7 @@
 
 #include "JFJochReceiverLite.h"
 #include "../image_analysis/indexing/IndexerFactory.h"
+#include "../common/CUDAWrapper.h"
 
 using namespace std::chrono_literals;
 
@@ -34,7 +35,6 @@ JFJochReceiverLite::JFJochReceiverLite(const DiffractionExperiment &in_experimen
                                        ImagePusher &in_image_pusher,
                                        Logger &in_logger,
                                        int64_t forward_and_sum_nthreads,
-                                       const NUMAHWPolicy &in_numa_policy,
                                        const SpotFindingSettings &in_spot_finding_settings,
                                        JFJochReceiverCurrentStatus &in_current_status,
                                        JFJochReceiverPlots &in_plots,
@@ -49,7 +49,6 @@ JFJochReceiverLite::JFJochReceiverLite(const DiffractionExperiment &in_experimen
                      in_plots,
                      in_spot_finding_settings,
                      in_logger,
-                     in_numa_policy,
                      in_pixel_mask,
                      in_zmq_preview_socket,
                      in_zmq_metadata_socket,
@@ -231,14 +230,12 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
     logger.Debug("Thread {} started", id);
 
     try {
-        numa_policy.Bind(id);
-        data_analysis_started.count_down();
+        pin_gpu();
     } catch (const JFJochException &e) {
-        data_analysis_started.count_down();
-        Cancel(e);
-        return;
+        logger.Warning("Error pinning GPU {}", e.what());
     }
 
+    data_analysis_started.count_down();
     measurement_started.wait();
 
     try {
diff --git a/receiver/JFJochReceiverLite.h b/receiver/JFJochReceiverLite.h
index b8c1b546..33a0d0aa 100644
--- a/receiver/JFJochReceiverLite.h
+++ b/receiver/JFJochReceiverLite.h
@@ -12,7 +12,6 @@
 #include "../common/ImageBuffer.h"
 #include "../common/Logger.h"
 #include "../image_pusher/ImagePusher.h"
-#include "../common/NUMAHWPolicy.h"
 #include "../preview/PreviewImage.h"
 #include "../preview/ZMQPreviewSocket.h"
 #include "../preview/ZMQMetadataSocket.h"
@@ -53,7 +52,6 @@ public:
                        ImagePuller &image_puller,
                        ImagePusher &image_pusher,
                        Logger &logger, int64_t forward_and_sum_nthreads,
-                       const NUMAHWPolicy &numa_policy,
                        const SpotFindingSettings &spot_finding_settings,
                        JFJochReceiverCurrentStatus &current_status,
                        JFJochReceiverPlots &plots,
diff --git a/receiver/JFJochReceiverService.cpp b/receiver/JFJochReceiverService.cpp
index a6e92f49..63b7b5b4 100644
--- a/receiver/JFJochReceiverService.cpp
+++ b/receiver/JFJochReceiverService.cpp
@@ -24,16 +24,6 @@ JFJochReceiverService &JFJochReceiverService::NumThreads(int64_t input) {
     return *this;
 }
 
-JFJochReceiverService &JFJochReceiverService::NUMAPolicy(const NUMAHWPolicy &policy) {
-    numa_policy = policy;
-    return *this;
-}
-
-JFJochReceiverService &JFJochReceiverService::NUMAPolicy(const std::string &policy) {
-    numa_policy = NUMAHWPolicy(policy);
-    return *this;
-}
-
 void JFJochReceiverService::FinalizeMeasurementChangeState() {
     std::unique_lock ul(state_mutex);
     state = ReceiverState::Idle;
@@ -80,7 +70,6 @@ void JFJochReceiverService::Start(const DiffractionExperiment &experiment,
                                                                 aq_devices, image_pusher,
                                                                 logger,
                                                                 nthreads_local,
-                                                                numa_policy,
                                                                 spot_finding_settings,
                                                                 receiver_status,
                                                                 plots,
@@ -102,7 +91,6 @@ void JFJochReceiverService::Start(const DiffractionExperiment &experiment,
                                                                 image_pusher,
                                                                 logger,
                                                                 nthreads_local,
-                                                                numa_policy,
                                                                 spot_finding_settings,
                                                                 receiver_status,
                                                                 plots,
diff --git a/receiver/JFJochReceiverService.h b/receiver/JFJochReceiverService.h
index 1edec952..5c4748fd 100644
--- a/receiver/JFJochReceiverService.h
+++ b/receiver/JFJochReceiverService.h
@@ -9,12 +9,10 @@
 #include "JFJochReceiver.h"
 #include "../acquisition_device/AcquisitionDeviceGroup.h"
 
-#include "../common/NUMAHWPolicy.h"
 #include "../preview/ZMQMetadataSocket.h"
 #include "../preview/ZMQPreviewSocket.h"
 
 class JFJochReceiverService {
-    NUMAHWPolicy numa_policy;
     std::unique_ptr<JFJochReceiver> receiver;
     AcquisitionDeviceGroup &aq_devices;
     Logger &logger;
@@ -45,8 +43,6 @@ public:
                           ImagePusher &pusher,
                           size_t send_buffer_size_MiB = 512);
     JFJochReceiverService& NumThreads(int64_t input);
-    JFJochReceiverService& NUMAPolicy(const NUMAHWPolicy& policy);
-    JFJochReceiverService& NUMAPolicy(const std::string& policy);
     JFJochReceiverService& PreviewSocket(const std::string &addr, const std::optional<int32_t> &watermark = {});
     JFJochReceiverService& MetadataSocket(const std::string &addr);
 
diff --git a/receiver/JFJochReceiverTest.cpp b/receiver/JFJochReceiverTest.cpp
index 1e00e7ab..3bd87105 100644
--- a/receiver/JFJochReceiverTest.cpp
+++ b/receiver/JFJochReceiverTest.cpp
@@ -38,7 +38,6 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
                         const DiffractionExperiment &x,
                         const PixelMask &pixel_mask,
                         uint16_t nthreads,
-                        const std::string &numa_policy,
                         size_t send_buf_size_MiB,
                         bool quick_integrate) {
 
@@ -47,8 +46,8 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
     for (int i = 0; i < raw_expected_image.size(); i++)
         raw_expected_image[i] = i % 65536;
 
-    return JFJochReceiverTest(output, logger, aq_devices, x, pixel_mask, raw_expected_image, nthreads, numa_policy, send_buf_size_MiB,
-                              quick_integrate);
+    return JFJochReceiverTest(output, logger, aq_devices, x, pixel_mask, raw_expected_image, nthreads,
+        send_buf_size_MiB, quick_integrate);
 }
 
 bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
@@ -57,7 +56,6 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
                         const PixelMask &pixel_mask,
                         const std::vector<uint16_t> &raw_expected_image,
                         uint16_t nthreads,
-                        const std::string &numa_policy,
                         size_t send_buf_size_MiB,
                         bool quick_integrate) {
     std::vector<uint16_t> raw_expected_image_with_mask = raw_expected_image;
@@ -79,7 +77,7 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
     TestImagePusher pusher(image_number);
 
     JFJochReceiverService service(aq_devices, logger, pusher, send_buf_size_MiB);
-    service.NumThreads(nthreads).NUMAPolicy(numa_policy);
+    service.NumThreads(nthreads);
     service.LoadInternalGeneratorImage(x, raw_expected_image, 0);
     service.Indexing(x.GetIndexingSettings());
 
diff --git a/receiver/JFJochReceiverTest.h b/receiver/JFJochReceiverTest.h
index 89281494..2cc03ee0 100644
--- a/receiver/JFJochReceiverTest.h
+++ b/receiver/JFJochReceiverTest.h
@@ -10,7 +10,6 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
                         const DiffractionExperiment &x,
                         const PixelMask &pixel_mask,
                         uint16_t nthreads,
-                        const std::string &numa_policy = "",
                         size_t send_buf_size_MiB = 1024,
                         bool quick_integrate = false);
 
@@ -20,6 +19,5 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
                         const PixelMask &pixel_mask,
                         const std::vector<uint16_t> &data,
                         uint16_t nthreads,
-                        const std::string &numa_policy = "",
                         size_t send_buf_size_MiB = 1024,
                         bool quick_integrate = false);
diff --git a/tools/jfjoch_fpga_test.cpp b/tools/jfjoch_fpga_test.cpp
index 9cd98e3a..b4359252 100644
--- a/tools/jfjoch_fpga_test.cpp
+++ b/tools/jfjoch_fpga_test.cpp
@@ -23,7 +23,6 @@ void print_usage(Logger &logger) {
     logger.Info("   -m<num>    Number of modules");
     logger.Info("   -i<num>    Number of images");
     logger.Info("   -N<num>    Number of image processing threads");
-    logger.Info("   -P<txt>    NUMA Policy (none|n2g2|n8g4|n8g4_hbm), none is default");
     logger.Info("   -B<num>    Size of send buffer in MiB (default 2048)");
     logger.Info("   -q<num>    Use Poisson lossy compression, with square root of counts");
     logger.Info("   -T<num>    Use thresholding for low counts");
@@ -53,7 +52,6 @@ int main(int argc, char **argv) {
     std::optional<int64_t> fft_num_vectors;
 
     bool verbose = false;
-    std::string numa_policy_name;
     bool raw_data = false;
     bool force_32bit = false;
     bool force_8bit = false;
@@ -100,7 +98,7 @@ int main(int argc, char **argv) {
                 verbose = true;
                 break;
             case 'P':
-                numa_policy_name = std::string(optarg);
+                logger.Warning("NUMA policy is deprecated and ignored");
                 break;
             case 'R':
                 raw_data = true;
@@ -247,7 +245,7 @@ int main(int argc, char **argv) {
     bool ret;
     std::thread run_thread([&] {
         try {
-            ret = JFJochReceiverTest(output, logger, aq_devices, x, mask, input, nthreads, numa_policy_name,
+            ret = JFJochReceiverTest(output, logger, aq_devices, x, mask, input, nthreads,
                                      send_buffer_size_MiB, quick_integrate);
         } catch (std::exception &e) {
             logger.Error(e.what());
diff --git a/tools/jfjoch_lite_perf_test.cpp b/tools/jfjoch_lite_perf_test.cpp
index 5840d25f..13ba0103 100644
--- a/tools/jfjoch_lite_perf_test.cpp
+++ b/tools/jfjoch_lite_perf_test.cpp
@@ -18,7 +18,6 @@ void print_usage(Logger &logger) {
     logger.Info("Options:");
     logger.Info("   -i<num>      Number of images");
     logger.Info("   -N<num>      Number of image processing threads (default: 8)");
-    logger.Info("   -P<txt>      NUMA policy: none|n2g2|n8g4|n8g4_hbm (default: none)");
     logger.Info("   -F{<txt>}    Write file, optional parameter is name (default: lyso_lite_perf_test)");
     logger.Info("   -X<txt>      Indexing (none|fft|fftw|ffbidx), ffbidx is default");
     logger.Info("   -t<num>      Indexing thread pool size (default: 4)");
@@ -58,7 +57,7 @@ int main(int argc, char **argv) {
                 nthreads = atol(optarg);
                 break;
             case 'P':
-                numa_policy_name = std::string(optarg);
+                logger.Warning("NUMA policy is deprecated and ignored");
                 break;
             case 'i':
                 nimages = atol(optarg);
@@ -166,7 +165,6 @@ int main(int argc, char **argv) {
     AcquisitionDeviceGroup group;
     JFJochReceiverService service(group, logger, pusher);
 
-    service.NUMAPolicy(numa_policy_name);
     service.NumThreads(nthreads);
 
     IndexingSettings i_settings;
-- 
2.52.0


From 58910274bf257e8f53bd5ecaaab66a5f7d363073 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 21:15:54 +0200
Subject: [PATCH 072/228] image_analysis: compute ROI statistics in the
 non-FPGA path

MXAnalysisWithoutFPGA never filled DataMessage.roi, so ROI integrals were
only available on the FPGA path. Add a software ROI engine that mirrors the
FPGA roi_calc kernel: per-ROI sum, sum of squares, good-pixel count, max and
intensity-weighted centre of mass, with each pixel carrying a 16-bit mask so
it can contribute to any subset of up to 16 ROIs.

New image_analysis/roi/ library (JFJochROIIntegration), structured like azint:
a base that precomputes the per-pixel mask and names, a templated CPU engine
(generic over pixel type for a future 16-bit path), and a GPU kernel using
per-block shared-memory atomics for the STXM case (half-detector ROIs).

Masked pixels are excluded entirely; saturated pixels are excluded from the
sums but still count towards the max, matching roi_calc exactly. The engine is
only constructed when at least one ROI is defined. Downstream CBOR/HDF5 already
consume message.roi, so no further changes are needed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/CMakeLists.txt            |   3 +-
 image_analysis/MXAnalysisWithoutFPGA.cpp |   9 ++
 image_analysis/MXAnalysisWithoutFPGA.h   |   2 +
 image_analysis/roi/CMakeLists.txt        |   5 +
 image_analysis/roi/ROIIntegration.cpp    |  34 +++++
 image_analysis/roi/ROIIntegration.h      |  46 +++++++
 image_analysis/roi/ROIIntegrationCPU.cpp |  11 ++
 image_analysis/roi/ROIIntegrationCPU.h   |  71 +++++++++++
 image_analysis/roi/ROIIntegrationGPU.cu  | 152 +++++++++++++++++++++++
 image_analysis/roi/ROIIntegrationGPU.h   |  37 ++++++
 tests/CMakeLists.txt                     |   1 +
 tests/ROIIntegrationCPUTest.cpp          |  95 ++++++++++++++
 12 files changed, 465 insertions(+), 1 deletion(-)
 create mode 100644 image_analysis/roi/CMakeLists.txt
 create mode 100644 image_analysis/roi/ROIIntegration.cpp
 create mode 100644 image_analysis/roi/ROIIntegration.h
 create mode 100644 image_analysis/roi/ROIIntegrationCPU.cpp
 create mode 100644 image_analysis/roi/ROIIntegrationCPU.h
 create mode 100644 image_analysis/roi/ROIIntegrationGPU.cu
 create mode 100644 image_analysis/roi/ROIIntegrationGPU.h
 create mode 100644 tests/ROIIntegrationCPUTest.cpp

diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 1bf6e448..00996187 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -50,6 +50,7 @@ ADD_SUBDIRECTORY(lattice_search)
 ADD_SUBDIRECTORY(scale_merge)
 ADD_SUBDIRECTORY(image_preprocessing)
 ADD_SUBDIRECTORY(azint)
+ADD_SUBDIRECTORY(roi)
 ADD_SUBDIRECTORY(pixel_refinement)
 
-TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochPixelRefine gemmi)
+TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochROIIntegration JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochPixelRefine gemmi)
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index 7bade492..cbe26e6a 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -11,9 +11,11 @@
 #include "image_preprocessing/ImagePreprocessorCPU.h"
 
 #include "azint/AzIntEngineCPU.h"
+#include "roi/ROIIntegrationCPU.h"
 #include "spot_finding/ImageSpotFinderCPU.h"
 #ifdef JFJOCH_USE_CUDA
 #include "azint/AzIntEngineGPU.h"
+#include "roi/ROIIntegrationGPU.h"
 #include "spot_finding/ImageSpotFinderGPU.h"
 #include "image_preprocessing/ImagePreprocessorGPU.h"
 #include "image_preprocessing/ImagePreprocessorBufferGPU.h"
@@ -42,6 +44,8 @@ MXAnalysisWithoutFPGA::MXAnalysisWithoutFPGA(const DiffractionExperiment &in_exp
         spotFinder = std::make_unique<ImageSpotFinderCPU>(experiment.GetXPixelsNum(), experiment.GetYPixelsNum());
         azint = std::make_unique<AzIntEngineCPU>(integration);
         preprocessor = std::make_unique<ImagePreprocessorCPU>(in_experiment, in_mask);
+        if (experiment.ROI().size() >= 1)
+            roi = std::make_unique<ROIIntegrationCPU>(experiment);
 #ifdef JFJOCH_USE_CUDA
     } else {
         auto stream = std::make_shared<CudaStream>();
@@ -49,6 +53,8 @@ MXAnalysisWithoutFPGA::MXAnalysisWithoutFPGA(const DiffractionExperiment &in_exp
         preprocessor = std::make_unique<ImagePreprocessorGPU>(in_experiment, in_mask, stream);
         spotFinder = std::make_unique<ImageSpotFinderGPU>(experiment.GetXPixelsNum(), experiment.GetYPixelsNum(), stream);
         azint = std::make_unique<AzIntEngineGPU>(integration, stream);
+        if (experiment.ROI().size() >= 1)
+            roi = std::make_unique<ROIIntegrationGPU>(experiment, stream);
     }
 #endif
 }
@@ -77,6 +83,9 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
     const auto azint_end_time = std::chrono::steady_clock::now();
     output.azint_time_s = std::chrono::duration<float>(azint_end_time - azint_start_time).count();
 
+    if (roi)
+        roi->Run(*preprocessor_buffer, output.roi);
+
     if (spot_finding_settings.enable) {
         // Update resolution mask
         if (mask_high_res != spot_finding_settings.high_resolution_limit
diff --git a/image_analysis/MXAnalysisWithoutFPGA.h b/image_analysis/MXAnalysisWithoutFPGA.h
index e5864d41..9d6bd0a9 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.h
+++ b/image_analysis/MXAnalysisWithoutFPGA.h
@@ -14,6 +14,7 @@
 #include "spot_finding/ImageSpotFinder.h"
 #include "indexing/IndexerThreadPool.h"
 #include "azint/AzIntEngine.h"
+#include "roi/ROIIntegration.h"
 #include "IndexAndRefine.h"
 #include "image_preprocessing/ImagePreprocessor.h"
 #include "image_preprocessing/ImagePreprocessorBuffer.h"
@@ -31,6 +32,7 @@ class MXAnalysisWithoutFPGA {
     size_t xpixels;
 
     std::unique_ptr<AzIntEngine> azint;
+    std::unique_ptr<ROIIntegration> roi;
     std::unique_ptr<ImageSpotFinder> spotFinder;
     IndexAndRefine &indexer;
     std::unique_ptr<BraggPrediction> prediction;
diff --git a/image_analysis/roi/CMakeLists.txt b/image_analysis/roi/CMakeLists.txt
new file mode 100644
index 00000000..afa1daa6
--- /dev/null
+++ b/image_analysis/roi/CMakeLists.txt
@@ -0,0 +1,5 @@
+ADD_LIBRARY(JFJochROIIntegration STATIC ROIIntegration.cpp ROIIntegration.h ROIIntegrationCPU.cpp ROIIntegrationCPU.h)
+TARGET_LINK_LIBRARIES(JFJochROIIntegration JFJochCommon)
+IF (JFJOCH_CUDA_AVAILABLE)
+    TARGET_SOURCES(JFJochROIIntegration PRIVATE ../indexing/CUDAMemHelpers.h ROIIntegrationGPU.cu ROIIntegrationGPU.h)
+ENDIF()
diff --git a/image_analysis/roi/ROIIntegration.cpp b/image_analysis/roi/ROIIntegration.cpp
new file mode 100644
index 00000000..0cef8cca
--- /dev/null
+++ b/image_analysis/roi/ROIIntegration.cpp
@@ -0,0 +1,34 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "ROIIntegration.h"
+#include "../../common/DiffractionExperiment.h"
+
+ROIIntegration::ROIIntegration(const DiffractionExperiment &experiment)
+    : roi_map(experiment.ExportROIMap()),
+      width(experiment.GetXPixelsNumConv()),
+      npixel(roi_map.size()),
+      roi_count(experiment.ROI().size()),
+      roi_name(roi_count),
+      roi_sum(roi_count),
+      roi_sum2(roi_count),
+      roi_pixels(roi_count),
+      roi_x_weighted(roi_count),
+      roi_y_weighted(roi_count),
+      roi_max(roi_count) {
+    for (const auto &[name, id] : experiment.ROI().GetROINameMap())
+        roi_name[id] = name;
+}
+
+void ROIIntegration::Export(std::map<std::string, ROIMessage> &out) const {
+    for (uint16_t r = 0; r < roi_count; r++)
+        out[roi_name[r]] = ROIMessage{
+            .sum           = roi_sum[r],
+            .sum_square    = roi_sum2[r],
+            .max_count     = roi_max[r],
+            .pixels        = roi_pixels[r],
+            .pixels_masked = 0,
+            .x_weighted    = roi_x_weighted[r],
+            .y_weighted    = roi_y_weighted[r],
+        };
+}
diff --git a/image_analysis/roi/ROIIntegration.h b/image_analysis/roi/ROIIntegration.h
new file mode 100644
index 00000000..2d0ddd26
--- /dev/null
+++ b/image_analysis/roi/ROIIntegration.h
@@ -0,0 +1,46 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <cstdint>
+#include <map>
+#include <string>
+#include <vector>
+
+#include "../../common/JFJochMessages.h"
+#include "../image_preprocessing/ImagePreprocessorBuffer.h"
+
+class DiffractionExperiment;
+
+// Computes per-ROI statistics over an assembled image: sum, sum of squares,
+// good-pixel count, maximum and intensity-weighted centre of mass. Each pixel
+// carries a 16-bit mask selecting which of up to 16 ROIs it belongs to, so a
+// single pixel can contribute to none, one, or several ROIs at once. This is
+// the software counterpart of the FPGA roi_calc kernel.
+class ROIIntegration {
+protected:
+    std::vector<uint16_t> roi_map;   // per-pixel ROI bitmask, assembled (converted) geometry
+    size_t width;                    // assembled image width, to recover x/y from a pixel index
+    size_t npixel;
+    uint16_t roi_count;
+    std::vector<std::string> roi_name;  // ROI name indexed by bit position
+
+    // Result accumulators, filled by Run() in the derived class
+    std::vector<int64_t>  roi_sum;
+    std::vector<uint64_t> roi_sum2;
+    std::vector<uint64_t> roi_pixels;
+    std::vector<int64_t>  roi_x_weighted;
+    std::vector<int64_t>  roi_y_weighted;
+    std::vector<int64_t>  roi_max;
+
+    void Export(std::map<std::string, ROIMessage> &out) const;
+public:
+    explicit ROIIntegration(const DiffractionExperiment &experiment);
+    virtual ~ROIIntegration() = default;
+
+    [[nodiscard]] uint16_t Count() const { return roi_count; }
+    [[nodiscard]] bool empty() const { return roi_count == 0; }
+
+    virtual void Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) = 0;
+};
diff --git a/image_analysis/roi/ROIIntegrationCPU.cpp b/image_analysis/roi/ROIIntegrationCPU.cpp
new file mode 100644
index 00000000..432b2ca4
--- /dev/null
+++ b/image_analysis/roi/ROIIntegrationCPU.cpp
@@ -0,0 +1,11 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "ROIIntegrationCPU.h"
+
+ROIIntegrationCPU::ROIIntegrationCPU(const DiffractionExperiment &experiment)
+    : ROIIntegration(experiment) {}
+
+void ROIIntegrationCPU::Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) {
+    RunROI(image, out);
+}
diff --git a/image_analysis/roi/ROIIntegrationCPU.h b/image_analysis/roi/ROIIntegrationCPU.h
new file mode 100644
index 00000000..0e5fb4eb
--- /dev/null
+++ b/image_analysis/roi/ROIIntegrationCPU.h
@@ -0,0 +1,71 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <limits>
+#include <type_traits>
+
+#include "ROIIntegration.h"
+#include "../../common/JFJochException.h"
+
+class ROIIntegrationCPU : public ROIIntegration {
+public:
+    explicit ROIIntegrationCPU(const DiffractionExperiment &experiment);
+
+    // image is anything indexable with operator[] and size(). Templated on the
+    // pixel type so a future narrow-integer (e.g. 16-bit) path works as well.
+    template <class T>
+    void RunROI(const T &image, std::map<std::string, ROIMessage> &out) {
+        if (image.size() != npixel)
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "ROIIntegration: mismatch in image size");
+
+        for (uint16_t r = 0; r < roi_count; r++) {
+            roi_sum[r] = 0;
+            roi_sum2[r] = 0;
+            roi_pixels[r] = 0;
+            roi_x_weighted[r] = 0;
+            roi_y_weighted[r] = 0;
+            roi_max[r] = INT64_MIN;
+        }
+
+        using pixel_t = std::remove_cv_t<std::remove_reference_t<decltype(image[0])>>;
+
+        for (size_t i = 0; i < npixel; i++) {
+            const uint16_t mask = roi_map[i];
+            if (mask == 0)
+                continue;
+
+            const pixel_t v = image[i];
+            // masked/bad pixels (signed types only) are excluded entirely
+            if constexpr (std::is_signed_v<pixel_t>) {
+                if (v == std::numeric_limits<pixel_t>::min())
+                    continue;
+            }
+            // saturated pixels still count towards the max, but not the sums
+            const bool saturated = (v == std::numeric_limits<pixel_t>::max());
+
+            const int64_t val = static_cast<int64_t>(v);
+            const int64_t x = static_cast<int64_t>(i % width);
+            const int64_t y = static_cast<int64_t>(i / width);
+
+            for (uint16_t r = 0; r < roi_count; r++) {
+                if (!(mask & (1u << r)))
+                    continue;
+                if (!saturated) {
+                    roi_sum[r] += val;
+                    roi_sum2[r] += static_cast<uint64_t>(val * val);
+                    roi_pixels[r] += 1;
+                    roi_x_weighted[r] += val * x;
+                    roi_y_weighted[r] += val * y;
+                }
+                if (val > roi_max[r])
+                    roi_max[r] = val;
+            }
+        }
+        Export(out);
+    }
+
+    void Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) override;
+};
diff --git a/image_analysis/roi/ROIIntegrationGPU.cu b/image_analysis/roi/ROIIntegrationGPU.cu
new file mode 100644
index 00000000..66701cfa
--- /dev/null
+++ b/image_analysis/roi/ROIIntegrationGPU.cu
@@ -0,0 +1,152 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <climits>
+
+#include "ROIIntegrationGPU.h"
+#include "../../common/DiffractionExperiment.h"
+
+inline void cuda_err(cudaError_t val) {
+    if (val != cudaSuccess)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
+}
+
+// One pixel carries a 16-bit mask, so it can feed any subset of the ROIs.
+// Each block reduces into shared memory first to keep global atomics low.
+__global__
+void gpu_roi(
+    const uint16_t *__restrict__ roi_map,
+    const int32_t  *__restrict__ input_buffer,
+    size_t num_pixels,
+    size_t width,
+    int roi_count,
+    unsigned long long *__restrict__ roi_sum,
+    unsigned long long *__restrict__ roi_sum2,
+    unsigned long long *__restrict__ roi_pixels,
+    unsigned long long *__restrict__ roi_x_weighted,
+    unsigned long long *__restrict__ roi_y_weighted,
+    int *__restrict__ roi_max) {
+    extern __shared__ unsigned long long shared[];
+    unsigned long long *s_sum    = shared;
+    unsigned long long *s_sum2   = &s_sum[roi_count];
+    unsigned long long *s_pixels = &s_sum2[roi_count];
+    unsigned long long *s_xw     = &s_pixels[roi_count];
+    unsigned long long *s_yw     = &s_xw[roi_count];
+    int *s_max = (int *) &s_yw[roi_count];
+
+    for (int r = threadIdx.x; r < roi_count; r += blockDim.x) {
+        s_sum[r] = 0;
+        s_sum2[r] = 0;
+        s_pixels[r] = 0;
+        s_xw[r] = 0;
+        s_yw[r] = 0;
+        s_max[r] = INT_MIN;
+    }
+    __syncthreads();
+
+    for (size_t idx = blockIdx.x * blockDim.x + threadIdx.x;
+         idx < num_pixels;
+         idx += blockDim.x * gridDim.x) {
+        const uint16_t mask = roi_map[idx];
+        if (mask == 0)
+            continue;
+
+        const int32_t v = input_buffer[idx];
+        if (v == INT32_MIN)        // masked/bad pixel
+            continue;
+        const bool saturated = (v == INT32_MAX);
+
+        const long long val = v;
+        const long long x = idx % width;
+        const long long y = idx / width;
+        const unsigned long long val_u  = (unsigned long long) val;
+        const unsigned long long val2_u = (unsigned long long) (val * val);
+        const unsigned long long vx_u   = (unsigned long long) (val * x);
+        const unsigned long long vy_u   = (unsigned long long) (val * y);
+
+        for (int r = 0; r < roi_count; r++) {
+            if (!(mask & (1u << r)))
+                continue;
+            if (!saturated) {
+                atomicAdd(&s_sum[r], val_u);
+                atomicAdd(&s_sum2[r], val2_u);
+                atomicAdd(&s_pixels[r], 1ULL);
+                atomicAdd(&s_xw[r], vx_u);
+                atomicAdd(&s_yw[r], vy_u);
+            }
+            atomicMax(&s_max[r], v);
+        }
+    }
+    __syncthreads();
+
+    for (int r = threadIdx.x; r < roi_count; r += blockDim.x) {
+        atomicAdd(&roi_sum[r], s_sum[r]);
+        atomicAdd(&roi_sum2[r], s_sum2[r]);
+        atomicAdd(&roi_pixels[r], s_pixels[r]);
+        atomicAdd(&roi_x_weighted[r], s_xw[r]);
+        atomicAdd(&roi_y_weighted[r], s_yw[r]);
+        atomicMax(&roi_max[r], s_max[r]);
+    }
+}
+
+ROIIntegrationGPU::ROIIntegrationGPU(const DiffractionExperiment &experiment, std::shared_ptr<CudaStream> stream)
+    : ROIIntegration(experiment),
+      stream(stream),
+      gpu_roi_map(npixel),
+      gpu_sum(roi_count),
+      gpu_sum2(roi_count),
+      gpu_pixels(roi_count),
+      gpu_x_weighted(roi_count),
+      gpu_y_weighted(roi_count),
+      gpu_max(roi_count),
+      host_sum(roi_count),
+      host_sum2(roi_count),
+      host_pixels(roi_count),
+      host_x_weighted(roi_count),
+      host_y_weighted(roi_count),
+      host_max(roi_count),
+      max_init(roi_count, INT_MIN) {
+
+    cudaDeviceProp prop{};
+    cuda_err(cudaGetDeviceProperties(&prop, 0));
+    threads = 128;
+    blocks = 4 * prop.multiProcessorCount;
+    shared_needed = roi_count * (5 * sizeof(unsigned long long) + sizeof(int));
+
+    cuda_err(cudaMemcpy(gpu_roi_map, roi_map.data(), sizeof(uint16_t) * npixel, cudaMemcpyHostToDevice));
+}
+
+void ROIIntegrationGPU::Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) {
+    if (image.size() != npixel)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "ROIIntegration: mismatch in image size");
+
+    cuda_err(cudaMemsetAsync(gpu_sum, 0, sizeof(unsigned long long) * roi_count, *stream));
+    cuda_err(cudaMemsetAsync(gpu_sum2, 0, sizeof(unsigned long long) * roi_count, *stream));
+    cuda_err(cudaMemsetAsync(gpu_pixels, 0, sizeof(unsigned long long) * roi_count, *stream));
+    cuda_err(cudaMemsetAsync(gpu_x_weighted, 0, sizeof(unsigned long long) * roi_count, *stream));
+    cuda_err(cudaMemsetAsync(gpu_y_weighted, 0, sizeof(unsigned long long) * roi_count, *stream));
+    cuda_err(cudaMemcpyAsync(gpu_max, max_init.data(), sizeof(int) * roi_count, cudaMemcpyHostToDevice, *stream));
+
+    gpu_roi<<<blocks, threads, shared_needed, *stream>>>(
+        gpu_roi_map, image.getGPUBuffer(), npixel, width, roi_count,
+        gpu_sum, gpu_sum2, gpu_pixels, gpu_x_weighted, gpu_y_weighted, gpu_max);
+
+    cudaMemcpyAsync(host_sum.data(), gpu_sum, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cudaMemcpyAsync(host_sum2.data(), gpu_sum2, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cudaMemcpyAsync(host_pixels.data(), gpu_pixels, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cudaMemcpyAsync(host_x_weighted.data(), gpu_x_weighted, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cudaMemcpyAsync(host_y_weighted.data(), gpu_y_weighted, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cudaMemcpyAsync(host_max.data(), gpu_max, sizeof(int) * roi_count, cudaMemcpyDeviceToHost, *stream);
+    cuda_err(cudaStreamSynchronize(*stream));
+
+    for (uint16_t r = 0; r < roi_count; r++) {
+        roi_sum[r] = static_cast<int64_t>(host_sum[r]);
+        roi_sum2[r] = host_sum2[r];
+        roi_pixels[r] = host_pixels[r];
+        roi_x_weighted[r] = static_cast<int64_t>(host_x_weighted[r]);
+        roi_y_weighted[r] = static_cast<int64_t>(host_y_weighted[r]);
+        roi_max[r] = (host_max[r] == INT_MIN) ? INT64_MIN : static_cast<int64_t>(host_max[r]);
+    }
+    Export(out);
+}
diff --git a/image_analysis/roi/ROIIntegrationGPU.h b/image_analysis/roi/ROIIntegrationGPU.h
new file mode 100644
index 00000000..5528b37b
--- /dev/null
+++ b/image_analysis/roi/ROIIntegrationGPU.h
@@ -0,0 +1,37 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <memory>
+
+#include "ROIIntegration.h"
+#include "../indexing/CUDAMemHelpers.h"
+
+class ROIIntegrationGPU : public ROIIntegration {
+    std::shared_ptr<CudaStream> stream;
+    int threads;
+    int blocks;
+    size_t shared_needed;
+
+    CudaDevicePtr<uint16_t> gpu_roi_map;
+    // 64-bit sums are accumulated as unsigned long long (two's-complement bit
+    // pattern) because CUDA atomicAdd has no signed 64-bit overload.
+    CudaDevicePtr<unsigned long long> gpu_sum;
+    CudaDevicePtr<unsigned long long> gpu_sum2;
+    CudaDevicePtr<unsigned long long> gpu_pixels;
+    CudaDevicePtr<unsigned long long> gpu_x_weighted;
+    CudaDevicePtr<unsigned long long> gpu_y_weighted;
+    CudaDevicePtr<int> gpu_max;
+
+    std::vector<unsigned long long> host_sum;
+    std::vector<unsigned long long> host_sum2;
+    std::vector<unsigned long long> host_pixels;
+    std::vector<unsigned long long> host_x_weighted;
+    std::vector<unsigned long long> host_y_weighted;
+    std::vector<int> host_max;
+    std::vector<int> max_init;   // INT_MIN seed copied into gpu_max each frame
+public:
+    ROIIntegrationGPU(const DiffractionExperiment &experiment, std::shared_ptr<CudaStream> stream);
+    void Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) override;
+};
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 751e8f64..59af6e96 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -32,6 +32,7 @@ ADD_EXECUTABLE(jfjoch_test
         JPEGTest.cpp
         HistogramTest.cpp
         ROIMapTest.cpp
+        ROIIntegrationCPUTest.cpp
         LossyFilterTest.cpp
         ImageBufferTest.cpp
         PixelMaskTest.cpp
diff --git a/tests/ROIIntegrationCPUTest.cpp b/tests/ROIIntegrationCPUTest.cpp
new file mode 100644
index 00000000..747d9b16
--- /dev/null
+++ b/tests/ROIIntegrationCPUTest.cpp
@@ -0,0 +1,95 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include "../image_analysis/roi/ROIIntegrationCPU.h"
+#include "../common/DiffractionExperiment.h"
+
+TEST_CASE("ROIIntegrationCPU") {
+    DiffractionExperiment experiment(DetJF(1));
+    experiment.ROI().SetROI(ROIDefinition{.boxes = {
+        ROIBox("roiA", 10, 20, 30, 40),
+        ROIBox("roiB", 15, 25, 35, 45)
+    }});
+
+    ROIIntegrationCPU roi(experiment);
+    REQUIRE(roi.Count() == 2);
+    REQUIRE_FALSE(roi.empty());
+
+    const auto roi_map = experiment.ExportROIMap();
+    const size_t width = experiment.GetXPixelsNumConv();
+    const size_t npixel = roi_map.size();
+
+    ImagePreprocessorBuffer image(npixel);
+    for (size_t i = 0; i < npixel; i++)
+        image[i] = static_cast<int32_t>((i * 7 + 3) % 251); // deterministic, well below INT32_MAX
+
+    // Inject one saturated pixel into roiA (bit 0) and one masked pixel into roiB (bit 1)
+    int64_t saturated_index = -1;
+    int64_t masked_index = -1;
+    for (size_t i = 0; i < npixel && (saturated_index < 0 || masked_index < 0); i++) {
+        if (saturated_index < 0 && (roi_map[i] & (1 << 0)))
+            saturated_index = static_cast<int64_t>(i);
+        else if (masked_index < 0 && (roi_map[i] & (1 << 1)))
+            masked_index = static_cast<int64_t>(i);
+    }
+    REQUIRE(saturated_index >= 0);
+    REQUIRE(masked_index >= 0);
+    image[saturated_index] = INT32_MAX;
+    image[masked_index] = INT32_MIN;
+
+    // Independent reference matching the documented semantics (masked excluded
+    // entirely; saturated excluded from sums but counted towards the max)
+    struct Ref { int64_t sum = 0; uint64_t sum2 = 0; uint64_t pixels = 0;
+                 int64_t xw = 0; int64_t yw = 0; int64_t max = INT64_MIN; };
+    Ref ref[2];
+    for (size_t i = 0; i < npixel; i++) {
+        const uint16_t mask = roi_map[i];
+        if (mask == 0)
+            continue;
+        const int32_t v = image[i];
+        if (v == INT32_MIN)
+            continue;
+        const bool saturated = (v == INT32_MAX);
+        const int64_t val = v;
+        const int64_t x = static_cast<int64_t>(i % width);
+        const int64_t y = static_cast<int64_t>(i / width);
+        for (int r = 0; r < 2; r++) {
+            if (!(mask & (1 << r)))
+                continue;
+            if (!saturated) {
+                ref[r].sum += val;
+                ref[r].sum2 += static_cast<uint64_t>(val * val);
+                ref[r].pixels += 1;
+                ref[r].xw += val * x;
+                ref[r].yw += val * y;
+            }
+            if (val > ref[r].max)
+                ref[r].max = val;
+        }
+    }
+
+    std::map<std::string, ROIMessage> out;
+    roi.Run(image, out);
+
+    REQUIRE(out.size() == 2);
+    REQUIRE(out.contains("roiA"));
+    REQUIRE(out.contains("roiB"));
+
+    const std::pair<std::string, int> roi_ids[2] = {{"roiA", 0}, {"roiB", 1}};
+    for (const auto &[name, r] : roi_ids) {
+        const auto &msg = out.at(name);
+        CHECK(msg.sum == ref[r].sum);
+        CHECK(msg.sum_square == ref[r].sum2);
+        CHECK(msg.pixels == ref[r].pixels);
+        CHECK(msg.x_weighted == ref[r].xw);
+        CHECK(msg.y_weighted == ref[r].yw);
+        CHECK(msg.max_count == ref[r].max);
+        CHECK(msg.pixels_masked == 0);
+    }
+
+    // Targeted checks: saturated pixel sets the max for roiA but is not summed
+    CHECK(out.at("roiA").max_count == INT32_MAX);
+    CHECK(ref[0].pixels > 0);
+}
-- 
2.52.0


From c0a4801bc47c998c6ad771a14c5b43edae2d9065 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 22:02:09 +0200
Subject: [PATCH 073/228] TCPStreamPusher: fix zero-copy buffer reuse and make
 send/END timeouts progress-based

Three robustness fixes for the writer-facing TCP stream, addressing the
spurious "wrong number of images" / connection failures seen under load.

1. Never MSG_ZEROCOPY a transient buffer. The synchronous SendImage path
   passes a caller-owned buffer with z == nullptr and reuses it for the next
   frame immediately. With MSG_ZEROCOPY the kernel still references that buffer
   after send() returns, so the peer could receive corrupted frames and drop
   the connection mid-stream, truncating the run. Zero-copy is now gated on a
   ZeroCopyReturnValue that keeps the buffer alive until completion.

2. Make the SendAll watchdog measure lack of progress, not total wall-clock.
   The previous absolute deadline tore down a healthy but back-pressured
   connection (slow/starved writer) after a fixed window; the watchdog now
   resets on every byte actually sent, so only a genuinely stuck socket is
   closed. Dead peers are still caught by OS keepalive and POLLHUP/POLLERR.

3. Make the END-ack wait progress-based (WaitForEndAck). The writer may still
   be draining a backlog of DATA frames when END is sent; each DATA ACK is
   progress, so the timeout only arms once the writer falls silent rather than
   firing while images are legitimately still being drained.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_pusher/TCPStreamPusher.cpp | 52 +++++++++++++++++++++++++++++---
 image_pusher/TCPStreamPusher.h   |  1 +
 2 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/image_pusher/TCPStreamPusher.cpp b/image_pusher/TCPStreamPusher.cpp
index d3184d2c..d4a4295b 100644
--- a/image_pusher/TCPStreamPusher.cpp
+++ b/image_pusher/TCPStreamPusher.cpp
@@ -197,7 +197,10 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
     bool zc_used = false;
     uint32_t zc_first = 0;
     uint32_t zc_last = 0;
-    const auto deadline = std::chrono::steady_clock::now() + send_total_timeout;
+    // Watchdog on *lack of progress*, not total time: a slow but advancing transfer
+    // (a writer applying back-pressure) must not be torn down, only a socket that
+    // stops moving bytes altogether. Reset on every byte actually handed to the kernel.
+    auto last_progress = std::chrono::steady_clock::now();
 
     bool try_zerocopy = false;
 #if defined(MSG_ZEROCOPY)
@@ -213,7 +216,7 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
             return false;
         }
 
-        if (std::chrono::steady_clock::now() >= deadline) {
+        if (std::chrono::steady_clock::now() - last_progress >= send_total_timeout) {
             c.broken = true;
             CloseFd(c.fd);
             if (zc_used_out) *zc_used_out = zc_used;
@@ -288,6 +291,9 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
         }
 #endif
 
+        if (rc > 0)
+            last_progress = std::chrono::steady_clock::now();
+
         sent += static_cast<size_t>(rc);
     }
 
@@ -315,7 +321,12 @@ bool TCPStreamPusher::SendFrame(Connection& c, const uint8_t* data, size_t size,
     uint32_t zc_last = 0;
 
     if (size > 0) {
-        const bool allow_zerocopy = (type == TCPFrameType::DATA || type == TCPFrameType::CALIBRATION);
+        // MSG_ZEROCOPY leaves the kernel referencing the caller's buffer after send()
+        // returns, so it is only safe when a ZeroCopyReturnValue keeps that buffer alive
+        // until the completion notification. The synchronous path passes a transient
+        // buffer (z == nullptr) that the caller reuses immediately — never zero-copy it.
+        const bool allow_zerocopy = (z != nullptr)
+                                    && (type == TCPFrameType::DATA || type == TCPFrameType::CALIBRATION);
         if (!SendAll(c, data, size, allow_zerocopy, &zc_used, &zc_first, &zc_last)) {
             if (z) {
                 if (zc_used) EnqueueZeroCopyPending(c, z, zc_first, zc_last);
@@ -899,6 +910,39 @@ bool TCPStreamPusher::WaitForAck(Connection& c, TCPFrameType ack_for, std::chron
     return ack_ok;
 }
 
+bool TCPStreamPusher::WaitForEndAck(Connection& c, std::chrono::milliseconds no_progress_timeout, std::string* error_text) {
+    std::unique_lock ul(c.ack_mutex);
+
+    // After END is sent the writer may still be draining a backlog of DATA frames.
+    // Each DATA ACK that arrives is forward progress, so the END timer is effectively
+    // armed only once the writer falls silent: the timeout fires when neither a DATA
+    // ACK nor the END ACK is seen for the whole window, not while images still drain.
+    uint64_t last_acked = c.data_acked_total.load(std::memory_order_relaxed);
+
+    while (!c.end_ack_received && !c.broken) {
+        const bool progressed = c.ack_cv.wait_for(ul, no_progress_timeout, [&] {
+            return c.end_ack_received || c.broken.load()
+                   || c.data_acked_total.load(std::memory_order_relaxed) != last_acked;
+        });
+
+        if (!progressed) {
+            if (error_text) *error_text = "END ACK timeout (writer stalled)";
+            return false;
+        }
+        last_acked = c.data_acked_total.load(std::memory_order_relaxed);
+    }
+
+    if (c.broken) {
+        if (error_text) *error_text = c.last_ack_error.empty() ? "Socket broken" : c.last_ack_error;
+        return false;
+    }
+
+    if (!c.end_ack_ok && error_text)
+        *error_text = c.last_ack_error.empty() ? "END ACK rejected" : c.last_ack_error;
+
+    return c.end_ack_ok;
+}
+
 void TCPStreamPusher::StartDataCollection(StartMessage& message) {
     if (message.images_per_file < 1)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Images per file cannot be zero or negative");
@@ -1076,7 +1120,7 @@ bool TCPStreamPusher::EndDataCollection(const EndMessage& message) {
         }
 
         std::string ack_err;
-        if (!WaitForAck(c, TCPFrameType::END, std::chrono::seconds(10), &ack_err))
+        if (!WaitForEndAck(c, std::chrono::seconds(10), &ack_err))
             ret = false;
     }
 
diff --git a/image_pusher/TCPStreamPusher.h b/image_pusher/TCPStreamPusher.h
index 1b6eb0ef..bd5dfed6 100644
--- a/image_pusher/TCPStreamPusher.h
+++ b/image_pusher/TCPStreamPusher.h
@@ -161,6 +161,7 @@ class TCPStreamPusher : public ImagePusher {
     bool WaitForZeroCopyDrain(Connection& c, std::chrono::milliseconds timeout);
 
     bool WaitForAck(Connection& c, TCPFrameType ack_for, std::chrono::milliseconds timeout, std::string* error_text);
+    bool WaitForEndAck(Connection& c, std::chrono::milliseconds no_progress_timeout, std::string* error_text);
 public:
     explicit TCPStreamPusher(const std::string& addr,
                              size_t in_max_connections,
-- 
2.52.0


From 188cbb659dc190b657583bdd13bae0c34583339d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Wed, 17 Jun 2026 22:28:42 +0200
Subject: [PATCH 074/228] tests: add GPU/CPU equivalence test for ROI
 integration

Runs ROIIntegrationGPU and ROIIntegrationCPU on identical input and asserts
every per-ROI field (sum, sum_square, max, pixels, weighted centre, masked
count) matches bit-for-bit. Uses overlapping ROI boxes (multi-bit masks),
negative pixel values (signed weighted-sum path), and an injected saturated
and masked pixel per ROI to cover the "max only" and "fully excluded" branches.

Guarded by JFJOCH_USE_CUDA and skips with a warning when no CUDA GPU is present,
mirroring ImageSpotFinderGPUTest.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/CMakeLists.txt            |   1 +
 tests/ROIIntegrationGPUTest.cpp | 114 ++++++++++++++++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 tests/ROIIntegrationGPUTest.cpp

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 59af6e96..bc6539d3 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -33,6 +33,7 @@ ADD_EXECUTABLE(jfjoch_test
         HistogramTest.cpp
         ROIMapTest.cpp
         ROIIntegrationCPUTest.cpp
+        ROIIntegrationGPUTest.cpp
         LossyFilterTest.cpp
         ImageBufferTest.cpp
         PixelMaskTest.cpp
diff --git a/tests/ROIIntegrationGPUTest.cpp b/tests/ROIIntegrationGPUTest.cpp
new file mode 100644
index 00000000..dc6d2841
--- /dev/null
+++ b/tests/ROIIntegrationGPUTest.cpp
@@ -0,0 +1,114 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+#include "../common/CUDAWrapper.h"
+
+#ifdef JFJOCH_USE_CUDA
+
+#include <map>
+#include <string>
+#include <vector>
+
+#include "../image_analysis/roi/ROIIntegrationCPU.h"
+#include "../image_analysis/roi/ROIIntegrationGPU.h"
+#include "../image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.h"
+#include "../common/DiffractionExperiment.h"
+
+namespace {
+DiffractionExperiment make_roi_experiment() {
+    DiffractionExperiment experiment(DetJF(1));
+    // Overlapping boxes so some pixels belong to several ROIs at once (multi-bit
+    // mask), exercising the per-bit accumulation that has to match between CPU and GPU.
+    // ROIBox is (name, x_min, x_max, y_min, y_max), kept within the JF module bounds.
+    experiment.ROI().SetROI(ROIDefinition{.boxes = {
+        ROIBox("roiA", 10, 210, 20, 220),
+        ROIBox("roiB", 100, 300, 100, 300),
+        ROIBox("roiC", 0, 150, 0, 150),
+        ROIBox("roiD", 50, 250, 50, 250),
+    }});
+    return experiment;
+}
+
+void compare_results(const std::map<std::string, ROIMessage> &cpu,
+                     const std::map<std::string, ROIMessage> &gpu) {
+    REQUIRE(cpu.size() == gpu.size());
+    for (const auto &[name, c] : cpu) {
+        INFO("ROI " << name);
+        REQUIRE(gpu.contains(name));
+        const auto &g = gpu.at(name);
+        CHECK(g.sum           == c.sum);
+        CHECK(g.sum_square    == c.sum_square);
+        CHECK(g.max_count     == c.max_count);
+        CHECK(g.pixels        == c.pixels);
+        CHECK(g.x_weighted    == c.x_weighted);
+        CHECK(g.y_weighted    == c.y_weighted);
+        CHECK(g.pixels_masked == c.pixels_masked);
+    }
+}
+} // namespace
+
+// The GPU kernel reduces with atomics and two's-complement unsigned accumulators,
+// while the CPU path is a plain serial loop. On identical input every per-ROI
+// statistic must be bit-for-bit identical, so we run both and compare.
+TEST_CASE("ROIIntegrationGPU_MatchesCPU") {
+    if (get_gpu_count() == 0) {
+        WARN("No CUDA GPU present. Skipping ROIIntegrationGPU_MatchesCPU");
+        return;
+    }
+
+    const DiffractionExperiment experiment = make_roi_experiment();
+    const auto roi_map = experiment.ExportROIMap();
+    const size_t npixel = roi_map.size();
+    const uint16_t roi_count = experiment.ROI().size();
+    REQUIRE(roi_count == 4);
+
+    // Deterministic image with both positive and negative values; negatives exercise
+    // the signed weighted-sum path (val * x can be negative).
+    std::vector<int32_t> values(npixel);
+    for (size_t i = 0; i < npixel; i++)
+        values[i] = static_cast<int32_t>((i * 2654435761u) % 1000) - 500;
+
+    // Inject one saturated (INT32_MAX) and one masked (INT32_MIN) pixel into every ROI
+    // so both the "max only, not summed" and "fully excluded" branches are covered.
+    for (uint16_t r = 0; r < roi_count; r++) {
+        bool injected_sat = false, injected_mask = false;
+        for (size_t i = 0; i < npixel && !(injected_sat && injected_mask); i++) {
+            if (!(roi_map[i] & (1u << r)))
+                continue;
+            if (!injected_sat) { values[i] = INT32_MAX; injected_sat = true; }
+            else if (!injected_mask) { values[i] = INT32_MIN; injected_mask = true; }
+        }
+        REQUIRE(injected_sat);
+        REQUIRE(injected_mask);
+    }
+
+    // CPU reference
+    ImagePreprocessorBuffer cpu_image(npixel);
+    for (size_t i = 0; i < npixel; i++)
+        cpu_image[i] = values[i];
+
+    ROIIntegrationCPU cpu(experiment);
+    std::map<std::string, ROIMessage> out_cpu;
+    cpu.Run(cpu_image, out_cpu);
+
+    // GPU under test — identical input uploaded to the device
+    auto stream = std::make_shared<CudaStream>();
+    ImagePreprocessorBufferGPU gpu_image(npixel);
+    for (size_t i = 0; i < npixel; i++)
+        gpu_image[i] = values[i];
+
+    REQUIRE(cudaMemcpyAsync(gpu_image.getGPUBuffer(),
+                            gpu_image.getBuffer().data(),
+                            npixel * sizeof(int32_t),
+                            cudaMemcpyHostToDevice,
+                            *stream) == cudaSuccess);
+
+    ROIIntegrationGPU gpu(experiment, stream);
+    std::map<std::string, ROIMessage> out_gpu;
+    gpu.Run(gpu_image, out_gpu);
+
+    compare_results(out_cpu, out_gpu);
+}
+
+#endif
-- 
2.52.0


From 56ddfaef96bfcf725711385d18c4d6f4c0203a8d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 08:13:07 +0200
Subject: [PATCH 075/228] viewer: live detector status bar + dataset-follow
 sync mode

Add a status-bar cluster, shown when connected over HTTP, that surfaces
the broker state and live acquisition info:
- broker state box (QProgressBar) with progress drawn as the bar fill,
  polled ~1 Hz on its own timer independent of image sync
- Live/Disconnected connection badge (host:port in tooltip)
- "+N new" badge and effective live-rate (Hz) readout
All widgets are fixed-width and only blanked in place, so the bar never
reflows when things appear/disappear.

Add a third autoload mode (HTTPSyncDataset): manually selecting an image
while following live now freezes the displayed image but keeps the dataset,
plots and image count updating. Surfaced via a tri-state HTTP Sync button
(off / live / data-only).

Also fix GetBrokerStatus() dropping the message field and a couple of
copy-pasted exception strings in JFJochHttpReader.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHttpReader.cpp                 |  32 +++++-
 reader/JFJochHttpReader.h                   |   4 +
 viewer/JFJochImageReadingWorker.cpp         |  75 +++++++++++-
 viewer/JFJochImageReadingWorker.h           |  16 ++-
 viewer/JFJochViewerStatusBar.cpp            | 120 +++++++++++++++++++-
 viewer/JFJochViewerStatusBar.h              |  34 +++++-
 viewer/JFJochViewerWindow.cpp               |  12 ++
 viewer/toolbar/JFJochViewerToolbarImage.cpp |  33 +++++-
 8 files changed, 308 insertions(+), 18 deletions(-)

diff --git a/reader/JFJochHttpReader.cpp b/reader/JFJochHttpReader.cpp
index 30784ed9..dd383d27 100644
--- a/reader/JFJochHttpReader.cpp
+++ b/reader/JFJochHttpReader.cpp
@@ -50,7 +50,7 @@ BrokerStatus JFJochHttpReader::GetBrokerStatus() const {
     auto res = cli_cmd.Get("/status");
     if (!res || res->status != httplib::StatusCode::OK_200)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Could not get image buffer status");
+                              "Could not get broker status");
 
     try {
         org::openapitools::server::model::Broker_status input = nlohmann::json::parse(res->body);
@@ -59,6 +59,8 @@ BrokerStatus JFJochHttpReader::GetBrokerStatus() const {
         ret.gpu_count = input.getGpuCount();
         if (input.progressIsSet())
             ret.progress = input.getProgress();
+        if (input.messageIsSet())
+            ret.message = input.getMessage();
 
         if (input.getState() == "Inactive")
             ret.state = JFJochState::Inactive;
@@ -87,7 +89,7 @@ BrokerStatus JFJochHttpReader::GetBrokerStatus() const {
         return ret;
     } catch (std::exception &e) {
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Could not parse image buffer status");
+                              "Could not parse broker status");
     }
 }
 
@@ -209,6 +211,30 @@ void JFJochHttpReader::ReadURL(const std::string &url) {
         SetStartMessage(UpdateDataset_i());
 }
 
+std::shared_ptr<const JFJochReaderDataset> JFJochHttpReader::RefreshDatasetIfChanged(int64_t &num_images_out) {
+    std::unique_lock ul(http_mutex);
+
+    num_images_out = 0;
+    if (addr.empty())
+        return {};
+
+    auto status = GetImageBufferStatus();
+    num_images_out = status.max_image_number + 1;
+
+    // Re-fetch the dataset (start message + plots) only when the buffer actually changed,
+    // so the dataset-only follow mode does not hammer the broker with plot requests.
+    const bool buffer_changed = !last_image_buffer_counter.has_value()
+        || !status.current_counter.has_value()
+        || last_image_buffer_counter.value() != status.current_counter.value();
+    last_image_buffer_counter = status.current_counter;
+
+    if (!buffer_changed)
+        return {};
+
+    SetStartMessage(UpdateDataset_i());
+    return GetDataset();
+}
+
 bool JFJochHttpReader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
                                    DataMessage &message,
                                    std::vector<uint8_t> &buffer,
@@ -342,7 +368,7 @@ std::vector<float> JFJochHttpReader::GetPlot_i(const std::string &plot_type, flo
             return {};
     } catch (nlohmann::json::parse_error &e) {
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Could not parse image buffer status");
+                              "Could not parse plot " + plot_type);
     }
 }
 
diff --git a/reader/JFJochHttpReader.h b/reader/JFJochHttpReader.h
index 13dc6911..e558d98a 100644
--- a/reader/JFJochHttpReader.h
+++ b/reader/JFJochHttpReader.h
@@ -30,6 +30,10 @@ public:
     uint64_t GetNumberOfImages() const override;
     void Close() override;
 
+    // Refresh dataset/plots if the image buffer changed since the last poll (returns nullptr if
+    // unchanged). Always writes the current number of images to num_images_out. Does not load an image.
+    std::shared_ptr<const JFJochReaderDataset> RefreshDatasetIfChanged(int64_t &num_images_out);
+
     void UploadUserMask(const std::vector<uint32_t>& mask);
 
     BrokerStatus GetBrokerStatus() const;
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index a10ded30..15a441d4 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -68,7 +68,8 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
       indexing_settings(experiment.GetIndexingSettings()),
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
     qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
-    spot_finding_settings = settings;;
+    qRegisterMetaType<BrokerStatus>("BrokerStatus");
+    spot_finding_settings = settings;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
     http_reader.Experiment(experiment);
@@ -78,6 +79,10 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
     autoload_timer->setInterval(autoload_interval);
     connect(autoload_timer, &QTimer::timeout, this, &JFJochImageReadingWorker::AutoLoadTimerExpired);
 
+    status_timer = new QTimer(this);
+    status_timer->setInterval(status_interval);
+    connect(status_timer, &QTimer::timeout, this, &JFJochImageReadingWorker::StatusTimerExpired);
+
     file_open_retry_timer = new QTimer(this);
     file_open_retry_timer->setSingleShot(true);
     connect(file_open_retry_timer, &QTimer::timeout, this, &JFJochImageReadingWorker::FileOpenRetryTimerExpired);
@@ -171,6 +176,8 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
             http_reader.ReadURL(filename.toStdString());
             total_images = http_reader.GetNumberOfImages();
             dataset = http_reader.GetDataset();
+            SetHttpConnected_i(true, filename);
+            status_timer->start();
             if (image_number < 0)
                 setAutoLoadMode_i(AutoloadMode::HTTPSync);
             else
@@ -178,6 +185,8 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
 
         } else {
             http_mode = false;
+            status_timer->stop();
+            SetHttpConnected_i(false, "");
 
             if (retry) {
                 pending_load.filename = filename;
@@ -279,6 +288,10 @@ void JFJochImageReadingWorker::CloseFile() {
     else
         file_reader.Close();
 
+    status_timer->stop();
+    setAutoLoadMode_i(AutoloadMode::None);
+    SetHttpConnected_i(false, "");
+
     current_image_ptr.reset();
     current_image.reset();
     current_summation = 1;
@@ -290,7 +303,12 @@ void JFJochImageReadingWorker::CloseFile() {
 
 void JFJochImageReadingWorker::LoadImage(int64_t image_number, int64_t summation) {
     QMutexLocker ul(&m);
-    setAutoLoadMode_i(AutoloadMode::None);
+    // Manually selecting an image while following live drops to dataset-only follow:
+    // the chosen image stays put while plots and image count keep updating.
+    if (autoload_mode == AutoloadMode::HTTPSync || autoload_mode == AutoloadMode::HTTPSyncDataset)
+        setAutoLoadMode_i(AutoloadMode::HTTPSyncDataset);
+    else
+        setAutoLoadMode_i(AutoloadMode::None);
     if ((image_number == current_image) && (current_summation == summation))
         return;
     LoadImage_i(image_number, summation);
@@ -366,6 +384,9 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
                     autoload_timer->setInterval(autoload_interval);
                 }
             }
+
+            if (autoload_mode == AutoloadMode::HTTPSync)
+                emit liveRateChanged(autoload_interval > 0 ? 1000.0 / autoload_interval : 0.0);
         }
 
         logger.Info("Loaded image {} in {}/{} ms Autoload timer set to {} ms", image_number, duration_1, duration_2, autoload_interval);
@@ -656,6 +677,10 @@ void JFJochImageReadingWorker::AutoLoadTimerExpired() {
             if (http_mode)
                 LoadImage_i(-1 , 1);
             break;
+        case AutoloadMode::HTTPSyncDataset:
+            if (http_mode)
+                RefreshDatasetOnly_i();
+            break;
         case AutoloadMode::Movie: {
             if (total_images == 0 || !current_image)
                 return;
@@ -668,12 +693,57 @@ void JFJochImageReadingWorker::AutoLoadTimerExpired() {
     }
 }
 
+void JFJochImageReadingWorker::SetHttpConnected_i(bool connected, const QString &addr) {
+    // Assumes m locked! Only signals on a real change so the status bar does not flicker.
+    if (connected == http_connected)
+        return;
+    http_connected = connected;
+    emit httpConnectionChanged(connected, addr);
+}
+
+void JFJochImageReadingWorker::RefreshDatasetOnly_i() {
+    // Assumes m locked! Updates dataset/plots and image count without touching the displayed image.
+    if (!http_mode)
+        return;
+    try {
+        int64_t num_images = 0;
+        auto dataset = http_reader.RefreshDatasetIfChanged(num_images);
+        SetHttpConnected_i(true, current_file);
+
+        if (num_images != total_images) {
+            total_images = num_images;
+            if (current_image.has_value())
+                emit imageNumberChanged(total_images, current_image.value());
+        }
+        if (dataset)
+            emit datasetLoaded(dataset);
+    } catch (std::exception &e) {
+        logger.Debug("Dataset refresh failed: {}", e.what());
+        SetHttpConnected_i(false, current_file);
+    }
+}
+
+void JFJochImageReadingWorker::StatusTimerExpired() {
+    QMutexLocker locker(&m);
+    if (!http_mode)
+        return;
+    try {
+        BrokerStatus status = http_reader.GetBrokerStatus();
+        SetHttpConnected_i(true, current_file);
+        emit brokerStatusUpdated(status);
+    } catch (std::exception &e) {
+        SetHttpConnected_i(false, current_file);
+    }
+}
+
 void JFJochImageReadingWorker::setAutoLoadMode_i(AutoloadMode in_mode) {
     autoload_mode = in_mode;
     if (autoload_mode == AutoloadMode::None)
         autoload_timer->stop();
     else
         autoload_timer->start();
+    if (autoload_mode != AutoloadMode::HTTPSync)
+        emit liveRateChanged(0.0);
     emit autoloadChanged(autoload_mode);
 }
 
@@ -682,6 +752,7 @@ void JFJochImageReadingWorker::setAutoLoadMode(AutoloadMode mode) {
 
     switch (mode) {
         case AutoloadMode::HTTPSync:
+        case AutoloadMode::HTTPSyncDataset:
             if (http_mode)
                 setAutoLoadMode_i(mode);
             else
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index fcf74d5d..07144f52 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -30,12 +30,15 @@ Q_DECLARE_METATYPE(AzimuthalIntegrationSettings)
 
 Q_DECLARE_METATYPE(UnitCell)
 Q_DECLARE_METATYPE(std::shared_ptr<const SimpleImage>)
+Q_DECLARE_METATYPE(BrokerStatus)
 
 class JFJochImageReadingWorker : public QObject {
     Q_OBJECT
 
 public:
-    enum class AutoloadMode {HTTPSync, Movie, None};
+    // HTTPSync: follow latest image + dataset. HTTPSyncDataset: follow dataset/plots/image count
+    // but keep the displayed image frozen (entered by manually selecting an image while following).
+    enum class AutoloadMode {HTTPSync, HTTPSyncDataset, Movie, None};
     Q_ENUM(AutoloadMode)
 private:
     mutable QMutex m;
@@ -76,6 +79,11 @@ private:
     QTimer *autoload_timer;
     int autoload_interval = 500; // milliseconds
 
+    // Broker status polling (independent of image sync, runs whenever connected over HTTP)
+    QTimer *status_timer = nullptr;
+    int status_interval = 1000; // milliseconds
+    bool http_connected = false;
+
     // Adaptive autoload interval based on recent load+analysis time
     MovingAverage autoload_ms_ma{8};          // window size (tune as needed)
     int autoload_interval_min_ms = 50;        // 20 Hz is the top performance!
@@ -103,6 +111,8 @@ private:
 
     void LoadFile_i(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void LoadImage_i(int64_t image_number, int64_t summation);
+    void RefreshDatasetOnly_i();
+    void SetHttpConnected_i(bool connected, const QString &addr);
     void ReanalyzeImage_i();
     void UpdateDataset_i(const std::optional<DiffractionExperiment>& experiment);
     void UpdateAzint_i(const JFJochReaderDataset *dataset);
@@ -120,6 +130,9 @@ signals:
     void autoloadChanged(AutoloadMode mode);
     void fileLoadError(QString title, QString message);
     void fileLoadRetryStatus(bool active, QString message);
+    void brokerStatusUpdated(BrokerStatus status);
+    void httpConnectionChanged(bool connected, QString addr);
+    void liveRateChanged(double hz);
 
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
@@ -127,6 +140,7 @@ public:
 
 private slots:
     void AutoLoadTimerExpired();
+    void StatusTimerExpired();
     void FileOpenRetryTimerExpired();
 
 public slots:
diff --git a/viewer/JFJochViewerStatusBar.cpp b/viewer/JFJochViewerStatusBar.cpp
index 445d48f7..680f7ede 100644
--- a/viewer/JFJochViewerStatusBar.cpp
+++ b/viewer/JFJochViewerStatusBar.cpp
@@ -3,8 +3,126 @@
 
 #include "JFJochViewerStatusBar.h"
 
-JFJochViewerStatusBar::JFJochViewerStatusBar(QWidget *parent) : QStatusBar(parent) {}
+#include <algorithm>
+
+JFJochViewerStatusBar::JFJochViewerStatusBar(QWidget *parent) : QStatusBar(parent) {
+    // Added left-to-right within the permanent (right-aligned) area.
+    conn_label = new QLabel(this);
+    conn_label->setFixedWidth(100);
+    conn_label->setAlignment(Qt::AlignCenter);
+    addPermanentWidget(conn_label);
+
+    state_box = new QProgressBar(this);
+    state_box->setFixedWidth(110);
+    state_box->setRange(0, 1000);
+    state_box->setValue(0);
+    state_box->setTextVisible(true);
+    state_box->setAlignment(Qt::AlignCenter);
+    state_box->setFormat("");
+    addPermanentWidget(state_box);
+
+    new_label = new QLabel(this);
+    new_label->setFixedWidth(70);
+    new_label->setAlignment(Qt::AlignCenter);
+    addPermanentWidget(new_label);
+
+    rate_label = new QLabel(this);
+    rate_label->setFixedWidth(60);
+    rate_label->setAlignment(Qt::AlignCenter);
+    addPermanentWidget(rate_label);
+}
 
 void JFJochViewerStatusBar::display(QString input) {
     showMessage(input, 60000);
 }
+
+void JFJochViewerStatusBar::setBrokerStatus(BrokerStatus status) {
+    QString text;
+    switch (status.state) {
+        case JFJochState::Inactive:    text = "Inactive"; break;
+        case JFJochState::Idle:        text = "Idle"; break;
+        case JFJochState::Measuring:   text = "Measuring"; break;
+        case JFJochState::Error:       text = "Error"; break;
+        case JFJochState::Busy:        text = "Busy"; break;
+        case JFJochState::Calibration: text = "Calibration"; break;
+    }
+    state_box->setFormat(text);
+
+    if (status.progress.has_value())
+        state_box->setValue(std::clamp(static_cast<int>(status.progress.value() * 1000.0f), 0, 1000));
+    else
+        state_box->setValue(0);
+
+    const QString chunk = (status.state == JFJochState::Error) ? "#d9534f" : "#5cb85c";
+    state_box->setStyleSheet(QString(
+        "QProgressBar { border: 1px solid #aaa; border-radius: 2px; background: transparent; }"
+        "QProgressBar::chunk { background-color: %1; }").arg(chunk));
+
+    if (status.message.has_value() && !status.message.value().empty())
+        state_box->setToolTip(QString::fromStdString(status.message.value()));
+    else
+        state_box->setToolTip(text);
+}
+
+void JFJochViewerStatusBar::setHttpConnection(bool connected, QString addr) {
+    if (addr.isEmpty()) {
+        // No detector session at all -> blank the whole cluster (but keep the reserved space).
+        conn_label->setText("");
+        conn_label->setToolTip("");
+        conn_label->setStyleSheet("");
+        state_box->setFormat("");
+        state_box->setValue(0);
+        state_box->setStyleSheet("");
+        state_box->setToolTip("");
+        rate_label->setText("");
+        new_label->setText("");
+        new_label->setStyleSheet("");
+        return;
+    }
+
+    conn_label->setToolTip(addr);
+    if (connected) {
+        conn_label->setText("Live");
+        conn_label->setStyleSheet("color: white; background-color: #5cb85c; border-radius: 3px;");
+    } else {
+        conn_label->setText("Disconnected");
+        conn_label->setStyleSheet("color: white; background-color: #d9534f; border-radius: 3px;");
+        // Connection lost: clear live readouts but keep the badge so the user sees why.
+        state_box->setFormat("");
+        state_box->setValue(0);
+        state_box->setToolTip("");
+        rate_label->setText("");
+        new_label->setText("");
+    }
+}
+
+void JFJochViewerStatusBar::setAutoloadMode(JFJochImageReadingWorker::AutoloadMode mode) {
+    autoload_mode = mode;
+    UpdateNewLabel();
+}
+
+void JFJochViewerStatusBar::setImageNumber(int64_t in_total_images, int64_t in_current_image) {
+    total_images = in_total_images;
+    current_image = in_current_image;
+    UpdateNewLabel();
+}
+
+void JFJochViewerStatusBar::setLiveRate(double hz) {
+    if (hz > 0.0)
+        rate_label->setText(QString::number(hz, 'f', 1) + " Hz");
+    else
+        rate_label->setText("");
+}
+
+void JFJochViewerStatusBar::UpdateNewLabel() {
+    if (autoload_mode == JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset) {
+        const int64_t n = total_images - 1 - current_image;
+        if (n > 0) {
+            new_label->setText(QString("+%1 new").arg(n));
+            new_label->setStyleSheet("color: #f0ad4e; font-weight: bold;");
+            return;
+        }
+    }
+    new_label->setText("");
+    new_label->setStyleSheet("");
+}
diff --git a/viewer/JFJochViewerStatusBar.h b/viewer/JFJochViewerStatusBar.h
index 59d2de0a..7592f523 100644
--- a/viewer/JFJochViewerStatusBar.h
+++ b/viewer/JFJochViewerStatusBar.h
@@ -4,14 +4,36 @@
 #pragma once
 
 #include <QStatusBar>
+#include <QLabel>
+#include <QProgressBar>
+
+#include "../common/BrokerStatus.h"
+#include "JFJochImageReadingWorker.h"
 
 class JFJochViewerStatusBar : public QStatusBar {
+    Q_OBJECT
+
+    // Permanent (right-side) widgets. These are created once and never shown/hidden or resized,
+    // so the status bar never reflows; when not applicable they are just blanked in place.
+    QLabel *conn_label;       // "Live" / "Disconnected" (host:port in tooltip)
+    QProgressBar *state_box;  // Jungfraujoch state text, progress drawn as the bar fill
+    QLabel *new_label;        // "+N new" when following the dataset with a frozen image
+    QLabel *rate_label;       // effective live update rate
+
+    JFJochImageReadingWorker::AutoloadMode autoload_mode = JFJochImageReadingWorker::AutoloadMode::None;
+    int64_t total_images = 0;
+    int64_t current_image = 0;
+
+    void UpdateNewLabel();
+
+public:
+    explicit JFJochViewerStatusBar(QWidget *parent = nullptr);
+
 public slots:
     void display(QString input);
-public:
-    JFJochViewerStatusBar(QWidget * parent = nullptr);
-
+    void setBrokerStatus(BrokerStatus status);
+    void setHttpConnection(bool connected, QString addr);
+    void setAutoloadMode(JFJochImageReadingWorker::AutoloadMode mode);
+    void setImageNumber(int64_t total_images, int64_t current_image);
+    void setLiveRate(double hz);
 };
-
-
-
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 903b7528..eab463ca 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -294,6 +294,18 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(side_panel, &JFJochViewerSidePanel::writeStatusBar,
             statusbar, &JFJochViewerStatusBar::display);
 
+    // Detector connection / broker state / live readouts in the status bar
+    connect(reading_worker, &JFJochImageReadingWorker::brokerStatusUpdated,
+            statusbar, &JFJochViewerStatusBar::setBrokerStatus);
+    connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
+            statusbar, &JFJochViewerStatusBar::setHttpConnection);
+    connect(reading_worker, &JFJochImageReadingWorker::autoloadChanged,
+            statusbar, &JFJochViewerStatusBar::setAutoloadMode);
+    connect(reading_worker, &JFJochImageReadingWorker::imageNumberChanged,
+            statusbar, &JFJochViewerStatusBar::setImageNumber);
+    connect(reading_worker, &JFJochImageReadingWorker::liveRateChanged,
+            statusbar, &JFJochViewerStatusBar::setLiveRate);
+
     connect(metadataWindow, &JFJochViewerMetadataWindow::datasetUpdated,
             reading_worker, &JFJochImageReadingWorker::UpdateDataset);
 
diff --git a/viewer/toolbar/JFJochViewerToolbarImage.cpp b/viewer/toolbar/JFJochViewerToolbarImage.cpp
index ea6f99e9..b570194e 100644
--- a/viewer/toolbar/JFJochViewerToolbarImage.cpp
+++ b/viewer/toolbar/JFJochViewerToolbarImage.cpp
@@ -62,9 +62,11 @@ JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(p
     movie_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_M));
     addWidget(movie_button);
 
-    autoload_button = new QPushButton("HTTP &Sync");
+    autoload_button = new QPushButton("HTTP Sync");
     autoload_button->setCheckable(true);
     autoload_button->setChecked(false);
+    // Fixed width so the tri-state glyph prefix never reflows the toolbar.
+    autoload_button->setFixedWidth(120);
     autoload_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_S));
     addWidget(autoload_button);
 
@@ -195,10 +197,18 @@ void JFJochViewerToolbarImage::setSummation(int val) {
 }
 
 void JFJochViewerToolbarImage::autoloadButtonPressed() {
-    if (autoload_button->isChecked())
-        emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::HTTPSync);
-    else
-        emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::None);
+    // The button either starts/resumes live following or stops it; the data-only "frozen" state
+    // is entered automatically by manually selecting an image while following.
+    switch (autoload_mode) {
+        case JFJochImageReadingWorker::AutoloadMode::HTTPSync:
+            emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::None);
+            break;
+        case JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset:
+        case JFJochImageReadingWorker::AutoloadMode::Movie:
+        case JFJochImageReadingWorker::AutoloadMode::None:
+            emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::HTTPSync);
+            break;
+    }
 }
 
 void JFJochViewerToolbarImage::movieButtonPressed() {
@@ -213,16 +223,29 @@ void JFJochViewerToolbarImage::reanalyzeButtonPressed() {
 }
 
 void JFJochViewerToolbarImage::setAutoloadMode(JFJochImageReadingWorker::AutoloadMode input) {
+    autoload_mode = input;
     switch (input) {
         case JFJochImageReadingWorker::AutoloadMode::HTTPSync:
+            autoload_button->setText("▣ HTTP Sync");
+            autoload_button->setToolTip("Following live (image + data)");
+            autoload_button->setChecked(true);
+            movie_button->setChecked(false);
+            break;
+        case JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset:
+            autoload_button->setText("◐ HTTP Sync");
+            autoload_button->setToolTip("Following data only — image frozen (click to resume live)");
             autoload_button->setChecked(true);
             movie_button->setChecked(false);
             break;
         case JFJochImageReadingWorker::AutoloadMode::Movie:
+            autoload_button->setText("HTTP Sync");
+            autoload_button->setToolTip("");
             autoload_button->setChecked(false);
             movie_button->setChecked(true);
             break;
         case JFJochImageReadingWorker::AutoloadMode::None:
+            autoload_button->setText("HTTP Sync");
+            autoload_button->setToolTip("");
             autoload_button->setChecked(false);
             movie_button->setChecked(false);
             break;
-- 
2.52.0


From b29b870ef2b672a6d282990e64d1c41170b84294 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 13:45:04 +0200
Subject: [PATCH 076/228] broker/gen: gitignore generated cpp-pistache-server
 output

Only gen/model/ is compiled (into JFJochAPI) and tracked; the REST server is
hand-written on cpp-httplib, so the generated Pistache server stubs (api/,
impl/, main-api-server.cpp, CMakeLists.txt, README.md, .openapi-generator*) are
regeneration debris that was previously left untracked and tended to carry a
newer spec version than the committed models. Ignore it so it can't be
committed by accident.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/gen/.gitignore | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 broker/gen/.gitignore

diff --git a/broker/gen/.gitignore b/broker/gen/.gitignore
new file mode 100644
index 00000000..c24e5b6c
--- /dev/null
+++ b/broker/gen/.gitignore
@@ -0,0 +1,14 @@
+# Generated OpenAPI cpp-pistache-server output.
+#
+# Only model/ is compiled (into the JFJochAPI library) and tracked. The REST
+# server is hand-written on cpp-httplib (see broker/JFJochBrokerHttp.cpp), so the
+# generated Pistache server stubs below are regeneration debris: never compiled,
+# and they tend to carry a newer spec version than the committed models. Keep
+# them out of git to avoid accidentally committing mismatched artefacts.
+/api/
+/impl/
+/main-api-server.cpp
+/CMakeLists.txt
+/README.md
+/.openapi-generator/
+/.openapi-generator-ignore
-- 
2.52.0


From ec1308f4a9d0da504171774bd21e0657d988d631 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 13:50:49 +0200
Subject: [PATCH 077/228] viewer: guard Linux-only constructs for Windows/MSVC
 builds

Step toward building jfjoch_viewer on Windows/MSVC. No change to the Linux
build: D-Bus stays on by default and the XCB plugin is still used.

- CMake: make Qt6::DBus optional via JFJOCH_VIEWER_DBUS (ON on Linux, OFF on
  Windows/macOS where Qt6::DBus does not exist); compile/link/install the dbus/
  adaptor + service file only when enabled. Select the platform integration
  plugin per-OS (QXcb on Linux, QWindows on Windows, QCocoa on macOS) instead
  of hard-coding QXcbIntegrationPlugin.
- JFJochViewerWindow: wrap the adaptor include and D-Bus registration in
  #ifdef JFJOCH_VIEWER_DBUS.
- JFJochImageReadingWorker: the POSIX open()/fstat()/NFS-errno preflight is now
  #ifndef _WIN32, with a portable QFileInfo fallback elsewhere; POSIX-only
  headers are guarded too.
- Replace the POSIX M_PI/M_PI_2 extension with C++20 std::numbers::pi across the
  viewer (not defined by MSVC without _USE_MATH_DEFINES).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         | 42 ++++++++++++++-----
 viewer/JFJochImageReadingWorker.cpp           | 27 ++++++++++--
 viewer/JFJochViewerWindow.cpp                 |  6 +++
 viewer/image_viewer/JFJochAzIntImage.cpp      |  3 +-
 .../image_viewer/JFJochDiffractionImage.cpp   | 15 +++----
 viewer/widgets/PowderCalibrationWidget.cpp    |  3 +-
 viewer/windows/JFJochViewerMetadataWindow.cpp |  9 ++--
 7 files changed, 79 insertions(+), 26 deletions(-)

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index d7f0875c..b8a54837 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -5,7 +5,19 @@ SET(CMAKE_AUTOMOC ON)
 SET(CMAKE_AUTORCC ON)
 SET(CMAKE_AUTOUIC ON)
 
-FIND_PACKAGE(Qt6 COMPONENTS Core Gui Widgets Charts DBus Concurrent OpenGL OpenGLWidgets REQUIRED)
+# D-Bus (single-instance / remote control) is Linux-only: Qt6::DBus does not
+# exist on Windows or macOS. Default ON on Linux, OFF elsewhere.
+IF(UNIX AND NOT APPLE)
+    OPTION(JFJOCH_VIEWER_DBUS "Build viewer with D-Bus support (Linux only)" ON)
+ELSE()
+    OPTION(JFJOCH_VIEWER_DBUS "Build viewer with D-Bus support (Linux only)" OFF)
+ENDIF()
+
+SET(JFJOCH_VIEWER_QT_COMPONENTS Core Gui Widgets Charts Concurrent OpenGL OpenGLWidgets)
+IF(JFJOCH_VIEWER_DBUS)
+    LIST(APPEND JFJOCH_VIEWER_QT_COMPONENTS DBus)
+ENDIF()
+FIND_PACKAGE(Qt6 COMPONENTS ${JFJOCH_VIEWER_QT_COMPONENTS} REQUIRED)
 
 QT_ADD_RESOURCES(APP_RESOURCES resources/resources.qrc)
 
@@ -34,8 +46,6 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         JFJochViewerStatusBar.h
         windows/JFJochViewerImageListWindow.cpp
         windows/JFJochViewerImageListWindow.h
-        dbus/JFJochViewerAdaptor.h
-        dbus/JFJochViewerAdaptor.cpp
         widgets/NumericComboBox.cpp
         widgets/NumericComboBox.h
         windows/JFJochViewerMetadataWindow.cpp
@@ -90,16 +100,21 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJochMagnifierWindow.h
 )
 
-TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::DBus Qt6::Concurrent
+TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::Concurrent
         Qt6::OpenGL Qt6::OpenGLWidgets
         JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis)
 INSTALL(TARGETS jfjoch_viewer RUNTIME COMPONENT viewer)
 
-INSTALL(
-        FILES ${CMAKE_CURRENT_SOURCE_DIR}/dbus/ch.psi.jfjoch_viewer.service
-        DESTINATION share/dbus-1/services
-        COMPONENT viewer
-)
+IF(JFJOCH_VIEWER_DBUS)
+    TARGET_SOURCES(jfjoch_viewer PRIVATE dbus/JFJochViewerAdaptor.cpp dbus/JFJochViewerAdaptor.h)
+    TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::DBus)
+    TARGET_COMPILE_DEFINITIONS(jfjoch_viewer PRIVATE JFJOCH_VIEWER_DBUS)
+    INSTALL(
+            FILES ${CMAKE_CURRENT_SOURCE_DIR}/dbus/ch.psi.jfjoch_viewer.service
+            DESTINATION share/dbus-1/services
+            COMPONENT viewer
+    )
+ENDIF()
 
 INSTALL(
         FILES resources/jfjoch.png
@@ -113,7 +128,14 @@ INSTALL(
         COMPONENT viewer
 )
 
-qt_import_plugins(jfjoch_viewer INCLUDE Qt::QXcbIntegrationPlugin)
+# Platform integration plugin: XCB on Linux, native plugin on Windows/macOS.
+IF(WIN32)
+    qt_import_plugins(jfjoch_viewer INCLUDE Qt::QWindowsIntegrationPlugin)
+ELSEIF(APPLE)
+    qt_import_plugins(jfjoch_viewer INCLUDE Qt::QCocoaIntegrationPlugin)
+ELSE()
+    qt_import_plugins(jfjoch_viewer INCLUDE Qt::QXcbIntegrationPlugin)
+ENDIF()
 
 IF(HAS_FFTW3_H AND FFTWF_LIBRARY)
     TARGET_LINK_LIBRARIES(jfjoch_viewer ${FFTWF_LIBRARY})
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 15a441d4..67496478 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -1,11 +1,14 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include <cerrno>
+#include <cstring>
+#include <numbers>
+#ifndef _WIN32
 #include <sys/stat.h>
 #include <fcntl.h>
 #include <unistd.h>
-#include <cerrno>
-#include <cstring>
+#endif
 
 #include "JFJochImageReadingWorker.h"
 #include "../reader/JFJochReaderImage.h"   // JFJochReaderImage + GAP/ERROR/SATURATED sentinels
@@ -31,6 +34,7 @@ namespace {
     PreflightResult preflight_open_ro(const QString& filename, std::string& reason_out) {
         reason_out.clear();
 
+#ifndef _WIN32
         const QByteArray path = filename.toLocal8Bit();
         errno = 0;
         const int fd = ::open(path.constData(), O_RDONLY | O_CLOEXEC);
@@ -59,6 +63,23 @@ namespace {
             return PreflightResult::IsDirectory;
 
         return PreflightResult::OtherError;
+#else
+        // No NFS-style transient-errno semantics off POSIX; use a portable check.
+        const QFileInfo info(filename);
+        if (!info.exists()) {
+            reason_out = "File not visible yet";
+            return PreflightResult::NotYetVisible;
+        }
+        if (info.isDir()) {
+            reason_out = "Path is a directory";
+            return PreflightResult::IsDirectory;
+        }
+        if (!info.isReadable()) {
+            reason_out = "Permission denied";
+            return PreflightResult::PermissionDenied;
+        }
+        return PreflightResult::Ok;
+#endif
     }
 }
 
@@ -518,7 +539,7 @@ void JFJochImageReadingWorker::FindCenter(const UnitCell& calibrant, bool guess)
 
     QVector<float> rings;
     for (int i = 0; i < 15 && i < ring_Q.size(); i++) {
-        rings.push_back(2 * M_PI / ring_Q[i]);
+        rings.push_back(2 * std::numbers::pi / ring_Q[i]);
     }
     emit setRings(rings);
 }
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index eab463ca..7763b9e1 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -15,7 +15,9 @@
 #include "../common/CUDAWrapper.h"
 #include "windows/JFJochViewerImageListWindow.h"
 #include "windows/JFJochViewerMetadataWindow.h"
+#ifdef JFJOCH_VIEWER_DBUS
 #include "dbus/JFJochViewerAdaptor.h"
+#endif
 #include "windows/JFJochViewerProcessingWindow.h"
 #include "windows/JFJochViewerSpotListWindow.h"
 #include "windows/JFJochViewerReflectionListWindow.h"
@@ -119,6 +121,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
 
+#ifdef JFJOCH_VIEWER_DBUS
     if (dbus) {
         // Create adaptor attached to this window
         new JFJochViewerAdaptor(this);
@@ -132,6 +135,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             }
         }
     }
+#else
+    (void) dbus;
+#endif
 
     connect(this, &JFJochViewerWindow::LoadFileRequest,
             reading_worker, &JFJochImageReadingWorker::LoadFile);
diff --git a/viewer/image_viewer/JFJochAzIntImage.cpp b/viewer/image_viewer/JFJochAzIntImage.cpp
index e055f729..74c86733 100644
--- a/viewer/image_viewer/JFJochAzIntImage.cpp
+++ b/viewer/image_viewer/JFJochAzIntImage.cpp
@@ -5,6 +5,7 @@
 #include <QVBoxLayout>
 
 #include "../../common/JFJochException.h"
+#include <numbers>
 
 JFJochAzIntImage::JFJochAzIntImage(QWidget *parent)
     : JFJochImage(parent) {
@@ -109,7 +110,7 @@ void JFJochAzIntImage::mouseDoubleClickEvent(QMouseEvent *event) {
         float phi = image->Dataset().az_int_bin_to_phi[idx];
 
         auto geom = image->Dataset().experiment.GetDiffractionGeometry();
-        auto coord = geom.ResPhiToPxl(2 * M_PI / q, phi / 180.0 * M_PI);
+        auto coord = geom.ResPhiToPxl(2 * std::numbers::pi / q, phi / 180.0 * std::numbers::pi);
         emit zoomOnBin(QPointF(coord.first, coord.second));
     }
 }
\ No newline at end of file
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index b204a624..51dde0f3 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -3,6 +3,7 @@
 
 #include "JFJochDiffractionImage.h"
 #include "../../common/DiffractionGeometry.h"
+#include <numbers>
 
 #include <QGraphicsPixmapItem>
 #include <QGraphicsSimpleTextItem>
@@ -239,9 +240,9 @@ void JFJochDiffractionImage::DrawResolutionRings() {
             continue;
 
         auto [x1,y1] = geom.ResPhiToPxl(d, 0);
-        auto [x2,y2] = geom.ResPhiToPxl(d, M_PI_2);
-        auto [x3,y3] = geom.ResPhiToPxl(d, M_PI);
-        auto [x4,y4] = geom.ResPhiToPxl(d, 3.0 * M_PI_2);
+        auto [x2,y2] = geom.ResPhiToPxl(d, std::numbers::pi / 2);
+        auto [x3,y3] = geom.ResPhiToPxl(d, std::numbers::pi);
+        auto [x4,y4] = geom.ResPhiToPxl(d, 3.0 * std::numbers::pi / 2);
 
         auto x_min = std::min({x1, x2, x3, x4});
         auto x_max = std::max({x1, x2, x3, x4});
@@ -252,9 +253,9 @@ void JFJochDiffractionImage::DrawResolutionRings() {
         addOverlayItem(scene()->addEllipse(boundingRect, pen));
 
         auto [x5,y5] = geom.ResPhiToPxl(d, phi_offset + 0);
-        auto [x6,y6] = geom.ResPhiToPxl(d, phi_offset + M_PI_2);
-        auto [x7,y7] = geom.ResPhiToPxl(d, phi_offset + M_PI);
-        auto [x8,y8] = geom.ResPhiToPxl(d, phi_offset + 3.0 * M_PI_2);
+        auto [x6,y6] = geom.ResPhiToPxl(d, phi_offset + std::numbers::pi / 2);
+        auto [x7,y7] = geom.ResPhiToPxl(d, phi_offset + std::numbers::pi);
+        auto [x8,y8] = geom.ResPhiToPxl(d, phi_offset + 3.0 * std::numbers::pi / 2);
 
         QPointF point_1(x5, y5);
         QPointF point_2(x6, y6);
@@ -285,7 +286,7 @@ void JFJochDiffractionImage::DrawResolutionRings() {
             scene()->addItem(textItem);
             addOverlayItem(textItem);
         }
-        phi_offset += 4.0 / 180.0 * M_PI;
+        phi_offset += 4.0 / 180.0 * std::numbers::pi;
     }
 }
 
diff --git a/viewer/widgets/PowderCalibrationWidget.cpp b/viewer/widgets/PowderCalibrationWidget.cpp
index d6d9c31d..b7a78076 100644
--- a/viewer/widgets/PowderCalibrationWidget.cpp
+++ b/viewer/widgets/PowderCalibrationWidget.cpp
@@ -5,6 +5,7 @@
 #include <QPushButton>
 #include <QGridLayout>
 #include <QLabel>
+#include <numbers>
 
 #include "../image_analysis/geom_refinement/AssignSpotsToRings.h"
 
@@ -25,7 +26,7 @@ PowderCalibrationWidget::PowderCalibrationWidget(QWidget *parent) : QWidget(pare
         std::vector<float> rings = CalculateXtalRings(GetCalibrant(), 10);
         QVector<float> q_rings;
         for (float ring : rings) {
-            q_rings.append(2 * M_PI / ring);
+            q_rings.append(2 * std::numbers::pi / ring);
         }
         emit ringsFromCalibration(q_rings);
     });
diff --git a/viewer/windows/JFJochViewerMetadataWindow.cpp b/viewer/windows/JFJochViewerMetadataWindow.cpp
index 85d0e430..97db7e02 100644
--- a/viewer/windows/JFJochViewerMetadataWindow.cpp
+++ b/viewer/windows/JFJochViewerMetadataWindow.cpp
@@ -10,6 +10,7 @@
 #include <QMessageBox>
 
 #include "JFJochViewerMetadataWindow.h"
+#include <numbers>
 
 JFJochViewerMetadataWindow::JFJochViewerMetadataWindow(QWidget *parent) : JFJochHelperWindow(parent) {
 
@@ -135,8 +136,8 @@ void JFJochViewerMetadataWindow::datasetUpdate() {
             tmp.BeamX_pxl(beam_center_x->value());
             tmp.BeamY_pxl(beam_center_y->value());
             tmp.IncidentEnergy_keV(WVL_1A_IN_KEV / wavelength_A->value());
-            tmp.PoniRot1_rad(poni_rot1_deg->value() * M_PI / 180.0);
-            tmp.PoniRot2_rad(poni_rot2_deg->value() * M_PI / 180.0);
+            tmp.PoniRot1_rad(poni_rot1_deg->value() * std::numbers::pi / 180.0);
+            tmp.PoniRot2_rad(poni_rot2_deg->value() * std::numbers::pi / 180.0);
             tmp.DetectIceRings(detect_ice_rings->isChecked());
 
             if (unit_cell_enabled->isChecked()) {
@@ -176,8 +177,8 @@ void JFJochViewerMetadataWindow::datasetLoaded(std::shared_ptr<const JFJochReade
     beam_center_x->setValue(dataset->experiment.GetBeamX_pxl());
     beam_center_y->setValue(dataset->experiment.GetBeamY_pxl());
     wavelength_A->setValue(dataset->experiment.GetWavelength_A());
-    poni_rot1_deg->setValue(dataset->experiment.GetPoniRot1_rad() * 180.0 / M_PI);
-    poni_rot2_deg->setValue(dataset->experiment.GetPoniRot2_rad() * 180.0 / M_PI);
+    poni_rot1_deg->setValue(dataset->experiment.GetPoniRot1_rad() * 180.0 / std::numbers::pi);
+    poni_rot2_deg->setValue(dataset->experiment.GetPoniRot2_rad() * 180.0 / std::numbers::pi);
     detect_ice_rings->setChecked(dataset->experiment.IsDetectIceRings());
 
     auto unit_cell = dataset->experiment.GetUnitCell();
-- 
2.52.0


From e1622c3750e5631634f04fd6b0d991fbf0a10364 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 13:52:41 +0200
Subject: [PATCH 078/228] plots: expose compression_ratio over the REST/UI plot
 path

The receiver already computes and stores the compression ratio per image
(JFJochReceiverPlots Add/GetPlots/GetPlotRaw all handle PlotType::CompressionRatio),
but the type was unreachable from the API: it was missing from ConvertPlotType,
the OpenAPI plot_type enum, and the TS client, so requesting it returned 500 and
no UI menu entry existed.

Wire it through all layers:
- broker: add the compression_ratio -> PlotType::CompressionRatio case in
  ConvertPlotType.
- spec: add compression_ratio to the plot_type parameter enum.
- frontend: add COMPRESSION_RATIO to the generated plot_type enum (matches what
  regeneration would produce), a "Compression ratio" menu entry, and a Y-axis
  label.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/OpenAPIConvert.cpp                       | 1 +
 broker/jfjoch_api.yaml                          | 1 +
 frontend/src/components/DataProcessingPlot.tsx  | 2 ++
 frontend/src/components/DataProcessingPlots.tsx | 1 +
 frontend/src/openapi/models/plot_type.ts        | 1 +
 5 files changed, 6 insertions(+)

diff --git a/broker/OpenAPIConvert.cpp b/broker/OpenAPIConvert.cpp
index c601f594..ff273c16 100644
--- a/broker/OpenAPIConvert.cpp
+++ b/broker/OpenAPIConvert.cpp
@@ -886,6 +886,7 @@ PlotType ConvertPlotType(const std::optional<std::string>& input) {
     if (input == "image_scale_factor") return PlotType::ImageScaleFactor;
     if (input == "image_scale_cc") return PlotType::ImageScaleCC;
     if (input == "image_scale_b") return PlotType::ImageScaleBFactor;
+    if (input == "compression_ratio") return PlotType::CompressionRatio;
     if (input == "indexing_lattice_count") return PlotType::IndexingLatticeCount;
     throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                           "Plot type not recognized");
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 6e2b42db..1a44430a 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -120,6 +120,7 @@ components:
           - image_scale_factor
           - image_scale_cc
           - image_scale_b
+          - compression_ratio
     roi:
       in: query
       name: roi
diff --git a/frontend/src/components/DataProcessingPlot.tsx b/frontend/src/components/DataProcessingPlot.tsx
index d2ab2d61..e0faae69 100644
--- a/frontend/src/components/DataProcessingPlot.tsx
+++ b/frontend/src/components/DataProcessingPlot.tsx
@@ -90,6 +90,8 @@ function AxisTypeY(plot: plot_type) : string | ReactNode {
         case plot_type.BEAM_CENTER_X:
         case plot_type.BEAM_CENTER_Y:
             return "Beam center [pixel]";
+        case plot_type.COMPRESSION_RATIO:
+            return "Compression ratio";
         default:
             return "?";
     }
diff --git a/frontend/src/components/DataProcessingPlots.tsx b/frontend/src/components/DataProcessingPlots.tsx
index cc632a0e..49162e35 100644
--- a/frontend/src/components/DataProcessingPlots.tsx
+++ b/frontend/src/components/DataProcessingPlots.tsx
@@ -80,6 +80,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
                             <MenuItem value={plot_type.INDEXING_LATTICE_COUNT}>Indexed lattice count</MenuItem>
                             <MenuItem value={plot_type.INTEGRATED_REFLECTIONS}>Integrated reflections</MenuItem>
                             <MenuItem value={plot_type.IMAGE_COLLECTION_EFFICIENCY}>Image collection efficiency</MenuItem>
+                            <MenuItem value={plot_type.COMPRESSION_RATIO}>Compression ratio</MenuItem>
                             <MenuItem value={plot_type.PROCESSING_TIME}> Processing time</MenuItem>
                             <MenuItem value={plot_type.RECEIVER_DELAY}>Receiver delay (internal debugging)</MenuItem>
                             <MenuItem value={plot_type.RECEIVER_FREE_SEND_BUF}>Receiver free send buffers (internal debugging)</MenuItem>
diff --git a/frontend/src/openapi/models/plot_type.ts b/frontend/src/openapi/models/plot_type.ts
index 370ee04d..26ac39b2 100644
--- a/frontend/src/openapi/models/plot_type.ts
+++ b/frontend/src/openapi/models/plot_type.ts
@@ -44,4 +44,5 @@ export enum plot_type {
     IMAGE_SCALE_FACTOR = 'image_scale_factor',
     IMAGE_SCALE_CC = 'image_scale_cc',
     IMAGE_SCALE_B = 'image_scale_b',
+    COMPRESSION_RATIO = 'compression_ratio',
 }
-- 
2.52.0


From 086129f767ef8562c5b2538b1c8e399491097c99 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:12:14 +0200
Subject: [PATCH 079/228] receiver: count only images the pusher accepted

images_sent was incremented right after image_pusher.SendImage(*loc), but the
ZeroCopyReturnValue overload was void and, for the TCP pusher, asynchronous: it
silently drops the image (releases the slot and returns) when there is no live
connection or the 2 s enqueue deadline expires. So images_sent over-counted on a
broken/slow writer connection and disagreed with the ACK-based GetImagesWritten().

Make SendImage(ZeroCopyReturnValue&) return whether the image was accepted
(enqueued/handed off) and only increment images_sent on success. The slot is
still released on the drop path. The authoritative delivered count remains
GetImagesWritten() (total_data_acked_ok for TCP). File/ZMQ pushers return true on
accept, preserving their previous always-counted behaviour.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_pusher/HDF5FilePusher.cpp   |  3 ++-
 image_pusher/HDF5FilePusher.h     |  2 +-
 image_pusher/ImagePusher.cpp      |  5 +++--
 image_pusher/ImagePusher.h        |  7 ++++++-
 image_pusher/TCPStreamPusher.cpp  | 11 ++++++-----
 image_pusher/TCPStreamPusher.h    |  2 +-
 image_pusher/ZMQStream2Pusher.cpp |  7 +++++--
 image_pusher/ZMQStream2Pusher.h   |  2 +-
 receiver/JFJochReceiverFPGA.cpp   |  6 ++++--
 receiver/JFJochReceiverLite.cpp   |  6 ++++--
 10 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/image_pusher/HDF5FilePusher.cpp b/image_pusher/HDF5FilePusher.cpp
index a5f9138c..5c93f24e 100644
--- a/image_pusher/HDF5FilePusher.cpp
+++ b/image_pusher/HDF5FilePusher.cpp
@@ -91,12 +91,13 @@ bool HDF5FilePusher::SendImage(const uint8_t *image_data, size_t image_size, int
     return true;
 }
 
-void HDF5FilePusher::SendImage(ZeroCopyReturnValue &z) {
+bool HDF5FilePusher::SendImage(ZeroCopyReturnValue &z) {
     writer_queue.PutBlocking(ImagePusherQueueElement{
         .image_data = (uint8_t *) z.GetImage(),
         .z = &z,
         .end = false
     });
+    return true;
 }
 
 bool HDF5FilePusher::SendCalibration(const CompressedImage &message) {
diff --git a/image_pusher/HDF5FilePusher.h b/image_pusher/HDF5FilePusher.h
index 4039135e..f7fcbdc3 100644
--- a/image_pusher/HDF5FilePusher.h
+++ b/image_pusher/HDF5FilePusher.h
@@ -34,7 +34,7 @@ public:
     void StartDataCollection(StartMessage &message) override;
     bool EndDataCollection(const EndMessage &message) override;
     bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
-    void SendImage(ZeroCopyReturnValue &z) override;
+    bool SendImage(ZeroCopyReturnValue &z) override;
     bool SendCalibration(const CompressedImage &message) override;
 
     std::string PrintSetup() const override;
diff --git a/image_pusher/ImagePusher.cpp b/image_pusher/ImagePusher.cpp
index cca67c54..8c518ba6 100644
--- a/image_pusher/ImagePusher.cpp
+++ b/image_pusher/ImagePusher.cpp
@@ -25,7 +25,8 @@ std::string ImagePusher::GetWriterNotificationSocketAddress() const {
     return "";
 }
 
-void ImagePusher::SendImage(ZeroCopyReturnValue &z) {
-    SendImage((uint8_t *) z.GetImage(), z.GetImageSize(), z.GetImageNumber());
+bool ImagePusher::SendImage(ZeroCopyReturnValue &z) {
+    const bool accepted = SendImage((uint8_t *) z.GetImage(), z.GetImageSize(), z.GetImageNumber());
     z.release();
+    return accepted;
 }
diff --git a/image_pusher/ImagePusher.h b/image_pusher/ImagePusher.h
index 17d543ed..065d4ef1 100644
--- a/image_pusher/ImagePusher.h
+++ b/image_pusher/ImagePusher.h
@@ -41,7 +41,12 @@ public:
     virtual void StartDataCollection(StartMessage& message) = 0;
     virtual bool EndDataCollection(const EndMessage& message) = 0; // Non-blocking
     virtual bool SendImage(const uint8_t *image_data, size_t image_size,  int64_t image_number) = 0;
-    virtual void SendImage(ZeroCopyReturnValue &z);
+    // Returns true if the image was accepted (handed to the writer / enqueued for
+    // sending), false if it was dropped (e.g. no TCP connection, or the enqueue
+    // deadline expired). Ownership is settled either way: on a false return the
+    // slot has already been release()d. The authoritative count of images actually
+    // delivered is GetImagesWritten() (ACK-based for TCP).
+    virtual bool SendImage(ZeroCopyReturnValue &z);
     virtual bool SendCalibration(const CompressedImage& message) = 0;
     virtual std::string Finalize(); // Ensure that all streams are closed, can throw exception
     virtual std::string GetWriterNotificationSocketAddress() const;
diff --git a/image_pusher/TCPStreamPusher.cpp b/image_pusher/TCPStreamPusher.cpp
index d4a4295b..892b1bbc 100644
--- a/image_pusher/TCPStreamPusher.cpp
+++ b/image_pusher/TCPStreamPusher.cpp
@@ -1051,7 +1051,7 @@ bool TCPStreamPusher::SendImage(const uint8_t *image_data, size_t image_size, in
     return SendFrame(c, image_data, image_size, TCPFrameType::DATA, image_number, nullptr);
 }
 
-void TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
+bool TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
     // Look up the target connection while holding the mutex, but do NOT call
     // PutBlocking while holding it — that can block indefinitely and deadlock
     // against AcceptorThread/KeepaliveThread.
@@ -1061,7 +1061,7 @@ void TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
         const auto& use = (!session_connections.empty() ? session_connections : connections);
         if (use.empty()) {
             z.release();
-            return;
+            return false;
         }
 
         auto idx = static_cast<size_t>((z.GetImageNumber() / images_per_file) % static_cast<int64_t>(use.size()));
@@ -1070,14 +1070,14 @@ void TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
 
     if (!target || target->broken || !target->active) {
         z.release();
-        return;
+        return false;
     }
 
     const auto deadline = std::chrono::steady_clock::now() + std::chrono::seconds(2);
     while (std::chrono::steady_clock::now() < deadline) {
         if (target->broken || !target->active) {
             z.release();
-            return;
+            return false;
         }
 
         if (target->queue.PutTimeout(ImagePusherQueueElement{
@@ -1085,12 +1085,13 @@ void TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
                 .z = &z,
                 .end = false
             }, std::chrono::milliseconds(50))) {
-            return;
+            return true;
             }
     }
 
     target->broken = true;
     z.release();
+    return false;
 }
 
 bool TCPStreamPusher::EndDataCollection(const EndMessage& message) {
diff --git a/image_pusher/TCPStreamPusher.h b/image_pusher/TCPStreamPusher.h
index bd5dfed6..dfa62c03 100644
--- a/image_pusher/TCPStreamPusher.h
+++ b/image_pusher/TCPStreamPusher.h
@@ -177,7 +177,7 @@ public:
     void StartDataCollection(StartMessage& message) override;
     bool EndDataCollection(const EndMessage& message) override;
     bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
-    void SendImage(ZeroCopyReturnValue &z) override;
+    bool SendImage(ZeroCopyReturnValue &z) override;
     bool SendCalibration(const CompressedImage& message) override;
 
     std::string Finalize() override;
diff --git a/image_pusher/ZMQStream2Pusher.cpp b/image_pusher/ZMQStream2Pusher.cpp
index f115ce94..a29ca5fd 100644
--- a/image_pusher/ZMQStream2Pusher.cpp
+++ b/image_pusher/ZMQStream2Pusher.cpp
@@ -26,12 +26,15 @@ bool ZMQStream2Pusher::SendImage(const uint8_t *image_data, size_t image_size, i
 }
 
 
-void ZMQStream2Pusher::SendImage(ZeroCopyReturnValue &z) {
+bool ZMQStream2Pusher::SendImage(ZeroCopyReturnValue &z) {
     if (!socket.empty()) {
         auto socket_number = (z.GetImageNumber() / images_per_file) % socket.size();
         socket[socket_number]->SendImage(z);
-    } else
+        return true;
+    } else {
         z.release();
+        return false;
+    }
 }
 
 void ZMQStream2Pusher::StartDataCollection(StartMessage& message) {
diff --git a/image_pusher/ZMQStream2Pusher.h b/image_pusher/ZMQStream2Pusher.h
index 9d58f7a3..3fc17de4 100644
--- a/image_pusher/ZMQStream2Pusher.h
+++ b/image_pusher/ZMQStream2Pusher.h
@@ -37,7 +37,7 @@ public:
     bool SendCalibration(const CompressedImage& message) override;
 
     // Thread-safe
-    void SendImage(ZeroCopyReturnValue &z) override;
+    bool SendImage(ZeroCopyReturnValue &z) override;
     bool SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) override;
 
     std::string Finalize() override;
diff --git a/receiver/JFJochReceiverFPGA.cpp b/receiver/JFJochReceiverFPGA.cpp
index 3b2cbbb8..63745408 100644
--- a/receiver/JFJochReceiverFPGA.cpp
+++ b/receiver/JFJochReceiverFPGA.cpp
@@ -481,8 +481,10 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
                         zmq_metadata_socket->AddDataMessage(message);
 
                     if (push_images_to_writer) {
-                        image_pusher.SendImage(*loc);
-                        ++images_sent; // Handle case when image not sent properly
+                        // Only count images the pusher accepted; TCP can drop on a
+                        // broken/absent connection or an expired enqueue deadline.
+                        if (image_pusher.SendImage(*loc))
+                            ++images_sent;
                     } else
                         loc->release();
                     UpdateMaxImageSent(message.number);
diff --git a/receiver/JFJochReceiverLite.cpp b/receiver/JFJochReceiverLite.cpp
index cc8fbcad..b88972e2 100644
--- a/receiver/JFJochReceiverLite.cpp
+++ b/receiver/JFJochReceiverLite.cpp
@@ -328,8 +328,10 @@ void JFJochReceiverLite::DataAnalysisThread(uint32_t id) {
                             zmq_metadata_socket->AddDataMessage(data_msg);
 
                         if (push_images_to_writer) {
-                            image_pusher.SendImage(*loc);
-                            ++images_sent; // Handle case when image not sent properly
+                            // Only count images the pusher accepted; TCP can drop on a
+                            // broken/absent connection or an expired enqueue deadline.
+                            if (image_pusher.SendImage(*loc))
+                                ++images_sent;
                         } else
                             loc->release();
                         UpdateMaxImageSent(data_msg.number);
-- 
2.52.0


From 52f349b9f151c54c3e7568fd536fb9ae7d3641c8 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:13:03 +0200
Subject: [PATCH 080/228] frame_serialize: use reentrant gmtime in CBOR date
 decoding

gmtime() returns a pointer to a shared static buffer, so concurrent
deserialization of CborUnixTime_tTag values was a data race. Decode into a local
struct tm via gmtime_r (gmtime_s on Windows) instead.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frame_serialize/CBORStream2Deserializer.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index 2a598de6..06241be0 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -85,8 +85,14 @@ namespace {
             return GetCBORString(value);
         else if (tag == CborUnixTime_tTag) {
             time_t t = GetCBORUInt(value);
+            struct tm tm_buf{};
+#ifdef _WIN32
+            gmtime_s(&tm_buf, &t);
+#else
+            gmtime_r(&t, &tm_buf);
+#endif
             char buf1[255];
-            strftime(buf1, sizeof(buf1), "%FT%T", gmtime(&t));
+            strftime(buf1, sizeof(buf1), "%FT%T", &tm_buf);
             return std::string(buf1) + "Z";
         } else
             throw JFJochException(JFJochExceptionCategory::CBORError, "Time/date tag error");
-- 
2.52.0


From 01a97d61feb7d14ae8e00646909b85033bf225d6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:15:22 +0200
Subject: [PATCH 081/228] common: spell the azimuthal d-spacing unit d_A
 consistently

PlotAzintUnit used D_A while MultiLinePlotUnits used d_A for the same
d-spacing-in-angstrom unit. Align PlotAzintUnit to the lowercase crystallographic
convention already used by MultiLinePlotUnits. Generated Plot_unit_x::D_A is
left as-is (controlled by the OpenAPI generator's C++ enum casing).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/JFJochBrokerHttp.cpp            | 2 +-
 common/AzimuthalIntegrationProfile.cpp | 2 +-
 common/Plot.h                          | 2 +-
 receiver/JFJochReceiverPlots.cpp       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/broker/JFJochBrokerHttp.cpp b/broker/JFJochBrokerHttp.cpp
index ec2d90bf..8166fb87 100644
--- a/broker/JFJochBrokerHttp.cpp
+++ b/broker/JFJochBrokerHttp.cpp
@@ -880,7 +880,7 @@ void JFJochBrokerHttp::preview_plot_get(const std::optional<std::string> &type,
         if (azintUnit == "Q_recipA" || azintUnit == "q_recipa")
             unit = PlotAzintUnit::Q_recipA;
         else if (azintUnit == "d_A" || azintUnit == "d_a")
-            unit = PlotAzintUnit::D_A;
+            unit = PlotAzintUnit::d_A;
         else if (azintUnit == "two_theta_deg")
             unit = PlotAzintUnit::TwoTheta_deg;
     }
diff --git a/common/AzimuthalIntegrationProfile.cpp b/common/AzimuthalIntegrationProfile.cpp
index 4ccfb609..dc31a79d 100644
--- a/common/AzimuthalIntegrationProfile.cpp
+++ b/common/AzimuthalIntegrationProfile.cpp
@@ -120,7 +120,7 @@ const std::vector<float> &AzimuthalIntegrationProfile::GetXAxis(PlotAzintUnit un
     switch (unit) {
         case PlotAzintUnit::TwoTheta_deg:
             return bin_to_2theta;
-        case PlotAzintUnit::D_A:
+        case PlotAzintUnit::d_A:
             return bin_to_d;
         default:
         case PlotAzintUnit::Q_recipA:
diff --git a/common/Plot.h b/common/Plot.h
index 1075b5c4..943d0135 100644
--- a/common/Plot.h
+++ b/common/Plot.h
@@ -19,7 +19,7 @@ enum class PlotType {
 };
 
 enum class PlotAzintUnit {
-    Q_recipA, TwoTheta_deg, D_A
+    Q_recipA, TwoTheta_deg, d_A
 };
 
 struct PlotRequest {
diff --git a/receiver/JFJochReceiverPlots.cpp b/receiver/JFJochReceiverPlots.cpp
index 3f7e2599..553b99ce 100644
--- a/receiver/JFJochReceiverPlots.cpp
+++ b/receiver/JFJochReceiverPlots.cpp
@@ -250,7 +250,7 @@ MultiLinePlot JFJochReceiverPlots::GetPlots(const PlotRequest &request) {
             case PlotAzintUnit::TwoTheta_deg:
                 units = MultiLinePlotUnits::Angle_deg;
                 break;
-            case PlotAzintUnit::D_A:
+            case PlotAzintUnit::d_A:
                 units = MultiLinePlotUnits::d_A;
                 break;
         }
-- 
2.52.0


From 1558dddbb8e78ab13edbe44b480627cb8e7c1469 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:19:23 +0200
Subject: [PATCH 082/228] indexing: make the resolved-algorithm invariant
 explicit in the pool

IndexerThreadPool dispatches on DiffractionExperiment::GetIndexingAlgorithm(),
which already resolves Auto to a concrete algorithm (FFTW/FFT/FFBIDX) or None;
the pool has no policy to resolve Auto itself. The worker handled a stray Auto
with a dead branch and silently produced no result when the resolved algorithm
had no matching indexer built.

- Document on GetIndexingAlgorithm() that it never returns Auto.
- Throw a clear internal error at the pool boundary if Auto ever arrives.
- In the worker, replace the dead Auto branch with a loud failure for any
  resolved algorithm that has no matching indexer (e.g. a GPU algorithm on a
  host without a GPU), instead of returning no result silently.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/DiffractionExperiment.h                |  3 +++
 image_analysis/indexing/IndexerThreadPool.cpp | 19 ++++++++++++++++---
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/common/DiffractionExperiment.h b/common/DiffractionExperiment.h
index a8bbb9a8..a542ad03 100644
--- a/common/DiffractionExperiment.h
+++ b/common/DiffractionExperiment.h
@@ -392,6 +392,9 @@ public:
     void CalcSpotFinderResolutionMap(float *data, size_t module_number) const;
     CompressedImageMode GetImageMode() const;
 
+    // Resolves the configured algorithm to a concrete one from GPU availability and
+    // unit-cell presence: Auto -> FFTW/FFT/FFBIDX, and FFBIDX without a cell -> None.
+    // Never returns Auto - the indexer pool relies on this and cannot resolve Auto itself.
     IndexingAlgorithmEnum GetIndexingAlgorithm() const;
     GeomRefinementAlgorithmEnum GetGeomRefinementAlgorithm() const;
     float GetIndexingTolerance() const;
diff --git a/image_analysis/indexing/IndexerThreadPool.cpp b/image_analysis/indexing/IndexerThreadPool.cpp
index 51913d9a..262aa4b6 100644
--- a/image_analysis/indexing/IndexerThreadPool.cpp
+++ b/image_analysis/indexing/IndexerThreadPool.cpp
@@ -118,9 +118,14 @@ void IndexerThread::Worker(const IndexingSettings &settings, int threadid) {
                     indexer = ffbidx_indexer.get();
                 } else if (algorithm == IndexingAlgorithmEnum::FFTW && fftw_indexer) {
                     indexer = fftw_indexer.get();
-                } else if (algorithm == IndexingAlgorithmEnum::Auto) {
+                } else {
+                    // Algorithm is already resolved here (never Auto/None - see
+                    // IndexerThreadPool::Run). Reaching this means the resolved algorithm
+                    // has no matching indexer in this worker (e.g. a GPU algorithm on a
+                    // host without a GPU) - fail loudly instead of silently not indexing.
                     throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                                          "Internal error: Invalid indexing algorithm provided");
+                                          "Internal error: no indexer available for the resolved "
+                                          "indexing algorithm");
                 }
 
                 if (indexer) {
@@ -206,9 +211,17 @@ int IndexerThreadPool::GetFreeWorker() {
 }
 
 IndexerResult IndexerThreadPool::Run(const DiffractionExperiment &experiment, const std::vector<Coord> &recip) {
-    if (experiment.GetIndexingAlgorithm() == IndexingAlgorithmEnum::None)
+    const auto algorithm = experiment.GetIndexingAlgorithm();
+    if (algorithm == IndexingAlgorithmEnum::None)
         return IndexerResult{.lattice = {}, .indexing_time_s = 0, .executed = false};
 
+    // GetIndexingAlgorithm() must already have resolved Auto to a concrete algorithm;
+    // the pool has no policy to resolve it, so Auto here is an upstream contract bug.
+    if (algorithm == IndexingAlgorithmEnum::Auto)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Internal error: indexing algorithm must be resolved (not Auto) "
+                              "before reaching the indexer pool");
+
     // Check if there is available worker
    const int task = GetFreeWorker();
 
-- 
2.52.0


From d0a1175c65da776f7d5516efad769a6101119508 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:29:53 +0200
Subject: [PATCH 083/228] Clean-up of OpenAPI code

---
 broker/gen/model/Dataset_settings.h             | 2 +-
 broker/gen/model/Jfjoch_settings.h              | 2 +-
 broker/redoc-static.html                        | 8 ++++----
 docs/python_client/docs/DatasetSettings.md      | 2 +-
 docs/python_client/docs/JfjochSettings.md       | 2 +-
 frontend/src/openapi/models/dataset_settings.ts | 2 +-
 frontend/src/openapi/models/jfjoch_settings.ts  | 3 ++-
 frontend/src/openapi/services/DefaultService.ts | 4 ++--
 8 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/broker/gen/model/Dataset_settings.h b/broker/gen/model/Dataset_settings.h
index c9e5d574..8a06b8e0 100644
--- a/broker/gen/model/Dataset_settings.h
+++ b/broker/gen/model/Dataset_settings.h
@@ -168,7 +168,7 @@ public:
     bool gridScanIsSet() const;
     void unsetGrid_scan();
     /// <summary>
-    /// Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file.  However, if values are placed in \&quot;hdf5\&quot; object, &#x60;jfjoch_writer&#x60; will write them in /entry/data of the HDF5 file.  This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\&quot;hdf5\&quot;: {\&quot;val1\&quot;:1, \&quot;val2\&quot;:\&quot;xyz\&quot;}}, will write /entry/user/val1 and /entry/user/val2. 
+    /// Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file.  However, if values are placed in \&quot;hdf5\&quot; object, &#x60;jfjoch_writer&#x60; will write them in /entry/user of the HDF5 file.  This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\&quot;hdf5\&quot;: {\&quot;val1\&quot;:1, \&quot;val2\&quot;:\&quot;xyz\&quot;}}, will write /entry/user/val1 and /entry/user/val2. 
     /// </summary>
     nlohmann::json getHeaderAppendix() const;
     void setHeaderAppendix(nlohmann::json const& value);
diff --git a/broker/gen/model/Jfjoch_settings.h b/broker/gen/model/Jfjoch_settings.h
index e1e2ab26..8661427a 100644
--- a/broker/gen/model/Jfjoch_settings.h
+++ b/broker/gen/model/Jfjoch_settings.h
@@ -164,7 +164,7 @@ public:
     bool receiverThreadsIsSet() const;
     void unsetReceiver_threads();
     /// <summary>
-    /// NUMA policy to bind CPUs
+    /// Ignored value
     /// </summary>
     std::string getNumaPolicy() const;
     void setNumaPolicy(std::string const& value);
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 7475bf3e..e6a0dbfc 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -466,7 +466,7 @@ Transmission of attenuator (filter) [no units]</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="grid_scan"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand grid_scan"><span class="property-name">grid_scan</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->grid_scan<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Definition of a grid scan (mutually exclusive with <code>rotation_axis</code>)</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="header_appendix"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">header_appendix</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">any</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
 In general, it is not saved in HDF5 file.</p>
-<p>However, if values are placed in &quot;hdf5&quot; object, <code>jfjoch_writer</code> will write them in /entry/data of the HDF5 file. 
+<p>However, if values are placed in &quot;hdf5&quot; object, <code>jfjoch_writer</code> will write them in /entry/user of the HDF5 file. 
 This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
 For example {&quot;hdf5&quot;: {&quot;val1&quot;:1, &quot;val2&quot;:&quot;xyz&quot;}}, will write /entry/user/val1 and /entry/user/val2.</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="image_appendix"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">image_appendix</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">any</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)
@@ -868,7 +868,7 @@ User mask is not automatically applied - i.e. pixels with user mask will have a
 </div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>No calibration recorded so far</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/preview/pedestal.tiff</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/preview/pedestal.tiff</div></div></div></div></div></div></div></div><div id="/paths/~1preview~1plot/get" data-section-id="/paths/~1preview~1plot/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1preview~1plot/get" aria-label="/paths/~1preview~1plot/get"></a>Generate 1D plot from Jungfraujoch<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="binning"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">binning</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">integer</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">1</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Binning of frames for the plot (0 = default binning)</p>
-</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
+</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;compression_ratio&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="fill"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">fill</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">number</span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr"> <!-- -->&lt;<!-- -->float<!-- -->&gt;<!-- --> </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Fill value for elements that were missed during data collection</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="experimental_coord"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">experimental_coord</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">boolean</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">false</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>If measurement has goniometer axis defined, plot X-axis will represent rotation angle
 If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
@@ -880,7 +880,7 @@ For still measurement the number is ignored</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/preview/plot</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pra_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pra_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pra_0" aria-labelledby="tab_R_9pra_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"unit_x"</span>: <span class="token string">&quot;image_number&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"size_x"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"size_y"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"plot"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"x"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"y"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"z"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1preview~1plot.bin/get" data-section-id="/paths/~1preview~1plot.bin/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1preview~1plot.bin/get" aria-label="/paths/~1preview~1plot.bin/get"></a>Generate 1D plot from Jungfraujoch and send in raw binary format.
 Data are provided as (32-bit) float binary array.
 This format doesn&#x27;t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
-<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
+<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;compression_ratio&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
 </div></div></div></td></tr><tr class="last "><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="roi"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">roi</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span><span> <span class="sc-Nxspf sc-fxwrCY cXxAXt eMVOei"> <!-- -->non-empty<!-- --> </span></span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Name of ROI for which plot is requested</p>
 </div></div></div></td></tr></tbody></table></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK.</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Input parsing or validation error</p>
@@ -933,7 +933,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
-      const __redoc_state = {"menu":{"activeItemIdx":-1},"spec":{"data":{"openapi":"3.0.3","info":{"title":"Jungfraujoch","description":"API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).\nJungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.\nJungfraujoch uses FPGA boards to acquire data at high data rates.\n\n# License Clarification\n\nWhile this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**\nwhen this file is used solely to generate OpenAPI clients or when implementing applications that\ninteract with the API. Generated client code and applications using this API definition are not\nsubject to the GPL license requirements and may be distributed under terms of your choosing.\n\nThis exception is similar in spirit to the Linux Kernel's approach to userspace API headers and\nthe GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.148","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","image_scale_b"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"},"saturation":{"in":"query","name":"saturation","required":false,"schema":{"type":"number","format":"float","minimum":-32767,"maximum":32767},"description":"Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"},"background":{"in":"query","name":"background","required":false,"schema":{"type":"number","format":"float","default":0,"minimum":-32767,"maximum":32767},"description":"Background value to set contrast in the preview image"},"show_spots":{"in":"query","name":"show_spots","schema":{"type":"boolean","default":true},"description":"Show spot finding results on the image"},"show_beam_center":{"in":"query","name":"show_beam_center","schema":{"type":"boolean","default":true},"description":"Show beam center on the image"},"show_roi":{"in":"query","name":"show_roi","schema":{"type":"boolean","default":false},"description":"Show ROI areas on the image"},"jpeg_quality":{"in":"query","name":"jpeg_quality","description":"Quality of JPEG image (100 - highest; 0 - lowest)","schema":{"type":"integer","format":"int64","default":100,"minimum":0,"maximum":100}},"show_user_mask":{"in":"query","name":"show_user_mask","schema":{"type":"boolean","default":false},"description":"Show user mask"},"resolution_ring":{"in":"query","name":"show_res_ring","description":"Show resolution ring, provided in Angstrom","schema":{"type":"number","format":"float","default":0.1,"minimum":0.1,"maximum":100}},"resolution_estimate":{"in":"query","name":"show_res_est","description":"Show resolution estimation as a ring","schema":{"type":"boolean","default":false}},"color_scale":{"in":"query","name":"color","description":"Color scale for preview image","schema":{"type":"string","enum":["indigo","viridis","bw","wb","green","heat","magma","inferno"],"default":"indigo"}}},"schemas":{"grid_scan":{"description":"Definition of a grid scan (mutually exclusive with `rotation_axis`)","type":"object","required":["n_fast","step_x_um","step_y_um"],"properties":{"n_fast":{"type":"integer","format":"int64","minimum":1,"example":20,"description":"Number of elements in the fast direction"},"step_x_um":{"type":"number","format":"float","example":5,"description":"Step in grid along the fast direction. Can be negative. \nPositive number: left to right\nNegative number: right to left\n"},"step_y_um":{"type":"number","format":"float","example":-3,"description":"Step in grid along the slow direction. Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\n","enum":["BeamCenter","OrientationOnly","None"]},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. If left empty, no file will be saved."},"images_per_file":{"type":"integer","format":"int64","minimum":0,"default":1000,"description":"Number of files in a single HDF5 data file (0 = write all images to a single data file)."},"space_group_number":{"type":"integer","format":"int64","minimum":1,"maximum":194,"description":"Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. \nThis applies solely to string and number (double floating-point). 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This is optional parameter.\nThis option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.\n"}}},"azim_int_settings":{"type":"object","required":["solid_angle_corr","polarization_corr","high_q_recipA","low_q_recipA","q_spacing"],"properties":{"polarization_corr":{"type":"boolean","description":"Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)","default":true},"solid_angle_corr":{"type":"boolean","description":"Apply solid angle correction for azimuthal integration","default":true},"high_q_recipA":{"type":"number","format":"float"},"low_q_recipA":{"type":"number","format":"float"},"q_spacing":{"type":"number","format":"float"},"azimuthal_bins":{"type":"integer","format":"int64","minimum":1,"maximum":256,"default":1,"description":"Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration"}}},"detector_list_element":{"type":"object","required":["id","nmodules","description","width","height","serial_number","base_ipv4_addr","udp_interface_count","readout_time_ns","min_frame_time_ns","min_count_time_ns"],"properties":{"id":{"type":"integer","format":"int64","minimum":0},"description":{"type":"string","example":"JUNGFRAU 4 Mpixel"},"serial_number":{"type":"string","example":"JF17T16V01"},"base_ipv4_addr":{"type":"string","example":"10.10.10.1"},"udp_interface_count":{"type":"integer","format":"int64","example":2,"description":"Number of UDP interfaces per detector module"},"nmodules":{"type":"integer","format":"int64","example":18},"width":{"type":"integer","format":"int64","example":2068},"height":{"type":"integer","format":"int64","example":2164},"pixel_size_mm":{"type":"number","format":"float","example":0.075},"readout_time_ns":{"type":"integer","format":"int64"},"min_frame_time_ns":{"type":"integer","format":"int64"},"min_count_time_ns":{"type":"integer","format":"int64"},"type":{"$ref":"#/components/schemas/detector_type"}}},"detector_list":{"type":"object","required":["detectors","current_id"],"properties":{"detectors":{"type":"array","items":{"$ref":"#/components/schemas/detector_list_element"}},"current_id":{"type":"integer","format":"int64","example":0}}},"detector_selection":{"type":"object","required":["id"],"properties":{"id":{"type":"integer","format":"int64","example":1}}},"measurement_statistics":{"type":"object","properties":{"file_prefix":{"type":"string"},"run_number":{"type":"integer","format":"int64","description":"Number of data collection run. This can be either automatically incremented or provided externally for each data collection.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number).\n"},"images_expected":{"type":"integer","format":"int64"},"images_collected":{"type":"integer","format":"int64","description":"Images collected by the receiver. 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NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. \nhttps://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource\nNXsource allows the following:\n\nSpallation Neutron Source\nPulsed Reactor Neutron Source\nReactor Neutron Source\nSynchrotron X-ray Source\nPulsed Muon Source\nRotating Anode X-ray\nFixed Tube X-ray\nUV Laser\nFree-Electron Laser\nOptical Laser\nIon Source\nUV Plasma Source\nMetal Jet X-ray\n","example":"Synchrotron X-ray Source","default":""},"instrument_name":{"type":"string","example":"CristallinaMX"},"pulsed_source":{"type":"boolean","description":"Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)\n","default":false},"electron_source":{"type":"boolean","description":"Settings specific to electron source (e.g., wavelength definition)\n","default":false}}},"detector_module_direction":{"type":"string","enum":["Xp","Xn","Yp","Yn"]},"detector_type":{"type":"string","enum":["EIGER","JUNGFRAU","DECTRIS"]},"image_pusher_type":{"type":"string","default":"None","enum":["ZeroMQ","HDF5","CBOR","TCP","None"]},"standard_detector_geometry":{"type":"object","description":"Regular rectangular geometry, first module is in the bottom left corner of the detector","required":["nmodules"],"properties":{"nmodules":{"type":"integer","minimum":1,"description":"Number of modules in the detector"},"gap_x":{"type":"integer","default":8,"minimum":0,"description":"Gap size in X direction [pixels]"},"gap_y":{"type":"integer","minimum":0,"default":36,"description":"Gap size in Y direction [pixels]"},"modules_in_row":{"type":"integer","minimum":1,"default":1,"description":"Number of modules in one row"}}},"detector_module":{"type":"object","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number"},"y0":{"type":"number"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. 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Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - 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see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask.tiff":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (TIFF)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as TIFF (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. \nUser mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.\n","requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/preview/pedestal.tiff":{"get":{"parameters":[{"in":"query","name":"gain_level","required":true,"schema":{"type":"integer"},"description":"Gain level (0, 1, 2)"},{"in":"query","name":"sc","schema":{"type":"integer"},"description":"Storage cell number"}],"summary":"Get pedestal in TIFF format","responses":{"200":{"description":"Calibration image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Invalid gain level or storage cell number"},"404":{"description":"No calibration recorded so far"}}}},"/preview/plot":{"get":{"summary":"Generate 1D plot from Jungfraujoch","parameters":[{"$ref":"#/components/parameters/binning"},{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/fill_value"},{"$ref":"#/components/parameters/experimental_coord"},{"$ref":"#/components/parameters/azint_unit"}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/plots"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/preview/plot.bin":{"get":{"summary":"Generate 1D plot from Jungfraujoch and send in raw binary format.\nData are provided as (32-bit) float binary array.\nThis format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.\n","parameters":[{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/roi"}],"responses":{"200":{"description":"Everything OK.","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/result/scan":{"get":{"summary":"Get full scan result","responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/scan_result"}}}},"404":{"description":"No grid scan recorded"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/start.cbor":{"get":{"summary":"Get Start message in CBOR format","description":"Contains metadata for a dataset (e.g., experimental geometry)","responses":{"200":{"description":"Return start message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"No measurement so far"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.cbor":{"get":{"summary":"Get image message in CBOR format","description":"Contains full image data and metadata. The image must come from the latest data collection.","parameters":[{"$ref":"#/components/parameters/image_id"}],"responses":{"200":{"description":"Return image message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.jpeg":{"get":{"summary":"Get preview image in JPEG format using custom settings","parameters":[{"$ref":"#/components/parameters/image_id"},{"$ref":"#/components/parameters/show_user_mask"},{"$ref":"#/components/parameters/show_roi"},{"$ref":"#/components/parameters/show_spots"},{"$ref":"#/components/parameters/show_beam_center"},{"$ref":"#/components/parameters/saturation"},{"$ref":"#/components/parameters/jpeg_quality"},{"$ref":"#/components/parameters/resolution_ring"},{"$ref":"#/components/parameters/color_scale"},{"$ref":"#/components/parameters/resolution_estimate"}],"responses":{"200":{"description":"Preview image","content":{"image/jpeg":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.tiff":{"get":{"summary":"Get preview image in TIFF format","parameters":[{"$ref":"#/components/parameters/image_id"}],"responses":{"200":{"description":"Preview image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"No preview image recorded so far"}}}},"/image_buffer/clear":{"post":{"summary":"Clear image buffer","description":"Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.","responses":{"200":{"description":"Done"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/status":{"get":{"summary":"Get status of the image buffers","description":"Can be run at any stage of Jungfraujoch operation, including during data collection.\nThe status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,\nthen image might be replaced in the buffer between calling /images and /image.cbor.\n","responses":{"200":{"description":"Done","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_buffer_status"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/version":{"get":{"summary":"Get Jungfraujoch version of jfjoch_broker","responses":{"200":{"description":"Release number of 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voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real 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One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; 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 **grid_scan** | [**GridScan**](GridScan.md) |  | [optional] 
-**header_appendix** | **object** | Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file.  However, if values are placed in \&quot;hdf5\&quot; object, &#x60;jfjoch_writer&#x60; will write them in /entry/data of the HDF5 file.  This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\&quot;hdf5\&quot;: {\&quot;val1\&quot;:1, \&quot;val2\&quot;:\&quot;xyz\&quot;}}, will write /entry/user/val1 and /entry/user/val2.  | [optional] 
+**header_appendix** | **object** | Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file.  However, if values are placed in \&quot;hdf5\&quot; object, &#x60;jfjoch_writer&#x60; will write them in /entry/user of the HDF5 file.  This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\&quot;hdf5\&quot;: {\&quot;val1\&quot;:1, \&quot;val2\&quot;:\&quot;xyz\&quot;}}, will write /entry/user/val1 and /entry/user/val2.  | [optional] 
 **image_appendix** | **object** | Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file  | [optional] 
 **data_reduction_factor_serialmx** | **float** | Rate at which non-indexed images are accepted to be forwarded to writer.  Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability.  | [optional] [default to 1.0]
 **pixel_value_low_threshold** | **int** | Set all counts lower than the value to zero.  When the value is set, negative numbers other than error pixel value are always set to zero. Setting to zero is equivalent to turning the option off.  | [optional] 
diff --git a/docs/python_client/docs/JfjochSettings.md b/docs/python_client/docs/JfjochSettings.md
index 360eb37b..1952a1c3 100644
--- a/docs/python_client/docs/JfjochSettings.md
+++ b/docs/python_client/docs/JfjochSettings.md
@@ -19,7 +19,7 @@ Name | Type | Description | Notes
 **image_buffer_mi_b** | **int** | Size of internal buffer in MiB for images before they are sent to a stream | [optional] [default to 2048]
 **verbose** | **bool** | Print extra debug information | [optional] [default to False]
 **receiver_threads** | **int** | Number of threads used by the receiver | [optional] [default to 64]
-**numa_policy** | **str** | NUMA policy to bind CPUs | [optional] 
+**numa_policy** | **str** | Ignored value | [optional] 
 **frontend_directory** | **str** | Location of built JavaScript web frontend | 
 **spot_finding** | [**SpotFindingSettings**](SpotFindingSettings.md) |  | [optional] 
 **image_pusher** | [**ImagePusherType**](ImagePusherType.md) |  | [default to ImagePusherType.NONE]
diff --git a/frontend/src/openapi/models/dataset_settings.ts b/frontend/src/openapi/models/dataset_settings.ts
index 3d2998a0..81d0dbe9 100644
--- a/frontend/src/openapi/models/dataset_settings.ts
+++ b/frontend/src/openapi/models/dataset_settings.ts
@@ -92,7 +92,7 @@ export type dataset_settings = {
      * Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
      * In general, it is not saved in HDF5 file.
      *
-     * However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file.
+     * However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file.
      * This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
      * For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.
      *
diff --git a/frontend/src/openapi/models/jfjoch_settings.ts b/frontend/src/openapi/models/jfjoch_settings.ts
index c266d3d7..205c178c 100644
--- a/frontend/src/openapi/models/jfjoch_settings.ts
+++ b/frontend/src/openapi/models/jfjoch_settings.ts
@@ -48,7 +48,8 @@ export type jfjoch_settings = {
      */
     receiver_threads?: number;
     /**
-     * NUMA policy to bind CPUs
+     * Ignored value
+     * @deprecated
      */
     numa_policy?: string;
     /**
diff --git a/frontend/src/openapi/services/DefaultService.ts b/frontend/src/openapi/services/DefaultService.ts
index 7ad810e6..959f5957 100644
--- a/frontend/src/openapi/services/DefaultService.ts
+++ b/frontend/src/openapi/services/DefaultService.ts
@@ -1031,7 +1031,7 @@ export class DefaultService {
      * @throws ApiError
      */
     public static getPreviewPlot(
-        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b',
+        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio',
         binning: number = 1,
         fill?: number,
         experimentalCoord: boolean = false,
@@ -1064,7 +1064,7 @@ export class DefaultService {
      * @throws ApiError
      */
     public static getPreviewPlotBin(
-        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b',
+        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio',
         roi?: string,
     ): CancelablePromise<Blob> {
         return __request(OpenAPI, {
-- 
2.52.0


From 5d9e1be8141017afabd937a3667b2c5e159d154f Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 14:54:01 +0200
Subject: [PATCH 084/228] portability: replace M_PI / std::numbers::pi with a
 host+device-safe PI

M_PI is a POSIX <math.h> extension that MSVC does not define without
_USE_MATH_DEFINES. std::numbers::pi (introduced in the viewer guard commit) is
C++20, but CUDA here is compiled as C++17 (CMAKE_CUDA_STANDARD 17) and several
common/ headers are pulled into .cu device translation units, so std::numbers is
not available there.

Add common/JFJochMath.h with a dependency-free `constexpr double PI` that works
in host code (including MSVC), in CUDA device code, and under C++17/20, and use
it everywhere:
- common/ and image_analysis/ (incl. CUDA .cu): 78 M_PI occurrences, 22 files
- broker/OpenAPIConvert.cpp
- viewer/: the 5 files that used std::numbers::pi now use PI, for one consistent
  convention across the codebase

Verified to build: JFJochImageAnalysis (incl. CUDA), jfjoch_viewer, JFJochBroker.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/OpenAPIConvert.cpp                     |  5 ++--
 common/AzimuthalIntegrationMapping.cpp        | 11 +++----
 common/AzimuthalIntegrationSettings.h         |  5 ++--
 common/Coord.cpp                              |  3 +-
 common/CrystalLattice.cpp                     |  3 +-
 common/DiffractionGeometry.cpp                |  7 +++--
 common/GoniometerAxis.cpp                     |  3 +-
 common/JFJochMath.h                           | 10 +++++++
 common/ROIAzimuthal.cpp                       |  5 ++--
 .../bragg_prediction/BraggPrediction.cpp      |  3 +-
 .../bragg_prediction/BraggPredictionGPU.cu    |  3 +-
 .../bragg_prediction/BraggPredictionRot.cpp   |  7 +++--
 .../bragg_prediction/BraggPredictionRotGPU.cu |  7 +++--
 .../geom_refinement/AssignSpotsToRings.cpp    |  9 +++---
 .../geom_refinement/LatticeReduction.cpp      |  7 +++--
 .../geom_refinement/RingOptimizer.cpp         |  3 +-
 .../geom_refinement/XtalOptimizer.cpp         | 29 ++++++++++---------
 image_analysis/indexing/AnalyzeIndexing.cpp   | 11 +++----
 image_analysis/indexing/FFTIndexer.cpp        |  7 +++--
 .../indexing/PostIndexingRefinement.cpp       |  7 +++--
 .../lattice_search/LatticeSearch.cpp          |  7 +++--
 .../pixel_refinement/PixelRefine.cpp          |  5 ++--
 .../rotation_indexer/RotationIndexer.cpp      |  3 +-
 image_analysis/spot_finding/SpotUtils.cpp     |  9 +++---
 viewer/JFJochImageReadingWorker.cpp           |  4 +--
 viewer/image_viewer/JFJochAzIntImage.cpp      |  4 +--
 .../image_viewer/JFJochDiffractionImage.cpp   | 16 +++++-----
 viewer/widgets/PowderCalibrationWidget.cpp    |  4 +--
 viewer/windows/JFJochViewerMetadataWindow.cpp | 10 +++----
 29 files changed, 120 insertions(+), 87 deletions(-)
 create mode 100644 common/JFJochMath.h

diff --git a/broker/OpenAPIConvert.cpp b/broker/OpenAPIConvert.cpp
index ff273c16..cc296d52 100644
--- a/broker/OpenAPIConvert.cpp
+++ b/broker/OpenAPIConvert.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../common/JFJochMath.h"
 #include "OpenAPIConvert.h"
 
 // From https://en.cppreference.com/w/cpp/string/byte/tolower
@@ -460,8 +461,8 @@ ROIDefinition Convert(const org::openapitools::server::model::Roi_definitions& i
         output.circles.emplace_back(ROICircle(i.getName(), i.getCenterXPxl(), i.getCenterYPxl(), i.getRadiusPxl()));
     for (const auto &i: input.getAzim().getRois())
         output.azimuthal.emplace_back(ROIAzimuthal(i.getName(),
-                                                   (i.getQMaxRecipA() == 0.0) ? 0.0 : 2.0f * M_PI / i.getQMaxRecipA(),
-                                                   (i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * M_PI / i.getQMinRecipA()));
+                                                   (i.getQMaxRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMaxRecipA(),
+                                                   (i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMinRecipA()));
     return output;
 }
 
diff --git a/common/AzimuthalIntegrationMapping.cpp b/common/AzimuthalIntegrationMapping.cpp
index 4c558f02..b72337ef 100644
--- a/common/AzimuthalIntegrationMapping.cpp
+++ b/common/AzimuthalIntegrationMapping.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include <cmath>
 #include <thread>
 #include <future>
@@ -145,8 +146,8 @@ void AzimuthalIntegrationMapping::SetupPixel(const DiffractionGeometry &geom,
     corrections[pxl] = corr;
 
     if (d > 0) {
-        float q = 2.0f * static_cast<float>(M_PI) / d;
-        pixel_to_bin[pxl] = settings.GetBin(q, phi_rad * 180.0 / M_PI);
+        float q = 2.0f * static_cast<float>(PI) / d;
+        pixel_to_bin[pxl] = settings.GetBin(q, phi_rad * 180.0 / PI);
     }
 }
 
@@ -187,9 +188,9 @@ void AzimuthalIntegrationMapping::UpdateMaxBinNumber() {
     for (int j = 0; j < settings.GetAzimuthalBinCount(); j++) {
         for (int i = 0; i < settings.GetQBinCount(); i++) {
             bin_to_q[j * settings.GetQBinCount() + i] = static_cast<float>(settings.GetQSpacing_recipA() * (i + 0.5) + settings.GetLowQ_recipA());
-            bin_to_d[j * settings.GetQBinCount() + i] = 2.0f * static_cast<float>(M_PI) / bin_to_q[j * settings.GetQBinCount() + i];
-            bin_to_2theta[j * settings.GetQBinCount() + i] = 2.0f * asinf(bin_to_q[i] * wavelength / (4.0f * static_cast<float>(M_PI))) * 180.0f /
-                               static_cast<float>(M_PI);
+            bin_to_d[j * settings.GetQBinCount() + i] = 2.0f * static_cast<float>(PI) / bin_to_q[j * settings.GetQBinCount() + i];
+            bin_to_2theta[j * settings.GetQBinCount() + i] = 2.0f * asinf(bin_to_q[i] * wavelength / (4.0f * static_cast<float>(PI))) * 180.0f /
+                               static_cast<float>(PI);
             bin_to_phi[j * settings.GetQBinCount() + i] = static_cast<float>(j) * 360.0f / static_cast<float>(settings.GetAzimuthalBinCount());
         }
     }
diff --git a/common/AzimuthalIntegrationSettings.h b/common/AzimuthalIntegrationSettings.h
index eafb97f5..7f7ee8e2 100644
--- a/common/AzimuthalIntegrationSettings.h
+++ b/common/AzimuthalIntegrationSettings.h
@@ -3,6 +3,7 @@
 
 #pragma once
 
+#include "JFJochMath.h"
 #include <optional>
 #include <cstdint>
 
@@ -11,8 +12,8 @@ class AzimuthalIntegrationSettings {
     bool polarization_correction = true;
     float high_q_recipA = 5.0;
     float low_q_recipA = 0.1;
-    float bkg_estimate_high_q_recipA = 2.0f * M_PI / 3.0;
-    float bkg_estimate_low_q_recipA = 2.0f * M_PI / 5.0;
+    float bkg_estimate_high_q_recipA = 2.0f * PI / 3.0;
+    float bkg_estimate_low_q_recipA = 2.0f * PI / 5.0;
     float q_spacing = 0.05;
     int32_t azim_bins = 1;
 
diff --git a/common/Coord.cpp b/common/Coord.cpp
index 54809077..8595c40a 100644
--- a/common/Coord.cpp
+++ b/common/Coord.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include <cmath>
 #include "Coord.h"
 #include "JFJochException.h"
@@ -143,7 +144,7 @@ float angle_deg(const Coord &c1, const Coord &c2) {
     else if (cos_ang < -1.0f && cos_ang > -1.0f - epsilon)
         cos_ang = -1.0f;
 
-    return acosf(cos_ang) * (180.0f / static_cast<float>(M_PI));
+    return acosf(cos_ang) * (180.0f / static_cast<float>(PI));
 }
 
 void Coord::swap(Coord &other) noexcept {
diff --git a/common/CrystalLattice.cpp b/common/CrystalLattice.cpp
index 17dbca65..ac3583c5 100644
--- a/common/CrystalLattice.cpp
+++ b/common/CrystalLattice.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include <cmath>
 #include "CrystalLattice.h"
 #include "JFJochException.h"
@@ -9,7 +10,7 @@
 #include "gemmi/unitcell.hpp"
 #include "gemmi/cellred.hpp"
 
-#define DEG_TO_RAD static_cast<float>(M_PI/180.0)
+#define DEG_TO_RAD static_cast<float>(PI/180.0)
 
 CrystalLattice::CrystalLattice(const UnitCell &cell) {
     vec[0] = {cell.a, 0, 0};
diff --git a/common/DiffractionGeometry.cpp b/common/DiffractionGeometry.cpp
index 51163a59..1234ffa8 100644
--- a/common/DiffractionGeometry.cpp
+++ b/common/DiffractionGeometry.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include <cmath>
 
 #include "DiffractionGeometry.h"
@@ -48,7 +49,7 @@ float DiffractionGeometry::Phi_rad(float x, float y) const {
     auto lab = LabCoord(x, y);
     auto v = atan2f(lab.y, lab.x);
     if (v < 0)
-        v += 2.0f * M_PI;
+        v += 2.0f * PI;
     return v;
 }
 
@@ -58,7 +59,7 @@ float DiffractionGeometry::PxlToRes(float x, float y) const {
 }
 
 float DiffractionGeometry::PxlToQ(float x, float y) const {
-    return 2.0f * M_PI / PxlToRes(x,y);
+    return 2.0f * PI / PxlToRes(x,y);
 }
 
 float DiffractionGeometry::PxlToRes(float dist_pxl) const {
@@ -87,7 +88,7 @@ float DiffractionGeometry::DistFromEwaldSphere(const Coord &recip) const {
 }
 
 float DiffractionGeometry::CalcAzIntSolidAngleCorr(float q) const {
-    float sin_theta = q * wavelength_A / (4 * static_cast<float>(M_PI));
+    float sin_theta = q * wavelength_A / (4 * static_cast<float>(PI));
     float cos_2theta = 1.0f - 2.0f * sin_theta * sin_theta; // cos(2*alpha) = 1 - 2 * sin(alpha)^2
     float cos_2theta_3 = cos_2theta * cos_2theta * cos_2theta;
     return cos_2theta_3;
diff --git a/common/GoniometerAxis.cpp b/common/GoniometerAxis.cpp
index bfe9dedf..bd56d392 100644
--- a/common/GoniometerAxis.cpp
+++ b/common/GoniometerAxis.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include <cmath>
 #include <algorithm>
 
@@ -138,6 +139,6 @@ std::vector<double> GoniometerAxis::GetAngleContainerEnd(int64_t max_image_numbe
 }
 
 RotMatrix GoniometerAxis::GetTransformationAngle(float angle_deg) const {
-    auto angle_rad = angle_deg / 180.0f * static_cast<float>(M_PI);
+    auto angle_rad = angle_deg / 180.0f * static_cast<float>(PI);
     return {angle_rad, axis};
 }
\ No newline at end of file
diff --git a/common/JFJochMath.h b/common/JFJochMath.h
new file mode 100644
index 00000000..d6d9d579
--- /dev/null
+++ b/common/JFJochMath.h
@@ -0,0 +1,10 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+// pi as a plain constexpr so it is usable everywhere:
+//  - host code on MSVC, which does not define M_PI without _USE_MATH_DEFINES;
+//  - CUDA device code, which is compiled as C++17 here, so PI
+//    (C++20) is not available.
+constexpr double PI = 3.14159265358979323846;
diff --git a/common/ROIAzimuthal.cpp b/common/ROIAzimuthal.cpp
index 60dbc6a9..d9321b68 100644
--- a/common/ROIAzimuthal.cpp
+++ b/common/ROIAzimuthal.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include "ROIAzimuthal.h"
 #include "JFJochException.h"
 
@@ -31,11 +32,11 @@ bool ROIAzimuthal::CheckROI(int64_t x, int64_t y, float resolution) const {
 }
 
 float ROIAzimuthal::GetQMax_recipA() const {
-    return 2.0f * M_PI / d_min_A;
+    return 2.0f * PI / d_min_A;
 }
 
 float ROIAzimuthal::GetQMin_recipA() const {
-    return 2.0f * M_PI / d_max_A;
+    return 2.0f * PI / d_max_A;
 }
 
 ROIConfig ROIAzimuthal::ExportMetadata() const {
diff --git a/image_analysis/bragg_prediction/BraggPrediction.cpp b/image_analysis/bragg_prediction/BraggPrediction.cpp
index 4c134e38..70ebea71 100644
--- a/image_analysis/bragg_prediction/BraggPrediction.cpp
+++ b/image_analysis/bragg_prediction/BraggPrediction.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "BraggPrediction.h"
 #include "../bragg_integration/SystematicAbsence.h"
 
@@ -46,7 +47,7 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
 
     const float epsilon = 1e-5f;
     const float s0_sq = S0 * S0;
-    const float rad_to_deg = 180.0f / static_cast<float>(M_PI);
+    const float rad_to_deg = 180.0f / static_cast<float>(PI);
 
     int i = 0;
 
diff --git a/image_analysis/bragg_prediction/BraggPredictionGPU.cu b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
index cf8f8cc6..04e4da64 100644
--- a/image_analysis/bragg_prediction/BraggPredictionGPU.cu
+++ b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "BraggPredictionGPU.h"
 
 #ifdef JFJOCH_USE_CUDA
@@ -16,7 +17,7 @@ namespace {
 
     __device__ inline float angle_from_ewald_sphere_deg(const Coord &S0, float recip_x, float recip_y, float recip_z, float recip_sq) {
         const float epsilon = 1e-5f;
-        const float rad_to_deg = 180.0f / static_cast<float>(M_PI);
+        const float rad_to_deg = 180.0f / static_cast<float>(PI);
 
         const float s0_sq = S0.x * S0.x + S0.y * S0.y + S0.z * S0.z;
         const float s0_p0 = S0.x * recip_x + S0.y * recip_y + S0.z * recip_z;
diff --git a/image_analysis/bragg_prediction/BraggPredictionRot.cpp b/image_analysis/bragg_prediction/BraggPredictionRot.cpp
index c349fe3d..1743736e 100644
--- a/image_analysis/bragg_prediction/BraggPredictionRot.cpp
+++ b/image_analysis/bragg_prediction/BraggPredictionRot.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "BraggPredictionRot.h"
 #include "../bragg_integration/SystematicAbsence.h"
 
@@ -46,8 +47,8 @@ int BraggPredictionRot::Calc(const DiffractionExperiment &experiment, const Crys
 
     int i = 0;
 
-    const float mos_angle_rad = settings.mosaicity_deg * static_cast<float>(M_PI) / 180.f;
-    const float half_wedge_angle_rad = settings.wedge_deg * static_cast<float>(M_PI) / 180.f / 2.0f ;
+    const float mos_angle_rad = settings.mosaicity_deg * static_cast<float>(PI) / 180.f;
+    const float half_wedge_angle_rad = settings.wedge_deg * static_cast<float>(PI) / 180.f / 2.0f ;
 
     for (int h = -settings.max_hkl; h <= settings.max_hkl; h++) {
         // Precompute A* h contribution
@@ -134,7 +135,7 @@ int BraggPredictionRot::Calc(const DiffractionExperiment &experiment, const Crys
                         .h = h,
                         .k = k,
                         .l = l,
-                        .delta_phi_deg = phi * 180.0f / static_cast<float>(M_PI),
+                        .delta_phi_deg = phi * 180.0f / static_cast<float>(PI),
                         .predicted_x = x,
                         .predicted_y = y,
                         .observed_x = NAN,
diff --git a/image_analysis/bragg_prediction/BraggPredictionRotGPU.cu b/image_analysis/bragg_prediction/BraggPredictionRotGPU.cu
index f86061f6..a06de212 100644
--- a/image_analysis/bragg_prediction/BraggPredictionRotGPU.cu
+++ b/image_analysis/bragg_prediction/BraggPredictionRotGPU.cu
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "BraggPredictionRotGPU.h"
 
 #ifdef JFJOCH_USE_CUDA
@@ -150,7 +151,7 @@ namespace {
             out[count].h = h;
             out[count].k = k;
             out[count].l = l;
-            out[count].delta_phi_deg = phi * 180.0 / M_PI;
+            out[count].delta_phi_deg = phi * 180.0 / PI;
             out[count].predicted_x = x;
             out[count].predicted_y = y;
             out[count].observed_x = NAN;
@@ -209,8 +210,8 @@ namespace {
          kc.one_over_wavelength = 1.0f / geom.GetWavelength_A();
 
          // Store mosaicity and wedge in radians for partiality calculation
-         kc.mos_angle_rad = settings.mosaicity_deg * static_cast<float>(M_PI) / 180.0f;
-         kc.wedge_angle_rad = settings.wedge_deg * static_cast<float>(M_PI) / 180.0f;
+         kc.mos_angle_rad = settings.mosaicity_deg * static_cast<float>(PI) / 180.0f;
+         kc.wedge_angle_rad = settings.wedge_deg * static_cast<float>(PI) / 180.0f;
          kc.min_zeta = settings.min_zeta;
          kc.mosaicity_multiplier = settings.mosaicity_multiplier;
 
diff --git a/image_analysis/geom_refinement/AssignSpotsToRings.cpp b/image_analysis/geom_refinement/AssignSpotsToRings.cpp
index c50d0ef0..01691ddd 100644
--- a/image_analysis/geom_refinement/AssignSpotsToRings.cpp
+++ b/image_analysis/geom_refinement/AssignSpotsToRings.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "AssignSpotsToRings.h"
 
 #include <vector>
@@ -163,7 +164,7 @@ std::vector<float> CalculateXtalRings(const UnitCell &cell, int hkl_max) {
             for (int l = 0; l <= hkl_max; l++) {
                 if (h == 0 && k == 0 && l == 0) continue;
                 auto p = Astar * h + Bstar * k + Cstar * l;
-                float Q = 2.0f * M_PI * p.Length();
+                float Q = 2.0f * PI * p.Length();
                 u.push_back(Q);
             }
         }
@@ -222,7 +223,7 @@ void GuessGeometry(DiffractionGeometry &geom,  const std::vector<SpotToSave> &v,
     std::vector<float> ring_q = CalculateXtalRings(calibrant_uc);
     if (ring_q.empty())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unit cell problem");
-    auto cluster_annot = GuessInitialGeometry(geom, v, 2 * M_PI / ring_q[0]);
+    auto cluster_annot = GuessInitialGeometry(geom, v, 2 * PI / ring_q[0]);
 
     std::vector<RingOptimizerInput> optimizer_input;
 
@@ -231,7 +232,7 @@ void GuessGeometry(DiffractionGeometry &geom,  const std::vector<SpotToSave> &v,
 
     while (cluster_idx < cluster_annot.size() && ring_idx < ring_q.size()) {
 
-        float obs_q = 2 * M_PI / geom.PxlToRes(cluster_annot[cluster_idx].R_obs);
+        float obs_q = 2 * PI / geom.PxlToRes(cluster_annot[cluster_idx].R_obs);
         if (std::fabs(ring_q[ring_idx] - obs_q) < 0.1) {
             std::cout << "Found ring " << ring_idx
                     << " with q_ring = " << ring_q[ring_idx]
@@ -263,7 +264,7 @@ void OptimizeGeometry(DiffractionGeometry &geom, const std::vector<SpotToSave> &
     std::vector<RingOptimizerInput> optimizer_input;
 
     for (const auto& s: v) {
-        float q_obs = 2 * M_PI / geom.PxlToRes(s.x, s.y);
+        float q_obs = 2 * PI / geom.PxlToRes(s.x, s.y);
         for (const auto &q : q_ring) {
             if (std::fabs(q - q_obs) < 0.1) {
                 optimizer_input.push_back({s.x, s.y, q});
diff --git a/image_analysis/geom_refinement/LatticeReduction.cpp b/image_analysis/geom_refinement/LatticeReduction.cpp
index 7da10261..d0cd4836 100644
--- a/image_analysis/geom_refinement/LatticeReduction.cpp
+++ b/image_analysis/geom_refinement/LatticeReduction.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "LatticeReduction.h"
 
 #include <Eigen/Dense>
@@ -251,7 +252,7 @@ CrystalLattice AngleAxisAndCellToLattice(const double rod[3],
 
 CrystalLattice AngleAxisAndLengthsToLattice(const double rod[3], const double lengths[3], bool hex) {
     return AngleAxisAndCellToLattice(rod, lengths,
-                                     /*alpha=*/M_PI / 2.0,
-                                     /*beta =*/M_PI / 2.0,
-                                     /*gamma=*/hex ? 2.0 * M_PI / 3.0 : M_PI / 2.0);
+                                     /*alpha=*/PI / 2.0,
+                                     /*beta =*/PI / 2.0,
+                                     /*gamma=*/hex ? 2.0 * PI / 3.0 : PI / 2.0);
 }
diff --git a/image_analysis/geom_refinement/RingOptimizer.cpp b/image_analysis/geom_refinement/RingOptimizer.cpp
index af214bf4..626f66f8 100644
--- a/image_analysis/geom_refinement/RingOptimizer.cpp
+++ b/image_analysis/geom_refinement/RingOptimizer.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "RingOptimizer.h"
 #include "ceres/ceres.h"
 
@@ -11,7 +12,7 @@ struct RingResidual {
             : obs_x(x), obs_y(y),
               lambda(lambda),
               pixel_size(pixel_size),
-              expected_len_recip_sq(expected_q * expected_q / (4.0 * M_PI * M_PI)) {}
+              expected_len_recip_sq(expected_q * expected_q / (4.0 * PI * PI)) {}
 
     template<typename T>
     bool operator()(const T* const center_x, const T* const center_y,
diff --git a/image_analysis/geom_refinement/XtalOptimizer.cpp b/image_analysis/geom_refinement/XtalOptimizer.cpp
index 03d5ce08..a4676450 100644
--- a/image_analysis/geom_refinement/XtalOptimizer.cpp
+++ b/image_analysis/geom_refinement/XtalOptimizer.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include <Eigen/Dense>
 
 #include "XtalOptimizer.h"
@@ -293,9 +294,9 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
                 // Triclinic: initialize a,b,c and α,β,γ from current unit cell
                 LatticeToRodriguesAndLengths_GS(data.latt, latt_vec0, latt_vec1);
                 auto uc = data.latt.GetUnitCell();
-                latt_vec2[0] = uc.alpha * M_PI / 180.0;
-                latt_vec2[1] = uc.beta * M_PI / 180.0;
-                latt_vec2[2] = uc.gamma * M_PI / 180.0;
+                latt_vec2[0] = uc.alpha * PI / 180.0;
+                latt_vec2[1] = uc.beta * PI / 180.0;
+                latt_vec2[2] = uc.gamma * PI / 180.0;
                 break;
         }
 
@@ -316,7 +317,7 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
 
             if (data.axis) {
                 const float angle_deg = data.axis->GetAngle_deg(i) + data.axis->GetWedge_deg() / 2.0;
-                angle_rad = angle_deg * M_PI / 180.0;
+                angle_rad = angle_deg * PI / 180.0;
                 rot_matr = data.axis->GetTransformationAngle(angle_deg);
             }
 
@@ -380,7 +381,7 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
         if (!data.refine_detector_angles) {
             problem.SetParameterBlockConstant(detector_rot);
         } else {
-            const double rot_range = 3.0 / 180.0 * M_PI;
+            const double rot_range = 3.0 / 180.0 * PI;
             for (int i = 0; i < 2; ++i) {
                 problem.SetParameterLowerBound(detector_rot, i, detector_rot[i] - rot_range);
                 problem.SetParameterUpperBound(detector_rot, i, detector_rot[i] + rot_range);
@@ -403,14 +404,14 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
             }
 
             if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
-                const double beta_lo = std::max(1e-6, M_PI * (data.min_angle_deg / 180.0));
-                const double beta_hi = std::min(M_PI - 1e-6, M_PI * (data.max_angle_deg / 180.0));
+                const double beta_lo = std::max(1e-6, PI * (data.min_angle_deg / 180.0));
+                const double beta_hi = std::min(PI - 1e-6, PI * (data.max_angle_deg / 180.0));
                 problem.SetParameterLowerBound(latt_vec2, 0, beta_lo);
                 problem.SetParameterUpperBound(latt_vec2, 0, beta_hi);
             } else if (data.crystal_system == gemmi::CrystalSystem::Triclinic) {
                 // α, β, γ bounds (radians)
-                const double alo = M_PI * (data.min_angle_deg / 180.0);
-                const double ahi = M_PI * (data.max_angle_deg / 180.0);
+                const double alo = PI * (data.min_angle_deg / 180.0);
+                const double ahi = PI * (data.max_angle_deg / 180.0);
                 for (int i = 0; i < 3; ++i) {
                     problem.SetParameterLowerBound(latt_vec2, i, alo);
                     problem.SetParameterUpperBound(latt_vec2, i, ahi);
@@ -450,19 +451,19 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
             data.axis.value().Axis(Coord(rot_vec[0], rot_vec[1], rot_vec[2]));
 
         if (data.crystal_system == gemmi::CrystalSystem::Orthorhombic)
-            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI / 2.0, M_PI / 2.0, M_PI / 2.0);
+            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
         else if (data.crystal_system == gemmi::CrystalSystem::Tetragonal) {
             latt_vec1[1] = latt_vec1[0];
-            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI / 2.0, M_PI / 2.0, M_PI / 2.0);
+            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
         } else if (data.crystal_system == gemmi::CrystalSystem::Cubic) {
             latt_vec1[1] = latt_vec1[0];
             latt_vec1[2] = latt_vec1[0];
-            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI / 2.0, M_PI / 2.0, M_PI / 2.0);
+            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
         } else if (data.crystal_system == gemmi::CrystalSystem::Hexagonal) {
             latt_vec1[1] = latt_vec1[0];
-            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,M_PI / 2.0, M_PI / 2.0, 2.0 * M_PI / 3.0);
+            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,PI / 2.0, PI / 2.0, 2.0 * PI / 3.0);
         } else if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
-            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, M_PI / 2.0, latt_vec2[0], M_PI / 2.0);
+            data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, latt_vec2[0], PI / 2.0);
         } else {
             // Triclinic via the same generic builder
             data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, latt_vec2[0], latt_vec2[1], latt_vec2[2]);
diff --git a/image_analysis/indexing/AnalyzeIndexing.cpp b/image_analysis/indexing/AnalyzeIndexing.cpp
index 2a11ffd1..5da8f709 100644
--- a/image_analysis/indexing/AnalyzeIndexing.cpp
+++ b/image_analysis/indexing/AnalyzeIndexing.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include <cstdint>
 #include <vector>
 #include <cmath>
@@ -20,11 +21,11 @@ namespace {
     }
 
     inline float deg_to_rad(float deg) {
-        return deg * (static_cast<float>(M_PI) / 180.0f);
+        return deg * (static_cast<float>(PI) / 180.0f);
     }
 
     inline float rad_to_deg(float rad) {
-        return rad * (180.0f / static_cast<float>(M_PI));
+        return rad * (180.0f / static_cast<float>(PI));
     }
 
     // Wrap to [-180, 180] (useful for residuals)
@@ -139,7 +140,7 @@ namespace {
         float s1 = phi_ref + delta;
         float s2 = phi_ref - delta;
 
-        const float two_pi = 2.0f * static_cast<float>(M_PI);
+        const float two_pi = 2.0f * static_cast<float>(PI);
         auto shift_near = [&](float x) {
             if (!std::isfinite(x))
                 return std::numeric_limits<float>::quiet_NaN();
@@ -153,9 +154,9 @@ namespace {
                 return std::numeric_limits<float>::quiet_NaN();
 
             // fmod can return negative values; normalize to [-π, π]
-            if (shifted < -static_cast<float>(M_PI))
+            if (shifted < -static_cast<float>(PI))
                 shifted += two_pi;
-            else if (shifted > static_cast<float>(M_PI))
+            else if (shifted > static_cast<float>(PI))
                 shifted -= two_pi;
 
             return shifted + span_center;
diff --git a/image_analysis/indexing/FFTIndexer.cpp b/image_analysis/indexing/FFTIndexer.cpp
index 2578d589..c5fbb0f9 100644
--- a/image_analysis/indexing/FFTIndexer.cpp
+++ b/image_analysis/indexing/FFTIndexer.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "FFTIndexer.h"
 #include <Eigen/Eigen>
 #include "PostIndexingRefinement.h"
@@ -23,7 +24,7 @@ FFTIndexer::FFTIndexer(const IndexingSettings &settings)
     // from when the extent was mistakenly written as 2*pi/d (the Q convention); it is kept
     // because the exact amount sets which marginal frames index - rounding it to a nearby
     // integer shifts the indexing rate ~0.5-1% (validated on the lyso datasets).
-    const float oversampling = 2.0f * static_cast<float>(M_PI);
+    const float oversampling = 2.0f * static_cast<float>(PI);
     const float one_over_d_max = 1.0f / settings.GetFFT_HighResolution_A();
 
     histogram_spacing = 1.0f / (2.0f * max_length_A);
@@ -52,7 +53,7 @@ void FFTIndexer::SetupDirectionVectors() {
     direction_vectors.reserve(static_cast<size_t>(nDirections));
 
     const double phi = (1.0 + std::sqrt(5.0)) / 2.0; // Golden ratio
-    const double golden_angle = 2.0 * M_PI / phi;
+    const double golden_angle = 2.0 * PI / phi;
 
     for (int i = 0; i < nDirections; i++) {
         // Half-sphere distribution (z in [0,1])
@@ -148,7 +149,7 @@ std::vector<Coord> FFTIndexer::FilterFFTResults() const {
     std::vector<Coord> ret;
 
     // Remove vectors less than 5 deg apart, as most likely these are colinear
-    const float COS_5_DEG = std::cos(5.0f * M_PI / 180.0f);
+    const float COS_5_DEG = std::cos(5.0f * PI / 180.0f);
 
     // Minimum relative amplitude to accept a shorter vector (fundamental)
     // over a longer one (harmonic).
diff --git a/image_analysis/indexing/PostIndexingRefinement.cpp b/image_analysis/indexing/PostIndexingRefinement.cpp
index 45960eca..75e21f58 100644
--- a/image_analysis/indexing/PostIndexingRefinement.cpp
+++ b/image_analysis/indexing/PostIndexingRefinement.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "PostIndexingRefinement.h"
 
 #include <iostream>
@@ -175,9 +176,9 @@ std::vector<CrystalLattice> Refine(const std::vector<Coord> &in_spots,
         }
 
         // Filter for wrong angles
-        float alpha = std::acos(cell_rows.row(1).normalized().dot(cell_rows.row(2).normalized())) * 180.0f / M_PI;
-        float beta = std::acos(cell_rows.row(0).normalized().dot(cell_rows.row(2).normalized())) * 180.0f / M_PI;
-        float gamma = std::acos(cell_rows.row(0).normalized().dot(cell_rows.row(1).normalized())) * 180.0f / M_PI;
+        float alpha = std::acos(cell_rows.row(1).normalized().dot(cell_rows.row(2).normalized())) * 180.0f / PI;
+        float beta = std::acos(cell_rows.row(0).normalized().dot(cell_rows.row(2).normalized())) * 180.0f / PI;
+        float gamma = std::acos(cell_rows.row(0).normalized().dot(cell_rows.row(1).normalized())) * 180.0f / PI;
 
         if (alpha < p.min_angle_deg || alpha > p.max_angle_deg ||
             beta < p.min_angle_deg || beta > p.max_angle_deg ||
diff --git a/image_analysis/lattice_search/LatticeSearch.cpp b/image_analysis/lattice_search/LatticeSearch.cpp
index c2257a68..1648338a 100644
--- a/image_analysis/lattice_search/LatticeSearch.cpp
+++ b/image_analysis/lattice_search/LatticeSearch.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "LatticeSearch.h"
 #include <gemmi/cellred.hpp>
 
@@ -315,9 +316,9 @@ LatticeSearchResult LatticeSearch(const CrystalLattice &L, double dist_tolerance
         if (c.cond_BC && fabs((uc_reduced.b - uc_reduced.c) / (0.5 * (uc_reduced.b + uc_reduced.c))) > dist_tolerance)
             ok = false;
 
-        double expected_alpha = acos(c.cond_D / sqrt(B*C)) * 180 / M_PI;
-        double expected_beta = acos(c.cond_E / sqrt(A*C)) * 180 / M_PI;
-        double expected_gamma = acos(c.cond_F / sqrt(A*B)) * 180 / M_PI;
+        double expected_alpha = acos(c.cond_D / sqrt(B*C)) * 180 / PI;
+        double expected_beta = acos(c.cond_E / sqrt(A*C)) * 180 / PI;
+        double expected_gamma = acos(c.cond_F / sqrt(A*B)) * 180 / PI;
 
         if (fabs(expected_alpha - uc_reduced.alpha) > angle_tolerance)
             ok = false;
diff --git a/image_analysis/pixel_refinement/PixelRefine.cpp b/image_analysis/pixel_refinement/PixelRefine.cpp
index b9014d82..59d92de2 100644
--- a/image_analysis/pixel_refinement/PixelRefine.cpp
+++ b/image_analysis/pixel_refinement/PixelRefine.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "PixelRefine.h"
 
 #include <algorithm>
@@ -499,7 +500,7 @@ void PixelRefine::Run(const T *image,
                                beam, dist_mm, detector_rot, latt_vec0, latt_vec1, latt_vec2,
                                q_sq, eps_r, eps_t_sq))
                 continue;
-            const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
+            const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (PI * R1 * R1);
             const double R0_eff_sq = R0 * R0 + g.R_bw_sq;
             const double P_rad = std::exp(-eps_r * eps_r / R0_eff_sq);
             const double v = std::max(g.Ibkg, 1.0);
@@ -597,7 +598,7 @@ void PixelRefine::Run(const T *image,
                 // Tangential profile shape (area-normalized) -> the fit template, using the
                 // per-reflection R1_eff (Term 2).
                 const double R1 = g.R1_eff;
-                const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (M_PI * R1 * R1);
+                const double P_t = std::exp(-eps_t_sq / (R1 * R1)) / (PI * R1 * R1);
                 prof_full += P_t; // whole shoebox, on- or off-detector
 
                 // Only real, unmasked detector pixels carry signal.
diff --git a/image_analysis/rotation_indexer/RotationIndexer.cpp b/image_analysis/rotation_indexer/RotationIndexer.cpp
index f004959a..66f0dc98 100644
--- a/image_analysis/rotation_indexer/RotationIndexer.cpp
+++ b/image_analysis/rotation_indexer/RotationIndexer.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "RotationIndexer.h"
 
 #include "../geom_refinement/XtalOptimizer.h"
@@ -84,7 +85,7 @@ void RotationIndexer::RunIndexing() {
                     break;
 
                 // Ignore lattices oriented by less than 3.0 degree
-                if (l.rotation_vector.Length() < 3.0 * M_PI / 180.0)
+                if (l.rotation_vector.Length() < 3.0 * PI / 180.0)
                     continue;
 
                 RotMatrix rot(l.rotation_vector.Length(), l.rotation_vector.Normalize());
diff --git a/image_analysis/spot_finding/SpotUtils.cpp b/image_analysis/spot_finding/SpotUtils.cpp
index 1605b0f1..8dcf3254 100644
--- a/image_analysis/spot_finding/SpotUtils.cpp
+++ b/image_analysis/spot_finding/SpotUtils.cpp
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "../../common/JFJochMath.h"
 #include "SpotUtils.h"
 #include "../../common/ResolutionShells.h"
 
@@ -25,10 +26,10 @@ void MarkIceRings(std::vector<SpotToSave> &spots, float tolerance_q_recipA) {
     std::vector<float> ice_rings_q;
 
     for (const auto &i: ICE_RING_RES_A)
-        ice_rings_q.push_back(2 * M_PI / i);
+        ice_rings_q.push_back(2 * PI / i);
 
     for (auto &s: spots) {
-        auto spot_q = 2 * M_PI / s.d_A;
+        auto spot_q = 2 * PI / s.d_A;
         bool tmp = false;
         for (const auto &q: ice_rings_q)
             tmp |= (fabs(spot_q - q) < tolerance_q_recipA);
@@ -65,8 +66,8 @@ void FilterSpuriousHighResolutionSpots(std::vector<SpotToSave> &spots, float thr
             // Avoid division by zero; d_A should be > 0 in valid data
             if (d1 <= 0.0f || d2 <= 0.0f)
                 continue;
-            float q1 = 2 * M_PI / d1;
-            float q2 = 2 * M_PI / d2;
+            float q1 = 2 * PI / d1;
+            float q2 = 2 * PI / d2;
             float dq = q2 - q1; // should be >= 0 due to sorting
             if (dq > threshold) {
                 cut_index = i + 1; // keep up to i inclusive
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 67496478..f6aaedef 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -3,7 +3,7 @@
 
 #include <cerrno>
 #include <cstring>
-#include <numbers>
+#include "../common/JFJochMath.h"
 #ifndef _WIN32
 #include <sys/stat.h>
 #include <fcntl.h>
@@ -539,7 +539,7 @@ void JFJochImageReadingWorker::FindCenter(const UnitCell& calibrant, bool guess)
 
     QVector<float> rings;
     for (int i = 0; i < 15 && i < ring_Q.size(); i++) {
-        rings.push_back(2 * std::numbers::pi / ring_Q[i]);
+        rings.push_back(2 * PI / ring_Q[i]);
     }
     emit setRings(rings);
 }
diff --git a/viewer/image_viewer/JFJochAzIntImage.cpp b/viewer/image_viewer/JFJochAzIntImage.cpp
index 74c86733..4588de53 100644
--- a/viewer/image_viewer/JFJochAzIntImage.cpp
+++ b/viewer/image_viewer/JFJochAzIntImage.cpp
@@ -5,7 +5,7 @@
 #include <QVBoxLayout>
 
 #include "../../common/JFJochException.h"
-#include <numbers>
+#include "../../common/JFJochMath.h"
 
 JFJochAzIntImage::JFJochAzIntImage(QWidget *parent)
     : JFJochImage(parent) {
@@ -110,7 +110,7 @@ void JFJochAzIntImage::mouseDoubleClickEvent(QMouseEvent *event) {
         float phi = image->Dataset().az_int_bin_to_phi[idx];
 
         auto geom = image->Dataset().experiment.GetDiffractionGeometry();
-        auto coord = geom.ResPhiToPxl(2 * std::numbers::pi / q, phi / 180.0 * std::numbers::pi);
+        auto coord = geom.ResPhiToPxl(2 * PI / q, phi / 180.0 * PI);
         emit zoomOnBin(QPointF(coord.first, coord.second));
     }
 }
\ No newline at end of file
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 51dde0f3..9b744348 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -3,7 +3,7 @@
 
 #include "JFJochDiffractionImage.h"
 #include "../../common/DiffractionGeometry.h"
-#include <numbers>
+#include "../../common/JFJochMath.h"
 
 #include <QGraphicsPixmapItem>
 #include <QGraphicsSimpleTextItem>
@@ -240,9 +240,9 @@ void JFJochDiffractionImage::DrawResolutionRings() {
             continue;
 
         auto [x1,y1] = geom.ResPhiToPxl(d, 0);
-        auto [x2,y2] = geom.ResPhiToPxl(d, std::numbers::pi / 2);
-        auto [x3,y3] = geom.ResPhiToPxl(d, std::numbers::pi);
-        auto [x4,y4] = geom.ResPhiToPxl(d, 3.0 * std::numbers::pi / 2);
+        auto [x2,y2] = geom.ResPhiToPxl(d, PI / 2);
+        auto [x3,y3] = geom.ResPhiToPxl(d, PI);
+        auto [x4,y4] = geom.ResPhiToPxl(d, 3.0 * PI / 2);
 
         auto x_min = std::min({x1, x2, x3, x4});
         auto x_max = std::max({x1, x2, x3, x4});
@@ -253,9 +253,9 @@ void JFJochDiffractionImage::DrawResolutionRings() {
         addOverlayItem(scene()->addEllipse(boundingRect, pen));
 
         auto [x5,y5] = geom.ResPhiToPxl(d, phi_offset + 0);
-        auto [x6,y6] = geom.ResPhiToPxl(d, phi_offset + std::numbers::pi / 2);
-        auto [x7,y7] = geom.ResPhiToPxl(d, phi_offset + std::numbers::pi);
-        auto [x8,y8] = geom.ResPhiToPxl(d, phi_offset + 3.0 * std::numbers::pi / 2);
+        auto [x6,y6] = geom.ResPhiToPxl(d, phi_offset + PI / 2);
+        auto [x7,y7] = geom.ResPhiToPxl(d, phi_offset + PI);
+        auto [x8,y8] = geom.ResPhiToPxl(d, phi_offset + 3.0 * PI / 2);
 
         QPointF point_1(x5, y5);
         QPointF point_2(x6, y6);
@@ -286,7 +286,7 @@ void JFJochDiffractionImage::DrawResolutionRings() {
             scene()->addItem(textItem);
             addOverlayItem(textItem);
         }
-        phi_offset += 4.0 / 180.0 * std::numbers::pi;
+        phi_offset += 4.0 / 180.0 * PI;
     }
 }
 
diff --git a/viewer/widgets/PowderCalibrationWidget.cpp b/viewer/widgets/PowderCalibrationWidget.cpp
index b7a78076..286f3c8a 100644
--- a/viewer/widgets/PowderCalibrationWidget.cpp
+++ b/viewer/widgets/PowderCalibrationWidget.cpp
@@ -5,7 +5,7 @@
 #include <QPushButton>
 #include <QGridLayout>
 #include <QLabel>
-#include <numbers>
+#include "../../common/JFJochMath.h"
 
 #include "../image_analysis/geom_refinement/AssignSpotsToRings.h"
 
@@ -26,7 +26,7 @@ PowderCalibrationWidget::PowderCalibrationWidget(QWidget *parent) : QWidget(pare
         std::vector<float> rings = CalculateXtalRings(GetCalibrant(), 10);
         QVector<float> q_rings;
         for (float ring : rings) {
-            q_rings.append(2 * std::numbers::pi / ring);
+            q_rings.append(2 * PI / ring);
         }
         emit ringsFromCalibration(q_rings);
     });
diff --git a/viewer/windows/JFJochViewerMetadataWindow.cpp b/viewer/windows/JFJochViewerMetadataWindow.cpp
index 97db7e02..47f214ad 100644
--- a/viewer/windows/JFJochViewerMetadataWindow.cpp
+++ b/viewer/windows/JFJochViewerMetadataWindow.cpp
@@ -10,7 +10,7 @@
 #include <QMessageBox>
 
 #include "JFJochViewerMetadataWindow.h"
-#include <numbers>
+#include "../../common/JFJochMath.h"
 
 JFJochViewerMetadataWindow::JFJochViewerMetadataWindow(QWidget *parent) : JFJochHelperWindow(parent) {
 
@@ -136,8 +136,8 @@ void JFJochViewerMetadataWindow::datasetUpdate() {
             tmp.BeamX_pxl(beam_center_x->value());
             tmp.BeamY_pxl(beam_center_y->value());
             tmp.IncidentEnergy_keV(WVL_1A_IN_KEV / wavelength_A->value());
-            tmp.PoniRot1_rad(poni_rot1_deg->value() * std::numbers::pi / 180.0);
-            tmp.PoniRot2_rad(poni_rot2_deg->value() * std::numbers::pi / 180.0);
+            tmp.PoniRot1_rad(poni_rot1_deg->value() * PI / 180.0);
+            tmp.PoniRot2_rad(poni_rot2_deg->value() * PI / 180.0);
             tmp.DetectIceRings(detect_ice_rings->isChecked());
 
             if (unit_cell_enabled->isChecked()) {
@@ -177,8 +177,8 @@ void JFJochViewerMetadataWindow::datasetLoaded(std::shared_ptr<const JFJochReade
     beam_center_x->setValue(dataset->experiment.GetBeamX_pxl());
     beam_center_y->setValue(dataset->experiment.GetBeamY_pxl());
     wavelength_A->setValue(dataset->experiment.GetWavelength_A());
-    poni_rot1_deg->setValue(dataset->experiment.GetPoniRot1_rad() * 180.0 / std::numbers::pi);
-    poni_rot2_deg->setValue(dataset->experiment.GetPoniRot2_rad() * 180.0 / std::numbers::pi);
+    poni_rot1_deg->setValue(dataset->experiment.GetPoniRot1_rad() * 180.0 / PI);
+    poni_rot2_deg->setValue(dataset->experiment.GetPoniRot2_rad() * 180.0 / PI);
     detect_ice_rings->setChecked(dataset->experiment.IsDetectIceRings());
 
     auto unit_cell = dataset->experiment.GetUnitCell();
-- 
2.52.0


From bee35f7a25ce170c6bb1f83e81c51d57f2151a08 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 15:02:39 +0200
Subject: [PATCH 085/228] frame_serialize: write CBOR length big-endian without
 bswap intrinsic

AppendImage wrote the CBOR byte-string length (major type 2, 8-byte length,
which is defined big-endian) via __builtin_bswap64 under #ifdef LITTLE_ENDIAN.
That is broken two ways off GCC/Clang+glibc: __builtin_bswap64 is not available
on MSVC, and LITTLE_ENDIAN is not defined there, so the #else path skipped the
swap and emitted a little-endian length on a little-endian host -> corrupt
frames.

Write the 8 length bytes most-significant-first directly. This is big-endian by
construction on any host, needs no byte-swap intrinsic and no endianness macro,
and is byte-for-byte identical to the previous output on little-endian hosts.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frame_serialize/CBORStream2Serializer.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index a79370f1..dee8591f 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -917,12 +917,13 @@ void CBORStream2Serializer::AppendImage(size_t image_size) {
 
     buffer[curr_size - 2] = 0x40 + 27;
     curr_size--;
-#ifdef LITTLE_ENDIAN
-    size_t image_size_be = __builtin_bswap64(image_size);
-#else
-    size_t image_size_be = image_size;
-#endif
-    memcpy(buffer + curr_size, &image_size_be, sizeof(size_t));
+    // CBOR encodes the byte-string length as a big-endian 64-bit integer (major
+    // type 2, additional info 27). Write it big-endian byte-by-byte so the result
+    // is correct on any host endianness and needs no compiler-specific byte-swap
+    // intrinsic (__builtin_bswap64 is GCC/Clang-only; MSVC lacks it).
+    const uint64_t image_size_be = image_size;
+    for (size_t k = 0; k < sizeof(uint64_t); ++k)
+        buffer[curr_size + k] = static_cast<uint8_t>(image_size_be >> (8 * (sizeof(uint64_t) - 1 - k)));
     curr_size += sizeof(size_t);
     curr_size += image_size + 0;
     buffer[curr_size] = 0xFF;
-- 
2.52.0


From 57ae1455553a12985436ff52c625e5303266f65b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 15:02:39 +0200
Subject: [PATCH 086/228] writer: drop unused <sys/stat.h> include from
 HDF5DataFile

Nothing in HDF5DataFile.cpp uses sys/stat.h (no stat/mkdir/S_* etc.); it relies
on <filesystem>. Removing the dead POSIX include also avoids a needless
non-portable header for the eventual MSVC build.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 writer/HDF5DataFile.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/writer/HDF5DataFile.cpp b/writer/HDF5DataFile.cpp
index bee8b278..378b1ca3 100644
--- a/writer/HDF5DataFile.cpp
+++ b/writer/HDF5DataFile.cpp
@@ -1,7 +1,6 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#include <sys/stat.h>
 #include <filesystem>
 #include <iostream>
 
-- 
2.52.0


From 0f5271f14c196a5bee7d75b745fae35bf10f05c6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 16:05:04 +0200
Subject: [PATCH 087/228] mask: accept any-bit-depth TIFF for user mask upload

PUT /config/user_mask.tiff only accepted 32-bit unsigned TIFF, so masks
exported by tools like PyFAI (8-bit) failed. Route the upload through the
universal ReadTIFF reader and let PixelMask take a CompressedImage directly:
it validates the 2D shape against the detector's converted/raw layouts,
binarizes any 8/16/32-bit integer image (non-zero == masked), and rejects
float/multi-channel images.

Also dedupe the TIFF readers: ReadTIFFFromString16 is now a thin wrapper over
ReadTIFF, and the now-unused ReadTIFFFromString32 is removed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/JFJochBrokerHttp.cpp   |  5 +--
 broker/JFJochStateMachine.cpp | 15 +++++++
 broker/JFJochStateMachine.h   |  1 +
 broker/jfjoch_api.yaml        |  6 ++-
 common/PixelMask.cpp          | 49 +++++++++++++++++++++++
 common/PixelMask.h            |  2 +
 preview/JFJochTIFF.cpp        | 75 ++++-------------------------------
 preview/JFJochTIFF.h          |  1 -
 tests/PixelMaskTest.cpp       | 38 ++++++++++++++++++
 tests/TIFFTest.cpp            | 55 ++++++++++++++++++++-----
 10 files changed, 165 insertions(+), 82 deletions(-)

diff --git a/broker/JFJochBrokerHttp.cpp b/broker/JFJochBrokerHttp.cpp
index 8166fb87..bf46c6a9 100644
--- a/broker/JFJochBrokerHttp.cpp
+++ b/broker/JFJochBrokerHttp.cpp
@@ -743,9 +743,8 @@ void JFJochBrokerHttp::config_user_mask_tiff_get(httplib::Response &response) {
 
 void JFJochBrokerHttp::config_user_mask_tiff_put(const httplib::Request &request,
                                                  httplib::Response &response) {
-    uint32_t cols, lines;
-    auto v = ReadTIFFFromString32(request.body, cols, lines);
-    state_machine.SetUserPixelMask(v);
+    std::vector<uint8_t> buffer;
+    state_machine.SetUserPixelMask(ReadTIFF(request.body, buffer));
     response.status = 200;
 }
 
diff --git a/broker/JFJochStateMachine.cpp b/broker/JFJochStateMachine.cpp
index 10e4193b..b2daa353 100644
--- a/broker/JFJochStateMachine.cpp
+++ b/broker/JFJochStateMachine.cpp
@@ -903,6 +903,21 @@ void JFJochStateMachine::SetUserPixelMask(const std::vector<uint32_t> &v) {
     }
 }
 
+void JFJochStateMachine::SetUserPixelMask(const CompressedImage &image) {
+    std::unique_lock ul(m);
+
+    if (state != JFJochState::Idle)
+        throw WrongDAQStateException("User mask can be only modified in Idle state");
+
+    try {
+        pixel_mask.LoadUserMask(experiment, image);
+        UpdatePixelMaskStatistics(pixel_mask.GetStatistics());
+    } catch (const JFJochException &e) {
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Problem handling user mask " + std::string(e.what()));
+    }
+}
+
 InstrumentMetadata JFJochStateMachine::GetInstrumentMetadata() const {
     std::unique_lock ul(experiment_instrument_metadata_mutex);
     return experiment.GetInstrumentMetadata();
diff --git a/broker/JFJochStateMachine.h b/broker/JFJochStateMachine.h
index 1d5fb56a..aff240c6 100644
--- a/broker/JFJochStateMachine.h
+++ b/broker/JFJochStateMachine.h
@@ -220,6 +220,7 @@ public:
     std::vector<uint32_t> GetUserPixelMask() const;
 
     void SetUserPixelMask(const std::vector<uint32_t> &v);
+    void SetUserPixelMask(const CompressedImage &image);
 
     std::vector<DeviceStatus> GetDeviceStatus() const;
 
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 1a44430a..8096f853 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -3244,9 +3244,9 @@ paths:
         Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
         If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
         In the latter case - module gaps are ignored and don't need to be assigned value.
-        Mask is expected as TIFF (4-byte; unsigned).
+        Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
         0 - good pixel, other value - masked
-        User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. 
+        User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
         User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
       requestBody:
         content:
@@ -3257,6 +3257,8 @@ paths:
       responses:
         "200":
           description: All good
+        "400":
+          description: Not a valid single-channel TIFF or size doesn't match the detector
         "500":
           description: Error within Jungfraujoch code - see output message.
           content:
diff --git a/common/PixelMask.cpp b/common/PixelMask.cpp
index c25aec66..2b2dfd81 100644
--- a/common/PixelMask.cpp
+++ b/common/PixelMask.cpp
@@ -218,6 +218,55 @@ void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const std:
                               "Size of input user mask invalid");
 }
 
+void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const CompressedImage& image) {
+    const size_t width = image.GetWidth();
+    const size_t height = image.GetHeight();
+
+    // The image has to match one of the two layouts handled by the vector
+    // overload below: converted geometry, or raw stacked modules.
+    const bool converted = (width == static_cast<size_t>(experiment.GetXPixelsNumConv()))
+                           && (height == static_cast<size_t>(experiment.GetYPixelsNumConv()));
+    const bool raw = (width == static_cast<size_t>(RAW_MODULE_COLS))
+                     && (height == static_cast<size_t>(RAW_MODULE_LINES * experiment.GetModulesNum()));
+    if (!converted && !raw)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "User mask image size doesn't match the detector");
+
+    std::vector<uint8_t> buffer;
+    const uint8_t *bytes = image.GetUncompressedPtr(buffer);
+
+    // A pixel is masked when its value is non-zero. Read each pixel as an
+    // unsigned integer of the matching width - the sign is irrelevant when
+    // comparing against zero.
+    std::vector<uint32_t> mask(width * height);
+    auto binarize = [&](auto sample) {
+        using sample_t = decltype(sample);
+        const auto *typed = reinterpret_cast<const sample_t *>(bytes);
+        for (size_t i = 0; i < mask.size(); i++)
+            mask[i] = (typed[i] != 0) ? 1 : 0;
+    };
+
+    switch (image.GetMode()) {
+        case CompressedImageMode::Uint8:
+        case CompressedImageMode::Int8:
+            binarize(uint8_t{});
+            break;
+        case CompressedImageMode::Uint16:
+        case CompressedImageMode::Int16:
+            binarize(uint16_t{});
+            break;
+        case CompressedImageMode::Uint32:
+        case CompressedImageMode::Int32:
+            binarize(uint32_t{});
+            break;
+        default:
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "User mask must be an 8-, 16- or 32-bit integer image");
+    }
+
+    LoadUserMask(experiment, mask);
+}
+
 void PixelMask::LoadDECTRISBadPixelMask(const std::vector<uint32_t> &input_mask)  {
     if (input_mask.size() != mask.size())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
diff --git a/common/PixelMask.h b/common/PixelMask.h
index 5f9ae7c7..f151c4d1 100644
--- a/common/PixelMask.h
+++ b/common/PixelMask.h
@@ -3,6 +3,7 @@
 
 #pragma once
 
+#include "CompressedImage.h"
 #include "DetectorSetup.h"
 #include "DiffractionExperiment.h"
 #include "../jungfrau/JFCalibration.h"
@@ -41,6 +42,7 @@ public:
 
     void CalcEdgePixels(const DiffractionExperiment& experiment);
     void LoadUserMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
+    void LoadUserMask(const DiffractionExperiment& experiment, const CompressedImage& image);
     void LoadDECTRISBadPixelMask(const std::vector<uint32_t>& mask);
     void LoadDarkBadPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
     void LoadDetectorBadPixelMask(const DiffractionExperiment& experiment, const JFCalibration *calib);
diff --git a/preview/JFJochTIFF.cpp b/preview/JFJochTIFF.cpp
index 25c4f8ed..25369b3b 100644
--- a/preview/JFJochTIFF.cpp
+++ b/preview/JFJochTIFF.cpp
@@ -3,6 +3,7 @@
 
 #include <tiffio.h>
 #include <tiffio.hxx>
+#include <cstring>
 #include <sstream>
 
 #include "JFJochTIFF.h"
@@ -144,78 +145,18 @@ CompressedImage ReadTIFF(const std::string &s, std::vector<uint8_t> &buffer) {
     return CompressedImage(buffer, cols, lines, mode);
 }
 
-std::vector<uint32_t> ReadTIFFFromString32(const std::string &s, uint32_t &cols, uint32_t &lines) {
-    if (s.empty())
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "No TIFF file provided");
-
-    uint32_t rows_per_string = 0;
-
-    std::vector<uint32_t> ret;
-
-    uint16_t elem_size;
-
-    std::istringstream input_TIFF_stream(s);
-    TIFF* tiff = TIFFStreamOpen("MemTIFF", &input_TIFF_stream);
-    if (tiff == nullptr)
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError,"Not a proper TIFF file");
-
-    TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &cols);  // get the width of the image
-    TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &lines);    // get the height of the image
-    TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &elem_size);    // get the size of the channels
-    TIFFGetField(tiff, TIFFTAG_ROWSPERSTRIP, &rows_per_string);
-
-    if (elem_size != 32)
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "Only 32-bit format supported");
-
-    ret.resize(cols * lines);
-
-    if (cols * sizeof(uint32_t) != TIFFScanlineSize(tiff))
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFScanlineSize mismatch");
-
-    for (int i = 0; i < lines; i++) {
-        if (TIFFReadScanline(tiff, ret.data() + i * cols, i, 0) < 0)
-            throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFReadScanline error");
-    }
-
-    TIFFClose(tiff);
-    return ret;
-}
-
 std::vector<uint16_t> ReadTIFFFromString16(const std::string &s, uint32_t &cols, uint32_t &lines) {
-    if (s.empty())
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "No TIFF file provided");
+    std::vector<uint8_t> buffer;
+    CompressedImage image = ReadTIFF(s, buffer);
 
-    uint32_t rows_per_string = 0;
-
-    std::vector<uint16_t> ret;
-
-    uint16_t elem_size;
-
-    std::istringstream input_TIFF_stream(s);
-    TIFF* tiff = TIFFStreamOpen("MemTIFF", &input_TIFF_stream);
-    if (tiff == nullptr)
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError,
-            "TIFF format error");
-
-    TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &cols);  // get the width of the image
-    TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &lines);    // get the height of the image
-    TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &elem_size);    // get the size of the channels
-    TIFFGetField(tiff, TIFFTAG_ROWSPERSTRIP, &rows_per_string);
-
-    if (elem_size != 16)
+    if (image.GetByteDepth() != sizeof(uint16_t) || image.GetNumChannels() != 1)
         throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "Only 16-bit format supported");
 
-    ret.resize(cols * lines);
+    cols = image.GetWidth();
+    lines = image.GetHeight();
 
-    if (cols * sizeof(uint16_t) != TIFFScanlineSize(tiff))
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFScanlineSize mismatch");
-
-    for (int i = 0; i < lines; i++) {
-        if (TIFFReadScanline(tiff, ret.data() + i * cols, i, 0) < 0)
-            throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFReadScanline error");
-    }
-
-    TIFFClose(tiff);
+    std::vector<uint16_t> ret(static_cast<size_t>(cols) * lines);
+    memcpy(ret.data(), buffer.data(), buffer.size());
     return ret;
 }
 
diff --git a/preview/JFJochTIFF.h b/preview/JFJochTIFF.h
index ec0dbc10..12db8758 100644
--- a/preview/JFJochTIFF.h
+++ b/preview/JFJochTIFF.h
@@ -12,7 +12,6 @@ void WriteTIFFToFile(const std::string &filename, const CompressedImage& image);
 
 CompressedImage ReadTIFF(const std::string &s, std::vector<uint8_t> &buffer);
 
-std::vector<uint32_t> ReadTIFFFromString32(const std::string& s, uint32_t &cols, uint32_t &lines);
 std::vector<uint16_t> ReadTIFFFromString16(const std::string& s, uint32_t &cols, uint32_t &lines);
 
 void SuppressTIFFErrors();
diff --git a/tests/PixelMaskTest.cpp b/tests/PixelMaskTest.cpp
index 361c35d0..d8342eca 100644
--- a/tests/PixelMaskTest.cpp
+++ b/tests/PixelMaskTest.cpp
@@ -306,6 +306,44 @@ TEST_CASE("PixelMask_LoadUserMaskRaw_UpdatesCachedRawMask", "[PixelMask]") {
     CHECK((raw_mask_out[0] & (1u << PixelMask::ModuleEdgePixelBit)) != 0);
 }
 
+TEST_CASE("PixelMask_LoadUserMask_CompressedImage","[PixelMask]") {
+    DiffractionExperiment experiment(DetJF(4, 1, 8, 36, false));
+    experiment.MaskModuleEdges(false).MaskChipEdges(false);
+
+    const uint32_t cols = experiment.GetXPixelsNumConv();
+    const uint32_t lines = experiment.GetYPixelsNumConv();
+
+    // 8-bit single-channel mask, as e.g. PyFAI produces; non-zero == masked
+    std::vector<uint8_t> values(static_cast<size_t>(cols) * lines, 0);
+    values[1030 * 700 + 300] = 255;
+    CompressedImage image(values, cols, lines, CompressedImageMode::Uint8);
+
+    PixelMask mask(experiment);
+    REQUIRE_NOTHROW(mask.LoadUserMask(experiment, image));
+
+    REQUIRE(mask.GetMask()[1030 * 700 + 300] == (1 << PixelMask::UserMaskedPixelBit));
+    REQUIRE(mask.GetUserMask()[1030 * 700 + 300] == 1);
+    REQUIRE(mask.GetStatistics().user_mask == 1);
+
+    // 32-bit mask goes through the same path
+    std::vector<uint32_t> values32(static_cast<size_t>(cols) * lines, 0);
+    values32[1030 * 700 + 300] = 7;
+    CompressedImage image32(values32, cols, lines);
+    PixelMask mask32(experiment);
+    REQUIRE_NOTHROW(mask32.LoadUserMask(experiment, image32));
+    REQUIRE(mask32.GetUserMask()[1030 * 700 + 300] == 1);
+
+    // Float images are rejected outright
+    std::vector<float> valuesf(static_cast<size_t>(cols) * lines, 0.0f);
+    CompressedImage imagef(valuesf, cols, lines);
+    REQUIRE_THROWS(mask.LoadUserMask(experiment, imagef));
+
+    // Image whose shape doesn't match the detector is rejected
+    std::vector<uint8_t> wrong(static_cast<size_t>(cols) * (lines + 1), 0);
+    CompressedImage bad(wrong, cols, lines + 1, CompressedImageMode::Uint8);
+    REQUIRE_THROWS(mask.LoadUserMask(experiment, bad));
+}
+
 TEST_CASE("PixelMask_GetMaskRaw_ThrowsForDECTRIS", "[PixelMask]") {
     DiffractionExperiment experiment(DetDECTRIS(2068, 2164, "Test", ""));
     PixelMask mask(experiment);
diff --git a/tests/TIFFTest.cpp b/tests/TIFFTest.cpp
index 4c44ea24..df5e13b5 100644
--- a/tests/TIFFTest.cpp
+++ b/tests/TIFFTest.cpp
@@ -18,22 +18,59 @@ TEST_CASE("TIFFTest","[TIFF]") {
 }
 
 TEST_CASE("TIFFTest_Write_Read","[TIFF]") {
-    std::vector<uint32_t> values(512*1024), values_out;
-    for (int i = 0; i < values.size(); i++) {
+    std::vector<uint32_t> values(512*1024);
+    for (int i = 0; i < values.size(); i++)
         values[i] = (i * 17 + 2);
-    }
 
     CompressedImage image(values, 1024, 512);
 
     std::string s;
     REQUIRE_NOTHROW(s = WriteTIFFToString(image));
-    uint32_t lines, cols;
 
-    REQUIRE_NOTHROW(values_out = ReadTIFFFromString32(s, cols, lines));
-    REQUIRE(lines == 512);
-    REQUIRE(cols == 1024);
-    REQUIRE(values.size() == values_out.size());
-    REQUIRE(memcmp(values.data(), values_out.data(), cols * lines * sizeof(uint32_t)) == 0);
+    std::vector<uint8_t> buffer;
+    CompressedImage out = ReadTIFF(s, buffer);
+    REQUIRE(out.GetMode() == CompressedImageMode::Uint32);
+    REQUIRE(out.GetWidth() == 1024);
+    REQUIRE(out.GetHeight() == 512);
+    REQUIRE(buffer.size() == values.size() * sizeof(uint32_t));
+    REQUIRE(memcmp(values.data(), buffer.data(), buffer.size()) == 0);
+}
+
+TEST_CASE("TIFFTest_Write_Read_8bit","[TIFF]") {
+    std::vector<uint8_t> values(512*1024);
+    for (int i = 0; i < values.size(); i++)
+        values[i] = static_cast<uint8_t>(i * 17 + 2);
+
+    CompressedImage image(values, 1024, 512, CompressedImageMode::Uint8);
+
+    std::string s;
+    REQUIRE_NOTHROW(s = WriteTIFFToString(image));
+
+    std::vector<uint8_t> buffer;
+    CompressedImage out = ReadTIFF(s, buffer);
+    REQUIRE(out.GetMode() == CompressedImageMode::Uint8);
+    REQUIRE(out.GetWidth() == 1024);
+    REQUIRE(out.GetHeight() == 512);
+    REQUIRE(buffer == values);
+}
+
+TEST_CASE("TIFFTest_Write_Read_16bit","[TIFF]") {
+    std::vector<uint16_t> values(512*1024);
+    for (int i = 0; i < values.size(); i++)
+        values[i] = static_cast<uint16_t>(i * 17 + 2);
+
+    CompressedImage image(values, 1024, 512);
+
+    std::string s;
+    REQUIRE_NOTHROW(s = WriteTIFFToString(image));
+
+    std::vector<uint8_t> buffer;
+    CompressedImage out = ReadTIFF(s, buffer);
+    REQUIRE(out.GetMode() == CompressedImageMode::Uint16);
+    REQUIRE(out.GetWidth() == 1024);
+    REQUIRE(out.GetHeight() == 512);
+    REQUIRE(buffer.size() == values.size() * sizeof(uint16_t));
+    REQUIRE(memcmp(values.data(), buffer.data(), buffer.size()) == 0);
 }
 
 TEST_CASE("TIFFTest_File","[TIFF]") {
-- 
2.52.0


From a7c77f1f080cbef0ec6525ad2c0214cc8eea4a0b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 16:09:05 +0200
Subject: [PATCH 088/228] internal generator: compare raw image width to
 RAW_MODULE_COLS

The raw stacked-module layout check compared the image width (cols) against
RAW_MODULE_SIZE (the per-module pixel count, 524288) instead of
RAW_MODULE_COLS (1024), so a raw-geometry TIFF could never be accepted.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/JFJochStateMachine.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/broker/JFJochStateMachine.cpp b/broker/JFJochStateMachine.cpp
index b2daa353..00eae79d 100644
--- a/broker/JFJochStateMachine.cpp
+++ b/broker/JFJochStateMachine.cpp
@@ -812,7 +812,7 @@ void JFJochStateMachine::LoadInternalGeneratorImageTIFF(const std::string &s, ui
     uint32_t cols, lines;
     auto v = ReadTIFFFromString16(s, cols, lines);
     if (((cols == experiment.GetXPixelsNum()) && (lines == experiment.GetYPixelsNum()))
-        || ((cols == RAW_MODULE_SIZE) && (lines == RAW_MODULE_LINES * experiment.GetModulesNum())))
+        || ((cols == RAW_MODULE_COLS) && (lines == RAW_MODULE_LINES * experiment.GetModulesNum())))
         services.LoadInternalGeneratorImage(experiment, v, image_number);
     else
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-- 
2.52.0


From b71da6238e327d59fddbb86a755fcba2461161ea Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 18:54:31 +0200
Subject: [PATCH 089/228] Clean-up unused tools

---
 docs/TOOLS.md                       |  6 ----
 tools/CMakeLists.txt                |  7 -----
 tools/jfjoch_azint_test.cpp         | 45 -----------------------------
 tools/jfjoch_pcie_read_register.cpp | 32 --------------------
 4 files changed, 90 deletions(-)
 delete mode 100644 tools/jfjoch_azint_test.cpp
 delete mode 100644 tools/jfjoch_pcie_read_register.cpp

diff --git a/docs/TOOLS.md b/docs/TOOLS.md
index cddd655e..8e6aecfa 100644
--- a/docs/TOOLS.md
+++ b/docs/TOOLS.md
@@ -49,9 +49,6 @@ Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run fr
 ./jfjoch_pcie_clear_net_counters /dev/jfjoch0
 ```
 
-### jfjoch_pcie_read_register
-Reads raw Jungfraujoch FPGA registers.
-
 ## Testing, benchmarking and simulation
 
 ### jfjoch_udp_simulator
@@ -68,9 +65,6 @@ writing.
 ### jfjoch_hdf5_test
 Tests single-threaded HDF5 writer performance.
 
-### jfjoch_azint_test
-Tests the azimuthal integration code on synthetic data.
-
 ### jfjoch_simplon_test
 Minimal test client for a DECTRIS SIMPLON detector API.
 
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index d24e900c..c31e6f00 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -19,10 +19,6 @@ ADD_EXECUTABLE(jfjoch_pcie_clear_net_counters jfjoch_pcie_clear_net_counters.cpp
 TARGET_LINK_LIBRARIES(jfjoch_pcie_clear_net_counters JFJochDevice JFJochCommon)
 INSTALL(TARGETS jfjoch_pcie_clear_net_counters RUNTIME COMPONENT jfjoch )
 
-ADD_EXECUTABLE(jfjoch_pcie_read_register jfjoch_pcie_read_register.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_pcie_read_register JFJochDevice JFJochCommon)
-INSTALL(TARGETS jfjoch_pcie_read_register RUNTIME COMPONENT jfjoch )
-
 ADD_EXECUTABLE(jfjoch_fpga_test jfjoch_fpga_test.cpp)
 TARGET_LINK_LIBRARIES(jfjoch_fpga_test JFJochReceiver)
 INSTALL(TARGETS jfjoch_fpga_test RUNTIME COMPONENT jfjoch)
@@ -41,9 +37,6 @@ ADD_EXECUTABLE(jfjoch_extract_hkl jfjoch_extract_hkl.cpp
 TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
 INSTALL(TARGETS jfjoch_extract_hkl RUNTIME COMPONENT viewer)
 
-ADD_EXECUTABLE(jfjoch_azint_test jfjoch_azint_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_azint_test JFJochImageAnalysis JFJochCommon)
-
 ADD_EXECUTABLE(jfjoch_process jfjoch_process.cpp)
 TARGET_LINK_LIBRARIES(jfjoch_process JFJochReader JFJochImageAnalysis JFJochWriter JFJochReceiver)
 INSTALL(TARGETS jfjoch_process RUNTIME COMPONENT viewer)
diff --git a/tools/jfjoch_azint_test.cpp b/tools/jfjoch_azint_test.cpp
deleted file mode 100644
index 5b99e614..00000000
--- a/tools/jfjoch_azint_test.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#include <cstdint>
-#include <chrono>
-#include <random>
-
-#include "../common/DiffractionExperiment.h"
-#include "../common/AzimuthalIntegrationMapping.h"
-#include "../common/AzimuthalIntegrationProfile.h"
-#include "../common/AzimuthalIntegrationProfile.h"
-#include "../common/Logger.h"
-#include "../image_analysis/azint/AzIntEngineCPU.h"
-
-int main(int argc, char** argv) {
-    constexpr const uint32_t nimages = 1000;
-
-    DiffractionExperiment experiment(DetEIGER(18, 3, 36, 8));
-
-    AzimuthalIntegrationSettings azim_settings;
-    azim_settings.QSpacing_recipA(0.01).QRange_recipA(0.005, 5.0).AzimuthalBinCount(64);
-    experiment.ImportAzimuthalIntegrationSettings(azim_settings).DetectorDistance_mm(100).BeamX_pxl(1500).BeamY_pxl(1500);
-
-    PixelMask pixel_mask(experiment);
-    AzimuthalIntegrationMapping mapping(experiment, pixel_mask);
-    spdlog::info("Bins {}", mapping.GetBinNumber());
-
-    std::vector<uint16_t> image(experiment.GetPixelsNum());
-
-    std::mt19937 rng(42); // seed
-    std::poisson_distribution<int> poisson(20.0); // mean = 20 photons
-
-    for (auto& pixel : image)
-        pixel = static_cast<uint16_t>(poisson(rng));
-
-    spdlog::info("Generated image");
-
-    AzIntEngineCPU azint_engine(mapping);
-    AzimuthalIntegrationProfile profile(mapping);
-
-    auto start_time = std::chrono::steady_clock::now();
-    for (int i = 0; i < nimages; i++)
-        azint_engine.RunAzint(image, profile);
-
-    auto end_time = std::chrono::steady_clock::now();
-    auto duration = std::chrono::duration<double>(end_time - start_time).count();
-    spdlog::info("Time: {} ms", duration/nimages * 1000.0);
-}
\ No newline at end of file
diff --git a/tools/jfjoch_pcie_read_register.cpp b/tools/jfjoch_pcie_read_register.cpp
deleted file mode 100644
index 3c49e566..00000000
--- a/tools/jfjoch_pcie_read_register.cpp
+++ /dev/null
@@ -1,32 +0,0 @@
-// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "../common/Logger.h"
-#include "../common/JFJochException.h"
-#include "../fpga/host_library/JungfraujochDevice.h"
-#include "../common/NetworkAddressConvert.h"
-
-
-int main(int argc, char **argv) {
-    Logger logger("jfjoch_pcie_read_register");
-
-    if (argc != 3) {
-        std::cout << "Usage: ./jfjoch_pcie_status <device name> <reg number hex>" << std::endl;
-        exit(EXIT_FAILURE);
-    }
-
-    logger.Info("Device {}", argv[1]);
-
-    char *endptr;
-    uint32_t reg_number = std::strtol(argv[2], &endptr, 16);
-    if (*endptr != '\0') {
-        logger.Error("Invalid hexadecimal number: {} ", argv[2]);
-        exit(EXIT_FAILURE);
-    }
-
-    JungfraujochDevice dev(argv[1], false);
-    logger.Info("Reg 0x{:x} = 0x{:x}", reg_number,dev.ReadRegister(reg_number));
-}
-- 
2.52.0


From eb9b4632638bab4cf76f6f8416c14e7b05bf7429 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 19:26:15 +0200
Subject: [PATCH 090/228] VERSION: 1.0.0-rc.153

---
 VERSION                                           |  2 +-
 broker/gen/model/Azim_int_settings.cpp            |  2 +-
 broker/gen/model/Azim_int_settings.h              |  2 +-
 broker/gen/model/Broker_status.cpp                |  2 +-
 broker/gen/model/Broker_status.h                  |  2 +-
 broker/gen/model/Calibration_statistics_inner.cpp |  2 +-
 broker/gen/model/Calibration_statistics_inner.h   |  2 +-
 broker/gen/model/Dark_mask_settings.cpp           |  2 +-
 broker/gen/model/Dark_mask_settings.h             |  2 +-
 broker/gen/model/Dataset_settings.cpp             |  2 +-
 broker/gen/model/Dataset_settings.h               |  2 +-
 ...ataset_settings_xray_fluorescence_spectrum.cpp |  2 +-
 .../Dataset_settings_xray_fluorescence_spectrum.h |  2 +-
 broker/gen/model/Detector.cpp                     |  2 +-
 broker/gen/model/Detector.h                       |  2 +-
 broker/gen/model/Detector_list.cpp                |  2 +-
 broker/gen/model/Detector_list.h                  |  2 +-
 broker/gen/model/Detector_list_element.cpp        |  2 +-
 broker/gen/model/Detector_list_element.h          |  2 +-
 broker/gen/model/Detector_module.cpp              |  2 +-
 broker/gen/model/Detector_module.h                |  2 +-
 broker/gen/model/Detector_module_direction.cpp    |  2 +-
 broker/gen/model/Detector_module_direction.h      |  2 +-
 broker/gen/model/Detector_power_state.cpp         |  2 +-
 broker/gen/model/Detector_power_state.h           |  2 +-
 broker/gen/model/Detector_selection.cpp           |  2 +-
 broker/gen/model/Detector_selection.h             |  2 +-
 broker/gen/model/Detector_settings.cpp            |  2 +-
 broker/gen/model/Detector_settings.h              |  2 +-
 broker/gen/model/Detector_state.cpp               |  2 +-
 broker/gen/model/Detector_state.h                 |  2 +-
 broker/gen/model/Detector_status.cpp              |  2 +-
 broker/gen/model/Detector_status.h                |  2 +-
 broker/gen/model/Detector_timing.cpp              |  2 +-
 broker/gen/model/Detector_timing.h                |  2 +-
 broker/gen/model/Detector_type.cpp                |  2 +-
 broker/gen/model/Detector_type.h                  |  2 +-
 broker/gen/model/Error_message.cpp                |  2 +-
 broker/gen/model/Error_message.h                  |  2 +-
 broker/gen/model/File_writer_format.cpp           |  2 +-
 broker/gen/model/File_writer_format.h             |  2 +-
 broker/gen/model/File_writer_settings.cpp         |  2 +-
 broker/gen/model/File_writer_settings.h           |  2 +-
 broker/gen/model/Fpga_status_inner.cpp            |  2 +-
 broker/gen/model/Fpga_status_inner.h              |  2 +-
 broker/gen/model/Geom_refinement_algorithm.cpp    |  2 +-
 broker/gen/model/Geom_refinement_algorithm.h      |  2 +-
 broker/gen/model/Grid_scan.cpp                    |  2 +-
 broker/gen/model/Grid_scan.h                      |  2 +-
 broker/gen/model/Helpers.cpp                      |  2 +-
 broker/gen/model/Helpers.h                        |  2 +-
 broker/gen/model/Image_buffer_status.cpp          |  2 +-
 broker/gen/model/Image_buffer_status.h            |  2 +-
 broker/gen/model/Image_format_settings.cpp        |  2 +-
 broker/gen/model/Image_format_settings.h          |  2 +-
 broker/gen/model/Image_pusher_status.cpp          |  2 +-
 broker/gen/model/Image_pusher_status.h            |  2 +-
 broker/gen/model/Image_pusher_type.cpp            |  2 +-
 broker/gen/model/Image_pusher_type.h              |  2 +-
 broker/gen/model/Indexing_algorithm.cpp           |  2 +-
 broker/gen/model/Indexing_algorithm.h             |  2 +-
 broker/gen/model/Indexing_settings.cpp            |  2 +-
 broker/gen/model/Indexing_settings.h              |  2 +-
 broker/gen/model/Instrument_metadata.cpp          |  2 +-
 broker/gen/model/Instrument_metadata.h            |  2 +-
 broker/gen/model/Jfjoch_settings.cpp              |  2 +-
 broker/gen/model/Jfjoch_settings.h                |  2 +-
 broker/gen/model/Jfjoch_statistics.cpp            |  2 +-
 broker/gen/model/Jfjoch_statistics.h              |  2 +-
 broker/gen/model/Measurement_statistics.cpp       |  2 +-
 broker/gen/model/Measurement_statistics.h         |  2 +-
 broker/gen/model/Pcie_devices_inner.cpp           |  2 +-
 broker/gen/model/Pcie_devices_inner.h             |  2 +-
 broker/gen/model/Pixel_mask_statistics.cpp        |  2 +-
 broker/gen/model/Pixel_mask_statistics.h          |  2 +-
 broker/gen/model/Plot.cpp                         |  2 +-
 broker/gen/model/Plot.h                           |  2 +-
 broker/gen/model/Plot_unit_x.cpp                  |  2 +-
 broker/gen/model/Plot_unit_x.h                    |  2 +-
 broker/gen/model/Plots.cpp                        |  2 +-
 broker/gen/model/Plots.h                          |  2 +-
 broker/gen/model/Roi_azim_list.cpp                |  2 +-
 broker/gen/model/Roi_azim_list.h                  |  2 +-
 broker/gen/model/Roi_azimuthal.cpp                |  2 +-
 broker/gen/model/Roi_azimuthal.h                  |  2 +-
 broker/gen/model/Roi_box.cpp                      |  2 +-
 broker/gen/model/Roi_box.h                        |  2 +-
 broker/gen/model/Roi_box_list.cpp                 |  2 +-
 broker/gen/model/Roi_box_list.h                   |  2 +-
 broker/gen/model/Roi_circle.cpp                   |  2 +-
 broker/gen/model/Roi_circle.h                     |  2 +-
 broker/gen/model/Roi_circle_list.cpp              |  2 +-
 broker/gen/model/Roi_circle_list.h                |  2 +-
 broker/gen/model/Roi_definitions.cpp              |  2 +-
 broker/gen/model/Roi_definitions.h                |  2 +-
 broker/gen/model/Rotation_axis.cpp                |  2 +-
 broker/gen/model/Rotation_axis.h                  |  2 +-
 broker/gen/model/Scan_result.cpp                  |  2 +-
 broker/gen/model/Scan_result.h                    |  2 +-
 broker/gen/model/Scan_result_images_inner.cpp     |  2 +-
 broker/gen/model/Scan_result_images_inner.h       |  2 +-
 broker/gen/model/Spot_finding_settings.cpp        |  2 +-
 broker/gen/model/Spot_finding_settings.h          |  2 +-
 broker/gen/model/Standard_detector_geometry.cpp   |  2 +-
 broker/gen/model/Standard_detector_geometry.h     |  2 +-
 broker/gen/model/Tcp_settings.cpp                 |  2 +-
 broker/gen/model/Tcp_settings.h                   |  2 +-
 broker/gen/model/Unit_cell.cpp                    |  2 +-
 broker/gen/model/Unit_cell.h                      |  2 +-
 broker/gen/model/Zeromq_metadata_settings.cpp     |  2 +-
 broker/gen/model/Zeromq_metadata_settings.h       |  2 +-
 broker/gen/model/Zeromq_preview_settings.cpp      |  2 +-
 broker/gen/model/Zeromq_preview_settings.h        |  2 +-
 broker/gen/model/Zeromq_settings.cpp              |  2 +-
 broker/gen/model/Zeromq_settings.h                |  2 +-
 broker/jfjoch_api.yaml                            |  2 +-
 broker/redoc-static.html                          | 15 ++++++++-------
 docs/CHANGELOG.md                                 | 10 ++++++++++
 docs/conf.py                                      |  2 +-
 docs/python_client/README.md                      |  4 ++--
 docs/python_client/docs/DefaultApi.md             |  5 +++--
 fpga/hdl/action_config.v                          |  2 +-
 fpga/pcie_driver/dkms.conf                        |  2 +-
 fpga/pcie_driver/install_dkms.sh                  |  2 +-
 fpga/pcie_driver/jfjoch_drv.c                     |  2 +-
 fpga/pcie_driver/postinstall.sh                   |  2 +-
 fpga/pcie_driver/preuninstall.sh                  |  2 +-
 frontend/package-lock.json                        |  4 ++--
 frontend/package.json                             |  2 +-
 frontend/src/openapi/core/OpenAPI.ts              |  2 +-
 frontend/src/openapi/services/DefaultService.ts   |  3 ++-
 frontend/src/version.ts                           |  2 +-
 132 files changed, 153 insertions(+), 140 deletions(-)

diff --git a/VERSION b/VERSION
index a9cf07ad..9f1ff589 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.0.0-rc.152
+1.0.0-rc.153
diff --git a/broker/gen/model/Azim_int_settings.cpp b/broker/gen/model/Azim_int_settings.cpp
index da2ee80d..826ea5ae 100644
--- a/broker/gen/model/Azim_int_settings.cpp
+++ b/broker/gen/model/Azim_int_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Azim_int_settings.h b/broker/gen/model/Azim_int_settings.h
index 92f86d19..158c8922 100644
--- a/broker/gen/model/Azim_int_settings.h
+++ b/broker/gen/model/Azim_int_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Broker_status.cpp b/broker/gen/model/Broker_status.cpp
index 92c041d8..6cec1ee2 100644
--- a/broker/gen/model/Broker_status.cpp
+++ b/broker/gen/model/Broker_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Broker_status.h b/broker/gen/model/Broker_status.h
index f3fb07b3..f18ca782 100644
--- a/broker/gen/model/Broker_status.h
+++ b/broker/gen/model/Broker_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Calibration_statistics_inner.cpp b/broker/gen/model/Calibration_statistics_inner.cpp
index 9265878e..9556ade6 100644
--- a/broker/gen/model/Calibration_statistics_inner.cpp
+++ b/broker/gen/model/Calibration_statistics_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Calibration_statistics_inner.h b/broker/gen/model/Calibration_statistics_inner.h
index e250f9fd..3f67f0b6 100644
--- a/broker/gen/model/Calibration_statistics_inner.h
+++ b/broker/gen/model/Calibration_statistics_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dark_mask_settings.cpp b/broker/gen/model/Dark_mask_settings.cpp
index 4f345a4b..8b1ca257 100644
--- a/broker/gen/model/Dark_mask_settings.cpp
+++ b/broker/gen/model/Dark_mask_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dark_mask_settings.h b/broker/gen/model/Dark_mask_settings.h
index 4b5ec2ec..4f9c9823 100644
--- a/broker/gen/model/Dark_mask_settings.h
+++ b/broker/gen/model/Dark_mask_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings.cpp b/broker/gen/model/Dataset_settings.cpp
index 6f7c7343..7e07777c 100644
--- a/broker/gen/model/Dataset_settings.cpp
+++ b/broker/gen/model/Dataset_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings.h b/broker/gen/model/Dataset_settings.h
index 952e2d2d..510286d3 100644
--- a/broker/gen/model/Dataset_settings.h
+++ b/broker/gen/model/Dataset_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
index aa9fb930..157d97d2 100644
--- a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
+++ b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
index d13e31e8..7bfa5137 100644
--- a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
+++ b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector.cpp b/broker/gen/model/Detector.cpp
index a3f77897..e7bbd72d 100644
--- a/broker/gen/model/Detector.cpp
+++ b/broker/gen/model/Detector.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector.h b/broker/gen/model/Detector.h
index 8d12e503..999949c4 100644
--- a/broker/gen/model/Detector.h
+++ b/broker/gen/model/Detector.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list.cpp b/broker/gen/model/Detector_list.cpp
index a907fe2c..de7e27e2 100644
--- a/broker/gen/model/Detector_list.cpp
+++ b/broker/gen/model/Detector_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list.h b/broker/gen/model/Detector_list.h
index e2876a3f..445f8481 100644
--- a/broker/gen/model/Detector_list.h
+++ b/broker/gen/model/Detector_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list_element.cpp b/broker/gen/model/Detector_list_element.cpp
index cbe51df0..7c59cfe3 100644
--- a/broker/gen/model/Detector_list_element.cpp
+++ b/broker/gen/model/Detector_list_element.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list_element.h b/broker/gen/model/Detector_list_element.h
index 9a1890d0..32793439 100644
--- a/broker/gen/model/Detector_list_element.h
+++ b/broker/gen/model/Detector_list_element.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module.cpp b/broker/gen/model/Detector_module.cpp
index 9a4b5e0e..f28cc957 100644
--- a/broker/gen/model/Detector_module.cpp
+++ b/broker/gen/model/Detector_module.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module.h b/broker/gen/model/Detector_module.h
index 5f5d20ed..f04863c1 100644
--- a/broker/gen/model/Detector_module.h
+++ b/broker/gen/model/Detector_module.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module_direction.cpp b/broker/gen/model/Detector_module_direction.cpp
index 2d0a47c4..068dc6e7 100644
--- a/broker/gen/model/Detector_module_direction.cpp
+++ b/broker/gen/model/Detector_module_direction.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module_direction.h b/broker/gen/model/Detector_module_direction.h
index d1068069..19f22005 100644
--- a/broker/gen/model/Detector_module_direction.h
+++ b/broker/gen/model/Detector_module_direction.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_power_state.cpp b/broker/gen/model/Detector_power_state.cpp
index 8c9558ab..9ee53908 100644
--- a/broker/gen/model/Detector_power_state.cpp
+++ b/broker/gen/model/Detector_power_state.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_power_state.h b/broker/gen/model/Detector_power_state.h
index d5500210..d1a6c5cb 100644
--- a/broker/gen/model/Detector_power_state.h
+++ b/broker/gen/model/Detector_power_state.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_selection.cpp b/broker/gen/model/Detector_selection.cpp
index 97e53716..3cf0fa77 100644
--- a/broker/gen/model/Detector_selection.cpp
+++ b/broker/gen/model/Detector_selection.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_selection.h b/broker/gen/model/Detector_selection.h
index b5480072..bba38849 100644
--- a/broker/gen/model/Detector_selection.h
+++ b/broker/gen/model/Detector_selection.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_settings.cpp b/broker/gen/model/Detector_settings.cpp
index 34104542..d8bf158a 100644
--- a/broker/gen/model/Detector_settings.cpp
+++ b/broker/gen/model/Detector_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_settings.h b/broker/gen/model/Detector_settings.h
index 40dbe2ec..6546179d 100644
--- a/broker/gen/model/Detector_settings.h
+++ b/broker/gen/model/Detector_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_state.cpp b/broker/gen/model/Detector_state.cpp
index 79a6bccb..c4ab8f1b 100644
--- a/broker/gen/model/Detector_state.cpp
+++ b/broker/gen/model/Detector_state.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_state.h b/broker/gen/model/Detector_state.h
index 29d8afde..b372129d 100644
--- a/broker/gen/model/Detector_state.h
+++ b/broker/gen/model/Detector_state.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_status.cpp b/broker/gen/model/Detector_status.cpp
index ce479f66..0e8b2a95 100644
--- a/broker/gen/model/Detector_status.cpp
+++ b/broker/gen/model/Detector_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_status.h b/broker/gen/model/Detector_status.h
index 38eb8ac6..e3b2ccca 100644
--- a/broker/gen/model/Detector_status.h
+++ b/broker/gen/model/Detector_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_timing.cpp b/broker/gen/model/Detector_timing.cpp
index 59cfc0da..de423c69 100644
--- a/broker/gen/model/Detector_timing.cpp
+++ b/broker/gen/model/Detector_timing.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_timing.h b/broker/gen/model/Detector_timing.h
index 5c05c179..e7110f99 100644
--- a/broker/gen/model/Detector_timing.h
+++ b/broker/gen/model/Detector_timing.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_type.cpp b/broker/gen/model/Detector_type.cpp
index 64ad5bb5..9399377a 100644
--- a/broker/gen/model/Detector_type.cpp
+++ b/broker/gen/model/Detector_type.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_type.h b/broker/gen/model/Detector_type.h
index 83dcea72..7e9532b7 100644
--- a/broker/gen/model/Detector_type.h
+++ b/broker/gen/model/Detector_type.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Error_message.cpp b/broker/gen/model/Error_message.cpp
index bd6bc10f..416ac4e6 100644
--- a/broker/gen/model/Error_message.cpp
+++ b/broker/gen/model/Error_message.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Error_message.h b/broker/gen/model/Error_message.h
index 29e51933..517ebc30 100644
--- a/broker/gen/model/Error_message.h
+++ b/broker/gen/model/Error_message.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_format.cpp b/broker/gen/model/File_writer_format.cpp
index 49250ebc..1032d71a 100644
--- a/broker/gen/model/File_writer_format.cpp
+++ b/broker/gen/model/File_writer_format.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_format.h b/broker/gen/model/File_writer_format.h
index bdf52aa7..0cbca1c6 100644
--- a/broker/gen/model/File_writer_format.h
+++ b/broker/gen/model/File_writer_format.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_settings.cpp b/broker/gen/model/File_writer_settings.cpp
index c19f6234..dc5c16aa 100644
--- a/broker/gen/model/File_writer_settings.cpp
+++ b/broker/gen/model/File_writer_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_settings.h b/broker/gen/model/File_writer_settings.h
index 32c52db4..3ef56e2a 100644
--- a/broker/gen/model/File_writer_settings.h
+++ b/broker/gen/model/File_writer_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Fpga_status_inner.cpp b/broker/gen/model/Fpga_status_inner.cpp
index 09a94333..0851c88a 100644
--- a/broker/gen/model/Fpga_status_inner.cpp
+++ b/broker/gen/model/Fpga_status_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Fpga_status_inner.h b/broker/gen/model/Fpga_status_inner.h
index c2072482..75153cdd 100644
--- a/broker/gen/model/Fpga_status_inner.h
+++ b/broker/gen/model/Fpga_status_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Geom_refinement_algorithm.cpp b/broker/gen/model/Geom_refinement_algorithm.cpp
index 7f4f1561..d56046ad 100644
--- a/broker/gen/model/Geom_refinement_algorithm.cpp
+++ b/broker/gen/model/Geom_refinement_algorithm.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Geom_refinement_algorithm.h b/broker/gen/model/Geom_refinement_algorithm.h
index 4f25608f..1267dcc4 100644
--- a/broker/gen/model/Geom_refinement_algorithm.h
+++ b/broker/gen/model/Geom_refinement_algorithm.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Grid_scan.cpp b/broker/gen/model/Grid_scan.cpp
index 12817267..b610bce2 100644
--- a/broker/gen/model/Grid_scan.cpp
+++ b/broker/gen/model/Grid_scan.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Grid_scan.h b/broker/gen/model/Grid_scan.h
index 5afd301a..077ccebb 100644
--- a/broker/gen/model/Grid_scan.h
+++ b/broker/gen/model/Grid_scan.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Helpers.cpp b/broker/gen/model/Helpers.cpp
index 4af047c9..f24789fc 100644
--- a/broker/gen/model/Helpers.cpp
+++ b/broker/gen/model/Helpers.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Helpers.h b/broker/gen/model/Helpers.h
index 408053f7..6d6c04a0 100644
--- a/broker/gen/model/Helpers.h
+++ b/broker/gen/model/Helpers.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_buffer_status.cpp b/broker/gen/model/Image_buffer_status.cpp
index 7eb055b5..7291140c 100644
--- a/broker/gen/model/Image_buffer_status.cpp
+++ b/broker/gen/model/Image_buffer_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_buffer_status.h b/broker/gen/model/Image_buffer_status.h
index aea1c8e0..4678e21b 100644
--- a/broker/gen/model/Image_buffer_status.h
+++ b/broker/gen/model/Image_buffer_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_format_settings.cpp b/broker/gen/model/Image_format_settings.cpp
index 309ea9d0..50b354dc 100644
--- a/broker/gen/model/Image_format_settings.cpp
+++ b/broker/gen/model/Image_format_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_format_settings.h b/broker/gen/model/Image_format_settings.h
index b5d27a50..4f3cc8db 100644
--- a/broker/gen/model/Image_format_settings.h
+++ b/broker/gen/model/Image_format_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_status.cpp b/broker/gen/model/Image_pusher_status.cpp
index b5a46f3a..4a637f45 100644
--- a/broker/gen/model/Image_pusher_status.cpp
+++ b/broker/gen/model/Image_pusher_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_status.h b/broker/gen/model/Image_pusher_status.h
index 8cd79bc3..d1cdf1aa 100644
--- a/broker/gen/model/Image_pusher_status.h
+++ b/broker/gen/model/Image_pusher_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_type.cpp b/broker/gen/model/Image_pusher_type.cpp
index a0d0362e..320ec448 100644
--- a/broker/gen/model/Image_pusher_type.cpp
+++ b/broker/gen/model/Image_pusher_type.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_type.h b/broker/gen/model/Image_pusher_type.h
index 03d609d9..0a54762f 100644
--- a/broker/gen/model/Image_pusher_type.h
+++ b/broker/gen/model/Image_pusher_type.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_algorithm.cpp b/broker/gen/model/Indexing_algorithm.cpp
index cbe69731..31f4a0ab 100644
--- a/broker/gen/model/Indexing_algorithm.cpp
+++ b/broker/gen/model/Indexing_algorithm.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_algorithm.h b/broker/gen/model/Indexing_algorithm.h
index 244e2c74..80f7762e 100644
--- a/broker/gen/model/Indexing_algorithm.h
+++ b/broker/gen/model/Indexing_algorithm.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_settings.cpp b/broker/gen/model/Indexing_settings.cpp
index 1475e07b..bf4a805f 100644
--- a/broker/gen/model/Indexing_settings.cpp
+++ b/broker/gen/model/Indexing_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_settings.h b/broker/gen/model/Indexing_settings.h
index 6dc1ad52..50003d68 100644
--- a/broker/gen/model/Indexing_settings.h
+++ b/broker/gen/model/Indexing_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Instrument_metadata.cpp b/broker/gen/model/Instrument_metadata.cpp
index cd644077..ec9f8815 100644
--- a/broker/gen/model/Instrument_metadata.cpp
+++ b/broker/gen/model/Instrument_metadata.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Instrument_metadata.h b/broker/gen/model/Instrument_metadata.h
index 4e698f0e..1b6e0a11 100644
--- a/broker/gen/model/Instrument_metadata.h
+++ b/broker/gen/model/Instrument_metadata.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_settings.cpp b/broker/gen/model/Jfjoch_settings.cpp
index d49a9345..8db1ff0f 100644
--- a/broker/gen/model/Jfjoch_settings.cpp
+++ b/broker/gen/model/Jfjoch_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_settings.h b/broker/gen/model/Jfjoch_settings.h
index 9ea5cca0..85982af3 100644
--- a/broker/gen/model/Jfjoch_settings.h
+++ b/broker/gen/model/Jfjoch_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_statistics.cpp b/broker/gen/model/Jfjoch_statistics.cpp
index 6f41bf40..37b4b262 100644
--- a/broker/gen/model/Jfjoch_statistics.cpp
+++ b/broker/gen/model/Jfjoch_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_statistics.h b/broker/gen/model/Jfjoch_statistics.h
index b8066389..eee784f5 100644
--- a/broker/gen/model/Jfjoch_statistics.h
+++ b/broker/gen/model/Jfjoch_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Measurement_statistics.cpp b/broker/gen/model/Measurement_statistics.cpp
index bdbf113a..c8278f09 100644
--- a/broker/gen/model/Measurement_statistics.cpp
+++ b/broker/gen/model/Measurement_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Measurement_statistics.h b/broker/gen/model/Measurement_statistics.h
index ad76374c..3fc19a24 100644
--- a/broker/gen/model/Measurement_statistics.h
+++ b/broker/gen/model/Measurement_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pcie_devices_inner.cpp b/broker/gen/model/Pcie_devices_inner.cpp
index 2d1c3da4..d91cb19f 100644
--- a/broker/gen/model/Pcie_devices_inner.cpp
+++ b/broker/gen/model/Pcie_devices_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pcie_devices_inner.h b/broker/gen/model/Pcie_devices_inner.h
index 891ea047..7612c1c6 100644
--- a/broker/gen/model/Pcie_devices_inner.h
+++ b/broker/gen/model/Pcie_devices_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pixel_mask_statistics.cpp b/broker/gen/model/Pixel_mask_statistics.cpp
index 504536df..f132990b 100644
--- a/broker/gen/model/Pixel_mask_statistics.cpp
+++ b/broker/gen/model/Pixel_mask_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pixel_mask_statistics.h b/broker/gen/model/Pixel_mask_statistics.h
index 80b57a27..a9e3a2e6 100644
--- a/broker/gen/model/Pixel_mask_statistics.h
+++ b/broker/gen/model/Pixel_mask_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot.cpp b/broker/gen/model/Plot.cpp
index 70750a5f..fea50f58 100644
--- a/broker/gen/model/Plot.cpp
+++ b/broker/gen/model/Plot.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot.h b/broker/gen/model/Plot.h
index cefb8c29..01aa18ca 100644
--- a/broker/gen/model/Plot.h
+++ b/broker/gen/model/Plot.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot_unit_x.cpp b/broker/gen/model/Plot_unit_x.cpp
index 6e4e051e..50c0fe12 100644
--- a/broker/gen/model/Plot_unit_x.cpp
+++ b/broker/gen/model/Plot_unit_x.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot_unit_x.h b/broker/gen/model/Plot_unit_x.h
index ba8f9220..c4a008e2 100644
--- a/broker/gen/model/Plot_unit_x.h
+++ b/broker/gen/model/Plot_unit_x.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plots.cpp b/broker/gen/model/Plots.cpp
index 79c6af6d..3353b009 100644
--- a/broker/gen/model/Plots.cpp
+++ b/broker/gen/model/Plots.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plots.h b/broker/gen/model/Plots.h
index 1b2920f5..ab6d44c5 100644
--- a/broker/gen/model/Plots.h
+++ b/broker/gen/model/Plots.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azim_list.cpp b/broker/gen/model/Roi_azim_list.cpp
index 4f9e81b8..50a0eb11 100644
--- a/broker/gen/model/Roi_azim_list.cpp
+++ b/broker/gen/model/Roi_azim_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azim_list.h b/broker/gen/model/Roi_azim_list.h
index 4b832050..f0125932 100644
--- a/broker/gen/model/Roi_azim_list.h
+++ b/broker/gen/model/Roi_azim_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azimuthal.cpp b/broker/gen/model/Roi_azimuthal.cpp
index 76dccaf5..dfed1827 100644
--- a/broker/gen/model/Roi_azimuthal.cpp
+++ b/broker/gen/model/Roi_azimuthal.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azimuthal.h b/broker/gen/model/Roi_azimuthal.h
index 2660fa11..8913039b 100644
--- a/broker/gen/model/Roi_azimuthal.h
+++ b/broker/gen/model/Roi_azimuthal.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box.cpp b/broker/gen/model/Roi_box.cpp
index 1f55c5a4..c9732767 100644
--- a/broker/gen/model/Roi_box.cpp
+++ b/broker/gen/model/Roi_box.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box.h b/broker/gen/model/Roi_box.h
index 3159b221..286ffb08 100644
--- a/broker/gen/model/Roi_box.h
+++ b/broker/gen/model/Roi_box.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box_list.cpp b/broker/gen/model/Roi_box_list.cpp
index 439261c5..556dede5 100644
--- a/broker/gen/model/Roi_box_list.cpp
+++ b/broker/gen/model/Roi_box_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box_list.h b/broker/gen/model/Roi_box_list.h
index 2a8bfa07..c18a0702 100644
--- a/broker/gen/model/Roi_box_list.h
+++ b/broker/gen/model/Roi_box_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle.cpp b/broker/gen/model/Roi_circle.cpp
index 1e27e7bb..0e897514 100644
--- a/broker/gen/model/Roi_circle.cpp
+++ b/broker/gen/model/Roi_circle.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle.h b/broker/gen/model/Roi_circle.h
index 18bf66bd..0b7ee690 100644
--- a/broker/gen/model/Roi_circle.h
+++ b/broker/gen/model/Roi_circle.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle_list.cpp b/broker/gen/model/Roi_circle_list.cpp
index 536cee7b..88f1bc6d 100644
--- a/broker/gen/model/Roi_circle_list.cpp
+++ b/broker/gen/model/Roi_circle_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle_list.h b/broker/gen/model/Roi_circle_list.h
index edb63267..e6219a9e 100644
--- a/broker/gen/model/Roi_circle_list.h
+++ b/broker/gen/model/Roi_circle_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_definitions.cpp b/broker/gen/model/Roi_definitions.cpp
index fdb7c902..18c6d380 100644
--- a/broker/gen/model/Roi_definitions.cpp
+++ b/broker/gen/model/Roi_definitions.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_definitions.h b/broker/gen/model/Roi_definitions.h
index ef972e18..7c75eafd 100644
--- a/broker/gen/model/Roi_definitions.h
+++ b/broker/gen/model/Roi_definitions.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rotation_axis.cpp b/broker/gen/model/Rotation_axis.cpp
index 66d7ed71..45928b50 100644
--- a/broker/gen/model/Rotation_axis.cpp
+++ b/broker/gen/model/Rotation_axis.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rotation_axis.h b/broker/gen/model/Rotation_axis.h
index 4fde353b..54e72f01 100644
--- a/broker/gen/model/Rotation_axis.h
+++ b/broker/gen/model/Rotation_axis.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result.cpp b/broker/gen/model/Scan_result.cpp
index 78ba7b56..d61f4c0c 100644
--- a/broker/gen/model/Scan_result.cpp
+++ b/broker/gen/model/Scan_result.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result.h b/broker/gen/model/Scan_result.h
index 570a3bf0..03733748 100644
--- a/broker/gen/model/Scan_result.h
+++ b/broker/gen/model/Scan_result.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result_images_inner.cpp b/broker/gen/model/Scan_result_images_inner.cpp
index 5550477e..c1ccfade 100644
--- a/broker/gen/model/Scan_result_images_inner.cpp
+++ b/broker/gen/model/Scan_result_images_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result_images_inner.h b/broker/gen/model/Scan_result_images_inner.h
index 3c0e22f8..fac1cdfd 100644
--- a/broker/gen/model/Scan_result_images_inner.h
+++ b/broker/gen/model/Scan_result_images_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Spot_finding_settings.cpp b/broker/gen/model/Spot_finding_settings.cpp
index 22a53efb..c7155a5a 100644
--- a/broker/gen/model/Spot_finding_settings.cpp
+++ b/broker/gen/model/Spot_finding_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Spot_finding_settings.h b/broker/gen/model/Spot_finding_settings.h
index fdcf402e..4eb59121 100644
--- a/broker/gen/model/Spot_finding_settings.h
+++ b/broker/gen/model/Spot_finding_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Standard_detector_geometry.cpp b/broker/gen/model/Standard_detector_geometry.cpp
index f90f137a..38d22564 100644
--- a/broker/gen/model/Standard_detector_geometry.cpp
+++ b/broker/gen/model/Standard_detector_geometry.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Standard_detector_geometry.h b/broker/gen/model/Standard_detector_geometry.h
index 17b8942c..e50c21a9 100644
--- a/broker/gen/model/Standard_detector_geometry.h
+++ b/broker/gen/model/Standard_detector_geometry.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Tcp_settings.cpp b/broker/gen/model/Tcp_settings.cpp
index 59df788f..883ab4b7 100644
--- a/broker/gen/model/Tcp_settings.cpp
+++ b/broker/gen/model/Tcp_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Tcp_settings.h b/broker/gen/model/Tcp_settings.h
index 2e175560..2c933bdd 100644
--- a/broker/gen/model/Tcp_settings.h
+++ b/broker/gen/model/Tcp_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Unit_cell.cpp b/broker/gen/model/Unit_cell.cpp
index def6e873..75b301d7 100644
--- a/broker/gen/model/Unit_cell.cpp
+++ b/broker/gen/model/Unit_cell.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Unit_cell.h b/broker/gen/model/Unit_cell.h
index 78e96633..48499fac 100644
--- a/broker/gen/model/Unit_cell.h
+++ b/broker/gen/model/Unit_cell.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_metadata_settings.cpp b/broker/gen/model/Zeromq_metadata_settings.cpp
index 7bb949ca..dd409b32 100644
--- a/broker/gen/model/Zeromq_metadata_settings.cpp
+++ b/broker/gen/model/Zeromq_metadata_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_metadata_settings.h b/broker/gen/model/Zeromq_metadata_settings.h
index a21043aa..8fdaeea4 100644
--- a/broker/gen/model/Zeromq_metadata_settings.h
+++ b/broker/gen/model/Zeromq_metadata_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_preview_settings.cpp b/broker/gen/model/Zeromq_preview_settings.cpp
index 77b772dd..52a16b37 100644
--- a/broker/gen/model/Zeromq_preview_settings.cpp
+++ b/broker/gen/model/Zeromq_preview_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_preview_settings.h b/broker/gen/model/Zeromq_preview_settings.h
index 2bac15c4..e33df9c7 100644
--- a/broker/gen/model/Zeromq_preview_settings.h
+++ b/broker/gen/model/Zeromq_preview_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_settings.cpp b/broker/gen/model/Zeromq_settings.cpp
index 351bc128..8643b5fa 100644
--- a/broker/gen/model/Zeromq_settings.cpp
+++ b/broker/gen/model/Zeromq_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_settings.h b/broker/gen/model/Zeromq_settings.h
index b8fb83e9..1697b1ab 100644
--- a/broker/gen/model/Zeromq_settings.h
+++ b/broker/gen/model/Zeromq_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.152
+* The version of the OpenAPI document: 1.0.0-rc.153
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 828c952a..573288da 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -22,7 +22,7 @@ info:
     requirements on applications that merely interact with the API, regardless of whether they
     communicate through network calls or other mechanisms.
 
-  version: 1.0.0-rc.152
+  version: 1.0.0-rc.153
   contact:
     name: Filip Leonarski (Paul Scherrer Institute)
     email: filip.leonarski@psi.ch
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 7fa87fe9..73cd15d5 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -399,7 +399,7 @@ This format doesn&#x27;t transmit information about X-axis, only values, so it i
           55.627 l 55.6165,55.627 -231.245496,231.24803 c -127.185,127.1864
           -231.5279,231.248 -231.873,231.248 -0.3451,0 -104.688,
           -104.0616 -231.873,-231.248 z
-        " fill="currentColor"></path></g></svg></div></div><div class="sc-eulNck iEaKWZ api-content"><div class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx api-info"><h1 class="sc-imWYAI sc-ktJbId cILgPb UQJzT">Jungfraujoch<!-- --> <span>(<!-- -->1.0.0-rc.152<!-- -->)</span></h1><p>Download OpenAPI specification<!-- -->:</p><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><div class="sc-fiCwlc iQovLz"><div class="sc-jIGnZt cKLRU"><span class="sc-kMkxaj csEIgT">Filip Leonarski (Paul Scherrer Institute)<!-- -->:<!-- --> <a href="mailto:filip.leonarski@psi.ch">filip.leonarski@psi.ch</a></span> <!-- --> <span class="sc-kMkxaj csEIgT">License:<!-- --> <a href="https://www.gnu.org/licenses/gpl-3.0.html">GPL-3.0</a></span> </div></div></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-summary"></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-description"><p>API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
+        " fill="currentColor"></path></g></svg></div></div><div class="sc-eulNck iEaKWZ api-content"><div class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx api-info"><h1 class="sc-imWYAI sc-ktJbId cILgPb UQJzT">Jungfraujoch<!-- --> <span>(<!-- -->1.0.0-rc.153<!-- -->)</span></h1><p>Download OpenAPI specification<!-- -->:</p><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><div class="sc-fiCwlc iQovLz"><div class="sc-jIGnZt cKLRU"><span class="sc-kMkxaj csEIgT">Filip Leonarski (Paul Scherrer Institute)<!-- -->:<!-- --> <a href="mailto:filip.leonarski@psi.ch">filip.leonarski@psi.ch</a></span> <!-- --> <span class="sc-kMkxaj csEIgT">License:<!-- --> <a href="https://www.gnu.org/licenses/gpl-3.0.html">GPL-3.0</a></span> </div></div></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-summary"></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-description"><p>API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
 Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.
 Jungfraujoch uses FPGA boards to acquire data at high data rates.</p>
 </div></div></div></div><div id="section/License-Clarification" data-section-id="section/License-Clarification" class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#section/License-Clarification" aria-label="section/License-Clarification"></a>License Clarification</h2></div></div><div class="sc-fqkvVR diIqQJ"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru redoc-markdown "><p>While this API definition is licensed under GPL-3.0, <strong>the GPL copyleft provisions do not apply</strong>
@@ -466,7 +466,7 @@ Transmission of attenuator (filter) [no units]</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="grid_scan"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand grid_scan"><span class="property-name">grid_scan</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->grid_scan<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Definition of a grid scan (mutually exclusive with <code>rotation_axis</code>)</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="header_appendix"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">header_appendix</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">any</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
 In general, it is not saved in HDF5 file.</p>
-<p>However, if values are placed in &quot;hdf5&quot; object, <code>jfjoch_writer</code> will write them in /entry/data of the HDF5 file. 
+<p>However, if values are placed in &quot;hdf5&quot; object, <code>jfjoch_writer</code> will write them in /entry/user of the HDF5 file. 
 This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
 For example {&quot;hdf5&quot;: {&quot;val1&quot;:1, &quot;val2&quot;:&quot;xyz&quot;}}, will write /entry/user/val1 and /entry/user/val2.</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="image_appendix"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">image_appendix</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">any</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)
@@ -857,11 +857,12 @@ Get user mask of the detector (TIFF)
 Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
 If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
 In the latter case - module gaps are ignored and don&#39;t need to be assigned value.
-Mask is expected as TIFF (4-byte; unsigned).
+Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
 0 - good pixel, other value - masked
-User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. 
+User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
 User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.</p>
 </div></div><h5 class="sc-dAlyuH jbQuod">Request Body schema: <span class="sc-cWSHoV fzNksy">image/tiff</span></h5><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"></div><div><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr"> <!-- -->&lt;<!-- -->binary<!-- -->&gt;<!-- --> </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"></div></div></div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jkjMMR" disabled=""><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>All good</p>
+</div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Not a valid single-channel TIFF or size doesn&#39;t match the detector</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">500<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Error within Jungfraujoch code - see output message.</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="put" class="sc-eZYNyq cnqpVw http-verb put">put</span><span class="sc-iEXKAA gUNSDu">/config/user_mask.tiff</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/config/user_mask.tiff</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-error react-tabs__tab--selected" role="tab" id="tab_R_9pqa_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pqa_0" tabindex="0" data-rttab="true">500</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pqa_0" aria-labelledby="tab_R_9pqa_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"msg"</span>: <span class="token string">&quot;Detector in wrong state&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"reason"</span>: <span class="token string">&quot;WrongDAQState&quot;</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1preview~1pedestal.tiff/get" data-section-id="/paths/~1preview~1pedestal.tiff/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1preview~1pedestal.tiff/get" aria-label="/paths/~1preview~1pedestal.tiff/get"></a>Get pedestal in TIFF format<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="gain_level"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">gain_level</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">integer</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Gain level (0, 1, 2)</p>
@@ -871,7 +872,7 @@ User mask is not automatically applied - i.e. pixels with user mask will have a
 </div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>No calibration recorded so far</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/preview/pedestal.tiff</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/preview/pedestal.tiff</div></div></div></div></div></div></div></div><div id="/paths/~1preview~1plot/get" data-section-id="/paths/~1preview~1plot/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1preview~1plot/get" aria-label="/paths/~1preview~1plot/get"></a>Generate 1D plot from Jungfraujoch<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="binning"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">binning</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">integer</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">1</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Binning of frames for the plot (0 = default binning)</p>
-</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
+</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;compression_ratio&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="fill"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">fill</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">number</span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr"> <!-- -->&lt;<!-- -->float<!-- -->&gt;<!-- --> </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Fill value for elements that were missed during data collection</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="experimental_coord"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">experimental_coord</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">boolean</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">false</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>If measurement has goniometer axis defined, plot X-axis will represent rotation angle
 If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
@@ -883,7 +884,7 @@ For still measurement the number is ignored</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/preview/plot</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pra_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pra_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pra_0" aria-labelledby="tab_R_9pra_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"unit_x"</span>: <span class="token string">&quot;image_number&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"size_x"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"size_y"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"plot"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"x"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"y"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"z"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0.1</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1preview~1plot.bin/get" data-section-id="/paths/~1preview~1plot.bin/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1preview~1plot.bin/get" aria-label="/paths/~1preview~1plot.bin/get"></a>Generate 1D plot from Jungfraujoch and send in raw binary format.
 Data are provided as (32-bit) float binary array.
 This format doesn&#x27;t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
-<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
+<!-- --> </h2><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;bkg_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;azint_1d&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_low_res&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_indexed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;spot_count_ice&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_rate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_lattice_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_length&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;indexing_unit_cell_angle&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;profile_radius&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;mosaicity&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;b_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;error_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;saturated_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_collection_efficiency&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_delay&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;receiver_free_send_buf&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;strong_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_mean&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_max_count&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_pixels&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;roi_weighted_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;packets_received&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;max_pixel_value&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;resolution_estimate&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;pixel_sum&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;processing_time&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_x&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;beam_center_y&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;integrated_reflections&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_factor&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_cc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;image_scale_b&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;compression_ratio&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Type of requested plot</p>
 </div></div></div></td></tr><tr class="last "><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="roi"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">roi</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span><span> <span class="sc-Nxspf sc-fxwrCY cXxAXt eMVOei"> <!-- -->non-empty<!-- --> </span></span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Name of ROI for which plot is requested</p>
 </div></div></div></td></tr></tbody></table></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK.</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Input parsing or validation error</p>
@@ -936,7 +937,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
-      const __redoc_state = {"menu":{"activeItemIdx":-1},"spec":{"data":{"openapi":"3.0.3","info":{"title":"Jungfraujoch","description":"API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).\nJungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.\nJungfraujoch uses FPGA boards to acquire data at high data rates.\n\n# License Clarification\n\nWhile this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**\nwhen this file is used solely to generate OpenAPI clients or when implementing applications that\ninteract with the API. Generated client code and applications using this API definition are not\nsubject to the GPL license requirements and may be distributed under terms of your choosing.\n\nThis exception is similar in spirit to the Linux Kernel's approach to userspace API headers and\nthe GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.152","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","image_scale_b"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"},"saturation":{"in":"query","name":"saturation","required":false,"schema":{"type":"number","format":"float","minimum":-32767,"maximum":32767},"description":"Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"},"background":{"in":"query","name":"background","required":false,"schema":{"type":"number","format":"float","default":0,"minimum":-32767,"maximum":32767},"description":"Background value to set contrast in the preview image"},"show_spots":{"in":"query","name":"show_spots","schema":{"type":"boolean","default":true},"description":"Show spot finding results on the image"},"show_beam_center":{"in":"query","name":"show_beam_center","schema":{"type":"boolean","default":true},"description":"Show beam center on the image"},"show_roi":{"in":"query","name":"show_roi","schema":{"type":"boolean","default":false},"description":"Show ROI areas on the image"},"jpeg_quality":{"in":"query","name":"jpeg_quality","description":"Quality of JPEG image (100 - highest; 0 - lowest)","schema":{"type":"integer","format":"int64","default":100,"minimum":0,"maximum":100}},"show_user_mask":{"in":"query","name":"show_user_mask","schema":{"type":"boolean","default":false},"description":"Show user mask"},"resolution_ring":{"in":"query","name":"show_res_ring","description":"Show resolution ring, provided in Angstrom","schema":{"type":"number","format":"float","default":0.1,"minimum":0.1,"maximum":100}},"resolution_estimate":{"in":"query","name":"show_res_est","description":"Show resolution estimation as a ring","schema":{"type":"boolean","default":false}},"color_scale":{"in":"query","name":"color","description":"Color scale for preview image","schema":{"type":"string","enum":["indigo","viridis","bw","wb","green","heat","magma","inferno"],"default":"indigo"}}},"schemas":{"grid_scan":{"description":"Definition of a grid scan (mutually exclusive with `rotation_axis`)","type":"object","required":["n_fast","step_x_um","step_y_um"],"properties":{"n_fast":{"type":"integer","format":"int64","minimum":1,"example":20,"description":"Number of elements in the fast direction"},"step_x_um":{"type":"number","format":"float","example":5,"description":"Step in grid along the fast direction. Can be negative. \nPositive number: left to right\nNegative number: right to left\n"},"step_y_um":{"type":"number","format":"float","example":-3,"description":"Step in grid along the slow direction. Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\n","enum":["BeamCenter","OrientationOnly","None"]},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. If left empty, no file will be saved."},"images_per_file":{"type":"integer","format":"int64","minimum":0,"default":1000,"description":"Number of files in a single HDF5 data file (0 = write all images to a single data file)."},"space_group_number":{"type":"integer","format":"int64","minimum":1,"maximum":194,"description":"Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. 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This can be either automatically incremented or provided externally for each data collection.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number).\n"},"images_expected":{"type":"integer","format":"int64"},"images_collected":{"type":"integer","format":"int64","description":"Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.\n"},"images_sent":{"type":"integer","format":"int64","description":"Images sent to the writer. \nThe value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.\n"},"images_written":{"type":"integer","format":"int64","description":"Images successfully written to disk.\nThe value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.\n"},"images_discarded_lossy_compression":{"type":"integer","format":"int64","description":"Images discarded by the lossy compression 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NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. \nhttps://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource\nNXsource allows the following:\n\nSpallation Neutron Source\nPulsed Reactor Neutron Source\nReactor Neutron Source\nSynchrotron X-ray Source\nPulsed Muon Source\nRotating Anode X-ray\nFixed Tube X-ray\nUV Laser\nFree-Electron Laser\nOptical Laser\nIon Source\nUV Plasma Source\nMetal Jet X-ray\n","example":"Synchrotron X-ray Source","default":""},"instrument_name":{"type":"string","example":"CristallinaMX"},"pulsed_source":{"type":"boolean","description":"Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)\n","default":false},"electron_source":{"type":"boolean","description":"Settings specific to electron source (e.g., wavelength definition)\n","default":false}}},"detector_module_direction":{"type":"string","enum":["Xp","Xn","Yp","Yn"]},"detector_type":{"type":"string","enum":["EIGER","JUNGFRAU","DECTRIS"]},"image_pusher_type":{"type":"string","default":"None","enum":["ZeroMQ","HDF5","CBOR","TCP","None"]},"standard_detector_geometry":{"type":"object","description":"Regular rectangular geometry, first module is in the bottom left corner of the detector","required":["nmodules"],"properties":{"nmodules":{"type":"integer","minimum":1,"description":"Number of modules in the detector"},"gap_x":{"type":"integer","default":8,"minimum":0,"description":"Gap size in X direction [pixels]"},"gap_y":{"type":"integer","minimum":0,"default":36,"description":"Gap size in Y direction [pixels]"},"modules_in_row":{"type":"integer","minimum":1,"default":1,"description":"Number of modules in one row"}}},"detector_module":{"type":"object","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number"},"y0":{"type":"number"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. 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Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - 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see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask.tiff":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (TIFF)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as TIFF (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. \nUser mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.\n","requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/preview/pedestal.tiff":{"get":{"parameters":[{"in":"query","name":"gain_level","required":true,"schema":{"type":"integer"},"description":"Gain level (0, 1, 2)"},{"in":"query","name":"sc","schema":{"type":"integer"},"description":"Storage cell number"}],"summary":"Get pedestal in TIFF format","responses":{"200":{"description":"Calibration image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Invalid gain level or storage cell number"},"404":{"description":"No calibration recorded so far"}}}},"/preview/plot":{"get":{"summary":"Generate 1D plot from Jungfraujoch","parameters":[{"$ref":"#/components/parameters/binning"},{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/fill_value"},{"$ref":"#/components/parameters/experimental_coord"},{"$ref":"#/components/parameters/azint_unit"}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/plots"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/preview/plot.bin":{"get":{"summary":"Generate 1D plot from Jungfraujoch and send in raw binary format.\nData are provided as (32-bit) float binary array.\nThis format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.\n","parameters":[{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/roi"}],"responses":{"200":{"description":"Everything OK.","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/result/scan":{"get":{"summary":"Get full scan result","responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/scan_result"}}}},"404":{"description":"No grid scan recorded"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/start.cbor":{"get":{"summary":"Get Start message in CBOR format","description":"Contains metadata for a dataset (e.g., experimental geometry)","responses":{"200":{"description":"Return start message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"No measurement so far"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.cbor":{"get":{"summary":"Get image message in CBOR format","description":"Contains full image data and metadata. The image must come from the latest data collection.","parameters":[{"$ref":"#/components/parameters/image_id"}],"responses":{"200":{"description":"Return image message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.jpeg":{"get":{"summary":"Get preview image in JPEG format using custom settings","parameters":[{"$ref":"#/components/parameters/image_id"},{"$ref":"#/components/parameters/show_user_mask"},{"$ref":"#/components/parameters/show_roi"},{"$ref":"#/components/parameters/show_spots"},{"$ref":"#/components/parameters/show_beam_center"},{"$ref":"#/components/parameters/saturation"},{"$ref":"#/components/parameters/jpeg_quality"},{"$ref":"#/components/parameters/resolution_ring"},{"$ref":"#/components/parameters/color_scale"},{"$ref":"#/components/parameters/resolution_estimate"}],"responses":{"200":{"description":"Preview image","content":{"image/jpeg":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.tiff":{"get":{"summary":"Get preview image in TIFF format","parameters":[{"$ref":"#/components/parameters/image_id"}],"responses":{"200":{"description":"Preview image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"404":{"description":"No preview image recorded so far"}}}},"/image_buffer/clear":{"post":{"summary":"Clear image buffer","description":"Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.","responses":{"200":{"description":"Done"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/status":{"get":{"summary":"Get status of the image buffers","description":"Can be run at any stage of Jungfraujoch operation, including during data collection.\nThe status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,\nthen image might be replaced in the buffer between calling /images and /image.cbor.\n","responses":{"200":{"description":"Done","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_buffer_status"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/version":{"get":{"summary":"Get Jungfraujoch version of jfjoch_broker","responses":{"200":{"description":"Release number of 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voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real 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One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; 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       var container = document.getElementById('redoc');
       Redoc.hydrate(__redoc_state, container);
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index ce7f67a6..cae444e1 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Changelog
 ## 1.0.0
+### 1.0.0-rc.153
+This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.
+
+* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
+* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
+* jfjoch_broker: Add ROI calculation in non-FPGA workflow
+* jfjoch_broker: Fixes to TCP image pusher
+* jfjoch_broker: Remove NUMA bindings
+* jfjoch_broker: Improvements to indexing
+
 ### 1.0.0-rc.152
 * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5)
 * jfjoch_viewer: Adjust Q bounds for azimuthal integration
diff --git a/docs/conf.py b/docs/conf.py
index adab566d..029de2d0 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -9,7 +9,7 @@
 project = 'Jungfraujoch'
 copyright = '2024, Paul Scherrer Institute'
 author = 'Filip Leonarski'
-release = '1.0.0-rc.152'
+release = '1.0.0-rc.153'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/docs/python_client/README.md b/docs/python_client/README.md
index 4fc31bd8..5dff536f 100644
--- a/docs/python_client/README.md
+++ b/docs/python_client/README.md
@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.152
-- Package version: 1.0.0-rc.152
+- API version: 1.0.0-rc.153
+- Package version: 1.0.0-rc.153
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 
diff --git a/docs/python_client/docs/DefaultApi.md b/docs/python_client/docs/DefaultApi.md
index 7db29ad4..2c5169c6 100644
--- a/docs/python_client/docs/DefaultApi.md
+++ b/docs/python_client/docs/DefaultApi.md
@@ -2069,9 +2069,9 @@ Should be in `Idle` state.
 Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
 If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
 In the latter case - module gaps are ignored and don't need to be assigned value.
-Mask is expected as TIFF (4-byte; unsigned).
+Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
 0 - good pixel, other value - masked
-User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. 
+User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
 User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
 
 
@@ -2130,6 +2130,7 @@ No authorization required
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
 **200** | All good |  -  |
+**400** | Not a valid single-channel TIFF or size doesn&#39;t match the detector |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
diff --git a/fpga/hdl/action_config.v b/fpga/hdl/action_config.v
index 99f37906..7b27a15c 100644
--- a/fpga/hdl/action_config.v
+++ b/fpga/hdl/action_config.v
@@ -10,7 +10,7 @@ localparam signed [31:0] INT32_MIN = 32'sh80000000;
 `define JFJOCH_FPGA_MAJOR_VERSION 8'd1
 `define JFJOCH_FPGA_MINOR_VERSION 8'd0
 `define JFJOCH_FPGA_PATCH_VERSION 8'd0
-`define JFJOCH_FPGA_PRERELEASE 64'h3235312E6372
+`define JFJOCH_FPGA_PRERELEASE 64'h3335312E6372
 
 `define GIT_SHA1 32'h
 `define MAX_MODULES_FPGA 32'd16
diff --git a/fpga/pcie_driver/dkms.conf b/fpga/pcie_driver/dkms.conf
index 297e130e..e0b05757 100644
--- a/fpga/pcie_driver/dkms.conf
+++ b/fpga/pcie_driver/dkms.conf
@@ -1,5 +1,5 @@
 PACKAGE_NAME=jfjoch
-PACKAGE_VERSION=1.0.0-rc.152
+PACKAGE_VERSION=1.0.0-rc.153
 
 DEST_MODULE_LOCATION=/extra
 BUILT_MODULE_NAME=jfjoch
diff --git a/fpga/pcie_driver/install_dkms.sh b/fpga/pcie_driver/install_dkms.sh
index 60971356..b6d0d4e6 100755
--- a/fpga/pcie_driver/install_dkms.sh
+++ b/fpga/pcie_driver/install_dkms.sh
@@ -2,7 +2,7 @@
 
 # Copyright (2019-2024) Paul Scherrer Institute
 
-VERSION=1.0.0-rc.152
+VERSION=1.0.0-rc.153
 
 mkdir -p /usr/src/jfjoch-${VERSION}/src
 cp dkms.conf /usr/src/jfjoch-${VERSION}
diff --git a/fpga/pcie_driver/jfjoch_drv.c b/fpga/pcie_driver/jfjoch_drv.c
index 8eca024b..54f91a98 100644
--- a/fpga/pcie_driver/jfjoch_drv.c
+++ b/fpga/pcie_driver/jfjoch_drv.c
@@ -12,7 +12,7 @@
 MODULE_AUTHOR("Filip Leonarski; Paul Scherrer Institute");
 MODULE_DESCRIPTION("Jungfraujoch device module");
 MODULE_LICENSE("GPL");
-MODULE_VERSION("1.0.0-rc.152");
+MODULE_VERSION("1.0.0-rc.153");
 
 #define PCI_DEV_ID_JUNGFRAUJOCH        (0x3450)
 
diff --git a/fpga/pcie_driver/postinstall.sh b/fpga/pcie_driver/postinstall.sh
index 3521df6d..c1b69fa9 100644
--- a/fpga/pcie_driver/postinstall.sh
+++ b/fpga/pcie_driver/postinstall.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
 
-VERSION=1.0.0-rc.152
+VERSION=1.0.0-rc.153
 
 occurrences=`/usr/sbin/dkms status | grep jfjoch | grep ${VERSION} | wc -l`
 
diff --git a/fpga/pcie_driver/preuninstall.sh b/fpga/pcie_driver/preuninstall.sh
index 00e44da5..06c49080 100644
--- a/fpga/pcie_driver/preuninstall.sh
+++ b/fpga/pcie_driver/preuninstall.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
 
-VERSION=1.0.0-rc.152
+VERSION=1.0.0-rc.153
 
 /usr/sbin/dkms remove -m jfjoch -v ${VERSION} --all
 
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 78e9bb57..6d84e871 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.151",
+  "version": "1.0.0-rc.152",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "jungfraujoch-frontend",
-      "version": "1.0.0-rc.151",
+      "version": "1.0.0-rc.152",
       "license": "GPL-3.0",
       "dependencies": {
         "@emotion/react": "^11.10.4",
diff --git a/frontend/package.json b/frontend/package.json
index ebaf626a..d4ce664d 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -1,6 +1,6 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.152",
+  "version": "1.0.0-rc.153",
   "license": "GPL-3.0",
   "private": true,
   "homepage": "/frontend",
diff --git a/frontend/src/openapi/core/OpenAPI.ts b/frontend/src/openapi/core/OpenAPI.ts
index 3a8317d6..104efe50 100644
--- a/frontend/src/openapi/core/OpenAPI.ts
+++ b/frontend/src/openapi/core/OpenAPI.ts
@@ -21,7 +21,7 @@ export type OpenAPIConfig = {
 
 export const OpenAPI: OpenAPIConfig = {
     BASE: 'http://localhost:5232',
-    VERSION: '1.0.0-rc.152',
+    VERSION: '1.0.0-rc.153',
     WITH_CREDENTIALS: false,
     CREDENTIALS: 'include',
     TOKEN: undefined,
diff --git a/frontend/src/openapi/services/DefaultService.ts b/frontend/src/openapi/services/DefaultService.ts
index 959f5957..0d737f15 100644
--- a/frontend/src/openapi/services/DefaultService.ts
+++ b/frontend/src/openapi/services/DefaultService.ts
@@ -967,7 +967,7 @@ export class DefaultService {
      * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
      * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
      * In the latter case - module gaps are ignored and don't need to be assigned value.
-     * Mask is expected as TIFF (4-byte; unsigned).
+     * Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
      * 0 - good pixel, other value - masked
      * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
      * User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
@@ -985,6 +985,7 @@ export class DefaultService {
             body: requestBody,
             mediaType: 'image/tiff',
             errors: {
+                400: `Not a valid single-channel TIFF or size doesn't match the detector`,
                 500: `Error within Jungfraujoch code - see output message.`,
             },
         });
diff --git a/frontend/src/version.ts b/frontend/src/version.ts
index f8de158b..416dfe51 100644
--- a/frontend/src/version.ts
+++ b/frontend/src/version.ts
@@ -1 +1 @@
-export const JFJOCH_VERSION : string = "1.0.0-rc.152";
\ No newline at end of file
+export const JFJOCH_VERSION : string = "1.0.0-rc.153";
\ No newline at end of file
-- 
2.52.0


From ceb7d31eacb4ca8188a0c4a8ac1866606538e581 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 20:30:15 +0200
Subject: [PATCH 091/228] frontend: generate OpenAPI client with
 @hey-api/openapi-ts

Replace the unmaintained openapi-typescript-codegen generator with
@hey-api/openapi-ts.

- openapi-ts.config.ts generates src/client from ../broker/jfjoch_api.yaml
  (client-fetch + typescript + sdk plugins; enums as const objects via
  mode: 'javascript', type names preserved)
- npm "openapi" script now runs openapi-ts; drop openapi-typescript-codegen
- migrate all imports from src/openapi to src/client
- DefaultService.foo() -> standalone foo({ body|query, throwOnError })
- OpenAPI.BASE='' -> client.setConfig({ baseUrl: '' }); ButtonWithSnackbar
  uses the relative path directly
- adapt hey-api's inlined enums: broker_status.state/message_severity and
  bit_depth_image/eiger_bit_depth become string/number literal unions;
  file_writer_format NXMX_* -> N_XMX_*
- remove generated src/openapi

Build (tsc + vite) passes.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/openapi-ts.config.ts                 |   17 +
 frontend/package-lock.json                    |  623 +++-
 frontend/package.json                         |    6 +-
 frontend/src/App.tsx                          |   13 +-
 frontend/src/client/client.gen.ts             |   16 +
 frontend/src/client/client/client.gen.ts      |  277 ++
 frontend/src/client/client/index.ts           |   27 +
 frontend/src/client/client/types.gen.ts       |  218 ++
 frontend/src/client/client/utils.gen.ts       |  316 ++
 frontend/src/client/core/auth.gen.ts          |   48 +
 .../src/client/core/bodySerializer.gen.ts     |   82 +
 frontend/src/client/core/params.gen.ts        |  171 +
 .../src/client/core/pathSerializer.gen.ts     |  171 +
 .../src/client/core/queryKeySerializer.gen.ts |  117 +
 .../src/client/core/serverSentEvents.gen.ts   |  242 ++
 frontend/src/client/core/types.gen.ts         |  110 +
 frontend/src/client/core/utils.gen.ts         |  140 +
 frontend/src/client/index.ts                  |    4 +
 frontend/src/client/sdk.gen.ts                |  640 ++++
 frontend/src/client/types.gen.ts              | 3219 +++++++++++++++++
 frontend/src/components/AzIntSettings.tsx     |    2 +-
 .../src/components/ButtonWithSnackbar.tsx     |    4 +-
 frontend/src/components/Calibration.tsx       |    2 +-
 frontend/src/components/DarkMaskSettings.tsx  |    2 +-
 frontend/src/components/DataCollection.tsx    |    2 +-
 .../src/components/DataProcessingPlot.tsx     |    6 +-
 .../src/components/DataProcessingPlots.tsx    |    2 +-
 .../src/components/DataProcessingSettings.tsx |    4 +-
 frontend/src/components/DetectorSelection.tsx |    2 +-
 frontend/src/components/DetectorSettings.tsx  |   18 +-
 frontend/src/components/DetectorStatus.tsx    |    2 +-
 frontend/src/components/ErrorMessage.tsx      |   12 +-
 .../src/components/FileWriterSettings.tsx     |   16 +-
 frontend/src/components/FpgaStatus.tsx        |    2 +-
 .../src/components/ImageFormatSettings.tsx    |   22 +-
 frontend/src/components/ImagePusherStatus.tsx |    2 +-
 frontend/src/components/IndexingSettings.tsx  |    2 +-
 .../src/components/InstrumentMetadata.tsx     |    2 +-
 .../src/components/MeasurementStatistics.tsx  |    2 +-
 frontend/src/components/PixelMask.tsx         |    4 +-
 frontend/src/components/PreviewImage.tsx      |    2 +-
 frontend/src/components/ROI.tsx               |    6 +-
 frontend/src/components/StatusBar.tsx         |    5 +-
 frontend/src/components/ZeroMQPreview.tsx     |    2 +-
 frontend/src/openapi/core/ApiError.ts         |   25 -
 .../src/openapi/core/ApiRequestOptions.ts     |   17 -
 frontend/src/openapi/core/ApiResult.ts        |   11 -
 .../src/openapi/core/CancelablePromise.ts     |  131 -
 frontend/src/openapi/core/OpenAPI.ts          |   32 -
 frontend/src/openapi/core/request.ts          |  320 --
 frontend/src/openapi/index.ts                 |   83 -
 .../src/openapi/models/azim_int_settings.ts   |   30 -
 frontend/src/openapi/models/azint_unit.ts     |   14 -
 frontend/src/openapi/models/background.ts     |    9 -
 frontend/src/openapi/models/binning.ts        |    9 -
 frontend/src/openapi/models/broker_status.ts  |   56 -
 .../openapi/models/calibration_statistics.ts  |   16 -
 frontend/src/openapi/models/color_scale.ts    |   18 -
 .../src/openapi/models/crystal_lattice.ts     |   11 -
 .../src/openapi/models/dark_mask_settings.ts  |   31 -
 .../src/openapi/models/dataset_settings.ts    |  231 --
 frontend/src/openapi/models/detector.ts       |   68 -
 frontend/src/openapi/models/detector_list.ts  |   12 -
 .../openapi/models/detector_list_element.ts   |   26 -
 .../src/openapi/models/detector_module.ts     |   14 -
 .../models/detector_module_direction.ts       |   11 -
 .../openapi/models/detector_power_state.ts    |   13 -
 .../src/openapi/models/detector_selection.ts  |    9 -
 .../src/openapi/models/detector_settings.ts   |   92 -
 frontend/src/openapi/models/detector_state.ts |   15 -
 .../src/openapi/models/detector_status.ts     |   29 -
 .../src/openapi/models/detector_timing.ts     |   11 -
 frontend/src/openapi/models/detector_type.ts  |   10 -
 frontend/src/openapi/models/error_message.ts  |   29 -
 .../src/openapi/models/experimental_coord.ts  |   12 -
 .../src/openapi/models/file_writer_format.ts  |   24 -
 .../openapi/models/file_writer_settings.ts    |   16 -
 frontend/src/openapi/models/fill_value.ts     |   10 -
 frontend/src/openapi/models/fpga_status.ts    |   27 -
 .../models/geom_refinement_algorithm.ts       |   16 -
 frontend/src/openapi/models/grid_scan.ts      |   40 -
 .../src/openapi/models/image_buffer_status.ts |   47 -
 .../openapi/models/image_format_settings.ts   |   84 -
 frontend/src/openapi/models/image_id.ts       |    9 -
 .../src/openapi/models/image_pusher_status.ts |   51 -
 .../src/openapi/models/image_pusher_type.ts   |   12 -
 .../src/openapi/models/indexing_algorithm.ts  |   16 -
 .../src/openapi/models/indexing_settings.ts   |   66 -
 .../src/openapi/models/instrument_metadata.ts |   44 -
 .../src/openapi/models/jfjoch_settings.ts     |   65 -
 .../src/openapi/models/jfjoch_statistics.ts   |   52 -
 frontend/src/openapi/models/jpeg_quality.ts   |    9 -
 .../openapi/models/measurement_statistics.ts  |   82 -
 frontend/src/openapi/models/pcie_devices.ts   |   15 -
 .../openapi/models/pixel_mask_statistics.ts   |   20 -
 frontend/src/openapi/models/plot.ts           |   15 -
 frontend/src/openapi/models/plot_type.ts      |   48 -
 frontend/src/openapi/models/plot_unit_x.ts    |   13 -
 frontend/src/openapi/models/plots.ts          |   22 -
 .../src/openapi/models/resolution_estimate.ts |    9 -
 .../src/openapi/models/resolution_ring.ts     |    9 -
 frontend/src/openapi/models/roi.ts            |    9 -
 frontend/src/openapi/models/roi_azim_list.ts  |   14 -
 frontend/src/openapi/models/roi_azimuthal.ts  |   23 -
 frontend/src/openapi/models/roi_box.ts        |   31 -
 frontend/src/openapi/models/roi_box_list.ts   |   14 -
 frontend/src/openapi/models/roi_circle.ts     |   27 -
 .../src/openapi/models/roi_circle_list.ts     |   14 -
 .../src/openapi/models/roi_definitions.ts     |   18 -
 frontend/src/openapi/models/rotation_axis.ts  |   35 -
 frontend/src/openapi/models/saturation.ts     |    9 -
 frontend/src/openapi/models/scan_result.ts    |   97 -
 .../src/openapi/models/show_beam_center.ts    |    9 -
 frontend/src/openapi/models/show_roi.ts       |    9 -
 frontend/src/openapi/models/show_spots.ts     |    9 -
 frontend/src/openapi/models/show_user_mask.ts |    9 -
 .../openapi/models/spot_finding_settings.ts   |   53 -
 .../models/standard_detector_geometry.ts      |   27 -
 frontend/src/openapi/models/tcp_settings.ts   |   27 -
 frontend/src/openapi/models/unit_cell.ts      |   17 -
 .../models/zeromq_metadata_settings.ts        |   25 -
 .../openapi/models/zeromq_preview_settings.ts |   27 -
 .../src/openapi/models/zeromq_settings.ts     |   38 -
 .../src/openapi/services/DefaultService.ts    | 1258 -------
 124 files changed, 6418 insertions(+), 4179 deletions(-)
 create mode 100644 frontend/openapi-ts.config.ts
 create mode 100644 frontend/src/client/client.gen.ts
 create mode 100644 frontend/src/client/client/client.gen.ts
 create mode 100644 frontend/src/client/client/index.ts
 create mode 100644 frontend/src/client/client/types.gen.ts
 create mode 100644 frontend/src/client/client/utils.gen.ts
 create mode 100644 frontend/src/client/core/auth.gen.ts
 create mode 100644 frontend/src/client/core/bodySerializer.gen.ts
 create mode 100644 frontend/src/client/core/params.gen.ts
 create mode 100644 frontend/src/client/core/pathSerializer.gen.ts
 create mode 100644 frontend/src/client/core/queryKeySerializer.gen.ts
 create mode 100644 frontend/src/client/core/serverSentEvents.gen.ts
 create mode 100644 frontend/src/client/core/types.gen.ts
 create mode 100644 frontend/src/client/core/utils.gen.ts
 create mode 100644 frontend/src/client/index.ts
 create mode 100644 frontend/src/client/sdk.gen.ts
 create mode 100644 frontend/src/client/types.gen.ts
 delete mode 100644 frontend/src/openapi/core/ApiError.ts
 delete mode 100644 frontend/src/openapi/core/ApiRequestOptions.ts
 delete mode 100644 frontend/src/openapi/core/ApiResult.ts
 delete mode 100644 frontend/src/openapi/core/CancelablePromise.ts
 delete mode 100644 frontend/src/openapi/core/OpenAPI.ts
 delete mode 100644 frontend/src/openapi/core/request.ts
 delete mode 100644 frontend/src/openapi/index.ts
 delete mode 100644 frontend/src/openapi/models/azim_int_settings.ts
 delete mode 100644 frontend/src/openapi/models/azint_unit.ts
 delete mode 100644 frontend/src/openapi/models/background.ts
 delete mode 100644 frontend/src/openapi/models/binning.ts
 delete mode 100644 frontend/src/openapi/models/broker_status.ts
 delete mode 100644 frontend/src/openapi/models/calibration_statistics.ts
 delete mode 100644 frontend/src/openapi/models/color_scale.ts
 delete mode 100644 frontend/src/openapi/models/crystal_lattice.ts
 delete mode 100644 frontend/src/openapi/models/dark_mask_settings.ts
 delete mode 100644 frontend/src/openapi/models/dataset_settings.ts
 delete mode 100644 frontend/src/openapi/models/detector.ts
 delete mode 100644 frontend/src/openapi/models/detector_list.ts
 delete mode 100644 frontend/src/openapi/models/detector_list_element.ts
 delete mode 100644 frontend/src/openapi/models/detector_module.ts
 delete mode 100644 frontend/src/openapi/models/detector_module_direction.ts
 delete mode 100644 frontend/src/openapi/models/detector_power_state.ts
 delete mode 100644 frontend/src/openapi/models/detector_selection.ts
 delete mode 100644 frontend/src/openapi/models/detector_settings.ts
 delete mode 100644 frontend/src/openapi/models/detector_state.ts
 delete mode 100644 frontend/src/openapi/models/detector_status.ts
 delete mode 100644 frontend/src/openapi/models/detector_timing.ts
 delete mode 100644 frontend/src/openapi/models/detector_type.ts
 delete mode 100644 frontend/src/openapi/models/error_message.ts
 delete mode 100644 frontend/src/openapi/models/experimental_coord.ts
 delete mode 100644 frontend/src/openapi/models/file_writer_format.ts
 delete mode 100644 frontend/src/openapi/models/file_writer_settings.ts
 delete mode 100644 frontend/src/openapi/models/fill_value.ts
 delete mode 100644 frontend/src/openapi/models/fpga_status.ts
 delete mode 100644 frontend/src/openapi/models/geom_refinement_algorithm.ts
 delete mode 100644 frontend/src/openapi/models/grid_scan.ts
 delete mode 100644 frontend/src/openapi/models/image_buffer_status.ts
 delete mode 100644 frontend/src/openapi/models/image_format_settings.ts
 delete mode 100644 frontend/src/openapi/models/image_id.ts
 delete mode 100644 frontend/src/openapi/models/image_pusher_status.ts
 delete mode 100644 frontend/src/openapi/models/image_pusher_type.ts
 delete mode 100644 frontend/src/openapi/models/indexing_algorithm.ts
 delete mode 100644 frontend/src/openapi/models/indexing_settings.ts
 delete mode 100644 frontend/src/openapi/models/instrument_metadata.ts
 delete mode 100644 frontend/src/openapi/models/jfjoch_settings.ts
 delete mode 100644 frontend/src/openapi/models/jfjoch_statistics.ts
 delete mode 100644 frontend/src/openapi/models/jpeg_quality.ts
 delete mode 100644 frontend/src/openapi/models/measurement_statistics.ts
 delete mode 100644 frontend/src/openapi/models/pcie_devices.ts
 delete mode 100644 frontend/src/openapi/models/pixel_mask_statistics.ts
 delete mode 100644 frontend/src/openapi/models/plot.ts
 delete mode 100644 frontend/src/openapi/models/plot_type.ts
 delete mode 100644 frontend/src/openapi/models/plot_unit_x.ts
 delete mode 100644 frontend/src/openapi/models/plots.ts
 delete mode 100644 frontend/src/openapi/models/resolution_estimate.ts
 delete mode 100644 frontend/src/openapi/models/resolution_ring.ts
 delete mode 100644 frontend/src/openapi/models/roi.ts
 delete mode 100644 frontend/src/openapi/models/roi_azim_list.ts
 delete mode 100644 frontend/src/openapi/models/roi_azimuthal.ts
 delete mode 100644 frontend/src/openapi/models/roi_box.ts
 delete mode 100644 frontend/src/openapi/models/roi_box_list.ts
 delete mode 100644 frontend/src/openapi/models/roi_circle.ts
 delete mode 100644 frontend/src/openapi/models/roi_circle_list.ts
 delete mode 100644 frontend/src/openapi/models/roi_definitions.ts
 delete mode 100644 frontend/src/openapi/models/rotation_axis.ts
 delete mode 100644 frontend/src/openapi/models/saturation.ts
 delete mode 100644 frontend/src/openapi/models/scan_result.ts
 delete mode 100644 frontend/src/openapi/models/show_beam_center.ts
 delete mode 100644 frontend/src/openapi/models/show_roi.ts
 delete mode 100644 frontend/src/openapi/models/show_spots.ts
 delete mode 100644 frontend/src/openapi/models/show_user_mask.ts
 delete mode 100644 frontend/src/openapi/models/spot_finding_settings.ts
 delete mode 100644 frontend/src/openapi/models/standard_detector_geometry.ts
 delete mode 100644 frontend/src/openapi/models/tcp_settings.ts
 delete mode 100644 frontend/src/openapi/models/unit_cell.ts
 delete mode 100644 frontend/src/openapi/models/zeromq_metadata_settings.ts
 delete mode 100644 frontend/src/openapi/models/zeromq_preview_settings.ts
 delete mode 100644 frontend/src/openapi/models/zeromq_settings.ts
 delete mode 100644 frontend/src/openapi/services/DefaultService.ts

diff --git a/frontend/openapi-ts.config.ts b/frontend/openapi-ts.config.ts
new file mode 100644
index 00000000..a35193eb
--- /dev/null
+++ b/frontend/openapi-ts.config.ts
@@ -0,0 +1,17 @@
+import { defineConfig } from '@hey-api/openapi-ts';
+
+export default defineConfig({
+    input: '../broker/jfjoch_api.yaml',
+    output: {
+        path: 'src/client',
+    },
+    plugins: [
+        '@hey-api/client-fetch',
+        {
+            name: '@hey-api/typescript',
+            case: 'preserve',
+            enums: { mode: 'javascript' },
+        },
+        '@hey-api/sdk',
+    ],
+});
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 6d84e871..619f1e11 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.152",
+  "version": "1.0.0-rc.153",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "jungfraujoch-frontend",
-      "version": "1.0.0-rc.152",
+      "version": "1.0.0-rc.153",
       "license": "GPL-3.0",
       "dependencies": {
         "@emotion/react": "^11.10.4",
@@ -30,11 +30,11 @@
         "vite-tsconfig-paths": "^6.1.1"
       },
       "devDependencies": {
+        "@hey-api/openapi-ts": "^0.98.2",
         "@redocly/cli": "^2.28.1",
         "@types/lodash": "^4.17.10",
         "@types/react-plotly.js": "^2.6.3",
-        "esbuild-style-plugin": "^1.6.3",
-        "openapi-typescript-codegen": "^0.25.0"
+        "esbuild-style-plugin": "^1.6.3"
       }
     },
     "node_modules/@ampproject/remapping": {
@@ -49,18 +49,6 @@
         "node": ">=6.0.0"
       }
     },
-    "node_modules/@apidevtools/json-schema-ref-parser": {
-      "version": "9.0.9",
-      "resolved": "https://registry.npmjs.org/@apidevtools/json-schema-ref-parser/-/json-schema-ref-parser-9.0.9.tgz",
-      "integrity": "sha512-GBD2Le9w2+lVFoc4vswGI/TjkNIZSVp7+9xPf+X3uidBfWnAeUWmquteSyt0+VCrhNMWj/FTABISQrD3Z/YA+w==",
-      "dev": true,
-      "dependencies": {
-        "@jsdevtools/ono": "^7.1.3",
-        "@types/json-schema": "^7.0.6",
-        "call-me-maybe": "^1.0.1",
-        "js-yaml": "^4.1.0"
-      }
-    },
     "node_modules/@babel/code-frame": {
       "version": "7.26.2",
       "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.26.2.tgz",
@@ -928,6 +916,127 @@
         "npm": ">=6.0.0"
       }
     },
+    "node_modules/@hey-api/codegen-core": {
+      "version": "0.9.0",
+      "resolved": "https://registry.npmjs.org/@hey-api/codegen-core/-/codegen-core-0.9.0.tgz",
+      "integrity": "sha512-OK9/R8WuujwgvnrDIPnEiIf6WnfUOi3GaEr6kIngqoI5FUQwYbeDKHE/frTVUl2A76ZQPCrMknHtPx6Gqtwf8Q==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@hey-api/types": "0.1.4",
+        "ansi-colors": "4.1.3",
+        "c12": "3.3.4",
+        "color-support": "1.1.3"
+      },
+      "engines": {
+        "node": ">=22.18.0"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/hey-api"
+      }
+    },
+    "node_modules/@hey-api/json-schema-ref-parser": {
+      "version": "1.4.3",
+      "resolved": "https://registry.npmjs.org/@hey-api/json-schema-ref-parser/-/json-schema-ref-parser-1.4.3.tgz",
+      "integrity": "sha512-UzGSDzh3QUhrnwl4atnHc2YqDO6KemYVEOwl1Ynowm/tcr0XlpdHOpyWr5UaWIJfiXTXdYRIC9k2Yxm19pcPzQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@jsdevtools/ono": "7.1.3",
+        "@types/json-schema": "7.0.15",
+        "js-yaml": "4.1.1"
+      },
+      "engines": {
+        "node": ">=22.18.0"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/hey-api"
+      }
+    },
+    "node_modules/@hey-api/openapi-ts": {
+      "version": "0.98.2",
+      "resolved": "https://registry.npmjs.org/@hey-api/openapi-ts/-/openapi-ts-0.98.2.tgz",
+      "integrity": "sha512-2nVJXH8tpFPGTBOhxyjEd1Jw0hsRqJqeTQW3kltAjVdSU4YWxeu97x5sgNOmsbsfeg6Dqz7Wfzs26walBOuswA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@hey-api/codegen-core": "0.9.0",
+        "@hey-api/json-schema-ref-parser": "1.4.3",
+        "@hey-api/shared": "0.4.8",
+        "@hey-api/spec-types": "0.2.0",
+        "@hey-api/types": "0.1.4",
+        "@lukeed/ms": "2.0.2",
+        "ansi-colors": "4.1.3",
+        "color-support": "1.1.3",
+        "commander": "15.0.0",
+        "get-tsconfig": "4.14.0"
+      },
+      "bin": {
+        "openapi-ts": "bin/run.js"
+      },
+      "engines": {
+        "node": ">=22.18.0"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/hey-api"
+      },
+      "peerDependencies": {
+        "typescript": ">=5.5.3 || >=6.0.0 || 6.0.1-rc"
+      }
+    },
+    "node_modules/@hey-api/openapi-ts/node_modules/commander": {
+      "version": "15.0.0",
+      "resolved": "https://registry.npmjs.org/commander/-/commander-15.0.0.tgz",
+      "integrity": "sha512-z67u4ZhzCL/Tydu1lJARtEZYWbWaN7oYLHbsuzocr6y4N6WZAagG3RQ4FW61V1/0+jImpj293XfrcYnd1qxtPg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=22.12.0"
+      }
+    },
+    "node_modules/@hey-api/shared": {
+      "version": "0.4.8",
+      "resolved": "https://registry.npmjs.org/@hey-api/shared/-/shared-0.4.8.tgz",
+      "integrity": "sha512-29Pg2FB0UW20pplYgcfiQn1hQYpbZ9D2gdDJc7nDK3xh3pvHOTGP0v3R2ueFpFnw9GN1SRhIdhiVuAYWMDimjA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@hey-api/codegen-core": "0.9.0",
+        "@hey-api/json-schema-ref-parser": "1.4.3",
+        "@hey-api/spec-types": "0.2.0",
+        "@hey-api/types": "0.1.4",
+        "ansi-colors": "4.1.3",
+        "cross-spawn": "7.0.6",
+        "open": "11.0.0",
+        "semver": "7.8.2"
+      },
+      "engines": {
+        "node": ">=22.18.0"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/hey-api"
+      }
+    },
+    "node_modules/@hey-api/spec-types": {
+      "version": "0.2.0",
+      "resolved": "https://registry.npmjs.org/@hey-api/spec-types/-/spec-types-0.2.0.tgz",
+      "integrity": "sha512-ibQ8Is7evMavzr8GNyJCcTg975d8DpaMUyLmOrQ85UBdy1l6t1KuRAwgChAbesJsIlNV6gjmlXruWyegDX18Fg==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@hey-api/types": "0.1.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/hey-api"
+      }
+    },
+    "node_modules/@hey-api/types": {
+      "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/@hey-api/types/-/types-0.1.4.tgz",
+      "integrity": "sha512-thWfawrDIP7wSI9ioT13I5soaaqB5vAPIiZmgD8PbeEVKNrkonc0N/Sjj97ezl7oQgusZmaNphGdMKipPO6IBg==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/@humanwhocodes/momoa": {
       "version": "2.0.4",
       "resolved": "https://registry.npmjs.org/@humanwhocodes/momoa/-/momoa-2.0.4.tgz",
@@ -1094,6 +1203,16 @@
       "integrity": "sha512-4JQNk+3mVzK3xh2rqd6RB4J46qUR19azEHBneZyTZM+c456qOrbbM/5xcR8huNCCcbVt7+UmizG6GuUvPvKUYg==",
       "dev": true
     },
+    "node_modules/@lukeed/ms": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/@lukeed/ms/-/ms-2.0.2.tgz",
+      "integrity": "sha512-9I2Zn6+NJLfaGoz9jN3lpwDgAYvfGeNYdbAIjJOqzs4Tpc+VU3Jqq4IofSUBKajiDS8k9fZIg18/z13mpk1bsA==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/@mapbox/geojson-rewind": {
       "version": "0.5.2",
       "resolved": "https://registry.npmjs.org/@mapbox/geojson-rewind/-/geojson-rewind-0.5.2.tgz",
@@ -3702,6 +3821,16 @@
       "integrity": "sha512-0V/PkoculFl5+0Lp47JoxUcO0xSxhIBvm+BxHdD/OgXNmdRpRHCFnKVuUoWyS9EzQP+otSGv0m9Lb4yVkQBn2A==",
       "peer": true
     },
+    "node_modules/ansi-colors": {
+      "version": "4.1.3",
+      "resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-4.1.3.tgz",
+      "integrity": "sha512-/6w/C21Pm1A7aZitlI5Ni/2J6FFQN8i1Cvz3kHABAAbw93v/NlvKdVOqz7CCWz/3iv/JplRSEEZ83XION15ovw==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=6"
+      }
+    },
     "node_modules/ansi-regex": {
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz",
@@ -3968,6 +4097,64 @@
       "integrity": "sha512-E+XQCRwSbaaiChtv6k6Dwgc+bx+Bs6vuKJHHl5kox/BaKbhiXzqQOwK4cO22yElGp2OCmjwVhT3HmxgyPGnJfQ==",
       "peer": true
     },
+    "node_modules/bundle-name": {
+      "version": "4.1.0",
+      "resolved": "https://registry.npmjs.org/bundle-name/-/bundle-name-4.1.0.tgz",
+      "integrity": "sha512-tjwM5exMg6BGRI+kNmTntNsvdZS1X8BFYS6tnJ2hdH0kVxM6/eVZ2xy+FqStSWvYmtfFMDLIxurorHwDKfDz5Q==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "run-applescript": "^7.0.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/c12": {
+      "version": "3.3.4",
+      "resolved": "https://registry.npmjs.org/c12/-/c12-3.3.4.tgz",
+      "integrity": "sha512-cM0ApFQSBXuourJejzwv/AuPRvAxordTyParRVcHjjtXirtkzM0uK2L9TTn9s0cXZbG7E55jCivRQzoxYmRAlA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "chokidar": "^5.0.0",
+        "confbox": "^0.2.4",
+        "defu": "^6.1.6",
+        "dotenv": "^17.3.1",
+        "exsolve": "^1.0.8",
+        "giget": "^3.2.0",
+        "jiti": "^2.6.1",
+        "ohash": "^2.0.11",
+        "pathe": "^2.0.3",
+        "perfect-debounce": "^2.1.0",
+        "pkg-types": "^2.3.0",
+        "rc9": "^3.0.1"
+      },
+      "peerDependencies": {
+        "magicast": "*"
+      },
+      "peerDependenciesMeta": {
+        "magicast": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/c12/node_modules/dotenv": {
+      "version": "17.4.2",
+      "resolved": "https://registry.npmjs.org/dotenv/-/dotenv-17.4.2.tgz",
+      "integrity": "sha512-nI4U3TottKAcAD9LLud4Cb7b2QztQMUEfHbvhTH09bqXTxnSie8WnjPALV/WMCrJZ6UV/qHJ6L03OqO3LcdYZw==",
+      "dev": true,
+      "license": "BSD-2-Clause",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://dotenvx.com"
+      }
+    },
     "node_modules/call-me-maybe": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/call-me-maybe/-/call-me-maybe-1.0.2.tgz",
@@ -4049,6 +4236,22 @@
         "url": "https://github.com/chalk/chalk?sponsor=1"
       }
     },
+    "node_modules/chokidar": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-5.0.0.tgz",
+      "integrity": "sha512-TQMmc3w+5AxjpL8iIiwebF73dRDF4fBIieAqGn9RGCWaEVwQ6Fb2cGe31Yns0RRIzii5goJ1Y7xbMwo1TxMplw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "readdirp": "^5.0.0"
+      },
+      "engines": {
+        "node": ">= 20.19.0"
+      },
+      "funding": {
+        "url": "https://paulmillr.com/funding/"
+      }
+    },
     "node_modules/clamp": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/clamp/-/clamp-1.0.1.tgz",
@@ -4176,6 +4379,16 @@
         "mumath": "^3.3.4"
       }
     },
+    "node_modules/color-support": {
+      "version": "1.1.3",
+      "resolved": "https://registry.npmjs.org/color-support/-/color-support-1.1.3.tgz",
+      "integrity": "sha512-qiBjkpbMLO/HL68y+lh4q0/O1MZFj2RX6X/KmMa3+gJD3z+WwI1ZzDHysvqHGS3mP6mznPckpXmw1nI9cJjyRg==",
+      "dev": true,
+      "license": "ISC",
+      "bin": {
+        "color-support": "bin.js"
+      }
+    },
     "node_modules/colorette": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/colorette/-/colorette-1.4.0.tgz",
@@ -4183,14 +4396,12 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/commander": {
-      "version": "11.1.0",
-      "resolved": "https://registry.npmjs.org/commander/-/commander-11.1.0.tgz",
-      "integrity": "sha512-yPVavfyCcRhmorC7rWlkHn15b4wDVgVmBA7kV4QVBsF7kv/9TKJAbAXVTxvTnwP8HHKjRCJDClKbciiYS7p0DQ==",
+    "node_modules/confbox": {
+      "version": "0.2.4",
+      "resolved": "https://registry.npmjs.org/confbox/-/confbox-0.2.4.tgz",
+      "integrity": "sha512-ysOGlgTFbN2/Y6Cg3Iye8YKulHw+R2fNXHrgSmXISQdMnomY6eNDprVdW9R5xBguEqI954+S6709UyiO7B+6OQ==",
       "dev": true,
-      "engines": {
-        "node": ">=16"
-      }
+      "license": "MIT"
     },
     "node_modules/convert-source-map": {
       "version": "1.9.0",
@@ -4564,6 +4775,49 @@
       "integrity": "sha512-m8FnyHXV1QX+S1cl+KPFDIl6NMkxtKsy6+U/aYyjrOqWMuwAwYWu7ePqrsUHtDR5Y8Yk2pi/KIDSgF+vT4cPOQ==",
       "dev": true
     },
+    "node_modules/default-browser": {
+      "version": "5.5.0",
+      "resolved": "https://registry.npmjs.org/default-browser/-/default-browser-5.5.0.tgz",
+      "integrity": "sha512-H9LMLr5zwIbSxrmvikGuI/5KGhZ8E2zH3stkMgM5LpOWDutGM2JZaj460Udnf1a+946zc7YBgrqEWwbk7zHvGw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "bundle-name": "^4.1.0",
+        "default-browser-id": "^5.0.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/default-browser-id": {
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/default-browser-id/-/default-browser-id-5.0.1.tgz",
+      "integrity": "sha512-x1VCxdX4t+8wVfd1so/9w+vQ4vx7lKd2Qp5tDRutErwmR85OgmfX7RlLRMWafRMY7hbEiXIbudNrjOAPa/hL8Q==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/define-lazy-prop": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/define-lazy-prop/-/define-lazy-prop-3.0.0.tgz",
+      "integrity": "sha512-N+MeXYoqr3pOgn8xfyRPREN7gHakLYjhsHhWGT3fWAiL4IkAt0iDw14QiiEm2bE30c5XX5q0FtAA3CK5f9/BUg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/defined": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/defined/-/defined-1.0.1.tgz",
@@ -4573,6 +4827,20 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
+    "node_modules/defu": {
+      "version": "6.1.7",
+      "resolved": "https://registry.npmjs.org/defu/-/defu-6.1.7.tgz",
+      "integrity": "sha512-7z22QmUWiQ/2d0KkdYmANbRUVABpZ9SNYyH5vx6PZ+nE5bcC0l7uFvEfHlyld/HcGBFTL536ClDt3DEcSlEJAQ==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/destr": {
+      "version": "2.0.5",
+      "resolved": "https://registry.npmjs.org/destr/-/destr-2.0.5.tgz",
+      "integrity": "sha512-ugFTXCtDZunbzasqBxrK93Ik/DRYsO6S/fedkWEMKqt04xZ4csmnmwGDBAb07QWNaGMAmnTIemsYZCksjATwsA==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/detect-kerning": {
       "version": "2.1.2",
       "resolved": "https://registry.npmjs.org/detect-kerning/-/detect-kerning-2.1.2.tgz",
@@ -5063,6 +5331,13 @@
         "node": ">=0.8.x"
       }
     },
+    "node_modules/exsolve": {
+      "version": "1.0.8",
+      "resolved": "https://registry.npmjs.org/exsolve/-/exsolve-1.0.8.tgz",
+      "integrity": "sha512-LmDxfWXwcTArk8fUEnOfSZpHOJ6zOMUJKOtFLFqJLoKJetuQG874Uc7/Kki7zFLzYybmZhp1M7+98pfMqeX8yA==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/ext": {
       "version": "1.7.0",
       "resolved": "https://registry.npmjs.org/ext/-/ext-1.7.0.tgz",
@@ -5279,20 +5554,6 @@
         "safe-buffer": "~5.1.0"
       }
     },
-    "node_modules/fs-extra": {
-      "version": "11.3.0",
-      "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-11.3.0.tgz",
-      "integrity": "sha512-Z4XaCL6dUDHfP/jT25jJKMmtxvuwbkrD1vNSMFlo9lNLY2c5FHYSQgHPRZUjAB26TpDEoW9HCOgplrdbaPV/ew==",
-      "dev": true,
-      "dependencies": {
-        "graceful-fs": "^4.2.0",
-        "jsonfile": "^6.0.1",
-        "universalify": "^2.0.0"
-      },
-      "engines": {
-        "node": ">=14.14"
-      }
-    },
     "node_modules/fsevents": {
       "version": "2.3.3",
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@@ -5365,6 +5626,29 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/get-tsconfig": {
+      "version": "4.14.0",
+      "resolved": "https://registry.npmjs.org/get-tsconfig/-/get-tsconfig-4.14.0.tgz",
+      "integrity": "sha512-yTb+8DXzDREzgvYmh6s9vHsSVCHeC0G3PI5bEXNBHtmshPnO+S5O7qgLEOn0I5QvMy6kpZN8K1NKGyilLb93wA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "resolve-pkg-maps": "^1.0.0"
+      },
+      "funding": {
+        "url": "https://github.com/privatenumber/get-tsconfig?sponsor=1"
+      }
+    },
+    "node_modules/giget": {
+      "version": "3.3.0",
+      "resolved": "https://registry.npmjs.org/giget/-/giget-3.3.0.tgz",
+      "integrity": "sha512-gzi2D96p+AMfDcmJHGDj3KJ9NRiwvlFAU5yfa3ROwWZmFUjX4P43x3BcyRaOMMLto1vUo7C+86+MFhYTl6Ryiw==",
+      "dev": true,
+      "license": "MIT",
+      "bin": {
+        "giget": "dist/cli.mjs"
+      }
+    },
     "node_modules/gl-mat4": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/gl-mat4/-/gl-mat4-1.2.0.tgz",
@@ -5745,7 +6029,8 @@
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       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
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+      "integrity": "sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==",
+      "peer": true
     },
     "node_modules/grid-index": {
       "version": "1.1.0",
@@ -5968,6 +6253,22 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
+    "node_modules/is-docker": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/is-docker/-/is-docker-3.0.0.tgz",
+      "integrity": "sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ==",
+      "dev": true,
+      "license": "MIT",
+      "bin": {
+        "is-docker": "cli.js"
+      },
+      "engines": {
+        "node": "^12.20.0 || ^14.13.1 || >=16.0.0"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/is-extglob": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/is-extglob/-/is-extglob-2.1.1.tgz",
@@ -6030,6 +6331,38 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/is-in-ssh": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/is-in-ssh/-/is-in-ssh-1.0.0.tgz",
+      "integrity": "sha512-jYa6Q9rH90kR1vKB6NM7qqd1mge3Fx4Dhw5TVlK1MUBqhEOuCagrEHMevNuCcbECmXZ0ThXkRm+Ymr51HwEPAw==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/is-inside-container": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/is-inside-container/-/is-inside-container-1.0.0.tgz",
+      "integrity": "sha512-KIYLCCJghfHZxqjYBE7rEy0OBuTd5xCHS7tHVgvCLkx7StIoaxwNW3hCALgEUjFfeRk+MG/Qxmp/vtETEF3tRA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "is-docker": "^3.0.0"
+      },
+      "bin": {
+        "is-inside-container": "cli.js"
+      },
+      "engines": {
+        "node": ">=14.16"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/is-mobile": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/is-mobile/-/is-mobile-4.0.0.tgz",
@@ -6076,6 +6409,22 @@
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       "peer": true
     },
+    "node_modules/is-wsl": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/is-wsl/-/is-wsl-3.1.1.tgz",
+      "integrity": "sha512-e6rvdUCiQCAuumZslxRJWR/Doq4VpPR82kqclvcS0efgt430SlGIk05vdCN58+VrzgtIcfNODjozVielycD4Sw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "is-inside-container": "^1.0.0"
+      },
+      "engines": {
+        "node": ">=16"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/isarray": {
       "version": "2.0.5",
       "resolved": "https://registry.npmjs.org/isarray/-/isarray-2.0.5.tgz",
@@ -6106,6 +6455,16 @@
         "@pkgjs/parseargs": "^0.11.0"
       }
     },
+    "node_modules/jiti": {
+      "version": "2.7.0",
+      "resolved": "https://registry.npmjs.org/jiti/-/jiti-2.7.0.tgz",
+      "integrity": "sha512-AC/7JofJvZGrrneWNaEnJeOLUx+JlGt7tNa0wZiRPT4MY1wmfKjt2+6O2p2uz2+skll8OZZmJMNqeke7kKbNgQ==",
+      "devOptional": true,
+      "license": "MIT",
+      "bin": {
+        "jiti": "lib/jiti-cli.mjs"
+      }
+    },
     "node_modules/js-levenshtein": {
       "version": "1.1.6",
       "resolved": "https://registry.npmjs.org/js-levenshtein/-/js-levenshtein-1.1.6.tgz",
@@ -6159,19 +6518,6 @@
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-    "node_modules/json-schema-ref-parser": {
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-      "resolved": "https://registry.npmjs.org/json-schema-ref-parser/-/json-schema-ref-parser-9.0.9.tgz",
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-      "deprecated": "Please switch to @apidevtools/json-schema-ref-parser",
-      "dev": true,
-      "dependencies": {
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-      },
-      "engines": {
-        "node": ">=10"
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-    },
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@@ -6211,18 +6557,6 @@
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-      "version": "6.1.0",
-      "resolved": "https://registry.npmjs.org/jsonfile/-/jsonfile-6.1.0.tgz",
-      "integrity": "sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==",
-      "dev": true,
-      "dependencies": {
-        "universalify": "^2.0.0"
-      },
-      "optionalDependencies": {
-        "graceful-fs": "^4.1.6"
-      }
-    },
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       "resolved": "https://registry.npmjs.org/jsonpath-rfc9535/-/jsonpath-rfc9535-1.3.0.tgz",
@@ -6959,6 +7293,13 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/ohash": {
+      "version": "2.0.11",
+      "resolved": "https://registry.npmjs.org/ohash/-/ohash-2.0.11.tgz",
+      "integrity": "sha512-RdR9FQrFwNBNXAr4GixM8YaRZRJ5PUWbKYbE5eOsrwAjJW0q2REGcf79oYPsLyskQCZG1PLN+S/K1V00joZAoQ==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/once": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz",
@@ -6968,6 +7309,27 @@
         "wrappy": "1"
       }
     },
+    "node_modules/open": {
+      "version": "11.0.0",
+      "resolved": "https://registry.npmjs.org/open/-/open-11.0.0.tgz",
+      "integrity": "sha512-smsWv2LzFjP03xmvFoJ331ss6h+jixfA4UUV/Bsiyuu4YJPfN+FIQGOIiv4w9/+MoHkfkJ22UIaQWRVFRfH6Vw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "default-browser": "^5.4.0",
+        "define-lazy-prop": "^3.0.0",
+        "is-in-ssh": "^1.0.0",
+        "is-inside-container": "^1.0.0",
+        "powershell-utils": "^0.1.0",
+        "wsl-utils": "^0.3.0"
+      },
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/openapi-sampler": {
       "version": "1.7.2",
       "resolved": "https://registry.npmjs.org/openapi-sampler/-/openapi-sampler-1.7.2.tgz",
@@ -6980,22 +7342,6 @@
         "json-pointer": "0.6.2"
       }
     },
-    "node_modules/openapi-typescript-codegen": {
-      "version": "0.25.0",
-      "resolved": "https://registry.npmjs.org/openapi-typescript-codegen/-/openapi-typescript-codegen-0.25.0.tgz",
-      "integrity": "sha512-nN/TnIcGbP58qYgwEEy5FrAAjePcYgfMaCe3tsmYyTgI3v4RR9v8os14L+LEWDvV50+CmqiyTzRkKKtJeb6Ybg==",
-      "dev": true,
-      "dependencies": {
-        "camelcase": "^6.3.0",
-        "commander": "^11.0.0",
-        "fs-extra": "^11.1.1",
-        "handlebars": "^4.7.7",
-        "json-schema-ref-parser": "^9.0.9"
-      },
-      "bin": {
-        "openapi": "bin/index.js"
-      }
-    },
     "node_modules/outdent": {
       "version": "0.8.0",
       "resolved": "https://registry.npmjs.org/outdent/-/outdent-0.8.0.tgz",
@@ -7131,6 +7477,13 @@
         "node": ">=8"
       }
     },
+    "node_modules/pathe": {
+      "version": "2.0.3",
+      "resolved": "https://registry.npmjs.org/pathe/-/pathe-2.0.3.tgz",
+      "integrity": "sha512-WUjGcAqP1gQacoQe+OBJsFA7Ld4DyXuUIjZ5cc75cLHvJ7dtNsTugphxIADwspS+AraAUePCKrSVtPLFj/F88w==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/pbf": {
       "version": "3.3.0",
       "resolved": "https://registry.npmjs.org/pbf/-/pbf-3.3.0.tgz",
@@ -7144,6 +7497,13 @@
         "pbf": "bin/pbf"
       }
     },
+    "node_modules/perfect-debounce": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/perfect-debounce/-/perfect-debounce-2.1.0.tgz",
+      "integrity": "sha512-LjgdTytVFXeUgtHZr9WYViYSM/g8MkcTPYDlPa3cDqMirHjKiSZPYd6DoL7pK8AJQr+uWkQvCjHNdiMqsrJs+g==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/perfect-scrollbar": {
       "version": "1.5.6",
       "resolved": "https://registry.npmjs.org/perfect-scrollbar/-/perfect-scrollbar-1.5.6.tgz",
@@ -7181,6 +7541,18 @@
         "url": "https://github.com/sponsors/jonschlinkert"
       }
     },
+    "node_modules/pkg-types": {
+      "version": "2.3.1",
+      "resolved": "https://registry.npmjs.org/pkg-types/-/pkg-types-2.3.1.tgz",
+      "integrity": "sha512-y+ichcgc2LrADuhLNAx8DFjVfgz91pRxfZdI3UDhxHvcVEZsenLO+7XaU5vOp0u/7V/wZ+plyuQxtrDlZJ+yeg==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "confbox": "^0.2.4",
+        "exsolve": "^1.0.8",
+        "pathe": "^2.0.3"
+      }
+    },
     "node_modules/plotly.js": {
       "version": "3.3.1",
       "resolved": "https://registry.npmjs.org/plotly.js/-/plotly.js-3.3.1.tgz",
@@ -7431,6 +7803,19 @@
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       "peer": true
     },
+    "node_modules/powershell-utils": {
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/powershell-utils/-/powershell-utils-0.1.0.tgz",
+      "integrity": "sha512-dM0jVuXJPsDN6DvRpea484tCUaMiXWjuCn++HGTqUWzGDjv5tZkEZldAJ/UMlqRYGFrD/etByo4/xOuC/snX2A==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/prismjs": {
       "version": "1.30.0",
       "resolved": "https://registry.npmjs.org/prismjs/-/prismjs-1.30.0.tgz",
@@ -7551,6 +7936,17 @@
         "safe-buffer": "^5.1.0"
       }
     },
+    "node_modules/rc9": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/rc9/-/rc9-3.0.1.tgz",
+      "integrity": "sha512-gMDyleLWVE+i6Sgtc0QbbY6pEKqYs97NGi6isHQPqYlLemPoO8dxQ3uGi0f4NiP98c+jMW6cG1Kx9dDwfvqARQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "defu": "^6.1.6",
+        "destr": "^2.0.5"
+      }
+    },
     "node_modules/react": {
       "version": "19.2.4",
       "resolved": "https://registry.npmjs.org/react/-/react-19.2.4.tgz",
@@ -7648,6 +8044,20 @@
         "node": ">= 6"
       }
     },
+    "node_modules/readdirp": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-5.0.0.tgz",
+      "integrity": "sha512-9u/XQ1pvrQtYyMpZe7DXKv2p5CNvyVwzUB6uhLAnQwHMSgKMBR62lc7AHljaeteeHXn11XTAaLLUVZYVZyuRBQ==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">= 20.19.0"
+      },
+      "funding": {
+        "type": "individual",
+        "url": "https://paulmillr.com/funding/"
+      }
+    },
     "node_modules/redoc": {
       "version": "2.5.1",
       "resolved": "https://registry.npmjs.org/redoc/-/redoc-2.5.1.tgz",
@@ -7878,6 +8288,16 @@
         "node": ">=4"
       }
     },
+    "node_modules/resolve-pkg-maps": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/resolve-pkg-maps/-/resolve-pkg-maps-1.0.0.tgz",
+      "integrity": "sha512-seS2Tj26TBVOC2NIc2rOe2y2ZO7efxITtLZcGSOnHHNOQ7CkiUBfw0Iw2ck6xkIhPwLhKNLS8BO+hEpngQlqzw==",
+      "dev": true,
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/privatenumber/resolve-pkg-maps?sponsor=1"
+      }
+    },
     "node_modules/resolve-protobuf-schema": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/resolve-protobuf-schema/-/resolve-protobuf-schema-2.1.0.tgz",
@@ -7937,6 +8357,19 @@
         "fsevents": "~2.3.2"
       }
     },
+    "node_modules/run-applescript": {
+      "version": "7.1.0",
+      "resolved": "https://registry.npmjs.org/run-applescript/-/run-applescript-7.1.0.tgz",
+      "integrity": "sha512-DPe5pVFaAsinSaV6QjQ6gdiedWDcRCbUuiQfQa2wmWV7+xC9bGulGI8+TdRmoFkAPaBXk8CrAbnlY2ISniJ47Q==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/rw": {
       "version": "1.3.3",
       "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz",
@@ -8031,9 +8464,9 @@
       "license": "MIT"
     },
     "node_modules/semver": {
-      "version": "7.7.4",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.4.tgz",
-      "integrity": "sha512-vFKC2IEtQnVhpT78h1Yp8wzwrf8CM+MzKMHGJZfBtzhZNycRFnXsHk6E5TxIkkMsgNS7mdX3AGB7x2QM2di4lA==",
+      "version": "7.8.2",
+      "resolved": "https://registry.npmjs.org/semver/-/semver-7.8.2.tgz",
+      "integrity": "sha512-c8jsqUZm3omBOI66G90z1Dyw5z622G8oLG+omfsHBJf3CWQTlOcwOjvOG6wtiNfW6anKm/eA39LMwMtMez2TiQ==",
       "dev": true,
       "license": "ISC",
       "bin": {
@@ -8894,15 +9327,6 @@
       "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==",
       "license": "MIT"
     },
-    "node_modules/universalify": {
-      "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/universalify/-/universalify-2.0.1.tgz",
-      "integrity": "sha512-gptHNQghINnc/vTGIk0SOFGFNXw7JVrlRUtConJRlvaw6DuX0wO5Jeko9sWrMBhh+PsYAZ7oXAiOnf/UKogyiw==",
-      "dev": true,
-      "engines": {
-        "node": ">= 10.0.0"
-      }
-    },
     "node_modules/unquote": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/unquote/-/unquote-1.1.1.tgz",
@@ -9235,6 +9659,23 @@
         }
       }
     },
+    "node_modules/wsl-utils": {
+      "version": "0.3.1",
+      "resolved": "https://registry.npmjs.org/wsl-utils/-/wsl-utils-0.3.1.tgz",
+      "integrity": "sha512-g/eziiSUNBSsdDJtCLB8bdYEUMj4jR7AGeUo96p/3dTafgjHhpF4RiCFPiRILwjQoDXx5MqkBr4fwWtR3Ky4Wg==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "is-wsl": "^3.1.0",
+        "powershell-utils": "^0.1.0"
+      },
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/xml-naming": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/xml-naming/-/xml-naming-0.1.0.tgz",
diff --git a/frontend/package.json b/frontend/package.json
index d4ce664d..a28a1bfa 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -32,7 +32,7 @@
     "serve": "vite preview",
     "redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=dist/openapi.html",
     "redocly4broker": "redocly build-docs ../broker/jfjoch_api.yaml --output=../broker/redoc-static.html",
-    "openapi": "./node_modules/openapi-typescript-codegen/bin/index.js -i ../broker/jfjoch_api.yaml --output ./src/openapi"
+    "openapi": "openapi-ts"
   },
   "overrides": {
     "styled-components": "5.3.11"
@@ -50,10 +50,10 @@
     ]
   },
   "devDependencies": {
+    "@hey-api/openapi-ts": "^0.98.2",
     "@redocly/cli": "^2.28.1",
     "@types/lodash": "^4.17.10",
     "@types/react-plotly.js": "^2.6.3",
-    "esbuild-style-plugin": "^1.6.3",
-    "openapi-typescript-codegen": "^0.25.0"
+    "esbuild-style-plugin": "^1.6.3"
   }
 }
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index b3570596..83974b4d 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -18,8 +18,9 @@ import ImageFormatSettings from "./components/ImageFormatSettings";
 import InstrumentMetadata from "./components/InstrumentMetadata";
 import {JFJOCH_VERSION} from "./version";
 import FpgaStatus from "./components/FpgaStatus";
-import {broker_status, DefaultService, OpenAPI, plot_type} from "./openapi";
-import {jfjoch_statistics} from "./openapi";
+import {getStatistics, plot_type} from "./client";
+import {client} from "./client/client.gen";
+import {jfjoch_statistics} from "./client";
 import DataCollection from "./components/DataCollection";
 import ZeroMQPreview from "./components/ZeroMQPreview";
 import PixelMask from "./components/PixelMask";
@@ -65,8 +66,8 @@ class App extends Component<MyProps, MyState> {
     }
 
     getValues = () => {
-        DefaultService.getStatistics()
-            .then(data => this.setState({s: data, connection_error: false}))
+        getStatistics({ throwOnError: true })
+            .then(({data}) => this.setState({s: data, connection_error: false}))
             .catch(_ => {
                 this.setState({s: {}, connection_error: true});
             });
@@ -76,7 +77,7 @@ class App extends Component<MyProps, MyState> {
         clearInterval(this.interval);
     }
     componentDidMount() {
-        OpenAPI.BASE='';
+        client.setConfig({ baseUrl: '' });
         this.getValues();
         this.interval = setInterval(() => this.getValues(), 1000);
     }
@@ -126,7 +127,7 @@ class App extends Component<MyProps, MyState> {
 
     isMeasuring() : boolean {
         return (this.state.s.broker !== undefined)
-            && (this.state.s.broker.state == broker_status.state.MEASURING);
+            && (this.state.s.broker.state == 'Measuring');
     }
 
     render() {
diff --git a/frontend/src/client/client.gen.ts b/frontend/src/client/client.gen.ts
new file mode 100644
index 00000000..85e4a5b3
--- /dev/null
+++ b/frontend/src/client/client.gen.ts
@@ -0,0 +1,16 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import { type Client, type ClientOptions, type Config, createClient, createConfig } from './client';
+import type { ClientOptions as ClientOptions2 } from './types.gen';
+
+/**
+ * The `createClientConfig()` function will be called on client initialization
+ * and the returned object will become the client's initial configuration.
+ *
+ * You may want to initialize your client this way instead of calling
+ * `setConfig()`. This is useful for example if you're using Next.js
+ * to ensure your client always has the correct values.
+ */
+export type CreateClientConfig<T extends ClientOptions = ClientOptions2> = (override?: Config<ClientOptions & T>) => Config<Required<ClientOptions> & T>;
+
+export const client: Client = createClient(createConfig<ClientOptions2>({ baseUrl: 'http://localhost:5232' }));
diff --git a/frontend/src/client/client/client.gen.ts b/frontend/src/client/client/client.gen.ts
new file mode 100644
index 00000000..fc3f037f
--- /dev/null
+++ b/frontend/src/client/client/client.gen.ts
@@ -0,0 +1,277 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import { createSseClient } from '../core/serverSentEvents.gen';
+import type { HttpMethod } from '../core/types.gen';
+import { getValidRequestBody } from '../core/utils.gen';
+import type { Client, Config, RequestOptions, ResolvedRequestOptions } from './types.gen';
+import {
+  buildUrl,
+  createConfig,
+  createInterceptors,
+  getParseAs,
+  mergeConfigs,
+  mergeHeaders,
+  setAuthParams,
+} from './utils.gen';
+
+type ReqInit = Omit<RequestInit, 'body' | 'headers'> & {
+  body?: any;
+  headers: ReturnType<typeof mergeHeaders>;
+};
+
+export const createClient = (config: Config = {}): Client => {
+  let _config = mergeConfigs(createConfig(), config);
+
+  const getConfig = (): Config => ({ ..._config });
+
+  const setConfig = (config: Config): Config => {
+    _config = mergeConfigs(_config, config);
+    return getConfig();
+  };
+
+  const interceptors = createInterceptors<Request, Response, unknown, ResolvedRequestOptions>();
+
+  const beforeRequest = async <
+    TData = unknown,
+    TResponseStyle extends 'data' | 'fields' = 'fields',
+    ThrowOnError extends boolean = boolean,
+    Url extends string = string,
+  >(
+    options: RequestOptions<TData, TResponseStyle, ThrowOnError, Url>,
+  ) => {
+    const opts = {
+      ..._config,
+      ...options,
+      fetch: options.fetch ?? _config.fetch ?? globalThis.fetch,
+      headers: mergeHeaders(_config.headers, options.headers),
+      serializedBody: undefined as string | undefined,
+    };
+
+    if (opts.security) {
+      await setAuthParams(opts);
+    }
+
+    if (opts.requestValidator) {
+      await opts.requestValidator(opts);
+    }
+
+    if (opts.body !== undefined && opts.bodySerializer) {
+      opts.serializedBody = opts.bodySerializer(opts.body) as string | undefined;
+    }
+
+    // remove Content-Type header if body is empty to avoid sending invalid requests
+    if (opts.body === undefined || opts.serializedBody === '') {
+      opts.headers.delete('Content-Type');
+    }
+
+    const resolvedOpts = opts as typeof opts &
+      ResolvedRequestOptions<TResponseStyle, ThrowOnError, Url>;
+    const url = buildUrl(resolvedOpts);
+
+    return { opts: resolvedOpts, url };
+  };
+
+  const request: Client['request'] = async (options) => {
+    const throwOnError = options.throwOnError ?? _config.throwOnError;
+    const responseStyle = options.responseStyle ?? _config.responseStyle;
+
+    let request: Request | undefined;
+    let response: Response | undefined;
+
+    try {
+      const { opts, url } = await beforeRequest(options);
+      const requestInit: ReqInit = {
+        redirect: 'follow',
+        ...opts,
+        body: getValidRequestBody(opts),
+      };
+
+      request = new Request(url, requestInit);
+
+      for (const fn of interceptors.request.fns) {
+        if (fn) {
+          request = await fn(request, opts);
+        }
+      }
+
+      // fetch must be assigned here, otherwise it would throw the error:
+      // TypeError: Failed to execute 'fetch' on 'Window': Illegal invocation
+      const _fetch = opts.fetch!;
+
+      response = await _fetch(request);
+
+      for (const fn of interceptors.response.fns) {
+        if (fn) {
+          response = await fn(response, request, opts);
+        }
+      }
+
+      const result = {
+        request,
+        response,
+      };
+
+      if (response.ok) {
+        const parseAs =
+          (opts.parseAs === 'auto'
+            ? getParseAs(response.headers.get('Content-Type'))
+            : opts.parseAs) ?? 'json';
+
+        if (response.status === 204 || response.headers.get('Content-Length') === '0') {
+          let emptyData: any;
+          switch (parseAs) {
+            case 'arrayBuffer':
+            case 'blob':
+            case 'text':
+              emptyData = await response[parseAs]();
+              break;
+            case 'formData':
+              emptyData = new FormData();
+              break;
+            case 'stream':
+              emptyData = response.body;
+              break;
+            case 'json':
+            default:
+              emptyData = {};
+              break;
+          }
+          return opts.responseStyle === 'data'
+            ? emptyData
+            : {
+                data: emptyData,
+                ...result,
+              };
+        }
+
+        let data: any;
+        switch (parseAs) {
+          case 'arrayBuffer':
+          case 'blob':
+          case 'formData':
+          case 'text':
+            data = await response[parseAs]();
+            break;
+          case 'json': {
+            // Some servers return 200 with no Content-Length and empty body.
+            // response.json() would throw; read as text and parse if non-empty.
+            const text = await response.text();
+            data = text ? JSON.parse(text) : {};
+            break;
+          }
+          case 'stream':
+            return opts.responseStyle === 'data'
+              ? response.body
+              : {
+                  data: response.body,
+                  ...result,
+                };
+        }
+
+        if (parseAs === 'json') {
+          if (opts.responseValidator) {
+            await opts.responseValidator(data);
+          }
+
+          if (opts.responseTransformer) {
+            data = await opts.responseTransformer(data);
+          }
+        }
+
+        return opts.responseStyle === 'data'
+          ? data
+          : {
+              data,
+              ...result,
+            };
+      }
+
+      const textError = await response.text();
+      let jsonError: unknown;
+
+      try {
+        jsonError = JSON.parse(textError);
+      } catch {
+        // noop
+      }
+
+      throw jsonError ?? textError;
+    } catch (error) {
+      let finalError = error;
+
+      for (const fn of interceptors.error.fns) {
+        if (fn) {
+          finalError = await fn(finalError, response, request, options as ResolvedRequestOptions);
+        }
+      }
+
+      finalError = finalError || {};
+
+      if (throwOnError) {
+        throw finalError;
+      }
+
+      // TODO: we probably want to return error and improve types
+      return responseStyle === 'data'
+        ? undefined
+        : {
+            error: finalError,
+            request,
+            response,
+          };
+    }
+  };
+
+  const makeMethodFn = (method: Uppercase<HttpMethod>) => (options: RequestOptions) =>
+    request({ ...options, method });
+
+  const makeSseFn = (method: Uppercase<HttpMethod>) => async (options: RequestOptions) => {
+    const { opts, url } = await beforeRequest(options);
+    return createSseClient({
+      ...opts,
+      body: opts.body as BodyInit | null | undefined,
+      method,
+      onRequest: async (url, init) => {
+        let request = new Request(url, init);
+        for (const fn of interceptors.request.fns) {
+          if (fn) {
+            request = await fn(request, opts);
+          }
+        }
+        return request;
+      },
+      serializedBody: getValidRequestBody(opts) as BodyInit | null | undefined,
+      url,
+    });
+  };
+
+  const _buildUrl: Client['buildUrl'] = (options) => buildUrl({ ..._config, ...options });
+
+  return {
+    buildUrl: _buildUrl,
+    connect: makeMethodFn('CONNECT'),
+    delete: makeMethodFn('DELETE'),
+    get: makeMethodFn('GET'),
+    getConfig,
+    head: makeMethodFn('HEAD'),
+    interceptors,
+    options: makeMethodFn('OPTIONS'),
+    patch: makeMethodFn('PATCH'),
+    post: makeMethodFn('POST'),
+    put: makeMethodFn('PUT'),
+    request,
+    setConfig,
+    sse: {
+      connect: makeSseFn('CONNECT'),
+      delete: makeSseFn('DELETE'),
+      get: makeSseFn('GET'),
+      head: makeSseFn('HEAD'),
+      options: makeSseFn('OPTIONS'),
+      patch: makeSseFn('PATCH'),
+      post: makeSseFn('POST'),
+      put: makeSseFn('PUT'),
+      trace: makeSseFn('TRACE'),
+    },
+    trace: makeMethodFn('TRACE'),
+  } as Client;
+};
diff --git a/frontend/src/client/client/index.ts b/frontend/src/client/client/index.ts
new file mode 100644
index 00000000..8c693310
--- /dev/null
+++ b/frontend/src/client/client/index.ts
@@ -0,0 +1,27 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export type { Auth } from '../core/auth.gen';
+export type { QuerySerializerOptions } from '../core/bodySerializer.gen';
+export {
+  formDataBodySerializer,
+  jsonBodySerializer,
+  urlSearchParamsBodySerializer,
+} from '../core/bodySerializer.gen';
+export { buildClientParams } from '../core/params.gen';
+export { serializeQueryKeyValue } from '../core/queryKeySerializer.gen';
+export type { ServerSentEventsResult } from '../core/serverSentEvents.gen';
+export type { ClientMeta } from '../core/types.gen';
+export { createClient } from './client.gen';
+export type {
+  Client,
+  ClientOptions,
+  Config,
+  CreateClientConfig,
+  Options,
+  RequestOptions,
+  RequestResult,
+  ResolvedRequestOptions,
+  ResponseStyle,
+  TDataShape,
+} from './types.gen';
+export { createConfig, mergeHeaders } from './utils.gen';
diff --git a/frontend/src/client/client/types.gen.ts b/frontend/src/client/client/types.gen.ts
new file mode 100644
index 00000000..193646cd
--- /dev/null
+++ b/frontend/src/client/client/types.gen.ts
@@ -0,0 +1,218 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { Auth } from '../core/auth.gen';
+import type {
+  ServerSentEventsOptions,
+  ServerSentEventsResult,
+} from '../core/serverSentEvents.gen';
+import type { Client as CoreClient, Config as CoreConfig } from '../core/types.gen';
+import type { Middleware } from './utils.gen';
+
+export type ResponseStyle = 'data' | 'fields';
+
+export interface Config<T extends ClientOptions = ClientOptions>
+  extends Omit<RequestInit, 'body' | 'headers' | 'method'>, CoreConfig {
+  /**
+   * Base URL for all requests made by this client.
+   */
+  baseUrl?: T['baseUrl'];
+  /**
+   * Fetch API implementation. You can use this option to provide a custom
+   * fetch instance.
+   *
+   * @default globalThis.fetch
+   */
+  fetch?: typeof fetch;
+  /**
+   * Please don't use the Fetch client for Next.js applications. The `next`
+   * options won't have any effect.
+   *
+   * Install {@link https://www.npmjs.com/package/@hey-api/client-next `@hey-api/client-next`} instead.
+   */
+  next?: never;
+  /**
+   * Return the response data parsed in a specified format. By default, `auto`
+   * will infer the appropriate method from the `Content-Type` response header.
+   * You can override this behavior with any of the {@link Body} methods.
+   * Select `stream` if you don't want to parse response data at all.
+   *
+   * @default 'auto'
+   */
+  parseAs?: 'arrayBuffer' | 'auto' | 'blob' | 'formData' | 'json' | 'stream' | 'text';
+  /**
+   * Should we return only data or multiple fields (data, error, response, etc.)?
+   *
+   * @default 'fields'
+   */
+  responseStyle?: ResponseStyle;
+  /**
+   * Throw an error instead of returning it in the response?
+   *
+   * @default false
+   */
+  throwOnError?: T['throwOnError'];
+}
+
+export interface RequestOptions<
+  TData = unknown,
+  TResponseStyle extends ResponseStyle = 'fields',
+  ThrowOnError extends boolean = boolean,
+  Url extends string = string,
+>
+  extends
+    Config<{
+      responseStyle: TResponseStyle;
+      throwOnError: ThrowOnError;
+    }>,
+    Pick<
+      ServerSentEventsOptions<TData>,
+      | 'onRequest'
+      | 'onSseError'
+      | 'onSseEvent'
+      | 'sseDefaultRetryDelay'
+      | 'sseMaxRetryAttempts'
+      | 'sseMaxRetryDelay'
+    > {
+  /**
+   * Any body that you want to add to your request.
+   *
+   * {@link https://developer.mozilla.org/docs/Web/API/fetch#body}
+   */
+  body?: unknown;
+  path?: Record<string, unknown>;
+  query?: Record<string, unknown>;
+  /**
+   * Security mechanism(s) to use for the request.
+   */
+  security?: ReadonlyArray<Auth>;
+  url: Url;
+}
+
+export interface ResolvedRequestOptions<
+  TResponseStyle extends ResponseStyle = 'fields',
+  ThrowOnError extends boolean = boolean,
+  Url extends string = string,
+> extends RequestOptions<unknown, TResponseStyle, ThrowOnError, Url> {
+  headers: Headers;
+  serializedBody?: string;
+}
+
+export type RequestResult<
+  TData = unknown,
+  TError = unknown,
+  ThrowOnError extends boolean = boolean,
+  TResponseStyle extends ResponseStyle = 'fields',
+> = ThrowOnError extends true
+  ? Promise<
+      TResponseStyle extends 'data'
+        ? TData extends Record<string, unknown>
+          ? TData[keyof TData]
+          : TData
+        : {
+            data: TData extends Record<string, unknown> ? TData[keyof TData] : TData;
+            request: Request;
+            response: Response;
+          }
+    >
+  : Promise<
+      TResponseStyle extends 'data'
+        ? (TData extends Record<string, unknown> ? TData[keyof TData] : TData) | undefined
+        : (
+            | {
+                data: TData extends Record<string, unknown> ? TData[keyof TData] : TData;
+                error: undefined;
+              }
+            | {
+                data: undefined;
+                error: TError extends Record<string, unknown> ? TError[keyof TError] : TError;
+              }
+          ) & {
+            /** request may be undefined, because error may be from building the request object itself */
+            request?: Request;
+            /** response may be undefined, because error may be from building the request object itself or from a network error */
+            response?: Response;
+          }
+    >;
+
+export interface ClientOptions {
+  baseUrl?: string;
+  responseStyle?: ResponseStyle;
+  throwOnError?: boolean;
+}
+
+type MethodFn = <
+  TData = unknown,
+  TError = unknown,
+  ThrowOnError extends boolean = false,
+  TResponseStyle extends ResponseStyle = 'fields',
+>(
+  options: Omit<RequestOptions<TData, TResponseStyle, ThrowOnError>, 'method'>,
+) => RequestResult<TData, TError, ThrowOnError, TResponseStyle>;
+
+type SseFn = <
+  TData = unknown,
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  _TError = unknown,
+  ThrowOnError extends boolean = false,
+  TResponseStyle extends ResponseStyle = 'fields',
+>(
+  options: Omit<RequestOptions<never, TResponseStyle, ThrowOnError>, 'method'>,
+) => Promise<ServerSentEventsResult<TData>>;
+
+type RequestFn = <
+  TData = unknown,
+  TError = unknown,
+  ThrowOnError extends boolean = false,
+  TResponseStyle extends ResponseStyle = 'fields',
+>(
+  options: Omit<RequestOptions<TData, TResponseStyle, ThrowOnError>, 'method'> &
+    Pick<Required<RequestOptions<TData, TResponseStyle, ThrowOnError>>, 'method'>,
+) => RequestResult<TData, TError, ThrowOnError, TResponseStyle>;
+
+type BuildUrlFn = <
+  TData extends {
+    body?: unknown;
+    path?: Record<string, unknown>;
+    query?: Record<string, unknown>;
+    url: string;
+  },
+>(
+  options: TData & Options<TData>,
+) => string;
+
+export type Client = CoreClient<RequestFn, Config, MethodFn, BuildUrlFn, SseFn> & {
+  interceptors: Middleware<Request, Response, unknown, ResolvedRequestOptions>;
+};
+
+/**
+ * The `createClientConfig()` function will be called on client initialization
+ * and the returned object will become the client's initial configuration.
+ *
+ * You may want to initialize your client this way instead of calling
+ * `setConfig()`. This is useful for example if you're using Next.js
+ * to ensure your client always has the correct values.
+ */
+export type CreateClientConfig<T extends ClientOptions = ClientOptions> = (
+  override?: Config<ClientOptions & T>,
+) => Config<Required<ClientOptions> & T>;
+
+export interface TDataShape {
+  body?: unknown;
+  headers?: unknown;
+  path?: unknown;
+  query?: unknown;
+  url: string;
+}
+
+type OmitKeys<T, K> = Pick<T, Exclude<keyof T, K>>;
+
+export type Options<
+  TData extends TDataShape = TDataShape,
+  ThrowOnError extends boolean = boolean,
+  TResponse = unknown,
+  TResponseStyle extends ResponseStyle = 'fields',
+> = OmitKeys<
+  RequestOptions<TResponse, TResponseStyle, ThrowOnError>,
+  'body' | 'path' | 'query' | 'url'
+> &
+  ([TData] extends [never] ? unknown : Omit<TData, 'url'>);
diff --git a/frontend/src/client/client/utils.gen.ts b/frontend/src/client/client/utils.gen.ts
new file mode 100644
index 00000000..d4a72843
--- /dev/null
+++ b/frontend/src/client/client/utils.gen.ts
@@ -0,0 +1,316 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import { getAuthToken } from '../core/auth.gen';
+import type { QuerySerializerOptions } from '../core/bodySerializer.gen';
+import { jsonBodySerializer } from '../core/bodySerializer.gen';
+import {
+  serializeArrayParam,
+  serializeObjectParam,
+  serializePrimitiveParam,
+} from '../core/pathSerializer.gen';
+import { getUrl } from '../core/utils.gen';
+import type { Client, ClientOptions, Config, RequestOptions } from './types.gen';
+
+export const createQuerySerializer = <T = unknown>({
+  parameters = {},
+  ...args
+}: QuerySerializerOptions = {}): ((queryParams: T) => string) => {
+  const querySerializer = (queryParams: T): string => {
+    const search: string[] = [];
+    if (queryParams && typeof queryParams === 'object') {
+      for (const name in queryParams) {
+        const value = queryParams[name];
+
+        if (value === undefined || value === null) {
+          continue;
+        }
+
+        const options = parameters[name] || args;
+
+        if (Array.isArray(value)) {
+          const serializedArray = serializeArrayParam({
+            allowReserved: options.allowReserved,
+            explode: true,
+            name,
+            style: 'form',
+            value,
+            ...options.array,
+          });
+          if (serializedArray) search.push(serializedArray);
+        } else if (typeof value === 'object') {
+          const serializedObject = serializeObjectParam({
+            allowReserved: options.allowReserved,
+            explode: true,
+            name,
+            style: 'deepObject',
+            value: value as Record<string, unknown>,
+            ...options.object,
+          });
+          if (serializedObject) search.push(serializedObject);
+        } else {
+          const serializedPrimitive = serializePrimitiveParam({
+            allowReserved: options.allowReserved,
+            name,
+            value: value as string,
+          });
+          if (serializedPrimitive) search.push(serializedPrimitive);
+        }
+      }
+    }
+    return search.join('&');
+  };
+  return querySerializer;
+};
+
+/**
+ * Infers parseAs value from provided Content-Type header.
+ */
+export const getParseAs = (contentType: string | null): Exclude<Config['parseAs'], 'auto'> => {
+  if (!contentType) {
+    // If no Content-Type header is provided, the best we can do is return the raw response body,
+    // which is effectively the same as the 'stream' option.
+    return 'stream';
+  }
+
+  const cleanContent = contentType.split(';')[0]?.trim();
+
+  if (!cleanContent) {
+    return;
+  }
+
+  if (cleanContent.startsWith('application/json') || cleanContent.endsWith('+json')) {
+    return 'json';
+  }
+
+  if (cleanContent === 'multipart/form-data') {
+    return 'formData';
+  }
+
+  if (
+    ['application/', 'audio/', 'image/', 'video/'].some((type) => cleanContent.startsWith(type))
+  ) {
+    return 'blob';
+  }
+
+  if (cleanContent.startsWith('text/')) {
+    return 'text';
+  }
+
+  return;
+};
+
+const checkForExistence = (
+  options: Pick<RequestOptions, 'auth' | 'query'> & {
+    headers: Headers;
+  },
+  name?: string,
+): boolean => {
+  if (!name) {
+    return false;
+  }
+  if (
+    options.headers.has(name) ||
+    options.query?.[name] ||
+    options.headers.get('Cookie')?.includes(`${name}=`)
+  ) {
+    return true;
+  }
+  return false;
+};
+
+export async function setAuthParams(
+  options: Pick<RequestOptions, 'auth' | 'query' | 'security'> & {
+    headers: Headers;
+  },
+): Promise<void> {
+  for (const auth of options.security ?? []) {
+    if (checkForExistence(options, auth.name)) {
+      continue;
+    }
+
+    const token = await getAuthToken(auth, options.auth);
+
+    if (!token) {
+      continue;
+    }
+
+    const name = auth.name ?? 'Authorization';
+
+    switch (auth.in) {
+      case 'query':
+        if (!options.query) {
+          options.query = {};
+        }
+        options.query[name] = token;
+        break;
+      case 'cookie':
+        options.headers.append('Cookie', `${name}=${token}`);
+        break;
+      case 'header':
+      default:
+        options.headers.set(name, token);
+        break;
+    }
+  }
+}
+
+export const buildUrl: Client['buildUrl'] = (options) =>
+  getUrl({
+    baseUrl: options.baseUrl as string,
+    path: options.path,
+    query: options.query,
+    querySerializer:
+      typeof options.querySerializer === 'function'
+        ? options.querySerializer
+        : createQuerySerializer(options.querySerializer),
+    url: options.url,
+  });
+
+export const mergeConfigs = (a: Config, b: Config): Config => {
+  const config = { ...a, ...b };
+  if (config.baseUrl?.endsWith('/')) {
+    config.baseUrl = config.baseUrl.substring(0, config.baseUrl.length - 1);
+  }
+  config.headers = mergeHeaders(a.headers, b.headers);
+  return config;
+};
+
+const headersEntries = (headers: Headers): Array<[string, string]> => {
+  const entries: Array<[string, string]> = [];
+  headers.forEach((value, key) => {
+    entries.push([key, value]);
+  });
+  return entries;
+};
+
+export const mergeHeaders = (
+  ...headers: Array<Required<Config>['headers'] | undefined>
+): Headers => {
+  const mergedHeaders = new Headers();
+  for (const header of headers) {
+    if (!header) {
+      continue;
+    }
+
+    const iterator = header instanceof Headers ? headersEntries(header) : Object.entries(header);
+
+    for (const [key, value] of iterator) {
+      if (value === null) {
+        mergedHeaders.delete(key);
+      } else if (Array.isArray(value)) {
+        for (const v of value) {
+          mergedHeaders.append(key, v as string);
+        }
+      } else if (value !== undefined) {
+        // assume object headers are meant to be JSON stringified, i.e., their
+        // content value in OpenAPI specification is 'application/json'
+        mergedHeaders.set(
+          key,
+          typeof value === 'object' ? JSON.stringify(value) : (value as string),
+        );
+      }
+    }
+  }
+  return mergedHeaders;
+};
+
+type ErrInterceptor<Err, Res, Req, Options> = (
+  error: Err,
+  /** response may be undefined due to a network error where no response object is produced */
+  response: Res | undefined,
+  /** request may be undefined, because error may be from building the request object itself */
+  request: Req | undefined,
+  options: Options,
+) => Err | Promise<Err>;
+
+type ReqInterceptor<Req, Options> = (request: Req, options: Options) => Req | Promise<Req>;
+
+type ResInterceptor<Res, Req, Options> = (
+  response: Res,
+  request: Req,
+  options: Options,
+) => Res | Promise<Res>;
+
+class Interceptors<Interceptor> {
+  fns: Array<Interceptor | null> = [];
+
+  clear(): void {
+    this.fns = [];
+  }
+
+  eject(id: number | Interceptor): void {
+    const index = this.getInterceptorIndex(id);
+    if (this.fns[index]) {
+      this.fns[index] = null;
+    }
+  }
+
+  exists(id: number | Interceptor): boolean {
+    const index = this.getInterceptorIndex(id);
+    return Boolean(this.fns[index]);
+  }
+
+  getInterceptorIndex(id: number | Interceptor): number {
+    if (typeof id === 'number') {
+      return this.fns[id] ? id : -1;
+    }
+    return this.fns.indexOf(id);
+  }
+
+  update(id: number | Interceptor, fn: Interceptor): number | Interceptor | false {
+    const index = this.getInterceptorIndex(id);
+    if (this.fns[index]) {
+      this.fns[index] = fn;
+      return id;
+    }
+    return false;
+  }
+
+  use(fn: Interceptor): number {
+    this.fns.push(fn);
+    return this.fns.length - 1;
+  }
+}
+
+export interface Middleware<Req, Res, Err, Options> {
+  error: Interceptors<ErrInterceptor<Err, Res, Req, Options>>;
+  request: Interceptors<ReqInterceptor<Req, Options>>;
+  response: Interceptors<ResInterceptor<Res, Req, Options>>;
+}
+
+export const createInterceptors = <Req, Res, Err, Options>(): Middleware<
+  Req,
+  Res,
+  Err,
+  Options
+> => ({
+  error: new Interceptors<ErrInterceptor<Err, Res, Req, Options>>(),
+  request: new Interceptors<ReqInterceptor<Req, Options>>(),
+  response: new Interceptors<ResInterceptor<Res, Req, Options>>(),
+});
+
+const defaultQuerySerializer = createQuerySerializer({
+  allowReserved: false,
+  array: {
+    explode: true,
+    style: 'form',
+  },
+  object: {
+    explode: true,
+    style: 'deepObject',
+  },
+});
+
+const defaultHeaders = {
+  'Content-Type': 'application/json',
+};
+
+export const createConfig = <T extends ClientOptions = ClientOptions>(
+  override: Config<Omit<ClientOptions, keyof T> & T> = {},
+): Config<Omit<ClientOptions, keyof T> & T> => ({
+  ...jsonBodySerializer,
+  headers: defaultHeaders,
+  parseAs: 'auto',
+  querySerializer: defaultQuerySerializer,
+  ...override,
+});
diff --git a/frontend/src/client/core/auth.gen.ts b/frontend/src/client/core/auth.gen.ts
new file mode 100644
index 00000000..c6636644
--- /dev/null
+++ b/frontend/src/client/core/auth.gen.ts
@@ -0,0 +1,48 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export type AuthToken = string | undefined;
+
+export interface Auth {
+  /**
+   * Which part of the request do we use to send the auth?
+   *
+   * @default 'header'
+   */
+  in?: 'header' | 'query' | 'cookie';
+  /**
+   * A unique identifier for the security scheme.
+   *
+   * Defined only when there are multiple security schemes whose `Auth`
+   * shape would otherwise be identical.
+   */
+  key?: string;
+  /**
+   * Header or query parameter name.
+   *
+   * @default 'Authorization'
+   */
+  name?: string;
+  scheme?: 'basic' | 'bearer';
+  type: 'apiKey' | 'http';
+}
+
+export const getAuthToken = async (
+  auth: Auth,
+  callback: ((auth: Auth) => Promise<AuthToken> | AuthToken) | AuthToken,
+): Promise<string | undefined> => {
+  const token = typeof callback === 'function' ? await callback(auth) : callback;
+
+  if (!token) {
+    return;
+  }
+
+  if (auth.scheme === 'bearer') {
+    return `Bearer ${token}`;
+  }
+
+  if (auth.scheme === 'basic') {
+    return `Basic ${btoa(token)}`;
+  }
+
+  return token;
+};
diff --git a/frontend/src/client/core/bodySerializer.gen.ts b/frontend/src/client/core/bodySerializer.gen.ts
new file mode 100644
index 00000000..67daca60
--- /dev/null
+++ b/frontend/src/client/core/bodySerializer.gen.ts
@@ -0,0 +1,82 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { ArrayStyle, ObjectStyle, SerializerOptions } from './pathSerializer.gen';
+
+export type QuerySerializer = (query: Record<string, unknown>) => string;
+
+export type BodySerializer = (body: unknown) => unknown;
+
+type QuerySerializerOptionsObject = {
+  allowReserved?: boolean;
+  array?: Partial<SerializerOptions<ArrayStyle>>;
+  object?: Partial<SerializerOptions<ObjectStyle>>;
+};
+
+export type QuerySerializerOptions = QuerySerializerOptionsObject & {
+  /**
+   * Per-parameter serialization overrides. When provided, these settings
+   * override the global array/object settings for specific parameter names.
+   */
+  parameters?: Record<string, QuerySerializerOptionsObject>;
+};
+
+const serializeFormDataPair = (data: FormData, key: string, value: unknown): void => {
+  if (typeof value === 'string' || value instanceof Blob) {
+    data.append(key, value);
+  } else if (value instanceof Date) {
+    data.append(key, value.toISOString());
+  } else {
+    data.append(key, JSON.stringify(value));
+  }
+};
+
+const serializeUrlSearchParamsPair = (data: URLSearchParams, key: string, value: unknown): void => {
+  if (typeof value === 'string') {
+    data.append(key, value);
+  } else {
+    data.append(key, JSON.stringify(value));
+  }
+};
+
+export const formDataBodySerializer = {
+  bodySerializer: (body: unknown): FormData => {
+    const data = new FormData();
+
+    Object.entries(body as Record<string, unknown>).forEach(([key, value]) => {
+      if (value === undefined || value === null) {
+        return;
+      }
+      if (Array.isArray(value)) {
+        value.forEach((v) => serializeFormDataPair(data, key, v));
+      } else {
+        serializeFormDataPair(data, key, value);
+      }
+    });
+
+    return data;
+  },
+};
+
+export const jsonBodySerializer = {
+  bodySerializer: (body: unknown): string =>
+    JSON.stringify(body, (_key, value) => (typeof value === 'bigint' ? value.toString() : value)),
+};
+
+export const urlSearchParamsBodySerializer = {
+  bodySerializer: (body: unknown): string => {
+    const data = new URLSearchParams();
+
+    Object.entries(body as Record<string, unknown>).forEach(([key, value]) => {
+      if (value === undefined || value === null) {
+        return;
+      }
+      if (Array.isArray(value)) {
+        value.forEach((v) => serializeUrlSearchParamsPair(data, key, v));
+      } else {
+        serializeUrlSearchParamsPair(data, key, value);
+      }
+    });
+
+    return data.toString();
+  },
+};
diff --git a/frontend/src/client/core/params.gen.ts b/frontend/src/client/core/params.gen.ts
new file mode 100644
index 00000000..0f50047b
--- /dev/null
+++ b/frontend/src/client/core/params.gen.ts
@@ -0,0 +1,171 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+type Slot = 'body' | 'headers' | 'path' | 'query';
+
+export type Field =
+  | {
+      in: Exclude<Slot, 'body'>;
+      /**
+       * Field name. This is the name we want the user to see and use.
+       */
+      key: string;
+      /**
+       * Field mapped name. This is the name we want to use in the request.
+       * If omitted, we use the same value as `key`.
+       */
+      map?: string;
+    }
+  | {
+      in: Extract<Slot, 'body'>;
+      /**
+       * Key isn't required for bodies.
+       */
+      key?: string;
+      map?: string;
+    }
+  | {
+      /**
+       * Field name. This is the name we want the user to see and use.
+       */
+      key: string;
+      /**
+       * Field mapped name. This is the name we want to use in the request.
+       * If `in` is omitted, `map` aliases `key` to the transport layer.
+       */
+      map: Slot;
+    };
+
+export interface Fields {
+  allowExtra?: Partial<Record<Slot, boolean>>;
+  args?: ReadonlyArray<Field>;
+}
+
+export type FieldsConfig = ReadonlyArray<Field | Fields>;
+
+const extraPrefixesMap: Record<string, Slot> = {
+  $body_: 'body',
+  $headers_: 'headers',
+  $path_: 'path',
+  $query_: 'query',
+};
+const extraPrefixes = Object.entries(extraPrefixesMap);
+
+type KeyMap = Map<
+  string,
+  | {
+      in: Slot;
+      map?: string;
+    }
+  | {
+      in?: never;
+      map: Slot;
+    }
+>;
+
+function buildKeyMap(fields: FieldsConfig, map?: KeyMap): KeyMap {
+  if (!map) {
+    map = new Map();
+  }
+
+  for (const config of fields) {
+    if ('in' in config) {
+      if (config.key) {
+        map.set(config.key, {
+          in: config.in,
+          map: config.map,
+        });
+      }
+    } else if ('key' in config) {
+      map.set(config.key, {
+        map: config.map,
+      });
+    } else if (config.args) {
+      buildKeyMap(config.args, map);
+    }
+  }
+
+  return map;
+}
+
+interface Params {
+  body: unknown;
+  headers: Record<string, unknown>;
+  path: Record<string, unknown>;
+  query: Record<string, unknown>;
+}
+
+type ParamsSlotMap = Record<Slot, unknown>;
+
+function stripEmptySlots(params: ParamsSlotMap): void {
+  for (const [slot, value] of Object.entries(params)) {
+    if (value && typeof value === 'object' && !Array.isArray(value) && !Object.keys(value).length) {
+      delete params[slot as Slot];
+    }
+  }
+}
+
+export function buildClientParams(args: ReadonlyArray<unknown>, fields: FieldsConfig): Params {
+  const params: ParamsSlotMap = {
+    body: Object.create(null),
+    headers: Object.create(null),
+    path: Object.create(null),
+    query: Object.create(null),
+  };
+
+  const map = buildKeyMap(fields);
+
+  let config: FieldsConfig[number] | undefined;
+
+  for (const [index, arg] of args.entries()) {
+    if (fields[index]) {
+      config = fields[index];
+    }
+
+    if (!config) {
+      continue;
+    }
+
+    if ('in' in config) {
+      if (config.key) {
+        const field = map.get(config.key)!;
+        const name = field.map || config.key;
+        if (field.in) {
+          (params[field.in] as Record<string, unknown>)[name] = arg;
+        }
+      } else {
+        params.body = arg;
+      }
+    } else {
+      for (const [key, value] of Object.entries(arg ?? {})) {
+        const field = map.get(key);
+
+        if (field) {
+          if (field.in) {
+            const name = field.map || key;
+            (params[field.in] as Record<string, unknown>)[name] = value;
+          } else {
+            params[field.map] = value;
+          }
+        } else {
+          const extra = extraPrefixes.find(([prefix]) => key.startsWith(prefix));
+
+          if (extra) {
+            const [prefix, slot] = extra;
+            (params[slot] as Record<string, unknown>)[key.slice(prefix.length)] = value;
+          } else if ('allowExtra' in config && config.allowExtra) {
+            for (const [slot, allowed] of Object.entries(config.allowExtra)) {
+              if (allowed) {
+                (params[slot as Slot] as Record<string, unknown>)[key] = value;
+                break;
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
+  stripEmptySlots(params);
+
+  return params as Params;
+}
diff --git a/frontend/src/client/core/pathSerializer.gen.ts b/frontend/src/client/core/pathSerializer.gen.ts
new file mode 100644
index 00000000..fab1ed4b
--- /dev/null
+++ b/frontend/src/client/core/pathSerializer.gen.ts
@@ -0,0 +1,171 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+interface SerializeOptions<T> extends SerializePrimitiveOptions, SerializerOptions<T> {}
+
+interface SerializePrimitiveOptions {
+  allowReserved?: boolean;
+  name: string;
+}
+
+export interface SerializerOptions<T> {
+  /**
+   * @default true
+   */
+  explode: boolean;
+  style: T;
+}
+
+export type ArrayStyle = 'form' | 'spaceDelimited' | 'pipeDelimited';
+export type ArraySeparatorStyle = ArrayStyle | MatrixStyle;
+type MatrixStyle = 'label' | 'matrix' | 'simple';
+export type ObjectStyle = 'form' | 'deepObject';
+type ObjectSeparatorStyle = ObjectStyle | MatrixStyle;
+
+interface SerializePrimitiveParam extends SerializePrimitiveOptions {
+  value: string;
+}
+
+export const separatorArrayExplode = (style: ArraySeparatorStyle): '.' | ';' | ',' | '&' => {
+  switch (style) {
+    case 'label':
+      return '.';
+    case 'matrix':
+      return ';';
+    case 'simple':
+      return ',';
+    default:
+      return '&';
+  }
+};
+
+export const separatorArrayNoExplode = (style: ArraySeparatorStyle): ',' | '|' | '%20' => {
+  switch (style) {
+    case 'form':
+      return ',';
+    case 'pipeDelimited':
+      return '|';
+    case 'spaceDelimited':
+      return '%20';
+    default:
+      return ',';
+  }
+};
+
+export const separatorObjectExplode = (style: ObjectSeparatorStyle): '.' | ';' | ',' | '&' => {
+  switch (style) {
+    case 'label':
+      return '.';
+    case 'matrix':
+      return ';';
+    case 'simple':
+      return ',';
+    default:
+      return '&';
+  }
+};
+
+export const serializeArrayParam = ({
+  allowReserved,
+  explode,
+  name,
+  style,
+  value,
+}: SerializeOptions<ArraySeparatorStyle> & {
+  value: unknown[];
+}): string => {
+  if (!explode) {
+    const joinedValues = (
+      allowReserved ? value : value.map((v) => encodeURIComponent(v as string))
+    ).join(separatorArrayNoExplode(style));
+    switch (style) {
+      case 'label':
+        return `.${joinedValues}`;
+      case 'matrix':
+        return `;${name}=${joinedValues}`;
+      case 'simple':
+        return joinedValues;
+      default:
+        return `${name}=${joinedValues}`;
+    }
+  }
+
+  const separator = separatorArrayExplode(style);
+  const joinedValues = value
+    .map((v) => {
+      if (style === 'label' || style === 'simple') {
+        return allowReserved ? v : encodeURIComponent(v as string);
+      }
+
+      return serializePrimitiveParam({
+        allowReserved,
+        name,
+        value: v as string,
+      });
+    })
+    .join(separator);
+  return style === 'label' || style === 'matrix' ? separator + joinedValues : joinedValues;
+};
+
+export const serializePrimitiveParam = ({
+  allowReserved,
+  name,
+  value,
+}: SerializePrimitiveParam): string => {
+  if (value === undefined || value === null) {
+    return '';
+  }
+
+  if (typeof value === 'object') {
+    throw new Error(
+      'Deeply-nested arrays/objects aren’t supported. Provide your own `querySerializer()` to handle these.',
+    );
+  }
+
+  return `${name}=${allowReserved ? value : encodeURIComponent(value)}`;
+};
+
+export const serializeObjectParam = ({
+  allowReserved,
+  explode,
+  name,
+  style,
+  value,
+  valueOnly,
+}: SerializeOptions<ObjectSeparatorStyle> & {
+  value: Record<string, unknown> | Date;
+  valueOnly?: boolean;
+}): string => {
+  if (value instanceof Date) {
+    return valueOnly ? value.toISOString() : `${name}=${value.toISOString()}`;
+  }
+
+  if (style !== 'deepObject' && !explode) {
+    let values: string[] = [];
+    Object.entries(value).forEach(([key, v]) => {
+      values = [...values, key, allowReserved ? (v as string) : encodeURIComponent(v as string)];
+    });
+    const joinedValues = values.join(',');
+    switch (style) {
+      case 'form':
+        return `${name}=${joinedValues}`;
+      case 'label':
+        return `.${joinedValues}`;
+      case 'matrix':
+        return `;${name}=${joinedValues}`;
+      default:
+        return joinedValues;
+    }
+  }
+
+  const separator = separatorObjectExplode(style);
+  const joinedValues = Object.entries(value)
+    .map(([key, v]) =>
+      serializePrimitiveParam({
+        allowReserved,
+        name: style === 'deepObject' ? `${name}[${key}]` : key,
+        value: v as string,
+      }),
+    )
+    .join(separator);
+  return style === 'label' || style === 'matrix' ? separator + joinedValues : joinedValues;
+};
diff --git a/frontend/src/client/core/queryKeySerializer.gen.ts b/frontend/src/client/core/queryKeySerializer.gen.ts
new file mode 100644
index 00000000..773b0650
--- /dev/null
+++ b/frontend/src/client/core/queryKeySerializer.gen.ts
@@ -0,0 +1,117 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+/**
+ * JSON-friendly union that mirrors what Pinia Colada can hash.
+ */
+export type JsonValue =
+  | null
+  | string
+  | number
+  | boolean
+  | JsonValue[]
+  | { [key: string]: JsonValue };
+
+/**
+ * Replacer that converts non-JSON values (bigint, Date, etc.) to safe substitutes.
+ */
+export const queryKeyJsonReplacer = (_key: string, value: unknown): unknown | undefined => {
+  if (value === undefined || typeof value === 'function' || typeof value === 'symbol') {
+    return undefined;
+  }
+  if (typeof value === 'bigint') {
+    return value.toString();
+  }
+  if (value instanceof Date) {
+    return value.toISOString();
+  }
+  return value;
+};
+
+/**
+ * Safely stringifies a value and parses it back into a JsonValue.
+ */
+export const stringifyToJsonValue = (input: unknown): JsonValue | undefined => {
+  try {
+    const json = JSON.stringify(input, queryKeyJsonReplacer);
+    if (json === undefined) {
+      return undefined;
+    }
+    return JSON.parse(json) as JsonValue;
+  } catch {
+    return undefined;
+  }
+};
+
+/**
+ * Detects plain objects (including objects with a null prototype).
+ */
+const isPlainObject = (value: unknown): value is Record<string, unknown> => {
+  if (value === null || typeof value !== 'object') {
+    return false;
+  }
+  const prototype = Object.getPrototypeOf(value as object);
+  return prototype === Object.prototype || prototype === null;
+};
+
+/**
+ * Turns URLSearchParams into a sorted JSON object for deterministic keys.
+ */
+const serializeSearchParams = (params: URLSearchParams): JsonValue => {
+  const entries = Array.from(params.entries()).sort(([a], [b]) => a.localeCompare(b));
+  const result: Record<string, JsonValue> = {};
+
+  for (const [key, value] of entries) {
+    const existing = result[key];
+    if (existing === undefined) {
+      result[key] = value;
+      continue;
+    }
+
+    if (Array.isArray(existing)) {
+      (existing as string[]).push(value);
+    } else {
+      result[key] = [existing, value];
+    }
+  }
+
+  return result;
+};
+
+/**
+ * Normalizes any accepted value into a JSON-friendly shape for query keys.
+ */
+export const serializeQueryKeyValue = (value: unknown): JsonValue | undefined => {
+  if (value === null) {
+    return null;
+  }
+
+  if (typeof value === 'string' || typeof value === 'number' || typeof value === 'boolean') {
+    return value;
+  }
+
+  if (value === undefined || typeof value === 'function' || typeof value === 'symbol') {
+    return undefined;
+  }
+
+  if (typeof value === 'bigint') {
+    return value.toString();
+  }
+
+  if (value instanceof Date) {
+    return value.toISOString();
+  }
+
+  if (Array.isArray(value)) {
+    return stringifyToJsonValue(value);
+  }
+
+  if (typeof URLSearchParams !== 'undefined' && value instanceof URLSearchParams) {
+    return serializeSearchParams(value);
+  }
+
+  if (isPlainObject(value)) {
+    return stringifyToJsonValue(value);
+  }
+
+  return undefined;
+};
diff --git a/frontend/src/client/core/serverSentEvents.gen.ts b/frontend/src/client/core/serverSentEvents.gen.ts
new file mode 100644
index 00000000..ddf3c4d1
--- /dev/null
+++ b/frontend/src/client/core/serverSentEvents.gen.ts
@@ -0,0 +1,242 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { Config } from './types.gen';
+
+export type ServerSentEventsOptions<TData = unknown> = Omit<RequestInit, 'method'> &
+  Pick<Config, 'method' | 'responseTransformer' | 'responseValidator'> & {
+    /**
+     * Fetch API implementation. You can use this option to provide a custom
+     * fetch instance.
+     *
+     * @default globalThis.fetch
+     */
+    fetch?: typeof fetch;
+    /**
+     * Implementing clients can call request interceptors inside this hook.
+     */
+    onRequest?: (url: string, init: RequestInit) => Promise<Request>;
+    /**
+     * Callback invoked when a network or parsing error occurs during streaming.
+     *
+     * This option applies only if the endpoint returns a stream of events.
+     *
+     * @param error The error that occurred.
+     */
+    onSseError?: (error: unknown) => void;
+    /**
+     * Callback invoked when an event is streamed from the server.
+     *
+     * This option applies only if the endpoint returns a stream of events.
+     *
+     * @param event Event streamed from the server.
+     * @returns Nothing (void).
+     */
+    onSseEvent?: (event: StreamEvent<TData>) => void;
+    serializedBody?: RequestInit['body'];
+    /**
+     * Default retry delay in milliseconds.
+     *
+     * This option applies only if the endpoint returns a stream of events.
+     *
+     * @default 3000
+     */
+    sseDefaultRetryDelay?: number;
+    /**
+     * Maximum number of retry attempts before giving up.
+     */
+    sseMaxRetryAttempts?: number;
+    /**
+     * Maximum retry delay in milliseconds.
+     *
+     * Applies only when exponential backoff is used.
+     *
+     * This option applies only if the endpoint returns a stream of events.
+     *
+     * @default 30000
+     */
+    sseMaxRetryDelay?: number;
+    /**
+     * Optional sleep function for retry backoff.
+     *
+     * Defaults to using `setTimeout`.
+     */
+    sseSleepFn?: (ms: number) => Promise<void>;
+    url: string;
+  };
+
+export interface StreamEvent<TData = unknown> {
+  data: TData;
+  event?: string;
+  id?: string;
+  retry?: number;
+}
+
+export type ServerSentEventsResult<TData = unknown, TReturn = void, TNext = unknown> = {
+  stream: AsyncGenerator<
+    TData extends Record<string, unknown> ? TData[keyof TData] : TData,
+    TReturn,
+    TNext
+  >;
+};
+
+export function createSseClient<TData = unknown>({
+  onRequest,
+  onSseError,
+  onSseEvent,
+  responseTransformer,
+  responseValidator,
+  sseDefaultRetryDelay,
+  sseMaxRetryAttempts,
+  sseMaxRetryDelay,
+  sseSleepFn,
+  url,
+  ...options
+}: ServerSentEventsOptions): ServerSentEventsResult<TData> {
+  let lastEventId: string | undefined;
+
+  const sleep = sseSleepFn ?? ((ms: number) => new Promise((resolve) => setTimeout(resolve, ms)));
+
+  const createStream = async function* () {
+    let retryDelay: number = sseDefaultRetryDelay ?? 3000;
+    let attempt = 0;
+    const signal = options.signal ?? new AbortController().signal;
+
+    while (true) {
+      if (signal.aborted) break;
+
+      attempt++;
+
+      const headers =
+        options.headers instanceof Headers
+          ? options.headers
+          : new Headers(options.headers as Record<string, string> | undefined);
+
+      if (lastEventId !== undefined) {
+        headers.set('Last-Event-ID', lastEventId);
+      }
+
+      try {
+        const requestInit: RequestInit = {
+          redirect: 'follow',
+          ...options,
+          body: options.serializedBody,
+          headers,
+          signal,
+        };
+        let request = new Request(url, requestInit);
+        if (onRequest) {
+          request = await onRequest(url, requestInit);
+        }
+        // fetch must be assigned here, otherwise it would throw the error:
+        // TypeError: Failed to execute 'fetch' on 'Window': Illegal invocation
+        const _fetch = options.fetch ?? globalThis.fetch;
+        const response = await _fetch(request);
+
+        if (!response.ok) throw new Error(`SSE failed: ${response.status} ${response.statusText}`);
+
+        if (!response.body) throw new Error('No body in SSE response');
+
+        const reader = response.body.pipeThrough(new TextDecoderStream()).getReader();
+
+        let buffer = '';
+
+        const abortHandler = () => {
+          try {
+            reader.cancel();
+          } catch {
+            // noop
+          }
+        };
+
+        signal.addEventListener('abort', abortHandler);
+
+        try {
+          while (true) {
+            const { done, value } = await reader.read();
+            if (done) break;
+            buffer += value;
+            buffer = buffer.replace(/\r\n?/g, '\n'); // normalize line endings
+
+            const chunks = buffer.split('\n\n');
+            buffer = chunks.pop() ?? '';
+
+            for (const chunk of chunks) {
+              const lines = chunk.split('\n');
+              const dataLines: Array<string> = [];
+              let eventName: string | undefined;
+
+              for (const line of lines) {
+                if (line.startsWith('data:')) {
+                  dataLines.push(line.replace(/^data:\s*/, ''));
+                } else if (line.startsWith('event:')) {
+                  eventName = line.replace(/^event:\s*/, '');
+                } else if (line.startsWith('id:')) {
+                  lastEventId = line.replace(/^id:\s*/, '');
+                } else if (line.startsWith('retry:')) {
+                  const parsed = Number.parseInt(line.replace(/^retry:\s*/, ''), 10);
+                  if (!Number.isNaN(parsed)) {
+                    retryDelay = parsed;
+                  }
+                }
+              }
+
+              let data: unknown;
+              let parsedJson = false;
+
+              if (dataLines.length) {
+                const rawData = dataLines.join('\n');
+                try {
+                  data = JSON.parse(rawData);
+                  parsedJson = true;
+                } catch {
+                  data = rawData;
+                }
+              }
+
+              if (parsedJson) {
+                if (responseValidator) {
+                  await responseValidator(data);
+                }
+
+                if (responseTransformer) {
+                  data = await responseTransformer(data);
+                }
+              }
+
+              onSseEvent?.({
+                data,
+                event: eventName,
+                id: lastEventId,
+                retry: retryDelay,
+              });
+
+              if (dataLines.length) {
+                yield data as any;
+              }
+            }
+          }
+        } finally {
+          signal.removeEventListener('abort', abortHandler);
+          reader.releaseLock();
+        }
+
+        break; // exit loop on normal completion
+      } catch (error) {
+        // connection failed or aborted; retry after delay
+        onSseError?.(error);
+
+        if (sseMaxRetryAttempts !== undefined && attempt >= sseMaxRetryAttempts) {
+          break; // stop after firing error
+        }
+
+        // exponential backoff: double retry each attempt, cap at 30s
+        const backoff = Math.min(retryDelay * 2 ** (attempt - 1), sseMaxRetryDelay ?? 30000);
+        await sleep(backoff);
+      }
+    }
+  };
+
+  const stream = createStream();
+
+  return { stream };
+}
diff --git a/frontend/src/client/core/types.gen.ts b/frontend/src/client/core/types.gen.ts
new file mode 100644
index 00000000..c657c859
--- /dev/null
+++ b/frontend/src/client/core/types.gen.ts
@@ -0,0 +1,110 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { Auth, AuthToken } from './auth.gen';
+import type { BodySerializer, QuerySerializer, QuerySerializerOptions } from './bodySerializer.gen';
+
+export type HttpMethod =
+  | 'connect'
+  | 'delete'
+  | 'get'
+  | 'head'
+  | 'options'
+  | 'patch'
+  | 'post'
+  | 'put'
+  | 'trace';
+
+export type Client<
+  RequestFn = never,
+  Config = unknown,
+  MethodFn = never,
+  BuildUrlFn = never,
+  SseFn = never,
+> = {
+  /**
+   * Returns the final request URL.
+   */
+  buildUrl: BuildUrlFn;
+  getConfig: () => Config;
+  request: RequestFn;
+  setConfig: (config: Config) => Config;
+} & {
+  [K in HttpMethod]: MethodFn;
+} & ([SseFn] extends [never] ? { sse?: never } : { sse: { [K in HttpMethod]: SseFn } });
+
+export interface Config {
+  /**
+   * Auth token or a function returning auth token. The resolved value will be
+   * added to the request payload as defined by its `security` array.
+   */
+  auth?: ((auth: Auth) => Promise<AuthToken> | AuthToken) | AuthToken;
+  /**
+   * A function for serializing request body parameter. By default,
+   * {@link JSON.stringify()} will be used.
+   */
+  bodySerializer?: BodySerializer | null;
+  /**
+   * An object containing any HTTP headers that you want to pre-populate your
+   * `Headers` object with.
+   *
+   * {@link https://developer.mozilla.org/docs/Web/API/Headers/Headers#init See more}
+   */
+  headers?:
+    | RequestInit['headers']
+    | Record<
+        string,
+        string | number | boolean | (string | number | boolean)[] | null | undefined | unknown
+      >;
+  /**
+   * The request method.
+   *
+   * {@link https://developer.mozilla.org/docs/Web/API/fetch#method See more}
+   */
+  method?: Uppercase<HttpMethod>;
+  /**
+   * A function for serializing request query parameters. By default, arrays
+   * will be exploded in form style, objects will be exploded in deepObject
+   * style, and reserved characters are percent-encoded.
+   *
+   * This method will have no effect if the native `paramsSerializer()` Axios
+   * API function is used.
+   *
+   * {@link https://swagger.io/docs/specification/serialization/#query View examples}
+   */
+  querySerializer?: QuerySerializer | QuerySerializerOptions;
+  /**
+   * A function validating request data. This is useful if you want to ensure
+   * the request conforms to the desired shape, so it can be safely sent to
+   * the server.
+   */
+  requestValidator?: (data: unknown) => Promise<unknown>;
+  /**
+   * A function transforming response data before it's returned. This is useful
+   * for post-processing data, e.g., converting ISO strings into Date objects.
+   */
+  responseTransformer?: (data: unknown) => Promise<unknown>;
+  /**
+   * A function validating response data. This is useful if you want to ensure
+   * the response conforms to the desired shape, so it can be safely passed to
+   * the transformers and returned to the user.
+   */
+  responseValidator?: (data: unknown) => Promise<unknown>;
+}
+
+/**
+ * Arbitrary metadata passed through the `meta` request option.
+ */
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
+export interface ClientMeta {}
+
+type IsExactlyNeverOrNeverUndefined<T> = [T] extends [never]
+  ? true
+  : [T] extends [never | undefined]
+    ? [undefined] extends [T]
+      ? false
+      : true
+    : false;
+
+export type OmitNever<T extends Record<string, unknown>> = {
+  [K in keyof T as IsExactlyNeverOrNeverUndefined<T[K]> extends true ? never : K]: T[K];
+};
diff --git a/frontend/src/client/core/utils.gen.ts b/frontend/src/client/core/utils.gen.ts
new file mode 100644
index 00000000..af56e071
--- /dev/null
+++ b/frontend/src/client/core/utils.gen.ts
@@ -0,0 +1,140 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { BodySerializer, QuerySerializer } from './bodySerializer.gen';
+import {
+  type ArraySeparatorStyle,
+  serializeArrayParam,
+  serializeObjectParam,
+  serializePrimitiveParam,
+} from './pathSerializer.gen';
+
+export interface PathSerializer {
+  path: Record<string, unknown>;
+  url: string;
+}
+
+export const PATH_PARAM_RE: RegExp = /\{[^{}]+\}/g;
+
+export const defaultPathSerializer = ({ path, url: _url }: PathSerializer): string => {
+  let url = _url;
+  const matches = _url.match(PATH_PARAM_RE);
+  if (matches) {
+    for (const match of matches) {
+      let explode = false;
+      let name = match.substring(1, match.length - 1);
+      let style: ArraySeparatorStyle = 'simple';
+
+      if (name.endsWith('*')) {
+        explode = true;
+        name = name.substring(0, name.length - 1);
+      }
+
+      if (name.startsWith('.')) {
+        name = name.substring(1);
+        style = 'label';
+      } else if (name.startsWith(';')) {
+        name = name.substring(1);
+        style = 'matrix';
+      }
+
+      const value = path[name];
+
+      if (value === undefined || value === null) {
+        continue;
+      }
+
+      if (Array.isArray(value)) {
+        url = url.replace(match, serializeArrayParam({ explode, name, style, value }));
+        continue;
+      }
+
+      if (typeof value === 'object') {
+        url = url.replace(
+          match,
+          serializeObjectParam({
+            explode,
+            name,
+            style,
+            value: value as Record<string, unknown>,
+            valueOnly: true,
+          }),
+        );
+        continue;
+      }
+
+      if (style === 'matrix') {
+        url = url.replace(
+          match,
+          `;${serializePrimitiveParam({
+            name,
+            value: value as string,
+          })}`,
+        );
+        continue;
+      }
+
+      const replaceValue = encodeURIComponent(
+        style === 'label' ? `.${value as string}` : (value as string),
+      );
+      url = url.replace(match, replaceValue);
+    }
+  }
+  return url;
+};
+
+export const getUrl = ({
+  baseUrl,
+  path,
+  query,
+  querySerializer,
+  url: _url,
+}: {
+  baseUrl?: string;
+  path?: Record<string, unknown>;
+  query?: Record<string, unknown>;
+  querySerializer: QuerySerializer;
+  url: string;
+}): string => {
+  const pathUrl = _url.startsWith('/') ? _url : `/${_url}`;
+  let url = (baseUrl ?? '') + pathUrl;
+  if (path) {
+    url = defaultPathSerializer({ path, url });
+  }
+  let search = query ? querySerializer(query) : '';
+  if (search.startsWith('?')) {
+    search = search.substring(1);
+  }
+  if (search) {
+    url += `?${search}`;
+  }
+  return url;
+};
+
+export function getValidRequestBody(options: {
+  body?: unknown;
+  bodySerializer?: BodySerializer | null;
+  serializedBody?: unknown;
+}): unknown {
+  const hasBody = options.body !== undefined;
+  const isSerializedBody = hasBody && options.bodySerializer;
+
+  if (isSerializedBody) {
+    if ('serializedBody' in options) {
+      const hasSerializedBody =
+        options.serializedBody !== undefined && options.serializedBody !== '';
+
+      return hasSerializedBody ? options.serializedBody : null;
+    }
+
+    // not all clients implement a serializedBody property (i.e., client-axios)
+    return options.body !== '' ? options.body : null;
+  }
+
+  // plain/text body
+  if (hasBody) {
+    return options.body;
+  }
+
+  // no body was provided
+  return undefined;
+}
diff --git a/frontend/src/client/index.ts b/frontend/src/client/index.ts
new file mode 100644
index 00000000..7eb1c36d
--- /dev/null
+++ b/frontend/src/client/index.ts
@@ -0,0 +1,4 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export { getConfigAzimInt, getConfigDarkMask, getConfigDetector, getConfigFileWriter, getConfigImageFormat, getConfigIndexing, getConfigInstrument, getConfigMask, getConfigMaskTiff, getConfigRoi, getConfigSelectDetector, getConfigSpotFinding, getConfigUserMask, getConfigUserMaskTiff, getConfigZeromqMetadata, getConfigZeromqPreview, getDetectorStatus, getFpgaStatus, getImageBufferImageCbor, getImageBufferImageJpeg, getImageBufferImageTiff, getImageBufferStartCbor, getImageBufferStatus, getImagePusherStatus, getPreviewPedestalTiff, getPreviewPlot, getPreviewPlotBin, getResultScan, getStatistics, getStatisticsCalibration, getStatisticsDataCollection, getStatus, getVersion, getXfelEventCode, getXfelPulseId, type Options, postCancel, postConfigImageFormatConversion, postConfigImageFormatRaw, postDeactivate, postImageBufferClear, postInitialize, postPedestal, postStart, postTrigger, postWaitTillDone, postWaitUntilRunning, putConfigAzimInt, putConfigDarkMask, putConfigDetector, putConfigFileWriter, putConfigImageFormat, putConfigIndexing, putConfigInstrument, putConfigInternalGeneratorImage, putConfigInternalGeneratorImageTiff, putConfigRoi, putConfigSelectDetector, putConfigSpotFinding, putConfigUserMask, putConfigUserMaskTiff, putConfigZeromqMetadata, putConfigZeromqPreview } from './sdk.gen';
+export { type azim_int_settings, azint_unit, type background, type binning, type broker_status, type calibration_statistics, type ClientOptions, color_scale, type crystal_lattice, type dark_mask_settings, type dataset_settings, type detector, type detector_list, type detector_list_element, type detector_module, detector_module_direction, detector_power_state, type detector_selection, type detector_settings, detector_state, type detector_status, detector_timing, detector_type, type error_message, type experimental_coord, file_writer_format, type file_writer_settings, type fill_value, type fpga_status, geom_refinement_algorithm, type getConfigAzimIntData, type getConfigAzimIntResponse, type getConfigAzimIntResponses, type getConfigDarkMaskData, type getConfigDarkMaskResponse, type getConfigDarkMaskResponses, type getConfigDetectorData, type getConfigDetectorResponse, type getConfigDetectorResponses, type getConfigFileWriterData, type getConfigFileWriterResponse, type getConfigFileWriterResponses, type getConfigImageFormatData, type getConfigImageFormatResponse, type getConfigImageFormatResponses, type getConfigIndexingData, type getConfigIndexingResponse, type getConfigIndexingResponses, type getConfigInstrumentData, type getConfigInstrumentResponse, type getConfigInstrumentResponses, type getConfigMaskData, type getConfigMaskResponse, type getConfigMaskResponses, type getConfigMaskTiffData, type getConfigMaskTiffResponse, type getConfigMaskTiffResponses, type getConfigRoiData, type getConfigRoiResponse, type getConfigRoiResponses, type getConfigSelectDetectorData, type getConfigSelectDetectorResponse, type getConfigSelectDetectorResponses, type getConfigSpotFindingData, type getConfigSpotFindingResponse, type getConfigSpotFindingResponses, type getConfigUserMaskData, type getConfigUserMaskResponse, type getConfigUserMaskResponses, type getConfigUserMaskTiffData, type getConfigUserMaskTiffResponse, type getConfigUserMaskTiffResponses, type getConfigZeromqMetadataData, type getConfigZeromqMetadataResponse, type getConfigZeromqMetadataResponses, type getConfigZeromqPreviewData, type getConfigZeromqPreviewResponse, type getConfigZeromqPreviewResponses, type getDetectorStatusData, type getDetectorStatusError, type getDetectorStatusErrors, type getDetectorStatusResponse, type getDetectorStatusResponses, type getFpgaStatusData, type getFpgaStatusResponse, type getFpgaStatusResponses, type getImageBufferImageCborData, type getImageBufferImageCborError, type getImageBufferImageCborErrors, type getImageBufferImageCborResponse, type getImageBufferImageCborResponses, type getImageBufferImageJpegData, type getImageBufferImageJpegError, type getImageBufferImageJpegErrors, type getImageBufferImageJpegResponse, type getImageBufferImageJpegResponses, type getImageBufferImageTiffData, type getImageBufferImageTiffErrors, type getImageBufferImageTiffResponse, type getImageBufferImageTiffResponses, type getImageBufferStartCborData, type getImageBufferStartCborError, type getImageBufferStartCborErrors, type getImageBufferStartCborResponse, type getImageBufferStartCborResponses, type getImageBufferStatusData, type getImageBufferStatusError, type getImageBufferStatusErrors, type getImageBufferStatusResponse, type getImageBufferStatusResponses, type getImagePusherStatusData, type getImagePusherStatusError, type getImagePusherStatusErrors, type getImagePusherStatusResponse, type getImagePusherStatusResponses, type getPreviewPedestalTiffData, type getPreviewPedestalTiffErrors, type getPreviewPedestalTiffResponse, type getPreviewPedestalTiffResponses, type getPreviewPlotBinData, type getPreviewPlotBinError, type getPreviewPlotBinErrors, type getPreviewPlotBinResponse, type getPreviewPlotBinResponses, type getPreviewPlotData, type getPreviewPlotError, type getPreviewPlotErrors, type getPreviewPlotResponse, type getPreviewPlotResponses, type getResultScanData, type getResultScanError, type getResultScanErrors, type getResultScanResponse, type getResultScanResponses, type getStatisticsCalibrationData, type getStatisticsCalibrationResponse, type getStatisticsCalibrationResponses, type getStatisticsData, type getStatisticsDataCollectionData, type getStatisticsDataCollectionErrors, type getStatisticsDataCollectionResponse, type getStatisticsDataCollectionResponses, type getStatisticsResponse, type getStatisticsResponses, type getStatusData, type getStatusResponse, type getStatusResponses, type getVersionData, type getVersionResponse, type getVersionResponses, type getXfelEventCodeData, type getXfelEventCodeErrors, type getXfelEventCodeResponse, type getXfelEventCodeResponses, type getXfelPulseIdData, type getXfelPulseIdErrors, type getXfelPulseIdResponse, type getXfelPulseIdResponses, type grid_scan, type image_buffer_status, type image_format_settings, type image_id, type image_pusher_status, image_pusher_type, indexing_algorithm, type indexing_settings, type instrument_metadata, type jfjoch_settings, type jfjoch_statistics, type jpeg_quality, type measurement_statistics, type pcie_devices, type pixel_mask_statistics, type plot, plot_type, plot_unit_x, type plots, type postCancelData, type postCancelResponses, type postConfigImageFormatConversionData, type postConfigImageFormatConversionError, type postConfigImageFormatConversionErrors, type postConfigImageFormatConversionResponses, type postConfigImageFormatRawData, type postConfigImageFormatRawError, type postConfigImageFormatRawErrors, type postConfigImageFormatRawResponses, type postDeactivateData, type postDeactivateError, type postDeactivateErrors, type postDeactivateResponses, type postImageBufferClearData, type postImageBufferClearError, type postImageBufferClearErrors, type postImageBufferClearResponses, type postInitializeData, type postInitializeError, type postInitializeErrors, type postInitializeResponses, type postPedestalData, type postPedestalError, type postPedestalErrors, type postPedestalResponses, type postStartData, type postStartError, type postStartErrors, type postStartResponses, type postTriggerData, type postTriggerResponses, type postWaitTillDoneData, type postWaitTillDoneError, type postWaitTillDoneErrors, type postWaitTillDoneResponses, type postWaitUntilRunningData, type postWaitUntilRunningError, type postWaitUntilRunningErrors, type postWaitUntilRunningResponses, type putConfigAzimIntData, type putConfigAzimIntError, type putConfigAzimIntErrors, type putConfigAzimIntResponses, type putConfigDarkMaskData, type putConfigDarkMaskError, type putConfigDarkMaskErrors, type putConfigDarkMaskResponses, type putConfigDetectorData, type putConfigDetectorError, type putConfigDetectorErrors, type putConfigDetectorResponses, type putConfigFileWriterData, type putConfigFileWriterError, type putConfigFileWriterErrors, type putConfigFileWriterResponses, type putConfigImageFormatData, type putConfigImageFormatError, type putConfigImageFormatErrors, type putConfigImageFormatResponses, type putConfigIndexingData, type putConfigIndexingError, type putConfigIndexingErrors, type putConfigIndexingResponses, type putConfigInstrumentData, type putConfigInstrumentError, type putConfigInstrumentErrors, type putConfigInstrumentResponses, type putConfigInternalGeneratorImageData, type putConfigInternalGeneratorImageError, type putConfigInternalGeneratorImageErrors, type putConfigInternalGeneratorImageResponses, type putConfigInternalGeneratorImageTiffData, type putConfigInternalGeneratorImageTiffError, type putConfigInternalGeneratorImageTiffErrors, type putConfigInternalGeneratorImageTiffResponses, type putConfigRoiData, type putConfigRoiError, type putConfigRoiErrors, type putConfigRoiResponses, type putConfigSelectDetectorData, type putConfigSelectDetectorError, type putConfigSelectDetectorErrors, type putConfigSelectDetectorResponses, type putConfigSpotFindingData, type putConfigSpotFindingError, type putConfigSpotFindingErrors, type putConfigSpotFindingResponses, type putConfigUserMaskData, type putConfigUserMaskError, type putConfigUserMaskErrors, type putConfigUserMaskResponses, type putConfigUserMaskTiffData, type putConfigUserMaskTiffError, type putConfigUserMaskTiffErrors, type putConfigUserMaskTiffResponses, type putConfigZeromqMetadataData, type putConfigZeromqMetadataError, type putConfigZeromqMetadataErrors, type putConfigZeromqMetadataResponses, type putConfigZeromqPreviewData, type putConfigZeromqPreviewError, type putConfigZeromqPreviewErrors, type putConfigZeromqPreviewResponses, type resolution_estimate, type resolution_ring, type roi, type roi_azim_list, type roi_azimuthal, type roi_box, type roi_box_list, type roi_circle, type roi_circle_list, type roi_definitions, type rotation_axis, type saturation, type scan_result, type show_beam_center, type show_roi, type show_spots, type show_user_mask, type spot_finding_settings, type standard_detector_geometry, type tcp_settings, type unit_cell, type zeromq_metadata_settings, type zeromq_preview_settings, type zeromq_settings } from './types.gen';
diff --git a/frontend/src/client/sdk.gen.ts b/frontend/src/client/sdk.gen.ts
new file mode 100644
index 00000000..e36c8a41
--- /dev/null
+++ b/frontend/src/client/sdk.gen.ts
@@ -0,0 +1,640 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import type { Client, ClientMeta, Options as Options2, RequestResult, TDataShape } from './client';
+import { client } from './client.gen';
+import type { getConfigAzimIntData, getConfigAzimIntResponses, getConfigDarkMaskData, getConfigDarkMaskResponses, getConfigDetectorData, getConfigDetectorResponses, getConfigFileWriterData, getConfigFileWriterResponses, getConfigImageFormatData, getConfigImageFormatResponses, getConfigIndexingData, getConfigIndexingResponses, getConfigInstrumentData, getConfigInstrumentResponses, getConfigMaskData, getConfigMaskResponses, getConfigMaskTiffData, getConfigMaskTiffResponses, getConfigRoiData, getConfigRoiResponses, getConfigSelectDetectorData, getConfigSelectDetectorResponses, getConfigSpotFindingData, getConfigSpotFindingResponses, getConfigUserMaskData, getConfigUserMaskResponses, getConfigUserMaskTiffData, getConfigUserMaskTiffResponses, getConfigZeromqMetadataData, getConfigZeromqMetadataResponses, getConfigZeromqPreviewData, getConfigZeromqPreviewResponses, getDetectorStatusData, getDetectorStatusErrors, getDetectorStatusResponses, getFpgaStatusData, getFpgaStatusResponses, getImageBufferImageCborData, getImageBufferImageCborErrors, getImageBufferImageCborResponses, getImageBufferImageJpegData, getImageBufferImageJpegErrors, getImageBufferImageJpegResponses, getImageBufferImageTiffData, getImageBufferImageTiffErrors, getImageBufferImageTiffResponses, getImageBufferStartCborData, getImageBufferStartCborErrors, getImageBufferStartCborResponses, getImageBufferStatusData, getImageBufferStatusErrors, getImageBufferStatusResponses, getImagePusherStatusData, getImagePusherStatusErrors, getImagePusherStatusResponses, getPreviewPedestalTiffData, getPreviewPedestalTiffErrors, getPreviewPedestalTiffResponses, getPreviewPlotBinData, getPreviewPlotBinErrors, getPreviewPlotBinResponses, getPreviewPlotData, getPreviewPlotErrors, getPreviewPlotResponses, getResultScanData, getResultScanErrors, getResultScanResponses, getStatisticsCalibrationData, getStatisticsCalibrationResponses, getStatisticsData, getStatisticsDataCollectionData, getStatisticsDataCollectionErrors, getStatisticsDataCollectionResponses, getStatisticsResponses, getStatusData, getStatusResponses, getVersionData, getVersionResponses, getXfelEventCodeData, getXfelEventCodeErrors, getXfelEventCodeResponses, getXfelPulseIdData, getXfelPulseIdErrors, getXfelPulseIdResponses, postCancelData, postCancelResponses, postConfigImageFormatConversionData, postConfigImageFormatConversionErrors, postConfigImageFormatConversionResponses, postConfigImageFormatRawData, postConfigImageFormatRawErrors, postConfigImageFormatRawResponses, postDeactivateData, postDeactivateErrors, postDeactivateResponses, postImageBufferClearData, postImageBufferClearErrors, postImageBufferClearResponses, postInitializeData, postInitializeErrors, postInitializeResponses, postPedestalData, postPedestalErrors, postPedestalResponses, postStartData, postStartErrors, postStartResponses, postTriggerData, postTriggerResponses, postWaitTillDoneData, postWaitTillDoneErrors, postWaitTillDoneResponses, postWaitUntilRunningData, postWaitUntilRunningErrors, postWaitUntilRunningResponses, putConfigAzimIntData, putConfigAzimIntErrors, putConfigAzimIntResponses, putConfigDarkMaskData, putConfigDarkMaskErrors, putConfigDarkMaskResponses, putConfigDetectorData, putConfigDetectorErrors, putConfigDetectorResponses, putConfigFileWriterData, putConfigFileWriterErrors, putConfigFileWriterResponses, putConfigImageFormatData, putConfigImageFormatErrors, putConfigImageFormatResponses, putConfigIndexingData, putConfigIndexingErrors, putConfigIndexingResponses, putConfigInstrumentData, putConfigInstrumentErrors, putConfigInstrumentResponses, putConfigInternalGeneratorImageData, putConfigInternalGeneratorImageErrors, putConfigInternalGeneratorImageResponses, putConfigInternalGeneratorImageTiffData, putConfigInternalGeneratorImageTiffErrors, putConfigInternalGeneratorImageTiffResponses, putConfigRoiData, putConfigRoiErrors, putConfigRoiResponses, putConfigSelectDetectorData, putConfigSelectDetectorErrors, putConfigSelectDetectorResponses, putConfigSpotFindingData, putConfigSpotFindingErrors, putConfigSpotFindingResponses, putConfigUserMaskData, putConfigUserMaskErrors, putConfigUserMaskResponses, putConfigUserMaskTiffData, putConfigUserMaskTiffErrors, putConfigUserMaskTiffResponses, putConfigZeromqMetadataData, putConfigZeromqMetadataErrors, putConfigZeromqMetadataResponses, putConfigZeromqPreviewData, putConfigZeromqPreviewErrors, putConfigZeromqPreviewResponses } from './types.gen';
+
+export type Options<TData extends TDataShape = TDataShape, ThrowOnError extends boolean = boolean, TResponse = unknown> = Options2<TData, ThrowOnError, TResponse> & {
+    /**
+     * You can provide a client instance returned by `createClient()` instead of
+     * individual options. This might be also useful if you want to implement a
+     * custom client.
+     */
+    client?: Client;
+    /**
+     * You can pass arbitrary values through the `meta` object. This can be
+     * used to access values that aren't defined as part of the SDK function.
+     */
+    meta?: keyof ClientMeta extends never ? Record<string, unknown> : ClientMeta;
+};
+
+/**
+ * Initialize detector and data acquisition
+ *
+ * Should be used in two cases:
+ * - Detector is in `Inactive` state
+ * - Detector is in `Error` state
+ * X-ray shutter must be closed.
+ * This operation will reconfigure network interface of the detector.
+ * During operation of the detector it is recommended to use the `POST /pedestal` operation instead.
+ * If storage cells are used, the execution time might be few minutes.
+ *
+ * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
+ *
+ */
+export const postInitialize = <ThrowOnError extends boolean = false>(options?: Options<postInitializeData, ThrowOnError>): RequestResult<postInitializeResponses, postInitializeErrors, ThrowOnError> => (options?.client ?? client).post<postInitializeResponses, postInitializeErrors, ThrowOnError>({ url: '/initialize', ...options });
+
+/**
+ * Collect dark current for the detector
+ *
+ * Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.
+ *
+ * X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).
+ *
+ * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
+ *
+ */
+export const postPedestal = <ThrowOnError extends boolean = false>(options?: Options<postPedestalData, ThrowOnError>): RequestResult<postPedestalResponses, postPedestalErrors, ThrowOnError> => (options?.client ?? client).post<postPedestalResponses, postPedestalErrors, ThrowOnError>({ url: '/pedestal', ...options });
+
+/**
+ * Start detector
+ *
+ * Start data acquisition.
+ * Detector must be in `Idle` state.
+ * Default behavior is for the call to block until detector is ready to accept soft/TTL triggers.
+ * However, this behavior can be changed by settings `async_start` to true in the request body,
+ * in which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.
+ *
+ */
+export const postStart = <ThrowOnError extends boolean = false>(options?: Options<postStartData, ThrowOnError>): RequestResult<postStartResponses, postStartErrors, ThrowOnError> => (options?.client ?? client).post<postStartResponses, postStartErrors, ThrowOnError>({
+    url: '/start',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Wait for acquisition running
+ *
+ * Block execution of external script till detector and Jungfraujoch are ready to collect data.
+ * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
+ * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
+ *
+ */
+export const postWaitUntilRunning = <ThrowOnError extends boolean = false>(options?: Options<postWaitUntilRunningData, ThrowOnError>): RequestResult<postWaitUntilRunningResponses, postWaitUntilRunningErrors, ThrowOnError> => (options?.client ?? client).post<postWaitUntilRunningResponses, postWaitUntilRunningErrors, ThrowOnError>({ url: '/wait_until_running', ...options });
+
+/**
+ * Wait for acquisition done
+ *
+ * Block execution of external script till initialization, data collection or pedestal is finished.
+ * Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.
+ *
+ * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
+ * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
+ *
+ */
+export const postWaitTillDone = <ThrowOnError extends boolean = false>(options?: Options<postWaitTillDoneData, ThrowOnError>): RequestResult<postWaitTillDoneResponses, postWaitTillDoneErrors, ThrowOnError> => (options?.client ?? client).post<postWaitTillDoneResponses, postWaitTillDoneErrors, ThrowOnError>({ url: '/wait_till_done', ...options });
+
+/**
+ * Send soft trigger to the detector
+ *
+ * Generate soft trigger
+ */
+export const postTrigger = <ThrowOnError extends boolean = false>(options?: Options<postTriggerData, ThrowOnError>): RequestResult<postTriggerResponses, unknown, ThrowOnError> => (options?.client ?? client).post<postTriggerResponses, unknown, ThrowOnError>({ url: '/trigger', ...options });
+
+/**
+ * Cancel running data collection
+ *
+ * Command will inform FPGA network card to stop pedestal or data collection at the current stage.
+ * Any frame that is currently being processed by CPU will be finished and sent to writer.
+ * Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.
+ *
+ * If data collection is not running, the command has no effect.
+ *
+ */
+export const postCancel = <ThrowOnError extends boolean = false>(options?: Options<postCancelData, ThrowOnError>): RequestResult<postCancelResponses, unknown, ThrowOnError> => (options?.client ?? client).post<postCancelResponses, unknown, ThrowOnError>({ url: '/cancel', ...options });
+
+/**
+ * Prepare detector to turn off
+ *
+ * Should be in `Idle` or `Error` state.
+ * Command deactivates data acquisition and turns off detector high voltage and ASIC.
+ * Should be used always before turning off power from the detector.
+ *
+ */
+export const postDeactivate = <ThrowOnError extends boolean = false>(options?: Options<postDeactivateData, ThrowOnError>): RequestResult<postDeactivateResponses, postDeactivateErrors, ThrowOnError> => (options?.client ?? client).post<postDeactivateResponses, postDeactivateErrors, ThrowOnError>({ url: '/deactivate', ...options });
+
+/**
+ * Get detector configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigDetector = <ThrowOnError extends boolean = false>(options?: Options<getConfigDetectorData, ThrowOnError>): RequestResult<getConfigDetectorResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigDetectorResponses, unknown, ThrowOnError>({ url: '/config/detector', ...options });
+
+/**
+ * Change detector configuration
+ *
+ * Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ * If detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.
+ * If detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.
+ *
+ */
+export const putConfigDetector = <ThrowOnError extends boolean = false>(options?: Options<putConfigDetectorData, ThrowOnError>): RequestResult<putConfigDetectorResponses, putConfigDetectorErrors, ThrowOnError> => (options?.client ?? client).put<putConfigDetectorResponses, putConfigDetectorErrors, ThrowOnError>({
+    url: '/config/detector',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get indexing configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigIndexing = <ThrowOnError extends boolean = false>(options?: Options<getConfigIndexingData, ThrowOnError>): RequestResult<getConfigIndexingResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigIndexingResponses, unknown, ThrowOnError>({ url: '/config/indexing', ...options });
+
+/**
+ * Change indexing algorithm settings
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigIndexing = <ThrowOnError extends boolean = false>(options?: Options<putConfigIndexingData, ThrowOnError>): RequestResult<putConfigIndexingResponses, putConfigIndexingErrors, ThrowOnError> => (options?.client ?? client).put<putConfigIndexingResponses, putConfigIndexingErrors, ThrowOnError>({
+    url: '/config/indexing',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get file writer settings
+ *
+ * Can be done anytime
+ */
+export const getConfigFileWriter = <ThrowOnError extends boolean = false>(options?: Options<getConfigFileWriterData, ThrowOnError>): RequestResult<getConfigFileWriterResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigFileWriterResponses, unknown, ThrowOnError>({ url: '/config/file_writer', ...options });
+
+/**
+ * Change file writer settings
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigFileWriter = <ThrowOnError extends boolean = false>(options?: Options<putConfigFileWriterData, ThrowOnError>): RequestResult<putConfigFileWriterResponses, putConfigFileWriterErrors, ThrowOnError> => (options?.client ?? client).put<putConfigFileWriterResponses, putConfigFileWriterErrors, ThrowOnError>({
+    url: '/config/file_writer',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get instrument metadata
+ *
+ * Can be done anytime
+ */
+export const getConfigInstrument = <ThrowOnError extends boolean = false>(options?: Options<getConfigInstrumentData, ThrowOnError>): RequestResult<getConfigInstrumentResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigInstrumentResponses, unknown, ThrowOnError>({ url: '/config/instrument', ...options });
+
+/**
+ * Change instrument metadata
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigInstrument = <ThrowOnError extends boolean = false>(options?: Options<putConfigInstrumentData, ThrowOnError>): RequestResult<putConfigInstrumentResponses, putConfigInstrumentErrors, ThrowOnError> => (options?.client ?? client).put<putConfigInstrumentResponses, putConfigInstrumentErrors, ThrowOnError>({
+    url: '/config/instrument',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get image output format
+ *
+ * Can be done anytime
+ */
+export const getConfigImageFormat = <ThrowOnError extends boolean = false>(options?: Options<getConfigImageFormatData, ThrowOnError>): RequestResult<getConfigImageFormatResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigImageFormatResponses, unknown, ThrowOnError>({ url: '/config/image_format', ...options });
+
+/**
+ * Change image output format
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigImageFormat = <ThrowOnError extends boolean = false>(options?: Options<putConfigImageFormatData, ThrowOnError>): RequestResult<putConfigImageFormatResponses, putConfigImageFormatErrors, ThrowOnError> => (options?.client ?? client).put<putConfigImageFormatResponses, putConfigImageFormatErrors, ThrowOnError>({
+    url: '/config/image_format',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Configure format for raw data collection
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const postConfigImageFormatRaw = <ThrowOnError extends boolean = false>(options?: Options<postConfigImageFormatRawData, ThrowOnError>): RequestResult<postConfigImageFormatRawResponses, postConfigImageFormatRawErrors, ThrowOnError> => (options?.client ?? client).post<postConfigImageFormatRawResponses, postConfigImageFormatRawErrors, ThrowOnError>({ url: '/config/image_format/raw', ...options });
+
+/**
+ * Configure format for data collection with full conversion
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const postConfigImageFormatConversion = <ThrowOnError extends boolean = false>(options?: Options<postConfigImageFormatConversionData, ThrowOnError>): RequestResult<postConfigImageFormatConversionResponses, postConfigImageFormatConversionErrors, ThrowOnError> => (options?.client ?? client).post<postConfigImageFormatConversionResponses, postConfigImageFormatConversionErrors, ThrowOnError>({ url: '/config/image_format/conversion', ...options });
+
+/**
+ * Get data processing configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigSpotFinding = <ThrowOnError extends boolean = false>(options?: Options<getConfigSpotFindingData, ThrowOnError>): RequestResult<getConfigSpotFindingResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigSpotFindingResponses, unknown, ThrowOnError>({ url: '/config/spot_finding', ...options });
+
+/**
+ * Configure spot finding
+ *
+ * Can be done anytime, also while data collection is running
+ */
+export const putConfigSpotFinding = <ThrowOnError extends boolean = false>(options?: Options<putConfigSpotFindingData, ThrowOnError>): RequestResult<putConfigSpotFindingResponses, putConfigSpotFindingErrors, ThrowOnError> => (options?.client ?? client).put<putConfigSpotFindingResponses, putConfigSpotFindingErrors, ThrowOnError>({
+    url: '/config/spot_finding',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get azimuthal integration configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigAzimInt = <ThrowOnError extends boolean = false>(options?: Options<getConfigAzimIntData, ThrowOnError>): RequestResult<getConfigAzimIntResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigAzimIntResponses, unknown, ThrowOnError>({ url: '/config/azim_int', ...options });
+
+/**
+ * Configure azimuthal integration
+ *
+ * Can be done when detector is Inactive or Idle
+ */
+export const putConfigAzimInt = <ThrowOnError extends boolean = false>(options?: Options<putConfigAzimIntData, ThrowOnError>): RequestResult<putConfigAzimIntResponses, putConfigAzimIntErrors, ThrowOnError> => (options?.client ?? client).put<putConfigAzimIntResponses, putConfigAzimIntErrors, ThrowOnError>({
+    url: '/config/azim_int',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Load binary image for internal FPGA generator
+ *
+ * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+ * Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates
+ * (depending on detector settings).
+ *
+ */
+export const putConfigInternalGeneratorImage = <ThrowOnError extends boolean = false>(options?: Options<putConfigInternalGeneratorImageData, ThrowOnError>): RequestResult<putConfigInternalGeneratorImageResponses, putConfigInternalGeneratorImageErrors, ThrowOnError> => (options?.client ?? client).put<putConfigInternalGeneratorImageResponses, putConfigInternalGeneratorImageErrors, ThrowOnError>({
+    bodySerializer: null,
+    url: '/config/internal_generator_image',
+    ...options,
+    headers: {
+        'Content-Type': 'application/octet-stream',
+        ...options?.headers
+    }
+});
+
+/**
+ * Load TIFF image for internal FPGA generator
+ *
+ * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+ * Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates
+ * (depending on detector settings).
+ *
+ */
+export const putConfigInternalGeneratorImageTiff = <ThrowOnError extends boolean = false>(options?: Options<putConfigInternalGeneratorImageTiffData, ThrowOnError>): RequestResult<putConfigInternalGeneratorImageTiffResponses, putConfigInternalGeneratorImageTiffErrors, ThrowOnError> => (options?.client ?? client).put<putConfigInternalGeneratorImageTiffResponses, putConfigInternalGeneratorImageTiffErrors, ThrowOnError>({
+    bodySerializer: null,
+    url: '/config/internal_generator_image.tiff',
+    ...options,
+    headers: {
+        'Content-Type': 'image/tiff',
+        ...options?.headers
+    }
+});
+
+/**
+ * List available detectors
+ *
+ * Configured detectors that can be selected by used
+ */
+export const getConfigSelectDetector = <ThrowOnError extends boolean = false>(options?: Options<getConfigSelectDetectorData, ThrowOnError>): RequestResult<getConfigSelectDetectorResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigSelectDetectorResponses, unknown, ThrowOnError>({ url: '/config/select_detector', ...options });
+
+/**
+ * Select detector
+ *
+ * Jungfraujoch allows to control multiple detectors and/or region-of-interests.
+ * The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).
+ * Changing detector will set detector to `Inactive` state and will require reinitialization.
+ *
+ */
+export const putConfigSelectDetector = <ThrowOnError extends boolean = false>(options?: Options<putConfigSelectDetectorData, ThrowOnError>): RequestResult<putConfigSelectDetectorResponses, putConfigSelectDetectorErrors, ThrowOnError> => (options?.client ?? client).put<putConfigSelectDetectorResponses, putConfigSelectDetectorErrors, ThrowOnError>({
+    url: '/config/select_detector',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get ZeroMQ preview settings
+ */
+export const getConfigZeromqPreview = <ThrowOnError extends boolean = false>(options?: Options<getConfigZeromqPreviewData, ThrowOnError>): RequestResult<getConfigZeromqPreviewResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigZeromqPreviewResponses, unknown, ThrowOnError>({ url: '/config/zeromq_preview', ...options });
+
+/**
+ * Set ZeroMQ preview settings
+ *
+ * Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.
+ * Here settings of the socket can be adjusted.
+ * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
+ * Options set with this PUT request have no effect on HTTP based preview.
+ *
+ */
+export const putConfigZeromqPreview = <ThrowOnError extends boolean = false>(options?: Options<putConfigZeromqPreviewData, ThrowOnError>): RequestResult<putConfigZeromqPreviewResponses, putConfigZeromqPreviewErrors, ThrowOnError> => (options?.client ?? client).put<putConfigZeromqPreviewResponses, putConfigZeromqPreviewErrors, ThrowOnError>({
+    url: '/config/zeromq_preview',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get ZeroMQ metadata socket settings
+ */
+export const getConfigZeromqMetadata = <ThrowOnError extends boolean = false>(options?: Options<getConfigZeromqMetadataData, ThrowOnError>): RequestResult<getConfigZeromqMetadataResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigZeromqMetadataResponses, unknown, ThrowOnError>({ url: '/config/zeromq_metadata', ...options });
+
+/**
+ * Set ZeroMQ metadata settings
+ *
+ * Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.
+ * Here settings of the socket can be adjusted.
+ * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
+ *
+ */
+export const putConfigZeromqMetadata = <ThrowOnError extends boolean = false>(options?: Options<putConfigZeromqMetadataData, ThrowOnError>): RequestResult<putConfigZeromqMetadataResponses, putConfigZeromqMetadataErrors, ThrowOnError> => (options?.client ?? client).put<putConfigZeromqMetadataResponses, putConfigZeromqMetadataErrors, ThrowOnError>({
+    url: '/config/zeromq_metadata',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get settings for dark data collection to calculate mask
+ */
+export const getConfigDarkMask = <ThrowOnError extends boolean = false>(options?: Options<getConfigDarkMaskData, ThrowOnError>): RequestResult<getConfigDarkMaskResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigDarkMaskResponses, unknown, ThrowOnError>({ url: '/config/dark_mask', ...options });
+
+/**
+ * Set configuration for dark data collection to calculate mask
+ *
+ * This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigDarkMask = <ThrowOnError extends boolean = false>(options?: Options<putConfigDarkMaskData, ThrowOnError>): RequestResult<putConfigDarkMaskResponses, putConfigDarkMaskErrors, ThrowOnError> => (options?.client ?? client).put<putConfigDarkMaskResponses, putConfigDarkMaskErrors, ThrowOnError>({
+    url: '/config/dark_mask',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get Jungfraujoch status
+ *
+ * Status of the data acquisition
+ */
+export const getStatus = <ThrowOnError extends boolean = false>(options?: Options<getStatusData, ThrowOnError>): RequestResult<getStatusResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getStatusResponses, unknown, ThrowOnError>({ url: '/status', ...options });
+
+/**
+ * Get status of FPGA devices
+ */
+export const getFpgaStatus = <ThrowOnError extends boolean = false>(options?: Options<getFpgaStatusData, ThrowOnError>): RequestResult<getFpgaStatusResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getFpgaStatusResponses, unknown, ThrowOnError>({ url: '/fpga_status', ...options });
+
+/**
+ * Return XFEL pulse IDs for the current data acquisition
+ *
+ * Return array of XFEL pulse IDs - (-1) if image not recorded
+ */
+export const getXfelPulseId = <ThrowOnError extends boolean = false>(options?: Options<getXfelPulseIdData, ThrowOnError>): RequestResult<getXfelPulseIdResponses, getXfelPulseIdErrors, ThrowOnError> => (options?.client ?? client).get<getXfelPulseIdResponses, getXfelPulseIdErrors, ThrowOnError>({ url: '/xfel/pulse_id', ...options });
+
+/**
+ * Return XFEL event codes for the current data acquisition
+ *
+ * Return array of XFEL event codes
+ */
+export const getXfelEventCode = <ThrowOnError extends boolean = false>(options?: Options<getXfelEventCodeData, ThrowOnError>): RequestResult<getXfelEventCodeResponses, getXfelEventCodeErrors, ThrowOnError> => (options?.client ?? client).get<getXfelEventCodeResponses, getXfelEventCodeErrors, ThrowOnError>({ url: '/xfel/event_code', ...options });
+
+/**
+ * Get status of image pusher
+ */
+export const getImagePusherStatus = <ThrowOnError extends boolean = false>(options?: Options<getImagePusherStatusData, ThrowOnError>): RequestResult<getImagePusherStatusResponses, getImagePusherStatusErrors, ThrowOnError> => (options?.client ?? client).get<getImagePusherStatusResponses, getImagePusherStatusErrors, ThrowOnError>({ url: '/image_pusher/status', ...options });
+
+/**
+ * Get detector status
+ *
+ * Status of the JUNGFRAU detector
+ */
+export const getDetectorStatus = <ThrowOnError extends boolean = false>(options?: Options<getDetectorStatusData, ThrowOnError>): RequestResult<getDetectorStatusResponses, getDetectorStatusErrors, ThrowOnError> => (options?.client ?? client).get<getDetectorStatusResponses, getDetectorStatusErrors, ThrowOnError>({ url: '/detector/status', ...options });
+
+/**
+ * Get ROI definitions
+ */
+export const getConfigRoi = <ThrowOnError extends boolean = false>(options?: Options<getConfigRoiData, ThrowOnError>): RequestResult<getConfigRoiResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigRoiResponses, unknown, ThrowOnError>({ url: '/config/roi', ...options });
+
+/**
+ * Upload ROI definitions
+ */
+export const putConfigRoi = <ThrowOnError extends boolean = false>(options?: Options<putConfigRoiData, ThrowOnError>): RequestResult<putConfigRoiResponses, putConfigRoiErrors, ThrowOnError> => (options?.client ?? client).put<putConfigRoiResponses, putConfigRoiErrors, ThrowOnError>({
+    url: '/config/roi',
+    ...options,
+    headers: {
+        'Content-Type': 'application/json',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get general statistics
+ */
+export const getStatistics = <ThrowOnError extends boolean = false>(options?: Options<getStatisticsData, ThrowOnError>): RequestResult<getStatisticsResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getStatisticsResponses, unknown, ThrowOnError>({ url: '/statistics', ...options });
+
+/**
+ * Get data collection statistics
+ *
+ * Results of the last data collection
+ */
+export const getStatisticsDataCollection = <ThrowOnError extends boolean = false>(options?: Options<getStatisticsDataCollectionData, ThrowOnError>): RequestResult<getStatisticsDataCollectionResponses, getStatisticsDataCollectionErrors, ThrowOnError> => (options?.client ?? client).get<getStatisticsDataCollectionResponses, getStatisticsDataCollectionErrors, ThrowOnError>({ url: '/statistics/data_collection', ...options });
+
+/**
+ * Get calibration statistics
+ *
+ * Statistics are provided for each module/storage cell separately
+ */
+export const getStatisticsCalibration = <ThrowOnError extends boolean = false>(options?: Options<getStatisticsCalibrationData, ThrowOnError>): RequestResult<getStatisticsCalibrationResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getStatisticsCalibrationResponses, unknown, ThrowOnError>({ url: '/statistics/calibration', ...options });
+
+/**
+ * Get mask of the detector (binary)
+ *
+ * Detector must be Initialized.
+ * Get full pixel mask of the detector.
+ * See NXmx standard for meaning of pixel values.
+ *
+ */
+export const getConfigMask = <ThrowOnError extends boolean = false>(options?: Options<getConfigMaskData, ThrowOnError>): RequestResult<getConfigMaskResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigMaskResponses, unknown, ThrowOnError>({ url: '/config/mask', ...options });
+
+/**
+ * Detector must be Initialized.
+ * Get user mask of the detector (binary)
+ *
+ *
+ * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+ */
+export const getConfigUserMask = <ThrowOnError extends boolean = false>(options?: Options<getConfigUserMaskData, ThrowOnError>): RequestResult<getConfigUserMaskResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigUserMaskResponses, unknown, ThrowOnError>({ url: '/config/user_mask', ...options });
+
+/**
+ * Upload user mask of the detector (binary)
+ *
+ * Should be in `Idle` state.
+ * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+ * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+ * In the latter case - module gaps are ignored and don't need to be assigned value.
+ * Mask is expected as binary array (4-byte; unsigned).
+ * 0 - good pixel, other value - masked
+ * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
+ *
+ */
+export const putConfigUserMask = <ThrowOnError extends boolean = false>(options?: Options<putConfigUserMaskData, ThrowOnError>): RequestResult<putConfigUserMaskResponses, putConfigUserMaskErrors, ThrowOnError> => (options?.client ?? client).put<putConfigUserMaskResponses, putConfigUserMaskErrors, ThrowOnError>({
+    bodySerializer: null,
+    url: '/config/user_mask',
+    ...options,
+    headers: {
+        'Content-Type': 'application/octet-stream',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get mask of the detector (TIFF)
+ *
+ * Should be in `Idle` state.
+ * Get full pixel mask of the detector
+ * See NXmx standard for meaning of pixel values
+ *
+ */
+export const getConfigMaskTiff = <ThrowOnError extends boolean = false>(options?: Options<getConfigMaskTiffData, ThrowOnError>): RequestResult<getConfigMaskTiffResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigMaskTiffResponses, unknown, ThrowOnError>({ url: '/config/mask.tiff', ...options });
+
+/**
+ * Detector must be Initialized.
+ * Get user mask of the detector (TIFF)
+ *
+ *
+ * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+ */
+export const getConfigUserMaskTiff = <ThrowOnError extends boolean = false>(options?: Options<getConfigUserMaskTiffData, ThrowOnError>): RequestResult<getConfigUserMaskTiffResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getConfigUserMaskTiffResponses, unknown, ThrowOnError>({ url: '/config/user_mask.tiff', ...options });
+
+/**
+ * Upload user mask of the detector
+ *
+ * Should be in `Idle` state.
+ * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+ * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+ * In the latter case - module gaps are ignored and don't need to be assigned value.
+ * Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
+ * 0 - good pixel, other value - masked
+ * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
+ * User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
+ *
+ */
+export const putConfigUserMaskTiff = <ThrowOnError extends boolean = false>(options?: Options<putConfigUserMaskTiffData, ThrowOnError>): RequestResult<putConfigUserMaskTiffResponses, putConfigUserMaskTiffErrors, ThrowOnError> => (options?.client ?? client).put<putConfigUserMaskTiffResponses, putConfigUserMaskTiffErrors, ThrowOnError>({
+    bodySerializer: null,
+    url: '/config/user_mask.tiff',
+    ...options,
+    headers: {
+        'Content-Type': 'image/tiff',
+        ...options?.headers
+    }
+});
+
+/**
+ * Get pedestal in TIFF format
+ */
+export const getPreviewPedestalTiff = <ThrowOnError extends boolean = false>(options: Options<getPreviewPedestalTiffData, ThrowOnError>): RequestResult<getPreviewPedestalTiffResponses, getPreviewPedestalTiffErrors, ThrowOnError> => (options.client ?? client).get<getPreviewPedestalTiffResponses, getPreviewPedestalTiffErrors, ThrowOnError>({ url: '/preview/pedestal.tiff', ...options });
+
+/**
+ * Generate 1D plot from Jungfraujoch
+ */
+export const getPreviewPlot = <ThrowOnError extends boolean = false>(options: Options<getPreviewPlotData, ThrowOnError>): RequestResult<getPreviewPlotResponses, getPreviewPlotErrors, ThrowOnError> => (options.client ?? client).get<getPreviewPlotResponses, getPreviewPlotErrors, ThrowOnError>({ url: '/preview/plot', ...options });
+
+/**
+ * Generate 1D plot from Jungfraujoch and send in raw binary format.
+ * Data are provided as (32-bit) float binary array.
+ * This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
+ *
+ */
+export const getPreviewPlotBin = <ThrowOnError extends boolean = false>(options: Options<getPreviewPlotBinData, ThrowOnError>): RequestResult<getPreviewPlotBinResponses, getPreviewPlotBinErrors, ThrowOnError> => (options.client ?? client).get<getPreviewPlotBinResponses, getPreviewPlotBinErrors, ThrowOnError>({ url: '/preview/plot.bin', ...options });
+
+/**
+ * Get full scan result
+ */
+export const getResultScan = <ThrowOnError extends boolean = false>(options?: Options<getResultScanData, ThrowOnError>): RequestResult<getResultScanResponses, getResultScanErrors, ThrowOnError> => (options?.client ?? client).get<getResultScanResponses, getResultScanErrors, ThrowOnError>({ url: '/result/scan', ...options });
+
+/**
+ * Get Start message in CBOR format
+ *
+ * Contains metadata for a dataset (e.g., experimental geometry)
+ */
+export const getImageBufferStartCbor = <ThrowOnError extends boolean = false>(options?: Options<getImageBufferStartCborData, ThrowOnError>): RequestResult<getImageBufferStartCborResponses, getImageBufferStartCborErrors, ThrowOnError> => (options?.client ?? client).get<getImageBufferStartCborResponses, getImageBufferStartCborErrors, ThrowOnError>({ url: '/image_buffer/start.cbor', ...options });
+
+/**
+ * Get image message in CBOR format
+ *
+ * Contains full image data and metadata. The image must come from the latest data collection.
+ */
+export const getImageBufferImageCbor = <ThrowOnError extends boolean = false>(options?: Options<getImageBufferImageCborData, ThrowOnError>): RequestResult<getImageBufferImageCborResponses, getImageBufferImageCborErrors, ThrowOnError> => (options?.client ?? client).get<getImageBufferImageCborResponses, getImageBufferImageCborErrors, ThrowOnError>({ url: '/image_buffer/image.cbor', ...options });
+
+/**
+ * Get preview image in JPEG format using custom settings
+ */
+export const getImageBufferImageJpeg = <ThrowOnError extends boolean = false>(options?: Options<getImageBufferImageJpegData, ThrowOnError>): RequestResult<getImageBufferImageJpegResponses, getImageBufferImageJpegErrors, ThrowOnError> => (options?.client ?? client).get<getImageBufferImageJpegResponses, getImageBufferImageJpegErrors, ThrowOnError>({ url: '/image_buffer/image.jpeg', ...options });
+
+/**
+ * Get preview image in TIFF format
+ */
+export const getImageBufferImageTiff = <ThrowOnError extends boolean = false>(options?: Options<getImageBufferImageTiffData, ThrowOnError>): RequestResult<getImageBufferImageTiffResponses, getImageBufferImageTiffErrors, ThrowOnError> => (options?.client ?? client).get<getImageBufferImageTiffResponses, getImageBufferImageTiffErrors, ThrowOnError>({ url: '/image_buffer/image.tiff', ...options });
+
+/**
+ * Clear image buffer
+ *
+ * Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.
+ */
+export const postImageBufferClear = <ThrowOnError extends boolean = false>(options?: Options<postImageBufferClearData, ThrowOnError>): RequestResult<postImageBufferClearResponses, postImageBufferClearErrors, ThrowOnError> => (options?.client ?? client).post<postImageBufferClearResponses, postImageBufferClearErrors, ThrowOnError>({ url: '/image_buffer/clear', ...options });
+
+/**
+ * Get status of the image buffers
+ *
+ * Can be run at any stage of Jungfraujoch operation, including during data collection.
+ * The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,
+ * then image might be replaced in the buffer between calling /images and /image.cbor.
+ *
+ */
+export const getImageBufferStatus = <ThrowOnError extends boolean = false>(options?: Options<getImageBufferStatusData, ThrowOnError>): RequestResult<getImageBufferStatusResponses, getImageBufferStatusErrors, ThrowOnError> => (options?.client ?? client).get<getImageBufferStatusResponses, getImageBufferStatusErrors, ThrowOnError>({ url: '/image_buffer/status', ...options });
+
+/**
+ * Get Jungfraujoch version of jfjoch_broker
+ */
+export const getVersion = <ThrowOnError extends boolean = false>(options?: Options<getVersionData, ThrowOnError>): RequestResult<getVersionResponses, unknown, ThrowOnError> => (options?.client ?? client).get<getVersionResponses, unknown, ThrowOnError>({ url: '/version', ...options });
diff --git a/frontend/src/client/types.gen.ts b/frontend/src/client/types.gen.ts
new file mode 100644
index 00000000..e7b33b4f
--- /dev/null
+++ b/frontend/src/client/types.gen.ts
@@ -0,0 +1,3219 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export type ClientOptions = {
+    baseUrl: 'http://localhost:5232' | (string & {});
+};
+
+/**
+ * Definition of a grid scan (mutually exclusive with `rotation_axis`)
+ */
+export type grid_scan = {
+    /**
+     * Number of elements in the fast direction
+     */
+    n_fast: number;
+    /**
+     * Step in grid along the fast direction. Can be negative.
+     * Positive number: left to right
+     * Negative number: right to left
+     *
+     */
+    step_x_um: number;
+    /**
+     * Step in grid along the slow direction. Can be negative.
+     * Positive number: top to bottom
+     * Negative number: bottom to top
+     *
+     */
+    step_y_um: number;
+    /**
+     * If disabled: fast direction = X, slow direction = Y
+     * If enabled: fast direction = Y, slow direction = X
+     *
+     */
+    vertical?: boolean;
+    /**
+     * Flip fast direction for every second row
+     *
+     */
+    snake?: boolean;
+};
+
+/**
+ * Definition of a crystal rotation axis
+ */
+export type rotation_axis = {
+    /**
+     * Name of rotation axis (e.g., omega, phi)
+     */
+    name?: string;
+    /**
+     * Angle step (per image) in degrees
+     */
+    step: number;
+    /**
+     * Start angle in degrees
+     */
+    start?: number;
+    /**
+     * Rotation axis
+     */
+    vector: [
+        number,
+        number,
+        number
+    ];
+    /**
+     * Translation (per image) for helical scan
+     */
+    helical_step_um?: [
+        number,
+        number,
+        number
+    ];
+    /**
+     * Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)
+     */
+    screening_wedge_deg?: number;
+};
+
+/**
+ * Selection of an indexing algorithm used by Jungfraujoch
+ *
+ */
+export const indexing_algorithm = {
+    FFBIDX: 'FFBIDX',
+    FFT: 'FFT',
+    FFTW: 'FFTW',
+    AUTO: 'Auto',
+    NONE: 'None'
+} as const;
+
+/**
+ * Selection of an indexing algorithm used by Jungfraujoch
+ *
+ */
+export type indexing_algorithm = typeof indexing_algorithm[keyof typeof indexing_algorithm];
+
+/**
+ * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
+ * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
+ * OrientationOnly - This option is refining only orientation of the lattice.
+ *
+ */
+export const geom_refinement_algorithm = {
+    BEAM_CENTER: 'BeamCenter',
+    ORIENTATION_ONLY: 'OrientationOnly',
+    NONE: 'None'
+} as const;
+
+/**
+ * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
+ * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
+ * OrientationOnly - This option is refining only orientation of the lattice.
+ *
+ */
+export type geom_refinement_algorithm = typeof geom_refinement_algorithm[keyof typeof geom_refinement_algorithm];
+
+export type dataset_settings = {
+    /**
+     * For standard synchrotron data collection - this is number of images collected per one TTL trigger
+     * For XFEL (pulsed source) - this number is ignored and set to 1
+     * For storage cell mode - this number is ignored and set to number of storage cells
+     *
+     */
+    images_per_trigger?: number;
+    /**
+     * Number of TTL trigger that the detector is expected to receive during data collection
+     *
+     */
+    ntrigger?: number;
+    /**
+     * Image time.
+     * If not provided (or zero value) the frame time is assumed as default.
+     * For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.
+     * In XFEL mode: summation happens for frames collected with multiple triggers.
+     * Ignored for storage cells and if raw data are saved.
+     *
+     */
+    image_time_us?: number;
+    /**
+     * /entry/detector/beam_center_x in NXmx
+     * Beam center in X direction [pixels]
+     *
+     */
+    beam_x_pxl: number;
+    /**
+     * /entry/detector/beam_center_y in NXmx
+     * Beam center in X direction [pixels]
+     *
+     */
+    beam_y_pxl: number;
+    /**
+     * /entry/detector/distance in NXmx Detector distance [mm]
+     */
+    detector_distance_mm: number;
+    /**
+     * Used to calculate /entry/beam/incident_wavelength in NXmx
+     * Incident particle (photon, electron) energy in keV
+     *
+     */
+    incident_energy_keV: number;
+    /**
+     * Prefix for filenames. If left empty, no file will be saved.
+     */
+    file_prefix?: string;
+    /**
+     * Number of files in a single HDF5 data file (0 = write all images to a single data file).
+     */
+    images_per_file?: number;
+    /**
+     * Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.
+     */
+    space_group_number?: number;
+    /**
+     * /entry/sample/name in NXmx
+     * Sample name
+     *
+     */
+    sample_name?: string;
+    /**
+     * Compression type for the images transferred over ZeroMQ and saved to HDF5 file.
+     *
+     */
+    compression?: 'bslz4' | 'bszstd' | 'bszstd_rle' | 'none';
+    /**
+     * /entry/beam/total_flux in NXmx
+     * Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]
+     *
+     */
+    total_flux?: number;
+    /**
+     * /entry/instrument/attenuator/attenuator_transmission
+     * Transmission of attenuator (filter) [no units]
+     *
+     */
+    transmission?: number;
+    goniometer?: rotation_axis;
+    grid_scan?: grid_scan;
+    /**
+     * Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
+     * In general, it is not saved in HDF5 file.
+     *
+     * However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file.
+     * This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
+     * For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.
+     *
+     */
+    header_appendix?: unknown;
+    /**
+     * Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)
+     * Not saved in HDF5 file
+     *
+     */
+    image_appendix?: unknown;
+    /**
+     * Rate at which non-indexed images are accepted to be forwarded to writer.
+     * Value of 1.0 (default) means that all images are written.
+     * Values below zero mean that non-indexed images will be accepted with a given probability.
+     *
+     */
+    data_reduction_factor_serialmx?: number;
+    /**
+     * Set all counts lower than the value to zero.
+     * When the value is set, negative numbers other than error pixel value are always set to zero.
+     * Setting to zero is equivalent to turning the option off.
+     *
+     */
+    pixel_value_low_threshold?: number;
+    /**
+     * Number of run within an experimental session.
+     * Transferred over CBOR stream as "series ID", though not saved in HDF5 file.
+     * It is highly recommended to keep this number unique for each data collection during experimental series.
+     * If not provided, the number will be automatically incremented.
+     *
+     */
+    run_number?: number;
+    /**
+     * Unique ID of run.
+     * Transferred over CBOR stream as "unique series ID", though not saved in HDF5 file.
+     * It is highly recommended to keep this name unique for each data collection during experimental series.
+     * If not provided, the name will be automatically generated as number + colon + file_prefix.
+     *
+     */
+    run_name?: string;
+    /**
+     * Name of group owning the data (e.g. p-group or proposal number).
+     * Transferred over CBOR stream, though not saved in HDF5 file.
+     *
+     */
+    experiment_group?: string;
+    /**
+     * Enable lossy compression of pixel values that preserves Poisson statistics.
+     * Requires to provide a numerical factor SQ.
+     * Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.
+     * Compression is turned off if the value is missing or it is set to zero.
+     *
+     */
+    poisson_compression?: number;
+    /**
+     * Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments
+     * and to turn off for other experiments.
+     *
+     */
+    write_nxmx_hdf5_master?: boolean;
+    /**
+     * Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.
+     * If parameter is not provided calibration will be saved only if more than 4 images are recorded.
+     *
+     */
+    save_calibration?: boolean;
+    /**
+     * Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization
+     */
+    polarization_factor?: number;
+    /**
+     * Ring current at the beginning of the data collection
+     */
+    ring_current_mA?: number;
+    /**
+     * Sample temperature in Kelvin
+     */
+    sample_temperature_K?: number;
+    /**
+     * PONI angle rot1 (see PyFAI documentation for details) in radians
+     */
+    poni_rot1_rad?: number;
+    /**
+     * PONI angle rot2 (see PyFAI documentation for details) in radians
+     */
+    poni_rot2_rad?: number;
+    /**
+     * PONI angle rot3 (see PyFAI documentation for details) in radians
+     */
+    poni_rot3_rad?: number;
+    unit_cell?: unit_cell;
+    /**
+     * Enable spot finding and save spots
+     */
+    spot_finding?: boolean;
+    /**
+     * Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected
+     */
+    max_spot_count?: number;
+    /**
+     * Flag spots as ice rings and reduce their effect on indexing
+     */
+    detect_ice_rings?: boolean;
+    /**
+     * When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement.
+     */
+    async_start?: boolean;
+    xray_fluorescence_spectrum?: {
+        /**
+         * X-ray fluorescence scan energy for each measurement point
+         */
+        energy_eV: Array<number>;
+        /**
+         * X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV
+         */
+        data: Array<number>;
+    };
+};
+
+/**
+ * Real-space crystal lattice 3D vectors in Angstrom.
+ * Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)
+ *
+ */
+export type crystal_lattice = [
+    number,
+    number,
+    number,
+    number,
+    number,
+    number,
+    number,
+    number,
+    number
+];
+
+/**
+ * Unit cell parameters. Necessary to run indexing. Units of angstrom and degree
+ */
+export type unit_cell = {
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+};
+
+/**
+ * NoFileWritten - no files are written at all
+ * NXmxOnlyData - only data files are written, no master file
+ * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
+ * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
+ * NXmxIntegrated - single HDF5 per dataset
+ * CBF - CBF format (limited metadata)
+ * TIFF - TIFF format (no metadata)
+ *
+ */
+export const file_writer_format = {
+    N_XMX_ONLY_DATA: 'NXmxOnlyData',
+    N_XMX_LEGACY: 'NXmxLegacy',
+    N_XMX_VDS: 'NXmxVDS',
+    N_XMX_INTEGRATED: 'NXmxIntegrated',
+    CBF: 'CBF',
+    TIFF: 'TIFF',
+    NO_FILE_WRITTEN: 'NoFileWritten'
+} as const;
+
+/**
+ * NoFileWritten - no files are written at all
+ * NXmxOnlyData - only data files are written, no master file
+ * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
+ * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
+ * NXmxIntegrated - single HDF5 per dataset
+ * CBF - CBF format (limited metadata)
+ * TIFF - TIFF format (no metadata)
+ *
+ */
+export type file_writer_format = typeof file_writer_format[keyof typeof file_writer_format];
+
+export type file_writer_settings = {
+    /**
+     * Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.
+     *
+     */
+    overwrite?: boolean;
+    format?: file_writer_format;
+};
+
+export type pixel_mask_statistics = {
+    /**
+     * Number of pixels masked using the user mask
+     */
+    user_mask?: number;
+    /**
+     * Number of pixels with G0 pedestal RMS higher than provided threshold
+     */
+    too_high_pedestal_rms?: number;
+    /**
+     * Number of pixels that show wrong gain level during the pedestal procedure
+     */
+    wrong_gain?: number;
+};
+
+export type image_buffer_status = {
+    /**
+     * Smallest image number available in the buffer
+     */
+    min_image_number: number;
+    /**
+     * Largest image number available in the buffer
+     */
+    max_image_number: number;
+    /**
+     * Image numbers currently present in the buffer.
+     */
+    image_numbers: Array<number>;
+    /**
+     * Number of slots in the image buffer. This number, compared to number of images in data collection and
+     * frame rate will determine "retention" rate of the image buffer.
+     *
+     */
+    total_slots: number;
+    /**
+     * Slots available for the data collection
+     */
+    available_slots: number;
+    /**
+     * Number of slots in the image buffer that are currently in preparation for sending.
+     *
+     */
+    in_preparation_slots: number;
+    /**
+     * Number of slots in the image buffer that are currently sending/writing data.
+     *
+     */
+    in_sending_slots: number;
+    /**
+     * Counter of changes in the image buffer - either new start message or new image added.
+     * For optimization one can only load new images/datasets from the HTTP if this value changes.
+     * Counter is optional as it was not implemented in older versions to avoid breaking change
+     *
+     */
+    current_counter?: number;
+};
+
+export type image_format_settings = {
+    /**
+     * Enable summation of images to a given image_time
+     * If disabled images are saved according to original detector speed, but image count is adjusted
+     *
+     */
+    summation: boolean;
+    /**
+     * Place module read-out into their location on composed detector and extend multipixels
+     *
+     */
+    geometry_transform: boolean;
+    /**
+     * Convert pixel value in ADU to photon counts/energy
+     * Only affects JUNGFRAU detector
+     *
+     */
+    jungfrau_conversion: boolean;
+    /**
+     * Used to convert energy deposited into pixel to counts
+     * If not provided incident_energy_keV is used
+     *
+     */
+    jungfrau_conversion_factor_keV?: number;
+    /**
+     * Bit depth of resulting image (it doesn't affect the detector read-out value)
+     * If not provided value is adjusted automatically
+     *
+     */
+    bit_depth_image?: 8 | 16 | 32;
+    /**
+     * Controls if pixels have signed output
+     * If not provided value is adjusted automatically
+     *
+     */
+    signed_output?: boolean;
+    /**
+     * Mask 1 pixel on the module boundary
+     *
+     */
+    mask_module_edges: boolean;
+    /**
+     * Mask multipixels on chip boundary
+     *
+     */
+    mask_chip_edges: boolean;
+    /**
+     * JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.
+     * This should be turned off for cases, where detector is operated at room temperature with long exposure time.
+     *
+     */
+    jungfrau_mask_pixels_without_g0?: boolean;
+    /**
+     * Masked pixels are set to special value in the images produced by Jungfraujoch
+     *
+     */
+    apply_mask: boolean;
+    /**
+     * Pixels with pedestal G0 RMS above the threshold are marked as masked pixels
+     */
+    jungfrau_pedestal_g0_rms_limit?: number;
+};
+
+/**
+ * Power on of ASICs
+ */
+export const detector_power_state = {
+    POWER_ON: 'PowerOn',
+    POWER_OFF: 'PowerOff',
+    PARTIAL: 'Partial'
+} as const;
+
+/**
+ * Power on of ASICs
+ */
+export type detector_power_state = typeof detector_power_state[keyof typeof detector_power_state];
+
+/**
+ * Current state of the detector
+ */
+export const detector_state = {
+    IDLE: 'Idle',
+    WAITING: 'Waiting',
+    BUSY: 'Busy',
+    ERROR: 'Error',
+    NOT_CONNECTED: 'Not connected'
+} as const;
+
+/**
+ * Current state of the detector
+ */
+export type detector_state = typeof detector_state[keyof typeof detector_state];
+
+export type detector_status = {
+    state: detector_state;
+    powerchip: detector_power_state;
+    /**
+     * Detector server (on read-out boards) version
+     */
+    server_version: string;
+    /**
+     * Remaining triggers to the detector (max of all modules)
+     */
+    number_of_triggers_left: number;
+    /**
+     * Temperature of detector FPGAs
+     */
+    fpga_temp_degC: Array<number>;
+    /**
+     * High voltage for detector modules
+     */
+    high_voltage_V: Array<number>;
+};
+
+export const detector_timing = {
+    AUTO: 'auto',
+    TRIGGER: 'trigger',
+    BURST: 'burst',
+    GATED: 'gated'
+} as const;
+
+export type detector_timing = typeof detector_timing[keyof typeof detector_timing];
+
+export type detector_settings = {
+    /**
+     * Interval between consecutive frames.
+     * This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.
+     * For EIGER detector this is default frame time, not used otherwise
+     *
+     */
+    frame_time_us: number;
+    /**
+     * Integration time of the detector.
+     * If not provided count time will be set to maximum value for a given frame time.
+     *
+     */
+    count_time_us?: number;
+    /**
+     * Use internal frame generator in FPGA instead of getting data from a real detector
+     */
+    internal_frame_generator?: boolean;
+    /**
+     * Number of images stored in the internal frame generator.
+     */
+    internal_frame_generator_images?: number;
+    /**
+     * Delay between TTL trigger and acquisition start [ns]
+     */
+    detector_trigger_delay_ns?: number;
+    timing?: detector_timing;
+    /**
+     * Threshold for the PSI EIGER detector and all DECTRIS detectors.
+     * If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.
+     * If value is not provided, threshold will be determined on start of acquisition as half of incident energy.
+     * This might lead to increased start time.
+     *
+     */
+    eiger_threshold_keV?: number;
+    /**
+     * Bit depth of PSI EIGER read-out. This is
+     * If value is not provided, depth will be determined based on the image time:
+     * * Exposure time < 500 microseconds depth of 8 bit will be used,
+     * * 500 <= exposure time < 2622 microseconds depth of 16 bit will be used
+     * * Exposure time >= 2622 microseconds depth of 32 bit will be used.
+     *
+     */
+    eiger_bit_depth?: 8 | 16 | 32;
+    jungfrau_pedestal_g0_frames?: number;
+    jungfrau_pedestal_g1_frames?: number;
+    jungfrau_pedestal_g2_frames?: number;
+    /**
+     * Minimum number of collected images for pedestal to consider it viable
+     */
+    jungfrau_pedestal_min_image_count?: number;
+    jungfrau_storage_cell_count?: number;
+    /**
+     * Delay between two storage cells [ns]
+     */
+    jungfrau_storage_cell_delay_ns?: number;
+    /**
+     * Fix gain to G1 (can be useful for storage cells)
+     */
+    jungfrau_fixed_gain_g1?: boolean;
+    /**
+     * Use high G0 (for low energy applications)
+     */
+    jungfrau_use_gain_hg0?: boolean;
+};
+
+export type spot_finding_settings = {
+    /**
+     * Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection.
+     * Even if disabled spot finding information will still be send and written, though always with zero spots.
+     *
+     */
+    enable: boolean;
+    /**
+     * Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.
+     *
+     */
+    indexing: boolean;
+    signal_to_noise_threshold: number;
+    photon_count_threshold: number;
+    min_pix_per_spot: number;
+    max_pix_per_spot: number;
+    /**
+     * High resolution limit for spot finding [Angstrom]
+     */
+    high_resolution_limit: number;
+    /**
+     * Low resolution limit for spot finding [Angstrom]
+     */
+    low_resolution_limit: number;
+    /**
+     * High resolution threshold to consider spot "low resolution" [Angstrom]
+     */
+    high_resolution_limit_for_spot_count_low_res: number;
+    /**
+     * Quick integration of Bragg spots in diffraction images.
+     * If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.
+     * (experimental feature)
+     *
+     */
+    quick_integration: boolean;
+    /**
+     * Width of ice ring in q-space in reciprocal space
+     */
+    ice_ring_width_q_recipA: number;
+    /**
+     * This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.
+     * If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.
+     * This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.
+     *
+     */
+    high_res_gap_Q_recipA?: number;
+};
+
+export type azim_int_settings = {
+    /**
+     * Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)
+     */
+    polarization_corr: boolean;
+    /**
+     * Apply solid angle correction for azimuthal integration
+     */
+    solid_angle_corr: boolean;
+    high_q_recipA: number;
+    low_q_recipA: number;
+    q_spacing: number;
+    /**
+     * Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration
+     */
+    azimuthal_bins?: number;
+    /**
+     * Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.
+     * This allows to extend number of azimuthal integration bins, as well as to calculate standard deviation
+     * of the azimuthal integration results.
+     *
+     */
+    force_cpu?: boolean;
+};
+
+export type detector_list_element = {
+    id: number;
+    description: string;
+    serial_number: string;
+    base_ipv4_addr: string;
+    /**
+     * Number of UDP interfaces per detector module
+     */
+    udp_interface_count: number;
+    nmodules: number;
+    width: number;
+    height: number;
+    pixel_size_mm?: number;
+    readout_time_ns: number;
+    min_frame_time_ns: number;
+    min_count_time_ns: number;
+    type?: detector_type;
+};
+
+export type detector_list = {
+    detectors: Array<detector_list_element>;
+    current_id: number;
+};
+
+export type detector_selection = {
+    id: number;
+};
+
+export type measurement_statistics = {
+    file_prefix?: string;
+    /**
+     * Number of data collection run. This can be either automatically incremented or provided externally for each data collection.
+     *
+     */
+    run_number?: number;
+    /**
+     * Name of group owning the data (e.g. p-group or proposal number).
+     *
+     */
+    experiment_group?: string;
+    images_expected?: number;
+    /**
+     * Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.
+     *
+     */
+    images_collected?: number;
+    /**
+     * Images sent to the writer.
+     * The value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.
+     *
+     */
+    images_sent?: number;
+    /**
+     * Images successfully written to disk.
+     * The value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.
+     *
+     */
+    images_written?: number;
+    /**
+     * Images discarded by the lossy compression filter
+     */
+    images_discarded_lossy_compression?: number;
+    max_image_number_sent?: number;
+    collection_efficiency?: number;
+    compression_ratio?: number;
+    cancelled?: boolean;
+    max_receiver_delay?: number;
+    indexing_rate?: number;
+    detector_width?: number;
+    detector_height?: number;
+    detector_pixel_depth?: 2 | 4;
+    bkg_estimate?: number;
+    unit_cell?: string;
+    /**
+     * Moving average of 1000 images counting number of error pixels on the detector
+     */
+    error_pixels?: number;
+    /**
+     * Moving average of 1000 images counting number of saturated pixels on the detector
+     */
+    saturated_pixels?: number;
+    /**
+     * If there is an ROI defined with name "beam", this number will hold moving average of 1000 images
+     * for number of valid pixels within this ROI
+     *
+     */
+    roi_beam_pixels?: number;
+    /**
+     * If there is an ROI defined with name "beam", this number will hold moving average of 1000 images
+     * for sum of valid pixels within this ROI
+     *
+     */
+    roi_beam_sum?: number;
+};
+
+export type fpga_status = Array<{
+    pci_dev_id: string;
+    serial_number: string;
+    fw_version: string;
+    base_mac_addr: string;
+    eth_link_count: number;
+    eth_link_status: number;
+    power_usage_W: number;
+    fpga_temp_C: number;
+    hbm_temp_C: number;
+    packets_udp: number;
+    packets_sls: number;
+    idle: boolean;
+    /**
+     * PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)
+     */
+    pcie_link_speed: number;
+    /**
+     * PCIe link width (expected value is 8 == x8)
+     */
+    pcie_link_width: number;
+}>;
+
+export type broker_status = {
+    state: 'Inactive' | 'Idle' | 'Busy' | 'Measuring' | 'Pedestal' | 'Error';
+    /**
+     * Progress of data collection (only available if receiving is running)
+     */
+    progress?: number;
+    /**
+     * Message to display besides state of the jfjoch_broker; mostly used for errors and warnings
+     * This matters especially for async functions (start/initialize), where API won't return reason
+     * for the error during async operation.
+     *
+     */
+    message?: string;
+    /**
+     * Level of the message to display
+     */
+    message_severity?: 'success' | 'info' | 'warning' | 'error';
+    /**
+     * Number of installed GPUs
+     */
+    gpu_count?: number;
+    /**
+     * Version of the jfjoch_broker
+     */
+    broker_version?: string;
+};
+
+/**
+ * Informs about status of the image pusher.
+ *
+ */
+export type image_pusher_status = {
+    pusher_type: image_pusher_type;
+    /**
+     * List of addresses of image pushers.
+     * For HDF5 socket - no addresses will be returned.
+     * For ZeroMQ - list of addresses for each socket will be provided.
+     * For TCP/IP - single address to connect all writers will be provided.
+     *
+     */
+    addr: Array<string>;
+    /**
+     * Number of connected writers
+     * For ZeroMQ image socket: number is constant
+     * For TCP/IP image socket: number is updated live during operation
+     *
+     */
+    connected_writers: number;
+    /**
+     * Number of images written to the image socket.
+     * This number is updated live during operation for TCP/IP image socket and direct HDF5 writer.
+     * It is updated at the end of experiment for ZeroMQ image socket.
+     *
+     */
+    images_written?: number;
+    /**
+     * Number of images that could not be written to the image socket.
+     * This number is updated live during operation for TCP/IP image socket.
+     * No other socket use it.
+     *
+     */
+    images_write_error?: number;
+    /**
+     * Utilization of internal writer FIFO.
+     * This number is updated live during operation for TCP/IP image socket.
+     * No other socket use it.
+     *
+     */
+    writer_fifo_utilization?: Array<number>;
+};
+
+/**
+ * x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly
+ */
+export type plot = {
+    title: string;
+    x: Array<number>;
+    y: Array<number | null>;
+    z?: Array<number | null>;
+};
+
+export const plot_unit_x = {
+    IMAGE_NUMBER: 'image_number',
+    Q_RECIP_A: 'q_recipA',
+    D_A: 'd_A',
+    ANGLE_DEG: 'angle_deg',
+    ADU: 'ADU',
+    GRID_UM: 'grid_um'
+} as const;
+
+export type plot_unit_x = typeof plot_unit_x[keyof typeof plot_unit_x];
+
+export type plots = {
+    title?: string;
+    unit_x: plot_unit_x;
+    /**
+     * Max X range of the plot
+     */
+    size_x?: number;
+    /**
+     * Max Y range of the plot
+     */
+    size_y?: number;
+    plot: Array<plot>;
+};
+
+/**
+ * Results of a scan
+ */
+export type scan_result = {
+    file_prefix?: string;
+    rotation_unit_cell?: unit_cell;
+    rotation_crystal_lattice?: crystal_lattice;
+    images: Array<{
+        efficiency: number;
+        /**
+         * Detector image number for a given cell
+         */
+        number: number;
+        /**
+         * Cell position in X for grid scan
+         */
+        nx?: number;
+        /**
+         * Cell position in Y for grid scan
+         */
+        ny?: number;
+        /**
+         * Rotation angle associated with the image
+         */
+        angle?: number;
+        /**
+         * Background estimate
+         */
+        bkg?: number;
+        /**
+         * Spot count
+         */
+        spots?: number;
+        /**
+         * Spot count in low resolution range
+         */
+        spots_low_res?: number;
+        /**
+         * Spot count within indexing tolerance
+         */
+        spots_indexed?: number;
+        /**
+         * Spot count within common ice ring resolutions
+         */
+        spots_ice?: number;
+        /**
+         * Indexing solution
+         */
+        index?: number;
+        /**
+         * Indexing lattice count
+         */
+        latt_count?: number;
+        /**
+         * Profile radius, i.e. how far reflections are from the Ewald sphere
+         */
+        pr?: number;
+        /**
+         * B-Factor estimate
+         */
+        b?: number;
+        uc?: unit_cell;
+        /**
+         * XFEL pulse ID
+         */
+        xfel_pulseid?: number;
+        /**
+         * Total sum of all pixels
+         */
+        pixel_sum?: number;
+        /**
+         * Max viable pixel
+         */
+        max?: number;
+        /**
+         * Number of saturated pixels
+         */
+        sat?: number;
+        /**
+         * Number of error pixels
+         */
+        err?: number;
+        /**
+         * Diffraction resolution estimate
+         */
+        res?: number;
+    }>;
+};
+
+export type calibration_statistics = Array<{
+    module_number: number;
+    storage_cell_number: number;
+    pedestal_g0_mean: number;
+    pedestal_g1_mean: number;
+    pedestal_g2_mean: number;
+    gain_g0_mean: number;
+    gain_g1_mean: number;
+    gain_g2_mean: number;
+    masked_pixels: number;
+}>;
+
+/**
+ * Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker
+ */
+export type jfjoch_statistics = {
+    detector?: detector_status;
+    detector_list?: detector_list;
+    detector_settings?: detector_settings;
+    image_format_settings?: image_format_settings;
+    instrument_metadata?: instrument_metadata;
+    file_writer_settings?: file_writer_settings;
+    data_processing_settings?: spot_finding_settings;
+    measurement?: measurement_statistics;
+    broker?: broker_status;
+    fpga?: fpga_status;
+    calibration?: calibration_statistics;
+    zeromq_preview?: zeromq_preview_settings;
+    zeromq_metadata?: zeromq_metadata_settings;
+    dark_mask?: dark_mask_settings;
+    pixel_mask?: pixel_mask_statistics;
+    roi?: roi_definitions;
+    az_int?: azim_int_settings;
+    buffer?: image_buffer_status;
+    indexing?: indexing_settings;
+    image_pusher?: image_pusher_status;
+};
+
+export type error_message = {
+    /**
+     * Human readable message
+     */
+    msg: string;
+    /**
+     * Enumerate field for automated analysis
+     */
+    reason: 'WrongDAQState' | 'Other';
+};
+
+/**
+ * ROI as Q-range (or resolution range)
+ */
+export type roi_azimuthal = {
+    /**
+     * Name for the ROI; used in the plots
+     */
+    name: string;
+    /**
+     * Minimum Q-range for the ROI
+     */
+    q_min_recipA: number;
+    /**
+     * Maximum Q-range for the ROI
+     */
+    q_max_recipA: number;
+};
+
+/**
+ * Circular ROI
+ */
+export type roi_circle = {
+    /**
+     * Name for the ROI; used in the plots
+     */
+    name: string;
+    /**
+     * X coordinate of center of the circle [pixels]
+     */
+    center_x_pxl: number;
+    /**
+     * Y coordinate of center of the circle [pixels]
+     */
+    center_y_pxl: number;
+    /**
+     * Radius of the circle [pixels]
+     */
+    radius_pxl: number;
+};
+
+/**
+ * Box ROI
+ */
+export type roi_box = {
+    /**
+     * Name for the ROI; used in the plots
+     */
+    name: string;
+    /**
+     * Lower bound (inclusive) in X coordinate for the box
+     */
+    min_x_pxl: number;
+    /**
+     * Upper bound (inclusive) in X coordinate for the box
+     */
+    max_x_pxl: number;
+    /**
+     * Lower bound (inclusive) in Y coordinate for the box
+     */
+    min_y_pxl: number;
+    /**
+     * Upper bound (inclusive) in Y coordinate for the box
+     */
+    max_y_pxl: number;
+};
+
+/**
+ * List of circular ROIs
+ */
+export type roi_circle_list = {
+    rois: Array<roi_circle>;
+};
+
+/**
+ * List of box ROIs
+ */
+export type roi_box_list = {
+    rois?: Array<roi_box>;
+};
+
+/**
+ * List of azimuthal ROIs
+ */
+export type roi_azim_list = {
+    rois?: Array<roi_azimuthal>;
+};
+
+/**
+ * ROI defintions
+ */
+export type roi_definitions = {
+    box: roi_box_list;
+    circle: roi_circle_list;
+    azim: roi_azim_list;
+};
+
+/**
+ * Settings for collection of dark images to be used for mask calculation
+ */
+export type dark_mask_settings = {
+    /**
+     * Energy threshold for dark image collection
+     */
+    detector_threshold_keV: number;
+    /**
+     * Time between frames for dark image collection
+     */
+    frame_time_us: number;
+    /**
+     * Number of frames for dark image collection; zero means no dark collection
+     */
+    number_of_frames: number;
+    /**
+     * Maximum count in a pixel considered normal (not-masked)
+     */
+    max_allowed_pixel_count: number;
+    /**
+     * Maximum number of frames with signal in a pixel considered normal (not-masked)
+     */
+    max_frames_with_signal: number;
+};
+
+/**
+ * Settings for crystallography indexing
+ */
+export type indexing_settings = {
+    algorithm: indexing_algorithm;
+    /**
+     * Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
+     */
+    fft_max_unit_cell_A: number;
+    /**
+     * Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
+     */
+    fft_min_unit_cell_A: number;
+    /**
+     * Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT.
+     * There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.
+     *
+     */
+    fft_high_resolution_A: number;
+    /**
+     * Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.
+     */
+    fft_num_vectors: number;
+    /**
+     * Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted
+     */
+    tolerance: number;
+    /**
+     * Thread count for indexing algorithm
+     */
+    thread_count: number;
+    geom_refinement_algorithm: geom_refinement_algorithm;
+    /**
+     * Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored
+     */
+    unit_cell_dist_tolerance: number;
+    /**
+     * Minimum number of indexed spots required for a cell to be considered viable
+     */
+    viable_cell_min_spots: number;
+    /**
+     * Include spots marked as ice rings in the indexing run.
+     * If `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.
+     *
+     */
+    index_ice_rings: boolean;
+    rotation_indexing: boolean;
+    rotation_indexing_min_angular_range_deg: number;
+    rotation_indexing_angular_stride_deg: number;
+    /**
+     * Indexing in Jungfraujoch goes with a dedicated thread pool.
+     * If set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates.
+     * If set to true, the thread pool will block until a thread is available.
+     *
+     */
+    blocking: boolean;
+};
+
+/**
+ * Metadata for a measurement instrument
+ */
+export type instrument_metadata = {
+    source_name: string;
+    /**
+     * Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance.
+     * https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource
+     * NXsource allows the following:
+     *
+     * Spallation Neutron Source
+     * Pulsed Reactor Neutron Source
+     * Reactor Neutron Source
+     * Synchrotron X-ray Source
+     * Pulsed Muon Source
+     * Rotating Anode X-ray
+     * Fixed Tube X-ray
+     * UV Laser
+     * Free-Electron Laser
+     * Optical Laser
+     * Ion Source
+     * UV Plasma Source
+     * Metal Jet X-ray
+     *
+     */
+    source_type?: string;
+    instrument_name: string;
+    /**
+     * Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)
+     *
+     */
+    pulsed_source?: boolean;
+    /**
+     * Settings specific to electron source (e.g., wavelength definition)
+     *
+     */
+    electron_source?: boolean;
+};
+
+export const detector_module_direction = {
+    XP: 'Xp',
+    XN: 'Xn',
+    YP: 'Yp',
+    YN: 'Yn'
+} as const;
+
+export type detector_module_direction = typeof detector_module_direction[keyof typeof detector_module_direction];
+
+export const detector_type = {
+    EIGER: 'EIGER',
+    JUNGFRAU: 'JUNGFRAU',
+    DECTRIS: 'DECTRIS'
+} as const;
+
+export type detector_type = typeof detector_type[keyof typeof detector_type];
+
+export const image_pusher_type = {
+    ZERO_MQ: 'ZeroMQ',
+    HDF5: 'HDF5',
+    CBOR: 'CBOR',
+    TCP: 'TCP',
+    NONE: 'None'
+} as const;
+
+export type image_pusher_type = typeof image_pusher_type[keyof typeof image_pusher_type];
+
+/**
+ * Regular rectangular geometry, first module is in the bottom left corner of the detector
+ */
+export type standard_detector_geometry = {
+    /**
+     * Number of modules in the detector
+     */
+    nmodules: number;
+    /**
+     * Gap size in X direction [pixels]
+     */
+    gap_x?: number;
+    /**
+     * Gap size in Y direction [pixels]
+     */
+    gap_y?: number;
+    /**
+     * Number of modules in one row
+     */
+    modules_in_row?: number;
+};
+
+export type detector_module = {
+    x0: number;
+    y0: number;
+    fast_axis: detector_module_direction;
+    slow_axis: detector_module_direction;
+};
+
+export type detector = {
+    description: string;
+    serial_number?: string;
+    type?: detector_type;
+    high_voltage_V?: number;
+    udp_interface_count?: number;
+    /**
+     * Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER).
+     */
+    module_sync?: boolean;
+    sensor_thickness_um?: number;
+    /**
+     * Minimum difference between frame time and count time in microseconds
+     * Defaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU
+     *
+     */
+    readout_time_ns?: number;
+    /**
+     * Minimum count time available for the detector.
+     */
+    min_count_time_ns?: number;
+    /**
+     * Minimum frame time available for the detector.
+     */
+    min_frame_time_ns?: number;
+    /**
+     * Can be empty for all detectors - default calibration used.
+     * For JUNGFRAU: list of gain files, one entry per module.
+     * For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.
+     *
+     */
+    calibration_file?: Array<string>;
+    /**
+     * Hostname for detector module. One entry per module
+     * One entry per module. Either empty or number of module entries.
+     *
+     */
+    hostname?: Array<string>;
+    sensor_material?: string;
+    tx_delay?: Array<number>;
+    base_data_ipv4_address?: string;
+    standard_geometry?: standard_detector_geometry;
+    custom_geometry?: Array<detector_module>;
+    /**
+     * ROI setting for DECTRIS detectors
+     */
+    roi_mode?: string;
+    /**
+     * Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner
+     */
+    mirror_y?: boolean;
+    /**
+     * Temperature threshold for JUNGFRAU detector modules
+     */
+    temp_thresold_degC?: number;
+    default_settings?: detector_settings;
+};
+
+/**
+ * ZeroMQ configuration for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export type zeromq_settings = {
+    /**
+     * Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)
+     */
+    send_watermark?: number;
+    /**
+     * Send buffer size for ZeroMQ socket
+     */
+    send_buffer_size?: number;
+    /**
+     * PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.
+     * Images are serialized using CBOR.
+     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.
+     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
+     *
+     */
+    image_socket?: Array<string>;
+    /**
+     * PULL ZeroMQ socket for notifications from writer that it finished operation.
+     * This allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.
+     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.
+     * 0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.
+     * Using * (star) instead of port number is allowed and it means a random free port number.
+     *
+     */
+    writer_notification_socket?: string;
+};
+
+/**
+ * TCP image stream configuration for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export type tcp_settings = {
+    /**
+     * Send buffer size for TCP/IP socket
+     */
+    send_buffer_size?: number;
+    /**
+     * tcp://<IP address>:<port>
+     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces
+     *
+     */
+    image_socket?: string;
+    /**
+     * Number of TCP/IP writers to be used for streaming images
+     */
+    nwriters?: number;
+};
+
+export type pcie_devices = Array<{
+    /**
+     * Block device name
+     */
+    blk?: string;
+    /**
+     * IPv4 address of the block device
+     */
+    ipv4?: string;
+}>;
+
+/**
+ * Default settings for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export type jfjoch_settings = {
+    pcie?: pcie_devices;
+    zeromq?: zeromq_settings;
+    tcp?: tcp_settings;
+    instrument?: instrument_metadata;
+    file_writer?: file_writer_settings;
+    detector: Array<detector>;
+    indexing?: indexing_settings;
+    detector_settings?: detector_settings;
+    azim_int?: azim_int_settings;
+    image_format?: image_format_settings;
+    /**
+     * Size of internal buffer in MiB for images before they are sent to a stream
+     */
+    image_buffer_MiB?: number;
+    /**
+     * Print extra debug information
+     */
+    verbose?: boolean;
+    /**
+     * Number of threads used by the receiver
+     */
+    receiver_threads?: number;
+    /**
+     * Ignored value
+     *
+     * @deprecated
+     */
+    numa_policy?: string;
+    /**
+     * Location of built JavaScript web frontend
+     */
+    frontend_directory: string;
+    spot_finding?: spot_finding_settings;
+    image_pusher: image_pusher_type;
+    zeromq_preview?: zeromq_preview_settings;
+    zeromq_metadata?: zeromq_metadata_settings;
+    dark_mask?: dark_mask_settings;
+};
+
+export type zeromq_metadata_settings = {
+    /**
+     * ZeroMQ metadata socket is enabled.
+     */
+    enabled: boolean;
+    /**
+     * Period for generating metadata package sent to the ZeroMQ interface in milliseconds.
+     *
+     */
+    period_ms: number;
+    /**
+     * PUB ZeroMQ socket for image metadata information.
+     * Image metadata are serialized using CBOR.
+     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.
+     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
+     *
+     */
+    socket_address?: string;
+};
+
+export type zeromq_preview_settings = {
+    /**
+     * ZeroMQ preview socket is enabled.
+     */
+    enabled: boolean;
+    /**
+     * Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second.
+     * If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).
+     * This has no effect on HTTP based preview, which updates always at rate of 1 second.
+     *
+     */
+    period_ms: number;
+    /**
+     * PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.
+     * Images are serialized using CBOR.
+     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.
+     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
+     *
+     */
+    socket_address?: string;
+};
+
+/**
+ * Binning of frames for the plot (0 = default binning)
+ */
+export type binning = number;
+
+/**
+ * If measurement has goniometer axis defined, plot X-axis will represent rotation angle
+ * If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
+ * For still measurement the number is ignored
+ *
+ */
+export type experimental_coord = boolean;
+
+/**
+ * Unit used for azim int.
+ *
+ */
+export const azint_unit = {
+    Q_RECIP_A: 'Q_recipA',
+    D_A: 'd_A',
+    TWO_THETA_DEG: 'two_theta_deg'
+} as const;
+
+/**
+ * Unit used for azim int.
+ *
+ */
+export type azint_unit = typeof azint_unit[keyof typeof azint_unit];
+
+/**
+ * Fill value for elements that were missed during data collection
+ *
+ */
+export type fill_value = number;
+
+/**
+ * Type of requested plot
+ */
+export const plot_type = {
+    BKG_ESTIMATE: 'bkg_estimate',
+    AZINT: 'azint',
+    AZINT_1D: 'azint_1d',
+    SPOT_COUNT: 'spot_count',
+    SPOT_COUNT_LOW_RES: 'spot_count_low_res',
+    SPOT_COUNT_INDEXED: 'spot_count_indexed',
+    SPOT_COUNT_ICE: 'spot_count_ice',
+    INDEXING_RATE: 'indexing_rate',
+    INDEXING_LATTICE_COUNT: 'indexing_lattice_count',
+    INDEXING_UNIT_CELL_LENGTH: 'indexing_unit_cell_length',
+    INDEXING_UNIT_CELL_ANGLE: 'indexing_unit_cell_angle',
+    PROFILE_RADIUS: 'profile_radius',
+    MOSAICITY: 'mosaicity',
+    B_FACTOR: 'b_factor',
+    ERROR_PIXELS: 'error_pixels',
+    SATURATED_PIXELS: 'saturated_pixels',
+    IMAGE_COLLECTION_EFFICIENCY: 'image_collection_efficiency',
+    RECEIVER_DELAY: 'receiver_delay',
+    RECEIVER_FREE_SEND_BUF: 'receiver_free_send_buf',
+    STRONG_PIXELS: 'strong_pixels',
+    ROI_SUM: 'roi_sum',
+    ROI_MEAN: 'roi_mean',
+    ROI_MAX_COUNT: 'roi_max_count',
+    ROI_PIXELS: 'roi_pixels',
+    ROI_WEIGHTED_X: 'roi_weighted_x',
+    ROI_WEIGHTED_Y: 'roi_weighted_y',
+    PACKETS_RECEIVED: 'packets_received',
+    MAX_PIXEL_VALUE: 'max_pixel_value',
+    RESOLUTION_ESTIMATE: 'resolution_estimate',
+    PIXEL_SUM: 'pixel_sum',
+    PROCESSING_TIME: 'processing_time',
+    BEAM_CENTER_X: 'beam_center_x',
+    BEAM_CENTER_Y: 'beam_center_y',
+    INTEGRATED_REFLECTIONS: 'integrated_reflections',
+    IMAGE_SCALE_FACTOR: 'image_scale_factor',
+    IMAGE_SCALE_CC: 'image_scale_cc',
+    IMAGE_SCALE_B: 'image_scale_b',
+    COMPRESSION_RATIO: 'compression_ratio'
+} as const;
+
+/**
+ * Type of requested plot
+ */
+export type plot_type = typeof plot_type[keyof typeof plot_type];
+
+/**
+ * Name of ROI for which plot is requested
+ */
+export type roi = string;
+
+/**
+ * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
+ */
+export type image_id = number;
+
+/**
+ * Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
+ */
+export type saturation = number;
+
+/**
+ * Background value to set contrast in the preview image
+ */
+export type background = number;
+
+/**
+ * Show spot finding results on the image
+ */
+export type show_spots = boolean;
+
+/**
+ * Show beam center on the image
+ */
+export type show_beam_center = boolean;
+
+/**
+ * Show ROI areas on the image
+ */
+export type show_roi = boolean;
+
+/**
+ * Quality of JPEG image (100 - highest; 0 - lowest)
+ */
+export type jpeg_quality = number;
+
+/**
+ * Show user mask
+ */
+export type show_user_mask = boolean;
+
+/**
+ * Show resolution ring, provided in Angstrom
+ */
+export type resolution_ring = number;
+
+/**
+ * Show resolution estimation as a ring
+ */
+export type resolution_estimate = boolean;
+
+/**
+ * Color scale for preview image
+ */
+export const color_scale = {
+    INDIGO: 'indigo',
+    VIRIDIS: 'viridis',
+    BW: 'bw',
+    WB: 'wb',
+    GREEN: 'green',
+    HEAT: 'heat',
+    MAGMA: 'magma',
+    INFERNO: 'inferno'
+} as const;
+
+/**
+ * Color scale for preview image
+ */
+export type color_scale = typeof color_scale[keyof typeof color_scale];
+
+export type postInitializeData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/initialize';
+};
+
+export type postInitializeErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postInitializeError = postInitializeErrors[keyof postInitializeErrors];
+
+export type postInitializeResponses = {
+    /**
+     * Initialization started
+     */
+    200: unknown;
+};
+
+export type postPedestalData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/pedestal';
+};
+
+export type postPedestalErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postPedestalError = postPedestalErrors[keyof postPedestalErrors];
+
+export type postPedestalResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type postStartData = {
+    body?: dataset_settings;
+    path?: never;
+    query?: never;
+    url: '/start';
+};
+
+export type postStartErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postStartError = postStartErrors[keyof postStartErrors];
+
+export type postStartResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type postWaitUntilRunningData = {
+    body?: never;
+    path?: never;
+    query?: {
+        /**
+         * Timeout in seconds (0 == immediate response)
+         */
+        timeout?: number;
+    };
+    url: '/wait_until_running';
+};
+
+export type postWaitUntilRunningErrors = {
+    /**
+     * Timeout parameter out of bounds
+     */
+    400: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+    /**
+     * Detector is inactive mode
+     */
+    502: unknown;
+    /**
+     * Timeout reached, need to restart operation
+     */
+    504: unknown;
+};
+
+export type postWaitUntilRunningError = postWaitUntilRunningErrors[keyof postWaitUntilRunningErrors];
+
+export type postWaitUntilRunningResponses = {
+    /**
+     * Detector in `Measuring` state
+     */
+    200: unknown;
+};
+
+export type postWaitTillDoneData = {
+    body?: never;
+    path?: never;
+    query?: {
+        /**
+         * Timeout in seconds (0 == immediate response)
+         */
+        timeout?: number;
+    };
+    url: '/wait_till_done';
+};
+
+export type postWaitTillDoneErrors = {
+    /**
+     * Timeout parameter out of bounds
+     */
+    400: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+    /**
+     * Detector is inactive mode
+     */
+    502: unknown;
+    /**
+     * Timeout reached, need to restart operation
+     */
+    504: unknown;
+};
+
+export type postWaitTillDoneError = postWaitTillDoneErrors[keyof postWaitTillDoneErrors];
+
+export type postWaitTillDoneResponses = {
+    /**
+     * Detector in `Idle` state, another data collection can start immediately
+     */
+    200: unknown;
+};
+
+export type postTriggerData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/trigger';
+};
+
+export type postTriggerResponses = {
+    /**
+     * Trigger sent
+     */
+    200: unknown;
+};
+
+export type postCancelData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/cancel';
+};
+
+export type postCancelResponses = {
+    /**
+     * Cancel request sent to FPGAs (or ignored, as data collection is not running)
+     */
+    200: unknown;
+};
+
+export type postDeactivateData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/deactivate';
+};
+
+export type postDeactivateErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postDeactivateError = postDeactivateErrors[keyof postDeactivateErrors];
+
+export type postDeactivateResponses = {
+    /**
+     * Detector ready to turn off
+     */
+    200: unknown;
+};
+
+export type getConfigDetectorData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/detector';
+};
+
+export type getConfigDetectorResponses = {
+    /**
+     * Everything OK
+     */
+    200: detector_settings;
+};
+
+export type getConfigDetectorResponse = getConfigDetectorResponses[keyof getConfigDetectorResponses];
+
+export type putConfigDetectorData = {
+    body?: detector_settings;
+    path?: never;
+    query?: never;
+    url: '/config/detector';
+};
+
+export type putConfigDetectorErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigDetectorError = putConfigDetectorErrors[keyof putConfigDetectorErrors];
+
+export type putConfigDetectorResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigIndexingData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/indexing';
+};
+
+export type getConfigIndexingResponses = {
+    /**
+     * Everything OK
+     */
+    200: indexing_settings;
+};
+
+export type getConfigIndexingResponse = getConfigIndexingResponses[keyof getConfigIndexingResponses];
+
+export type putConfigIndexingData = {
+    body?: indexing_settings;
+    path?: never;
+    query?: never;
+    url: '/config/indexing';
+};
+
+export type putConfigIndexingErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigIndexingError = putConfigIndexingErrors[keyof putConfigIndexingErrors];
+
+export type putConfigIndexingResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigFileWriterData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/file_writer';
+};
+
+export type getConfigFileWriterResponses = {
+    /**
+     * Everything OK
+     */
+    200: file_writer_settings;
+};
+
+export type getConfigFileWriterResponse = getConfigFileWriterResponses[keyof getConfigFileWriterResponses];
+
+export type putConfigFileWriterData = {
+    body?: file_writer_settings;
+    path?: never;
+    query?: never;
+    url: '/config/file_writer';
+};
+
+export type putConfigFileWriterErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigFileWriterError = putConfigFileWriterErrors[keyof putConfigFileWriterErrors];
+
+export type putConfigFileWriterResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigInstrumentData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/instrument';
+};
+
+export type getConfigInstrumentResponses = {
+    /**
+     * Everything OK
+     */
+    200: instrument_metadata;
+};
+
+export type getConfigInstrumentResponse = getConfigInstrumentResponses[keyof getConfigInstrumentResponses];
+
+export type putConfigInstrumentData = {
+    body?: instrument_metadata;
+    path?: never;
+    query?: never;
+    url: '/config/instrument';
+};
+
+export type putConfigInstrumentErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigInstrumentError = putConfigInstrumentErrors[keyof putConfigInstrumentErrors];
+
+export type putConfigInstrumentResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigImageFormatData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/image_format';
+};
+
+export type getConfigImageFormatResponses = {
+    /**
+     * Everything OK
+     */
+    200: image_format_settings;
+};
+
+export type getConfigImageFormatResponse = getConfigImageFormatResponses[keyof getConfigImageFormatResponses];
+
+export type putConfigImageFormatData = {
+    body?: image_format_settings;
+    path?: never;
+    query?: never;
+    url: '/config/image_format';
+};
+
+export type putConfigImageFormatErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigImageFormatError = putConfigImageFormatErrors[keyof putConfigImageFormatErrors];
+
+export type putConfigImageFormatResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type postConfigImageFormatRawData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/image_format/raw';
+};
+
+export type postConfigImageFormatRawErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postConfigImageFormatRawError = postConfigImageFormatRawErrors[keyof postConfigImageFormatRawErrors];
+
+export type postConfigImageFormatRawResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type postConfigImageFormatConversionData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/image_format/conversion';
+};
+
+export type postConfigImageFormatConversionErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postConfigImageFormatConversionError = postConfigImageFormatConversionErrors[keyof postConfigImageFormatConversionErrors];
+
+export type postConfigImageFormatConversionResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigSpotFindingData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/spot_finding';
+};
+
+export type getConfigSpotFindingResponses = {
+    /**
+     * Everything OK
+     */
+    200: spot_finding_settings;
+};
+
+export type getConfigSpotFindingResponse = getConfigSpotFindingResponses[keyof getConfigSpotFindingResponses];
+
+export type putConfigSpotFindingData = {
+    body?: spot_finding_settings;
+    path?: never;
+    query?: never;
+    url: '/config/spot_finding';
+};
+
+export type putConfigSpotFindingErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+};
+
+export type putConfigSpotFindingError = putConfigSpotFindingErrors[keyof putConfigSpotFindingErrors];
+
+export type putConfigSpotFindingResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigAzimIntData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/azim_int';
+};
+
+export type getConfigAzimIntResponses = {
+    /**
+     * Everything OK
+     */
+    200: azim_int_settings;
+};
+
+export type getConfigAzimIntResponse = getConfigAzimIntResponses[keyof getConfigAzimIntResponses];
+
+export type putConfigAzimIntData = {
+    body?: azim_int_settings;
+    path?: never;
+    query?: never;
+    url: '/config/azim_int';
+};
+
+export type putConfigAzimIntErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigAzimIntError = putConfigAzimIntErrors[keyof putConfigAzimIntErrors];
+
+export type putConfigAzimIntResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type putConfigInternalGeneratorImageData = {
+    body?: Blob | File;
+    path?: never;
+    query?: {
+        /**
+         * Image id to upload
+         */
+        id?: number;
+    };
+    url: '/config/internal_generator_image';
+};
+
+export type putConfigInternalGeneratorImageErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+};
+
+export type putConfigInternalGeneratorImageError = putConfigInternalGeneratorImageErrors[keyof putConfigInternalGeneratorImageErrors];
+
+export type putConfigInternalGeneratorImageResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type putConfigInternalGeneratorImageTiffData = {
+    body?: Blob | File;
+    path?: never;
+    query?: {
+        /**
+         * Image ID to upload
+         */
+        id?: number;
+    };
+    url: '/config/internal_generator_image.tiff';
+};
+
+export type putConfigInternalGeneratorImageTiffErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+};
+
+export type putConfigInternalGeneratorImageTiffError = putConfigInternalGeneratorImageTiffErrors[keyof putConfigInternalGeneratorImageTiffErrors];
+
+export type putConfigInternalGeneratorImageTiffResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigSelectDetectorData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/select_detector';
+};
+
+export type getConfigSelectDetectorResponses = {
+    /**
+     * Everything OK
+     */
+    200: detector_list;
+};
+
+export type getConfigSelectDetectorResponse = getConfigSelectDetectorResponses[keyof getConfigSelectDetectorResponses];
+
+export type putConfigSelectDetectorData = {
+    body?: detector_selection;
+    path?: never;
+    query?: never;
+    url: '/config/select_detector';
+};
+
+export type putConfigSelectDetectorErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigSelectDetectorError = putConfigSelectDetectorErrors[keyof putConfigSelectDetectorErrors];
+
+export type putConfigSelectDetectorResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigZeromqPreviewData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/zeromq_preview';
+};
+
+export type getConfigZeromqPreviewResponses = {
+    /**
+     * Everything OK
+     */
+    200: zeromq_preview_settings;
+};
+
+export type getConfigZeromqPreviewResponse = getConfigZeromqPreviewResponses[keyof getConfigZeromqPreviewResponses];
+
+export type putConfigZeromqPreviewData = {
+    body?: zeromq_preview_settings;
+    path?: never;
+    query?: never;
+    url: '/config/zeromq_preview';
+};
+
+export type putConfigZeromqPreviewErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigZeromqPreviewError = putConfigZeromqPreviewErrors[keyof putConfigZeromqPreviewErrors];
+
+export type putConfigZeromqPreviewResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigZeromqMetadataData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/zeromq_metadata';
+};
+
+export type getConfigZeromqMetadataResponses = {
+    /**
+     * Everything OK
+     */
+    200: zeromq_metadata_settings;
+};
+
+export type getConfigZeromqMetadataResponse = getConfigZeromqMetadataResponses[keyof getConfigZeromqMetadataResponses];
+
+export type putConfigZeromqMetadataData = {
+    body?: zeromq_metadata_settings;
+    path?: never;
+    query?: never;
+    url: '/config/zeromq_metadata';
+};
+
+export type putConfigZeromqMetadataErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigZeromqMetadataError = putConfigZeromqMetadataErrors[keyof putConfigZeromqMetadataErrors];
+
+export type putConfigZeromqMetadataResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getConfigDarkMaskData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/dark_mask';
+};
+
+export type getConfigDarkMaskResponses = {
+    /**
+     * Everything OK
+     */
+    200: dark_mask_settings;
+};
+
+export type getConfigDarkMaskResponse = getConfigDarkMaskResponses[keyof getConfigDarkMaskResponses];
+
+export type putConfigDarkMaskData = {
+    body?: dark_mask_settings;
+    path?: never;
+    query?: never;
+    url: '/config/dark_mask';
+};
+
+export type putConfigDarkMaskErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigDarkMaskError = putConfigDarkMaskErrors[keyof putConfigDarkMaskErrors];
+
+export type putConfigDarkMaskResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getStatusData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/status';
+};
+
+export type getStatusResponses = {
+    /**
+     * Everything OK
+     */
+    200: broker_status;
+};
+
+export type getStatusResponse = getStatusResponses[keyof getStatusResponses];
+
+export type getFpgaStatusData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/fpga_status';
+};
+
+export type getFpgaStatusResponses = {
+    /**
+     * Everything OK
+     */
+    200: fpga_status;
+};
+
+export type getFpgaStatusResponse = getFpgaStatusResponses[keyof getFpgaStatusResponses];
+
+export type getXfelPulseIdData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/xfel/pulse_id';
+};
+
+export type getXfelPulseIdErrors = {
+    /**
+     * Not in XFEL mode or no acquisition recorded
+     */
+    404: unknown;
+};
+
+export type getXfelPulseIdResponses = {
+    /**
+     * Pulse ID collected
+     */
+    200: Array<number>;
+};
+
+export type getXfelPulseIdResponse = getXfelPulseIdResponses[keyof getXfelPulseIdResponses];
+
+export type getXfelEventCodeData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/xfel/event_code';
+};
+
+export type getXfelEventCodeErrors = {
+    /**
+     * Not in XFEL mode or no acquisition recorded
+     */
+    404: unknown;
+};
+
+export type getXfelEventCodeResponses = {
+    /**
+     * Event codes collected
+     */
+    200: Array<number>;
+};
+
+export type getXfelEventCodeResponse = getXfelEventCodeResponses[keyof getXfelEventCodeResponses];
+
+export type getImagePusherStatusData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/image_pusher/status';
+};
+
+export type getImagePusherStatusErrors = {
+    /**
+     * Exception error
+     */
+    500: string;
+};
+
+export type getImagePusherStatusError = getImagePusherStatusErrors[keyof getImagePusherStatusErrors];
+
+export type getImagePusherStatusResponses = {
+    /**
+     * Everything OK
+     */
+    200: image_pusher_status;
+};
+
+export type getImagePusherStatusResponse = getImagePusherStatusResponses[keyof getImagePusherStatusResponses];
+
+export type getDetectorStatusData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/detector/status';
+};
+
+export type getDetectorStatusErrors = {
+    /**
+     * Running in "simulator" mode - no detector present
+     */
+    404: unknown;
+    /**
+     * Exception error
+     */
+    500: string;
+};
+
+export type getDetectorStatusError = getDetectorStatusErrors[keyof getDetectorStatusErrors];
+
+export type getDetectorStatusResponses = {
+    /**
+     * Everything OK
+     */
+    200: detector_status;
+};
+
+export type getDetectorStatusResponse = getDetectorStatusResponses[keyof getDetectorStatusResponses];
+
+export type getConfigRoiData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/roi';
+};
+
+export type getConfigRoiResponses = {
+    /**
+     * OK
+     */
+    200: roi_definitions;
+};
+
+export type getConfigRoiResponse = getConfigRoiResponses[keyof getConfigRoiResponses];
+
+export type putConfigRoiData = {
+    body?: roi_definitions;
+    path?: never;
+    query?: never;
+    url: '/config/roi';
+};
+
+export type putConfigRoiErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigRoiError = putConfigRoiErrors[keyof putConfigRoiErrors];
+
+export type putConfigRoiResponses = {
+    /**
+     * Everything OK
+     */
+    200: unknown;
+};
+
+export type getStatisticsData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/statistics';
+};
+
+export type getStatisticsResponses = {
+    /**
+     * Everything OK
+     */
+    200: jfjoch_statistics;
+};
+
+export type getStatisticsResponse = getStatisticsResponses[keyof getStatisticsResponses];
+
+export type getStatisticsDataCollectionData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/statistics/data_collection';
+};
+
+export type getStatisticsDataCollectionErrors = {
+    /**
+     * No data collection performed so far
+     */
+    404: unknown;
+};
+
+export type getStatisticsDataCollectionResponses = {
+    /**
+     * Everything OK
+     */
+    200: measurement_statistics;
+};
+
+export type getStatisticsDataCollectionResponse = getStatisticsDataCollectionResponses[keyof getStatisticsDataCollectionResponses];
+
+export type getStatisticsCalibrationData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/statistics/calibration';
+};
+
+export type getStatisticsCalibrationResponses = {
+    /**
+     * Everything OK
+     */
+    200: calibration_statistics;
+};
+
+export type getStatisticsCalibrationResponse = getStatisticsCalibrationResponses[keyof getStatisticsCalibrationResponses];
+
+export type getConfigMaskData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/mask';
+};
+
+export type getConfigMaskResponses = {
+    /**
+     * Binary array (4 byte; unsigned)
+     */
+    200: Blob | File;
+};
+
+export type getConfigMaskResponse = getConfigMaskResponses[keyof getConfigMaskResponses];
+
+export type getConfigUserMaskData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/user_mask';
+};
+
+export type getConfigUserMaskResponses = {
+    /**
+     * User mask in binary format (4 byte; unsigned)
+     */
+    200: Blob | File;
+};
+
+export type getConfigUserMaskResponse = getConfigUserMaskResponses[keyof getConfigUserMaskResponses];
+
+export type putConfigUserMaskData = {
+    body?: Blob | File;
+    path?: never;
+    query?: never;
+    url: '/config/user_mask';
+};
+
+export type putConfigUserMaskErrors = {
+    /**
+     * Mask is not 4-byte unsigned integer array or empty body
+     */
+    400: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigUserMaskError = putConfigUserMaskErrors[keyof putConfigUserMaskErrors];
+
+export type putConfigUserMaskResponses = {
+    /**
+     * All good
+     */
+    200: unknown;
+};
+
+export type getConfigMaskTiffData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/mask.tiff';
+};
+
+export type getConfigMaskTiffResponses = {
+    /**
+     * Pixel mask in TIFF format (4 byte; unsigned)
+     */
+    200: Blob | File;
+};
+
+export type getConfigMaskTiffResponse = getConfigMaskTiffResponses[keyof getConfigMaskTiffResponses];
+
+export type getConfigUserMaskTiffData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/user_mask.tiff';
+};
+
+export type getConfigUserMaskTiffResponses = {
+    /**
+     * User mask in TIFF format (4 byte; unsigned)
+     */
+    200: Blob | File;
+};
+
+export type getConfigUserMaskTiffResponse = getConfigUserMaskTiffResponses[keyof getConfigUserMaskTiffResponses];
+
+export type putConfigUserMaskTiffData = {
+    body?: Blob | File;
+    path?: never;
+    query?: never;
+    url: '/config/user_mask.tiff';
+};
+
+export type putConfigUserMaskTiffErrors = {
+    /**
+     * Not a valid single-channel TIFF or size doesn't match the detector
+     */
+    400: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type putConfigUserMaskTiffError = putConfigUserMaskTiffErrors[keyof putConfigUserMaskTiffErrors];
+
+export type putConfigUserMaskTiffResponses = {
+    /**
+     * All good
+     */
+    200: unknown;
+};
+
+export type getPreviewPedestalTiffData = {
+    body?: never;
+    path?: never;
+    query: {
+        /**
+         * Gain level (0, 1, 2)
+         */
+        gain_level: number;
+        /**
+         * Storage cell number
+         */
+        sc?: number;
+    };
+    url: '/preview/pedestal.tiff';
+};
+
+export type getPreviewPedestalTiffErrors = {
+    /**
+     * Invalid gain level or storage cell number
+     */
+    400: unknown;
+    /**
+     * No calibration recorded so far
+     */
+    404: unknown;
+};
+
+export type getPreviewPedestalTiffResponses = {
+    /**
+     * Calibration image
+     */
+    200: Blob | File;
+};
+
+export type getPreviewPedestalTiffResponse = getPreviewPedestalTiffResponses[keyof getPreviewPedestalTiffResponses];
+
+export type getPreviewPlotData = {
+    body?: never;
+    path?: never;
+    query: {
+        /**
+         * Binning of frames for the plot (0 = default binning)
+         */
+        binning?: number;
+        /**
+         * Type of requested plot
+         */
+        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio';
+        /**
+         * Fill value for elements that were missed during data collection
+         *
+         */
+        fill?: number;
+        /**
+         * If measurement has goniometer axis defined, plot X-axis will represent rotation angle
+         * If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
+         * For still measurement the number is ignored
+         *
+         */
+        experimental_coord?: boolean;
+        /**
+         * Unit used for azim int.
+         *
+         */
+        azint_unit?: 'Q_recipA' | 'd_A' | 'two_theta_deg';
+    };
+    url: '/preview/plot';
+};
+
+export type getPreviewPlotErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+};
+
+export type getPreviewPlotError = getPreviewPlotErrors[keyof getPreviewPlotErrors];
+
+export type getPreviewPlotResponses = {
+    /**
+     * Everything OK.
+     */
+    200: plots;
+};
+
+export type getPreviewPlotResponse = getPreviewPlotResponses[keyof getPreviewPlotResponses];
+
+export type getPreviewPlotBinData = {
+    body?: never;
+    path?: never;
+    query: {
+        /**
+         * Type of requested plot
+         */
+        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio';
+        /**
+         * Name of ROI for which plot is requested
+         */
+        roi?: string;
+    };
+    url: '/preview/plot.bin';
+};
+
+export type getPreviewPlotBinErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+};
+
+export type getPreviewPlotBinError = getPreviewPlotBinErrors[keyof getPreviewPlotBinErrors];
+
+export type getPreviewPlotBinResponses = {
+    /**
+     * Everything OK.
+     */
+    200: Blob | File;
+};
+
+export type getPreviewPlotBinResponse = getPreviewPlotBinResponses[keyof getPreviewPlotBinResponses];
+
+export type getResultScanData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/result/scan';
+};
+
+export type getResultScanErrors = {
+    /**
+     * No grid scan recorded
+     */
+    404: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type getResultScanError = getResultScanErrors[keyof getResultScanErrors];
+
+export type getResultScanResponses = {
+    /**
+     * Everything OK.
+     */
+    200: scan_result;
+};
+
+export type getResultScanResponse = getResultScanResponses[keyof getResultScanResponses];
+
+export type getImageBufferStartCborData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/image_buffer/start.cbor';
+};
+
+export type getImageBufferStartCborErrors = {
+    /**
+     * No measurement so far
+     */
+    404: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type getImageBufferStartCborError = getImageBufferStartCborErrors[keyof getImageBufferStartCborErrors];
+
+export type getImageBufferStartCborResponses = {
+    /**
+     * Return start message
+     */
+    200: Blob | File;
+};
+
+export type getImageBufferStartCborResponse = getImageBufferStartCborResponses[keyof getImageBufferStartCborResponses];
+
+export type getImageBufferImageCborData = {
+    body?: never;
+    path?: never;
+    query?: {
+        /**
+         * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
+         */
+        id?: number;
+    };
+    url: '/image_buffer/image.cbor';
+};
+
+export type getImageBufferImageCborErrors = {
+    /**
+     * Image not present in the buffer - either not yet measured or already replaced by a next image.
+     */
+    404: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type getImageBufferImageCborError = getImageBufferImageCborErrors[keyof getImageBufferImageCborErrors];
+
+export type getImageBufferImageCborResponses = {
+    /**
+     * Return image message
+     */
+    200: Blob | File;
+};
+
+export type getImageBufferImageCborResponse = getImageBufferImageCborResponses[keyof getImageBufferImageCborResponses];
+
+export type getImageBufferImageJpegData = {
+    body?: never;
+    path?: never;
+    query?: {
+        /**
+         * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
+         */
+        id?: number;
+        /**
+         * Show user mask
+         */
+        show_user_mask?: boolean;
+        /**
+         * Show ROI areas on the image
+         */
+        show_roi?: boolean;
+        /**
+         * Show spot finding results on the image
+         */
+        show_spots?: boolean;
+        /**
+         * Show beam center on the image
+         */
+        show_beam_center?: boolean;
+        /**
+         * Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
+         */
+        saturation?: number;
+        /**
+         * Quality of JPEG image (100 - highest; 0 - lowest)
+         */
+        jpeg_quality?: number;
+        /**
+         * Show resolution ring, provided in Angstrom
+         */
+        show_res_ring?: number;
+        /**
+         * Color scale for preview image
+         */
+        color?: 'indigo' | 'viridis' | 'bw' | 'wb' | 'green' | 'heat' | 'magma' | 'inferno';
+        /**
+         * Show resolution estimation as a ring
+         */
+        show_res_est?: boolean;
+    };
+    url: '/image_buffer/image.jpeg';
+};
+
+export type getImageBufferImageJpegErrors = {
+    /**
+     * Exception error
+     */
+    400: string;
+    /**
+     * Image not present in the buffer - either not yet measured or already replaced by a next image.
+     */
+    404: unknown;
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type getImageBufferImageJpegError = getImageBufferImageJpegErrors[keyof getImageBufferImageJpegErrors];
+
+export type getImageBufferImageJpegResponses = {
+    /**
+     * Preview image
+     */
+    200: Blob | File;
+};
+
+export type getImageBufferImageJpegResponse = getImageBufferImageJpegResponses[keyof getImageBufferImageJpegResponses];
+
+export type getImageBufferImageTiffData = {
+    body?: never;
+    path?: never;
+    query?: {
+        /**
+         * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
+         */
+        id?: number;
+    };
+    url: '/image_buffer/image.tiff';
+};
+
+export type getImageBufferImageTiffErrors = {
+    /**
+     * No preview image recorded so far
+     */
+    404: unknown;
+};
+
+export type getImageBufferImageTiffResponses = {
+    /**
+     * Preview image
+     */
+    200: Blob | File;
+};
+
+export type getImageBufferImageTiffResponse = getImageBufferImageTiffResponses[keyof getImageBufferImageTiffResponses];
+
+export type postImageBufferClearData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/image_buffer/clear';
+};
+
+export type postImageBufferClearErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type postImageBufferClearError = postImageBufferClearErrors[keyof postImageBufferClearErrors];
+
+export type postImageBufferClearResponses = {
+    /**
+     * Done
+     */
+    200: unknown;
+};
+
+export type getImageBufferStatusData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/image_buffer/status';
+};
+
+export type getImageBufferStatusErrors = {
+    /**
+     * Error within Jungfraujoch code - see output message.
+     */
+    500: error_message;
+};
+
+export type getImageBufferStatusError = getImageBufferStatusErrors[keyof getImageBufferStatusErrors];
+
+export type getImageBufferStatusResponses = {
+    /**
+     * Done
+     */
+    200: image_buffer_status;
+};
+
+export type getImageBufferStatusResponse = getImageBufferStatusResponses[keyof getImageBufferStatusResponses];
+
+export type getVersionData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/version';
+};
+
+export type getVersionResponses = {
+    /**
+     * Release number of Jungfraujoch
+     */
+    200: string;
+};
+
+export type getVersionResponse = getVersionResponses[keyof getVersionResponses];
diff --git a/frontend/src/components/AzIntSettings.tsx b/frontend/src/components/AzIntSettings.tsx
index f90ae3e2..4594813b 100644
--- a/frontend/src/components/AzIntSettings.tsx
+++ b/frontend/src/components/AzIntSettings.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 import Paper from '@mui/material/Paper';
 import {FormControlLabel, Checkbox, Stack, Tooltip, ListItem, List, Radio, RadioGroup, Typography} from "@mui/material";
 import NumberTextField from "./NumberTextField";
-import {azim_int_settings} from "../openapi";
+import {azim_int_settings} from "../client";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import FormControl from "@mui/material/FormControl";
diff --git a/frontend/src/components/ButtonWithSnackbar.tsx b/frontend/src/components/ButtonWithSnackbar.tsx
index 3d72e547..1a91afc8 100644
--- a/frontend/src/components/ButtonWithSnackbar.tsx
+++ b/frontend/src/components/ButtonWithSnackbar.tsx
@@ -3,7 +3,6 @@ import React, {Component} from 'react';
 import {
     Alert, SnackbarCloseReason
 } from "@mui/material";
-import {OpenAPI} from "../openapi";
 import Button from "@mui/material/Button";
 import Snackbar from "@mui/material/Snackbar";
 
@@ -58,8 +57,7 @@ class ButtonWithSnackbar extends Component<MyProps, MyState> {
     }
 
     startButton = () => {
-        const url = OpenAPI.BASE + this.props.path;
-        fetch(url, {
+        fetch(this.props.path, {
             method: (this.props.method === undefined) ? "POST" : this.props.method,
             body: this.props.input
         }).then(this.handleResponse);
diff --git a/frontend/src/components/Calibration.tsx b/frontend/src/components/Calibration.tsx
index b1f49059..4b9e9550 100644
--- a/frontend/src/components/Calibration.tsx
+++ b/frontend/src/components/Calibration.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 
 import Paper from '@mui/material/Paper';
 import {DataGrid, GridColDef} from "@mui/x-data-grid";
-import {calibration_statistics, DefaultService} from "../openapi";
+import {calibration_statistics} from "../client";
 
 type MyProps = {
     s?: calibration_statistics
diff --git a/frontend/src/components/DarkMaskSettings.tsx b/frontend/src/components/DarkMaskSettings.tsx
index d6896998..a4ff4ec5 100644
--- a/frontend/src/components/DarkMaskSettings.tsx
+++ b/frontend/src/components/DarkMaskSettings.tsx
@@ -4,7 +4,7 @@ import {Checkbox, FormControlLabel, Stack} from '@mui/material';
 import _ from 'lodash';
 import NumberTextField from './NumberTextField';
 import ButtonWithSnackbar from './ButtonWithSnackbar';
-import { dark_mask_settings } from '../openapi';
+import { dark_mask_settings } from '../client';
 
 type MyProps = {
     s?: dark_mask_settings;
diff --git a/frontend/src/components/DataCollection.tsx b/frontend/src/components/DataCollection.tsx
index de02f731..f2d5cacb 100644
--- a/frontend/src/components/DataCollection.tsx
+++ b/frontend/src/components/DataCollection.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 import Paper from '@mui/material/Paper';
 import {Stack, TextField, Radio, RadioGroup, FormControlLabel, FormControl, FormLabel, Checkbox} from "@mui/material";
 import NumberTextField from "./NumberTextField";
-import {dataset_settings, grid_scan, rotation_axis} from "../openapi";
+import {dataset_settings, grid_scan, rotation_axis} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 
 type MyProps = {
diff --git a/frontend/src/components/DataProcessingPlot.tsx b/frontend/src/components/DataProcessingPlot.tsx
index e0faae69..c47eb9bf 100644
--- a/frontend/src/components/DataProcessingPlot.tsx
+++ b/frontend/src/components/DataProcessingPlot.tsx
@@ -1,6 +1,6 @@
 import React, {Component, ReactNode} from 'react';
 
-import {azint_unit, DefaultService, plot_type, plot_unit_x, plots} from "../openapi";
+import {azint_unit, getPreviewPlot, plot_type, plot_unit_x, plots} from "../client";
 import MultiLinePlotWrapper from "./MultiLinePlotWrapper";
 
 type MyProps = {
@@ -115,8 +115,8 @@ class DataProcessingPlot extends Component<MyProps, MyState> {
     }
 
     getValues() {
-        DefaultService.getPreviewPlot(this.props.type, this.props.binning,  undefined, this.props.angle, this.props.azint)
-            .then(data => this.setState({plots: data, connection_error: false}))
+        getPreviewPlot({ throwOnError: true, query: { type: this.props.type, binning: this.props.binning, experimental_coord: this.props.angle, azint_unit: this.props.azint } })
+            .then(({data}) => this.setState({plots: data, connection_error: false}))
             .catch(error => {
                 this.setState({connection_error: true});
             });
diff --git a/frontend/src/components/DataProcessingPlots.tsx b/frontend/src/components/DataProcessingPlots.tsx
index 49162e35..303d5f99 100644
--- a/frontend/src/components/DataProcessingPlots.tsx
+++ b/frontend/src/components/DataProcessingPlots.tsx
@@ -7,7 +7,7 @@ import Toolbar from "@mui/material/Toolbar";
 import MenuItem from "@mui/material/MenuItem";
 import FormControl from "@mui/material/FormControl";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
-import {azint_unit, plot_type} from "../openapi";
+import {azint_unit, plot_type} from "../client";
 
 type MyProps = {
     type: plot_type,
diff --git a/frontend/src/components/DataProcessingSettings.tsx b/frontend/src/components/DataProcessingSettings.tsx
index c6352e96..8019a15c 100644
--- a/frontend/src/components/DataProcessingSettings.tsx
+++ b/frontend/src/components/DataProcessingSettings.tsx
@@ -2,7 +2,7 @@ import React, {Component} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Grid, Slider, Switch, Typography} from "@mui/material";
-import {DefaultService, spot_finding_settings} from "../openapi";
+import {putConfigSpotFinding, spot_finding_settings} from "../client";
 import _ from "lodash";
 
 type MyProps = {
@@ -39,7 +39,7 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
     }
 
     putValues(x: spot_finding_settings) {
-        DefaultService.putConfigSpotFinding(x)
+        putConfigSpotFinding({ body: x, throwOnError: true })
             .catch(error => console.log(error) );
     }
 
diff --git a/frontend/src/components/DetectorSelection.tsx b/frontend/src/components/DetectorSelection.tsx
index e49622eb..67192be0 100644
--- a/frontend/src/components/DetectorSelection.tsx
+++ b/frontend/src/components/DetectorSelection.tsx
@@ -6,7 +6,7 @@ import Paper from "@mui/material/Paper";
 import InputLabel from '@mui/material/InputLabel';
 import MenuItem from '@mui/material/MenuItem';
 import FormControl from '@mui/material/FormControl';
-import {detector_list, detector_list_element} from "../openapi";
+import {detector_list, detector_list_element} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import { ReactNode } from "react";
 
diff --git a/frontend/src/components/DetectorSettings.tsx b/frontend/src/components/DetectorSettings.tsx
index e9df194f..a12edc84 100644
--- a/frontend/src/components/DetectorSettings.tsx
+++ b/frontend/src/components/DetectorSettings.tsx
@@ -6,7 +6,7 @@ import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
-import {DefaultService, detector_settings, detector_timing} from "../openapi";
+import {detector_settings, detector_timing, postDeactivate} from "../client";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
@@ -38,11 +38,11 @@ type MyState = {
 function extractDepthForSelection(input: detector_settings) : string {
     if (input.eiger_bit_depth === undefined)
         return 'a';
-    else if (input.eiger_bit_depth === detector_settings.eiger_bit_depth._16)
+    else if (input.eiger_bit_depth === 16)
         return '16';
-    else if (input.eiger_bit_depth === detector_settings.eiger_bit_depth._32)
+    else if (input.eiger_bit_depth === 32)
         return '32';
-    else if (input.eiger_bit_depth === detector_settings.eiger_bit_depth._8)
+    else if (input.eiger_bit_depth === 8)
         return '8';
     else
         return "";
@@ -101,21 +101,21 @@ class DetectorSettings extends Component<MyProps, MyState> {
     }
 
     deactivate = () => {
-        DefaultService.postDeactivate()
+        postDeactivate({ throwOnError: true })
             .catch(error => {} );
     }
 
     handleBitWidthChange = (event: SelectChangeEvent) => {
-        let val: detector_settings.eiger_bit_depth|undefined = undefined;
+        let val: detector_settings['eiger_bit_depth'] = undefined;
 
         if (event.target.value === "a")
             val = undefined;
         else if (event.target.value === "8")
-            val = detector_settings.eiger_bit_depth._8;
+            val = 8;
         else if (event.target.value === "16")
-            val = detector_settings.eiger_bit_depth._16;
+            val = 16;
         else if (event.target.value === "32")
-            val = detector_settings.eiger_bit_depth._32;
+            val = 32;
 
         this.setState(prevState => ({
             bit_width_selection: event.target.value,
diff --git a/frontend/src/components/DetectorStatus.tsx b/frontend/src/components/DetectorStatus.tsx
index a2df4a64..e6dc0055 100644
--- a/frontend/src/components/DetectorStatus.tsx
+++ b/frontend/src/components/DetectorStatus.tsx
@@ -2,7 +2,7 @@ import React, {Component} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Stack, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
-import {detector_status, detector_state, detector_power_state} from "../openapi";
+import {detector_status, detector_state, detector_power_state} from "../client";
 
 type MyProps = {
     s?: detector_status
diff --git a/frontend/src/components/ErrorMessage.tsx b/frontend/src/components/ErrorMessage.tsx
index f5a2e858..0eef8ad5 100644
--- a/frontend/src/components/ErrorMessage.tsx
+++ b/frontend/src/components/ErrorMessage.tsx
@@ -1,6 +1,6 @@
 import React, {Component} from 'react';
 
-import {broker_status} from "../openapi";
+import {broker_status} from "../client";
 import {Alert, AlertColor} from "@mui/material";
 import { ReactNode } from "react";
 
@@ -11,18 +11,18 @@ type MyProps = {
 type MyState = {}
 
 class ErrorMessage extends Component<MyProps, MyState> {
-    severity(input?: broker_status.message_severity) : AlertColor {
+    severity(input?: broker_status['message_severity']) : AlertColor {
         if (input === undefined)
             return "error";
 
         switch (input) {
-            case broker_status.message_severity.INFO:
+            case 'info':
                 return "info";
-            case broker_status.message_severity.WARNING:
+            case 'warning':
                 return "warning";
-            case broker_status.message_severity.ERROR:
+            case 'error':
                 return "error";
-            case broker_status.message_severity.SUCCESS:
+            case 'success':
                 return "success";
         }
     }
diff --git a/frontend/src/components/FileWriterSettings.tsx b/frontend/src/components/FileWriterSettings.tsx
index b10ce4c0..90e0601b 100644
--- a/frontend/src/components/FileWriterSettings.tsx
+++ b/frontend/src/components/FileWriterSettings.tsx
@@ -2,7 +2,7 @@ import React from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Checkbox, FormControlLabel, FormGroup, Select, Stack} from "@mui/material";
-import {file_writer_format, file_writer_settings} from "../openapi";
+import {file_writer_format, file_writer_settings} from "../client";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import MenuItem from "@mui/material/MenuItem";
@@ -21,7 +21,7 @@ type MyState = {
 
 const default_file_writer_settings : file_writer_settings = {
     overwrite: false,
-    format: file_writer_format.NXMX_LEGACY
+    format: file_writer_format.N_XMX_LEGACY
 }
 
 // Function to convert a string to an enum value
@@ -30,8 +30,8 @@ function stringToEnum(value: string): file_writer_format {
         (v) => v === value
     ) as file_writer_format;
 
-    // If no match is found, default to file_writer_format.NXMX_ONLY_DATA
-    return enumValue || file_writer_format.NXMX_ONLY_DATA;
+    // If no match is found, default to file_writer_format.N_XMX_ONLY_DATA
+    return enumValue || file_writer_format.N_XMX_ONLY_DATA;
 }
 
 
@@ -107,10 +107,10 @@ class FileWriterSettings extends React.Component<MyProps, MyState> {
                             }));
                         }}
                     >
-                        <MenuItem value={file_writer_format.NXMX_LEGACY}>NXmx HDF5 master file with soft links (DECTRIS file writer compatibility)</MenuItem>
-                        <MenuItem value={file_writer_format.NXMX_VDS}>NXmx HDF5 master file with virtual datasets</MenuItem>
-                        <MenuItem value={file_writer_format.NXMX_INTEGRATED}>Single HDF5 file with data and metadata</MenuItem>
-                        <MenuItem value={file_writer_format.NXMX_ONLY_DATA}>No NXmx HDF5 master file (only data files)</MenuItem>
+                        <MenuItem value={file_writer_format.N_XMX_LEGACY}>NXmx HDF5 master file with soft links (DECTRIS file writer compatibility)</MenuItem>
+                        <MenuItem value={file_writer_format.N_XMX_VDS}>NXmx HDF5 master file with virtual datasets</MenuItem>
+                        <MenuItem value={file_writer_format.N_XMX_INTEGRATED}>Single HDF5 file with data and metadata</MenuItem>
+                        <MenuItem value={file_writer_format.N_XMX_ONLY_DATA}>No NXmx HDF5 master file (only data files)</MenuItem>
                         <MenuItem value={file_writer_format.CBF}>miniCBF (only data files; limited metadata)</MenuItem>
                         <MenuItem value={file_writer_format.TIFF}>TIFF (only data files; no metadata)</MenuItem>
                         <MenuItem value={file_writer_format.NO_FILE_WRITTEN}>No files saved</MenuItem>
diff --git a/frontend/src/components/FpgaStatus.tsx b/frontend/src/components/FpgaStatus.tsx
index 96e0d802..e96b02be 100644
--- a/frontend/src/components/FpgaStatus.tsx
+++ b/frontend/src/components/FpgaStatus.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 
 import Paper from '@mui/material/Paper';
 import {DataGrid, GridCellParams, GridColDef} from "@mui/x-data-grid";
-import { DefaultService, fpga_status} from "../openapi";
+import { fpga_status} from "../client";
 import { ReactNode } from "react";
 
 function Circles(val: boolean) : ReactNode {
diff --git a/frontend/src/components/ImageFormatSettings.tsx b/frontend/src/components/ImageFormatSettings.tsx
index a05dfb2f..6cc41002 100644
--- a/frontend/src/components/ImageFormatSettings.tsx
+++ b/frontend/src/components/ImageFormatSettings.tsx
@@ -7,7 +7,7 @@ import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
-import {DefaultService, image_format_settings} from "../openapi";
+import {image_format_settings, postConfigImageFormatConversion, postConfigImageFormatRaw, putConfigImageFormat} from "../client";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
@@ -53,11 +53,11 @@ function extractSignForSelection(input: image_format_settings) : string {
 function extractDepthForSelection(input: image_format_settings) : string {
     if (input.bit_depth_image === undefined)
         return 'a';
-    else if (input.bit_depth_image === image_format_settings.bit_depth_image._8)
+    else if (input.bit_depth_image === 8)
         return '8';
-    else if (input.bit_depth_image === image_format_settings.bit_depth_image._16)
+    else if (input.bit_depth_image === 16)
         return '16';
-    else if (input.bit_depth_image === image_format_settings.bit_depth_image._32)
+    else if (input.bit_depth_image === 32)
         return '32';
     else
         return "";
@@ -76,13 +76,13 @@ class ImageFormatSettings extends Component<MyProps, MyState> {
     }
 
     raw = () => {
-        DefaultService.postConfigImageFormatRaw()
+        postConfigImageFormatRaw({ throwOnError: true })
             .catch(error => console.log(error) );
         this.getValues();
     }
 
     conv = () => {
-        DefaultService.postConfigImageFormatConversion()
+        postConfigImageFormatConversion({ throwOnError: true })
             .catch(error => console.log(error) );
         this.getValues();
     }
@@ -90,7 +90,7 @@ class ImageFormatSettings extends Component<MyProps, MyState> {
     uploadButton = () => { this.putValues(); }
 
     putValues = () => {
-        DefaultService.putConfigImageFormat(this.state.s)
+        putConfigImageFormat({ body: this.state.s, throwOnError: true })
             .catch(error => console.log(error) );
     }
 
@@ -122,16 +122,16 @@ class ImageFormatSettings extends Component<MyProps, MyState> {
     }
 
     handleBitWidthChange = (event: SelectChangeEvent) => {
-        let val: image_format_settings.bit_depth_image|undefined = undefined;
+        let val: image_format_settings['bit_depth_image'] = undefined;
 
         if (event.target.value === "a")
             val = undefined;
         else if (event.target.value === "8")
-            val = image_format_settings.bit_depth_image._8;
+            val = 8;
         else if (event.target.value === "16")
-            val = image_format_settings.bit_depth_image._16;
+            val = 16;
         else if (event.target.value === "32")
-            val = image_format_settings.bit_depth_image._32;
+            val = 32;
 
         this.setState(prevState => ({
             bit_width_selection: event.target.value,
diff --git a/frontend/src/components/ImagePusherStatus.tsx b/frontend/src/components/ImagePusherStatus.tsx
index c39b43e7..d28633e5 100644
--- a/frontend/src/components/ImagePusherStatus.tsx
+++ b/frontend/src/components/ImagePusherStatus.tsx
@@ -6,7 +6,7 @@
 import React, {Component} from 'react';
 import Paper from '@mui/material/Paper';
 import {Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
-import {image_pusher_status, image_pusher_type} from "../openapi";
+import {image_pusher_status, image_pusher_type} from "../client";
 
 type MyProps = {
     s?: image_pusher_status
diff --git a/frontend/src/components/IndexingSettings.tsx b/frontend/src/components/IndexingSettings.tsx
index 08a1f1d3..5859146a 100644
--- a/frontend/src/components/IndexingSettings.tsx
+++ b/frontend/src/components/IndexingSettings.tsx
@@ -6,7 +6,7 @@ import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
-import {broker_status, geom_refinement_algorithm, indexing_algorithm, indexing_settings} from "../openapi";
+import {broker_status, geom_refinement_algorithm, indexing_algorithm, indexing_settings} from "../client";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
diff --git a/frontend/src/components/InstrumentMetadata.tsx b/frontend/src/components/InstrumentMetadata.tsx
index 99f438d8..661e1786 100644
--- a/frontend/src/components/InstrumentMetadata.tsx
+++ b/frontend/src/components/InstrumentMetadata.tsx
@@ -8,7 +8,7 @@ import {
     TextField
 } from "@mui/material";
 import Paper from "@mui/material/Paper";
-import {instrument_metadata} from "../openapi";
+import {instrument_metadata} from "../client";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 
diff --git a/frontend/src/components/MeasurementStatistics.tsx b/frontend/src/components/MeasurementStatistics.tsx
index eac52f88..28bc8736 100644
--- a/frontend/src/components/MeasurementStatistics.tsx
+++ b/frontend/src/components/MeasurementStatistics.tsx
@@ -2,7 +2,7 @@ import React, {Component} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Grid, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
-import {DefaultService, measurement_statistics} from "../openapi";
+import {measurement_statistics} from "../client";
 
 type MyProps = {
     s: measurement_statistics,
diff --git a/frontend/src/components/PixelMask.tsx b/frontend/src/components/PixelMask.tsx
index 82b64f5a..7130fabd 100644
--- a/frontend/src/components/PixelMask.tsx
+++ b/frontend/src/components/PixelMask.tsx
@@ -9,7 +9,7 @@ import {
     TableContainer,
     TableRow, TextField
 } from "@mui/material";
-import {DefaultService, pixel_mask_statistics} from "../openapi";
+import {putConfigUserMaskTiff, pixel_mask_statistics} from "../client";
 import Button from "@mui/material/Button";
 
 type MyProps = {
@@ -25,7 +25,7 @@ class PixelMask extends React.Component<MyProps, MyState> {
 
     handleUpload = () => {
         if (this.state.file)
-            DefaultService.putConfigUserMaskTiff(this.state.file);
+            putConfigUserMaskTiff({ body: this.state.file });
     };
 
     handleFileChange = (event: React.ChangeEvent<HTMLInputElement>) => {
diff --git a/frontend/src/components/PreviewImage.tsx b/frontend/src/components/PreviewImage.tsx
index 8c7c7da0..11d193bb 100644
--- a/frontend/src/components/PreviewImage.tsx
+++ b/frontend/src/components/PreviewImage.tsx
@@ -12,7 +12,7 @@ import {
     Stack
 } from "@mui/material";
 import {TransformComponent, TransformWrapper} from "react-zoom-pan-pinch";
-import {color_scale} from "../openapi";
+import {color_scale} from "../client";
 import InputLabel from "@mui/material/InputLabel";
 import MenuItem from "@mui/material/MenuItem";
 import FormControl from "@mui/material/FormControl";
diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index b8c13b13..76c7b754 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -2,13 +2,13 @@ import React from 'react';
 
 import Paper from '@mui/material/Paper';
 import {
-    DefaultService,
+    putConfigRoi,
     instrument_metadata,
     pixel_mask_statistics, roi_azimuthal,
     roi_box,
     roi_circle,
     roi_definitions
-} from "../openapi";
+} from "../client";
 import {Grid, Typography} from "@mui/material";
 import Button from "@mui/material/Button";
 import {DataGrid, GridActionsCellItem, GridColDef, GridRowModel} from "@mui/x-data-grid";
@@ -222,7 +222,7 @@ class ROI extends React.Component<MyProps, MyState> {
     }
 
     putValues = () => {
-        DefaultService.putConfigRoi(this.roiStruct()).catch(error => {} );
+        putConfigRoi({ body: this.roiStruct(), throwOnError: true }).catch(error => {} );
     }
 
 
diff --git a/frontend/src/components/StatusBar.tsx b/frontend/src/components/StatusBar.tsx
index cd4c996c..fd651bfc 100644
--- a/frontend/src/components/StatusBar.tsx
+++ b/frontend/src/components/StatusBar.tsx
@@ -3,9 +3,8 @@ import React, {Component} from 'react';
 import AppBar from '@mui/material/AppBar';
 import Toolbar from '@mui/material/Toolbar';
 import Typography from '@mui/material/Typography';
-import {broker_status} from "../openapi";
+import {broker_status} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
-import state = broker_status.state;
 import { ReactNode } from "react";
 
 type MyProps = {
@@ -52,7 +51,7 @@ class StatusBar extends Component<MyProps, MyState> {
                     text={"Pedestal"}
                     path={"/pedestal"}
                     color={"secondary"}
-                    disabled={(this.props.s === undefined) || (this.props.s.state !== state.IDLE)}
+                    disabled={(this.props.s === undefined) || (this.props.s.state !== 'Idle')}
                 />&nbsp;&nbsp;
                 <ButtonWithSnackbar
                     text={"Cancel"}
diff --git a/frontend/src/components/ZeroMQPreview.tsx b/frontend/src/components/ZeroMQPreview.tsx
index c61a00e8..268011e7 100644
--- a/frontend/src/components/ZeroMQPreview.tsx
+++ b/frontend/src/components/ZeroMQPreview.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 import Paper from '@mui/material/Paper';
 import {FormControlLabel, Radio, RadioGroup, Stack} from "@mui/material";
 import NumberTextField from "./NumberTextField";
-import {zeromq_preview_settings} from "../openapi";
+import {zeromq_preview_settings} from "../client";
 import _ from "lodash";
 import FormControl from "@mui/material/FormControl";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
diff --git a/frontend/src/openapi/core/ApiError.ts b/frontend/src/openapi/core/ApiError.ts
deleted file mode 100644
index d6b8fcc3..00000000
--- a/frontend/src/openapi/core/ApiError.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-import type { ApiRequestOptions } from './ApiRequestOptions';
-import type { ApiResult } from './ApiResult';
-
-export class ApiError extends Error {
-    public readonly url: string;
-    public readonly status: number;
-    public readonly statusText: string;
-    public readonly body: any;
-    public readonly request: ApiRequestOptions;
-
-    constructor(request: ApiRequestOptions, response: ApiResult, message: string) {
-        super(message);
-
-        this.name = 'ApiError';
-        this.url = response.url;
-        this.status = response.status;
-        this.statusText = response.statusText;
-        this.body = response.body;
-        this.request = request;
-    }
-}
diff --git a/frontend/src/openapi/core/ApiRequestOptions.ts b/frontend/src/openapi/core/ApiRequestOptions.ts
deleted file mode 100644
index c19adcc9..00000000
--- a/frontend/src/openapi/core/ApiRequestOptions.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-export type ApiRequestOptions = {
-    readonly method: 'GET' | 'PUT' | 'POST' | 'DELETE' | 'OPTIONS' | 'HEAD' | 'PATCH';
-    readonly url: string;
-    readonly path?: Record<string, any>;
-    readonly cookies?: Record<string, any>;
-    readonly headers?: Record<string, any>;
-    readonly query?: Record<string, any>;
-    readonly formData?: Record<string, any>;
-    readonly body?: any;
-    readonly mediaType?: string;
-    readonly responseHeader?: string;
-    readonly errors?: Record<number, string>;
-};
diff --git a/frontend/src/openapi/core/ApiResult.ts b/frontend/src/openapi/core/ApiResult.ts
deleted file mode 100644
index ad8fef2b..00000000
--- a/frontend/src/openapi/core/ApiResult.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-export type ApiResult = {
-    readonly url: string;
-    readonly ok: boolean;
-    readonly status: number;
-    readonly statusText: string;
-    readonly body: any;
-};
diff --git a/frontend/src/openapi/core/CancelablePromise.ts b/frontend/src/openapi/core/CancelablePromise.ts
deleted file mode 100644
index 55fef851..00000000
--- a/frontend/src/openapi/core/CancelablePromise.ts
+++ /dev/null
@@ -1,131 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-export class CancelError extends Error {
-
-    constructor(message: string) {
-        super(message);
-        this.name = 'CancelError';
-    }
-
-    public get isCancelled(): boolean {
-        return true;
-    }
-}
-
-export interface OnCancel {
-    readonly isResolved: boolean;
-    readonly isRejected: boolean;
-    readonly isCancelled: boolean;
-
-    (cancelHandler: () => void): void;
-}
-
-export class CancelablePromise<T> implements Promise<T> {
-    #isResolved: boolean;
-    #isRejected: boolean;
-    #isCancelled: boolean;
-    readonly #cancelHandlers: (() => void)[];
-    readonly #promise: Promise<T>;
-    #resolve?: (value: T | PromiseLike<T>) => void;
-    #reject?: (reason?: any) => void;
-
-    constructor(
-        executor: (
-            resolve: (value: T | PromiseLike<T>) => void,
-            reject: (reason?: any) => void,
-            onCancel: OnCancel
-        ) => void
-    ) {
-        this.#isResolved = false;
-        this.#isRejected = false;
-        this.#isCancelled = false;
-        this.#cancelHandlers = [];
-        this.#promise = new Promise<T>((resolve, reject) => {
-            this.#resolve = resolve;
-            this.#reject = reject;
-
-            const onResolve = (value: T | PromiseLike<T>): void => {
-                if (this.#isResolved || this.#isRejected || this.#isCancelled) {
-                    return;
-                }
-                this.#isResolved = true;
-                this.#resolve?.(value);
-            };
-
-            const onReject = (reason?: any): void => {
-                if (this.#isResolved || this.#isRejected || this.#isCancelled) {
-                    return;
-                }
-                this.#isRejected = true;
-                this.#reject?.(reason);
-            };
-
-            const onCancel = (cancelHandler: () => void): void => {
-                if (this.#isResolved || this.#isRejected || this.#isCancelled) {
-                    return;
-                }
-                this.#cancelHandlers.push(cancelHandler);
-            };
-
-            Object.defineProperty(onCancel, 'isResolved', {
-                get: (): boolean => this.#isResolved,
-            });
-
-            Object.defineProperty(onCancel, 'isRejected', {
-                get: (): boolean => this.#isRejected,
-            });
-
-            Object.defineProperty(onCancel, 'isCancelled', {
-                get: (): boolean => this.#isCancelled,
-            });
-
-            return executor(onResolve, onReject, onCancel as OnCancel);
-        });
-    }
-
-     get [Symbol.toStringTag]() {
-            return "Cancellable Promise";
-     }
-
-    public then<TResult1 = T, TResult2 = never>(
-        onFulfilled?: ((value: T) => TResult1 | PromiseLike<TResult1>) | null,
-        onRejected?: ((reason: any) => TResult2 | PromiseLike<TResult2>) | null
-    ): Promise<TResult1 | TResult2> {
-        return this.#promise.then(onFulfilled, onRejected);
-    }
-
-    public catch<TResult = never>(
-        onRejected?: ((reason: any) => TResult | PromiseLike<TResult>) | null
-    ): Promise<T | TResult> {
-        return this.#promise.catch(onRejected);
-    }
-
-    public finally(onFinally?: (() => void) | null): Promise<T> {
-        return this.#promise.finally(onFinally);
-    }
-
-    public cancel(): void {
-        if (this.#isResolved || this.#isRejected || this.#isCancelled) {
-            return;
-        }
-        this.#isCancelled = true;
-        if (this.#cancelHandlers.length) {
-            try {
-                for (const cancelHandler of this.#cancelHandlers) {
-                    cancelHandler();
-                }
-            } catch (error) {
-                console.warn('Cancellation threw an error', error);
-                return;
-            }
-        }
-        this.#cancelHandlers.length = 0;
-        this.#reject?.(new CancelError('Request aborted'));
-    }
-
-    public get isCancelled(): boolean {
-        return this.#isCancelled;
-    }
-}
diff --git a/frontend/src/openapi/core/OpenAPI.ts b/frontend/src/openapi/core/OpenAPI.ts
deleted file mode 100644
index 104efe50..00000000
--- a/frontend/src/openapi/core/OpenAPI.ts
+++ /dev/null
@@ -1,32 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-import type { ApiRequestOptions } from './ApiRequestOptions';
-
-type Resolver<T> = (options: ApiRequestOptions) => Promise<T>;
-type Headers = Record<string, string>;
-
-export type OpenAPIConfig = {
-    BASE: string;
-    VERSION: string;
-    WITH_CREDENTIALS: boolean;
-    CREDENTIALS: 'include' | 'omit' | 'same-origin';
-    TOKEN?: string | Resolver<string> | undefined;
-    USERNAME?: string | Resolver<string> | undefined;
-    PASSWORD?: string | Resolver<string> | undefined;
-    HEADERS?: Headers | Resolver<Headers> | undefined;
-    ENCODE_PATH?: ((path: string) => string) | undefined;
-};
-
-export const OpenAPI: OpenAPIConfig = {
-    BASE: 'http://localhost:5232',
-    VERSION: '1.0.0-rc.153',
-    WITH_CREDENTIALS: false,
-    CREDENTIALS: 'include',
-    TOKEN: undefined,
-    USERNAME: undefined,
-    PASSWORD: undefined,
-    HEADERS: undefined,
-    ENCODE_PATH: undefined,
-};
diff --git a/frontend/src/openapi/core/request.ts b/frontend/src/openapi/core/request.ts
deleted file mode 100644
index b018a07c..00000000
--- a/frontend/src/openapi/core/request.ts
+++ /dev/null
@@ -1,320 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-import { ApiError } from './ApiError';
-import type { ApiRequestOptions } from './ApiRequestOptions';
-import type { ApiResult } from './ApiResult';
-import { CancelablePromise } from './CancelablePromise';
-import type { OnCancel } from './CancelablePromise';
-import type { OpenAPIConfig } from './OpenAPI';
-
-export const isDefined = <T>(value: T | null | undefined): value is Exclude<T, null | undefined> => {
-    return value !== undefined && value !== null;
-};
-
-export const isString = (value: any): value is string => {
-    return typeof value === 'string';
-};
-
-export const isStringWithValue = (value: any): value is string => {
-    return isString(value) && value !== '';
-};
-
-export const isBlob = (value: any): value is Blob => {
-    return (
-        typeof value === 'object' &&
-        typeof value.type === 'string' &&
-        typeof value.stream === 'function' &&
-        typeof value.arrayBuffer === 'function' &&
-        typeof value.constructor === 'function' &&
-        typeof value.constructor.name === 'string' &&
-        /^(Blob|File)$/.test(value.constructor.name) &&
-        /^(Blob|File)$/.test(value[Symbol.toStringTag])
-    );
-};
-
-export const isFormData = (value: any): value is FormData => {
-    return value instanceof FormData;
-};
-
-export const base64 = (str: string): string => {
-    try {
-        return btoa(str);
-    } catch (err) {
-        // @ts-ignore
-        return Buffer.from(str).toString('base64');
-    }
-};
-
-export const getQueryString = (params: Record<string, any>): string => {
-    const qs: string[] = [];
-
-    const append = (key: string, value: any) => {
-        qs.push(`${encodeURIComponent(key)}=${encodeURIComponent(String(value))}`);
-    };
-
-    const process = (key: string, value: any) => {
-        if (isDefined(value)) {
-            if (Array.isArray(value)) {
-                value.forEach(v => {
-                    process(key, v);
-                });
-            } else if (typeof value === 'object') {
-                Object.entries(value).forEach(([k, v]) => {
-                    process(`${key}[${k}]`, v);
-                });
-            } else {
-                append(key, value);
-            }
-        }
-    };
-
-    Object.entries(params).forEach(([key, value]) => {
-        process(key, value);
-    });
-
-    if (qs.length > 0) {
-        return `?${qs.join('&')}`;
-    }
-
-    return '';
-};
-
-const getUrl = (config: OpenAPIConfig, options: ApiRequestOptions): string => {
-    const encoder = config.ENCODE_PATH || encodeURI;
-
-    const path = options.url
-        .replace('{api-version}', config.VERSION)
-        .replace(/{(.*?)}/g, (substring: string, group: string) => {
-            if (options.path?.hasOwnProperty(group)) {
-                return encoder(String(options.path[group]));
-            }
-            return substring;
-        });
-
-    const url = `${config.BASE}${path}`;
-    if (options.query) {
-        return `${url}${getQueryString(options.query)}`;
-    }
-    return url;
-};
-
-export const getFormData = (options: ApiRequestOptions): FormData | undefined => {
-    if (options.formData) {
-        const formData = new FormData();
-
-        const process = (key: string, value: any) => {
-            if (isString(value) || isBlob(value)) {
-                formData.append(key, value);
-            } else {
-                formData.append(key, JSON.stringify(value));
-            }
-        };
-
-        Object.entries(options.formData)
-            .filter(([_, value]) => isDefined(value))
-            .forEach(([key, value]) => {
-                if (Array.isArray(value)) {
-                    value.forEach(v => process(key, v));
-                } else {
-                    process(key, value);
-                }
-            });
-
-        return formData;
-    }
-    return undefined;
-};
-
-type Resolver<T> = (options: ApiRequestOptions) => Promise<T>;
-
-export const resolve = async <T>(options: ApiRequestOptions, resolver?: T | Resolver<T>): Promise<T | undefined> => {
-    if (typeof resolver === 'function') {
-        return (resolver as Resolver<T>)(options);
-    }
-    return resolver;
-};
-
-export const getHeaders = async (config: OpenAPIConfig, options: ApiRequestOptions): Promise<Headers> => {
-    const token = await resolve(options, config.TOKEN);
-    const username = await resolve(options, config.USERNAME);
-    const password = await resolve(options, config.PASSWORD);
-    const additionalHeaders = await resolve(options, config.HEADERS);
-
-    const headers = Object.entries({
-        Accept: 'application/json',
-        ...additionalHeaders,
-        ...options.headers,
-    })
-        .filter(([_, value]) => isDefined(value))
-        .reduce((headers, [key, value]) => ({
-            ...headers,
-            [key]: String(value),
-        }), {} as Record<string, string>);
-
-    if (isStringWithValue(token)) {
-        headers['Authorization'] = `Bearer ${token}`;
-    }
-
-    if (isStringWithValue(username) && isStringWithValue(password)) {
-        const credentials = base64(`${username}:${password}`);
-        headers['Authorization'] = `Basic ${credentials}`;
-    }
-
-    if (options.body) {
-        if (options.mediaType) {
-            headers['Content-Type'] = options.mediaType;
-        } else if (isBlob(options.body)) {
-            headers['Content-Type'] = options.body.type || 'application/octet-stream';
-        } else if (isString(options.body)) {
-            headers['Content-Type'] = 'text/plain';
-        } else if (!isFormData(options.body)) {
-            headers['Content-Type'] = 'application/json';
-        }
-    }
-
-    return new Headers(headers);
-};
-
-export const getRequestBody = (options: ApiRequestOptions): any => {
-    if (options.body !== undefined) {
-        if (options.mediaType?.includes('/json')) {
-            return JSON.stringify(options.body)
-        } else if (isString(options.body) || isBlob(options.body) || isFormData(options.body)) {
-            return options.body;
-        } else {
-            return JSON.stringify(options.body);
-        }
-    }
-    return undefined;
-};
-
-export const sendRequest = async (
-    config: OpenAPIConfig,
-    options: ApiRequestOptions,
-    url: string,
-    body: any,
-    formData: FormData | undefined,
-    headers: Headers,
-    onCancel: OnCancel
-): Promise<Response> => {
-    const controller = new AbortController();
-
-    const request: RequestInit = {
-        headers,
-        body: body ?? formData,
-        method: options.method,
-        signal: controller.signal,
-    };
-
-    if (config.WITH_CREDENTIALS) {
-        request.credentials = config.CREDENTIALS;
-    }
-
-    onCancel(() => controller.abort());
-
-    return await fetch(url, request);
-};
-
-export const getResponseHeader = (response: Response, responseHeader?: string): string | undefined => {
-    if (responseHeader) {
-        const content = response.headers.get(responseHeader);
-        if (isString(content)) {
-            return content;
-        }
-    }
-    return undefined;
-};
-
-export const getResponseBody = async (response: Response): Promise<any> => {
-    if (response.status !== 204) {
-        try {
-            const contentType = response.headers.get('Content-Type');
-            if (contentType) {
-                const jsonTypes = ['application/json', 'application/problem+json']
-                const isJSON = jsonTypes.some(type => contentType.toLowerCase().startsWith(type));
-                if (isJSON) {
-                    return await response.json();
-                } else {
-                    return await response.text();
-                }
-            }
-        } catch (error) {
-            console.error(error);
-        }
-    }
-    return undefined;
-};
-
-export const catchErrorCodes = (options: ApiRequestOptions, result: ApiResult): void => {
-    const errors: Record<number, string> = {
-        400: 'Bad Request',
-        401: 'Unauthorized',
-        403: 'Forbidden',
-        404: 'Not Found',
-        500: 'Internal Server Error',
-        502: 'Bad Gateway',
-        503: 'Service Unavailable',
-        ...options.errors,
-    }
-
-    const error = errors[result.status];
-    if (error) {
-        throw new ApiError(options, result, error);
-    }
-
-    if (!result.ok) {
-        const errorStatus = result.status ?? 'unknown';
-        const errorStatusText = result.statusText ?? 'unknown';
-        const errorBody = (() => {
-            try {
-                return JSON.stringify(result.body, null, 2);
-            } catch (e) {
-                return undefined;
-            }
-        })();
-
-        throw new ApiError(options, result,
-            `Generic Error: status: ${errorStatus}; status text: ${errorStatusText}; body: ${errorBody}`
-        );
-    }
-};
-
-/**
- * Request method
- * @param config The OpenAPI configuration object
- * @param options The request options from the service
- * @returns CancelablePromise<T>
- * @throws ApiError
- */
-export const request = <T>(config: OpenAPIConfig, options: ApiRequestOptions): CancelablePromise<T> => {
-    return new CancelablePromise(async (resolve, reject, onCancel) => {
-        try {
-            const url = getUrl(config, options);
-            const formData = getFormData(options);
-            const body = getRequestBody(options);
-            const headers = await getHeaders(config, options);
-
-            if (!onCancel.isCancelled) {
-                const response = await sendRequest(config, options, url, body, formData, headers, onCancel);
-                const responseBody = await getResponseBody(response);
-                const responseHeader = getResponseHeader(response, options.responseHeader);
-
-                const result: ApiResult = {
-                    url,
-                    ok: response.ok,
-                    status: response.status,
-                    statusText: response.statusText,
-                    body: responseHeader ?? responseBody,
-                };
-
-                catchErrorCodes(options, result);
-
-                resolve(result.body);
-            }
-        } catch (error) {
-            reject(error);
-        }
-    });
-};
diff --git a/frontend/src/openapi/index.ts b/frontend/src/openapi/index.ts
deleted file mode 100644
index e0bd0a1c..00000000
--- a/frontend/src/openapi/index.ts
+++ /dev/null
@@ -1,83 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-export { ApiError } from './core/ApiError';
-export { CancelablePromise, CancelError } from './core/CancelablePromise';
-export { OpenAPI } from './core/OpenAPI';
-export type { OpenAPIConfig } from './core/OpenAPI';
-
-export type { azim_int_settings } from './models/azim_int_settings';
-export { azint_unit } from './models/azint_unit';
-export type { background } from './models/background';
-export type { binning } from './models/binning';
-export { broker_status } from './models/broker_status';
-export type { calibration_statistics } from './models/calibration_statistics';
-export { color_scale } from './models/color_scale';
-export type { crystal_lattice } from './models/crystal_lattice';
-export type { dark_mask_settings } from './models/dark_mask_settings';
-export { dataset_settings } from './models/dataset_settings';
-export type { detector } from './models/detector';
-export type { detector_list } from './models/detector_list';
-export type { detector_list_element } from './models/detector_list_element';
-export type { detector_module } from './models/detector_module';
-export { detector_module_direction } from './models/detector_module_direction';
-export { detector_power_state } from './models/detector_power_state';
-export type { detector_selection } from './models/detector_selection';
-export { detector_settings } from './models/detector_settings';
-export { detector_state } from './models/detector_state';
-export type { detector_status } from './models/detector_status';
-export { detector_timing } from './models/detector_timing';
-export { detector_type } from './models/detector_type';
-export { error_message } from './models/error_message';
-export type { experimental_coord } from './models/experimental_coord';
-export { file_writer_format } from './models/file_writer_format';
-export type { file_writer_settings } from './models/file_writer_settings';
-export type { fill_value } from './models/fill_value';
-export type { fpga_status } from './models/fpga_status';
-export { geom_refinement_algorithm } from './models/geom_refinement_algorithm';
-export type { grid_scan } from './models/grid_scan';
-export type { image_buffer_status } from './models/image_buffer_status';
-export { image_format_settings } from './models/image_format_settings';
-export type { image_id } from './models/image_id';
-export type { image_pusher_status } from './models/image_pusher_status';
-export { image_pusher_type } from './models/image_pusher_type';
-export { indexing_algorithm } from './models/indexing_algorithm';
-export type { indexing_settings } from './models/indexing_settings';
-export type { instrument_metadata } from './models/instrument_metadata';
-export type { jfjoch_settings } from './models/jfjoch_settings';
-export type { jfjoch_statistics } from './models/jfjoch_statistics';
-export type { jpeg_quality } from './models/jpeg_quality';
-export { measurement_statistics } from './models/measurement_statistics';
-export type { pcie_devices } from './models/pcie_devices';
-export type { pixel_mask_statistics } from './models/pixel_mask_statistics';
-export type { plot } from './models/plot';
-export { plot_type } from './models/plot_type';
-export { plot_unit_x } from './models/plot_unit_x';
-export type { plots } from './models/plots';
-export type { resolution_estimate } from './models/resolution_estimate';
-export type { resolution_ring } from './models/resolution_ring';
-export type { roi } from './models/roi';
-export type { roi_azim_list } from './models/roi_azim_list';
-export type { roi_azimuthal } from './models/roi_azimuthal';
-export type { roi_box } from './models/roi_box';
-export type { roi_box_list } from './models/roi_box_list';
-export type { roi_circle } from './models/roi_circle';
-export type { roi_circle_list } from './models/roi_circle_list';
-export type { roi_definitions } from './models/roi_definitions';
-export type { rotation_axis } from './models/rotation_axis';
-export type { saturation } from './models/saturation';
-export type { scan_result } from './models/scan_result';
-export type { show_beam_center } from './models/show_beam_center';
-export type { show_roi } from './models/show_roi';
-export type { show_spots } from './models/show_spots';
-export type { show_user_mask } from './models/show_user_mask';
-export type { spot_finding_settings } from './models/spot_finding_settings';
-export type { standard_detector_geometry } from './models/standard_detector_geometry';
-export type { tcp_settings } from './models/tcp_settings';
-export type { unit_cell } from './models/unit_cell';
-export type { zeromq_metadata_settings } from './models/zeromq_metadata_settings';
-export type { zeromq_preview_settings } from './models/zeromq_preview_settings';
-export type { zeromq_settings } from './models/zeromq_settings';
-
-export { DefaultService } from './services/DefaultService';
diff --git a/frontend/src/openapi/models/azim_int_settings.ts b/frontend/src/openapi/models/azim_int_settings.ts
deleted file mode 100644
index e794beff..00000000
--- a/frontend/src/openapi/models/azim_int_settings.ts
+++ /dev/null
@@ -1,30 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type azim_int_settings = {
-    /**
-     * Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)
-     */
-    polarization_corr: boolean;
-    /**
-     * Apply solid angle correction for azimuthal integration
-     */
-    solid_angle_corr: boolean;
-    high_q_recipA: number;
-    low_q_recipA: number;
-    q_spacing: number;
-    /**
-     * Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration
-     */
-    azimuthal_bins?: number;
-    /**
-     * Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.
-     * This allows to extend number of azimuthal integration bins, as well as to calculate standard deviation
-     * of the azimuthal integration results.
-     *
-     */
-    force_cpu?: boolean;
-};
-
diff --git a/frontend/src/openapi/models/azint_unit.ts b/frontend/src/openapi/models/azint_unit.ts
deleted file mode 100644
index ebd2abbd..00000000
--- a/frontend/src/openapi/models/azint_unit.ts
+++ /dev/null
@@ -1,14 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Unit used for azim int.
- *
- */
-export enum azint_unit {
-    Q_RECIP_A = 'Q_recipA',
-    D_A = 'd_A',
-    TWO_THETA_DEG = 'two_theta_deg',
-}
diff --git a/frontend/src/openapi/models/background.ts b/frontend/src/openapi/models/background.ts
deleted file mode 100644
index 91e0ed23..00000000
--- a/frontend/src/openapi/models/background.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Background value to set contrast in the preview image
- */
-export type background = number;
diff --git a/frontend/src/openapi/models/binning.ts b/frontend/src/openapi/models/binning.ts
deleted file mode 100644
index 8b6d3bd4..00000000
--- a/frontend/src/openapi/models/binning.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Binning of frames for the plot (0 = default binning)
- */
-export type binning = number;
diff --git a/frontend/src/openapi/models/broker_status.ts b/frontend/src/openapi/models/broker_status.ts
deleted file mode 100644
index e8f1755f..00000000
--- a/frontend/src/openapi/models/broker_status.ts
+++ /dev/null
@@ -1,56 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type broker_status = {
-    state: broker_status.state;
-    /**
-     * Progress of data collection (only available if receiving is running)
-     */
-    progress?: number;
-    /**
-     * Message to display besides state of the jfjoch_broker; mostly used for errors and warnings
-     * This matters especially for async functions (start/initialize), where API won't return reason
-     * for the error during async operation.
-     *
-     */
-    message?: string;
-    /**
-     * Level of the message to display
-     */
-    message_severity?: broker_status.message_severity;
-    /**
-     * Number of installed GPUs
-     */
-    gpu_count?: number;
-    /**
-     * Version of the jfjoch_broker
-     */
-    broker_version?: string;
-};
-
-export namespace broker_status {
-
-    export enum state {
-        INACTIVE = 'Inactive',
-        IDLE = 'Idle',
-        BUSY = 'Busy',
-        MEASURING = 'Measuring',
-        PEDESTAL = 'Pedestal',
-        ERROR = 'Error',
-    }
-
-    /**
-     * Level of the message to display
-     */
-    export enum message_severity {
-        SUCCESS = 'success',
-        INFO = 'info',
-        WARNING = 'warning',
-        ERROR = 'error',
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/calibration_statistics.ts b/frontend/src/openapi/models/calibration_statistics.ts
deleted file mode 100644
index 7053e5bb..00000000
--- a/frontend/src/openapi/models/calibration_statistics.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type calibration_statistics = Array<{
-    module_number: number;
-    storage_cell_number: number;
-    pedestal_g0_mean: number;
-    pedestal_g1_mean: number;
-    pedestal_g2_mean: number;
-    gain_g0_mean: number;
-    gain_g1_mean: number;
-    gain_g2_mean: number;
-    masked_pixels: number;
-}>;
diff --git a/frontend/src/openapi/models/color_scale.ts b/frontend/src/openapi/models/color_scale.ts
deleted file mode 100644
index e7312ed2..00000000
--- a/frontend/src/openapi/models/color_scale.ts
+++ /dev/null
@@ -1,18 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Color scale for preview image
- */
-export enum color_scale {
-    INDIGO = 'indigo',
-    VIRIDIS = 'viridis',
-    BW = 'bw',
-    WB = 'wb',
-    GREEN = 'green',
-    HEAT = 'heat',
-    MAGMA = 'magma',
-    INFERNO = 'inferno',
-}
diff --git a/frontend/src/openapi/models/crystal_lattice.ts b/frontend/src/openapi/models/crystal_lattice.ts
deleted file mode 100644
index c8af6597..00000000
--- a/frontend/src/openapi/models/crystal_lattice.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Real-space crystal lattice 3D vectors in Angstrom.
- * Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)
- *
- */
-export type crystal_lattice = Array<number>;
diff --git a/frontend/src/openapi/models/dark_mask_settings.ts b/frontend/src/openapi/models/dark_mask_settings.ts
deleted file mode 100644
index 5fcde121..00000000
--- a/frontend/src/openapi/models/dark_mask_settings.ts
+++ /dev/null
@@ -1,31 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Settings for collection of dark images to be used for mask calculation
- */
-export type dark_mask_settings = {
-    /**
-     * Energy threshold for dark image collection
-     */
-    detector_threshold_keV: number;
-    /**
-     * Time between frames for dark image collection
-     */
-    frame_time_us: number;
-    /**
-     * Number of frames for dark image collection; zero means no dark collection
-     */
-    number_of_frames: number;
-    /**
-     * Maximum count in a pixel considered normal (not-masked)
-     */
-    max_allowed_pixel_count: number;
-    /**
-     * Maximum number of frames with signal in a pixel considered normal (not-masked)
-     */
-    max_frames_with_signal: number;
-};
-
diff --git a/frontend/src/openapi/models/dataset_settings.ts b/frontend/src/openapi/models/dataset_settings.ts
deleted file mode 100644
index 81d0dbe9..00000000
--- a/frontend/src/openapi/models/dataset_settings.ts
+++ /dev/null
@@ -1,231 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { grid_scan } from './grid_scan';
-import type { rotation_axis } from './rotation_axis';
-import type { unit_cell } from './unit_cell';
-
-export type dataset_settings = {
-    /**
-     * For standard synchrotron data collection - this is number of images collected per one TTL trigger
-     * For XFEL (pulsed source) - this number is ignored and set to 1
-     * For storage cell mode - this number is ignored and set to number of storage cells
-     *
-     */
-    images_per_trigger?: number;
-    /**
-     * Number of TTL trigger that the detector is expected to receive during data collection
-     *
-     */
-    ntrigger?: number;
-    /**
-     * Image time.
-     * If not provided (or zero value) the frame time is assumed as default.
-     * For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.
-     * In XFEL mode: summation happens for frames collected with multiple triggers.
-     * Ignored for storage cells and if raw data are saved.
-     *
-     */
-    image_time_us?: number;
-    /**
-     * /entry/detector/beam_center_x in NXmx
-     * Beam center in X direction [pixels]
-     *
-     */
-    beam_x_pxl: number;
-    /**
-     * /entry/detector/beam_center_y in NXmx
-     * Beam center in X direction [pixels]
-     *
-     */
-    beam_y_pxl: number;
-    /**
-     * /entry/detector/distance in NXmx Detector distance [mm]
-     */
-    detector_distance_mm: number;
-    /**
-     * Used to calculate /entry/beam/incident_wavelength in NXmx
-     * Incident particle (photon, electron) energy in keV
-     *
-     */
-    incident_energy_keV: number;
-    /**
-     * Prefix for filenames. If left empty, no file will be saved.
-     */
-    file_prefix?: string;
-    /**
-     * Number of files in a single HDF5 data file (0 = write all images to a single data file).
-     */
-    images_per_file?: number;
-    /**
-     * Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.
-     */
-    space_group_number?: number;
-    /**
-     * /entry/sample/name in NXmx
-     * Sample name
-     *
-     */
-    sample_name?: string;
-    /**
-     * Compression type for the images transferred over ZeroMQ and saved to HDF5 file.
-     *
-     */
-    compression?: dataset_settings.compression;
-    /**
-     * /entry/beam/total_flux in NXmx
-     * Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]
-     *
-     */
-    total_flux?: number;
-    /**
-     * /entry/instrument/attenuator/attenuator_transmission
-     * Transmission of attenuator (filter) [no units]
-     *
-     */
-    transmission?: number;
-    goniometer?: rotation_axis;
-    grid_scan?: grid_scan;
-    /**
-     * Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
-     * In general, it is not saved in HDF5 file.
-     *
-     * However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file.
-     * This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
-     * For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.
-     *
-     */
-    header_appendix?: any;
-    /**
-     * Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)
-     * Not saved in HDF5 file
-     *
-     */
-    image_appendix?: any;
-    /**
-     * Rate at which non-indexed images are accepted to be forwarded to writer.
-     * Value of 1.0 (default) means that all images are written.
-     * Values below zero mean that non-indexed images will be accepted with a given probability.
-     *
-     */
-    data_reduction_factor_serialmx?: number;
-    /**
-     * Set all counts lower than the value to zero.
-     * When the value is set, negative numbers other than error pixel value are always set to zero.
-     * Setting to zero is equivalent to turning the option off.
-     *
-     */
-    pixel_value_low_threshold?: number;
-    /**
-     * Number of run within an experimental session.
-     * Transferred over CBOR stream as "series ID", though not saved in HDF5 file.
-     * It is highly recommended to keep this number unique for each data collection during experimental series.
-     * If not provided, the number will be automatically incremented.
-     *
-     */
-    run_number?: number;
-    /**
-     * Unique ID of run.
-     * Transferred over CBOR stream as "unique series ID", though not saved in HDF5 file.
-     * It is highly recommended to keep this name unique for each data collection during experimental series.
-     * If not provided, the name will be automatically generated as number + colon + file_prefix.
-     *
-     */
-    run_name?: string;
-    /**
-     * Name of group owning the data (e.g. p-group or proposal number).
-     * Transferred over CBOR stream, though not saved in HDF5 file.
-     *
-     */
-    experiment_group?: string;
-    /**
-     * Enable lossy compression of pixel values that preserves Poisson statistics.
-     * Requires to provide a numerical factor SQ.
-     * Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.
-     * Compression is turned off if the value is missing or it is set to zero.
-     *
-     */
-    poisson_compression?: number;
-    /**
-     * Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments
-     * and to turn off for other experiments.
-     *
-     */
-    write_nxmx_hdf5_master?: boolean;
-    /**
-     * Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.
-     * If parameter is not provided calibration will be saved only if more than 4 images are recorded.
-     *
-     */
-    save_calibration?: boolean;
-    /**
-     * Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization
-     */
-    polarization_factor?: number;
-    /**
-     * Ring current at the beginning of the data collection
-     */
-    ring_current_mA?: number;
-    /**
-     * Sample temperature in Kelvin
-     */
-    sample_temperature_K?: number;
-    /**
-     * PONI angle rot1 (see PyFAI documentation for details) in radians
-     */
-    poni_rot1_rad?: number;
-    /**
-     * PONI angle rot2 (see PyFAI documentation for details) in radians
-     */
-    poni_rot2_rad?: number;
-    /**
-     * PONI angle rot3 (see PyFAI documentation for details) in radians
-     */
-    poni_rot3_rad?: number;
-    unit_cell?: unit_cell;
-    /**
-     * Enable spot finding and save spots
-     */
-    spot_finding?: boolean;
-    /**
-     * Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected
-     */
-    max_spot_count?: number;
-    /**
-     * Flag spots as ice rings and reduce their effect on indexing
-     */
-    detect_ice_rings?: boolean;
-    /**
-     * When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement.
-     */
-    async_start?: boolean;
-    xray_fluorescence_spectrum?: {
-        /**
-         * X-ray fluorescence scan energy for each measurement point
-         */
-        energy_eV: Array<number>;
-        /**
-         * X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV
-         */
-        data: Array<number>;
-    };
-};
-
-export namespace dataset_settings {
-
-    /**
-     * Compression type for the images transferred over ZeroMQ and saved to HDF5 file.
-     *
-     */
-    export enum compression {
-        BSLZ4 = 'bslz4',
-        BSZSTD = 'bszstd',
-        BSZSTD_RLE = 'bszstd_rle',
-        NONE = 'none',
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/detector.ts b/frontend/src/openapi/models/detector.ts
deleted file mode 100644
index 91c22b3d..00000000
--- a/frontend/src/openapi/models/detector.ts
+++ /dev/null
@@ -1,68 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_module } from './detector_module';
-import type { detector_settings } from './detector_settings';
-import type { detector_type } from './detector_type';
-import type { standard_detector_geometry } from './standard_detector_geometry';
-
-export type detector = {
-    description: string;
-    serial_number?: string;
-    type?: detector_type;
-    high_voltage_V?: number;
-    udp_interface_count?: number;
-    /**
-     * Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER).
-     */
-    module_sync?: boolean;
-    sensor_thickness_um?: number;
-    /**
-     * Minimum difference between frame time and count time in microseconds
-     * Defaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU
-     *
-     */
-    readout_time_ns?: number;
-    /**
-     * Minimum count time available for the detector.
-     */
-    min_count_time_ns?: number;
-    /**
-     * Minimum frame time available for the detector.
-     */
-    min_frame_time_ns?: number;
-    /**
-     * Can be empty for all detectors - default calibration used.
-     * For JUNGFRAU: list of gain files, one entry per module.
-     * For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.
-     *
-     */
-    calibration_file?: Array<string>;
-    /**
-     * Hostname for detector module. One entry per module
-     * One entry per module. Either empty or number of module entries.
-     *
-     */
-    hostname?: Array<string>;
-    sensor_material?: string;
-    tx_delay?: Array<number>;
-    base_data_ipv4_address?: string;
-    standard_geometry?: standard_detector_geometry;
-    custom_geometry?: Array<detector_module>;
-    /**
-     * ROI setting for DECTRIS detectors
-     */
-    roi_mode?: string;
-    /**
-     * Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner
-     */
-    mirror_y?: boolean;
-    /**
-     * Temperature threshold for JUNGFRAU detector modules
-     */
-    temp_thresold_degC?: number;
-    default_settings?: detector_settings;
-};
-
diff --git a/frontend/src/openapi/models/detector_list.ts b/frontend/src/openapi/models/detector_list.ts
deleted file mode 100644
index e080a40c..00000000
--- a/frontend/src/openapi/models/detector_list.ts
+++ /dev/null
@@ -1,12 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_list_element } from './detector_list_element';
-
-export type detector_list = {
-    detectors: Array<detector_list_element>;
-    current_id: number;
-};
-
diff --git a/frontend/src/openapi/models/detector_list_element.ts b/frontend/src/openapi/models/detector_list_element.ts
deleted file mode 100644
index abb03ef2..00000000
--- a/frontend/src/openapi/models/detector_list_element.ts
+++ /dev/null
@@ -1,26 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_type } from './detector_type';
-
-export type detector_list_element = {
-    id: number;
-    description: string;
-    serial_number: string;
-    base_ipv4_addr: string;
-    /**
-     * Number of UDP interfaces per detector module
-     */
-    udp_interface_count: number;
-    nmodules: number;
-    width: number;
-    height: number;
-    pixel_size_mm?: number;
-    readout_time_ns: number;
-    min_frame_time_ns: number;
-    min_count_time_ns: number;
-    type?: detector_type;
-};
-
diff --git a/frontend/src/openapi/models/detector_module.ts b/frontend/src/openapi/models/detector_module.ts
deleted file mode 100644
index 4e513b5e..00000000
--- a/frontend/src/openapi/models/detector_module.ts
+++ /dev/null
@@ -1,14 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_module_direction } from './detector_module_direction';
-
-export type detector_module = {
-    x0: number;
-    y0: number;
-    fast_axis: detector_module_direction;
-    slow_axis: detector_module_direction;
-};
-
diff --git a/frontend/src/openapi/models/detector_module_direction.ts b/frontend/src/openapi/models/detector_module_direction.ts
deleted file mode 100644
index 9df4db36..00000000
--- a/frontend/src/openapi/models/detector_module_direction.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export enum detector_module_direction {
-    XP = 'Xp',
-    XN = 'Xn',
-    YP = 'Yp',
-    YN = 'Yn',
-}
diff --git a/frontend/src/openapi/models/detector_power_state.ts b/frontend/src/openapi/models/detector_power_state.ts
deleted file mode 100644
index c44aa53b..00000000
--- a/frontend/src/openapi/models/detector_power_state.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Power on of ASICs
- */
-export enum detector_power_state {
-    POWER_ON = 'PowerOn',
-    POWER_OFF = 'PowerOff',
-    PARTIAL = 'Partial',
-}
diff --git a/frontend/src/openapi/models/detector_selection.ts b/frontend/src/openapi/models/detector_selection.ts
deleted file mode 100644
index a8b8a942..00000000
--- a/frontend/src/openapi/models/detector_selection.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type detector_selection = {
-    id: number;
-};
-
diff --git a/frontend/src/openapi/models/detector_settings.ts b/frontend/src/openapi/models/detector_settings.ts
deleted file mode 100644
index 23de3211..00000000
--- a/frontend/src/openapi/models/detector_settings.ts
+++ /dev/null
@@ -1,92 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_timing } from './detector_timing';
-
-export type detector_settings = {
-    /**
-     * Interval between consecutive frames.
-     * This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.
-     * For EIGER detector this is default frame time, not used otherwise
-     *
-     */
-    frame_time_us: number;
-    /**
-     * Integration time of the detector.
-     * If not provided count time will be set to maximum value for a given frame time.
-     *
-     */
-    count_time_us?: number;
-    /**
-     * Use internal frame generator in FPGA instead of getting data from a real detector
-     */
-    internal_frame_generator?: boolean;
-    /**
-     * Number of images stored in the internal frame generator.
-     */
-    internal_frame_generator_images?: number;
-    /**
-     * Delay between TTL trigger and acquisition start [ns]
-     */
-    detector_trigger_delay_ns?: number;
-    timing?: detector_timing;
-    /**
-     * Threshold for the PSI EIGER detector and all DECTRIS detectors.
-     * If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.
-     * If value is not provided, threshold will be determined on start of acquisition as half of incident energy.
-     * This might lead to increased start time.
-     *
-     */
-    eiger_threshold_keV?: number;
-    /**
-     * Bit depth of PSI EIGER read-out. This is
-     * If value is not provided, depth will be determined based on the image time:
-     * * Exposure time < 500 microseconds depth of 8 bit will be used,
-     * * 500 <= exposure time < 2622 microseconds depth of 16 bit will be used
-     * * Exposure time >= 2622 microseconds depth of 32 bit will be used.
-     *
-     */
-    eiger_bit_depth?: detector_settings.eiger_bit_depth;
-    jungfrau_pedestal_g0_frames?: number;
-    jungfrau_pedestal_g1_frames?: number;
-    jungfrau_pedestal_g2_frames?: number;
-    /**
-     * Minimum number of collected images for pedestal to consider it viable
-     */
-    jungfrau_pedestal_min_image_count?: number;
-    jungfrau_storage_cell_count?: number;
-    /**
-     * Delay between two storage cells [ns]
-     */
-    jungfrau_storage_cell_delay_ns?: number;
-    /**
-     * Fix gain to G1 (can be useful for storage cells)
-     */
-    jungfrau_fixed_gain_g1?: boolean;
-    /**
-     * Use high G0 (for low energy applications)
-     */
-    jungfrau_use_gain_hg0?: boolean;
-};
-
-export namespace detector_settings {
-
-    /**
-     * Bit depth of PSI EIGER read-out. This is
-     * If value is not provided, depth will be determined based on the image time:
-     * * Exposure time < 500 microseconds depth of 8 bit will be used,
-     * * 500 <= exposure time < 2622 microseconds depth of 16 bit will be used
-     * * Exposure time >= 2622 microseconds depth of 32 bit will be used.
-     *
-     */
-    export enum eiger_bit_depth {
-        '_8' = 8,
-        '_16' = 16,
-        '_32' = 32,
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/detector_state.ts b/frontend/src/openapi/models/detector_state.ts
deleted file mode 100644
index b941908d..00000000
--- a/frontend/src/openapi/models/detector_state.ts
+++ /dev/null
@@ -1,15 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Current state of the detector
- */
-export enum detector_state {
-    IDLE = 'Idle',
-    WAITING = 'Waiting',
-    BUSY = 'Busy',
-    ERROR = 'Error',
-    NOT_CONNECTED = 'Not connected',
-}
diff --git a/frontend/src/openapi/models/detector_status.ts b/frontend/src/openapi/models/detector_status.ts
deleted file mode 100644
index 6f5f2d24..00000000
--- a/frontend/src/openapi/models/detector_status.ts
+++ /dev/null
@@ -1,29 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { detector_power_state } from './detector_power_state';
-import type { detector_state } from './detector_state';
-
-export type detector_status = {
-    state: detector_state;
-    powerchip: detector_power_state;
-    /**
-     * Detector server (on read-out boards) version
-     */
-    server_version: string;
-    /**
-     * Remaining triggers to the detector (max of all modules)
-     */
-    number_of_triggers_left: number;
-    /**
-     * Temperature of detector FPGAs
-     */
-    fpga_temp_degC: Array<number>;
-    /**
-     * High voltage for detector modules
-     */
-    high_voltage_V: Array<number>;
-};
-
diff --git a/frontend/src/openapi/models/detector_timing.ts b/frontend/src/openapi/models/detector_timing.ts
deleted file mode 100644
index 1c0ce8d3..00000000
--- a/frontend/src/openapi/models/detector_timing.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export enum detector_timing {
-    AUTO = 'auto',
-    TRIGGER = 'trigger',
-    BURST = 'burst',
-    GATED = 'gated',
-}
diff --git a/frontend/src/openapi/models/detector_type.ts b/frontend/src/openapi/models/detector_type.ts
deleted file mode 100644
index 4cb1c6f2..00000000
--- a/frontend/src/openapi/models/detector_type.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export enum detector_type {
-    EIGER = 'EIGER',
-    JUNGFRAU = 'JUNGFRAU',
-    DECTRIS = 'DECTRIS',
-}
diff --git a/frontend/src/openapi/models/error_message.ts b/frontend/src/openapi/models/error_message.ts
deleted file mode 100644
index 87f49287..00000000
--- a/frontend/src/openapi/models/error_message.ts
+++ /dev/null
@@ -1,29 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type error_message = {
-    /**
-     * Human readable message
-     */
-    msg: string;
-    /**
-     * Enumerate field for automated analysis
-     */
-    reason: error_message.reason;
-};
-
-export namespace error_message {
-
-    /**
-     * Enumerate field for automated analysis
-     */
-    export enum reason {
-        WRONG_DAQSTATE = 'WrongDAQState',
-        OTHER = 'Other',
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/experimental_coord.ts b/frontend/src/openapi/models/experimental_coord.ts
deleted file mode 100644
index 77c01c29..00000000
--- a/frontend/src/openapi/models/experimental_coord.ts
+++ /dev/null
@@ -1,12 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * If measurement has goniometer axis defined, plot X-axis will represent rotation angle
- * If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
- * For still measurement the number is ignored
- *
- */
-export type experimental_coord = boolean;
diff --git a/frontend/src/openapi/models/file_writer_format.ts b/frontend/src/openapi/models/file_writer_format.ts
deleted file mode 100644
index 792ff42a..00000000
--- a/frontend/src/openapi/models/file_writer_format.ts
+++ /dev/null
@@ -1,24 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * NoFileWritten - no files are written at all
- * NXmxOnlyData - only data files are written, no master file
- * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
- * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
- * NXmxIntegrated - single HDF5 per dataset
- * CBF - CBF format (limited metadata)
- * TIFF - TIFF format (no metadata)
- *
- */
-export enum file_writer_format {
-    NXMX_ONLY_DATA = 'NXmxOnlyData',
-    NXMX_LEGACY = 'NXmxLegacy',
-    NXMX_VDS = 'NXmxVDS',
-    NXMX_INTEGRATED = 'NXmxIntegrated',
-    CBF = 'CBF',
-    TIFF = 'TIFF',
-    NO_FILE_WRITTEN = 'NoFileWritten',
-}
diff --git a/frontend/src/openapi/models/file_writer_settings.ts b/frontend/src/openapi/models/file_writer_settings.ts
deleted file mode 100644
index df4d99be..00000000
--- a/frontend/src/openapi/models/file_writer_settings.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { file_writer_format } from './file_writer_format';
-
-export type file_writer_settings = {
-    /**
-     * Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.
-     *
-     */
-    overwrite?: boolean;
-    format?: file_writer_format;
-};
-
diff --git a/frontend/src/openapi/models/fill_value.ts b/frontend/src/openapi/models/fill_value.ts
deleted file mode 100644
index 41c64406..00000000
--- a/frontend/src/openapi/models/fill_value.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Fill value for elements that were missed during data collection
- *
- */
-export type fill_value = number;
diff --git a/frontend/src/openapi/models/fpga_status.ts b/frontend/src/openapi/models/fpga_status.ts
deleted file mode 100644
index 90bae23a..00000000
--- a/frontend/src/openapi/models/fpga_status.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type fpga_status = Array<{
-    pci_dev_id: string;
-    serial_number: string;
-    fw_version: string;
-    base_mac_addr: string;
-    eth_link_count: number;
-    eth_link_status: number;
-    power_usage_W: number;
-    fpga_temp_C: number;
-    hbm_temp_C: number;
-    packets_udp: number;
-    packets_sls: number;
-    idle: boolean;
-    /**
-     * PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)
-     */
-    pcie_link_speed: number;
-    /**
-     * PCIe link width (expected value is 8 == x8)
-     */
-    pcie_link_width: number;
-}>;
diff --git a/frontend/src/openapi/models/geom_refinement_algorithm.ts b/frontend/src/openapi/models/geom_refinement_algorithm.ts
deleted file mode 100644
index 94ee46b0..00000000
--- a/frontend/src/openapi/models/geom_refinement_algorithm.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
- * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
- * OrientationOnly - This option is refining only orientation of the lattice.
- *
- */
-export enum geom_refinement_algorithm {
-    BEAM_CENTER = 'BeamCenter',
-    ORIENTATION_ONLY = 'OrientationOnly',
-    NONE = 'None',
-}
diff --git a/frontend/src/openapi/models/grid_scan.ts b/frontend/src/openapi/models/grid_scan.ts
deleted file mode 100644
index 73099975..00000000
--- a/frontend/src/openapi/models/grid_scan.ts
+++ /dev/null
@@ -1,40 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Definition of a grid scan (mutually exclusive with `rotation_axis`)
- */
-export type grid_scan = {
-    /**
-     * Number of elements in the fast direction
-     */
-    n_fast: number;
-    /**
-     * Step in grid along the fast direction. Can be negative.
-     * Positive number: left to right
-     * Negative number: right to left
-     *
-     */
-    step_x_um: number;
-    /**
-     * Step in grid along the slow direction. Can be negative.
-     * Positive number: top to bottom
-     * Negative number: bottom to top
-     *
-     */
-    step_y_um: number;
-    /**
-     * If disabled: fast direction = X, slow direction = Y
-     * If enabled: fast direction = Y, slow direction = X
-     *
-     */
-    vertical?: boolean;
-    /**
-     * Flip fast direction for every second row
-     *
-     */
-    snake?: boolean;
-};
-
diff --git a/frontend/src/openapi/models/image_buffer_status.ts b/frontend/src/openapi/models/image_buffer_status.ts
deleted file mode 100644
index a9dedc0e..00000000
--- a/frontend/src/openapi/models/image_buffer_status.ts
+++ /dev/null
@@ -1,47 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type image_buffer_status = {
-    /**
-     * Smallest image number available in the buffer
-     */
-    min_image_number: number;
-    /**
-     * Largest image number available in the buffer
-     */
-    max_image_number: number;
-    /**
-     * Image numbers currently present in the buffer.
-     */
-    image_numbers: Array<number>;
-    /**
-     * Number of slots in the image buffer. This number, compared to number of images in data collection and
-     * frame rate will determine "retention" rate of the image buffer.
-     *
-     */
-    total_slots: number;
-    /**
-     * Slots available for the data collection
-     */
-    available_slots: number;
-    /**
-     * Number of slots in the image buffer that are currently in preparation for sending.
-     *
-     */
-    in_preparation_slots: number;
-    /**
-     * Number of slots in the image buffer that are currently sending/writing data.
-     *
-     */
-    in_sending_slots: number;
-    /**
-     * Counter of changes in the image buffer - either new start message or new image added.
-     * For optimization one can only load new images/datasets from the HTTP if this value changes.
-     * Counter is optional as it was not implemented in older versions to avoid breaking change
-     *
-     */
-    current_counter?: number;
-};
-
diff --git a/frontend/src/openapi/models/image_format_settings.ts b/frontend/src/openapi/models/image_format_settings.ts
deleted file mode 100644
index 43077229..00000000
--- a/frontend/src/openapi/models/image_format_settings.ts
+++ /dev/null
@@ -1,84 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type image_format_settings = {
-    /**
-     * Enable summation of images to a given image_time
-     * If disabled images are saved according to original detector speed, but image count is adjusted
-     *
-     */
-    summation: boolean;
-    /**
-     * Place module read-out into their location on composed detector and extend multipixels
-     *
-     */
-    geometry_transform: boolean;
-    /**
-     * Convert pixel value in ADU to photon counts/energy
-     * Only affects JUNGFRAU detector
-     *
-     */
-    jungfrau_conversion: boolean;
-    /**
-     * Used to convert energy deposited into pixel to counts
-     * If not provided incident_energy_keV is used
-     *
-     */
-    jungfrau_conversion_factor_keV?: number;
-    /**
-     * Bit depth of resulting image (it doesn't affect the detector read-out value)
-     * If not provided value is adjusted automatically
-     *
-     */
-    bit_depth_image?: image_format_settings.bit_depth_image;
-    /**
-     * Controls if pixels have signed output
-     * If not provided value is adjusted automatically
-     *
-     */
-    signed_output?: boolean;
-    /**
-     * Mask 1 pixel on the module boundary
-     *
-     */
-    mask_module_edges: boolean;
-    /**
-     * Mask multipixels on chip boundary
-     *
-     */
-    mask_chip_edges: boolean;
-    /**
-     * JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.
-     * This should be turned off for cases, where detector is operated at room temperature with long exposure time.
-     *
-     */
-    jungfrau_mask_pixels_without_g0?: boolean;
-    /**
-     * Masked pixels are set to special value in the images produced by Jungfraujoch
-     *
-     */
-    apply_mask: boolean;
-    /**
-     * Pixels with pedestal G0 RMS above the threshold are marked as masked pixels
-     */
-    jungfrau_pedestal_g0_rms_limit?: number;
-};
-
-export namespace image_format_settings {
-
-    /**
-     * Bit depth of resulting image (it doesn't affect the detector read-out value)
-     * If not provided value is adjusted automatically
-     *
-     */
-    export enum bit_depth_image {
-        '_8' = 8,
-        '_16' = 16,
-        '_32' = 32,
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/image_id.ts b/frontend/src/openapi/models/image_id.ts
deleted file mode 100644
index 63380793..00000000
--- a/frontend/src/openapi/models/image_id.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
- */
-export type image_id = number;
diff --git a/frontend/src/openapi/models/image_pusher_status.ts b/frontend/src/openapi/models/image_pusher_status.ts
deleted file mode 100644
index 3e83eea3..00000000
--- a/frontend/src/openapi/models/image_pusher_status.ts
+++ /dev/null
@@ -1,51 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { image_pusher_type } from './image_pusher_type';
-
-/**
- * Informs about status of the image pusher.
- *
- */
-export type image_pusher_status = {
-    pusher_type: image_pusher_type;
-    /**
-     * List of addresses of image pushers.
-     * For HDF5 socket - no addresses will be returned.
-     * For ZeroMQ - list of addresses for each socket will be provided.
-     * For TCP/IP - single address to connect all writers will be provided.
-     *
-     */
-    addr: Array<string>;
-    /**
-     * Number of connected writers
-     * For ZeroMQ image socket: number is constant
-     * For TCP/IP image socket: number is updated live during operation
-     *
-     */
-    connected_writers: number;
-    /**
-     * Number of images written to the image socket.
-     * This number is updated live during operation for TCP/IP image socket and direct HDF5 writer.
-     * It is updated at the end of experiment for ZeroMQ image socket.
-     *
-     */
-    images_written?: number;
-    /**
-     * Number of images that could not be written to the image socket.
-     * This number is updated live during operation for TCP/IP image socket.
-     * No other socket use it.
-     *
-     */
-    images_write_error?: number;
-    /**
-     * Utilization of internal writer FIFO.
-     * This number is updated live during operation for TCP/IP image socket.
-     * No other socket use it.
-     *
-     */
-    writer_fifo_utilization?: Array<number>;
-};
-
diff --git a/frontend/src/openapi/models/image_pusher_type.ts b/frontend/src/openapi/models/image_pusher_type.ts
deleted file mode 100644
index 69b0494a..00000000
--- a/frontend/src/openapi/models/image_pusher_type.ts
+++ /dev/null
@@ -1,12 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export enum image_pusher_type {
-    ZERO_MQ = 'ZeroMQ',
-    HDF5 = 'HDF5',
-    CBOR = 'CBOR',
-    TCP = 'TCP',
-    NONE = 'None',
-}
diff --git a/frontend/src/openapi/models/indexing_algorithm.ts b/frontend/src/openapi/models/indexing_algorithm.ts
deleted file mode 100644
index 5f367ac7..00000000
--- a/frontend/src/openapi/models/indexing_algorithm.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Selection of an indexing algorithm used by Jungfraujoch
- *
- */
-export enum indexing_algorithm {
-    FFBIDX = 'FFBIDX',
-    FFT = 'FFT',
-    FFTW = 'FFTW',
-    AUTO = 'Auto',
-    NONE = 'None',
-}
diff --git a/frontend/src/openapi/models/indexing_settings.ts b/frontend/src/openapi/models/indexing_settings.ts
deleted file mode 100644
index fb6f3f8a..00000000
--- a/frontend/src/openapi/models/indexing_settings.ts
+++ /dev/null
@@ -1,66 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { geom_refinement_algorithm } from './geom_refinement_algorithm';
-import type { indexing_algorithm } from './indexing_algorithm';
-
-/**
- * Settings for crystallography indexing
- */
-export type indexing_settings = {
-    algorithm: indexing_algorithm;
-    /**
-     * Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
-     */
-    fft_max_unit_cell_A: number;
-    /**
-     * Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
-     */
-    fft_min_unit_cell_A: number;
-    /**
-     * Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT.
-     * There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.
-     *
-     */
-    fft_high_resolution_A: number;
-    /**
-     * Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.
-     */
-    fft_num_vectors: number;
-    /**
-     * Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted
-     */
-    tolerance: number;
-    /**
-     * Thread count for indexing algorithm
-     */
-    thread_count: number;
-    geom_refinement_algorithm: geom_refinement_algorithm;
-    /**
-     * Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored
-     */
-    unit_cell_dist_tolerance: number;
-    /**
-     * Minimum number of indexed spots required for a cell to be considered viable
-     */
-    viable_cell_min_spots: number;
-    /**
-     * Include spots marked as ice rings in the indexing run.
-     * If `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.
-     *
-     */
-    index_ice_rings: boolean;
-    rotation_indexing: boolean;
-    rotation_indexing_min_angular_range_deg: number;
-    rotation_indexing_angular_stride_deg: number;
-    /**
-     * Indexing in Jungfraujoch goes with a dedicated thread pool.
-     * If set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates.
-     * If set to true, the thread pool will block until a thread is available.
-     *
-     */
-    blocking: boolean;
-};
-
diff --git a/frontend/src/openapi/models/instrument_metadata.ts b/frontend/src/openapi/models/instrument_metadata.ts
deleted file mode 100644
index 609c5c7c..00000000
--- a/frontend/src/openapi/models/instrument_metadata.ts
+++ /dev/null
@@ -1,44 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Metadata for a measurement instrument
- */
-export type instrument_metadata = {
-    source_name: string;
-    /**
-     * Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance.
-     * https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource
-     * NXsource allows the following:
-     *
-     * Spallation Neutron Source
-     * Pulsed Reactor Neutron Source
-     * Reactor Neutron Source
-     * Synchrotron X-ray Source
-     * Pulsed Muon Source
-     * Rotating Anode X-ray
-     * Fixed Tube X-ray
-     * UV Laser
-     * Free-Electron Laser
-     * Optical Laser
-     * Ion Source
-     * UV Plasma Source
-     * Metal Jet X-ray
-     *
-     */
-    source_type?: string;
-    instrument_name: string;
-    /**
-     * Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)
-     *
-     */
-    pulsed_source?: boolean;
-    /**
-     * Settings specific to electron source (e.g., wavelength definition)
-     *
-     */
-    electron_source?: boolean;
-};
-
diff --git a/frontend/src/openapi/models/jfjoch_settings.ts b/frontend/src/openapi/models/jfjoch_settings.ts
deleted file mode 100644
index 205c178c..00000000
--- a/frontend/src/openapi/models/jfjoch_settings.ts
+++ /dev/null
@@ -1,65 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { azim_int_settings } from './azim_int_settings';
-import type { dark_mask_settings } from './dark_mask_settings';
-import type { detector } from './detector';
-import type { detector_settings } from './detector_settings';
-import type { file_writer_settings } from './file_writer_settings';
-import type { image_format_settings } from './image_format_settings';
-import type { image_pusher_type } from './image_pusher_type';
-import type { indexing_settings } from './indexing_settings';
-import type { instrument_metadata } from './instrument_metadata';
-import type { pcie_devices } from './pcie_devices';
-import type { spot_finding_settings } from './spot_finding_settings';
-import type { tcp_settings } from './tcp_settings';
-import type { zeromq_metadata_settings } from './zeromq_metadata_settings';
-import type { zeromq_preview_settings } from './zeromq_preview_settings';
-import type { zeromq_settings } from './zeromq_settings';
-
-/**
- * Default settings for Jungfraujoch software.
- * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
- *
- */
-export type jfjoch_settings = {
-    pcie?: pcie_devices;
-    zeromq?: zeromq_settings;
-    tcp?: tcp_settings;
-    instrument?: instrument_metadata;
-    file_writer?: file_writer_settings;
-    detector: Array<detector>;
-    indexing?: indexing_settings;
-    detector_settings?: detector_settings;
-    azim_int?: azim_int_settings;
-    image_format?: image_format_settings;
-    /**
-     * Size of internal buffer in MiB for images before they are sent to a stream
-     */
-    image_buffer_MiB?: number;
-    /**
-     * Print extra debug information
-     */
-    verbose?: boolean;
-    /**
-     * Number of threads used by the receiver
-     */
-    receiver_threads?: number;
-    /**
-     * Ignored value
-     * @deprecated
-     */
-    numa_policy?: string;
-    /**
-     * Location of built JavaScript web frontend
-     */
-    frontend_directory: string;
-    spot_finding?: spot_finding_settings;
-    image_pusher: image_pusher_type;
-    zeromq_preview?: zeromq_preview_settings;
-    zeromq_metadata?: zeromq_metadata_settings;
-    dark_mask?: dark_mask_settings;
-};
-
diff --git a/frontend/src/openapi/models/jfjoch_statistics.ts b/frontend/src/openapi/models/jfjoch_statistics.ts
deleted file mode 100644
index ac8f3512..00000000
--- a/frontend/src/openapi/models/jfjoch_statistics.ts
+++ /dev/null
@@ -1,52 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { azim_int_settings } from './azim_int_settings';
-import type { broker_status } from './broker_status';
-import type { calibration_statistics } from './calibration_statistics';
-import type { dark_mask_settings } from './dark_mask_settings';
-import type { detector_list } from './detector_list';
-import type { detector_settings } from './detector_settings';
-import type { detector_status } from './detector_status';
-import type { file_writer_settings } from './file_writer_settings';
-import type { fpga_status } from './fpga_status';
-import type { image_buffer_status } from './image_buffer_status';
-import type { image_format_settings } from './image_format_settings';
-import type { image_pusher_status } from './image_pusher_status';
-import type { indexing_settings } from './indexing_settings';
-import type { instrument_metadata } from './instrument_metadata';
-import type { measurement_statistics } from './measurement_statistics';
-import type { pixel_mask_statistics } from './pixel_mask_statistics';
-import type { roi_definitions } from './roi_definitions';
-import type { spot_finding_settings } from './spot_finding_settings';
-import type { zeromq_metadata_settings } from './zeromq_metadata_settings';
-import type { zeromq_preview_settings } from './zeromq_preview_settings';
-
-/**
- * Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker
- */
-export type jfjoch_statistics = {
-    detector?: detector_status;
-    detector_list?: detector_list;
-    detector_settings?: detector_settings;
-    image_format_settings?: image_format_settings;
-    instrument_metadata?: instrument_metadata;
-    file_writer_settings?: file_writer_settings;
-    data_processing_settings?: spot_finding_settings;
-    measurement?: measurement_statistics;
-    broker?: broker_status;
-    fpga?: fpga_status;
-    calibration?: calibration_statistics;
-    zeromq_preview?: zeromq_preview_settings;
-    zeromq_metadata?: zeromq_metadata_settings;
-    dark_mask?: dark_mask_settings;
-    pixel_mask?: pixel_mask_statistics;
-    roi?: roi_definitions;
-    az_int?: azim_int_settings;
-    buffer?: image_buffer_status;
-    indexing?: indexing_settings;
-    image_pusher?: image_pusher_status;
-};
-
diff --git a/frontend/src/openapi/models/jpeg_quality.ts b/frontend/src/openapi/models/jpeg_quality.ts
deleted file mode 100644
index a08f7806..00000000
--- a/frontend/src/openapi/models/jpeg_quality.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Quality of JPEG image (100 - highest; 0 - lowest)
- */
-export type jpeg_quality = number;
diff --git a/frontend/src/openapi/models/measurement_statistics.ts b/frontend/src/openapi/models/measurement_statistics.ts
deleted file mode 100644
index ee27d851..00000000
--- a/frontend/src/openapi/models/measurement_statistics.ts
+++ /dev/null
@@ -1,82 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type measurement_statistics = {
-    file_prefix?: string;
-    /**
-     * Number of data collection run. This can be either automatically incremented or provided externally for each data collection.
-     *
-     */
-    run_number?: number;
-    /**
-     * Name of group owning the data (e.g. p-group or proposal number).
-     *
-     */
-    experiment_group?: string;
-    images_expected?: number;
-    /**
-     * Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.
-     *
-     */
-    images_collected?: number;
-    /**
-     * Images sent to the writer.
-     * The value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.
-     *
-     */
-    images_sent?: number;
-    /**
-     * Images successfully written to disk.
-     * The value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.
-     *
-     */
-    images_written?: number;
-    /**
-     * Images discarded by the lossy compression filter
-     */
-    images_discarded_lossy_compression?: number;
-    max_image_number_sent?: number;
-    collection_efficiency?: number;
-    compression_ratio?: number;
-    cancelled?: boolean;
-    max_receiver_delay?: number;
-    indexing_rate?: number;
-    detector_width?: number;
-    detector_height?: number;
-    detector_pixel_depth?: measurement_statistics.detector_pixel_depth;
-    bkg_estimate?: number;
-    unit_cell?: string;
-    /**
-     * Moving average of 1000 images counting number of error pixels on the detector
-     */
-    error_pixels?: number;
-    /**
-     * Moving average of 1000 images counting number of saturated pixels on the detector
-     */
-    saturated_pixels?: number;
-    /**
-     * If there is an ROI defined with name "beam", this number will hold moving average of 1000 images
-     * for number of valid pixels within this ROI
-     *
-     */
-    roi_beam_pixels?: number;
-    /**
-     * If there is an ROI defined with name "beam", this number will hold moving average of 1000 images
-     * for sum of valid pixels within this ROI
-     *
-     */
-    roi_beam_sum?: number;
-};
-
-export namespace measurement_statistics {
-
-    export enum detector_pixel_depth {
-        '_2' = 2,
-        '_4' = 4,
-    }
-
-
-}
-
diff --git a/frontend/src/openapi/models/pcie_devices.ts b/frontend/src/openapi/models/pcie_devices.ts
deleted file mode 100644
index c7b303cc..00000000
--- a/frontend/src/openapi/models/pcie_devices.ts
+++ /dev/null
@@ -1,15 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type pcie_devices = Array<{
-    /**
-     * Block device name
-     */
-    blk?: string;
-    /**
-     * IPv4 address of the block device
-     */
-    ipv4?: string;
-}>;
diff --git a/frontend/src/openapi/models/pixel_mask_statistics.ts b/frontend/src/openapi/models/pixel_mask_statistics.ts
deleted file mode 100644
index 81437bdb..00000000
--- a/frontend/src/openapi/models/pixel_mask_statistics.ts
+++ /dev/null
@@ -1,20 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type pixel_mask_statistics = {
-    /**
-     * Number of pixels masked using the user mask
-     */
-    user_mask?: number;
-    /**
-     * Number of pixels with G0 pedestal RMS higher than provided threshold
-     */
-    too_high_pedestal_rms?: number;
-    /**
-     * Number of pixels that show wrong gain level during the pedestal procedure
-     */
-    wrong_gain?: number;
-};
-
diff --git a/frontend/src/openapi/models/plot.ts b/frontend/src/openapi/models/plot.ts
deleted file mode 100644
index 86f7e7fa..00000000
--- a/frontend/src/openapi/models/plot.ts
+++ /dev/null
@@ -1,15 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly
- */
-export type plot = {
-    title: string;
-    'x': Array<number>;
-    'y': Array<number | null>;
-    'z'?: Array<number | null>;
-};
-
diff --git a/frontend/src/openapi/models/plot_type.ts b/frontend/src/openapi/models/plot_type.ts
deleted file mode 100644
index 26ac39b2..00000000
--- a/frontend/src/openapi/models/plot_type.ts
+++ /dev/null
@@ -1,48 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Type of requested plot
- */
-export enum plot_type {
-    BKG_ESTIMATE = 'bkg_estimate',
-    AZINT = 'azint',
-    AZINT_1D = 'azint_1d',
-    SPOT_COUNT = 'spot_count',
-    SPOT_COUNT_LOW_RES = 'spot_count_low_res',
-    SPOT_COUNT_INDEXED = 'spot_count_indexed',
-    SPOT_COUNT_ICE = 'spot_count_ice',
-    INDEXING_RATE = 'indexing_rate',
-    INDEXING_LATTICE_COUNT = 'indexing_lattice_count',
-    INDEXING_UNIT_CELL_LENGTH = 'indexing_unit_cell_length',
-    INDEXING_UNIT_CELL_ANGLE = 'indexing_unit_cell_angle',
-    PROFILE_RADIUS = 'profile_radius',
-    MOSAICITY = 'mosaicity',
-    B_FACTOR = 'b_factor',
-    ERROR_PIXELS = 'error_pixels',
-    SATURATED_PIXELS = 'saturated_pixels',
-    IMAGE_COLLECTION_EFFICIENCY = 'image_collection_efficiency',
-    RECEIVER_DELAY = 'receiver_delay',
-    RECEIVER_FREE_SEND_BUF = 'receiver_free_send_buf',
-    STRONG_PIXELS = 'strong_pixels',
-    ROI_SUM = 'roi_sum',
-    ROI_MEAN = 'roi_mean',
-    ROI_MAX_COUNT = 'roi_max_count',
-    ROI_PIXELS = 'roi_pixels',
-    ROI_WEIGHTED_X = 'roi_weighted_x',
-    ROI_WEIGHTED_Y = 'roi_weighted_y',
-    PACKETS_RECEIVED = 'packets_received',
-    MAX_PIXEL_VALUE = 'max_pixel_value',
-    RESOLUTION_ESTIMATE = 'resolution_estimate',
-    PIXEL_SUM = 'pixel_sum',
-    PROCESSING_TIME = 'processing_time',
-    BEAM_CENTER_X = 'beam_center_x',
-    BEAM_CENTER_Y = 'beam_center_y',
-    INTEGRATED_REFLECTIONS = 'integrated_reflections',
-    IMAGE_SCALE_FACTOR = 'image_scale_factor',
-    IMAGE_SCALE_CC = 'image_scale_cc',
-    IMAGE_SCALE_B = 'image_scale_b',
-    COMPRESSION_RATIO = 'compression_ratio',
-}
diff --git a/frontend/src/openapi/models/plot_unit_x.ts b/frontend/src/openapi/models/plot_unit_x.ts
deleted file mode 100644
index ac609ba6..00000000
--- a/frontend/src/openapi/models/plot_unit_x.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export enum plot_unit_x {
-    IMAGE_NUMBER = 'image_number',
-    Q_RECIP_A = 'q_recipA',
-    D_A = 'd_A',
-    ANGLE_DEG = 'angle_deg',
-    ADU = 'ADU',
-    GRID_UM = 'grid_um',
-}
diff --git a/frontend/src/openapi/models/plots.ts b/frontend/src/openapi/models/plots.ts
deleted file mode 100644
index 1b0d8dfa..00000000
--- a/frontend/src/openapi/models/plots.ts
+++ /dev/null
@@ -1,22 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { plot } from './plot';
-import type { plot_unit_x } from './plot_unit_x';
-
-export type plots = {
-    title?: string;
-    unit_x: plot_unit_x;
-    /**
-     * Max X range of the plot
-     */
-    size_x?: number;
-    /**
-     * Max Y range of the plot
-     */
-    size_y?: number;
-    plot: Array<plot>;
-};
-
diff --git a/frontend/src/openapi/models/resolution_estimate.ts b/frontend/src/openapi/models/resolution_estimate.ts
deleted file mode 100644
index 5f51febf..00000000
--- a/frontend/src/openapi/models/resolution_estimate.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show resolution estimation as a ring
- */
-export type resolution_estimate = boolean;
diff --git a/frontend/src/openapi/models/resolution_ring.ts b/frontend/src/openapi/models/resolution_ring.ts
deleted file mode 100644
index f698210b..00000000
--- a/frontend/src/openapi/models/resolution_ring.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show resolution ring, provided in Angstrom
- */
-export type resolution_ring = number;
diff --git a/frontend/src/openapi/models/roi.ts b/frontend/src/openapi/models/roi.ts
deleted file mode 100644
index 24151c33..00000000
--- a/frontend/src/openapi/models/roi.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Name of ROI for which plot is requested
- */
-export type roi = string;
diff --git a/frontend/src/openapi/models/roi_azim_list.ts b/frontend/src/openapi/models/roi_azim_list.ts
deleted file mode 100644
index 84dde280..00000000
--- a/frontend/src/openapi/models/roi_azim_list.ts
+++ /dev/null
@@ -1,14 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { roi_azimuthal } from './roi_azimuthal';
-
-/**
- * List of azimuthal ROIs
- */
-export type roi_azim_list = {
-    rois?: Array<roi_azimuthal>;
-};
-
diff --git a/frontend/src/openapi/models/roi_azimuthal.ts b/frontend/src/openapi/models/roi_azimuthal.ts
deleted file mode 100644
index d0ccd135..00000000
--- a/frontend/src/openapi/models/roi_azimuthal.ts
+++ /dev/null
@@ -1,23 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * ROI as Q-range (or resolution range)
- */
-export type roi_azimuthal = {
-    /**
-     * Name for the ROI; used in the plots
-     */
-    name: string;
-    /**
-     * Minimum Q-range for the ROI
-     */
-    q_min_recipA: number;
-    /**
-     * Maximum Q-range for the ROI
-     */
-    q_max_recipA: number;
-};
-
diff --git a/frontend/src/openapi/models/roi_box.ts b/frontend/src/openapi/models/roi_box.ts
deleted file mode 100644
index 120a30a0..00000000
--- a/frontend/src/openapi/models/roi_box.ts
+++ /dev/null
@@ -1,31 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Box ROI
- */
-export type roi_box = {
-    /**
-     * Name for the ROI; used in the plots
-     */
-    name: string;
-    /**
-     * Lower bound (inclusive) in X coordinate for the box
-     */
-    min_x_pxl: number;
-    /**
-     * Upper bound (inclusive) in X coordinate for the box
-     */
-    max_x_pxl: number;
-    /**
-     * Lower bound (inclusive) in Y coordinate for the box
-     */
-    min_y_pxl: number;
-    /**
-     * Upper bound (inclusive) in Y coordinate for the box
-     */
-    max_y_pxl: number;
-};
-
diff --git a/frontend/src/openapi/models/roi_box_list.ts b/frontend/src/openapi/models/roi_box_list.ts
deleted file mode 100644
index 8cea4840..00000000
--- a/frontend/src/openapi/models/roi_box_list.ts
+++ /dev/null
@@ -1,14 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { roi_box } from './roi_box';
-
-/**
- * List of box ROIs
- */
-export type roi_box_list = {
-    rois?: Array<roi_box>;
-};
-
diff --git a/frontend/src/openapi/models/roi_circle.ts b/frontend/src/openapi/models/roi_circle.ts
deleted file mode 100644
index 410aa9ca..00000000
--- a/frontend/src/openapi/models/roi_circle.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Circular ROI
- */
-export type roi_circle = {
-    /**
-     * Name for the ROI; used in the plots
-     */
-    name: string;
-    /**
-     * X coordinate of center of the circle [pixels]
-     */
-    center_x_pxl: number;
-    /**
-     * Y coordinate of center of the circle [pixels]
-     */
-    center_y_pxl: number;
-    /**
-     * Radius of the circle [pixels]
-     */
-    radius_pxl: number;
-};
-
diff --git a/frontend/src/openapi/models/roi_circle_list.ts b/frontend/src/openapi/models/roi_circle_list.ts
deleted file mode 100644
index 7b93e116..00000000
--- a/frontend/src/openapi/models/roi_circle_list.ts
+++ /dev/null
@@ -1,14 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { roi_circle } from './roi_circle';
-
-/**
- * List of circular ROIs
- */
-export type roi_circle_list = {
-    rois: Array<roi_circle>;
-};
-
diff --git a/frontend/src/openapi/models/roi_definitions.ts b/frontend/src/openapi/models/roi_definitions.ts
deleted file mode 100644
index 9d40a881..00000000
--- a/frontend/src/openapi/models/roi_definitions.ts
+++ /dev/null
@@ -1,18 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { roi_azim_list } from './roi_azim_list';
-import type { roi_box_list } from './roi_box_list';
-import type { roi_circle_list } from './roi_circle_list';
-
-/**
- * ROI defintions
- */
-export type roi_definitions = {
-    box: roi_box_list;
-    circle: roi_circle_list;
-    azim: roi_azim_list;
-};
-
diff --git a/frontend/src/openapi/models/rotation_axis.ts b/frontend/src/openapi/models/rotation_axis.ts
deleted file mode 100644
index 57cb5190..00000000
--- a/frontend/src/openapi/models/rotation_axis.ts
+++ /dev/null
@@ -1,35 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Definition of a crystal rotation axis
- */
-export type rotation_axis = {
-    /**
-     * Name of rotation axis (e.g., omega, phi)
-     */
-    name?: string;
-    /**
-     * Angle step (per image) in degrees
-     */
-    step: number;
-    /**
-     * Start angle in degrees
-     */
-    start?: number;
-    /**
-     * Rotation axis
-     */
-    vector: Array<number>;
-    /**
-     * Translation (per image) for helical scan
-     */
-    helical_step_um?: Array<number>;
-    /**
-     * Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)
-     */
-    screening_wedge_deg?: number;
-};
-
diff --git a/frontend/src/openapi/models/saturation.ts b/frontend/src/openapi/models/saturation.ts
deleted file mode 100644
index 0402923c..00000000
--- a/frontend/src/openapi/models/saturation.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
- */
-export type saturation = number;
diff --git a/frontend/src/openapi/models/scan_result.ts b/frontend/src/openapi/models/scan_result.ts
deleted file mode 100644
index 41a7c73e..00000000
--- a/frontend/src/openapi/models/scan_result.ts
+++ /dev/null
@@ -1,97 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-import type { crystal_lattice } from './crystal_lattice';
-import type { unit_cell } from './unit_cell';
-
-/**
- * Results of a scan
- */
-export type scan_result = {
-    file_prefix?: string;
-    rotation_unit_cell?: unit_cell;
-    rotation_crystal_lattice?: crystal_lattice;
-    images: Array<{
-        efficiency: number;
-        /**
-         * Detector image number for a given cell
-         */
-        number: number;
-        /**
-         * Cell position in X for grid scan
-         */
-        nx?: number;
-        /**
-         * Cell position in Y for grid scan
-         */
-        ny?: number;
-        /**
-         * Rotation angle associated with the image
-         */
-        angle?: number;
-        /**
-         * Background estimate
-         */
-        bkg?: number;
-        /**
-         * Spot count
-         */
-        spots?: number;
-        /**
-         * Spot count in low resolution range
-         */
-        spots_low_res?: number;
-        /**
-         * Spot count within indexing tolerance
-         */
-        spots_indexed?: number;
-        /**
-         * Spot count within common ice ring resolutions
-         */
-        spots_ice?: number;
-        /**
-         * Indexing solution
-         */
-        index?: number;
-        /**
-         * Indexing lattice count
-         */
-        latt_count?: number;
-        /**
-         * Profile radius, i.e. how far reflections are from the Ewald sphere
-         */
-        pr?: number;
-        /**
-         * B-Factor estimate
-         */
-        'b'?: number;
-        uc?: unit_cell;
-        /**
-         * XFEL pulse ID
-         */
-        xfel_pulseid?: number;
-        /**
-         * Total sum of all pixels
-         */
-        pixel_sum?: number;
-        /**
-         * Max viable pixel
-         */
-        max?: number;
-        /**
-         * Number of saturated pixels
-         */
-        sat?: number;
-        /**
-         * Number of error pixels
-         */
-        err?: number;
-        /**
-         * Diffraction resolution estimate
-         */
-        res?: number;
-    }>;
-};
-
diff --git a/frontend/src/openapi/models/show_beam_center.ts b/frontend/src/openapi/models/show_beam_center.ts
deleted file mode 100644
index 6c24e388..00000000
--- a/frontend/src/openapi/models/show_beam_center.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show beam center on the image
- */
-export type show_beam_center = boolean;
diff --git a/frontend/src/openapi/models/show_roi.ts b/frontend/src/openapi/models/show_roi.ts
deleted file mode 100644
index e263d6c8..00000000
--- a/frontend/src/openapi/models/show_roi.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show ROI areas on the image
- */
-export type show_roi = boolean;
diff --git a/frontend/src/openapi/models/show_spots.ts b/frontend/src/openapi/models/show_spots.ts
deleted file mode 100644
index 66b1c07c..00000000
--- a/frontend/src/openapi/models/show_spots.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show spot finding results on the image
- */
-export type show_spots = boolean;
diff --git a/frontend/src/openapi/models/show_user_mask.ts b/frontend/src/openapi/models/show_user_mask.ts
deleted file mode 100644
index 8eedc479..00000000
--- a/frontend/src/openapi/models/show_user_mask.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Show user mask
- */
-export type show_user_mask = boolean;
diff --git a/frontend/src/openapi/models/spot_finding_settings.ts b/frontend/src/openapi/models/spot_finding_settings.ts
deleted file mode 100644
index ca4bea58..00000000
--- a/frontend/src/openapi/models/spot_finding_settings.ts
+++ /dev/null
@@ -1,53 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type spot_finding_settings = {
-    /**
-     * Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection.
-     * Even if disabled spot finding information will still be send and written, though always with zero spots.
-     *
-     */
-    enable: boolean;
-    /**
-     * Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.
-     *
-     */
-    indexing: boolean;
-    signal_to_noise_threshold: number;
-    photon_count_threshold: number;
-    min_pix_per_spot: number;
-    max_pix_per_spot: number;
-    /**
-     * High resolution limit for spot finding [Angstrom]
-     */
-    high_resolution_limit: number;
-    /**
-     * Low resolution limit for spot finding [Angstrom]
-     */
-    low_resolution_limit: number;
-    /**
-     * High resolution threshold to consider spot "low resolution" [Angstrom]
-     */
-    high_resolution_limit_for_spot_count_low_res: number;
-    /**
-     * Quick integration of Bragg spots in diffraction images.
-     * If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.
-     * (experimental feature)
-     *
-     */
-    quick_integration: boolean;
-    /**
-     * Width of ice ring in q-space in reciprocal space
-     */
-    ice_ring_width_q_recipA: number;
-    /**
-     * This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.
-     * If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.
-     * This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.
-     *
-     */
-    high_res_gap_Q_recipA?: number;
-};
-
diff --git a/frontend/src/openapi/models/standard_detector_geometry.ts b/frontend/src/openapi/models/standard_detector_geometry.ts
deleted file mode 100644
index cd2055f3..00000000
--- a/frontend/src/openapi/models/standard_detector_geometry.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Regular rectangular geometry, first module is in the bottom left corner of the detector
- */
-export type standard_detector_geometry = {
-    /**
-     * Number of modules in the detector
-     */
-    nmodules: number;
-    /**
-     * Gap size in X direction [pixels]
-     */
-    gap_x?: number;
-    /**
-     * Gap size in Y direction [pixels]
-     */
-    gap_y?: number;
-    /**
-     * Number of modules in one row
-     */
-    modules_in_row?: number;
-};
-
diff --git a/frontend/src/openapi/models/tcp_settings.ts b/frontend/src/openapi/models/tcp_settings.ts
deleted file mode 100644
index 9842ba7a..00000000
--- a/frontend/src/openapi/models/tcp_settings.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * TCP image stream configuration for Jungfraujoch software.
- * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
- *
- */
-export type tcp_settings = {
-    /**
-     * Send buffer size for TCP/IP socket
-     */
-    send_buffer_size?: number;
-    /**
-     * tcp://<IP address>:<port>
-     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces
-     *
-     */
-    image_socket?: string;
-    /**
-     * Number of TCP/IP writers to be used for streaming images
-     */
-    nwriters?: number;
-};
-
diff --git a/frontend/src/openapi/models/unit_cell.ts b/frontend/src/openapi/models/unit_cell.ts
deleted file mode 100644
index 8df1d143..00000000
--- a/frontend/src/openapi/models/unit_cell.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * Unit cell parameters. Necessary to run indexing. Units of angstrom and degree
- */
-export type unit_cell = {
-    'a': number;
-    'b': number;
-    'c': number;
-    alpha: number;
-    beta: number;
-    gamma: number;
-};
-
diff --git a/frontend/src/openapi/models/zeromq_metadata_settings.ts b/frontend/src/openapi/models/zeromq_metadata_settings.ts
deleted file mode 100644
index 7eac7bc3..00000000
--- a/frontend/src/openapi/models/zeromq_metadata_settings.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type zeromq_metadata_settings = {
-    /**
-     * ZeroMQ metadata socket is enabled.
-     */
-    enabled: boolean;
-    /**
-     * Period for generating metadata package sent to the ZeroMQ interface in milliseconds.
-     *
-     */
-    period_ms: number;
-    /**
-     * PUB ZeroMQ socket for image metadata information.
-     * Image metadata are serialized using CBOR.
-     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.
-     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
-     *
-     */
-    socket_address?: string;
-};
-
diff --git a/frontend/src/openapi/models/zeromq_preview_settings.ts b/frontend/src/openapi/models/zeromq_preview_settings.ts
deleted file mode 100644
index 120d6865..00000000
--- a/frontend/src/openapi/models/zeromq_preview_settings.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-export type zeromq_preview_settings = {
-    /**
-     * ZeroMQ preview socket is enabled.
-     */
-    enabled: boolean;
-    /**
-     * Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second.
-     * If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).
-     * This has no effect on HTTP based preview, which updates always at rate of 1 second.
-     *
-     */
-    period_ms: number;
-    /**
-     * PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.
-     * Images are serialized using CBOR.
-     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.
-     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
-     *
-     */
-    socket_address?: string;
-};
-
diff --git a/frontend/src/openapi/models/zeromq_settings.ts b/frontend/src/openapi/models/zeromq_settings.ts
deleted file mode 100644
index ef7b1546..00000000
--- a/frontend/src/openapi/models/zeromq_settings.ts
+++ /dev/null
@@ -1,38 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-
-/**
- * ZeroMQ configuration for Jungfraujoch software.
- * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
- *
- */
-export type zeromq_settings = {
-    /**
-     * Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)
-     */
-    send_watermark?: number;
-    /**
-     * Send buffer size for ZeroMQ socket
-     */
-    send_buffer_size?: number;
-    /**
-     * PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.
-     * Images are serialized using CBOR.
-     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.
-     * 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.
-     *
-     */
-    image_socket?: Array<string>;
-    /**
-     * PULL ZeroMQ socket for notifications from writer that it finished operation.
-     * This allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.
-     * Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.
-     * 0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.
-     * Using * (star) instead of port number is allowed and it means a random free port number.
-     *
-     */
-    writer_notification_socket?: string;
-};
-
diff --git a/frontend/src/openapi/services/DefaultService.ts b/frontend/src/openapi/services/DefaultService.ts
deleted file mode 100644
index 0d737f15..00000000
--- a/frontend/src/openapi/services/DefaultService.ts
+++ /dev/null
@@ -1,1258 +0,0 @@
-/* generated using openapi-typescript-codegen -- do no edit */
-/* istanbul ignore file */
-/* tslint:disable */
-/* eslint-disable */
-import type { azim_int_settings } from '../models/azim_int_settings';
-import type { broker_status } from '../models/broker_status';
-import type { calibration_statistics } from '../models/calibration_statistics';
-import type { dark_mask_settings } from '../models/dark_mask_settings';
-import type { dataset_settings } from '../models/dataset_settings';
-import type { detector_list } from '../models/detector_list';
-import type { detector_selection } from '../models/detector_selection';
-import type { detector_settings } from '../models/detector_settings';
-import type { detector_status } from '../models/detector_status';
-import type { file_writer_settings } from '../models/file_writer_settings';
-import type { fpga_status } from '../models/fpga_status';
-import type { image_buffer_status } from '../models/image_buffer_status';
-import type { image_format_settings } from '../models/image_format_settings';
-import type { image_pusher_status } from '../models/image_pusher_status';
-import type { indexing_settings } from '../models/indexing_settings';
-import type { instrument_metadata } from '../models/instrument_metadata';
-import type { jfjoch_statistics } from '../models/jfjoch_statistics';
-import type { measurement_statistics } from '../models/measurement_statistics';
-import type { plots } from '../models/plots';
-import type { roi_definitions } from '../models/roi_definitions';
-import type { scan_result } from '../models/scan_result';
-import type { spot_finding_settings } from '../models/spot_finding_settings';
-import type { zeromq_metadata_settings } from '../models/zeromq_metadata_settings';
-import type { zeromq_preview_settings } from '../models/zeromq_preview_settings';
-
-import type { CancelablePromise } from '../core/CancelablePromise';
-import { OpenAPI } from '../core/OpenAPI';
-import { request as __request } from '../core/request';
-
-export class DefaultService {
-
-    /**
-     * Initialize detector and data acquisition
-     * Should be used in two cases:
-     * - Detector is in `Inactive` state
-     * - Detector is in `Error` state
-     * X-ray shutter must be closed.
-     * This operation will reconfigure network interface of the detector.
-     * During operation of the detector it is recommended to use the `POST /pedestal` operation instead.
-     * If storage cells are used, the execution time might be few minutes.
-     *
-     * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
-     *
-     * @returns any Initialization started
-     * @throws ApiError
-     */
-    public static postInitialize(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/initialize',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Collect dark current for the detector
-     * Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.
-     *
-     * X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).
-     *
-     * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
-     *
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static postPedestal(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/pedestal',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Start detector
-     * Start data acquisition.
-     * Detector must be in `Idle` state.
-     * Default behavior is for the call to block until detector is ready to accept soft/TTL triggers.
-     * However, this behavior can be changed by settings `async_start` to true in the request body,
-     * in which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static postStart(
-        requestBody?: dataset_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/start',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Wait for acquisition running
-     * Block execution of external script till detector and Jungfraujoch are ready to collect data.
-     * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
-     * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
-     *
-     * @param timeout Timeout in seconds (0 == immediate response)
-     * @returns any Detector in `Measuring` state
-     * @throws ApiError
-     */
-    public static postWaitUntilRunning(
-        timeout: number = 60,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/wait_until_running',
-            query: {
-                'timeout': timeout,
-            },
-            errors: {
-                400: `Timeout parameter out of bounds`,
-                500: `Error within Jungfraujoch code - see output message.`,
-                502: `Detector is inactive mode`,
-                504: `Timeout reached, need to restart operation`,
-            },
-        });
-    }
-
-    /**
-     * Wait for acquisition done
-     * Block execution of external script till initialization, data collection or pedestal is finished.
-     * Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.
-     *
-     * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
-     * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
-     *
-     * @param timeout Timeout in seconds (0 == immediate response)
-     * @returns any Detector in `Idle` state, another data collection can start immediately
-     * @throws ApiError
-     */
-    public static postWaitTillDone(
-        timeout: number = 60,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/wait_till_done',
-            query: {
-                'timeout': timeout,
-            },
-            errors: {
-                400: `Timeout parameter out of bounds`,
-                500: `Error within Jungfraujoch code - see output message.`,
-                502: `Detector is inactive mode`,
-                504: `Timeout reached, need to restart operation`,
-            },
-        });
-    }
-
-    /**
-     * Send soft trigger to the detector
-     * Generate soft trigger
-     * @returns any Trigger sent
-     * @throws ApiError
-     */
-    public static postTrigger(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/trigger',
-        });
-    }
-
-    /**
-     * Cancel running data collection
-     * Command will inform FPGA network card to stop pedestal or data collection at the current stage.
-     * Any frame that is currently being processed by CPU will be finished and sent to writer.
-     * Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.
-     *
-     * If data collection is not running, the command has no effect.
-     *
-     * @returns any Cancel request sent to FPGAs (or ignored, as data collection is not running)
-     * @throws ApiError
-     */
-    public static postCancel(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/cancel',
-        });
-    }
-
-    /**
-     * Prepare detector to turn off
-     * Should be in `Idle` or `Error` state.
-     * Command deactivates data acquisition and turns off detector high voltage and ASIC.
-     * Should be used always before turning off power from the detector.
-     *
-     * @returns any Detector ready to turn off
-     * @throws ApiError
-     */
-    public static postDeactivate(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/deactivate',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Change detector configuration
-     * Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     * If detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.
-     * If detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigDetector(
-        requestBody?: detector_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/detector',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get detector configuration
-     * Can be done anytime
-     * @returns detector_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigDetector(): CancelablePromise<detector_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/detector',
-        });
-    }
-
-    /**
-     * Change indexing algorithm settings
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigIndexing(
-        requestBody?: indexing_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/indexing',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get indexing configuration
-     * Can be done anytime
-     * @returns indexing_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigIndexing(): CancelablePromise<indexing_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/indexing',
-        });
-    }
-
-    /**
-     * Change file writer settings
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigFileWriter(
-        requestBody?: file_writer_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/file_writer',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get file writer settings
-     * Can be done anytime
-     * @returns file_writer_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigFileWriter(): CancelablePromise<file_writer_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/file_writer',
-        });
-    }
-
-    /**
-     * Change instrument metadata
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigInstrument(
-        requestBody?: instrument_metadata,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/instrument',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get instrument metadata
-     * Can be done anytime
-     * @returns instrument_metadata Everything OK
-     * @throws ApiError
-     */
-    public static getConfigInstrument(): CancelablePromise<instrument_metadata> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/instrument',
-        });
-    }
-
-    /**
-     * Change image output format
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigImageFormat(
-        requestBody?: image_format_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/image_format',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get image output format
-     * Can be done anytime
-     * @returns image_format_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigImageFormat(): CancelablePromise<image_format_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/image_format',
-        });
-    }
-
-    /**
-     * Configure format for raw data collection
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static postConfigImageFormatRaw(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/config/image_format/raw',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Configure format for data collection with full conversion
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static postConfigImageFormatConversion(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/config/image_format/conversion',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Configure spot finding
-     * Can be done anytime, also while data collection is running
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigSpotFinding(
-        requestBody?: spot_finding_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/spot_finding',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-            },
-        });
-    }
-
-    /**
-     * Get data processing configuration
-     * Can be done anytime
-     * @returns spot_finding_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigSpotFinding(): CancelablePromise<spot_finding_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/spot_finding',
-        });
-    }
-
-    /**
-     * Configure azimuthal integration
-     * Can be done when detector is Inactive or Idle
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigAzimInt(
-        requestBody?: azim_int_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/azim_int',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get azimuthal integration configuration
-     * Can be done anytime
-     * @returns azim_int_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigAzimInt(): CancelablePromise<azim_int_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/azim_int',
-        });
-    }
-
-    /**
-     * Load binary image for internal FPGA generator
-     * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
-     * Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates
-     * (depending on detector settings).
-     *
-     * @param id Image id to upload
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigInternalGeneratorImage(
-        id?: number,
-        requestBody?: Blob,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/internal_generator_image',
-            query: {
-                'id': id,
-            },
-            body: requestBody,
-            mediaType: 'application/octet-stream',
-            errors: {
-                400: `Input parsing or validation error`,
-            },
-        });
-    }
-
-    /**
-     * Load TIFF image for internal FPGA generator
-     * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
-     * Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates
-     * (depending on detector settings).
-     *
-     * @param id Image ID to upload
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigInternalGeneratorImageTiff(
-        id?: number,
-        requestBody?: Blob,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/internal_generator_image.tiff',
-            query: {
-                'id': id,
-            },
-            body: requestBody,
-            mediaType: 'image/tiff',
-            errors: {
-                400: `Input parsing or validation error`,
-            },
-        });
-    }
-
-    /**
-     * Select detector
-     * Jungfraujoch allows to control multiple detectors and/or region-of-interests.
-     * The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).
-     * Changing detector will set detector to `Inactive` state and will require reinitialization.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigSelectDetector(
-        requestBody?: detector_selection,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/select_detector',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * List available detectors
-     * Configured detectors that can be selected by used
-     * @returns detector_list Everything OK
-     * @throws ApiError
-     */
-    public static getConfigSelectDetector(): CancelablePromise<detector_list> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/select_detector',
-        });
-    }
-
-    /**
-     * Set ZeroMQ preview settings
-     * Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.
-     * Here settings of the socket can be adjusted.
-     * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
-     * Options set with this PUT request have no effect on HTTP based preview.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigZeromqPreview(
-        requestBody?: zeromq_preview_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/zeromq_preview',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get ZeroMQ preview settings
-     * @returns zeromq_preview_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigZeromqPreview(): CancelablePromise<zeromq_preview_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/zeromq_preview',
-        });
-    }
-
-    /**
-     * Set ZeroMQ metadata settings
-     * Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.
-     * Here settings of the socket can be adjusted.
-     * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigZeromqMetadata(
-        requestBody?: zeromq_metadata_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/zeromq_metadata',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get ZeroMQ metadata socket settings
-     * @returns zeromq_metadata_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigZeromqMetadata(): CancelablePromise<zeromq_metadata_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/zeromq_metadata',
-        });
-    }
-
-    /**
-     * Set configuration for dark data collection to calculate mask
-     * This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.
-     * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
-     *
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigDarkMask(
-        requestBody?: dark_mask_settings,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/dark_mask',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get settings for dark data collection to calculate mask
-     * @returns dark_mask_settings Everything OK
-     * @throws ApiError
-     */
-    public static getConfigDarkMask(): CancelablePromise<dark_mask_settings> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/dark_mask',
-        });
-    }
-
-    /**
-     * Get Jungfraujoch status
-     * Status of the data acquisition
-     * @returns broker_status Everything OK
-     * @throws ApiError
-     */
-    public static getStatus(): CancelablePromise<broker_status> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/status',
-        });
-    }
-
-    /**
-     * Get status of FPGA devices
-     * @returns fpga_status Everything OK
-     * @throws ApiError
-     */
-    public static getFpgaStatus(): CancelablePromise<fpga_status> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/fpga_status',
-        });
-    }
-
-    /**
-     * Return XFEL pulse IDs for the current data acquisition
-     * Return array of XFEL pulse IDs - (-1) if image not recorded
-     * @returns number Pulse ID collected
-     * @throws ApiError
-     */
-    public static getXfelPulseId(): CancelablePromise<Array<number>> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/xfel/pulse_id',
-            errors: {
-                404: `Not in XFEL mode or no acquisition recorded`,
-            },
-        });
-    }
-
-    /**
-     * Return XFEL event codes for the current data acquisition
-     * Return array of XFEL event codes
-     * @returns number Event codes collected
-     * @throws ApiError
-     */
-    public static getXfelEventCode(): CancelablePromise<Array<number>> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/xfel/event_code',
-            errors: {
-                404: `Not in XFEL mode or no acquisition recorded`,
-            },
-        });
-    }
-
-    /**
-     * Get status of image pusher
-     * @returns image_pusher_status Everything OK
-     * @throws ApiError
-     */
-    public static getImagePusherStatus(): CancelablePromise<image_pusher_status> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_pusher/status',
-            errors: {
-                500: `Error encountered when trying to read status`,
-            },
-        });
-    }
-
-    /**
-     * Get detector status
-     * Status of the JUNGFRAU detector
-     * @returns detector_status Everything OK
-     * @throws ApiError
-     */
-    public static getDetectorStatus(): CancelablePromise<detector_status> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/detector/status',
-            errors: {
-                404: `Running in "simulator" mode - no detector present`,
-                500: `Error encountered when trying to read status`,
-            },
-        });
-    }
-
-    /**
-     * Get ROI definitions
-     * @returns roi_definitions OK
-     * @throws ApiError
-     */
-    public static getConfigRoi(): CancelablePromise<roi_definitions> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/roi',
-        });
-    }
-
-    /**
-     * Upload ROI definitions
-     * @param requestBody
-     * @returns any Everything OK
-     * @throws ApiError
-     */
-    public static putConfigRoi(
-        requestBody?: roi_definitions,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/roi',
-            body: requestBody,
-            mediaType: 'application/json',
-            errors: {
-                400: `Input parsing or validation error`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get general statistics
-     * @returns jfjoch_statistics Everything OK
-     * @throws ApiError
-     */
-    public static getStatistics(): CancelablePromise<jfjoch_statistics> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/statistics',
-        });
-    }
-
-    /**
-     * Get data collection statistics
-     * Results of the last data collection
-     * @returns measurement_statistics Everything OK
-     * @throws ApiError
-     */
-    public static getStatisticsDataCollection(): CancelablePromise<measurement_statistics> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/statistics/data_collection',
-            errors: {
-                404: `No data collection performed so far`,
-            },
-        });
-    }
-
-    /**
-     * Get calibration statistics
-     * Statistics are provided for each module/storage cell separately
-     * @returns calibration_statistics Everything OK
-     * @throws ApiError
-     */
-    public static getStatisticsCalibration(): CancelablePromise<calibration_statistics> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/statistics/calibration',
-        });
-    }
-
-    /**
-     * Get mask of the detector (binary)
-     * Detector must be Initialized.
-     * Get full pixel mask of the detector.
-     * See NXmx standard for meaning of pixel values.
-     *
-     * @returns binary Binary array (4 byte; unsigned)
-     * @throws ApiError
-     */
-    public static getConfigMask(): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/mask',
-        });
-    }
-
-    /**
-     * Detector must be Initialized.
-     * Get user mask of the detector (binary)
-     *
-     * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
-     * @returns binary User mask in binary format (4 byte; unsigned)
-     * @throws ApiError
-     */
-    public static getConfigUserMask(): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/user_mask',
-        });
-    }
-
-    /**
-     * Upload user mask of the detector (binary)
-     * Should be in `Idle` state.
-     * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
-     * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
-     * In the latter case - module gaps are ignored and don't need to be assigned value.
-     * Mask is expected as binary array (4-byte; unsigned).
-     * 0 - good pixel, other value - masked
-     * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
-     *
-     * @param requestBody
-     * @returns any All good
-     * @throws ApiError
-     */
-    public static putConfigUserMask(
-        requestBody?: Blob,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/user_mask',
-            body: requestBody,
-            mediaType: 'application/octet-stream',
-            errors: {
-                400: `Mask is not 4-byte unsigned integer array or empty body`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get mask of the detector (TIFF)
-     * Should be in `Idle` state.
-     * Get full pixel mask of the detector
-     * See NXmx standard for meaning of pixel values
-     *
-     * @returns binary Pixel mask in TIFF format (4 byte; unsigned)
-     * @throws ApiError
-     */
-    public static getConfigMaskTiff(): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/mask.tiff',
-        });
-    }
-
-    /**
-     * Detector must be Initialized.
-     * Get user mask of the detector (TIFF)
-     *
-     * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
-     * @returns binary User mask in TIFF format (4 byte; unsigned)
-     * @throws ApiError
-     */
-    public static getConfigUserMaskTiff(): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/config/user_mask.tiff',
-        });
-    }
-
-    /**
-     * Upload user mask of the detector
-     * Should be in `Idle` state.
-     * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
-     * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
-     * In the latter case - module gaps are ignored and don't need to be assigned value.
-     * Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
-     * 0 - good pixel, other value - masked
-     * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
-     * User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
-     *
-     * @param requestBody
-     * @returns any All good
-     * @throws ApiError
-     */
-    public static putConfigUserMaskTiff(
-        requestBody?: Blob,
-    ): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'PUT',
-            url: '/config/user_mask.tiff',
-            body: requestBody,
-            mediaType: 'image/tiff',
-            errors: {
-                400: `Not a valid single-channel TIFF or size doesn't match the detector`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get pedestal in TIFF format
-     * @param gainLevel Gain level (0, 1, 2)
-     * @param sc Storage cell number
-     * @returns binary Calibration image
-     * @throws ApiError
-     */
-    public static getPreviewPedestalTiff(
-        gainLevel: number,
-        sc?: number,
-    ): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/preview/pedestal.tiff',
-            query: {
-                'gain_level': gainLevel,
-                'sc': sc,
-            },
-            errors: {
-                400: `Invalid gain level or storage cell number`,
-                404: `No calibration recorded so far`,
-            },
-        });
-    }
-
-    /**
-     * Generate 1D plot from Jungfraujoch
-     * @param type Type of requested plot
-     * @param binning Binning of frames for the plot (0 = default binning)
-     * @param fill Fill value for elements that were missed during data collection
-     *
-     * @param experimentalCoord If measurement has goniometer axis defined, plot X-axis will represent rotation angle
-     * If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
-     * For still measurement the number is ignored
-     *
-     * @param azintUnit Unit used for azim int.
-     *
-     * @returns plots Everything OK.
-     * @throws ApiError
-     */
-    public static getPreviewPlot(
-        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio',
-        binning: number = 1,
-        fill?: number,
-        experimentalCoord: boolean = false,
-        azintUnit: 'Q_recipA' | 'd_A' | 'two_theta_deg' = 'Q_recipA',
-    ): CancelablePromise<plots> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/preview/plot',
-            query: {
-                'binning': binning,
-                'type': type,
-                'fill': fill,
-                'experimental_coord': experimentalCoord,
-                'azint_unit': azintUnit,
-            },
-            errors: {
-                400: `Input parsing or validation error`,
-            },
-        });
-    }
-
-    /**
-     * Generate 1D plot from Jungfraujoch and send in raw binary format.
-     * Data are provided as (32-bit) float binary array.
-     * This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
-     *
-     * @param type Type of requested plot
-     * @param roi Name of ROI for which plot is requested
-     * @returns binary Everything OK.
-     * @throws ApiError
-     */
-    public static getPreviewPlotBin(
-        type: 'bkg_estimate' | 'azint' | 'azint_1d' | 'spot_count' | 'spot_count_low_res' | 'spot_count_indexed' | 'spot_count_ice' | 'indexing_rate' | 'indexing_lattice_count' | 'indexing_unit_cell_length' | 'indexing_unit_cell_angle' | 'profile_radius' | 'mosaicity' | 'b_factor' | 'error_pixels' | 'saturated_pixels' | 'image_collection_efficiency' | 'receiver_delay' | 'receiver_free_send_buf' | 'strong_pixels' | 'roi_sum' | 'roi_mean' | 'roi_max_count' | 'roi_pixels' | 'roi_weighted_x' | 'roi_weighted_y' | 'packets_received' | 'max_pixel_value' | 'resolution_estimate' | 'pixel_sum' | 'processing_time' | 'beam_center_x' | 'beam_center_y' | 'integrated_reflections' | 'image_scale_factor' | 'image_scale_cc' | 'image_scale_b' | 'compression_ratio',
-        roi?: string,
-    ): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/preview/plot.bin',
-            query: {
-                'type': type,
-                'roi': roi,
-            },
-            errors: {
-                400: `Input parsing or validation error`,
-            },
-        });
-    }
-
-    /**
-     * Get full scan result
-     * @returns scan_result Everything OK.
-     * @throws ApiError
-     */
-    public static getResultScan(): CancelablePromise<scan_result> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/result/scan',
-            errors: {
-                404: `No grid scan recorded`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get Start message in CBOR format
-     * Contains metadata for a dataset (e.g., experimental geometry)
-     * @returns binary Return start message
-     * @throws ApiError
-     */
-    public static getImageBufferStartCbor(): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_buffer/start.cbor',
-            errors: {
-                404: `No measurement so far`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get image message in CBOR format
-     * Contains full image data and metadata. The image must come from the latest data collection.
-     * @param id Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
-     * @returns binary Return image message
-     * @throws ApiError
-     */
-    public static getImageBufferImageCbor(
-        id: number = -1,
-    ): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_buffer/image.cbor',
-            query: {
-                'id': id,
-            },
-            errors: {
-                404: `Image not present in the buffer - either not yet measured or already replaced by a next image.`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get preview image in JPEG format using custom settings
-     * @param id Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
-     * @param showUserMask Show user mask
-     * @param showRoi Show ROI areas on the image
-     * @param showSpots Show spot finding results on the image
-     * @param showBeamCenter Show beam center on the image
-     * @param saturation Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
-     * @param jpegQuality Quality of JPEG image (100 - highest; 0 - lowest)
-     * @param showResRing Show resolution ring, provided in Angstrom
-     * @param color Color scale for preview image
-     * @param showResEst Show resolution estimation as a ring
-     * @returns binary Preview image
-     * @throws ApiError
-     */
-    public static getImageBufferImageJpeg(
-        id: number = -1,
-        showUserMask: boolean = false,
-        showRoi: boolean = false,
-        showSpots: boolean = true,
-        showBeamCenter: boolean = true,
-        saturation?: number,
-        jpegQuality: number = 100,
-        showResRing: number = 0.1,
-        color: 'indigo' | 'viridis' | 'bw' | 'wb' | 'green' | 'heat' | 'magma' | 'inferno' = 'indigo',
-        showResEst: boolean = false,
-    ): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_buffer/image.jpeg',
-            query: {
-                'id': id,
-                'show_user_mask': showUserMask,
-                'show_roi': showRoi,
-                'show_spots': showSpots,
-                'show_beam_center': showBeamCenter,
-                'saturation': saturation,
-                'jpeg_quality': jpegQuality,
-                'show_res_ring': showResRing,
-                'color': color,
-                'show_res_est': showResEst,
-            },
-            errors: {
-                400: `Input parsing or validation error`,
-                404: `Image not present in the buffer - either not yet measured or already replaced by a next image.`,
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get preview image in TIFF format
-     * @param id Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
-     * @returns binary Preview image
-     * @throws ApiError
-     */
-    public static getImageBufferImageTiff(
-        id: number = -1,
-    ): CancelablePromise<Blob> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_buffer/image.tiff',
-            query: {
-                'id': id,
-            },
-            errors: {
-                404: `No preview image recorded so far`,
-            },
-        });
-    }
-
-    /**
-     * Clear image buffer
-     * Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.
-     * @returns any Done
-     * @throws ApiError
-     */
-    public static postImageBufferClear(): CancelablePromise<any> {
-        return __request(OpenAPI, {
-            method: 'POST',
-            url: '/image_buffer/clear',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get status of the image buffers
-     * Can be run at any stage of Jungfraujoch operation, including during data collection.
-     * The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,
-     * then image might be replaced in the buffer between calling /images and /image.cbor.
-     *
-     * @returns image_buffer_status Done
-     * @throws ApiError
-     */
-    public static getImageBufferStatus(): CancelablePromise<image_buffer_status> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/image_buffer/status',
-            errors: {
-                500: `Error within Jungfraujoch code - see output message.`,
-            },
-        });
-    }
-
-    /**
-     * Get Jungfraujoch version of jfjoch_broker
-     * @returns string Release number of Jungfraujoch
-     * @throws ApiError
-     */
-    public static getVersion(): CancelablePromise<string> {
-        return __request(OpenAPI, {
-            method: 'GET',
-            url: '/version',
-        });
-    }
-
-}
-- 
2.52.0


From 7ed424a4ca4f0110c9823246f6488e878c896d8a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 20:48:19 +0200
Subject: [PATCH 092/228] JFJochReceiverFPGA: Fix typo

---
 receiver/JFJochReceiverFPGA.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/receiver/JFJochReceiverFPGA.cpp b/receiver/JFJochReceiverFPGA.cpp
index 447521bc..470a9096 100644
--- a/receiver/JFJochReceiverFPGA.cpp
+++ b/receiver/JFJochReceiverFPGA.cpp
@@ -282,7 +282,7 @@ void JFJochReceiverFPGA::FrameTransformationThread(uint32_t threadid) {
     std::unique_ptr<MXAnalysisAfterFPGA> analyzer;
 
     try {
-        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, *az_int_mapping indexer);
+        analyzer = std::make_unique<MXAnalysisAfterFPGA>(experiment, *az_int_mapping, indexer);
     } catch (const JFJochException &e) {
         frame_transformation_ready.count_down();
         logger.Error("Thread setup error {}", e.what());
-- 
2.52.0


From 237de5a0fca548daa0f2acdb42c7a4dd997b1fdb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 21:32:36 +0200
Subject: [PATCH 093/228] frontend: convert to function components + TanStack
 Query

Replace all class components with function components and move server-state
polling to @tanstack/react-query.

- add @tanstack/react-query; generate query helpers via the hey-api
  @tanstack/react-query plugin (src/client/@tanstack)
- QueryClientProvider + one-time client.setConfig({ baseUrl: '' }) in index.tsx
- App polls statistics with useQuery(getStatisticsOptions, refetchInterval),
  DataProcessingPlot uses getPreviewPlotOptions; manual setInterval polling gone
- memo() on presentational children; with TanStack structural sharing this
  re-renders a child only when its own statistics slice changes
- PreviewImage stays imperative (binary JPEG -> object URL) using useEffect +
  a ref for the object-URL lifecycle
- fix AzIntSettings correction checkboxes that mutated state in place (relied on
  the poll re-render); they now use setState
- drop dead code uncovered during the port (unused upload/deactivate handlers
  and imports in ImageFormatSettings, DetectorSettings, ROI)

Build (tsc + vite) passes; dev server transforms all entry modules.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/openapi-ts.config.ts                 |    1 +
 frontend/package-lock.json                    |   27 +
 frontend/package.json                         |    1 +
 frontend/src/App.tsx                          |  362 ++---
 .../src/client/@tanstack/react-query.gen.ts   | 1317 +++++++++++++++++
 frontend/src/components/AzIntSettings.tsx     |  293 ++--
 .../src/components/ButtonWithSnackbar.tsx     |  109 +-
 frontend/src/components/Calibration.tsx       |   60 +-
 frontend/src/components/DarkMaskSettings.tsx  |  344 ++---
 frontend/src/components/DataCollection.tsx    |  564 ++++---
 .../src/components/DataProcessingPlot.tsx     |  117 +-
 .../src/components/DataProcessingPlots.tsx    |  224 ++-
 .../src/components/DataProcessingSettings.tsx |  384 ++---
 frontend/src/components/DetectorSelection.tsx |  122 +-
 frontend/src/components/DetectorSettings.tsx  |  795 +++++-----
 frontend/src/components/DetectorStatus.tsx    |  119 +-
 frontend/src/components/ErrorMessage.tsx      |   59 +-
 .../src/components/FileWriterSettings.tsx     |  157 +-
 frontend/src/components/FpgaStatus.tsx        |   78 +-
 .../src/components/ImageFormatSettings.tsx    |  502 +++----
 frontend/src/components/ImagePusherStatus.tsx |   71 +-
 frontend/src/components/IndexingSettings.tsx  |  573 ++++---
 .../src/components/InstrumentMetadata.tsx     |  182 +--
 .../src/components/MeasurementStatistics.tsx  |  145 +-
 frontend/src/components/NumberTextField.tsx   |  139 +-
 frontend/src/components/PixelMask.tsx         |  104 +-
 frontend/src/components/PreviewImage.tsx      |  695 ++++-----
 frontend/src/components/ROI.tsx               |  493 +++---
 frontend/src/components/StatusBar.tsx         |   78 +-
 frontend/src/components/ZeroMQPreview.tsx     |  202 ++-
 frontend/src/index.tsx                        |   15 +-
 31 files changed, 4408 insertions(+), 3924 deletions(-)
 create mode 100644 frontend/src/client/@tanstack/react-query.gen.ts

diff --git a/frontend/openapi-ts.config.ts b/frontend/openapi-ts.config.ts
index a35193eb..ed71a8a9 100644
--- a/frontend/openapi-ts.config.ts
+++ b/frontend/openapi-ts.config.ts
@@ -13,5 +13,6 @@ export default defineConfig({
             enums: { mode: 'javascript' },
         },
         '@hey-api/sdk',
+        '@tanstack/react-query',
     ],
 });
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 619f1e11..4e746d46 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -14,6 +14,7 @@
         "@mui/icons-material": "^6.1.2",
         "@mui/material": "^6.1.2",
         "@mui/x-data-grid": "^7.19.0",
+        "@tanstack/react-query": "^5.101.0",
         "@types/node": "^25.2.3",
         "@types/react": "^19.2.14",
         "@types/react-dom": "^19.2.3",
@@ -3492,6 +3493,32 @@
         "@swc/counter": "^0.1.3"
       }
     },
+    "node_modules/@tanstack/query-core": {
+      "version": "5.101.0",
+      "resolved": "https://registry.npmjs.org/@tanstack/query-core/-/query-core-5.101.0.tgz",
+      "integrity": "sha512-cQetA74EB+seWySv1TTKr828TnP0u39m6LykwDXIo84SNortpDkp30TMEjkqtYCNP9c40uT/iwl6MLiufEt0Ow==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/tannerlinsley"
+      }
+    },
+    "node_modules/@tanstack/react-query": {
+      "version": "5.101.0",
+      "resolved": "https://registry.npmjs.org/@tanstack/react-query/-/react-query-5.101.0.tgz",
+      "integrity": "sha512-rLlJXSpkqfizLWgkR5+eLeIk0MvTx/meEIR7LRjxic+qxiQP8zVjq7BqQkiCMNLQBlLfuOLqqr6KO5GtrDlmSg==",
+      "license": "MIT",
+      "dependencies": {
+        "@tanstack/query-core": "5.101.0"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/tannerlinsley"
+      },
+      "peerDependencies": {
+        "react": "^18 || ^19"
+      }
+    },
     "node_modules/@turf/area": {
       "version": "7.2.0",
       "resolved": "https://registry.npmjs.org/@turf/area/-/area-7.2.0.tgz",
diff --git a/frontend/package.json b/frontend/package.json
index a28a1bfa..da894318 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -11,6 +11,7 @@
     "@mui/icons-material": "^6.1.2",
     "@mui/material": "^6.1.2",
     "@mui/x-data-grid": "^7.19.0",
+    "@tanstack/react-query": "^5.101.0",
     "@types/node": "^25.2.3",
     "@types/react": "^19.2.14",
     "@types/react-dom": "^19.2.3",
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 83974b4d..97194c70 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -1,7 +1,8 @@
-import React, {Component} from 'react';
+import React, {useState} from 'react';
 
 import {createTheme, CssBaseline, Grid, Stack, Switch, ThemeProvider, Typography} from "@mui/material";
 import {indigo, lime} from "@mui/material/colors";
+import {useQuery} from "@tanstack/react-query";
 
 import DataProcessingSettings from "./components/DataProcessingSettings";
 import DetectorSettings from "./components/DetectorSettings";
@@ -18,9 +19,8 @@ import ImageFormatSettings from "./components/ImageFormatSettings";
 import InstrumentMetadata from "./components/InstrumentMetadata";
 import {JFJOCH_VERSION} from "./version";
 import FpgaStatus from "./components/FpgaStatus";
-import {getStatistics, plot_type} from "./client";
-import {client} from "./client/client.gen";
-import {jfjoch_statistics} from "./client";
+import {plot_type} from "./client";
+import {getStatisticsOptions} from "./client/@tanstack/react-query.gen";
 import DataCollection from "./components/DataCollection";
 import ZeroMQPreview from "./components/ZeroMQPreview";
 import PixelMask from "./components/PixelMask";
@@ -38,218 +38,162 @@ const jfjoch_theme = createTheme({
     },
 });
 
-type MyState = {
-    show_detector_setup: boolean,
-    show_module_calibration: boolean,
-    show_preview: boolean,
-    show_roi_setup: boolean,
-    show_fpga_status: boolean,
-    connection_error: boolean,
-    show_data_collection: boolean,
-    s: jfjoch_statistics
+function renderTitleWithSwitch(name: string, checked: boolean, func: ((event: React.ChangeEvent<HTMLInputElement>) => void)) {
+    return <Grid item xs={12}>
+        <Paper style={{textAlign: 'center'}} sx={{height: 60, width: '100%'}} component={Stack}
+               direction="column" justifyContent="center">
+            <Grid container spacing={0}>
+                <Grid xs={1}/>
+                <Grid xs={10}>
+                    <Typography variant="h5"> {name} </Typography>
+                </Grid>
+                <Grid xs={1}>
+                    <Switch checked={checked}
+                            onChange={func}
+                            name="Show detector setup"/>
+                </Grid>
+            </Grid>
+        </Paper>
+    </Grid>
 }
 
-type MyProps = {}
+function App() {
+    const [showDetectorSetup, setShowDetectorSetup] = useState(false);
+    const [showModuleCalibration, setShowModuleCalibration] = useState(false);
+    const [showPreview, setShowPreview] = useState(false);
+    const [showRoiSetup, setShowRoiSetup] = useState(false);
+    const [showFpgaStatus, setShowFpgaStatus] = useState(false);
+    const [showDataCollection, setShowDataCollection] = useState(false);
 
-class App extends Component<MyProps, MyState> {
-    interval: ReturnType<typeof setInterval> | undefined;
+    // Poll general statistics once per second; structural sharing keeps unchanged
+    // slices referentially stable so memoized children below only re-render when
+    // their own slice changes.
+    const {data, isError, refetch} = useQuery({
+        ...getStatisticsOptions(),
+        refetchInterval: 1000,
+    });
+    const s = isError || data === undefined ? {} : data;
 
-    state : MyState = {
-        show_detector_setup: false,
-        show_module_calibration: false,
-        show_preview: false,
-        show_roi_setup: false,
-        show_fpga_status: false,
-        connection_error: true,
-        show_data_collection: false,
-        s: {}
-    }
+    const isMeasuring = s.broker?.state === 'Measuring';
 
-    getValues = () => {
-        getStatistics({ throwOnError: true })
-            .then(({data}) => this.setState({s: data, connection_error: false}))
-            .catch(_ => {
-                this.setState({s: {}, connection_error: true});
-            });
-    }
-
-    componentWillUnmount() {
-        clearInterval(this.interval);
-    }
-    componentDidMount() {
-        client.setConfig({ baseUrl: '' });
-        this.getValues();
-        this.interval = setInterval(() => this.getValues(), 1000);
-    }
-
-    showPreviewToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_preview: event.target.checked});
-    }
-
-    showDetectorSetupToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_detector_setup: event.target.checked});
-    }
-
-    showModuleCalibrationToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_module_calibration: event.target.checked});
-    }
-
-    showROISetupToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_roi_setup: event.target.checked});
-    }
-
-    showFPGAStatusToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_fpga_status: event.target.checked});
-    }
-
-    showDataCollectionToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({show_data_collection: event.target.checked});
-    }
-
-    renderTitleWithSwitch = (name: string, checked: boolean, func: ((event: React.ChangeEvent<HTMLInputElement>) => void)) => {
-        return <Grid item xs={12}>
-            <Paper style={{textAlign: 'center'}} sx={{height: 60, width: '100%'}} component={Stack}
-                   direction="column" justifyContent="center">
-                <Grid container spacing={0}>
-                    <Grid xs={1}/>
-                    <Grid xs={10}>
-                        <Typography variant="h5"> {name} </Typography>
-                    </Grid>
-                    <Grid xs={1}>
-                        <Switch checked={checked}
-                                onChange={func}
-                                name="Show detector setup"/>
-                    </Grid>
+    return <ThemeProvider theme={jfjoch_theme}>
+        <CssBaseline enableColorScheme/>
+        <StatusBar s={s.broker}/> <br/><br/><br/><br/>
+        <div style={{
+            display: 'flex',
+            alignItems: 'center',
+            justifyContent: 'center'
+        }}>
+            <Grid container
+                  justifyContent="center"
+                  alignItems="center"
+                  spacing={3}
+                  sx={{width: "95%"}}>
+                <Grid item xs={2}/>
+                <Grid item xs={8}>
+                    <ErrorMessage s={s.broker}/>
                 </Grid>
-            </Paper>
-        </Grid>
-    };
-
-    isMeasuring() : boolean {
-        return (this.state.s.broker !== undefined)
-            && (this.state.s.broker.state == 'Measuring');
-    }
-
-    render() {
-        return <ThemeProvider theme={jfjoch_theme}>
-            <CssBaseline enableColorScheme/>
-            <StatusBar s={this.state.s.broker}/> <br/><br/><br/><br/>
-            <div style={{
-                display: 'flex',
-                alignItems: 'center',
-                justifyContent: 'center'
-            }}>
-                <Grid container
-                      justifyContent="center"
-                      alignItems="center"
-                      spacing={3}
-                      sx={{width: "95%"}}>
-                    <Grid item xs={2}/>
-                    <Grid item xs={8}>
-                        <ErrorMessage s={this.state.s.broker}/>
-                    </Grid>
-                    <Grid item xs={2}/>
-                    <Grid item xs={8}>
-                        <DataProcessingPlots height={550} type={plot_type.BKG_ESTIMATE}/>
-                    </Grid>
-                    <Grid item xs={4}>
-                        <MeasurementStatistics
-                            s={(this.state.s.measurement === undefined) ? {} : this.state.s.measurement}/>
-                    </Grid>
-                    <Grid item xs={8}>
-                        <DataProcessingPlots height={800} type={plot_type.INDEXING_RATE}/>
-                    </Grid>
-                    <Grid item xs={4}>
-                        <DataProcessingSettings s={this.state.s.data_processing_settings} update={this.getValues}/>
-                    </Grid>
-                    {
-                        this.renderTitleWithSwitch("Live image preview", this.state.show_preview, this.showPreviewToggle)
-                    }
-                    <Grid item xs={12}>
-                        {this.state.show_preview ? <PreviewImage measuring={this.isMeasuring()}
-                                                                 max_image_number={this.state.s.buffer?.max_image_number}
-                                                                 min_image_number={this.state.s.buffer?.min_image_number}/> : ""}
-                    </Grid>
-                    <br/><br/>
-                    {
-                        this.renderTitleWithSwitch("Data collection",
-                            this.state.show_data_collection, this.showDataCollectionToggle)
-                    }
-                    <Grid item xs={2}/>
-                    <Grid item xs={8}>
-                        {this.state.show_data_collection ? <DataCollection frame_time_us={
-                            this.state.s.detector_settings?.frame_time_us ?? 500
-                        }/> : ""}
-                    </Grid>
-                    <Grid item xs={2}/>
-                    <br/><br/>
-                    {
-                        this.renderTitleWithSwitch("Jungfraujoch expert configuration",
-                            this.state.show_detector_setup, this.showDetectorSetupToggle)
-                    }
-                    <Grid item xs={4}>
-                        {this.state.show_detector_setup ? <Stack spacing={2}>
-                            <DetectorSettings s={this.state.s.detector_settings}/>
-                            <PixelMask s={this.state.s.pixel_mask}/>
-                            <DarkMaskSettings s={this.state.s.dark_mask}/>
-                            <FileWriterSettings s={this.state.s.file_writer_settings}/>
-                        </Stack>: ""}
-                    </Grid>
-                    <Grid item xs={4}>
-                        {this.state.show_detector_setup ?
-                            <Stack spacing={2}>
-                                <DetectorSelection s={this.state.s.detector_list}/>
-                                <DetectorStatus s={this.state.s.detector}/>
-                                <ZeroMQPreview s={this.state.s.zeromq_preview}/>
-                                <IndexingSettings s={this.state.s.indexing} status={this.state.s.broker}/>
-                            </Stack> : ""}
-                    </Grid>
-                    <Grid item xs={4}>
-                        {this.state.show_detector_setup ?
-                            <Stack spacing={2}>
-                                <ImageFormatSettings s={this.state.s.image_format_settings}/>
-                                <InstrumentMetadata s={this.state.s.instrument_metadata}/>
-                                <AzIntSettings s={this.state.s.az_int}/>
-                                <ImagePusherStatus s={this.state.s.image_pusher}/>
-                            </Stack> : ""}
-                    </Grid>
-                    <br/><br/>
-                    {
-                        this.renderTitleWithSwitch("JUNGFRAU module calibration",
-                            this.state.show_module_calibration, this.showModuleCalibrationToggle)
-                    }
-                    <Grid item xs={12}>
-                        {this.state.show_module_calibration ? <Calibration s={this.state.s.calibration}/> : ""}
-                    </Grid>
-                    <br/><br/>
-                    {
-                        this.renderTitleWithSwitch("Region of interest (ROI)",
-                            this.state.show_roi_setup, this.showROISetupToggle)
-                    }
-                    <Grid item xs={12}>
-                        {this.state.show_roi_setup ? <ROI s={this.state.s.roi}/> : ""}
-                    </Grid>
-                    <br/><br/>
-                    {
-                        this.renderTitleWithSwitch("FPGA status",
-                            this.state.show_fpga_status, this.showFPGAStatusToggle)
-                    }
-                    <Grid item xs={12}>
-                        {this.state.show_fpga_status ? <FpgaStatus s={this.state.s.fpga}/> : ""}
-                    </Grid>
+                <Grid item xs={2}/>
+                <Grid item xs={8}>
+                    <DataProcessingPlots height={550} type={plot_type.BKG_ESTIMATE}/>
                 </Grid>
-            </div>
-            <br/>
-            <center>Developed at Paul Scherrer Institute (2019-2024). Main author: <a
-                href="mailto:filip.leonarski@psi.ch">Filip Leonarski</a> <br/>
-                For more information see <a href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron
-                    Rad.</i> (2023). <b>30</b>, 227–234</a> <br/>
-                Version: {JFJOCH_VERSION}&nbsp;&nbsp;&nbsp;
-                <a href="/frontend/openapi.html">API reference</a>&nbsp;&nbsp;&nbsp;
-                <a href="https://jungfraujoch.readthedocs.io/">Documentation</a></center>
-            <br/>
-        </ThemeProvider>
-    }
+                <Grid item xs={4}>
+                    <MeasurementStatistics
+                        s={(s.measurement === undefined) ? {} : s.measurement}/>
+                </Grid>
+                <Grid item xs={8}>
+                    <DataProcessingPlots height={800} type={plot_type.INDEXING_RATE}/>
+                </Grid>
+                <Grid item xs={4}>
+                    <DataProcessingSettings s={s.data_processing_settings} update={refetch}/>
+                </Grid>
+                {
+                    renderTitleWithSwitch("Live image preview", showPreview, e => setShowPreview(e.target.checked))
+                }
+                <Grid item xs={12}>
+                    {showPreview ? <PreviewImage measuring={isMeasuring}
+                                                 max_image_number={s.buffer?.max_image_number}
+                                                 min_image_number={s.buffer?.min_image_number}/> : ""}
+                </Grid>
+                <br/><br/>
+                {
+                    renderTitleWithSwitch("Data collection",
+                        showDataCollection, e => setShowDataCollection(e.target.checked))
+                }
+                <Grid item xs={2}/>
+                <Grid item xs={8}>
+                    {showDataCollection ? <DataCollection frame_time_us={
+                        s.detector_settings?.frame_time_us ?? 500
+                    }/> : ""}
+                </Grid>
+                <Grid item xs={2}/>
+                <br/><br/>
+                {
+                    renderTitleWithSwitch("Jungfraujoch expert configuration",
+                        showDetectorSetup, e => setShowDetectorSetup(e.target.checked))
+                }
+                <Grid item xs={4}>
+                    {showDetectorSetup ? <Stack spacing={2}>
+                        <DetectorSettings s={s.detector_settings}/>
+                        <PixelMask s={s.pixel_mask}/>
+                        <DarkMaskSettings s={s.dark_mask}/>
+                        <FileWriterSettings s={s.file_writer_settings}/>
+                    </Stack>: ""}
+                </Grid>
+                <Grid item xs={4}>
+                    {showDetectorSetup ?
+                        <Stack spacing={2}>
+                            <DetectorSelection s={s.detector_list}/>
+                            <DetectorStatus s={s.detector}/>
+                            <ZeroMQPreview s={s.zeromq_preview}/>
+                            <IndexingSettings s={s.indexing} status={s.broker}/>
+                        </Stack> : ""}
+                </Grid>
+                <Grid item xs={4}>
+                    {showDetectorSetup ?
+                        <Stack spacing={2}>
+                            <ImageFormatSettings s={s.image_format_settings}/>
+                            <InstrumentMetadata s={s.instrument_metadata}/>
+                            <AzIntSettings s={s.az_int}/>
+                            <ImagePusherStatus s={s.image_pusher}/>
+                        </Stack> : ""}
+                </Grid>
+                <br/><br/>
+                {
+                    renderTitleWithSwitch("JUNGFRAU module calibration",
+                        showModuleCalibration, e => setShowModuleCalibration(e.target.checked))
+                }
+                <Grid item xs={12}>
+                    {showModuleCalibration ? <Calibration s={s.calibration}/> : ""}
+                </Grid>
+                <br/><br/>
+                {
+                    renderTitleWithSwitch("Region of interest (ROI)",
+                        showRoiSetup, e => setShowRoiSetup(e.target.checked))
+                }
+                <Grid item xs={12}>
+                    {showRoiSetup ? <ROI s={s.roi}/> : ""}
+                </Grid>
+                <br/><br/>
+                {
+                    renderTitleWithSwitch("FPGA status",
+                        showFpgaStatus, e => setShowFpgaStatus(e.target.checked))
+                }
+                <Grid item xs={12}>
+                    {showFpgaStatus ? <FpgaStatus s={s.fpga}/> : ""}
+                </Grid>
+            </Grid>
+        </div>
+        <br/>
+        <center>Developed at Paul Scherrer Institute (2019-2024). Main author: <a
+            href="mailto:filip.leonarski@psi.ch">Filip Leonarski</a> <br/>
+            For more information see <a href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron
+                Rad.</i> (2023). <b>30</b>, 227–234</a> <br/>
+            Version: {JFJOCH_VERSION}&nbsp;&nbsp;&nbsp;
+            <a href="/frontend/openapi.html">API reference</a>&nbsp;&nbsp;&nbsp;
+            <a href="https://jungfraujoch.readthedocs.io/">Documentation</a></center>
+        <br/>
+    </ThemeProvider>
 }
 
 export default App;
diff --git a/frontend/src/client/@tanstack/react-query.gen.ts b/frontend/src/client/@tanstack/react-query.gen.ts
new file mode 100644
index 00000000..548c3c9d
--- /dev/null
+++ b/frontend/src/client/@tanstack/react-query.gen.ts
@@ -0,0 +1,1317 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import { type DefaultError, queryOptions, type UseMutationOptions } from '@tanstack/react-query';
+
+import { client } from '../client.gen';
+import { getConfigAzimInt, getConfigDarkMask, getConfigDetector, getConfigFileWriter, getConfigImageFormat, getConfigIndexing, getConfigInstrument, getConfigMask, getConfigMaskTiff, getConfigRoi, getConfigSelectDetector, getConfigSpotFinding, getConfigUserMask, getConfigUserMaskTiff, getConfigZeromqMetadata, getConfigZeromqPreview, getDetectorStatus, getFpgaStatus, getImageBufferImageCbor, getImageBufferImageJpeg, getImageBufferImageTiff, getImageBufferStartCbor, getImageBufferStatus, getImagePusherStatus, getPreviewPedestalTiff, getPreviewPlot, getPreviewPlotBin, getResultScan, getStatistics, getStatisticsCalibration, getStatisticsDataCollection, getStatus, getVersion, getXfelEventCode, getXfelPulseId, type Options, postCancel, postConfigImageFormatConversion, postConfigImageFormatRaw, postDeactivate, postImageBufferClear, postInitialize, postPedestal, postStart, postTrigger, postWaitTillDone, postWaitUntilRunning, putConfigAzimInt, putConfigDarkMask, putConfigDetector, putConfigFileWriter, putConfigImageFormat, putConfigIndexing, putConfigInstrument, putConfigInternalGeneratorImage, putConfigInternalGeneratorImageTiff, putConfigRoi, putConfigSelectDetector, putConfigSpotFinding, putConfigUserMask, putConfigUserMaskTiff, putConfigZeromqMetadata, putConfigZeromqPreview } from '../sdk.gen';
+import type { getConfigAzimIntData, getConfigAzimIntResponse, getConfigDarkMaskData, getConfigDarkMaskResponse, getConfigDetectorData, getConfigDetectorResponse, getConfigFileWriterData, getConfigFileWriterResponse, getConfigImageFormatData, getConfigImageFormatResponse, getConfigIndexingData, getConfigIndexingResponse, getConfigInstrumentData, getConfigInstrumentResponse, getConfigMaskData, getConfigMaskResponse, getConfigMaskTiffData, getConfigMaskTiffResponse, getConfigRoiData, getConfigRoiResponse, getConfigSelectDetectorData, getConfigSelectDetectorResponse, getConfigSpotFindingData, getConfigSpotFindingResponse, getConfigUserMaskData, getConfigUserMaskResponse, getConfigUserMaskTiffData, getConfigUserMaskTiffResponse, getConfigZeromqMetadataData, getConfigZeromqMetadataResponse, getConfigZeromqPreviewData, getConfigZeromqPreviewResponse, getDetectorStatusData, getDetectorStatusError, getDetectorStatusResponse, getFpgaStatusData, getFpgaStatusResponse, getImageBufferImageCborData, getImageBufferImageCborError, getImageBufferImageCborResponse, getImageBufferImageJpegData, getImageBufferImageJpegError, getImageBufferImageJpegResponse, getImageBufferImageTiffData, getImageBufferImageTiffResponse, getImageBufferStartCborData, getImageBufferStartCborError, getImageBufferStartCborResponse, getImageBufferStatusData, getImageBufferStatusError, getImageBufferStatusResponse, getImagePusherStatusData, getImagePusherStatusError, getImagePusherStatusResponse, getPreviewPedestalTiffData, getPreviewPedestalTiffResponse, getPreviewPlotBinData, getPreviewPlotBinError, getPreviewPlotBinResponse, getPreviewPlotData, getPreviewPlotError, getPreviewPlotResponse, getResultScanData, getResultScanError, getResultScanResponse, getStatisticsCalibrationData, getStatisticsCalibrationResponse, getStatisticsData, getStatisticsDataCollectionData, getStatisticsDataCollectionResponse, getStatisticsResponse, getStatusData, getStatusResponse, getVersionData, getVersionResponse, getXfelEventCodeData, getXfelEventCodeResponse, getXfelPulseIdData, getXfelPulseIdResponse, postCancelData, postConfigImageFormatConversionData, postConfigImageFormatConversionError, postConfigImageFormatRawData, postConfigImageFormatRawError, postDeactivateData, postDeactivateError, postImageBufferClearData, postImageBufferClearError, postInitializeData, postInitializeError, postPedestalData, postPedestalError, postStartData, postStartError, postTriggerData, postWaitTillDoneData, postWaitTillDoneError, postWaitUntilRunningData, postWaitUntilRunningError, putConfigAzimIntData, putConfigAzimIntError, putConfigDarkMaskData, putConfigDarkMaskError, putConfigDetectorData, putConfigDetectorError, putConfigFileWriterData, putConfigFileWriterError, putConfigImageFormatData, putConfigImageFormatError, putConfigIndexingData, putConfigIndexingError, putConfigInstrumentData, putConfigInstrumentError, putConfigInternalGeneratorImageData, putConfigInternalGeneratorImageError, putConfigInternalGeneratorImageTiffData, putConfigInternalGeneratorImageTiffError, putConfigRoiData, putConfigRoiError, putConfigSelectDetectorData, putConfigSelectDetectorError, putConfigSpotFindingData, putConfigSpotFindingError, putConfigUserMaskData, putConfigUserMaskError, putConfigUserMaskTiffData, putConfigUserMaskTiffError, putConfigZeromqMetadataData, putConfigZeromqMetadataError, putConfigZeromqPreviewData, putConfigZeromqPreviewError } from '../types.gen';
+
+/**
+ * Initialize detector and data acquisition
+ *
+ * Should be used in two cases:
+ * - Detector is in `Inactive` state
+ * - Detector is in `Error` state
+ * X-ray shutter must be closed.
+ * This operation will reconfigure network interface of the detector.
+ * During operation of the detector it is recommended to use the `POST /pedestal` operation instead.
+ * If storage cells are used, the execution time might be few minutes.
+ *
+ * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
+ *
+ */
+export const postInitializeMutation = (options?: Partial<Options<postInitializeData>>): UseMutationOptions<unknown, postInitializeError, Options<postInitializeData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postInitializeError, Options<postInitializeData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postInitialize({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Collect dark current for the detector
+ *
+ * Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.
+ *
+ * X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).
+ *
+ * This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
+ *
+ */
+export const postPedestalMutation = (options?: Partial<Options<postPedestalData>>): UseMutationOptions<unknown, postPedestalError, Options<postPedestalData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postPedestalError, Options<postPedestalData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postPedestal({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Start detector
+ *
+ * Start data acquisition.
+ * Detector must be in `Idle` state.
+ * Default behavior is for the call to block until detector is ready to accept soft/TTL triggers.
+ * However, this behavior can be changed by settings `async_start` to true in the request body,
+ * in which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.
+ *
+ */
+export const postStartMutation = (options?: Partial<Options<postStartData>>): UseMutationOptions<unknown, postStartError, Options<postStartData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postStartError, Options<postStartData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postStart({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Wait for acquisition running
+ *
+ * Block execution of external script till detector and Jungfraujoch are ready to collect data.
+ * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
+ * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
+ *
+ */
+export const postWaitUntilRunningMutation = (options?: Partial<Options<postWaitUntilRunningData>>): UseMutationOptions<unknown, postWaitUntilRunningError, Options<postWaitUntilRunningData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postWaitUntilRunningError, Options<postWaitUntilRunningData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postWaitUntilRunning({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Wait for acquisition done
+ *
+ * Block execution of external script till initialization, data collection or pedestal is finished.
+ * Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.
+ *
+ * To not block web server for a indefinite period of time, the procedure is provided with a timeout.
+ * Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.
+ *
+ */
+export const postWaitTillDoneMutation = (options?: Partial<Options<postWaitTillDoneData>>): UseMutationOptions<unknown, postWaitTillDoneError, Options<postWaitTillDoneData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postWaitTillDoneError, Options<postWaitTillDoneData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postWaitTillDone({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Send soft trigger to the detector
+ *
+ * Generate soft trigger
+ */
+export const postTriggerMutation = (options?: Partial<Options<postTriggerData>>): UseMutationOptions<unknown, DefaultError, Options<postTriggerData>> => {
+    const mutationOptions: UseMutationOptions<unknown, DefaultError, Options<postTriggerData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postTrigger({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Cancel running data collection
+ *
+ * Command will inform FPGA network card to stop pedestal or data collection at the current stage.
+ * Any frame that is currently being processed by CPU will be finished and sent to writer.
+ * Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.
+ *
+ * If data collection is not running, the command has no effect.
+ *
+ */
+export const postCancelMutation = (options?: Partial<Options<postCancelData>>): UseMutationOptions<unknown, DefaultError, Options<postCancelData>> => {
+    const mutationOptions: UseMutationOptions<unknown, DefaultError, Options<postCancelData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postCancel({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Prepare detector to turn off
+ *
+ * Should be in `Idle` or `Error` state.
+ * Command deactivates data acquisition and turns off detector high voltage and ASIC.
+ * Should be used always before turning off power from the detector.
+ *
+ */
+export const postDeactivateMutation = (options?: Partial<Options<postDeactivateData>>): UseMutationOptions<unknown, postDeactivateError, Options<postDeactivateData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postDeactivateError, Options<postDeactivateData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postDeactivate({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export type QueryKey<TOptions extends Options> = [
+    Pick<TOptions, 'baseUrl' | 'body' | 'headers' | 'path' | 'query'> & {
+        _id: string;
+        _infinite?: boolean;
+        tags?: ReadonlyArray<string>;
+    }
+];
+
+const createQueryKey = <TOptions extends Options>(id: string, options?: TOptions, infinite?: boolean, tags?: ReadonlyArray<string>): [
+    QueryKey<TOptions>[0]
+] => {
+    const params: QueryKey<TOptions>[0] = { _id: id, baseUrl: options?.baseUrl || (options?.client ?? client).getConfig().baseUrl } as QueryKey<TOptions>[0];
+    if (infinite) {
+        params._infinite = infinite;
+    }
+    if (tags) {
+        params.tags = tags;
+    }
+    if (options?.body) {
+        params.body = options.body;
+    }
+    if (options?.headers) {
+        params.headers = options.headers;
+    }
+    if (options?.path) {
+        params.path = options.path;
+    }
+    if (options?.query) {
+        params.query = options.query;
+    }
+    return [params];
+};
+
+export const getConfigDetectorQueryKey = (options?: Options<getConfigDetectorData>) => createQueryKey('getConfigDetector', options);
+
+/**
+ * Get detector configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigDetectorOptions = (options?: Options<getConfigDetectorData>) => queryOptions<getConfigDetectorResponse, DefaultError, getConfigDetectorResponse, ReturnType<typeof getConfigDetectorQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigDetector({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigDetectorQueryKey(options)
+});
+
+/**
+ * Change detector configuration
+ *
+ * Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ * If detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.
+ * If detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.
+ *
+ */
+export const putConfigDetectorMutation = (options?: Partial<Options<putConfigDetectorData>>): UseMutationOptions<unknown, putConfigDetectorError, Options<putConfigDetectorData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigDetectorError, Options<putConfigDetectorData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigDetector({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigIndexingQueryKey = (options?: Options<getConfigIndexingData>) => createQueryKey('getConfigIndexing', options);
+
+/**
+ * Get indexing configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigIndexingOptions = (options?: Options<getConfigIndexingData>) => queryOptions<getConfigIndexingResponse, DefaultError, getConfigIndexingResponse, ReturnType<typeof getConfigIndexingQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigIndexing({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigIndexingQueryKey(options)
+});
+
+/**
+ * Change indexing algorithm settings
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigIndexingMutation = (options?: Partial<Options<putConfigIndexingData>>): UseMutationOptions<unknown, putConfigIndexingError, Options<putConfigIndexingData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigIndexingError, Options<putConfigIndexingData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigIndexing({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigFileWriterQueryKey = (options?: Options<getConfigFileWriterData>) => createQueryKey('getConfigFileWriter', options);
+
+/**
+ * Get file writer settings
+ *
+ * Can be done anytime
+ */
+export const getConfigFileWriterOptions = (options?: Options<getConfigFileWriterData>) => queryOptions<getConfigFileWriterResponse, DefaultError, getConfigFileWriterResponse, ReturnType<typeof getConfigFileWriterQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigFileWriter({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigFileWriterQueryKey(options)
+});
+
+/**
+ * Change file writer settings
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigFileWriterMutation = (options?: Partial<Options<putConfigFileWriterData>>): UseMutationOptions<unknown, putConfigFileWriterError, Options<putConfigFileWriterData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigFileWriterError, Options<putConfigFileWriterData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigFileWriter({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigInstrumentQueryKey = (options?: Options<getConfigInstrumentData>) => createQueryKey('getConfigInstrument', options);
+
+/**
+ * Get instrument metadata
+ *
+ * Can be done anytime
+ */
+export const getConfigInstrumentOptions = (options?: Options<getConfigInstrumentData>) => queryOptions<getConfigInstrumentResponse, DefaultError, getConfigInstrumentResponse, ReturnType<typeof getConfigInstrumentQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigInstrument({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigInstrumentQueryKey(options)
+});
+
+/**
+ * Change instrument metadata
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigInstrumentMutation = (options?: Partial<Options<putConfigInstrumentData>>): UseMutationOptions<unknown, putConfigInstrumentError, Options<putConfigInstrumentData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigInstrumentError, Options<putConfigInstrumentData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigInstrument({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigImageFormatQueryKey = (options?: Options<getConfigImageFormatData>) => createQueryKey('getConfigImageFormat', options);
+
+/**
+ * Get image output format
+ *
+ * Can be done anytime
+ */
+export const getConfigImageFormatOptions = (options?: Options<getConfigImageFormatData>) => queryOptions<getConfigImageFormatResponse, DefaultError, getConfigImageFormatResponse, ReturnType<typeof getConfigImageFormatQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigImageFormat({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigImageFormatQueryKey(options)
+});
+
+/**
+ * Change image output format
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigImageFormatMutation = (options?: Partial<Options<putConfigImageFormatData>>): UseMutationOptions<unknown, putConfigImageFormatError, Options<putConfigImageFormatData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigImageFormatError, Options<putConfigImageFormatData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigImageFormat({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Configure format for raw data collection
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const postConfigImageFormatRawMutation = (options?: Partial<Options<postConfigImageFormatRawData>>): UseMutationOptions<unknown, postConfigImageFormatRawError, Options<postConfigImageFormatRawData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postConfigImageFormatRawError, Options<postConfigImageFormatRawData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postConfigImageFormatRaw({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Configure format for data collection with full conversion
+ *
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const postConfigImageFormatConversionMutation = (options?: Partial<Options<postConfigImageFormatConversionData>>): UseMutationOptions<unknown, postConfigImageFormatConversionError, Options<postConfigImageFormatConversionData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postConfigImageFormatConversionError, Options<postConfigImageFormatConversionData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postConfigImageFormatConversion({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigSpotFindingQueryKey = (options?: Options<getConfigSpotFindingData>) => createQueryKey('getConfigSpotFinding', options);
+
+/**
+ * Get data processing configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigSpotFindingOptions = (options?: Options<getConfigSpotFindingData>) => queryOptions<getConfigSpotFindingResponse, DefaultError, getConfigSpotFindingResponse, ReturnType<typeof getConfigSpotFindingQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigSpotFinding({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigSpotFindingQueryKey(options)
+});
+
+/**
+ * Configure spot finding
+ *
+ * Can be done anytime, also while data collection is running
+ */
+export const putConfigSpotFindingMutation = (options?: Partial<Options<putConfigSpotFindingData>>): UseMutationOptions<unknown, putConfigSpotFindingError, Options<putConfigSpotFindingData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigSpotFindingError, Options<putConfigSpotFindingData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigSpotFinding({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigAzimIntQueryKey = (options?: Options<getConfigAzimIntData>) => createQueryKey('getConfigAzimInt', options);
+
+/**
+ * Get azimuthal integration configuration
+ *
+ * Can be done anytime
+ */
+export const getConfigAzimIntOptions = (options?: Options<getConfigAzimIntData>) => queryOptions<getConfigAzimIntResponse, DefaultError, getConfigAzimIntResponse, ReturnType<typeof getConfigAzimIntQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigAzimInt({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigAzimIntQueryKey(options)
+});
+
+/**
+ * Configure azimuthal integration
+ *
+ * Can be done when detector is Inactive or Idle
+ */
+export const putConfigAzimIntMutation = (options?: Partial<Options<putConfigAzimIntData>>): UseMutationOptions<unknown, putConfigAzimIntError, Options<putConfigAzimIntData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigAzimIntError, Options<putConfigAzimIntData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigAzimInt({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Load binary image for internal FPGA generator
+ *
+ * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+ * Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates
+ * (depending on detector settings).
+ *
+ */
+export const putConfigInternalGeneratorImageMutation = (options?: Partial<Options<putConfigInternalGeneratorImageData>>): UseMutationOptions<unknown, putConfigInternalGeneratorImageError, Options<putConfigInternalGeneratorImageData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigInternalGeneratorImageError, Options<putConfigInternalGeneratorImageData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigInternalGeneratorImage({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+/**
+ * Load TIFF image for internal FPGA generator
+ *
+ * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+ * Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates
+ * (depending on detector settings).
+ *
+ */
+export const putConfigInternalGeneratorImageTiffMutation = (options?: Partial<Options<putConfigInternalGeneratorImageTiffData>>): UseMutationOptions<unknown, putConfigInternalGeneratorImageTiffError, Options<putConfigInternalGeneratorImageTiffData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigInternalGeneratorImageTiffError, Options<putConfigInternalGeneratorImageTiffData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigInternalGeneratorImageTiff({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigSelectDetectorQueryKey = (options?: Options<getConfigSelectDetectorData>) => createQueryKey('getConfigSelectDetector', options);
+
+/**
+ * List available detectors
+ *
+ * Configured detectors that can be selected by used
+ */
+export const getConfigSelectDetectorOptions = (options?: Options<getConfigSelectDetectorData>) => queryOptions<getConfigSelectDetectorResponse, DefaultError, getConfigSelectDetectorResponse, ReturnType<typeof getConfigSelectDetectorQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigSelectDetector({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigSelectDetectorQueryKey(options)
+});
+
+/**
+ * Select detector
+ *
+ * Jungfraujoch allows to control multiple detectors and/or region-of-interests.
+ * The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).
+ * Changing detector will set detector to `Inactive` state and will require reinitialization.
+ *
+ */
+export const putConfigSelectDetectorMutation = (options?: Partial<Options<putConfigSelectDetectorData>>): UseMutationOptions<unknown, putConfigSelectDetectorError, Options<putConfigSelectDetectorData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigSelectDetectorError, Options<putConfigSelectDetectorData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigSelectDetector({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigZeromqPreviewQueryKey = (options?: Options<getConfigZeromqPreviewData>) => createQueryKey('getConfigZeromqPreview', options);
+
+/**
+ * Get ZeroMQ preview settings
+ */
+export const getConfigZeromqPreviewOptions = (options?: Options<getConfigZeromqPreviewData>) => queryOptions<getConfigZeromqPreviewResponse, DefaultError, getConfigZeromqPreviewResponse, ReturnType<typeof getConfigZeromqPreviewQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigZeromqPreview({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigZeromqPreviewQueryKey(options)
+});
+
+/**
+ * Set ZeroMQ preview settings
+ *
+ * Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.
+ * Here settings of the socket can be adjusted.
+ * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
+ * Options set with this PUT request have no effect on HTTP based preview.
+ *
+ */
+export const putConfigZeromqPreviewMutation = (options?: Partial<Options<putConfigZeromqPreviewData>>): UseMutationOptions<unknown, putConfigZeromqPreviewError, Options<putConfigZeromqPreviewData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigZeromqPreviewError, Options<putConfigZeromqPreviewData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigZeromqPreview({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigZeromqMetadataQueryKey = (options?: Options<getConfigZeromqMetadataData>) => createQueryKey('getConfigZeromqMetadata', options);
+
+/**
+ * Get ZeroMQ metadata socket settings
+ */
+export const getConfigZeromqMetadataOptions = (options?: Options<getConfigZeromqMetadataData>) => queryOptions<getConfigZeromqMetadataResponse, DefaultError, getConfigZeromqMetadataResponse, ReturnType<typeof getConfigZeromqMetadataQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigZeromqMetadata({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigZeromqMetadataQueryKey(options)
+});
+
+/**
+ * Set ZeroMQ metadata settings
+ *
+ * Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.
+ * Here settings of the socket can be adjusted.
+ * While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.
+ *
+ */
+export const putConfigZeromqMetadataMutation = (options?: Partial<Options<putConfigZeromqMetadataData>>): UseMutationOptions<unknown, putConfigZeromqMetadataError, Options<putConfigZeromqMetadataData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigZeromqMetadataError, Options<putConfigZeromqMetadataData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigZeromqMetadata({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigDarkMaskQueryKey = (options?: Options<getConfigDarkMaskData>) => createQueryKey('getConfigDarkMask', options);
+
+/**
+ * Get settings for dark data collection to calculate mask
+ */
+export const getConfigDarkMaskOptions = (options?: Options<getConfigDarkMaskData>) => queryOptions<getConfigDarkMaskResponse, DefaultError, getConfigDarkMaskResponse, ReturnType<typeof getConfigDarkMaskQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigDarkMask({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigDarkMaskQueryKey(options)
+});
+
+/**
+ * Set configuration for dark data collection to calculate mask
+ *
+ * This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.
+ * This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+ *
+ */
+export const putConfigDarkMaskMutation = (options?: Partial<Options<putConfigDarkMaskData>>): UseMutationOptions<unknown, putConfigDarkMaskError, Options<putConfigDarkMaskData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigDarkMaskError, Options<putConfigDarkMaskData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigDarkMask({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getStatusQueryKey = (options?: Options<getStatusData>) => createQueryKey('getStatus', options);
+
+/**
+ * Get Jungfraujoch status
+ *
+ * Status of the data acquisition
+ */
+export const getStatusOptions = (options?: Options<getStatusData>) => queryOptions<getStatusResponse, DefaultError, getStatusResponse, ReturnType<typeof getStatusQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getStatus({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getStatusQueryKey(options)
+});
+
+export const getFpgaStatusQueryKey = (options?: Options<getFpgaStatusData>) => createQueryKey('getFpgaStatus', options);
+
+/**
+ * Get status of FPGA devices
+ */
+export const getFpgaStatusOptions = (options?: Options<getFpgaStatusData>) => queryOptions<getFpgaStatusResponse, DefaultError, getFpgaStatusResponse, ReturnType<typeof getFpgaStatusQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getFpgaStatus({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getFpgaStatusQueryKey(options)
+});
+
+export const getXfelPulseIdQueryKey = (options?: Options<getXfelPulseIdData>) => createQueryKey('getXfelPulseId', options);
+
+/**
+ * Return XFEL pulse IDs for the current data acquisition
+ *
+ * Return array of XFEL pulse IDs - (-1) if image not recorded
+ */
+export const getXfelPulseIdOptions = (options?: Options<getXfelPulseIdData>) => queryOptions<getXfelPulseIdResponse, DefaultError, getXfelPulseIdResponse, ReturnType<typeof getXfelPulseIdQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getXfelPulseId({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getXfelPulseIdQueryKey(options)
+});
+
+export const getXfelEventCodeQueryKey = (options?: Options<getXfelEventCodeData>) => createQueryKey('getXfelEventCode', options);
+
+/**
+ * Return XFEL event codes for the current data acquisition
+ *
+ * Return array of XFEL event codes
+ */
+export const getXfelEventCodeOptions = (options?: Options<getXfelEventCodeData>) => queryOptions<getXfelEventCodeResponse, DefaultError, getXfelEventCodeResponse, ReturnType<typeof getXfelEventCodeQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getXfelEventCode({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getXfelEventCodeQueryKey(options)
+});
+
+export const getImagePusherStatusQueryKey = (options?: Options<getImagePusherStatusData>) => createQueryKey('getImagePusherStatus', options);
+
+/**
+ * Get status of image pusher
+ */
+export const getImagePusherStatusOptions = (options?: Options<getImagePusherStatusData>) => queryOptions<getImagePusherStatusResponse, getImagePusherStatusError, getImagePusherStatusResponse, ReturnType<typeof getImagePusherStatusQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImagePusherStatus({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImagePusherStatusQueryKey(options)
+});
+
+export const getDetectorStatusQueryKey = (options?: Options<getDetectorStatusData>) => createQueryKey('getDetectorStatus', options);
+
+/**
+ * Get detector status
+ *
+ * Status of the JUNGFRAU detector
+ */
+export const getDetectorStatusOptions = (options?: Options<getDetectorStatusData>) => queryOptions<getDetectorStatusResponse, getDetectorStatusError, getDetectorStatusResponse, ReturnType<typeof getDetectorStatusQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getDetectorStatus({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getDetectorStatusQueryKey(options)
+});
+
+export const getConfigRoiQueryKey = (options?: Options<getConfigRoiData>) => createQueryKey('getConfigRoi', options);
+
+/**
+ * Get ROI definitions
+ */
+export const getConfigRoiOptions = (options?: Options<getConfigRoiData>) => queryOptions<getConfigRoiResponse, DefaultError, getConfigRoiResponse, ReturnType<typeof getConfigRoiQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigRoi({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigRoiQueryKey(options)
+});
+
+/**
+ * Upload ROI definitions
+ */
+export const putConfigRoiMutation = (options?: Partial<Options<putConfigRoiData>>): UseMutationOptions<unknown, putConfigRoiError, Options<putConfigRoiData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigRoiError, Options<putConfigRoiData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigRoi({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getStatisticsQueryKey = (options?: Options<getStatisticsData>) => createQueryKey('getStatistics', options);
+
+/**
+ * Get general statistics
+ */
+export const getStatisticsOptions = (options?: Options<getStatisticsData>) => queryOptions<getStatisticsResponse, DefaultError, getStatisticsResponse, ReturnType<typeof getStatisticsQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getStatistics({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getStatisticsQueryKey(options)
+});
+
+export const getStatisticsDataCollectionQueryKey = (options?: Options<getStatisticsDataCollectionData>) => createQueryKey('getStatisticsDataCollection', options);
+
+/**
+ * Get data collection statistics
+ *
+ * Results of the last data collection
+ */
+export const getStatisticsDataCollectionOptions = (options?: Options<getStatisticsDataCollectionData>) => queryOptions<getStatisticsDataCollectionResponse, DefaultError, getStatisticsDataCollectionResponse, ReturnType<typeof getStatisticsDataCollectionQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getStatisticsDataCollection({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getStatisticsDataCollectionQueryKey(options)
+});
+
+export const getStatisticsCalibrationQueryKey = (options?: Options<getStatisticsCalibrationData>) => createQueryKey('getStatisticsCalibration', options);
+
+/**
+ * Get calibration statistics
+ *
+ * Statistics are provided for each module/storage cell separately
+ */
+export const getStatisticsCalibrationOptions = (options?: Options<getStatisticsCalibrationData>) => queryOptions<getStatisticsCalibrationResponse, DefaultError, getStatisticsCalibrationResponse, ReturnType<typeof getStatisticsCalibrationQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getStatisticsCalibration({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getStatisticsCalibrationQueryKey(options)
+});
+
+export const getConfigMaskQueryKey = (options?: Options<getConfigMaskData>) => createQueryKey('getConfigMask', options);
+
+/**
+ * Get mask of the detector (binary)
+ *
+ * Detector must be Initialized.
+ * Get full pixel mask of the detector.
+ * See NXmx standard for meaning of pixel values.
+ *
+ */
+export const getConfigMaskOptions = (options?: Options<getConfigMaskData>) => queryOptions<getConfigMaskResponse, DefaultError, getConfigMaskResponse, ReturnType<typeof getConfigMaskQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigMask({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigMaskQueryKey(options)
+});
+
+export const getConfigUserMaskQueryKey = (options?: Options<getConfigUserMaskData>) => createQueryKey('getConfigUserMask', options);
+
+/**
+ * Detector must be Initialized.
+ * Get user mask of the detector (binary)
+ *
+ *
+ * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+ */
+export const getConfigUserMaskOptions = (options?: Options<getConfigUserMaskData>) => queryOptions<getConfigUserMaskResponse, DefaultError, getConfigUserMaskResponse, ReturnType<typeof getConfigUserMaskQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigUserMask({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigUserMaskQueryKey(options)
+});
+
+/**
+ * Upload user mask of the detector (binary)
+ *
+ * Should be in `Idle` state.
+ * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+ * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+ * In the latter case - module gaps are ignored and don't need to be assigned value.
+ * Mask is expected as binary array (4-byte; unsigned).
+ * 0 - good pixel, other value - masked
+ * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
+ *
+ */
+export const putConfigUserMaskMutation = (options?: Partial<Options<putConfigUserMaskData>>): UseMutationOptions<unknown, putConfigUserMaskError, Options<putConfigUserMaskData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigUserMaskError, Options<putConfigUserMaskData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigUserMask({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getConfigMaskTiffQueryKey = (options?: Options<getConfigMaskTiffData>) => createQueryKey('getConfigMaskTiff', options);
+
+/**
+ * Get mask of the detector (TIFF)
+ *
+ * Should be in `Idle` state.
+ * Get full pixel mask of the detector
+ * See NXmx standard for meaning of pixel values
+ *
+ */
+export const getConfigMaskTiffOptions = (options?: Options<getConfigMaskTiffData>) => queryOptions<getConfigMaskTiffResponse, DefaultError, getConfigMaskTiffResponse, ReturnType<typeof getConfigMaskTiffQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigMaskTiff({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigMaskTiffQueryKey(options)
+});
+
+export const getConfigUserMaskTiffQueryKey = (options?: Options<getConfigUserMaskTiffData>) => createQueryKey('getConfigUserMaskTiff', options);
+
+/**
+ * Detector must be Initialized.
+ * Get user mask of the detector (TIFF)
+ *
+ *
+ * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+ */
+export const getConfigUserMaskTiffOptions = (options?: Options<getConfigUserMaskTiffData>) => queryOptions<getConfigUserMaskTiffResponse, DefaultError, getConfigUserMaskTiffResponse, ReturnType<typeof getConfigUserMaskTiffQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getConfigUserMaskTiff({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getConfigUserMaskTiffQueryKey(options)
+});
+
+/**
+ * Upload user mask of the detector
+ *
+ * Should be in `Idle` state.
+ * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+ * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+ * In the latter case - module gaps are ignored and don't need to be assigned value.
+ * Mask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).
+ * 0 - good pixel, other value - masked
+ * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
+ * User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
+ *
+ */
+export const putConfigUserMaskTiffMutation = (options?: Partial<Options<putConfigUserMaskTiffData>>): UseMutationOptions<unknown, putConfigUserMaskTiffError, Options<putConfigUserMaskTiffData>> => {
+    const mutationOptions: UseMutationOptions<unknown, putConfigUserMaskTiffError, Options<putConfigUserMaskTiffData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await putConfigUserMaskTiff({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getPreviewPedestalTiffQueryKey = (options: Options<getPreviewPedestalTiffData>) => createQueryKey('getPreviewPedestalTiff', options);
+
+/**
+ * Get pedestal in TIFF format
+ */
+export const getPreviewPedestalTiffOptions = (options: Options<getPreviewPedestalTiffData>) => queryOptions<getPreviewPedestalTiffResponse, DefaultError, getPreviewPedestalTiffResponse, ReturnType<typeof getPreviewPedestalTiffQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getPreviewPedestalTiff({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getPreviewPedestalTiffQueryKey(options)
+});
+
+export const getPreviewPlotQueryKey = (options: Options<getPreviewPlotData>) => createQueryKey('getPreviewPlot', options);
+
+/**
+ * Generate 1D plot from Jungfraujoch
+ */
+export const getPreviewPlotOptions = (options: Options<getPreviewPlotData>) => queryOptions<getPreviewPlotResponse, getPreviewPlotError, getPreviewPlotResponse, ReturnType<typeof getPreviewPlotQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getPreviewPlot({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getPreviewPlotQueryKey(options)
+});
+
+export const getPreviewPlotBinQueryKey = (options: Options<getPreviewPlotBinData>) => createQueryKey('getPreviewPlotBin', options);
+
+/**
+ * Generate 1D plot from Jungfraujoch and send in raw binary format.
+ * Data are provided as (32-bit) float binary array.
+ * This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
+ *
+ */
+export const getPreviewPlotBinOptions = (options: Options<getPreviewPlotBinData>) => queryOptions<getPreviewPlotBinResponse, getPreviewPlotBinError, getPreviewPlotBinResponse, ReturnType<typeof getPreviewPlotBinQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getPreviewPlotBin({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getPreviewPlotBinQueryKey(options)
+});
+
+export const getResultScanQueryKey = (options?: Options<getResultScanData>) => createQueryKey('getResultScan', options);
+
+/**
+ * Get full scan result
+ */
+export const getResultScanOptions = (options?: Options<getResultScanData>) => queryOptions<getResultScanResponse, getResultScanError, getResultScanResponse, ReturnType<typeof getResultScanQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getResultScan({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getResultScanQueryKey(options)
+});
+
+export const getImageBufferStartCborQueryKey = (options?: Options<getImageBufferStartCborData>) => createQueryKey('getImageBufferStartCbor', options);
+
+/**
+ * Get Start message in CBOR format
+ *
+ * Contains metadata for a dataset (e.g., experimental geometry)
+ */
+export const getImageBufferStartCborOptions = (options?: Options<getImageBufferStartCborData>) => queryOptions<getImageBufferStartCborResponse, getImageBufferStartCborError, getImageBufferStartCborResponse, ReturnType<typeof getImageBufferStartCborQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImageBufferStartCbor({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImageBufferStartCborQueryKey(options)
+});
+
+export const getImageBufferImageCborQueryKey = (options?: Options<getImageBufferImageCborData>) => createQueryKey('getImageBufferImageCbor', options);
+
+/**
+ * Get image message in CBOR format
+ *
+ * Contains full image data and metadata. The image must come from the latest data collection.
+ */
+export const getImageBufferImageCborOptions = (options?: Options<getImageBufferImageCborData>) => queryOptions<getImageBufferImageCborResponse, getImageBufferImageCborError, getImageBufferImageCborResponse, ReturnType<typeof getImageBufferImageCborQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImageBufferImageCbor({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImageBufferImageCborQueryKey(options)
+});
+
+export const getImageBufferImageJpegQueryKey = (options?: Options<getImageBufferImageJpegData>) => createQueryKey('getImageBufferImageJpeg', options);
+
+/**
+ * Get preview image in JPEG format using custom settings
+ */
+export const getImageBufferImageJpegOptions = (options?: Options<getImageBufferImageJpegData>) => queryOptions<getImageBufferImageJpegResponse, getImageBufferImageJpegError, getImageBufferImageJpegResponse, ReturnType<typeof getImageBufferImageJpegQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImageBufferImageJpeg({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImageBufferImageJpegQueryKey(options)
+});
+
+export const getImageBufferImageTiffQueryKey = (options?: Options<getImageBufferImageTiffData>) => createQueryKey('getImageBufferImageTiff', options);
+
+/**
+ * Get preview image in TIFF format
+ */
+export const getImageBufferImageTiffOptions = (options?: Options<getImageBufferImageTiffData>) => queryOptions<getImageBufferImageTiffResponse, DefaultError, getImageBufferImageTiffResponse, ReturnType<typeof getImageBufferImageTiffQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImageBufferImageTiff({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImageBufferImageTiffQueryKey(options)
+});
+
+/**
+ * Clear image buffer
+ *
+ * Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.
+ */
+export const postImageBufferClearMutation = (options?: Partial<Options<postImageBufferClearData>>): UseMutationOptions<unknown, postImageBufferClearError, Options<postImageBufferClearData>> => {
+    const mutationOptions: UseMutationOptions<unknown, postImageBufferClearError, Options<postImageBufferClearData>> = {
+        mutationFn: async (fnOptions) => {
+            const { data } = await postImageBufferClear({
+                ...options,
+                ...fnOptions,
+                throwOnError: true
+            });
+            return data;
+        }
+    };
+    return mutationOptions;
+};
+
+export const getImageBufferStatusQueryKey = (options?: Options<getImageBufferStatusData>) => createQueryKey('getImageBufferStatus', options);
+
+/**
+ * Get status of the image buffers
+ *
+ * Can be run at any stage of Jungfraujoch operation, including during data collection.
+ * The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,
+ * then image might be replaced in the buffer between calling /images and /image.cbor.
+ *
+ */
+export const getImageBufferStatusOptions = (options?: Options<getImageBufferStatusData>) => queryOptions<getImageBufferStatusResponse, getImageBufferStatusError, getImageBufferStatusResponse, ReturnType<typeof getImageBufferStatusQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getImageBufferStatus({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getImageBufferStatusQueryKey(options)
+});
+
+export const getVersionQueryKey = (options?: Options<getVersionData>) => createQueryKey('getVersion', options);
+
+/**
+ * Get Jungfraujoch version of jfjoch_broker
+ */
+export const getVersionOptions = (options?: Options<getVersionData>) => queryOptions<getVersionResponse, DefaultError, getVersionResponse, ReturnType<typeof getVersionQueryKey>>({
+    queryFn: async ({ queryKey, signal }) => {
+        const { data } = await getVersion({
+            ...options,
+            ...queryKey[0],
+            signal,
+            throwOnError: true
+        });
+        return data;
+    },
+    queryKey: getVersionQueryKey(options)
+});
diff --git a/frontend/src/components/AzIntSettings.tsx b/frontend/src/components/AzIntSettings.tsx
index 4594813b..af00ab69 100644
--- a/frontend/src/components/AzIntSettings.tsx
+++ b/frontend/src/components/AzIntSettings.tsx
@@ -1,7 +1,7 @@
-import React from 'react';
+import {ChangeEvent, memo, useEffect, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
-import {FormControlLabel, Checkbox, Stack, Tooltip, ListItem, List, Radio, RadioGroup, Typography} from "@mui/material";
+import {FormControlLabel, Checkbox, Stack, Radio, RadioGroup, Typography} from "@mui/material";
 import NumberTextField from "./NumberTextField";
 import {azim_int_settings} from "../client";
 import _ from "lodash";
@@ -12,15 +12,6 @@ type MyProps = {
     s?: azim_int_settings
 };
 
-type MyState = {
-    s: azim_int_settings
-    last_downloaded_s: azim_int_settings
-    download_counter: number
-    low_q_error: boolean
-    high_q_error: boolean
-    q_spacing_error: boolean
-};
-
 const default_azim_int_settings : azim_int_settings = {
     solid_angle_corr: true,
     polarization_corr: true,
@@ -31,163 +22,139 @@ const default_azim_int_settings : azim_int_settings = {
     force_cpu: false
 }
 
-class AzIntSettings extends React.Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_azim_int_settings,
-        last_downloaded_s: default_azim_int_settings,
-        download_counter: 0,
-        low_q_error: false,
-        high_q_error: false,
-        q_spacing_error: false,
-    }
+function AzIntSettings({s: serverS}: MyProps) {
+    const [s, setS] = useState<azim_int_settings>(default_azim_int_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<azim_int_settings>(default_azim_int_settings);
+    const [downloadCounter, setDownloadCounter] = useState(0);
+    const [lowQError, setLowQError] = useState(false);
+    const [highQError, setHighQError] = useState(false);
+    const [qSpacingError, setQSpacingError] = useState(false);
 
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let format_set: azim_int_settings = this.props.s;
-            if (!_.isEqual(format_set, this.state.last_downloaded_s)) {
-                this.setState(prevState => ({
-                    s: format_set,
-                    last_downloaded_s: format_set,
-                    download_counter: prevState.download_counter + 1
-                }));
-            }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setDownloadCounter(c => c + 1);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
+    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+            marginLeft: '8%',
+            marginRight: '8%',
+        }}>
+            <div><strong>Azimuthal integration settings </strong></div>
+            <Stack spacing={2} direction="row">
+                <NumberTextField
+                    default={1.0}
+                    start_val={s.q_spacing}
+                    label={"Q spacing"}
+                    min={1e-5}
+                    units={"A-1"}
+                    float={true}
+                    counter={downloadCounter}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, q_spacing: val}));
+                        setQSpacingError(err);
+                    }}
+                    fullWidth/>
 
-    componentDidUpdate() {
-        this.getValues();
-    }
+                <NumberTextField
+                    default={0.1}
+                    start_val={s.low_q_recipA}
+                    label={"Low Q"}
+                    min={1e-5}
+                    max={10.0}
+                    units={"A-1"}
+                    float={true}
+                    counter={downloadCounter}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, low_q_recipA: val}));
+                        setLowQError(err);
+                    }}
+                    fullWidth/>
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-                marginLeft: '8%',
-                marginRight: '8%',
-            }}>
-                <div><strong>Azimuthal integration settings </strong></div>
-                <Stack spacing={2} direction="row">
-                    <NumberTextField
-                        default={1.0}
-                        start_val={this.state.s.q_spacing}
-                        label={"Q spacing"}
-                        min={1e-5}
-                        units={"A-1"}
-                        float={true}
-                        counter={this.state.download_counter}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                s: {...prevState.s, q_spacing: val},
-                                q_spacing_error: err
-                            }));
-                        }}
-                        fullWidth/>
-
-                    <NumberTextField
-                        default={0.1}
-                        start_val={this.state.s.low_q_recipA}
-                        label={"Low Q"}
-                        min={1e-5}
-                        max={10.0}
-                        units={"A-1"}
-                        float={true}
-                        counter={this.state.download_counter}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                s: {...prevState.s, low_q_recipA: val},
-                                low_q_error: err
-                            }));
-                        }}
-                        fullWidth/>
-
-                    <NumberTextField
-                        default={5}
-                        start_val={this.state.s.high_q_recipA}
-                        label={"High Q"}
-                        min={1e-5}
-                        max={10.0}
-                        units={"A-1"}
-                        float={true}
-                        counter={this.state.download_counter}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                s: {...prevState.s, high_q_recipA: val},
-                                high_q_error: err
-                            }));
-                        }}
-                        fullWidth/>
-                </Stack>
-                <FormControl>
-                <FormControlLabel control={
-                    <Checkbox
-                        checked={this.state.s.solid_angle_corr}
-                        onChange={
-                            (event: React.ChangeEvent<HTMLInputElement>) => {
-                                this.state.s.solid_angle_corr = event.target.checked;
-                            }}
-                    />} label="Solid angle correction"/>
-                <FormControlLabel control={
-                    <Checkbox
-                        checked={this.state.s.polarization_corr}
-                        onChange={
-                            (event: React.ChangeEvent<HTMLInputElement>) => {
-                                this.state.s.polarization_corr = event.target.checked;
-                            }}
-                    />} label="Polarization correction"/>
-                    <FormControlLabel control={
-                        <Checkbox
-                            checked={this.state.s.force_cpu ?? false}
-                            onChange={
-                                (event: React.ChangeEvent<HTMLInputElement>) => {
-                                    this.state.s.force_cpu = event.target.checked;
-                                }}
-                        />} label="Force CPU calculation in FPGA workflow"/>
-                </FormControl>
-                <Typography>Azimuthal bins</Typography>
-                <FormControl component="fieldset">
-                    <RadioGroup
-                        row
-                        value={this.state.s.azimuthal_bins}
-                        onChange={(event: React.ChangeEvent<HTMLInputElement>) => {
-                            this.setState(prevState => ({
-                                s: {...prevState.s, azimuthal_bins: Number(event.target.value)}
-                            }));
-                        }}
-                    >
-                        {[1, 2, 4, 8, 16, 32, 64, 128].map((value) => (
-                            <FormControlLabel
-                                key={value}
-                                value={value}
-                                control={<Radio/>}
-                                label={value.toString()}
-                            />
-                        ))}
-                    </RadioGroup>
-                </FormControl>
-
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/azim_int"}
-                    input={JSON.stringify(this.state.s)}
-                    method={"PUT"}
-                    text={"Upload"}
-                    disabled={
-                        (this.state.s.high_q_recipA <= this.state.s.low_q_recipA)
-                        || this.state.high_q_error
-                        || this.state.low_q_error
-                        || this.state.q_spacing_error
-                    }
-                />
+                <NumberTextField
+                    default={5}
+                    start_val={s.high_q_recipA}
+                    label={"High Q"}
+                    min={1e-5}
+                    max={10.0}
+                    units={"A-1"}
+                    float={true}
+                    counter={downloadCounter}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, high_q_recipA: val}));
+                        setHighQError(err);
+                    }}
+                    fullWidth/>
             </Stack>
-            <br/>
-        </Paper>
-    }
+            <FormControl>
+            <FormControlLabel control={
+                <Checkbox
+                    checked={s.solid_angle_corr}
+                    onChange={
+                        (event: ChangeEvent<HTMLInputElement>) => {
+                            setS(prev => ({...prev, solid_angle_corr: event.target.checked}));
+                        }}
+                />} label="Solid angle correction"/>
+            <FormControlLabel control={
+                <Checkbox
+                    checked={s.polarization_corr}
+                    onChange={
+                        (event: ChangeEvent<HTMLInputElement>) => {
+                            setS(prev => ({...prev, polarization_corr: event.target.checked}));
+                        }}
+                />} label="Polarization correction"/>
+                <FormControlLabel control={
+                    <Checkbox
+                        checked={s.force_cpu ?? false}
+                        onChange={
+                            (event: ChangeEvent<HTMLInputElement>) => {
+                                setS(prev => ({...prev, force_cpu: event.target.checked}));
+                            }}
+                    />} label="Force CPU calculation in FPGA workflow"/>
+            </FormControl>
+            <Typography>Azimuthal bins</Typography>
+            <FormControl component="fieldset">
+                <RadioGroup
+                    row
+                    value={s.azimuthal_bins}
+                    onChange={(event: ChangeEvent<HTMLInputElement>) => {
+                        setS(prev => ({...prev, azimuthal_bins: Number(event.target.value)}));
+                    }}
+                >
+                    {[1, 2, 4, 8, 16, 32, 64, 128].map((value) => (
+                        <FormControlLabel
+                            key={value}
+                            value={value}
+                            control={<Radio/>}
+                            label={value.toString()}
+                        />
+                    ))}
+                </RadioGroup>
+            </FormControl>
+
+            <ButtonWithSnackbar
+                color={"primary"}
+                path={"/config/azim_int"}
+                input={JSON.stringify(s)}
+                method={"PUT"}
+                text={"Upload"}
+                disabled={
+                    (s.high_q_recipA <= s.low_q_recipA)
+                    || highQError
+                    || lowQError
+                    || qSpacingError
+                }
+            />
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default AzIntSettings;
+export default memo(AzIntSettings);
diff --git a/frontend/src/components/ButtonWithSnackbar.tsx b/frontend/src/components/ButtonWithSnackbar.tsx
index 1a91afc8..7e000430 100644
--- a/frontend/src/components/ButtonWithSnackbar.tsx
+++ b/frontend/src/components/ButtonWithSnackbar.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {memo, SyntheticEvent, useState} from 'react';
 
 import {
     Alert, SnackbarCloseReason
@@ -15,86 +15,75 @@ type MyProps = {
     method?: "GET" | "POST" | "PUT"
 }
 
-type MyState = {
-    snackbar_open: boolean,
-    start_success: boolean,
-    start_error?: string
-}
+function ButtonWithSnackbar({input, disabled, path, text, color, method}: MyProps) {
+    const [snackbarOpen, setSnackbarOpen] = useState(false);
+    const [startSuccess, setStartSuccess] = useState(true);
+    const [startError, setStartError] = useState<string>();
 
-class ButtonWithSnackbar extends Component<MyProps, MyState> {
-    state : MyState = {
-        snackbar_open: false,
-        start_success: true
-    }
+    const printError = (msg: string) => {
+        setSnackbarOpen(true);
+        setStartSuccess(false);
+        setStartError(msg);
+    };
 
-
-    printError = (msg: string) => {
-        this.setState({
-            snackbar_open: true,
-            start_success: false,
-            start_error: msg
-        });
-    }
-
-    handleResponse = (response : Response) => {
+    const handleResponse = (response : Response) => {
         if (response.ok) {
-            this.setState({snackbar_open: true, start_success: true});
+            setSnackbarOpen(true);
+            setStartSuccess(true);
         } else {
             if (response.status == 404)
-                this.printError("404: Service not found");
+                printError("404: Service not found");
             else if (response.status == 400)
-                this.printError("400: Input parsing or validation error");
+                printError("400: Input parsing or validation error");
             else if (response.status == 500) {
                 response.text().then((val: string) => {
                     try {
-                        this.printError(JSON.parse(val).msg);
+                        printError(JSON.parse(val).msg);
                     } catch (e) {
-                        this.printError("500: Unknown error");
+                        printError("500: Unknown error");
                     }
                 });
             }
         }
-    }
+    };
 
-    startButton = () => {
-        fetch(this.props.path, {
-            method: (this.props.method === undefined) ? "POST" : this.props.method,
-            body: this.props.input
-        }).then(this.handleResponse);
-    }
+    const startButton = () => {
+        fetch(path, {
+            method: (method === undefined) ? "POST" : method,
+            body: input
+        }).then(handleResponse);
+    };
 
-    handleClose = (event?: React.SyntheticEvent | Event, reason?: SnackbarCloseReason) => {
+    const handleClose = (event?: SyntheticEvent | Event, reason?: SnackbarCloseReason) => {
         if (reason === 'clickaway') {
             return;
         }
-        this.setState({snackbar_open: false});
+        setSnackbarOpen(false);
     };
 
-    render() {
-        return <>
-            <Button
-                color={this.props.color}
-                onClick={this.startButton}
-                variant="contained"
-                disableElevation
-                disabled={this.props.disabled}
+    return <>
+        <Button
+            color={color}
+            onClick={startButton}
+            variant="contained"
+            disableElevation
+            disabled={disabled}
+        >
+            {text}
+        </Button>
+        <Snackbar open={snackbarOpen}
+                  autoHideDuration={5000}
+                  onClose={handleClose}>
+            <Alert
+                onClose={handleClose}
+                severity={startSuccess ? "success" : "error"}
+                variant="filled"
+                sx={{ width: '100%' }}
             >
-                {this.props.text}
-            </Button>
-            <Snackbar open={this.state.snackbar_open}
-                      autoHideDuration={5000}
-                      onClose={this.handleClose}>
-                <Alert
-                    onClose={this.handleClose}
-                    severity={this.state.start_success ? "success" : "error"}
-                    variant="filled"
-                    sx={{ width: '100%' }}
-                >
-                    {this.state.start_success ? "Ok!" : this.state.start_error}
-                </Alert>
-            </Snackbar>
-        </>
-    }
+                {startSuccess ? "Ok!" : startError}
+            </Alert>
+        </Snackbar>
+    </>
 }
 
-export default ButtonWithSnackbar;
\ No newline at end of file
+export default memo(ButtonWithSnackbar);
diff --git a/frontend/src/components/Calibration.tsx b/frontend/src/components/Calibration.tsx
index 4b9e9550..9f569922 100644
--- a/frontend/src/components/Calibration.tsx
+++ b/frontend/src/components/Calibration.tsx
@@ -1,5 +1,4 @@
-
-import React from 'react';
+import {memo} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {DataGrid, GridColDef} from "@mui/x-data-grid";
@@ -9,37 +8,32 @@ type MyProps = {
     s?: calibration_statistics
 };
 
-type MyState = {};
+const columns : GridColDef[] = [
+    { field: 'module_number', type: 'number', headerName: 'Module' },
+    { field: 'storage_cell_number', type: 'number', headerName: 'SC'},
+    { field: 'masked_pixels', headerName: 'Masked pxls', type: 'number'},
+    { field: 'pedestal_g0_mean', headerName: 'Pedestal G0', type: 'number'},
+    { field: 'pedestal_g1_mean', headerName: 'Pedestal G1', type: 'number'},
+    { field: 'pedestal_g2_mean', headerName: 'Pedestal G2', type: 'number'},
+    { field: 'gain_g0_mean', headerName: 'Gain G0', type: 'number'},
+    { field: 'gain_g1_mean', headerName: 'Gain G1', type: 'number'},
+    { field: 'gain_g2_mean', headerName: 'Gain G2', type: 'number'}
+];
 
-class Calibration extends React.Component<MyProps, MyState> {
-    columns : GridColDef[] = [
-        { field: 'module_number', type: 'number', headerName: 'Module' },
-        { field: 'storage_cell_number', type: 'number', headerName: 'SC'},
-        { field: 'masked_pixels', headerName: 'Masked pxls', type: 'number'},
-        { field: 'pedestal_g0_mean', headerName: 'Pedestal G0', type: 'number'},
-        { field: 'pedestal_g1_mean', headerName: 'Pedestal G1', type: 'number'},
-        { field: 'pedestal_g2_mean', headerName: 'Pedestal G2', type: 'number'},
-        { field: 'gain_g0_mean', headerName: 'Gain G0', type: 'number'},
-        { field: 'gain_g1_mean', headerName: 'Gain G1', type: 'number'},
-        { field: 'gain_g2_mean', headerName: 'Gain G2', type: 'number'}
-    ];
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 527, width: '100%' }}>
-            {((this.props.s !== undefined) && (this.props.s.length > 0)) ?
-            <DataGrid
-                getRowId={(row) => Number(row.module_number) * 64 + Number(row.storage_cell_number)}
-                rows={this.props.s}
-                columns={this.columns}
-                initialState={{
-                    pagination: { paginationModel: { pageSize: 8 } },
-                }}
-                pageSizeOptions={[4,8,16]}
-            /> : <div/>
-            }
-        </Paper>
-
-    }
+function Calibration({s}: MyProps) {
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 527, width: '100%' }}>
+        {((s !== undefined) && (s.length > 0)) ?
+        <DataGrid
+            getRowId={(row) => Number(row.module_number) * 64 + Number(row.storage_cell_number)}
+            rows={s}
+            columns={columns}
+            initialState={{
+                pagination: { paginationModel: { pageSize: 8 } },
+            }}
+            pageSizeOptions={[4,8,16]}
+        /> : <div/>
+        }
+    </Paper>
 }
 
-export default Calibration;
+export default memo(Calibration);
diff --git a/frontend/src/components/DarkMaskSettings.tsx b/frontend/src/components/DarkMaskSettings.tsx
index a4ff4ec5..9dac096c 100644
--- a/frontend/src/components/DarkMaskSettings.tsx
+++ b/frontend/src/components/DarkMaskSettings.tsx
@@ -1,4 +1,4 @@
-import React, { Component } from 'react';
+import {memo, useEffect, useState} from 'react';
 import Paper from '@mui/material/Paper';
 import {Checkbox, FormControlLabel, Stack} from '@mui/material';
 import _ from 'lodash';
@@ -10,18 +10,6 @@ type MyProps = {
     s?: dark_mask_settings;
 };
 
-type MyState = {
-    s: dark_mask_settings;
-    last_downloaded_s: dark_mask_settings;
-    download_counter: number;
-    threshold_err: boolean;
-    frame_time_err: boolean;
-    number_of_frames_err: boolean;
-    number_of_frames_old: number;
-    max_pixel_count_err: boolean;
-    max_frames_with_signal_err: boolean;
-};
-
 const default_dark_mask_settings: dark_mask_settings = {
     detector_threshold_keV: 4.0,
     frame_time_us: 1000,
@@ -30,203 +18,161 @@ const default_dark_mask_settings: dark_mask_settings = {
     max_frames_with_signal: 10,
 };
 
-class DarkMaskSettings extends Component<MyProps, MyState> {
-    state: MyState = {
-        s: default_dark_mask_settings,
-        last_downloaded_s: default_dark_mask_settings,
-        download_counter: 0,
-        threshold_err: false,
-        frame_time_err: false,
-        number_of_frames_err: false,
-        max_pixel_count_err: false,
-        max_frames_with_signal_err: false,
-        number_of_frames_old: 1000
-    };
+function DarkMaskSettings({s: serverS}: MyProps) {
+    const [s, setS] = useState<dark_mask_settings>(default_dark_mask_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<dark_mask_settings>(default_dark_mask_settings);
+    const [downloadCounter, setDownloadCounter] = useState(0);
+    const [thresholdErr, setThresholdErr] = useState(false);
+    const [frameTimeErr, setFrameTimeErr] = useState(false);
+    const [numberOfFramesErr, setNumberOfFramesErr] = useState(false);
+    const [numberOfFramesOld, setNumberOfFramesOld] = useState(1000);
+    const [maxPixelCountErr, setMaxPixelCountErr] = useState(false);
+    const [maxFramesWithSignalErr, setMaxFramesWithSignalErr] = useState(false);
 
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let incoming: dark_mask_settings = this.props.s;
-            if (!_.isEqual(incoming, this.state.last_downloaded_s)) {
-                this.setState((prev) => ({
-                    s: incoming,
-                    last_downloaded_s: incoming,
-                    download_counter: prev.download_counter + 1,
-                    threshold_err: false,
-                    frame_time_err: false,
-                    number_of_frames_err: false,
-                    number_of_frames_old:
-                        incoming.number_of_frames === 0 ? prev.number_of_frames_old : incoming.number_of_frames,
-                    max_pixel_count_err: false,
-                    max_frames_with_signal_err: false,
-                    enable: (this.props.s?.number_of_frames !== 0)
-                }));
-            }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setDownloadCounter(c => c + 1);
+            setThresholdErr(false);
+            setFrameTimeErr(false);
+            setNumberOfFramesErr(false);
+            setNumberOfFramesOld(serverS.number_of_frames === 0 ? numberOfFramesOld : serverS.number_of_frames);
+            setMaxPixelCountErr(false);
+            setMaxFramesWithSignalErr(false);
         }
-    };
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
+    const hasError = () =>
+        thresholdErr ||
+        frameTimeErr ||
+        numberOfFramesErr ||
+        maxPixelCountErr ||
+        maxFramesWithSignalErr;
 
-    componentDidUpdate() {
-        this.getValues();
-    }
+    return (
+        <Paper style={{ textAlign: 'center' }} sx={{ width: '100%' }}>
+            <br />
+            <Stack
+                spacing={3}
+                sx={{
+                    justifyContent: 'center',
+                    alignItems: 'center',
+                }}
+            >
+                <strong>Dark data collection settings for mask</strong>
+                <div>(DECTRIS detectors only)</div>
 
-    hasError = () =>
-        this.state.threshold_err ||
-        this.state.frame_time_err ||
-        this.state.number_of_frames_err ||
-        this.state.max_pixel_count_err ||
-        this.state.max_frames_with_signal_err;
+                <FormControlLabel
+                    control={
+                        <Checkbox
+                            checked={s.number_of_frames !== 0}
+                            onChange={(event) => {
+                                setDownloadCounter(c => c + 1);
+                                setNumberOfFramesErr(false);
+                                if (!event.target.checked)
+                                    setS(prev => ({...prev, number_of_frames: 0}));
+                                else
+                                    setS(prev => ({...prev, number_of_frames: numberOfFramesOld}));
+                            }}
+                        />
+                    }
+                    label="Enable dark data collection"
+                />
 
-    render() {
-        return (
-            <Paper style={{ textAlign: 'center' }} sx={{ width: '100%' }}>
-                <br />
-                <Stack
-                    spacing={3}
-                    sx={{
-                        justifyContent: 'center',
-                        alignItems: 'center',
-                    }}
-                >
-                    <strong>Dark data collection settings for mask</strong>
-                    <div>(DECTRIS detectors only)</div>
+                <Stack spacing={3} direction="row" sx={{ width: '80%' }}>
 
-                    <FormControlLabel
-                        control={
-                            <Checkbox
-                                checked={this.state.s.number_of_frames !== 0}
-                                onChange={(event) => {
-                                    if (!event.target.checked)
-                                        this.setState(prevState => ({
-                                            download_counter: this.state.download_counter + 1,
-                                            number_of_frames_err: false,
-                                            s: {
-                                                ...prevState.s,
-                                                number_of_frames: 0
-                                            }
-                                        }));
-                                    else
-                                        this.setState(prevState => ({
-                                            download_counter: this.state.download_counter + 1,
-                                            number_of_frames_err: false,
-                                            s: {
-                                                ...prevState.s,
-                                                number_of_frames: this.state.number_of_frames_old
-                                            }
-                                        }));
-                                }}
-                            />
-                        }
-                        label="Enable dark data collection"
+                    <NumberTextField
+                        start_val={s.detector_threshold_keV}
+                        label={'Detector threshold'}
+                        units={'keV'}
+                        float={true}
+                        min={0.001}
+                        default={4.0}
+                        counter={downloadCounter}
+                        disabled={s.number_of_frames === 0}
+                        callback={(val: number, err: boolean) => {
+                            setThresholdErr(err);
+                            setS(prev => ({ ...prev, detector_threshold_keV: val }));
+                        }}
                     />
 
-                    <Stack spacing={3} direction="row" sx={{ width: '80%' }}>
+                    <NumberTextField
+                        start_val={s.frame_time_us / 1000.0}
+                        label={'Frame time'}
+                        units={'ms'}
+                        float={false}
+                        min={1}
+                        max={1000}
+                        default={10}
+                        counter={downloadCounter}
+                        disabled={s.number_of_frames === 0}
+                        callback={(val: number, err: boolean) => {
+                            setFrameTimeErr(err);
+                            setS(prev => ({ ...prev, frame_time_us: val * 1000 }));
+                        }}
+                    />
+                    <NumberTextField
+                        start_val={s.number_of_frames}
+                        label={'Number of frames'}
+                        float={false}
+                        min={1}
+                        default={1000}
+                        counter={downloadCounter}
+                        disabled={s.number_of_frames === 0}
+                        callback={(val: number, err: boolean) => {
+                            if (!err)
+                                setNumberOfFramesOld(val);
+                            setNumberOfFramesErr(err);
+                            setS(prev => ({...prev, number_of_frames: val}));
+                        }}
 
-                        <NumberTextField
-                            start_val={this.state.s.detector_threshold_keV}
-                            label={'Detector threshold'}
-                            units={'keV'}
-                            float={true}
-                            min={0.001}
-                            default={4.0}
-                            counter={this.state.download_counter}
-                            disabled={this.state.s.number_of_frames === 0}
-                            callback={(val: number, err: boolean) => {
-                                this.setState((prev) => ({
-                                    threshold_err: err,
-                                    s: { ...prev.s, detector_threshold_keV: val },
-                                }));
-                            }}
-                        />
-
-                        <NumberTextField
-                            start_val={this.state.s.frame_time_us / 1000.0}
-                            label={'Frame time'}
-                            units={'ms'}
-                            float={false}
-                            min={1}
-                            max={1000}
-                            default={10}
-                            counter={this.state.download_counter}
-                            disabled={this.state.s.number_of_frames === 0}
-                            callback={(val: number, err: boolean) => {
-                                this.setState((prev) => ({
-                                    frame_time_err: err,
-                                    s: { ...prev.s, frame_time_us: val * 1000 },
-                                }));
-                            }}
-                        />
-                        <NumberTextField
-                            start_val={this.state.s.number_of_frames}
-                            label={'Number of frames'}
-                            float={false}
-                            min={1}
-                            default={1000}
-                            counter={this.state.download_counter}
-                            disabled={this.state.s.number_of_frames === 0}
-                            callback={(val: number, err: boolean) => {
-                                let old: number = this.state.number_of_frames_old;
-                                if (!err)
-                                    old = val;
-                                this.setState(prevState => ({
-                                    number_of_frames_err: err,
-                                    number_of_frames_old: old,
-                                    s: {...prevState.s, number_of_frames: val}
-                                }));
-                            }}
-
-                        />
-                    </Stack>
-                    <Stack spacing={3} direction="row" sx={{ width: '80%' }}>
-                        <NumberTextField
-                            start_val={this.state.s.max_allowed_pixel_count}
-                            label={'Max allowed pixel count for valid pixel'}
-                            float={false}
-                            min={0}
-                            default={1}
-                            fullWidth={true}
-                            disabled={this.state.s.number_of_frames === 0}
-                            counter={this.state.download_counter}
-                            callback={(val: number, err: boolean) => {
-                                this.setState((prev) => ({
-                                    max_pixel_count_err: err,
-                                    s: { ...prev.s, max_allowed_pixel_count: val },
-                                }));
-                            }}
-                        />
-
-                        <NumberTextField
-                            start_val={this.state.s.max_frames_with_signal}
-                            label={'Max frames with invalid pixel'}
-                            float={false}
-                            min={0}
-                            default={0}
-                            fullWidth={true}
-                            counter={this.state.download_counter}
-                            disabled={this.state.s.number_of_frames === 0}
-                            callback={(val: number, err: boolean) => {
-                                this.setState((prev) => ({
-                                    max_frames_with_signal_err: err,
-                                    s: { ...prev.s, max_frames_with_signal: val },
-                                }));
-                            }}
-                        />
-                    </Stack>
-                    <ButtonWithSnackbar
-                        path={'/config/dark_mask'}
-                        color={'primary'}
-                        method={'PUT'}
-                        disabled={this.hasError()}
-                        text={'Upload'}
-                        input={JSON.stringify(this.state.s)}
                     />
                 </Stack>
-                <br />
-            </Paper>
-        );
-    }
+                <Stack spacing={3} direction="row" sx={{ width: '80%' }}>
+                    <NumberTextField
+                        start_val={s.max_allowed_pixel_count}
+                        label={'Max allowed pixel count for valid pixel'}
+                        float={false}
+                        min={0}
+                        default={1}
+                        fullWidth={true}
+                        disabled={s.number_of_frames === 0}
+                        counter={downloadCounter}
+                        callback={(val: number, err: boolean) => {
+                            setMaxPixelCountErr(err);
+                            setS(prev => ({ ...prev, max_allowed_pixel_count: val }));
+                        }}
+                    />
+
+                    <NumberTextField
+                        start_val={s.max_frames_with_signal}
+                        label={'Max frames with invalid pixel'}
+                        float={false}
+                        min={0}
+                        default={0}
+                        fullWidth={true}
+                        counter={downloadCounter}
+                        disabled={s.number_of_frames === 0}
+                        callback={(val: number, err: boolean) => {
+                            setMaxFramesWithSignalErr(err);
+                            setS(prev => ({ ...prev, max_frames_with_signal: val }));
+                        }}
+                    />
+                </Stack>
+                <ButtonWithSnackbar
+                    path={'/config/dark_mask'}
+                    color={'primary'}
+                    method={'PUT'}
+                    disabled={hasError()}
+                    text={'Upload'}
+                    input={JSON.stringify(s)}
+                />
+            </Stack>
+            <br />
+        </Paper>
+    );
 }
 
-export default DarkMaskSettings;
+export default memo(DarkMaskSettings);
diff --git a/frontend/src/components/DataCollection.tsx b/frontend/src/components/DataCollection.tsx
index f2d5cacb..68a73e2e 100644
--- a/frontend/src/components/DataCollection.tsx
+++ b/frontend/src/components/DataCollection.tsx
@@ -1,7 +1,7 @@
-import React from 'react';
+import {ChangeEvent, memo, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
-import {Stack, TextField, Radio, RadioGroup, FormControlLabel, FormControl, FormLabel, Checkbox} from "@mui/material";
+import {Stack, TextField, Radio, RadioGroup, FormControlLabel, FormControl, Checkbox} from "@mui/material";
 import NumberTextField from "./NumberTextField";
 import {dataset_settings, grid_scan, rotation_axis} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
@@ -10,325 +10,261 @@ type MyProps = {
     frame_time_us: number
 };
 
-type MyState = {
-    s: dataset_settings,
-    beam_x_pxl_err: boolean,
-    beam_y_pxl_err: boolean,
-    detector_distance_mm_err: boolean,
-    incident_energy_kev_err: boolean,
-    images_per_trigger_err: boolean,
-    images_per_file_err: boolean,
-    image_time_us_err: boolean,
-    ntrigger_err: boolean,
-    mode: 'still' | 'rotation' | 'grid',
-    goniometer: rotation_axis,
-    grid: grid_scan,
-};
+function DataCollection({frame_time_us}: MyProps) {
+    const [s, setS] = useState<dataset_settings>(() => ({
+        beam_x_pxl: 0,
+        beam_y_pxl: 0,
+        detector_distance_mm: 100,
+        incident_energy_keV: 12.398,
+        images_per_trigger: 1,
+        image_time_us: frame_time_us,
+        ntrigger: 1,
+        images_per_file: 1000
+    }));
+    const [goniometer, setGoniometer] = useState<rotation_axis>({
+        start: 0,
+        step: 0.1,
+        name: "omega",
+        vector: [0,1,0]
+    });
+    const [grid, setGrid] = useState<grid_scan>({
+        n_fast: 10,
+        step_x_um: 10.0,
+        step_y_um: 10.0,
+        vertical: false,
+        snake: false
+    });
+    const [beamXPxlErr, setBeamXPxlErr] = useState(false);
+    const [beamYPxlErr, setBeamYPxlErr] = useState(false);
+    const [detectorDistanceMmErr, setDetectorDistanceMmErr] = useState(false);
+    const [incidentEnergyKevErr, setIncidentEnergyKevErr] = useState(false);
+    const [imagesPerTriggerErr, setImagesPerTriggerErr] = useState(false);
+    const [imageTimeUsErr, setImageTimeUsErr] = useState(false);
+    const [ntriggerErr, setNtriggerErr] = useState(false);
+    const [imagesPerFileErr, setImagesPerFileErr] = useState(false);
+    const [mode, setMode] = useState<'still' | 'rotation' | 'grid'>('still');
 
-class DataCollection extends React.Component<MyProps, MyState> {
-    state : MyState = {
-        s : {
-            beam_x_pxl: 0,
-            beam_y_pxl: 0,
-            detector_distance_mm: 100,
-            incident_energy_keV: 12.398,
-            images_per_trigger: 1,
-            image_time_us: this.props.frame_time_us,
-            ntrigger: 1,
-            images_per_file: 1000
-        },
-        goniometer : {
-          start: 0,
-          step: 0.1,
-          name: "omega",
-            vector: [0,1,0]
-        },
-        grid: {
-            n_fast: 10,
-            step_x_um: 10.0,
-            step_y_um: 10.0,
-            vertical: false,
-            snake: false
-        },
-        beam_x_pxl_err: false,
-        beam_y_pxl_err: false,
-        detector_distance_mm_err: false,
-        incident_energy_kev_err: false,
-        images_per_trigger_err: false,
-        image_time_us_err: false,
-        ntrigger_err: false,
-        images_per_file_err: false,
-        mode: 'still',
-    }
+    const error = () : boolean =>
+        beamXPxlErr
+        || beamYPxlErr
+        || detectorDistanceMmErr
+        || incidentEnergyKevErr
+        || imageTimeUsErr
+        || imagesPerTriggerErr
+        || imagesPerFileErr
+        || ntriggerErr;
 
-    error() : boolean {
-        return this.state.beam_x_pxl_err
-            || this.state.beam_y_pxl_err
-            || this.state.detector_distance_mm_err
-            || this.state.incident_energy_kev_err
-            || this.state.image_time_us_err
-            || this.state.images_per_trigger_err
-            || this.state.images_per_file_err
-            || this.state.ntrigger_err;
-    }
-
-    getDatasetSettings = () => {
-        let d = this.state.s;
-        if (this.state.mode === 'rotation')
-            d.goniometer = this.state.goniometer;
-        else if (this.state.mode === 'grid')
-            d.grid_scan = this.state.grid;
+    const getDatasetSettings = () : dataset_settings => {
+        let d = {...s};
+        if (mode === 'rotation')
+            d.goniometer = goniometer;
+        else if (mode === 'grid')
+            d.grid_scan = grid;
         return d;
-    }
+    };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-            <br/>
-            <Stack spacing={5} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-            }}>
-                <TextField label={"File prefix"}
-                           variant="outlined"
-                           onChange={
-                               (event: React.ChangeEvent<HTMLInputElement>) => {
-                                   this.setState(prevState => ({
-                                       s: {...prevState.s, file_prefix: event.target.value}
-                                   }));
-                               }
+    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
+        <br/>
+        <Stack spacing={5} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+        }}>
+            <TextField label={"File prefix"}
+                       variant="outlined"
+                       onChange={
+                           (event: ChangeEvent<HTMLInputElement>) => {
+                               setS(prev => ({...prev, file_prefix: event.target.value}));
                            }
-                           value={this.state.s.file_prefix}
-                           sx={{width:"90%"}}
+                       }
+                       value={s.file_prefix}
+                       sx={{width:"90%"}}
+            />
+            <Stack direction="row" spacing={2} sx={{width: '90%'}}>
+                <NumberTextField
+                    label={"Number of images per trigger"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, images_per_trigger: val}));
+                        setImagesPerTriggerErr(err);
+                    }}
+                    min={1}
+                    default={s.images_per_trigger}
+                />
+                <NumberTextField
+                    label={"Number of triggers"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, ntrigger: val}));
+                        setNtriggerErr(err);
+                    }}
+                    min={1}
+                    default={s.ntrigger}
+                />
+                <NumberTextField
+                    label={"Image time"}
+                    callback={(val: number, err: boolean) => {
+                        let image_time_us = Math.round(val * 1000.0);
+                        setS(prev => ({...prev, image_time_us: image_time_us}));
+                        setImageTimeUsErr(err);
+                    }}
+                    units={"ms"}
+                    float={true}
+                    min={0.01}
+                    default={(s.image_time_us ?? 500) / 1000.0}
                 />
-                <Stack direction="row" spacing={2} sx={{width: '90%'}}>
-                    <NumberTextField
-                        label={"Number of images per trigger"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, images_per_trigger: val},
-                                    images_per_trigger_err: err
-                                }
-                            ));
-                        }}
-                        min={1}
-                        default={this.state.s.images_per_trigger}
-                    />
-                    <NumberTextField
-                        label={"Number of triggers"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, ntrigger: val},
-                                    ntrigger_err: err
-                                }
-                            ));
-                        }}
-                        min={1}
-                        default={this.state.s.ntrigger}
-                    />
-                    <NumberTextField
-                        label={"Image time"}
-                        callback={(val: number, err: boolean) => {
-                            let image_time_us = Math.round(val * 1000.0);
 
-                            this.setState(prevState => ({
-                                    s: {...prevState.s,
-                                        image_time_us: image_time_us
-                                    },
-                                    image_time_us_err: err
-                                }
-                            ));
-                        }}
-                        units={"ms"}
-                        float={true}
-                        min={0.01}
-                        default={(this.state.s.image_time_us ?? 500) / 1000.0}
-                    />
-
-                    <NumberTextField
-                        label={"Images per file"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s,
-                                        images_per_file: val
-                                    },
-                                    images_per_file_err: err
-                                }
-                            ));
-                        }}
-                        float={false}
-                        min={1}
-                        default={this.state.s.images_per_file}
-                    />
-                </Stack>
-                <Stack direction="row" spacing={2} sx={{width: '90%'}}>
-                    <NumberTextField
-                        label={"Beam X [pxl]"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, beam_x_pxl: val},
-                                    beam_x_pxl_err: err
-                                }
-                            ));
-                        }}
-                        units={"pxl"}
-                        float={true}
-                        default={this.state.s.beam_x_pxl}
-                    />
-                    <NumberTextField
-                        label={"Beam Y"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, beam_y_pxl: val},
-                                    beam_y_pxl_err: err
-                                }
-                            ));
-                        }}
-                        units={"pxl"}
-                        float={true}
-                        default={this.state.s.beam_y_pxl}
-                    />
-                    <NumberTextField
-                        label={"Detector distance"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, detector_distance_mm: val},
-                                    detector_distance_mm_err: err
-                                }
-                            ));
-                        }}
-                        units={"mm"}
-                        min={0.1}
-                        float={true}
-                        default={this.state.s.detector_distance_mm}
-                    />
-                    <NumberTextField
-                        label={"Energy"}
-                        callback={(val: number, err: boolean) => {
-                            this.setState(prevState => ({
-                                    s: {...prevState.s, incident_energy_keV: val},
-                                    incident_energy_kev_err: err
-                                }
-                            ));
-                        }}
-                        min={0.1}
-                        max={500.0}
-                        units={"keV"}
-                        float={true}
-                        default={this.state.s.incident_energy_keV}
-                    />
-
-
-
-                </Stack>
-                <FormControl sx={{width: '90%'}}>
-                    <RadioGroup
-                        row
-                        value={this.state.mode}
-                        onChange={(event) => this.setState({mode: event.target.value as 'still' | 'rotation' | 'grid'})}>
-                        <FormControlLabel value="still" control={<Radio/>} label="Still"/>
-                        <FormControlLabel value="rotation" control={<Radio/>} label="Rotation"/>
-                        <FormControlLabel value="grid" control={<Radio/>} label="Grid scan"/>
-                    </RadioGroup>
-                </FormControl>
-                {this.state.mode === 'rotation' && (
-                    <Stack direction="row" spacing={2} sx={{width: '90%'}}>
-                        <NumberTextField
-                            label="Start angle"
-                            callback={(val: number) => this.setState(prevState => (
-                                {goniometer : {...prevState.goniometer, start: val}}
-                            ))}
-                            units="°"
-                            float={true}
-                            default={this.state.goniometer.start}
-                        />
-                        <NumberTextField
-                            label="Step"
-                            callback={(val: number) => this.setState(prevState => (
-                                {goniometer : {...prevState.goniometer, step: val}}
-                            ))}
-                            units="°"
-                            float={true}
-                            min={0.001}
-                            default={this.state.goniometer.step}
-                        />
-                        <TextField
-                            label="Axis name"
-                            value={this.state.goniometer.name}
-                            onChange={(e) => this.setState(prevState => (
-                                {goniometer : {...prevState.goniometer, name: e.target.value}}
-                                ))}
-                        />
-                    </Stack>
-                )}
-                {this.state.mode === 'grid' && (
-                    <Stack direction="row" spacing={2} sx={{width: '90%'}}>
-                        <NumberTextField
-                            label="Grid elements (fast dim.)"
-                            callback={(val: number) => this.setState(
-                                prevState => ({grid : {...prevState.grid, n_fast: val}}))}
-                            min={1}
-                            default={this.state.grid.n_fast}
-                        />
-                        <NumberTextField
-                            label="X step"
-                            callback={(val: number) => this.setState(
-                                prevState => ({grid : {...prevState.grid, step_x_um: val}}))}
-                            units="μm"
-                            float={true}
-                            default={this.state.grid.step_x_um}
-                        />
-                        <NumberTextField
-                            label="Y step"
-                            callback={(val: number) => this.setState(
-                                prevState => ({grid : {...prevState.grid, step_y_um: val}}))}
-                            units="μm"
-                            float={true}
-                            default={this.state.grid.step_y_um}
-                        />
-                        <FormControlLabel
-                            control={
-                                <Checkbox
-                                    checked={this.state.grid.snake}
-                                    onChange={(e) => this.setState(prevState => (
-                                        {grid : {...prevState.grid, snake: e.target.checked}}
-                                    ))}
-                                />
-                            }
-                            label="Snake scan"
-                        />
-                        <FormControlLabel
-                            control={
-                                <Checkbox
-                                    checked={this.state.grid.vertical}
-                                    onChange={(e) => this.setState(prevState => (
-                                        {grid : {...prevState.grid, vertical: e.target.checked}}
-                                    ))}
-                                />
-                            }
-                            label="Vertical scan"
-                        />
-                    </Stack>
-                )}
-
-                <Stack direction="row" spacing={2}>
-                    <ButtonWithSnackbar
-                        path={"/start"}
-                        text={"start"}
-                        disabled={this.error()}
-                        input={JSON.stringify(this.getDatasetSettings())}
-                        color={"primary"}
-                    />
-                    <ButtonWithSnackbar
-                        path={"/trigger"}
-                        text={"soft trigger"}
-                        disabled={this.error()}
-                        color={"primary"}
-                    />
-                </Stack>
+                <NumberTextField
+                    label={"Images per file"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, images_per_file: val}));
+                        setImagesPerFileErr(err);
+                    }}
+                    float={false}
+                    min={1}
+                    default={s.images_per_file}
+                />
             </Stack>
-            <br/>
-        </Paper>
-    }
+            <Stack direction="row" spacing={2} sx={{width: '90%'}}>
+                <NumberTextField
+                    label={"Beam X [pxl]"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, beam_x_pxl: val}));
+                        setBeamXPxlErr(err);
+                    }}
+                    units={"pxl"}
+                    float={true}
+                    default={s.beam_x_pxl}
+                />
+                <NumberTextField
+                    label={"Beam Y"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, beam_y_pxl: val}));
+                        setBeamYPxlErr(err);
+                    }}
+                    units={"pxl"}
+                    float={true}
+                    default={s.beam_y_pxl}
+                />
+                <NumberTextField
+                    label={"Detector distance"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, detector_distance_mm: val}));
+                        setDetectorDistanceMmErr(err);
+                    }}
+                    units={"mm"}
+                    min={0.1}
+                    float={true}
+                    default={s.detector_distance_mm}
+                />
+                <NumberTextField
+                    label={"Energy"}
+                    callback={(val: number, err: boolean) => {
+                        setS(prev => ({...prev, incident_energy_keV: val}));
+                        setIncidentEnergyKevErr(err);
+                    }}
+                    min={0.1}
+                    max={500.0}
+                    units={"keV"}
+                    float={true}
+                    default={s.incident_energy_keV}
+                />
+
+
+
+            </Stack>
+            <FormControl sx={{width: '90%'}}>
+                <RadioGroup
+                    row
+                    value={mode}
+                    onChange={(event) => setMode(event.target.value as 'still' | 'rotation' | 'grid')}>
+                    <FormControlLabel value="still" control={<Radio/>} label="Still"/>
+                    <FormControlLabel value="rotation" control={<Radio/>} label="Rotation"/>
+                    <FormControlLabel value="grid" control={<Radio/>} label="Grid scan"/>
+                </RadioGroup>
+            </FormControl>
+            {mode === 'rotation' && (
+                <Stack direction="row" spacing={2} sx={{width: '90%'}}>
+                    <NumberTextField
+                        label="Start angle"
+                        callback={(val: number) => setGoniometer(prev => ({...prev, start: val}))}
+                        units="°"
+                        float={true}
+                        default={goniometer.start}
+                    />
+                    <NumberTextField
+                        label="Step"
+                        callback={(val: number) => setGoniometer(prev => ({...prev, step: val}))}
+                        units="°"
+                        float={true}
+                        min={0.001}
+                        default={goniometer.step}
+                    />
+                    <TextField
+                        label="Axis name"
+                        value={goniometer.name}
+                        onChange={(e) => setGoniometer(prev => ({...prev, name: e.target.value}))}
+                    />
+                </Stack>
+            )}
+            {mode === 'grid' && (
+                <Stack direction="row" spacing={2} sx={{width: '90%'}}>
+                    <NumberTextField
+                        label="Grid elements (fast dim.)"
+                        callback={(val: number) => setGrid(prev => ({...prev, n_fast: val}))}
+                        min={1}
+                        default={grid.n_fast}
+                    />
+                    <NumberTextField
+                        label="X step"
+                        callback={(val: number) => setGrid(prev => ({...prev, step_x_um: val}))}
+                        units="μm"
+                        float={true}
+                        default={grid.step_x_um}
+                    />
+                    <NumberTextField
+                        label="Y step"
+                        callback={(val: number) => setGrid(prev => ({...prev, step_y_um: val}))}
+                        units="μm"
+                        float={true}
+                        default={grid.step_y_um}
+                    />
+                    <FormControlLabel
+                        control={
+                            <Checkbox
+                                checked={grid.snake}
+                                onChange={(e) => setGrid(prev => ({...prev, snake: e.target.checked}))}
+                            />
+                        }
+                        label="Snake scan"
+                    />
+                    <FormControlLabel
+                        control={
+                            <Checkbox
+                                checked={grid.vertical}
+                                onChange={(e) => setGrid(prev => ({...prev, vertical: e.target.checked}))}
+                            />
+                        }
+                        label="Vertical scan"
+                    />
+                </Stack>
+            )}
+
+            <Stack direction="row" spacing={2}>
+                <ButtonWithSnackbar
+                    path={"/start"}
+                    text={"start"}
+                    disabled={error()}
+                    input={JSON.stringify(getDatasetSettings())}
+                    color={"primary"}
+                />
+                <ButtonWithSnackbar
+                    path={"/trigger"}
+                    text={"soft trigger"}
+                    disabled={error()}
+                    color={"primary"}
+                />
+            </Stack>
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default DataCollection;
+export default memo(DataCollection);
diff --git a/frontend/src/components/DataProcessingPlot.tsx b/frontend/src/components/DataProcessingPlot.tsx
index c47eb9bf..b693e797 100644
--- a/frontend/src/components/DataProcessingPlot.tsx
+++ b/frontend/src/components/DataProcessingPlot.tsx
@@ -1,6 +1,8 @@
-import React, {Component, ReactNode} from 'react';
+import {ReactNode} from 'react';
 
-import {azint_unit, getPreviewPlot, plot_type, plot_unit_x, plots} from "../client";
+import {useQuery} from "@tanstack/react-query";
+import {azint_unit, plot_type, plot_unit_x} from "../client";
+import {getPreviewPlotOptions} from "../client/@tanstack/react-query.gen";
 import MultiLinePlotWrapper from "./MultiLinePlotWrapper";
 
 type MyProps = {
@@ -10,11 +12,6 @@ type MyProps = {
     azint: azint_unit;
 };
 
-type MyState = {
-    plots : plots,
-    connection_error: boolean
-}
-
 type PlotlyPlot = {
     x: number[],
     y: (number | null)[],
@@ -97,79 +94,49 @@ function AxisTypeY(plot: plot_type) : string | ReactNode {
     }
 }
 
-class DataProcessingPlot extends Component<MyProps, MyState> {
-    interval: ReturnType<typeof setInterval> | undefined;
+function DataProcessingPlot({type, binning, angle, azint}: MyProps) {
+    const {data: plots, isError} = useQuery({
+        ...getPreviewPlotOptions({ query: { type, binning, experimental_coord: angle, azint_unit: azint } }),
+        refetchInterval: 1000,
+    });
 
-    state: MyState = {
-        plots: {
-            plot : [
-                {
-                    x: [0, 100, 200, 300, 400, 500],
-                    y: [0.1, 0.3, 0.5, 0.2, 0.0, 0.1],
-                    title: "Example"
-                }
-            ],
-            unit_x: plot_unit_x.IMAGE_NUMBER
-        },
-        connection_error: true
-    }
+    if (isError
+        || (plots === undefined)
+        || (plots.plot === null)
+        || (plots.plot.length === 0))
+        return <div>No plots available</div>;
 
-    getValues() {
-        getPreviewPlot({ throwOnError: true, query: { type: this.props.type, binning: this.props.binning, experimental_coord: this.props.angle, azint_unit: this.props.azint } })
-            .then(({data}) => this.setState({plots: data, connection_error: false}))
-            .catch(error => {
-                this.setState({connection_error: true});
-            });
-    }
+    let data: PlotlyData = [];
+    if ((plots.plot[0].z !== undefined)
+        && (plots.plot[0].z.length > 0)) {
 
-    componentDidMount() {
-        this.getValues();
-        this.interval = setInterval(() => this.getValues(), 1000);
-    }
-
-    componentWillUnmount() {
-        clearInterval(this.interval);
-    }
-
-    render() {
-        if (this.state.connection_error
-            || (this.state.plots === undefined)
-            || (this.state.plots.plot === null)
-            || (this.state.plots.plot.length === 0))
-            return <div>No plots available</div>;
-
-        let data: PlotlyData = [];
-        if ((this.state.plots.plot[0].z !== undefined)
-            && (this.state.plots.plot[0].z.length > 0)) {
+        data.push({
+            x: plots.plot[0].x,
+            y: plots.plot[0].y,
+            z: plots.plot[0].z,
+            type: "heatmap",
+            colorscale: "Viridis"
+        })
+        return <MultiLinePlotWrapper xaxis={AxisTypeX(plots.unit_x)}
+                                     yaxis={AxisTypeY(type)}
+                                     data={data}
+                                     grid_scan={true}
+                                     range_x={plots.size_x}
+                                     range_y={plots.size_y}/>
 
+    } else {
+        plots.plot.map(d =>
             data.push({
-                x: this.state.plots.plot[0].x,
-                y: this.state.plots.plot[0].y,
-                z: this.state.plots.plot[0].z,
-                type: "heatmap",
-                colorscale: "Viridis"
-            })
-            return <MultiLinePlotWrapper xaxis={AxisTypeX(this.state.plots.unit_x)}
-                                         yaxis={AxisTypeY(this.props.type)}
-                                         data={data}
-                                         grid_scan={true}
-                                         range_x={this.state.plots.size_x}
-                                         range_y={this.state.plots.size_y}/>
-
-        } else {
-            this.state.plots.plot.map(d =>
-                data.push({
-                    x: d.x,
-                    y: d.y,
-                    type: "scatter",
-                    mode: "line",
-                    name: d.title
-                }));
-            return <MultiLinePlotWrapper xaxis={AxisTypeX(this.state.plots.unit_x)}
-                                         yaxis={AxisTypeY(this.props.type)}
-                                         data={data}
-                                         grid_scan={false}/>
-        }
+                x: d.x,
+                y: d.y,
+                type: "scatter",
+                mode: "line",
+                name: d.title
+            }));
+        return <MultiLinePlotWrapper xaxis={AxisTypeX(plots.unit_x)}
+                                     yaxis={AxisTypeY(type)}
+                                     data={data}
+                                     grid_scan={false}/>
     }
 }
 
diff --git a/frontend/src/components/DataProcessingPlots.tsx b/frontend/src/components/DataProcessingPlots.tsx
index 303d5f99..1e8206c2 100644
--- a/frontend/src/components/DataProcessingPlots.tsx
+++ b/frontend/src/components/DataProcessingPlots.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {memo, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Box, Checkbox, FormControlLabel, Grid} from "@mui/material";
@@ -14,131 +14,119 @@ type MyProps = {
     height: number
 }
 
-type MyState = {
-    type: plot_type,
-    binning: string,
-    tab : String,
-    angle_units: boolean,
-    azint_unit: azint_unit
-}
+function DataProcessingPlots({type: initialType, height}: MyProps) {
+    const [type, setType] = useState<plot_type>(initialType);
+    const [binning, setBinning] = useState("0");
+    const [tab, setTab] = useState<String>(initialType);
+    const [angleUnits, setAngleUnits] = useState(true);
+    const [azintUnit, setAzintUnit] = useState<azint_unit>(azint_unit.Q_RECIP_A);
 
-class DataProcessingPlots extends Component<MyProps, MyState> {
-    state: MyState = {
-        type: this.props.type,
-        binning: "0",
-        tab: this.props.type,
-        angle_units: true,
-        azint_unit: azint_unit.Q_RECIP_A
-    }
-
-    plotTypeChange = (event : SelectChangeEvent<String>) => {
+    const plotTypeChange = (event : SelectChangeEvent<String>) => {
         let val = String(event.target.value).toString();
-        this.setState({tab: val, type: val as plot_type});
+        setTab(val);
+        setType(val as plot_type);
     };
 
-    handleChange = (event : SelectChangeEvent<String>) => {
-        this.setState({ binning: String(event.target.value).toString() });
+    const handleChange = (event : SelectChangeEvent<String>) => {
+        setBinning(String(event.target.value).toString());
     };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: this.props.height, width: "100%" }}>
-            <Toolbar>
+    return <Paper style={{textAlign: 'center'}} sx={{ height: height, width: "100%" }}>
+        <Toolbar>
 
-                <Grid container sx={{ minWidth: 500 }} >
-                    <FormControl variant="standard" sx={{ m: 1, minWidth: 500 }}>
+            <Grid container sx={{ minWidth: 500 }} >
+                <FormControl variant="standard" sx={{ m: 1, minWidth: 500 }}>
 
-                        <Select
-                            value={this.state.tab}
-                            onChange={this.plotTypeChange}
-                            label="Plot category"
-                            sx={{fontWeight: "bold"}}
-                        >
-                            <MenuItem value={plot_type.INDEXING_RATE}>Indexing rate</MenuItem>
-                            <MenuItem value={plot_type.INDEXING_UNIT_CELL_LENGTH}>Indexing unit cell (length)</MenuItem>
-                            <MenuItem value={plot_type.INDEXING_UNIT_CELL_ANGLE}>Indexing unit cell (angle)</MenuItem>
-                            <MenuItem value={plot_type.SPOT_COUNT}>Spot count</MenuItem>
-                            <MenuItem value={plot_type.SPOT_COUNT_LOW_RES}>Spot count low res.</MenuItem>
-                            <MenuItem value={plot_type.SPOT_COUNT_INDEXED}>Spot count indexed</MenuItem>
-                            <MenuItem value={plot_type.SPOT_COUNT_ICE}>Spot count ice ring</MenuItem>
-                            <MenuItem value={plot_type.AZINT}>Azimuthal integration profile</MenuItem>
-                            <MenuItem value={plot_type.AZINT_1D}>Azimuthal integration profile (1D)</MenuItem>
-                            <MenuItem value={plot_type.BKG_ESTIMATE}>Background estimate</MenuItem>
-                            <MenuItem value={plot_type.RESOLUTION_ESTIMATE}>Diffraction resolution estimate</MenuItem>
-                            <MenuItem value={plot_type.ROI_SUM}>ROI area sum</MenuItem>
-                            <MenuItem value={plot_type.ROI_MEAN}>ROI area mean</MenuItem>
-                            <MenuItem value={plot_type.ROI_WEIGHTED_X}>ROI area weighted X position</MenuItem>
-                            <MenuItem value={plot_type.ROI_WEIGHTED_Y}>ROI area weighted Y position</MenuItem>
-                            <MenuItem value={plot_type.ROI_MAX_COUNT}>ROI area max count</MenuItem>
-                            <MenuItem value={plot_type.ERROR_PIXELS}>Error pixels</MenuItem>
-                            <MenuItem value={plot_type.SATURATED_PIXELS}>Saturated pixels</MenuItem>
-                            <MenuItem value={plot_type.STRONG_PIXELS}>Strong pixels (for spot finding)</MenuItem>
-                            <MenuItem value={plot_type.MAX_PIXEL_VALUE}>Maximum pixel value (excl. overloads)</MenuItem>
-                            <MenuItem value={plot_type.PROFILE_RADIUS}>Profile radius</MenuItem>
-                            <MenuItem value={plot_type.B_FACTOR}>Wilson B-factor</MenuItem>
-                            <MenuItem value={plot_type.BEAM_CENTER_X}>Beam center X (post-indexing geometry refinement)</MenuItem>
-                            <MenuItem value={plot_type.BEAM_CENTER_Y}>Beam center Y (post-indexing geometry refinement)</MenuItem>
-                            <MenuItem value={plot_type.INDEXING_LATTICE_COUNT}>Indexed lattice count</MenuItem>
-                            <MenuItem value={plot_type.INTEGRATED_REFLECTIONS}>Integrated reflections</MenuItem>
-                            <MenuItem value={plot_type.IMAGE_COLLECTION_EFFICIENCY}>Image collection efficiency</MenuItem>
-                            <MenuItem value={plot_type.COMPRESSION_RATIO}>Compression ratio</MenuItem>
-                            <MenuItem value={plot_type.PROCESSING_TIME}> Processing time</MenuItem>
-                            <MenuItem value={plot_type.RECEIVER_DELAY}>Receiver delay (internal debugging)</MenuItem>
-                            <MenuItem value={plot_type.RECEIVER_FREE_SEND_BUF}>Receiver free send buffers (internal debugging)</MenuItem>
-                        </Select>
+                    <Select
+                        value={tab}
+                        onChange={plotTypeChange}
+                        label="Plot category"
+                        sx={{fontWeight: "bold"}}
+                    >
+                        <MenuItem value={plot_type.INDEXING_RATE}>Indexing rate</MenuItem>
+                        <MenuItem value={plot_type.INDEXING_UNIT_CELL_LENGTH}>Indexing unit cell (length)</MenuItem>
+                        <MenuItem value={plot_type.INDEXING_UNIT_CELL_ANGLE}>Indexing unit cell (angle)</MenuItem>
+                        <MenuItem value={plot_type.SPOT_COUNT}>Spot count</MenuItem>
+                        <MenuItem value={plot_type.SPOT_COUNT_LOW_RES}>Spot count low res.</MenuItem>
+                        <MenuItem value={plot_type.SPOT_COUNT_INDEXED}>Spot count indexed</MenuItem>
+                        <MenuItem value={plot_type.SPOT_COUNT_ICE}>Spot count ice ring</MenuItem>
+                        <MenuItem value={plot_type.AZINT}>Azimuthal integration profile</MenuItem>
+                        <MenuItem value={plot_type.AZINT_1D}>Azimuthal integration profile (1D)</MenuItem>
+                        <MenuItem value={plot_type.BKG_ESTIMATE}>Background estimate</MenuItem>
+                        <MenuItem value={plot_type.RESOLUTION_ESTIMATE}>Diffraction resolution estimate</MenuItem>
+                        <MenuItem value={plot_type.ROI_SUM}>ROI area sum</MenuItem>
+                        <MenuItem value={plot_type.ROI_MEAN}>ROI area mean</MenuItem>
+                        <MenuItem value={plot_type.ROI_WEIGHTED_X}>ROI area weighted X position</MenuItem>
+                        <MenuItem value={plot_type.ROI_WEIGHTED_Y}>ROI area weighted Y position</MenuItem>
+                        <MenuItem value={plot_type.ROI_MAX_COUNT}>ROI area max count</MenuItem>
+                        <MenuItem value={plot_type.ERROR_PIXELS}>Error pixels</MenuItem>
+                        <MenuItem value={plot_type.SATURATED_PIXELS}>Saturated pixels</MenuItem>
+                        <MenuItem value={plot_type.STRONG_PIXELS}>Strong pixels (for spot finding)</MenuItem>
+                        <MenuItem value={plot_type.MAX_PIXEL_VALUE}>Maximum pixel value (excl. overloads)</MenuItem>
+                        <MenuItem value={plot_type.PROFILE_RADIUS}>Profile radius</MenuItem>
+                        <MenuItem value={plot_type.B_FACTOR}>Wilson B-factor</MenuItem>
+                        <MenuItem value={plot_type.BEAM_CENTER_X}>Beam center X (post-indexing geometry refinement)</MenuItem>
+                        <MenuItem value={plot_type.BEAM_CENTER_Y}>Beam center Y (post-indexing geometry refinement)</MenuItem>
+                        <MenuItem value={plot_type.INDEXING_LATTICE_COUNT}>Indexed lattice count</MenuItem>
+                        <MenuItem value={plot_type.INTEGRATED_REFLECTIONS}>Integrated reflections</MenuItem>
+                        <MenuItem value={plot_type.IMAGE_COLLECTION_EFFICIENCY}>Image collection efficiency</MenuItem>
+                        <MenuItem value={plot_type.COMPRESSION_RATIO}>Compression ratio</MenuItem>
+                        <MenuItem value={plot_type.PROCESSING_TIME}> Processing time</MenuItem>
+                        <MenuItem value={plot_type.RECEIVER_DELAY}>Receiver delay (internal debugging)</MenuItem>
+                        <MenuItem value={plot_type.RECEIVER_FREE_SEND_BUF}>Receiver free send buffers (internal debugging)</MenuItem>
+                    </Select>
 
-                    </FormControl>
-                </Grid>
-                <Grid container justifyContent="flex-end">
-                    <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
-                        <FormControlLabel
-                            control={
-                                <Checkbox
-                                    checked={this.state.angle_units}
-                                    onChange={(e) => this.setState(
-                                        {angle_units: e.target.checked})}
-                                />
-                            }
-                            label="X-axis exp. units"
-                        /></FormControl>
-                    <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
-                        <FormControlLabel
-                            control={
-                                <Checkbox
-                                    checked={this.state.azint_unit == azint_unit.TWO_THETA_DEG}
-                                    onChange={(e) => this.setState({
-                                        azint_unit: e.target.checked ? azint_unit.TWO_THETA_DEG : azint_unit.Q_RECIP_A
-                                    })}
-                                />
-                            }
-                            label="2θ (az. int.)"
-                        />
-                    </FormControl>
-                    <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
-                        <Select
-                            value={this.state.binning}
-                            onChange={this.handleChange}
-                            label="Binning"
-                        >
-                            <MenuItem value={0}>
-                                <em>Auto binning</em>
-                            </MenuItem>
-                            <MenuItem value={1}>1 image</MenuItem>
-                            <MenuItem value={10}>10 images</MenuItem>
-                            <MenuItem value={100}>100 images</MenuItem>
-                            <MenuItem value={500}>500 images</MenuItem>
-                            <MenuItem value={1000}>1000 images</MenuItem>
-                            <MenuItem value={5000}>5000 images</MenuItem>
-                            <MenuItem value={10000}>10000 images</MenuItem>
-                        </Select>
-                    </FormControl>
-                </Grid>
-            </Toolbar>
-            <Box sx={{width:"95%", height: this.props.height - 150}} >
-                <DataProcessingPlot type={this.state.type} binning={Number(this.state.binning)} angle={this.state.angle_units}
-                                    azint={this.state.azint_unit}/>
-            </Box>
-        </Paper>
-    }
+                </FormControl>
+            </Grid>
+            <Grid container justifyContent="flex-end">
+                <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
+                    <FormControlLabel
+                        control={
+                            <Checkbox
+                                checked={angleUnits}
+                                onChange={(e) => setAngleUnits(e.target.checked)}
+                            />
+                        }
+                        label="X-axis exp. units"
+                    /></FormControl>
+                <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
+                    <FormControlLabel
+                        control={
+                            <Checkbox
+                                checked={azintUnit == azint_unit.TWO_THETA_DEG}
+                                onChange={(e) => setAzintUnit(
+                                    e.target.checked ? azint_unit.TWO_THETA_DEG : azint_unit.Q_RECIP_A
+                                )}
+                            />
+                        }
+                        label="2θ (az. int.)"
+                    />
+                </FormControl>
+                <FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
+                    <Select
+                        value={binning}
+                        onChange={handleChange}
+                        label="Binning"
+                    >
+                        <MenuItem value={0}>
+                            <em>Auto binning</em>
+                        </MenuItem>
+                        <MenuItem value={1}>1 image</MenuItem>
+                        <MenuItem value={10}>10 images</MenuItem>
+                        <MenuItem value={100}>100 images</MenuItem>
+                        <MenuItem value={500}>500 images</MenuItem>
+                        <MenuItem value={1000}>1000 images</MenuItem>
+                        <MenuItem value={5000}>5000 images</MenuItem>
+                        <MenuItem value={10000}>10000 images</MenuItem>
+                    </Select>
+                </FormControl>
+            </Grid>
+        </Toolbar>
+        <Box sx={{width:"95%", height: height - 150}} >
+            <DataProcessingPlot type={type} binning={Number(binning)} angle={angleUnits}
+                                azint={azintUnit}/>
+        </Box>
+    </Paper>
 }
 
-export default DataProcessingPlots;
\ No newline at end of file
+export default memo(DataProcessingPlots);
diff --git a/frontend/src/components/DataProcessingSettings.tsx b/frontend/src/components/DataProcessingSettings.tsx
index 8019a15c..9a73519f 100644
--- a/frontend/src/components/DataProcessingSettings.tsx
+++ b/frontend/src/components/DataProcessingSettings.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, useEffect, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Grid, Slider, Switch, Typography} from "@mui/material";
@@ -10,12 +10,6 @@ type MyProps = {
     update: () => void
 };
 
-type MyState = {
-    s: spot_finding_settings,
-    last_downloaded_s: spot_finding_settings,
-    high_res_gap_Q_recipA: number
-}
-
 const default_spot_finding_settings: spot_finding_settings = {
     enable: true,
     indexing: true,
@@ -31,221 +25,165 @@ const default_spot_finding_settings: spot_finding_settings = {
     high_res_gap_Q_recipA: 1.5
 };
 
-class DataProcessingSettings extends Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_spot_finding_settings,
-        last_downloaded_s: default_spot_finding_settings,
-        high_res_gap_Q_recipA: 1.5
-    }
-
-    putValues(x: spot_finding_settings) {
-        putConfigSpotFinding({ body: x, throwOnError: true })
-            .catch(error => console.log(error) );
-    }
-
-    getValues() {
-        const incoming = this.props.s;
-
-        // Only adopt the server copy when it actually changed, otherwise the
-        // 1 s statistics poll would overwrite edits the user is making.
-        if ((incoming !== undefined) && !_.isEqual(incoming, this.state.last_downloaded_s))
-            this.setState(prevState => ({
-                s: incoming,
-                last_downloaded_s: incoming,
-                high_res_gap_Q_recipA: incoming.high_res_gap_Q_recipA ?? prevState.high_res_gap_Q_recipA
-            }));
-    }
-
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    setPhotonCountThreshold = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {...prevState.s, photon_count_threshold: newValue as number}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setSignalToNoiseThreshold = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {...prevState.s, signal_to_noise_threshold: newValue as number}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setMinPixPerSpot = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {...prevState.s, min_pix_per_spot: newValue as number}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setLowResolutionLimit = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {...prevState.s, low_resolution_limit: newValue as number}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setHighResolutionLimit = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {...prevState.s, high_resolution_limit: newValue as number}}),
-             () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setHighResolutionLimitForCountingLowResSpots = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {
-                    ...prevState.s,
-                    high_resolution_limit_for_spot_count_low_res: newValue as number
-        }}), () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    setIceRingWidth = (event: Event, newValue: number | number[]) => {
-        this.setState(prevState => ({s: {
-                ...prevState.s,
-                ice_ring_width_q_recipA: newValue as number
-            }}), () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-    enableSpotFindingToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s: {...prevState.s, enable: event.target.checked}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    enableIndexingToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s: {...prevState.s, indexing: event.target.checked}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-    enableQuickIntegrationToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s: {...prevState.s, quick_integration: event.target.checked}}),
-            () => {this.putValues(this.state.s);});
-        this.props.update();
-    }
-
-    enableHighResGapToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        const checked = event.target.checked;
-        this.setState(prevState => {
-            return {
-                s: {
-                    ...prevState.s,
-                    high_res_gap_Q_recipA: checked ? prevState.high_res_gap_Q_recipA : undefined
-                }
-            };
-        }, () => { this.putValues(this.state.s); });
-        this.props.update();
-    }
-
-    setHighResGap = (event: Event, newValue: number | number[]) => {
-        const v = newValue as number;
-        this.setState(prevState => ({
-            s: {
-                ...prevState.s,
-                high_res_gap_Q_recipA: v
-            },
-            high_res_gap_Q_recipA: v
-        }), () => { this.putValues(this.state.s); });
-        this.props.update();
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 800, width: '100%' }}>
-                    <Grid container spacing={0}>
-
-                        <Grid item xs={1}/>
-                        <Grid item xs={10}>
-                            <br/><strong>Spot finding parameters</strong><br/><br/>
-                            <Switch onChange={this.enableSpotFindingToggle} checked={this.state.s.enable}/>
-                            Spot finding
-                            <br/><br/>
-
-                            <Typography gutterBottom> Count threshold </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.photon_count_threshold)}
-                                    onChange={this.setPhotonCountThreshold}
-                                    min={1} max={50} step={1} valueLabelDisplay="auto"/>
-
-                            <br/><Typography> Signal-to-noise threshold </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.signal_to_noise_threshold)}
-                                    onChange={this.setSignalToNoiseThreshold}
-                                    min={2}
-                                    max={10}
-                                    step={0.5}
-                                    valueLabelDisplay="auto"
-                                    valueLabelFormat={(value) => value.toFixed(1)}
-                            />
-
-                            <br/><Typography> Minimum pixel / spot </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.min_pix_per_spot)}
-                                    onChange={this.setMinPixPerSpot}
-                                    min={1} max={8} step={1} valueLabelDisplay="auto"/>
-                            <Typography> Low resolution limit [&#8491;] </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.low_resolution_limit)}
-                                    onChange={this.setLowResolutionLimit}
-                                    min={10} max={100} step={0.1} valueLabelDisplay="auto"
-                                    valueLabelFormat={(value) => value.toFixed(1)}
-                            />
-
-                            <Typography> High resolution limit [&#8491;] </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.high_resolution_limit)}
-                                    onChange={this.setHighResolutionLimit}
-                                    min={1} max={5} step={0.1} valueLabelDisplay="auto"
-                                    valueLabelFormat={(value) => value.toFixed(1)}
-                            />
-                            <Typography> High resolution limit for counting low resolution spots [&#8491;] </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.high_resolution_limit_for_spot_count_low_res)}
-                                    onChange={this.setHighResolutionLimitForCountingLowResSpots}
-                                    min={2} max={8} step={0.1} valueLabelDisplay="auto"
-                                    valueLabelFormat={(value) => value.toFixed(1)}
-                            />
-                            <Typography> Ice ring width in Q-space [&#8491;<sup>-1</sup>] </Typography>
-                            <Slider disabled={!this.state.s.enable}
-                                    value={Number(this.state.s.ice_ring_width_q_recipA)}
-                                    onChange={this.setIceRingWidth}
-                                    min={0.0} max={0.2} step={0.001} valueLabelDisplay="auto"
-                                    valueLabelFormat={(value) => value.toFixed(3)}
-                            />
-
-                            <Switch
-                                onChange={this.enableHighResGapToggle}
-                                checked={this.state.s.high_res_gap_Q_recipA !== undefined}
-                                disabled={!this.state.s.enable}
-                            />
-                            High‑res gap Q-space filter [&#8491;<sup>-1</sup>]
-                            <Typography/>
-                            <Slider
-                                disabled={!this.state.s.enable || this.state.s.high_res_gap_Q_recipA === undefined}
-                                value={Number(this.state.s.high_res_gap_Q_recipA ?? this.state.high_res_gap_Q_recipA)}
-                                onChange={this.setHighResGap}
-                                min={0.1}
-                                max={5.0}
-                                step={0.01}
-                                valueLabelDisplay="auto"
-                                valueLabelFormat={(value) => value.toFixed(2)}
-                            />
-
-                            <br/><br/>
-                            <Switch onChange={this.enableIndexingToggle}
-                                    checked={this.state.s.indexing}
-                                    disabled={!this.state.s.enable}/>
-                            Indexing <br/><br/>
-                            <Switch onChange={this.enableQuickIntegrationToggle}
-                                    checked={this.state.s.quick_integration}
-                                    disabled={!this.state.s.enable}/>
-                            Quick MX integration
-                        </Grid>
-                        <Grid item xs={1}/>
-                    </Grid>
-                </Paper>
-    }
+function putValues(x: spot_finding_settings) {
+    putConfigSpotFinding({ body: x, throwOnError: true })
+        .catch(error => console.log(error) );
 }
 
-export default DataProcessingSettings;
\ No newline at end of file
+function DataProcessingSettings({s: serverS, update}: MyProps) {
+    const [s, setS] = useState<spot_finding_settings>(default_spot_finding_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<spot_finding_settings>(default_spot_finding_settings);
+    const [highResGap, setHighResGap] = useState(1.5);
+
+    // Only adopt the server copy when it actually changed, otherwise the
+    // 1 s statistics poll would overwrite edits the user is making.
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setHighResGap(serverS.high_res_gap_Q_recipA ?? highResGap);
+        }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
+
+    const apply = (next: spot_finding_settings) => {
+        setS(next);
+        putValues(next);
+        update();
+    };
+
+    const setPhotonCountThreshold = (event: Event, newValue: number | number[]) =>
+        apply({...s, photon_count_threshold: newValue as number});
+
+    const setSignalToNoiseThreshold = (event: Event, newValue: number | number[]) =>
+        apply({...s, signal_to_noise_threshold: newValue as number});
+
+    const setMinPixPerSpot = (event: Event, newValue: number | number[]) =>
+        apply({...s, min_pix_per_spot: newValue as number});
+
+    const setLowResolutionLimit = (event: Event, newValue: number | number[]) =>
+        apply({...s, low_resolution_limit: newValue as number});
+
+    const setHighResolutionLimit = (event: Event, newValue: number | number[]) =>
+        apply({...s, high_resolution_limit: newValue as number});
+
+    const setHighResolutionLimitForCountingLowResSpots = (event: Event, newValue: number | number[]) =>
+        apply({...s, high_resolution_limit_for_spot_count_low_res: newValue as number});
+
+    const setIceRingWidth = (event: Event, newValue: number | number[]) =>
+        apply({...s, ice_ring_width_q_recipA: newValue as number});
+
+    const enableSpotFindingToggle = (event: ChangeEvent<HTMLInputElement>) =>
+        apply({...s, enable: event.target.checked});
+
+    const enableIndexingToggle = (event: ChangeEvent<HTMLInputElement>) =>
+        apply({...s, indexing: event.target.checked});
+
+    const enableQuickIntegrationToggle = (event: ChangeEvent<HTMLInputElement>) =>
+        apply({...s, quick_integration: event.target.checked});
+
+    const enableHighResGapToggle = (event: ChangeEvent<HTMLInputElement>) =>
+        apply({...s, high_res_gap_Q_recipA: event.target.checked ? highResGap : undefined});
+
+    const handleHighResGap = (event: Event, newValue: number | number[]) => {
+        const v = newValue as number;
+        setHighResGap(v);
+        apply({...s, high_res_gap_Q_recipA: v});
+    };
+
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 800, width: '100%' }}>
+                <Grid container spacing={0}>
+
+                    <Grid item xs={1}/>
+                    <Grid item xs={10}>
+                        <br/><strong>Spot finding parameters</strong><br/><br/>
+                        <Switch onChange={enableSpotFindingToggle} checked={s.enable}/>
+                        Spot finding
+                        <br/><br/>
+
+                        <Typography gutterBottom> Count threshold </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.photon_count_threshold)}
+                                onChange={setPhotonCountThreshold}
+                                min={1} max={50} step={1} valueLabelDisplay="auto"/>
+
+                        <br/><Typography> Signal-to-noise threshold </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.signal_to_noise_threshold)}
+                                onChange={setSignalToNoiseThreshold}
+                                min={2}
+                                max={10}
+                                step={0.5}
+                                valueLabelDisplay="auto"
+                                valueLabelFormat={(value) => value.toFixed(1)}
+                        />
+
+                        <br/><Typography> Minimum pixel / spot </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.min_pix_per_spot)}
+                                onChange={setMinPixPerSpot}
+                                min={1} max={8} step={1} valueLabelDisplay="auto"/>
+                        <Typography> Low resolution limit [&#8491;] </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.low_resolution_limit)}
+                                onChange={setLowResolutionLimit}
+                                min={10} max={100} step={0.1} valueLabelDisplay="auto"
+                                valueLabelFormat={(value) => value.toFixed(1)}
+                        />
+
+                        <Typography> High resolution limit [&#8491;] </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.high_resolution_limit)}
+                                onChange={setHighResolutionLimit}
+                                min={1} max={5} step={0.1} valueLabelDisplay="auto"
+                                valueLabelFormat={(value) => value.toFixed(1)}
+                        />
+                        <Typography> High resolution limit for counting low resolution spots [&#8491;] </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.high_resolution_limit_for_spot_count_low_res)}
+                                onChange={setHighResolutionLimitForCountingLowResSpots}
+                                min={2} max={8} step={0.1} valueLabelDisplay="auto"
+                                valueLabelFormat={(value) => value.toFixed(1)}
+                        />
+                        <Typography> Ice ring width in Q-space [&#8491;<sup>-1</sup>] </Typography>
+                        <Slider disabled={!s.enable}
+                                value={Number(s.ice_ring_width_q_recipA)}
+                                onChange={setIceRingWidth}
+                                min={0.0} max={0.2} step={0.001} valueLabelDisplay="auto"
+                                valueLabelFormat={(value) => value.toFixed(3)}
+                        />
+
+                        <Switch
+                            onChange={enableHighResGapToggle}
+                            checked={s.high_res_gap_Q_recipA !== undefined}
+                            disabled={!s.enable}
+                        />
+                        High‑res gap Q-space filter [&#8491;<sup>-1</sup>]
+                        <Typography/>
+                        <Slider
+                            disabled={!s.enable || s.high_res_gap_Q_recipA === undefined}
+                            value={Number(s.high_res_gap_Q_recipA ?? highResGap)}
+                            onChange={handleHighResGap}
+                            min={0.1}
+                            max={5.0}
+                            step={0.01}
+                            valueLabelDisplay="auto"
+                            valueLabelFormat={(value) => value.toFixed(2)}
+                        />
+
+                        <br/><br/>
+                        <Switch onChange={enableIndexingToggle}
+                                checked={s.indexing}
+                                disabled={!s.enable}/>
+                        Indexing <br/><br/>
+                        <Switch onChange={enableQuickIntegrationToggle}
+                                checked={s.quick_integration}
+                                disabled={!s.enable}/>
+                        Quick MX integration
+                    </Grid>
+                    <Grid item xs={1}/>
+                </Grid>
+            </Paper>
+}
+
+export default memo(DataProcessingSettings);
diff --git a/frontend/src/components/DetectorSelection.tsx b/frontend/src/components/DetectorSelection.tsx
index 67192be0..9d7426fd 100644
--- a/frontend/src/components/DetectorSelection.tsx
+++ b/frontend/src/components/DetectorSelection.tsx
@@ -1,23 +1,18 @@
-import React, {Component} from 'react';
+import {memo, ReactNode, useEffect, useState} from 'react';
 
 import Select, { SelectChangeEvent } from '@mui/material/Select';
-import {Grid,Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
+import {Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
 import Paper from "@mui/material/Paper";
 import InputLabel from '@mui/material/InputLabel';
 import MenuItem from '@mui/material/MenuItem';
 import FormControl from '@mui/material/FormControl';
 import {detector_list, detector_list_element} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
-import { ReactNode } from "react";
 
 type MyProps = {
     s?: detector_list
 }
 
-type MyState = {
-    choice: string
-};
-
 type MapElement = {
     id: number
     name: string
@@ -42,30 +37,29 @@ const default_detector_element: detector_list_element = {
     min_count_time_ns: 0
 }
 
-class DetectorSelection extends Component<MyProps, MyState> {
-    state : MyState = {
-        choice: "0"
-    }
+function DetectorSelection({s}: MyProps) {
+    const [choice, setChoice] = useState("0");
 
-    componentDidMount() {
-        if (this.props.s !== undefined)
-            this.setState({choice: this.props.s.current_id.toString()});
-    }
+    useEffect(() => {
+        if (s !== undefined)
+            setChoice(s.current_id.toString());
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, []);
 
-    handleChange = (event : SelectChangeEvent<String>) => {
-        this.setState({ choice: String(event.target.value).toString() });
+    const handleChange = (event : SelectChangeEvent<String>) => {
+        setChoice(String(event.target.value).toString());
     };
 
-    current_detector_info = () : detector_list_element => {
-        if (this.props.s === undefined)
+    const current_detector_info = () : detector_list_element => {
+        if (s === undefined)
             return default_detector_element;
-        if (this.props.s.detectors.length <= this.props.s.current_id)
+        if (s.detectors.length <= s.current_id)
             return default_detector_element;
-        return this.props.s.detectors[this.props.s.current_id];
-    }
+        return s.detectors[s.current_id];
+    };
 
-    detector_info = () : ReactNode => {
-        let x : detector_list_element = this.current_detector_info();
+    const detector_info = () : ReactNode => {
+        let x : detector_list_element = current_detector_info();
 
         let arr: DetectorTableElement[] = [
             {title: "Current Detector", val: x.description},
@@ -95,58 +89,56 @@ class DetectorSelection extends Component<MyProps, MyState> {
                 </TableBody>
             </Table>
         </TableContainer>
-    }
+    };
 
-    detector_list() : MapElement[] {
+    const detector_options = () : MapElement[] => {
         let v: MapElement[] = [];
 
-        if (this.props.s !== undefined) {
-            let id: number = this.props.s.current_id;
-            v = this.props.s.detectors.map(d => ({
+        if (s !== undefined) {
+            let id: number = s.current_id;
+            v = s.detectors.map(d => ({
                 id: d.id,
                 name:  `${d.description} (${d.width}x${d.height} pxl) ` + ((d.id === id) ? "*** CURRENT ***" : "")
             }));
         }
 
         return v;
-    }
+    };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center"
-            }}>
-                <strong>Detector selection </strong>
+    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center"
+        }}>
+            <strong>Detector selection </strong>
 
-                {this.detector_info()}
+            {detector_info()}
 
-                <FormControl sx={{width: '80%'}}>
-                    <InputLabel id="detector-select-label">Detector</InputLabel>
-                    <Select
-                        labelId="detector-select-label"
-                        id="detector-select"
-                        value={this.state.choice}
-                        label="Detector"
-                        onChange={this.handleChange}
-                        disabled={this.props.s === undefined}
-                    >
-                        {this.detector_list().map(d => (<MenuItem value={d.id}> {d.name} </MenuItem>))}
-                    </Select>
-                </FormControl>
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/select_detector"}
-                    input={JSON.stringify({id: Number(this.state.choice)})}
-                    method={"PUT"}
-                    text={"Select detector"}
-                    disabled={this.props.s === undefined}
-                />
-            </Stack>
-            <br/>
-        </Paper>
-    }
+            <FormControl sx={{width: '80%'}}>
+                <InputLabel id="detector-select-label">Detector</InputLabel>
+                <Select
+                    labelId="detector-select-label"
+                    id="detector-select"
+                    value={choice}
+                    label="Detector"
+                    onChange={handleChange}
+                    disabled={s === undefined}
+                >
+                    {detector_options().map(d => (<MenuItem value={d.id}> {d.name} </MenuItem>))}
+                </Select>
+            </FormControl>
+            <ButtonWithSnackbar
+                color={"primary"}
+                path={"/config/select_detector"}
+                input={JSON.stringify({id: Number(choice)})}
+                method={"PUT"}
+                text={"Select detector"}
+                disabled={s === undefined}
+            />
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default DetectorSelection;
\ No newline at end of file
+export default memo(DetectorSelection);
diff --git a/frontend/src/components/DetectorSettings.tsx b/frontend/src/components/DetectorSettings.tsx
index a12edc84..8685d1b0 100644
--- a/frontend/src/components/DetectorSettings.tsx
+++ b/frontend/src/components/DetectorSettings.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, useEffect, useState} from 'react';
 
 import {Checkbox, FormControlLabel, FormGroup, Grid, List, ListItem, Switch, Tooltip} from "@mui/material";
 import Paper from "@mui/material/Paper";
@@ -6,7 +6,7 @@ import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
-import {detector_settings, detector_timing, postDeactivate} from "../client";
+import {detector_settings, detector_timing} from "../client";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
@@ -15,26 +15,6 @@ type MyProps = {
     s?: detector_settings
 }
 
-type MyState = {
-    s: detector_settings,
-    last_downloaded_s: detector_settings,
-    bit_width_selection: string,
-    storage_cell_list_value: string,
-    timing_mode_list_value: detector_timing,
-    frame_time_err: boolean,
-    count_time_err: boolean,
-    storage_cell_delay_err: boolean,
-    detector_trigger_delay_err: boolean,
-    internal_frame_generator_images_err: boolean,
-    pedestal_g0_frames_err: boolean,
-    pedestal_g1_frames_err: boolean,
-    pedestal_g2_frames_err: boolean,
-    pedestal_min_image_count_err: boolean,
-    eiger_threshold_err: boolean,
-    eiger_threshold_keV_old: number,
-    download_counter: number
-}
-
 function extractDepthForSelection(input: detector_settings) : string {
     if (input.eiger_bit_depth === undefined)
         return 'a';
@@ -48,64 +28,75 @@ function extractDepthForSelection(input: detector_settings) : string {
         return "";
 }
 
-class DetectorSettings extends Component<MyProps, MyState> {
-    state : MyState = {
-        s: {
-            frame_time_us: 1000
-        },
-        last_downloaded_s: {
-            frame_time_us: 1000
-        },
-        bit_width_selection: "a",
-        timing_mode_list_value: detector_timing.TRIGGER,
-        storage_cell_list_value: "1",
-        pedestal_g0_frames_err: false,
-        pedestal_g1_frames_err: false,
-        pedestal_g2_frames_err: false,
-        pedestal_min_image_count_err: false,
-        storage_cell_delay_err: false,
-        detector_trigger_delay_err: false,
-        frame_time_err: false,
-        count_time_err: false,
-        internal_frame_generator_images_err: false,
-        eiger_threshold_err: false,
-        eiger_threshold_keV_old: 6.0,
-        download_counter: 0
-    }
+function DetectorSettings({s: serverS}: MyProps) {
+    const [s, setS] = useState<detector_settings>({ frame_time_us: 1000 });
+    const [lastDownloadedS, setLastDownloadedS] = useState<detector_settings>({ frame_time_us: 1000 });
+    const [bitWidthSelection, setBitWidthSelection] = useState("a");
+    const [storageCellListValue, setStorageCellListValue] = useState("1");
+    const [timingModeListValue, setTimingModeListValue] = useState<detector_timing>(detector_timing.TRIGGER);
+    const [frameTimeErr, setFrameTimeErr] = useState(false);
+    const [countTimeErr, setCountTimeErr] = useState(false);
+    const [storageCellDelayErr, setStorageCellDelayErr] = useState(false);
+    const [detectorTriggerDelayErr, setDetectorTriggerDelayErr] = useState(false);
+    const [internalFrameGeneratorImagesErr, setInternalFrameGeneratorImagesErr] = useState(false);
+    const [pedestalG0FramesErr, setPedestalG0FramesErr] = useState(false);
+    const [pedestalG1FramesErr, setPedestalG1FramesErr] = useState(false);
+    const [pedestalG2FramesErr, setPedestalG2FramesErr] = useState(false);
+    const [pedestalMinImageCountErr, setPedestalMinImageCountErr] = useState(false);
+    const [eigerThresholdErr, setEigerThresholdErr] = useState(false);
+    const [eigerThresholdKeVOld, setEigerThresholdKeVOld] = useState(6.0);
+    const [downloadCounter, setDownloadCounter] = useState(0);
 
-    eigerThresholdToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setDownloadCounter(c => c + 1);
+            setS(serverS);
+            setBitWidthSelection(extractDepthForSelection(serverS));
+            setLastDownloadedS(serverS);
+            setStorageCellListValue(String(serverS.jungfrau_storage_cell_count ?? "1"));
+            setTimingModeListValue(serverS.timing ?? detector_timing.TRIGGER);
+            setPedestalG0FramesErr(false);
+            setPedestalG1FramesErr(false);
+            setPedestalG2FramesErr(false);
+            setPedestalMinImageCountErr(false);
+            setStorageCellDelayErr(false);
+            setDetectorTriggerDelayErr(false);
+            setFrameTimeErr(false);
+            setCountTimeErr(false);
+            setInternalFrameGeneratorImagesErr(false);
+            setEigerThresholdErr(false);
+            setEigerThresholdKeVOld(6.0);
+        }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
+
+    const eigerThresholdToggle = (event: ChangeEvent<HTMLInputElement>) => {
         if (event.target.checked)
-            this.setState(prevState => ({s : {...prevState.s,
-                    eiger_threshold_keV: prevState.eiger_threshold_keV_old}}));
+            setS(prev => ({...prev, eiger_threshold_keV: eigerThresholdKeVOld}));
         else
-            this.setState(prevState => ({s: {...prevState.s, eiger_threshold_keV: undefined}}));
-    }
+            setS(prev => ({...prev, eiger_threshold_keV: undefined}));
+    };
 
-    countTimeToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
+    const countTimeToggle = (event: ChangeEvent<HTMLInputElement>) => {
         if (event.target.checked)
-            this.setState(prevState => ({s : {...prevState.s, count_time_us: prevState.s.frame_time_us - 20}}));
+            setS(prev => ({...prev, count_time_us: prev.frame_time_us - 20}));
         else
-            this.setState(prevState => ({s : {...prevState.s, count_time_us: undefined}}));
-    }
+            setS(prev => ({...prev, count_time_us: undefined}));
+    };
 
-    internalFrameGeneratorToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s : {...prevState.s, internal_frame_generator: event.target.checked}}));
-    }
+    const internalFrameGeneratorToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        setS(prev => ({...prev, internal_frame_generator: event.target.checked}));
+    };
 
-    useGainHG0Toggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s : {...prevState.s, jungfrau_use_gain_hg0: event.target.checked}}));
-    }
+    const useGainHG0Toggle = (event: ChangeEvent<HTMLInputElement>) => {
+        setS(prev => ({...prev, jungfrau_use_gain_hg0: event.target.checked}));
+    };
 
-    fixedGainG1Toggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState(prevState => ({s : {...prevState.s, jungfrau_fixed_gain_g1: event.target.checked}}));
-    }
+    const fixedGainG1Toggle = (event: ChangeEvent<HTMLInputElement>) => {
+        setS(prev => ({...prev, jungfrau_fixed_gain_g1: event.target.checked}));
+    };
 
-    deactivate = () => {
-        postDeactivate({ throwOnError: true })
-            .catch(error => {} );
-    }
-
-    handleBitWidthChange = (event: SelectChangeEvent) => {
+    const handleBitWidthChange = (event: SelectChangeEvent) => {
         let val: detector_settings['eiger_bit_depth'] = undefined;
 
         if (event.target.value === "a")
@@ -117,16 +108,11 @@ class DetectorSettings extends Component<MyProps, MyState> {
         else if (event.target.value === "32")
             val = 32;
 
-        this.setState(prevState => ({
-            bit_width_selection: event.target.value,
-            s: {
-                ...prevState.s,
-                eiger_bit_depth: val
-            }
-        }));
+        setBitWidthSelection(event.target.value);
+        setS(prev => ({...prev, eiger_bit_depth: val}));
     };
 
-    handleTimingChange = (event : SelectChangeEvent<detector_timing>) => {
+    const handleTimingChange = (event : SelectChangeEvent<detector_timing>) => {
         let d : detector_timing = detector_timing.TRIGGER;
 
         switch (event.target.value) {
@@ -144,381 +130,312 @@ class DetectorSettings extends Component<MyProps, MyState> {
                 break;
         }
 
-        this.setState(prevState => ({
-                timing_mode_list_value: d,
-                s : {...prevState.s,
-                    timing: d
-                }
-            })
-        );
+        setTimingModeListValue(d);
+        setS(prev => ({...prev, timing: d}));
     };
 
-    handleChange = (event : SelectChangeEvent<String>) => {
-        this.setState(prevState => ({
-                storage_cell_list_value: String(event.target.value).toString(),
-                s : {...prevState.s,
-                    jungfrau_storage_cell_count: Number(event.target.value)
-                }
-            })
-        );
+    const handleChange = (event : SelectChangeEvent<String>) => {
+        setStorageCellListValue(String(event.target.value).toString());
+        setS(prev => ({...prev, jungfrau_storage_cell_count: Number(event.target.value)}));
     };
 
-    getValues() {
-        if (this.props.s !== undefined) {
-            let det_set: detector_settings = this.props.s;
-            if (!_.isEqual(det_set, this.state.last_downloaded_s)) {
-                this.setState(prevState => ({
-                    download_counter: prevState.download_counter + 1,
-                    s: det_set,
-                    bit_width_selection: extractDepthForSelection(det_set),
-                    last_downloaded_s: det_set,
-                    storage_cell_list_value: String(det_set.jungfrau_storage_cell_count ?? "1"),
-                    timing_mode_list_value: det_set.timing ?? detector_timing.TRIGGER,
-                    pedestal_g0_frames_err: false,
-                    pedestal_g1_frames_err: false,
-                    pedestal_g2_frames_err: false,
-                    pedestal_min_image_count_err: false,
-                    storage_cell_delay_err: false,
-                    detector_trigger_delay_err: false,
-                    frame_time_err: false,
-                    count_time_err: false,
-                    internal_frame_generator_images_err: false,
-                    eiger_threshold_err: false,
-                    eiger_threshold_keV_old: 6.0
-                }));
-            }
-        }
-    }
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 1150, width: '100%' }}>
 
-    componentDidMount() {
-        this.getValues();
-    }
+        <Grid container>
 
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 1150, width: '100%' }}>
-
-            <Grid container>
-
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <br/><strong>Detector settings </strong>
-                    <br/><br/><br/>
-                    <NumberTextField start_val={this.state.s.frame_time_us}
-                                     label={"Internal frame time"}
-                                     units={"us"}
-                                     min={450}
-                                     fullWidth
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             frame_time_err: err,
-                                             s: {...prevState.s, frame_time_us: val}
-                                         }));
-                                     }}/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={2}/>
-                <Grid item xs={8}>
-                    <List>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <br/><strong>Detector settings </strong>
+                <br/><br/><br/>
+                <NumberTextField start_val={s.frame_time_us}
+                                 label={"Internal frame time"}
+                                 units={"us"}
+                                 min={450}
+                                 fullWidth
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setFrameTimeErr(err);
+                                     setS(prev => ({...prev, frame_time_us: val}));
+                                 }}/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={2}/>
+            <Grid item xs={8}>
+                <List>
+                    <ListItem>
+                        <Switch onChange={countTimeToggle}
+                                checked={s.count_time_us !== undefined}/>
+                        <NumberTextField
+                            start_val={s.count_time_us}
+                            disabled={s.count_time_us === undefined}
+                            label={"Count time"}
+                            units={"us"}
+                            min={0}
+                            max={1980}
+                            fullWidth
+                            counter={downloadCounter}
+                            callback={(val: number, err: boolean) => {
+                                setCountTimeErr(err);
+                                setS(prev => ({...prev, count_time_us: val}));
+                            }}/>
+                    </ListItem>
+                </List>
+            </Grid>
+            <Grid item xs={2}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <NumberTextField start_val={s.detector_trigger_delay_ns}
+                                 label={"Detector delay"}
+                                 units={"ns"}
+                                 default={0}
+                                 min={0}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setDetectorTriggerDelayErr(err);
+                                     setS(prev => ({...prev, detector_trigger_delay_ns: val}));
+                                 }}
+                                 sx={{width: 120}}
+                />&nbsp;&nbsp;
+                <FormControl>
+                    <InputLabel id="timing-select-label">Timing mode</InputLabel>
+                    <Select
+                        sx={{width: 120}}
+                        labelId="timing-select-label"
+                        id="timing-select"
+                        value={timingModeListValue}
+                        label="Storage cell count"
+                        onChange={handleTimingChange}
+                    >
+                        <MenuItem value={"trigger"}>Trigger</MenuItem>
+                        <MenuItem value={"auto"}>Auto</MenuItem>
+                        <MenuItem value={"burst"}>Burst (EIGER)</MenuItem>
+                        <MenuItem value={"gated"}>Gated (EIGER)</MenuItem>
+                    </Select>
+                </FormControl>
+                <br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <b>Internal image generator (FPGA) </b><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={3}/>
+            <Grid item xs={6}>
+                <br/>
+                <List>
+                    <Tooltip title="Internal generator allows to test Jungfraujoch without having detector connected.">
                         <ListItem>
-                            <Switch onChange={this.countTimeToggle}
-                                    checked={this.state.s.count_time_us !== undefined}/>
-                            <NumberTextField
-                                start_val={this.state.s.count_time_us}
-                                disabled={this.state.s.count_time_us === undefined}
-                                label={"Count time"}
-                                units={"us"}
-                                min={0}
-                                max={1980}
-                                fullWidth
-                                counter={this.state.download_counter}
-                                callback={(val: number, err: boolean) => {
-                                    this.setState(prevState => ({
-                                        count_time_err: err,
-                                        s: {...prevState.s, count_time_us: val}
-                                    }));
-                                }}/>
+                            <Checkbox onChange={internalFrameGeneratorToggle}
+                                      checked={s.internal_frame_generator === true}/>
+                            <FormControl fullWidth>
+                                <NumberTextField start_val={s.internal_frame_generator_images}
+                                                 label={"Images"}
+                                                 min={1}
+                                                 default={1}
+                                                 max={128}
+                                                 counter={downloadCounter}
+                                                 callback={(val: number, err: boolean) => {
+                                                     setInternalFrameGeneratorImagesErr(err);
+                                                     setS(prev => ({...prev, internal_frame_generator_images: val}));
+                                                 }}
+                                                 disabled={!s.internal_frame_generator}
+                                                 fullWidth/>
+                            </FormControl>
                         </ListItem>
-                    </List>
-                </Grid>
-                <Grid item xs={2}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <NumberTextField start_val={this.state.s.detector_trigger_delay_ns}
-                                     label={"Detector delay"}
-                                     units={"ns"}
-                                     default={0}
-                                     min={0}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             detector_trigger_delay_err: err,
-                                             s: {...prevState.s, detector_trigger_delay_ns: val}
-                                         }));
-                                     }}
-                                     sx={{width: 120}}
-                    />&nbsp;&nbsp;
+                    </Tooltip>
+                </List>
+            </Grid>
+            <Grid item xs={3}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <b>JUNGFRAU settings </b><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={3}/>
+            <Grid item xs={6}>
+                <FormGroup>
+                    <FormControlLabel control={
+                        <Checkbox onChange={useGainHG0Toggle} checked={s.jungfrau_use_gain_hg0 === true}/>
+                    } label="HG0"/>
+                    <FormControlLabel control={
+                        <Checkbox onChange={fixedGainG1Toggle} checked={s.jungfrau_fixed_gain_g1 === true}/>
+                    } label="Fixed G1"/>
+                </FormGroup><br/>
+            </Grid>
+            <Grid item xs={3}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <b>JUNGFRAU storage cells </b><br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <FormControl>
+                    <InputLabel id="demo-simple-select-label">Count</InputLabel>
+                    <Select
+                        sx={{width: 120}}
+                        labelId="demo-simple-select-label"
+                        id="demo-simple-select"
+                        value={storageCellListValue}
+                        label="Storage cell count"
+                        onChange={handleChange}
+                    >
+                        <MenuItem value={"1"}>1</MenuItem>
+                        <MenuItem value={"2"}>2</MenuItem>
+                        <MenuItem value={"4"}>4</MenuItem>
+                        <MenuItem value={"8"}>8</MenuItem>
+                        <MenuItem value={"15"}>15</MenuItem>
+                        <MenuItem value={"16"}>16</MenuItem>
+                    </Select>
+                </FormControl>&nbsp;&nbsp;
+                <NumberTextField start_val={s.jungfrau_storage_cell_delay_ns}
+                                 label={"Delay"}
+                                 units={"ns"}
+                                 min={2100}
+                                 default={2100}
+                                 counter={downloadCounter}
+                                 sx={{ width: "140px" }}
+                                 callback={(val: number, err: boolean) => {
+                                     setStorageCellDelayErr(err);
+                                     setS(prev => ({...prev, jungfrau_storage_cell_delay_ns: val}));
+                                 }}
+                                 disabled={storageCellListValue === "1"}
+                                 fullWidth/>
+                <br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <b>JUNGFRAU Pedestal</b><br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <NumberTextField start_val={s.jungfrau_pedestal_g0_frames}
+                                 label={"G0"}
+                                 min={0}
+                                 default={2000}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setPedestalG0FramesErr(err);
+                                     setS(prev => ({...prev, jungfrau_pedestal_g0_frames: val}));
+                                 }}
+                                 sx={{width: "80px"}}/>&nbsp;
+                <NumberTextField start_val={s.jungfrau_pedestal_g1_frames}
+                                 label={"G1"}
+                                 min={0}
+                                 default={300}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setPedestalG1FramesErr(err);
+                                     setS(prev => ({...prev, jungfrau_pedestal_g1_frames: val}));
+                                 }}
+                                 sx={{width: "80px"}}/>&nbsp;
+                <NumberTextField start_val={s.jungfrau_pedestal_g2_frames}
+                                 label={"G2"}
+                                 min={0}
+                                 default={300}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setPedestalG2FramesErr(err);
+                                     setS(prev => ({...prev, jungfrau_pedestal_g2_frames: val}));
+                                 }}
+                                 sx={{width: "80px"}}/>
+                &nbsp;<br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+
+            <Grid item xs={10}>
+                <NumberTextField start_val={s.jungfrau_pedestal_min_image_count}
+                                 label={"Min. image count"}
+                                 min={0}
+                                 default={128}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setPedestalMinImageCountErr(err);
+                                     setS(prev => ({...prev, jungfrau_pedestal_min_image_count: val}));
+                                 }}
+                                 sx={{width: "120px"}}/><br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <b>EIGER settings </b><br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <ListItem>
+                    <Checkbox onChange={eigerThresholdToggle}
+                              checked={s.eiger_threshold_keV !== undefined}/>
+                    <FormControl fullWidth>
+                        <NumberTextField
+                            default={eigerThresholdKeVOld}
+                            start_val={s.eiger_threshold_keV}
+                            label={"Energy threshold"}
+                            min={1.0}
+                            max={100.0}
+                            units={"keV"}
+                            float={true}
+                            counter={downloadCounter}
+                            callback={(val: number, err: boolean) => {
+                                if (!err)
+                                    setEigerThresholdKeVOld(val);
+                                setEigerThresholdErr(err);
+                                setS(prev => ({...prev, eiger_threshold_keV: val}));
+                            }}
+                            disabled={s.eiger_threshold_keV === undefined}
+                            />
+                    </FormControl>&nbsp;
                     <FormControl>
-                        <InputLabel id="timing-select-label">Timing mode</InputLabel>
+                        <InputLabel id="demo-simple-select-label">Read-out</InputLabel>
                         <Select
-                            sx={{width: 120}}
-                            labelId="timing-select-label"
-                            id="timing-select"
-                            value={this.state.timing_mode_list_value}
-                            label="Storage cell count"
-                            onChange={this.handleTimingChange}
-                        >
-                            <MenuItem value={"trigger"}>Trigger</MenuItem>
-                            <MenuItem value={"auto"}>Auto</MenuItem>
-                            <MenuItem value={"burst"}>Burst (EIGER)</MenuItem>
-                            <MenuItem value={"gated"}>Gated (EIGER)</MenuItem>
-                        </Select>
-                    </FormControl>
-                    <br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <b>Internal image generator (FPGA) </b><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={3}/>
-                <Grid item xs={6}>
-                    <br/>
-                    <List>
-                        <Tooltip title="Internal generator allows to test Jungfraujoch without having detector connected.">
-                            <ListItem>
-                                <Checkbox onChange={this.internalFrameGeneratorToggle}
-                                          checked={this.state.s.internal_frame_generator === true}/>
-                                <FormControl fullWidth>
-                                    <NumberTextField start_val={this.state.s.internal_frame_generator_images}
-                                                     label={"Images"}
-                                                     min={1}
-                                                     default={1}
-                                                     max={128}
-                                                     counter={this.state.download_counter}
-                                                     callback={(val: number, err: boolean) => {
-                                                         this.setState(prevState => ({
-                                                             internal_frame_generator_images_err: err,
-                                                             s: {...prevState.s, internal_frame_generator_images: val}
-                                                         }));
-                                                     }}
-                                                     disabled={!this.state.s.internal_frame_generator}
-                                                     fullWidth/>
-                                </FormControl>
-                            </ListItem>
-                        </Tooltip>
-                    </List>
-                </Grid>
-                <Grid item xs={3}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <b>JUNGFRAU settings </b><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={3}/>
-                <Grid item xs={6}>
-                    <FormGroup>
-                        <FormControlLabel control={
-                            <Checkbox onChange={this.useGainHG0Toggle} checked={this.state.s.jungfrau_use_gain_hg0 === true}/>
-                        } label="HG0"/>
-                        <FormControlLabel control={
-                            <Checkbox onChange={this.fixedGainG1Toggle} checked={this.state.s.jungfrau_fixed_gain_g1 === true}/>
-                        } label="Fixed G1"/>
-                    </FormGroup><br/>
-                </Grid>
-                <Grid item xs={3}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <b>JUNGFRAU storage cells </b><br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <FormControl>
-                        <InputLabel id="demo-simple-select-label">Count</InputLabel>
-                        <Select
-                            sx={{width: 120}}
                             labelId="demo-simple-select-label"
                             id="demo-simple-select"
-                            value={this.state.storage_cell_list_value}
-                            label="Storage cell count"
-                            onChange={this.handleChange}
+                            label="Detector"
+                            value={bitWidthSelection}
+                            onChange={handleBitWidthChange}
+                            sx={{minWidth:106}}
                         >
-                            <MenuItem value={"1"}>1</MenuItem>
-                            <MenuItem value={"2"}>2</MenuItem>
-                            <MenuItem value={"4"}>4</MenuItem>
-                            <MenuItem value={"8"}>8</MenuItem>
-                            <MenuItem value={"15"}>15</MenuItem>
-                            <MenuItem value={"16"}>16</MenuItem>
+                            <MenuItem value={"a"}>Auto</MenuItem>
+                            <MenuItem value={"8"}>8-bit</MenuItem>
+                            <MenuItem value={"16"}>16-bit</MenuItem>
+                            <MenuItem value={"32"}>32-bit</MenuItem>
                         </Select>
-                    </FormControl>&nbsp;&nbsp;
-                    <NumberTextField start_val={this.state.s.jungfrau_storage_cell_delay_ns}
-                                     label={"Delay"}
-                                     units={"ns"}
-                                     min={2100}
-                                     default={2100}
-                                     counter={this.state.download_counter}
-                                     sx={{ width: "140px" }}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             storage_cell_delay_err: err,
-                                             s: {...prevState.s, jungfrau_storage_cell_delay_ns: val}
-                                         }));
-                                     }}
-                                     disabled={this.state.storage_cell_list_value === "1"}
-                                     fullWidth/>
-                    <br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <b>JUNGFRAU Pedestal</b><br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <NumberTextField start_val={this.state.s.jungfrau_pedestal_g0_frames}
-                                     label={"G0"}
-                                     min={0}
-                                     default={2000}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             pedestal_g0_frames_err: err,
-                                             s: {...prevState.s, jungfrau_pedestal_g0_frames: val}
-                                         }));
-                                     }}
-                                     sx={{width: "80px"}}/>&nbsp;
-                    <NumberTextField start_val={this.state.s.jungfrau_pedestal_g1_frames}
-                                     label={"G1"}
-                                     min={0}
-                                     default={300}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             pedestal_g1_frames_err: err,
-                                             s: {...prevState.s, jungfrau_pedestal_g1_frames: val}
-                                         }));
-                                     }}
-                                     sx={{width: "80px"}}/>&nbsp;
-                    <NumberTextField start_val={this.state.s.jungfrau_pedestal_g2_frames}
-                                     label={"G2"}
-                                     min={0}
-                                     default={300}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             pedestal_g2_frames_err: err,
-                                             s: {...prevState.s, jungfrau_pedestal_g2_frames: val}
-                                         }));
-                                     }}
-                                     sx={{width: "80px"}}/>
-                    &nbsp;<br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-
-                <Grid item xs={10}>
-                    <NumberTextField start_val={this.state.s.jungfrau_pedestal_min_image_count}
-                                     label={"Min. image count"}
-                                     min={0}
-                                     default={128}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             pedestal_min_image_count_err: err,
-                                             s: {...prevState.s, jungfrau_pedestal_min_image_count: val}
-                                         }));
-                                     }}
-                                     sx={{width: "120px"}}/><br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <b>EIGER settings </b><br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <ListItem>
-                        <Checkbox onChange={this.eigerThresholdToggle}
-                                  checked={this.state.s.eiger_threshold_keV !== undefined}/>
-                        <FormControl fullWidth>
-                            <NumberTextField
-                                default={this.state.eiger_threshold_keV_old}
-                                start_val={this.state.s.eiger_threshold_keV}
-                                label={"Energy threshold"}
-                                min={1.0}
-                                max={100.0}
-                                units={"keV"}
-                                float={true}
-                                counter={this.state.download_counter}
-                                callback={(val: number, err: boolean) => {
-                                    let old: number = this.state.eiger_threshold_keV_old;
-                                    if (!err)
-                                        old = val;
-                                    this.setState(prevState => ({
-                                        eiger_threshold_err: err,
-                                        eiger_threshold_keV_old: old,
-                                        s: {...prevState.s, eiger_threshold_keV: val}
-                                    }));
-                                }}
-                                disabled={this.state.s.eiger_threshold_keV === undefined}
-                                />
-                        </FormControl>&nbsp;
-                        <FormControl>
-                            <InputLabel id="demo-simple-select-label">Read-out</InputLabel>
-                            <Select
-                                labelId="demo-simple-select-label"
-                                id="demo-simple-select"
-                                label="Detector"
-                                value={this.state.bit_width_selection}
-                                onChange={this.handleBitWidthChange}
-                                sx={{minWidth:106}}
-                            >
-                                <MenuItem value={"a"}>Auto</MenuItem>
-                                <MenuItem value={"8"}>8-bit</MenuItem>
-                                <MenuItem value={"16"}>16-bit</MenuItem>
-                                <MenuItem value={"32"}>32-bit</MenuItem>
-                            </Select>
-                        </FormControl><br/><br/>
-                    </ListItem><br/>
-                </Grid>
-                <Grid item xs={1}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <ButtonWithSnackbar
-                        color={"primary"}
-                        path={"/config/detector"}
-                        disabled={this.state.count_time_err
-                            || this.state.frame_time_err
-                            || this.state.internal_frame_generator_images_err
-                            || this.state.detector_trigger_delay_err
-                            || this.state.storage_cell_delay_err
-                            || this.state.pedestal_g0_frames_err
-                            || this.state.pedestal_g1_frames_err
-                            || this.state.pedestal_g2_frames_err
-                            || this.state.pedestal_min_image_count_err}
-                        text={"Upload"}
-                        input={JSON.stringify(this.state.s)}
-                        method={"PUT"}
-                    />&nbsp;&nbsp;
-                    <ButtonWithSnackbar
-                        color={"primary"}
-                        path={"/deactivate"}
-                        text={"Deactivate"}
-                    />
-                    <br/><br/>
-                </Grid>
-                <Grid item xs={1}/>
+                    </FormControl><br/><br/>
+                </ListItem><br/>
             </Grid>
-        </Paper>
-    }
+            <Grid item xs={1}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <ButtonWithSnackbar
+                    color={"primary"}
+                    path={"/config/detector"}
+                    disabled={countTimeErr
+                        || frameTimeErr
+                        || internalFrameGeneratorImagesErr
+                        || detectorTriggerDelayErr
+                        || storageCellDelayErr
+                        || pedestalG0FramesErr
+                        || pedestalG1FramesErr
+                        || pedestalG2FramesErr
+                        || pedestalMinImageCountErr}
+                    text={"Upload"}
+                    input={JSON.stringify(s)}
+                    method={"PUT"}
+                />&nbsp;&nbsp;
+                <ButtonWithSnackbar
+                    color={"primary"}
+                    path={"/deactivate"}
+                    text={"Deactivate"}
+                />
+                <br/><br/>
+            </Grid>
+            <Grid item xs={1}/>
+        </Grid>
+    </Paper>
 }
 
-export default DetectorSettings;
\ No newline at end of file
+export default memo(DetectorSettings);
diff --git a/frontend/src/components/DetectorStatus.tsx b/frontend/src/components/DetectorStatus.tsx
index e6dc0055..1c4e84e7 100644
--- a/frontend/src/components/DetectorStatus.tsx
+++ b/frontend/src/components/DetectorStatus.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {memo} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Stack, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
@@ -8,8 +8,6 @@ type MyProps = {
     s?: detector_status
 }
 
-type MyState = {}
-
 function powerchipToString(s : detector_status) : string {
     switch (s.powerchip) {
         case detector_power_state.POWER_ON:
@@ -24,7 +22,7 @@ function powerchipToString(s : detector_status) : string {
 function reduce_array(arr: number[], unit: string) : string {
     if (arr.length == 0)
         return "N/A";
-    
+
     if (arr.every(val => val === arr[0]))
         return arr[0].toString() + " " + unit;
     else {
@@ -34,69 +32,62 @@ function reduce_array(arr: number[], unit: string) : string {
     }
 }
 
-class DetectorStatus extends Component<MyProps, MyState> {
-    det() : detector_status {
-        if (this.props.s === undefined)
-            return {
-                state: detector_state.NOT_CONNECTED,
-                powerchip: detector_power_state.POWER_OFF,
-                server_version: "N/A",
-                number_of_triggers_left: 0,
-                fpga_temp_degC: [],
-                high_voltage_V: []
-            }
-        else
-            return this.props.s;
-    }
+function DetectorStatus({s}: MyProps) {
+    const det : detector_status = s ?? {
+        state: detector_state.NOT_CONNECTED,
+        powerchip: detector_power_state.POWER_OFF,
+        server_version: "N/A",
+        number_of_triggers_left: 0,
+        fpga_temp_degC: [],
+        high_voltage_V: []
+    };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center"
-            }}>
+    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center"
+        }}>
 
-                <strong>Detector status</strong>
+            <strong>Detector status</strong>
 
-                <TableContainer component={Paper}
-                                style={{marginLeft: "auto", marginRight: "auto"}}
-                                sx={{width: '80%'}}
-                >
-                    <Table size="small" aria-label="simple table">
-                        <TableBody>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Detector state: </TableCell>
-                                <TableCell align="right">{(this.det().state.toString())}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Detector ASIC power: </TableCell>
-                                <TableCell align="right">{powerchipToString(this.det())}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Triggers remaining: </TableCell>
-                                <TableCell align="right">{this.det().number_of_triggers_left}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> FPGA temperature: </TableCell>
-                                <TableCell align="right">{reduce_array(this.det().fpga_temp_degC, "degC")}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> High voltage: </TableCell>
-                                <TableCell align="right">{reduce_array(this.det().high_voltage_V, "V")}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Detector server version: </TableCell>
-                                <TableCell align="right">{this.det().server_version} </TableCell>
-                            </TableRow>
-                        </TableBody>
-                    </Table>
-                </TableContainer>
+            <TableContainer component={Paper}
+                            style={{marginLeft: "auto", marginRight: "auto"}}
+                            sx={{width: '80%'}}
+            >
+                <Table size="small" aria-label="simple table">
+                    <TableBody>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> Detector state: </TableCell>
+                            <TableCell align="right">{(det.state.toString())}</TableCell>
+                        </TableRow>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> Detector ASIC power: </TableCell>
+                            <TableCell align="right">{powerchipToString(det)}</TableCell>
+                        </TableRow>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> Triggers remaining: </TableCell>
+                            <TableCell align="right">{det.number_of_triggers_left}</TableCell>
+                        </TableRow>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> FPGA temperature: </TableCell>
+                            <TableCell align="right">{reduce_array(det.fpga_temp_degC, "degC")}</TableCell>
+                        </TableRow>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> High voltage: </TableCell>
+                            <TableCell align="right">{reduce_array(det.high_voltage_V, "V")}</TableCell>
+                        </TableRow>
+                        <TableRow>
+                            <TableCell component="th" scope="row"> Detector server version: </TableCell>
+                            <TableCell align="right">{det.server_version} </TableCell>
+                        </TableRow>
+                    </TableBody>
+                </Table>
+            </TableContainer>
 
-            </Stack>
-            <br/>
-        </Paper>
-    }
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default DetectorStatus;
\ No newline at end of file
+export default memo(DetectorStatus);
diff --git a/frontend/src/components/ErrorMessage.tsx b/frontend/src/components/ErrorMessage.tsx
index 0eef8ad5..64fb2d92 100644
--- a/frontend/src/components/ErrorMessage.tsx
+++ b/frontend/src/components/ErrorMessage.tsx
@@ -1,45 +1,40 @@
-import React, {Component} from 'react';
+import {memo, ReactNode} from 'react';
 
 import {broker_status} from "../client";
 import {Alert, AlertColor} from "@mui/material";
-import { ReactNode } from "react";
 
 type MyProps = {
     s?: broker_status
 }
 
-type MyState = {}
+function severity(input?: broker_status['message_severity']) : AlertColor {
+    if (input === undefined)
+        return "error";
 
-class ErrorMessage extends Component<MyProps, MyState> {
-    severity(input?: broker_status['message_severity']) : AlertColor {
-        if (input === undefined)
+    switch (input) {
+        case 'info':
+            return "info";
+        case 'warning':
+            return "warning";
+        case 'error':
             return "error";
-
-        switch (input) {
-            case 'info':
-                return "info";
-            case 'warning':
-                return "warning";
-            case 'error':
-                return "error";
-            case 'success':
-                return "success";
-        }
-    }
-
-    alert(input: AlertColor, message: string) : ReactNode {
-        return <Alert severity={input}>{message}</Alert>
-    }
-
-    render() {
-        if (this.props.s === undefined)
-            return this.alert("error", "Not connected to Jungfraujoch instance; check if jfjoch_broker is running");
-
-        if (this.props.s.message === undefined)
-            return this.alert("info", "");
-
-        return this.alert(this.severity(this.props.s.message_severity),this.props.s.message);
+        case 'success':
+            return "success";
     }
 }
 
-export default ErrorMessage;
+function alert(input: AlertColor, message: string) : ReactNode {
+    return <Alert severity={input}>{message}</Alert>
+}
+
+function ErrorMessage({s}: MyProps) {
+    if (s === undefined)
+        return alert("error", "Not connected to Jungfraujoch instance; check if jfjoch_broker is running");
+
+    if (s.message === undefined)
+        return alert("info", "");
+
+    return alert(severity(s.message_severity), s.message);
+}
+
+export default memo(ErrorMessage);
diff --git a/frontend/src/components/FileWriterSettings.tsx b/frontend/src/components/FileWriterSettings.tsx
index 90e0601b..de07c66a 100644
--- a/frontend/src/components/FileWriterSettings.tsx
+++ b/frontend/src/components/FileWriterSettings.tsx
@@ -1,4 +1,4 @@
-import React from 'react';
+import {memo, useEffect, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Checkbox, FormControlLabel, FormGroup, Select, Stack} from "@mui/material";
@@ -13,12 +13,6 @@ type MyProps = {
     s?: file_writer_settings
 };
 
-type MyState = {
-    s: file_writer_settings,
-    last_downloaded_s: file_writer_settings,
-    download_counter: number
-};
-
 const default_file_writer_settings : file_writer_settings = {
     overwrite: false,
     format: file_writer_format.N_XMX_LEGACY
@@ -34,99 +28,68 @@ function stringToEnum(value: string): file_writer_format {
     return enumValue || file_writer_format.N_XMX_ONLY_DATA;
 }
 
+function FileWriterSettings({s: serverS}: MyProps) {
+    const [s, setS] = useState<file_writer_settings>(default_file_writer_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<file_writer_settings>(default_file_writer_settings);
 
-
-class FileWriterSettings extends React.Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_file_writer_settings,
-        last_downloaded_s: default_file_writer_settings,
-        download_counter: 0
-    }
-
-
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let format_set : file_writer_settings = this.props.s;
-            if (!_.isEqual(format_set, this.state.last_downloaded_s)) {
-                this.setState(prevState => ({
-                    s: format_set,
-                    last_downloaded_s: format_set,
-                    download_counter: prevState.download_counter + 1,
-                }));
-            }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-            }}>
-                <div><strong>File Writer settings </strong></div>
-                <FormGroup>
-                    <FormControlLabel
-                        control={
-                            <Checkbox
-                                checked={this.state.s.overwrite}
-                                onChange={(event) => {
-                                    this.setState(prevState => ({
-                                        s: {
-                                            ...prevState.s,
-                                            overwrite: event.target.checked
-                                        }
-                                    }));
-                                }}
-                            />
-                        }
-                        label="Overwrite existing files"
-                    />
-                </FormGroup>
-                <FormControl sx = {{width: "80%"}}>
-                    <InputLabel id="file-format-label">File format</InputLabel>
-                    <Select
-                        labelId="file-format-label"
-                        label="File format"
-                        value={this.state.s.format}
-                        variant="outlined"
-                        onChange={(event) => {
-                            this.setState(prevState => ({
-                                s: {
-                                    ...prevState.s,
-                                    format: stringToEnum(event.target.value)
-                                }
-                            }));
-                        }}
-                    >
-                        <MenuItem value={file_writer_format.N_XMX_LEGACY}>NXmx HDF5 master file with soft links (DECTRIS file writer compatibility)</MenuItem>
-                        <MenuItem value={file_writer_format.N_XMX_VDS}>NXmx HDF5 master file with virtual datasets</MenuItem>
-                        <MenuItem value={file_writer_format.N_XMX_INTEGRATED}>Single HDF5 file with data and metadata</MenuItem>
-                        <MenuItem value={file_writer_format.N_XMX_ONLY_DATA}>No NXmx HDF5 master file (only data files)</MenuItem>
-                        <MenuItem value={file_writer_format.CBF}>miniCBF (only data files; limited metadata)</MenuItem>
-                        <MenuItem value={file_writer_format.TIFF}>TIFF (only data files; no metadata)</MenuItem>
-                        <MenuItem value={file_writer_format.NO_FILE_WRITTEN}>No files saved</MenuItem>
-                    </Select>
-                </FormControl>
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/file_writer"}
-                    input={JSON.stringify(this.state.s)}
-                    method={"PUT"}
-                    text={"Upload"}
+    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+        }}>
+            <div><strong>File Writer settings </strong></div>
+            <FormGroup>
+                <FormControlLabel
+                    control={
+                        <Checkbox
+                            checked={s.overwrite}
+                            onChange={(event) => {
+                                setS(prev => ({...prev, overwrite: event.target.checked}));
+                            }}
+                        />
+                    }
+                    label="Overwrite existing files"
                 />
-            </Stack>
-            <br/>
-        </Paper>
-    }
+            </FormGroup>
+            <FormControl sx = {{width: "80%"}}>
+                <InputLabel id="file-format-label">File format</InputLabel>
+                <Select
+                    labelId="file-format-label"
+                    label="File format"
+                    value={s.format}
+                    variant="outlined"
+                    onChange={(event) => {
+                        setS(prev => ({...prev, format: stringToEnum(event.target.value)}));
+                    }}
+                >
+                    <MenuItem value={file_writer_format.N_XMX_LEGACY}>NXmx HDF5 master file with soft links (DECTRIS file writer compatibility)</MenuItem>
+                    <MenuItem value={file_writer_format.N_XMX_VDS}>NXmx HDF5 master file with virtual datasets</MenuItem>
+                    <MenuItem value={file_writer_format.N_XMX_INTEGRATED}>Single HDF5 file with data and metadata</MenuItem>
+                    <MenuItem value={file_writer_format.N_XMX_ONLY_DATA}>No NXmx HDF5 master file (only data files)</MenuItem>
+                    <MenuItem value={file_writer_format.CBF}>miniCBF (only data files; limited metadata)</MenuItem>
+                    <MenuItem value={file_writer_format.TIFF}>TIFF (only data files; no metadata)</MenuItem>
+                    <MenuItem value={file_writer_format.NO_FILE_WRITTEN}>No files saved</MenuItem>
+                </Select>
+            </FormControl>
+            <ButtonWithSnackbar
+                color={"primary"}
+                path={"/config/file_writer"}
+                input={JSON.stringify(s)}
+                method={"PUT"}
+                text={"Upload"}
+            />
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default FileWriterSettings;
+export default memo(FileWriterSettings);
diff --git a/frontend/src/components/FpgaStatus.tsx b/frontend/src/components/FpgaStatus.tsx
index e96b02be..c61b63d8 100644
--- a/frontend/src/components/FpgaStatus.tsx
+++ b/frontend/src/components/FpgaStatus.tsx
@@ -1,10 +1,8 @@
-
-import React from 'react';
+import {memo, ReactNode} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {DataGrid, GridCellParams, GridColDef} from "@mui/x-data-grid";
 import { fpga_status} from "../client";
-import { ReactNode } from "react";
 
 function Circles(val: boolean) : ReactNode {
     if (val)
@@ -63,46 +61,40 @@ type MyProps = {
     s?: fpga_status;
 };
 
-type MyState = {};
+const columns : GridColDef[] = [
+    { field: 'pci_dev_id', type: 'string', headerName: 'PCIe ID' },
+    { field: 'base_mac_addr', type: 'string', headerName: 'MAC address', width: 200 },
+    { field: 'eth_link_status', type: 'string', headerName: 'Link status', align: `center`,
+        renderCell: (params : GridCellParams) => EthLinkStatus(params.row.eth_link_count,
+            params.row.eth_link_status)
+    },
+    { field: 'idle', type: 'string', headerName: 'Idle', align: `center`,
+        renderCell: (params : GridCellParams) => CardIdle(params.row.idle)
+    },
+    { field: 'power_usage_W', type: 'number', headerName: 'Power usage [W]', width: 150},
+    { field: 'fpga_temp_C', type: 'number', headerName: 'FPGA temperature [C]', width: 200 },
+    { field: 'hbm_temp_C', type: 'number', headerName: 'HBM temperature [C]', width: 200 },
+    { field: 'packets_sls', type: 'number', headerName: 'Data (current data collection)', width: 150,
+    valueGetter: (params, row) => DataVolume(row.packets_sls)},
+    { field: "fw_version", type: 'string', headerName: 'Firmware version', width: 150 },
+    { field: "pcie_link", type: 'string', headerName: 'PCIe link', width: 100,  align: `center`,
+    renderCell: (params : GridCellParams) => LinkSpeed(params.row.pcie_link_speed, params.row.pcie_link_width)}
+];
 
-class FpgaStatus extends React.Component<MyProps, MyState> {
-
-    columns : GridColDef[] = [
-        { field: 'pci_dev_id', type: 'string', headerName: 'PCIe ID' },
-        { field: 'base_mac_addr', type: 'string', headerName: 'MAC address', width: 200 },
-        { field: 'eth_link_status', type: 'string', headerName: 'Link status', align: `center`,
-            renderCell: (params : GridCellParams) => EthLinkStatus(params.row.eth_link_count,
-                params.row.eth_link_status)
-        },
-        { field: 'idle', type: 'string', headerName: 'Idle', align: `center`,
-            renderCell: (params : GridCellParams) => CardIdle(params.row.idle)
-        },
-        { field: 'power_usage_W', type: 'number', headerName: 'Power usage [W]', width: 150},
-        { field: 'fpga_temp_C', type: 'number', headerName: 'FPGA temperature [C]', width: 200 },
-        { field: 'hbm_temp_C', type: 'number', headerName: 'HBM temperature [C]', width: 200 },
-        { field: 'packets_sls', type: 'number', headerName: 'Data (current data collection)', width: 150,
-        valueGetter: (params, row) => DataVolume(row.packets_sls)},
-        { field: "fw_version", type: 'string', headerName: 'Firmware version', width: 150 },
-        { field: "pcie_link", type: 'string', headerName: 'PCIe link', width: 100,  align: `center`,
-        renderCell: (params : GridCellParams) => LinkSpeed(params.row.pcie_link_speed, params.row.pcie_link_width)}
-    ];
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 500, width: '100%' }}>
-            {((this.props.s !== undefined) && (this.props.s.length > 0)) ?
-                <DataGrid
-                    rows={this.props.s}
-                    columns={this.columns}
-                    getRowId={(row) => row.pci_dev_id}
-                    autosizeOnMount={true}
-                    initialState={{
-                        pagination: { paginationModel: { pageSize: 8 } },
-                    }}
-                /> : <div> No FPGA available</div>
-            }
-        </Paper>
-
-    }
+function FpgaStatus({s}: MyProps) {
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 500, width: '100%' }}>
+        {((s !== undefined) && (s.length > 0)) ?
+            <DataGrid
+                rows={s}
+                columns={columns}
+                getRowId={(row) => row.pci_dev_id}
+                autosizeOnMount={true}
+                initialState={{
+                    pagination: { paginationModel: { pageSize: 8 } },
+                }}
+            /> : <div> No FPGA available</div>
+        }
+    </Paper>
 }
 
-export default FpgaStatus;
+export default memo(FpgaStatus);
diff --git a/frontend/src/components/ImageFormatSettings.tsx b/frontend/src/components/ImageFormatSettings.tsx
index 6cc41002..1c4eebef 100644
--- a/frontend/src/components/ImageFormatSettings.tsx
+++ b/frontend/src/components/ImageFormatSettings.tsx
@@ -1,13 +1,12 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, useEffect, useState} from 'react';
 
-import {Checkbox, FormControlLabel, FormGroup, Grid, List, ListItem, Stack, Switch, Tooltip} from "@mui/material";
-import Button from "@mui/material/Button";
+import {Checkbox, FormControlLabel, FormGroup, List, ListItem, Stack, Tooltip} from "@mui/material";
 import Paper from "@mui/material/Paper";
 import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
-import {image_format_settings, postConfigImageFormatConversion, postConfigImageFormatRaw, putConfigImageFormat} from "../client";
+import {image_format_settings} from "../client";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
@@ -16,17 +15,6 @@ type MyProps = {
     s?: image_format_settings
 }
 
-type MyState = {
-    s: image_format_settings,
-    last_downloaded_s: image_format_settings,
-    bit_width_selection: string,
-    sign_selection: string,
-    jungfrau_conversion_factor_err: boolean,
-    jungfrau_conversion_factor_old: number,
-    download_counter: number,
-    pedestal_g0_rms_limit_err: boolean
-}
-
 const default_image_format_settings: image_format_settings = {
     summation: true,
     geometry_transform: true,
@@ -63,65 +51,29 @@ function extractDepthForSelection(input: image_format_settings) : string {
         return "";
 }
 
-class ImageFormatSettings extends Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_image_format_settings,
-        last_downloaded_s: default_image_format_settings,
-        jungfrau_conversion_factor_err: false,
-        jungfrau_conversion_factor_old: 12.4,
-        bit_width_selection: "a",
-        sign_selection: "a",
-        download_counter: 0,
-        pedestal_g0_rms_limit_err: false
-    }
+function ImageFormatSettings({s: serverS}: MyProps) {
+    const [s, setS] = useState<image_format_settings>(default_image_format_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<image_format_settings>(default_image_format_settings);
+    const [bitWidthSelection, setBitWidthSelection] = useState("a");
+    const [signSelection, setSignSelection] = useState("a");
+    const [jungfrauConversionFactorErr, setJungfrauConversionFactorErr] = useState(false);
+    const [jungfrauConversionFactorOld, setJungfrauConversionFactorOld] = useState(12.4);
+    const [downloadCounter, setDownloadCounter] = useState(0);
 
-    raw = () => {
-        postConfigImageFormatRaw({ throwOnError: true })
-            .catch(error => console.log(error) );
-        this.getValues();
-    }
-
-    conv = () => {
-        postConfigImageFormatConversion({ throwOnError: true })
-            .catch(error => console.log(error) );
-        this.getValues();
-    }
-
-    uploadButton = () => { this.putValues(); }
-
-    putValues = () => {
-        putConfigImageFormat({ body: this.state.s, throwOnError: true })
-            .catch(error => console.log(error) );
-    }
-
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let format_set: image_format_settings = this.props.s;
-            if (!_.isEqual(format_set, this.state.last_downloaded_s)) {
-
-                this.setState(prevState => ({
-                    s: format_set,
-                    last_downloaded_s: format_set,
-                    jungfrau_conversion_factor_err: false,
-                    download_counter: prevState.download_counter + 1,
-                    jungfrau_conversion_factor_old: format_set.jungfrau_conversion_factor_keV
-                        ?? prevState.jungfrau_conversion_factor_old,
-                    bit_width_selection: extractDepthForSelection(format_set),
-                    sign_selection: extractSignForSelection(format_set)
-                }));
-            }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setJungfrauConversionFactorErr(false);
+            setDownloadCounter(c => c + 1);
+            setJungfrauConversionFactorOld(serverS.jungfrau_conversion_factor_keV ?? jungfrauConversionFactorOld);
+            setBitWidthSelection(extractDepthForSelection(serverS));
+            setSignSelection(extractSignForSelection(serverS));
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    handleBitWidthChange = (event: SelectChangeEvent) => {
+    const handleBitWidthChange = (event: SelectChangeEvent) => {
         let val: image_format_settings['bit_depth_image'] = undefined;
 
         if (event.target.value === "a")
@@ -133,16 +85,11 @@ class ImageFormatSettings extends Component<MyProps, MyState> {
         else if (event.target.value === "32")
             val = 32;
 
-        this.setState(prevState => ({
-            bit_width_selection: event.target.value,
-            s: {
-                ...prevState.s,
-                bit_depth_image: val
-            }
-        }));
+        setBitWidthSelection(event.target.value);
+        setS(prev => ({...prev, bit_depth_image: val}));
     };
 
-    handleSignChange = (event: SelectChangeEvent) => {
+    const handleSignChange = (event: SelectChangeEvent) => {
         let val: boolean|undefined = undefined;
 
         if (event.target.value === "a")
@@ -152,250 +99,173 @@ class ImageFormatSettings extends Component<MyProps, MyState> {
         else if (event.target.value === "s")
             val = true;
 
-        this.setState(prevState => ({
-            sign_selection: event.target.value,
-            s: {
-                ...prevState.s,
-                signed_output: val
-            }
-        }));
+        setSignSelection(event.target.value);
+        setS(prev => ({...prev, signed_output: val}));
     };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-            }}>
-                <strong>Output image format settings </strong>
-                <FormGroup>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.geometry_transform}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({
-                                                  s: {
-                                                      ...prevState.s,
-                                                      geometry_transform: event.target.checked
-                                                  }
-                                              })
-                                          );
-                                      }}/>
-                    } label="Geometry transformation"/>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.summation}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({s: {...prevState.s, summation: event.target.checked}})
-                                          );
-                                      }}/>
-                    } label="Image summation"/>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.mask_chip_edges}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({
-                                                  s: {
-                                                      ...prevState.s,
-                                                      mask_chip_edges: event.target.checked
-                                                  }
-                                              })
-                                          );
-                                      }}/>
-                    } label="Mask chip edges"/>
+    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+        }}>
+            <strong>Output image format settings </strong>
+            <FormGroup>
+                <FormControlLabel control={
+                    <Checkbox checked={s.geometry_transform}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, geometry_transform: event.target.checked}));
+                                  }}/>
+                } label="Geometry transformation"/>
+                <FormControlLabel control={
+                    <Checkbox checked={s.summation}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, summation: event.target.checked}));
+                                  }}/>
+                } label="Image summation"/>
+                <FormControlLabel control={
+                    <Checkbox checked={s.mask_chip_edges}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, mask_chip_edges: event.target.checked}));
+                                  }}/>
+                } label="Mask chip edges"/>
 
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.mask_module_edges}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({
-                                                  s: {
-                                                      ...prevState.s,
-                                                      mask_module_edges: event.target.checked
-                                                  }
-                                              })
-                                          );
-                                      }}/>
-                    } label="Mask module edges"/>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.apply_mask}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({
-                                                  s: {
-                                                      ...prevState.s,
-                                                      apply_mask: event.target.checked
-                                                  }
-                                              })
-                                          );
-                                      }}/>
-                    } label="Apply pixel masks on images"/>
-                </FormGroup>
+                <FormControlLabel control={
+                    <Checkbox checked={s.mask_module_edges}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, mask_module_edges: event.target.checked}));
+                                  }}/>
+                } label="Mask module edges"/>
+                <FormControlLabel control={
+                    <Checkbox checked={s.apply_mask}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, apply_mask: event.target.checked}));
+                                  }}/>
+                } label="Apply pixel masks on images"/>
+            </FormGroup>
 
-                <b>Output pixel value</b>
-                <Stack spacing={2} direction="row">
-                    <FormControl>
-                        <InputLabel id="demo-simple-select-label">Bit-width</InputLabel>
-                        <Select
-                            sx={{width: 150}}
-                            labelId="demo-simple-select-label"
-                            id="demo-simple-select"
-                            label="Detector"
-                            value={this.state.bit_width_selection}
-                            onChange={this.handleBitWidthChange}
-                        >
-                            <MenuItem value={"a"}>Auto</MenuItem>
-                            <MenuItem value={"8"}>8-bit</MenuItem>
-                            <MenuItem value={"16"}>16-bit</MenuItem>
-                            <MenuItem value={"32"}>32-bit</MenuItem>
-                        </Select>
-                    </FormControl>
-                    <FormControl>
-                        <InputLabel id="demo-simple-select-label">Sign</InputLabel>
-                        <Select
-                            sx={{width: 150}}
-                            labelId="demo-simple-select-label"
-                            id="demo-simple-select"
-                            label="Sign"
-                            value={this.state.sign_selection}
-                            onChange={this.handleSignChange}
-                        >
-                            <MenuItem value={"a"}>Auto</MenuItem>
-                            <MenuItem value={"s"}>Signed</MenuItem>
-                            <MenuItem value={"u"}>Unsigned</MenuItem>
-                        </Select>
-                    </FormControl>
-                </Stack>
-                <b>JUNGFRAU specific</b>
-                <FormGroup>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.jungfrau_mask_pixels_without_g0}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          this.setState(
-                                              prevState => ({
-                                                  s: {
-                                                      ...prevState.s,
-                                                      jungfrau_mask_pixels_without_g0: event.target.checked
-                                                  }
-                                              }));
-                                      }}/>
-                    } label="Mask pixels not switching to G0"/>
-                    <FormControlLabel control={
-                        <Checkbox checked={this.state.s.jungfrau_conversion}
-                                  onChange={
-                                      (event: React.ChangeEvent<HTMLInputElement>) => {
-                                          if (event.target.checked) {
-                                              this.setState(
-                                                  prevState => ({
-                                                      jungfrau_conversion_factor_err: false,
-                                                      s: {
-                                                          ...prevState.s,
-                                                          jungfrau_conversion: true,
-                                                          jungfrau_conversion_factor_keV: undefined
-                                                      }
-                                                  }));
-                                          } else {
-                                              this.setState(
-                                                  prevState => ({
-                                                      jungfrau_conversion_factor_err: false,
-                                                      s: {
-                                                          ...prevState.s,
-                                                          jungfrau_conversion: false,
-                                                          jungfrau_conversion_factor_keV: undefined
-                                                      }
-                                                  }));
-                                          }
-                                      }}/>
-                    } label="Conversion to photons"/>
+            <b>Output pixel value</b>
+            <Stack spacing={2} direction="row">
+                <FormControl>
+                    <InputLabel id="demo-simple-select-label">Bit-width</InputLabel>
+                    <Select
+                        sx={{width: 150}}
+                        labelId="demo-simple-select-label"
+                        id="demo-simple-select"
+                        label="Detector"
+                        value={bitWidthSelection}
+                        onChange={handleBitWidthChange}
+                    >
+                        <MenuItem value={"a"}>Auto</MenuItem>
+                        <MenuItem value={"8"}>8-bit</MenuItem>
+                        <MenuItem value={"16"}>16-bit</MenuItem>
+                        <MenuItem value={"32"}>32-bit</MenuItem>
+                    </Select>
+                </FormControl>
+                <FormControl>
+                    <InputLabel id="demo-simple-select-label">Sign</InputLabel>
+                    <Select
+                        sx={{width: 150}}
+                        labelId="demo-simple-select-label"
+                        id="demo-simple-select"
+                        label="Sign"
+                        value={signSelection}
+                        onChange={handleSignChange}
+                    >
+                        <MenuItem value={"a"}>Auto</MenuItem>
+                        <MenuItem value={"s"}>Signed</MenuItem>
+                        <MenuItem value={"u"}>Unsigned</MenuItem>
+                    </Select>
+                </FormControl>
+            </Stack>
+            <b>JUNGFRAU specific</b>
+            <FormGroup>
+                <FormControlLabel control={
+                    <Checkbox checked={s.jungfrau_mask_pixels_without_g0}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setS(prev => ({...prev, jungfrau_mask_pixels_without_g0: event.target.checked}));
+                                  }}/>
+                } label="Mask pixels not switching to G0"/>
+                <FormControlLabel control={
+                    <Checkbox checked={s.jungfrau_conversion}
+                              onChange={
+                                  (event: ChangeEvent<HTMLInputElement>) => {
+                                      setJungfrauConversionFactorErr(false);
+                                      setS(prev => ({
+                                          ...prev,
+                                          jungfrau_conversion: event.target.checked,
+                                          jungfrau_conversion_factor_keV: undefined
+                                      }));
+                                  }}/>
+                } label="Conversion to photons"/>
 
-                </FormGroup>
-                <List>
-                    <Tooltip
-                        title="JUNGFRAU conversion factor allows to get different unit than 1 photon count. If not provided incident_energy is used.">
-                        <ListItem>
-                            <Checkbox
-                                checked={this.state.s.jungfrau_conversion_factor_keV !== undefined}
-                                disabled={!this.state.s.jungfrau_conversion}
-                                onChange={
-                                    (event: React.ChangeEvent<HTMLInputElement>) => {
-                                        if (!event.target.checked)
-                                            this.setState(prevState => ({
-                                                download_counter: this.state.download_counter + 1,
-                                                jungfrau_conversion_factor_err: false,
-                                                s: {
-                                                    ...prevState.s,
-                                                    jungfrau_conversion_factor_keV: undefined
-                                                }
-                                            }));
-                                        else
-                                            this.setState(prevState => ({
-                                                download_counter: this.state.download_counter + 1,
-                                                jungfrau_conversion_factor_err: false,
-                                                s: {
-                                                    ...prevState.s,
-                                                    jungfrau_conversion_factor_keV: this.state.jungfrau_conversion_factor_old
-                                                }
-                                            }));
-                                    }}
-                            />
-                            <FormControl fullWidth>
-                                <NumberTextField
-                                    start_val={this.state.s.jungfrau_conversion_factor_keV}
-                                    disabled={this.state.s.jungfrau_conversion_factor_keV === undefined}
-                                    label={"JUNGFRAU conversion factor"}
-                                    units={"keV"}
-                                    float={true}
-                                    min={0.001}
-                                    fullWidth
-                                    counter={this.state.download_counter}
-                                    callback={(val: number, err: boolean) => {
-                                        let old: number = this.state.jungfrau_conversion_factor_old;
-                                        if (!err)
-                                            old = val;
-                                        this.setState(prevState => ({
-                                            jungfrau_conversion_factor_err: err,
-                                            jungfrau_conversion_factor_old: old,
-                                            s: {...prevState.s, jungfrau_conversion_factor_keV: val}
-                                        }));
-                                    }}/>
-                            </FormControl>
+            </FormGroup>
+            <List>
+                <Tooltip
+                    title="JUNGFRAU conversion factor allows to get different unit than 1 photon count. If not provided incident_energy is used.">
+                    <ListItem>
+                        <Checkbox
+                            checked={s.jungfrau_conversion_factor_keV !== undefined}
+                            disabled={!s.jungfrau_conversion}
+                            onChange={
+                                (event: ChangeEvent<HTMLInputElement>) => {
+                                    setDownloadCounter(c => c + 1);
+                                    setJungfrauConversionFactorErr(false);
+                                    if (!event.target.checked)
+                                        setS(prev => ({...prev, jungfrau_conversion_factor_keV: undefined}));
+                                    else
+                                        setS(prev => ({...prev, jungfrau_conversion_factor_keV: jungfrauConversionFactorOld}));
+                                }}
+                        />
+                        <FormControl fullWidth>
+                            <NumberTextField
+                                start_val={s.jungfrau_conversion_factor_keV}
+                                disabled={s.jungfrau_conversion_factor_keV === undefined}
+                                label={"JUNGFRAU conversion factor"}
+                                units={"keV"}
+                                float={true}
+                                min={0.001}
+                                fullWidth
+                                counter={downloadCounter}
+                                callback={(val: number, err: boolean) => {
+                                    if (!err)
+                                        setJungfrauConversionFactorOld(val);
+                                    setJungfrauConversionFactorErr(err);
+                                    setS(prev => ({...prev, jungfrau_conversion_factor_keV: val}));
+                                }}/>
+                        </FormControl>
 
-                        </ListItem>
-                    </Tooltip>
-                </List>
-                    <NumberTextField start_val={this.state.s.jungfrau_pedestal_g0_rms_limit}
-                                     label={"G0 max RMS"}
-                                     min={0}
-                                     default={100}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             pedestal_g0_rms_limit_err: err,
-                                             s: {...prevState.s, jungfrau_pedestal_g0_rms_limit: val}
-                                         }));
-                                     }}
-                    />
-
-                <ButtonWithSnackbar
-                    path={"/config/image_format"}
-                    color={"primary"}
-                    method={"PUT"}
-                    disabled={this.state.jungfrau_conversion_factor_err}
-                    text={"Upload"}
-                    input={JSON.stringify(this.state.s)}
+                    </ListItem>
+                </Tooltip>
+            </List>
+                <NumberTextField start_val={s.jungfrau_pedestal_g0_rms_limit}
+                                 label={"G0 max RMS"}
+                                 min={0}
+                                 default={100}
+                                 counter={downloadCounter}
+                                 callback={(val: number, _err: boolean) => {
+                                     setS(prev => ({...prev, jungfrau_pedestal_g0_rms_limit: val}));
+                                 }}
                 />
 
-            </Stack>
-            <br/>
-        </Paper>
-    }
+            <ButtonWithSnackbar
+                path={"/config/image_format"}
+                color={"primary"}
+                method={"PUT"}
+                disabled={jungfrauConversionFactorErr}
+                text={"Upload"}
+                input={JSON.stringify(s)}
+            />
+
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default ImageFormatSettings;
\ No newline at end of file
+export default memo(ImageFormatSettings);
diff --git a/frontend/src/components/ImagePusherStatus.tsx b/frontend/src/components/ImagePusherStatus.tsx
index d28633e5..0a21e00a 100644
--- a/frontend/src/components/ImagePusherStatus.tsx
+++ b/frontend/src/components/ImagePusherStatus.tsx
@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: GPL-3.0-only
  */
 
-import React, {Component} from 'react';
+import {memo} from 'react';
 import Paper from '@mui/material/Paper';
 import {Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
 import {image_pusher_status, image_pusher_type} from "../client";
@@ -32,41 +32,38 @@ function renderPusherType(type?: image_pusher_type): string {
     }
 }
 
-class ImagePusherStatus extends Component<MyProps> {
-    render() {
-        const { s } = this.props;
-        return (
-            <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-                <br/>
-                <Stack spacing={2} sx={{justifyContent: "center", alignItems: "center"}}>
-                    <strong>Image pusher status</strong>
-                    <TableContainer component={Paper} sx={{width: '90%'}} style={{marginLeft: "auto", marginRight: "auto"}}>
-                        <Table size="small">
-                            <TableBody>
-                                <TableRow>
-                                    <TableCell component="th" scope="row">Pusher type:</TableCell>
-                                    <TableCell align="right">{renderPusherType(s?.pusher_type)}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row">Images written:</TableCell>
-                                    <TableCell align="right">{s?.images_written ?? "N/A"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row">Images not written due to errors:</TableCell>
-                                    <TableCell align="right">{s?.images_write_error ?? "N/A"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row">FIFO utilization:</TableCell>
-                                    <TableCell align="right">{renderFifo(s?.writer_fifo_utilization)}</TableCell>
-                                </TableRow>
-                            </TableBody>
-                        </Table>
-                    </TableContainer>
-                </Stack>
-                <br/>
-            </Paper>
-        );
-    }
+function ImagePusherStatus({s}: MyProps) {
+    return (
+        <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+            <br/>
+            <Stack spacing={2} sx={{justifyContent: "center", alignItems: "center"}}>
+                <strong>Image pusher status</strong>
+                <TableContainer component={Paper} sx={{width: '90%'}} style={{marginLeft: "auto", marginRight: "auto"}}>
+                    <Table size="small">
+                        <TableBody>
+                            <TableRow>
+                                <TableCell component="th" scope="row">Pusher type:</TableCell>
+                                <TableCell align="right">{renderPusherType(s?.pusher_type)}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row">Images written:</TableCell>
+                                <TableCell align="right">{s?.images_written ?? "N/A"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row">Images not written due to errors:</TableCell>
+                                <TableCell align="right">{s?.images_write_error ?? "N/A"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row">FIFO utilization:</TableCell>
+                                <TableCell align="right">{renderFifo(s?.writer_fifo_utilization)}</TableCell>
+                            </TableRow>
+                        </TableBody>
+                    </Table>
+                </TableContainer>
+            </Stack>
+            <br/>
+        </Paper>
+    );
 }
 
-export default ImagePusherStatus;
\ No newline at end of file
+export default memo(ImagePusherStatus);
diff --git a/frontend/src/components/IndexingSettings.tsx b/frontend/src/components/IndexingSettings.tsx
index 5859146a..3e0c9b3b 100644
--- a/frontend/src/components/IndexingSettings.tsx
+++ b/frontend/src/components/IndexingSettings.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {memo, useEffect, useState} from 'react';
 
 import {Stack, Typography, FormControlLabel, Checkbox} from "@mui/material";
 import Paper from "@mui/material/Paper";
@@ -16,22 +16,6 @@ type MyProps = {
     status?: broker_status
 }
 
-type MyState = {
-    s: indexing_settings,
-    last_downloaded_s: indexing_settings,
-    download_counter: number,
-    viable_cell_min_spots_error: boolean,
-    fft_high_resolution_A_error: boolean,
-    fft_max_unit_cell_A_error: boolean,
-    fft_min_unit_cell_A_error: boolean,
-    fft_num_vectors_error: boolean,
-    tolerance_error: boolean,
-    thread_count_error: boolean,
-    unit_cell_dist_tolerance_error: boolean,
-    rotation_indexing_min_angular_range_deg_error: boolean,
-    rotation_indexing_angular_stride_deg_error: boolean
-}
-
 const default_indexing_settings: indexing_settings = {
     algorithm: indexing_algorithm.FFBIDX,
     geom_refinement_algorithm: geom_refinement_algorithm.NONE,
@@ -50,331 +34,274 @@ const default_indexing_settings: indexing_settings = {
     blocking: false
 };
 
-class IndexingSettings extends Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_indexing_settings,
-        last_downloaded_s: default_indexing_settings,
-        download_counter: 0,
-        fft_high_resolution_A_error: false,
-        fft_max_unit_cell_A_error: false,
-        fft_min_unit_cell_A_error: false,
-        fft_num_vectors_error: false,
-        tolerance_error: false,
-        thread_count_error: false,
-        unit_cell_dist_tolerance_error: false,
-        viable_cell_min_spots_error: false,
-        rotation_indexing_min_angular_range_deg_error: false,
-        rotation_indexing_angular_stride_deg_error: false
-    }
+function IndexingSettings({s: serverS, status}: MyProps) {
+    const [s, setS] = useState<indexing_settings>(default_indexing_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<indexing_settings>(default_indexing_settings);
+    const [downloadCounter, setDownloadCounter] = useState(0);
+    const [viableCellMinSpotsError, setViableCellMinSpotsError] = useState(false);
+    const [fftHighResolutionAError, setFftHighResolutionAError] = useState(false);
+    const [fftMaxUnitCellAError, setFftMaxUnitCellAError] = useState(false);
+    const [fftMinUnitCellAError, setFftMinUnitCellAError] = useState(false);
+    const [fftNumVectorsError, setFftNumVectorsError] = useState(false);
+    const [toleranceError, setToleranceError] = useState(false);
+    const [threadCountError, setThreadCountError] = useState(false);
+    const [unitCellDistToleranceError, setUnitCellDistToleranceError] = useState(false);
+    const [rotationIndexingMinAngularRangeDegError, setRotationIndexingMinAngularRangeDegError] = useState(false);
+    const [rotationIndexingAngularStrideDegError, setRotationIndexingAngularStrideDegError] = useState(false);
 
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let format_set: indexing_settings = this.props.s;
-            if (!_.isEqual(format_set, this.state.last_downloaded_s)) {
-
-                this.setState(prevState => ({
-                    s: format_set,
-                    last_downloaded_s: format_set,
-                    fft_high_resolution_A_error: false,
-                    fft_max_unit_cell_A_error: false,
-                    fft_min_unit_cell_A_error: false,
-                    fft_num_vectors_error: false,
-                    tolerance_error: false,
-                    thread_count_error: false,
-                    unit_cell_dist_tolerance_error: false,
-                    viable_cell_min_spots_error: false,
-                    download_counter: prevState.download_counter + 1,
-                }));
-            }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setFftHighResolutionAError(false);
+            setFftMaxUnitCellAError(false);
+            setFftMinUnitCellAError(false);
+            setFftNumVectorsError(false);
+            setToleranceError(false);
+            setThreadCountError(false);
+            setUnitCellDistToleranceError(false);
+            setViableCellMinSpotsError(false);
+            setDownloadCounter(c => c + 1);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    handleAlgorithmChange = (event: SelectChangeEvent) => {
-        this.setState(prevState => ({
-            s: {
-                ...prevState.s,
-                algorithm: event.target.value as indexing_algorithm
-            }
-        }));
+    const handleAlgorithmChange = (event: SelectChangeEvent) => {
+        setS(prev => ({...prev, algorithm: event.target.value as indexing_algorithm}));
     };
 
-    handleRefinementAlgorithmChange = (event: SelectChangeEvent) => {
-        this.setState(prevState => ({
-            s: {
-                ...prevState.s,
-                geom_refinement_algorithm: event.target.value as geom_refinement_algorithm
-            }
-        }));
+    const handleRefinementAlgorithmChange = (event: SelectChangeEvent) => {
+        setS(prev => ({...prev, geom_refinement_algorithm: event.target.value as geom_refinement_algorithm}));
     };
 
-    isError() {
-        return this.state.tolerance_error
-            || this.state.fft_high_resolution_A_error
-            || this.state.fft_min_unit_cell_A_error
-            || this.state.fft_max_unit_cell_A_error
-            || this.state.fft_num_vectors_error
-            || this.state.thread_count_error
-            || this.state.unit_cell_dist_tolerance_error
-            || this.state.viable_cell_min_spots_error
-            || this.state.rotation_indexing_angular_stride_deg_error
-            || this.state.rotation_indexing_min_angular_range_deg_error;
-    }
+    const isError = () =>
+        toleranceError
+        || fftHighResolutionAError
+        || fftMinUnitCellAError
+        || fftMaxUnitCellAError
+        || fftNumVectorsError
+        || threadCountError
+        || unitCellDistToleranceError
+        || viableCellMinSpotsError
+        || rotationIndexingAngularStrideDegError
+        || rotationIndexingMinAngularRangeDegError;
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-            }}>
-                <strong>Indexing settings </strong>
+    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+        }}>
+            <strong>Indexing settings </strong>
 
-                <b>Algorithm</b>
-                    <FormControl sx = {{width: "80%"}}>
-                        <InputLabel id="demo-simple-select-label">Algorithm</InputLabel>
-                        <Select
-                            labelId="demo-simple-select-label"
-                            id="demo-simple-select"
-                            label="Algorithm"
-                            value={this.state.s.algorithm}
-                            onChange={this.handleAlgorithmChange}
-                        >
-                            <MenuItem value={indexing_algorithm.FFBIDX}>FFBIDX (known unit cell) - GPU</MenuItem>
-                            <MenuItem value={indexing_algorithm.FFT}>FFT (guess unit cell) - GPU with CuFFT library</MenuItem>
-                            <MenuItem value={indexing_algorithm.FFTW}>FFT (guess unit cell) - CPU with FFTW library</MenuItem>
-                            <MenuItem value={indexing_algorithm.AUTO}>Auto (FFBIDX if unit cell provided, FFT otherwise)</MenuItem>
-                            <MenuItem value={indexing_algorithm.NONE}>No indexing</MenuItem>
-                        </Select>
-                    </FormControl>
-                <Stack spacing={2} direction="row" sx={{width: '80%'}}>
-                <NumberTextField start_val={this.state.s.tolerance}
-                                 label={"HKL tol."}
-                                 float={true}
-                                 min={0}
-                                 default={0.5}
-                                 counter={this.state.download_counter}
-                                 callback={(val: number, err: boolean) => {
-                                     this.setState(prevState => ({
-                                         tolerance_error: err,
-                                         s: {...prevState.s, tolerance: val}
-                                     }));
-                                 }}/>
-                <NumberTextField start_val={this.state.s.unit_cell_dist_tolerance * 100.0}
-                                 label={"UC dist. tol."}
-                                 float={true}
-                                 min={0.1}
-                                 default={5.0}
-                                 max={20.0}
-                                 units={"%"}
-                                 counter={this.state.download_counter}
-                                 callback={(val: number, err: boolean) => {
-                                     this.setState(prevState => ({
-                                         tolerance_error: err,
-                                         s: {...prevState.s,
-                                             unit_cell_dist_tolerance: val / 100.0}
-                                     }));
-                                 }}/>
-                    <NumberTextField start_val={this.state.s.viable_cell_min_spots}
-                                     label={"Min spots "}
-                                     float={false}
-                                     min={5}
-                                     default={10}
-                                     max={1000}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             viable_cell_min_spots_error: err,
-                                             s: {...prevState.s,
-                                                 viable_cell_min_spots: val}
-                                         }));
-                                     }}/></Stack>&nbsp;
+            <b>Algorithm</b>
                 <FormControl sx = {{width: "80%"}}>
-                    <InputLabel>Geometry refinement</InputLabel>
+                    <InputLabel id="demo-simple-select-label">Algorithm</InputLabel>
                     <Select
-                        label="Refinement algorithm"
-                        value={this.state.s.geom_refinement_algorithm}
-                        onChange={this.handleRefinementAlgorithmChange}
+                        labelId="demo-simple-select-label"
+                        id="demo-simple-select"
+                        label="Algorithm"
+                        value={s.algorithm}
+                        onChange={handleAlgorithmChange}
                     >
-                        <MenuItem value={geom_refinement_algorithm.NONE}>No refinement</MenuItem>
-                        <MenuItem value={geom_refinement_algorithm.ORIENTATION_ONLY}>Lattice orientation</MenuItem>
-                        <MenuItem value={geom_refinement_algorithm.BEAM_CENTER}>Beam center, lattice orientation and dimensions</MenuItem>
+                        <MenuItem value={indexing_algorithm.FFBIDX}>FFBIDX (known unit cell) - GPU</MenuItem>
+                        <MenuItem value={indexing_algorithm.FFT}>FFT (guess unit cell) - GPU with CuFFT library</MenuItem>
+                        <MenuItem value={indexing_algorithm.FFTW}>FFT (guess unit cell) - CPU with FFTW library</MenuItem>
+                        <MenuItem value={indexing_algorithm.AUTO}>Auto (FFBIDX if unit cell provided, FFT otherwise)</MenuItem>
+                        <MenuItem value={indexing_algorithm.NONE}>No indexing</MenuItem>
                     </Select>
                 </FormControl>
-                <FormControlLabel
-                    control={
-                        <Checkbox
-                            checked={this.state.s.index_ice_rings}
-                            onChange={(event) => {
-                                this.setState(prevState => ({
-                                    s: {...prevState.s, index_ice_rings: event.target.checked}
-                                }));
-                            }}
-                        />
-                    }
-                    label="Index ice rings"
-                />
-                <FormControlLabel
-                    control={
-                        <Checkbox
-                            checked={this.state.s.blocking}
-                            onChange={(event) => {
-                                this.setState(prevState => ({
-                                    s: {...prevState.s, blocking: event.target.checked}
-                                }));
-                            }}
-                        />
-                    }
-                    label="Blocking thread pool"
-                />
-                <b>Rotation (3D) indexing settings</b>
-                <Stack spacing={2} direction="row" sx={{width: '80%'}}>
-
-                <FormControlLabel
-                    control={
-                        <Checkbox
-                            checked={this.state.s.rotation_indexing}
-                            onChange={(event) => {
-                                this.setState(prevState => ({
-                                    s: {...prevState.s, rotation_indexing: event.target.checked}
-                                }));
-                            }}
-                        />
-                    }
-                    label="Enable"
-                />
-
-                    <NumberTextField start_val={this.state.s.rotation_indexing_min_angular_range_deg}
-                                     label={"Angular range"}
-                                     float={true}
-                                     units={"°"}
-                                     min={1.0}
-                                     max={360.0}
-                                     default={20.0}
-                                     counter={this.state.download_counter}
-                                     disabled={!this.state.s.rotation_indexing}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             rotation_indexing_min_angular_range_deg_error: err,
-                                             s: {...prevState.s, rotation_indexing_min_angular_range_deg: val}
-                                         }));
-                                     }}/>&nbsp;
-                    <NumberTextField start_val={this.state.s.rotation_indexing_angular_stride_deg}
-                                     label={"Angular stride"}
-                                     float={true}
-                                     units={"°"}
-                                     min={0.0001}
-                                     max={100.0}
-                                     default={0.1}
-                                     counter={this.state.download_counter}
-                                     disabled={!this.state.s.rotation_indexing}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             rotation_indexing_angular_stride_deg_error: err,
-                                             s: {...prevState.s, rotation_indexing_angular_stride_deg: val}
-                                         }));
-                                     }}/>&nbsp;
-
-                </Stack>
-
-                <b>FFT indexing settings</b>
-                <Stack spacing={2} direction="row" sx={{width: '80%'}}>
-                    <NumberTextField start_val={this.state.s.fft_min_unit_cell_A}
-                                     label={"Min Unit cell"}
-                                     float={true}
-                                     units={"Å"}
-                                     min={1.0}
-                                     max={40.0}
-                                     default={10.0}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             fft_min_unit_cell_A_error: err,
-                                             s: {...prevState.s, fft_min_unit_cell_A: val}
-                                         }));
-                                     }}/>&nbsp;
-                    <NumberTextField start_val={this.state.s.fft_max_unit_cell_A}
-                                     label={"Max Unit cell"}
-                                     float={true}
-                                     units={"Å"}
-                                     min={50.0}
-                                     max={400.0}
-                                     default={250.0}
-                                      counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             fft_max_unit_cell_A_error: err,
-                                             s: {...prevState.s, fft_max_unit_cell_A: val}
-                                         }));
-                                     }}/>&nbsp;
-
-                    <NumberTextField start_val={this.state.s.fft_high_resolution_A}
-                                     label={"High res."}
-                                     float={true}
-                                     units={"Å"}
-                                     min={0.5}
-                                     max={6.0}
-                                     default={2.0}
-                                     counter={this.state.download_counter}
-                                     callback={(val: number, err: boolean) => {
-                                         this.setState(prevState => ({
-                                             fft_high_resolution_A_error: err,
-                                             s: {...prevState.s, fft_high_resolution_A: val}
-                                         }));
-                                     }}/>&nbsp;
-                </Stack>
-                <NumberTextField start_val={this.state.s.fft_num_vectors}
-                                 label={"# vectors"}
+            <Stack spacing={2} direction="row" sx={{width: '80%'}}>
+            <NumberTextField start_val={s.tolerance}
+                             label={"HKL tol."}
+                             float={true}
+                             min={0}
+                             default={0.5}
+                             counter={downloadCounter}
+                             callback={(val: number, err: boolean) => {
+                                 setToleranceError(err);
+                                 setS(prev => ({...prev, tolerance: val}));
+                             }}/>
+            <NumberTextField start_val={s.unit_cell_dist_tolerance * 100.0}
+                             label={"UC dist. tol."}
+                             float={true}
+                             min={0.1}
+                             default={5.0}
+                             max={20.0}
+                             units={"%"}
+                             counter={downloadCounter}
+                             callback={(val: number, err: boolean) => {
+                                 setToleranceError(err);
+                                 setS(prev => ({...prev, unit_cell_dist_tolerance: val / 100.0}));
+                             }}/>
+                <NumberTextField start_val={s.viable_cell_min_spots}
+                                 label={"Min spots "}
                                  float={false}
-                                 min={128}
-                                 default={16384}
-                                 counter={this.state.download_counter}
+                                 min={5}
+                                 default={10}
+                                 max={1000}
+                                 counter={downloadCounter}
                                  callback={(val: number, err: boolean) => {
-                                     this.setState(prevState => ({
-                                         fft_num_vectors_error: err,
-                                         s: {...prevState.s, fft_num_vectors: val}
-                                     }));
-                                 }}
-                                 sx={{width: '80%'}}/>&nbsp;
-                <b>Computing resources</b>
-                <Typography> GPU count:  {this.props.status !== undefined ? this.props.status.gpu_count : "N/A"}</Typography>
+                                     setViableCellMinSpotsError(err);
+                                     setS(prev => ({...prev, viable_cell_min_spots: val}));
+                                 }}/></Stack>&nbsp;
+            <FormControl sx = {{width: "80%"}}>
+                <InputLabel>Geometry refinement</InputLabel>
+                <Select
+                    label="Refinement algorithm"
+                    value={s.geom_refinement_algorithm}
+                    onChange={handleRefinementAlgorithmChange}
+                >
+                    <MenuItem value={geom_refinement_algorithm.NONE}>No refinement</MenuItem>
+                    <MenuItem value={geom_refinement_algorithm.ORIENTATION_ONLY}>Lattice orientation</MenuItem>
+                    <MenuItem value={geom_refinement_algorithm.BEAM_CENTER}>Beam center, lattice orientation and dimensions</MenuItem>
+                </Select>
+            </FormControl>
+            <FormControlLabel
+                control={
+                    <Checkbox
+                        checked={s.index_ice_rings}
+                        onChange={(event) => {
+                            setS(prev => ({...prev, index_ice_rings: event.target.checked}));
+                        }}
+                    />
+                }
+                label="Index ice rings"
+            />
+            <FormControlLabel
+                control={
+                    <Checkbox
+                        checked={s.blocking}
+                        onChange={(event) => {
+                            setS(prev => ({...prev, blocking: event.target.checked}));
+                        }}
+                    />
+                }
+                label="Blocking thread pool"
+            />
+            <b>Rotation (3D) indexing settings</b>
+            <Stack spacing={2} direction="row" sx={{width: '80%'}}>
 
-                 <NumberTextField start_val={this.state.s.thread_count}
-                                 label={"CPU Thread count"}
-                                 float={false}
-                                 min={1}
-                                 max={64}
-                                 default={this.state.s.thread_count}
-                                 counter={this.state.download_counter}
+            <FormControlLabel
+                control={
+                    <Checkbox
+                        checked={s.rotation_indexing}
+                        onChange={(event) => {
+                            setS(prev => ({...prev, rotation_indexing: event.target.checked}));
+                        }}
+                    />
+                }
+                label="Enable"
+            />
+
+                <NumberTextField start_val={s.rotation_indexing_min_angular_range_deg}
+                                 label={"Angular range"}
+                                 float={true}
+                                 units={"°"}
+                                 min={1.0}
+                                 max={360.0}
+                                 default={20.0}
+                                 counter={downloadCounter}
+                                 disabled={!s.rotation_indexing}
                                  callback={(val: number, err: boolean) => {
-                                     this.setState(prevState => ({
-                                         thread_count_error: err,
-                                         s: {...prevState.s, thread_count: val}
-                                     }));
-                                 }}
-                                 sx={{width: '80%'}}/>
-
-                    <ButtonWithSnackbar
-                    path={"/config/indexing"}
-                    color={"primary"}
-                    method={"PUT"}
-                    disabled={this.isError()}
-                    text={"Upload"}
-                    input={JSON.stringify(this.state.s)}
-                />
+                                     setRotationIndexingMinAngularRangeDegError(err);
+                                     setS(prev => ({...prev, rotation_indexing_min_angular_range_deg: val}));
+                                 }}/>&nbsp;
+                <NumberTextField start_val={s.rotation_indexing_angular_stride_deg}
+                                 label={"Angular stride"}
+                                 float={true}
+                                 units={"°"}
+                                 min={0.0001}
+                                 max={100.0}
+                                 default={0.1}
+                                 counter={downloadCounter}
+                                 disabled={!s.rotation_indexing}
+                                 callback={(val: number, err: boolean) => {
+                                     setRotationIndexingAngularStrideDegError(err);
+                                     setS(prev => ({...prev, rotation_indexing_angular_stride_deg: val}));
+                                 }}/>&nbsp;
 
             </Stack>
-            <br/>
-        </Paper>
-    }
+
+            <b>FFT indexing settings</b>
+            <Stack spacing={2} direction="row" sx={{width: '80%'}}>
+                <NumberTextField start_val={s.fft_min_unit_cell_A}
+                                 label={"Min Unit cell"}
+                                 float={true}
+                                 units={"Å"}
+                                 min={1.0}
+                                 max={40.0}
+                                 default={10.0}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setFftMinUnitCellAError(err);
+                                     setS(prev => ({...prev, fft_min_unit_cell_A: val}));
+                                 }}/>&nbsp;
+                <NumberTextField start_val={s.fft_max_unit_cell_A}
+                                 label={"Max Unit cell"}
+                                 float={true}
+                                 units={"Å"}
+                                 min={50.0}
+                                 max={400.0}
+                                 default={250.0}
+                                  counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setFftMaxUnitCellAError(err);
+                                     setS(prev => ({...prev, fft_max_unit_cell_A: val}));
+                                 }}/>&nbsp;
+
+                <NumberTextField start_val={s.fft_high_resolution_A}
+                                 label={"High res."}
+                                 float={true}
+                                 units={"Å"}
+                                 min={0.5}
+                                 max={6.0}
+                                 default={2.0}
+                                 counter={downloadCounter}
+                                 callback={(val: number, err: boolean) => {
+                                     setFftHighResolutionAError(err);
+                                     setS(prev => ({...prev, fft_high_resolution_A: val}));
+                                 }}/>&nbsp;
+            </Stack>
+            <NumberTextField start_val={s.fft_num_vectors}
+                             label={"# vectors"}
+                             float={false}
+                             min={128}
+                             default={16384}
+                             counter={downloadCounter}
+                             callback={(val: number, err: boolean) => {
+                                 setFftNumVectorsError(err);
+                                 setS(prev => ({...prev, fft_num_vectors: val}));
+                             }}
+                             sx={{width: '80%'}}/>&nbsp;
+            <b>Computing resources</b>
+            <Typography> GPU count:  {status !== undefined ? status.gpu_count : "N/A"}</Typography>
+
+             <NumberTextField start_val={s.thread_count}
+                             label={"CPU Thread count"}
+                             float={false}
+                             min={1}
+                             max={64}
+                             default={s.thread_count}
+                             counter={downloadCounter}
+                             callback={(val: number, err: boolean) => {
+                                 setThreadCountError(err);
+                                 setS(prev => ({...prev, thread_count: val}));
+                             }}
+                             sx={{width: '80%'}}/>
+
+                <ButtonWithSnackbar
+                path={"/config/indexing"}
+                color={"primary"}
+                method={"PUT"}
+                disabled={isError()}
+                text={"Upload"}
+                input={JSON.stringify(s)}
+            />
+
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default IndexingSettings;
-
+export default memo(IndexingSettings);
diff --git a/frontend/src/components/InstrumentMetadata.tsx b/frontend/src/components/InstrumentMetadata.tsx
index 661e1786..0d91a1fd 100644
--- a/frontend/src/components/InstrumentMetadata.tsx
+++ b/frontend/src/components/InstrumentMetadata.tsx
@@ -1,10 +1,10 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, useEffect, useState} from 'react';
 
 import {
     Autocomplete,
     Checkbox,
     FormControlLabel, FormGroup,
-    Grid, Stack,
+    Stack,
     TextField
 } from "@mui/material";
 import Paper from "@mui/material/Paper";
@@ -16,11 +16,6 @@ type MyProps = {
     s?: instrument_metadata
 }
 
-type MyState = {
-    s: instrument_metadata
-    last_downloaded_s: instrument_metadata
-};
-
 const default_instrument_metadata: instrument_metadata = {
     source_name: "Swiss Light Source",
     instrument_name: "X06SA",
@@ -39,113 +34,86 @@ const source_types : string[] = [
     "Metal Jet X-ray"
 ];
 
-class ImageFormatSettings extends Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_instrument_metadata,
-        last_downloaded_s: default_instrument_metadata
-    }
+function InstrumentMetadata({s: serverS}: MyProps) {
+    const [s, setS] = useState<instrument_metadata>(default_instrument_metadata);
+    const [lastDownloadedS, setLastDownloadedS] = useState<instrument_metadata>(default_instrument_metadata);
 
-    getValues () {
-        if (this.props.s !== undefined) {
-            let instr_metadata: instrument_metadata = this.props.s;
-            if (!_.isEqual(instr_metadata, this.state.last_downloaded_s))
-                this.setState({
-                    s: instr_metadata,
-                    last_downloaded_s: instr_metadata
-                });
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setS(serverS);
+            setLastDownloadedS(serverS);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ width: '100%' }}>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-                marginLeft: '8%',
-                marginRight: '8%',
-            }}>
+    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%' }}>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+            marginLeft: '8%',
+            marginRight: '8%',
+        }}>
 
 
-                <div><strong>Source and instrument metadata</strong></div>
-                    <TextField id="source_name" label="Source name" variant="outlined"
-                               fullWidth
-                               onChange={(event: React.ChangeEvent<HTMLInputElement>) => {
-                                   this.setState(prevState => ({
-                                       s: {...prevState.s, source_name: event.target.value}
-                                   }))
-                               }}
-                               value={this.state.s.source_name}/>
-                    <TextField id="instrument_name" label="Instrument name" variant="outlined"
-                               fullWidth
-                               onChange={(event: React.ChangeEvent<HTMLInputElement>) => {
-                                   this.setState(prevState => ({
-                                       s: {...prevState.s, instrument_name: event.target.value}
-                                   }))
-                               }}
-                               value={this.state.s.instrument_name}/>
-                    <Autocomplete
-                        fullWidth
-                        freeSolo
-                        multiple={false}
-                        onChange={(event, newValue: string | null | undefined) => {
-                            if (typeof newValue === "string")
-                                this.setState(prevState => ({s: {...prevState.s, source_type: newValue}}));
-                        }}
+            <div><strong>Source and instrument metadata</strong></div>
+                <TextField id="source_name" label="Source name" variant="outlined"
+                           fullWidth
+                           onChange={(event: ChangeEvent<HTMLInputElement>) => {
+                               setS(prev => ({...prev, source_name: event.target.value}));
+                           }}
+                           value={s.source_name}/>
+                <TextField id="instrument_name" label="Instrument name" variant="outlined"
+                           fullWidth
+                           onChange={(event: ChangeEvent<HTMLInputElement>) => {
+                               setS(prev => ({...prev, instrument_name: event.target.value}));
+                           }}
+                           value={s.instrument_name}/>
+                <Autocomplete
+                    fullWidth
+                    freeSolo
+                    multiple={false}
+                    onChange={(event, newValue: string | null | undefined) => {
+                        if (typeof newValue === "string")
+                            setS(prev => ({...prev, source_type: newValue}));
+                    }}
 
-                        inputValue={this.state.s.source_type}
+                    inputValue={s.source_type}
 
-                        onInputChange={(_, newInputValue: string) => {
-                            this.setState(prevState => ({
-                                s: {...prevState.s, source_type: newInputValue}
-                            }));
-                        }}
-                        selectOnFocus
-                        clearOnBlur
-                        value={this.state.s.source_type}
-                        options={source_types}
-                        renderInput={(params) => <TextField {...params} label="Source type" variant="outlined"/>}
-                    />
-                    <FormGroup>
-                        <FormControlLabel control={
-                            <Checkbox checked={this.state.s.pulsed_source === true}
-                                      onChange={
-                                          (event: React.ChangeEvent<HTMLInputElement>) => {
-                                              this.setState(
-                                                  prevState => ({
-                                                      s: {...prevState.s, pulsed_source: event.target.checked}
-                                                  }));
-                                          }}/>
-                        } label="Pulsed source (XFEL)"/>
-                        <FormControlLabel control={
-                            <Checkbox checked={this.state.s.electron_source === true}
-                                      onChange={
-                                          (event: React.ChangeEvent<HTMLInputElement>) => {
-                                              this.setState(
-                                                  prevState => ({
-                                                      s: {...prevState.s, electron_source: event.target.checked}
-                                                  }));
-                                          }}/>
-                        } label="Electron source"/>
-                    </FormGroup>
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/instrument"}
-                    input={JSON.stringify(this.state.s)}
-                    method={"PUT"}
-                    text={"Upload"}
+                    onInputChange={(_event, newInputValue: string) => {
+                        setS(prev => ({...prev, source_type: newInputValue}));
+                    }}
+                    selectOnFocus
+                    clearOnBlur
+                    value={s.source_type}
+                    options={source_types}
+                    renderInput={(params) => <TextField {...params} label="Source type" variant="outlined"/>}
                 />
-            </Stack>
-            <br/>
-        </Paper>
-    }
+                <FormGroup>
+                    <FormControlLabel control={
+                        <Checkbox checked={s.pulsed_source === true}
+                                  onChange={
+                                      (event: ChangeEvent<HTMLInputElement>) => {
+                                          setS(prev => ({...prev, pulsed_source: event.target.checked}));
+                                      }}/>
+                    } label="Pulsed source (XFEL)"/>
+                    <FormControlLabel control={
+                        <Checkbox checked={s.electron_source === true}
+                                  onChange={
+                                      (event: ChangeEvent<HTMLInputElement>) => {
+                                          setS(prev => ({...prev, electron_source: event.target.checked}));
+                                      }}/>
+                    } label="Electron source"/>
+                </FormGroup>
+            <ButtonWithSnackbar
+                color={"primary"}
+                path={"/config/instrument"}
+                input={JSON.stringify(s)}
+                method={"PUT"}
+                text={"Upload"}
+            />
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default ImageFormatSettings;
\ No newline at end of file
+export default memo(InstrumentMetadata);
diff --git a/frontend/src/components/MeasurementStatistics.tsx b/frontend/src/components/MeasurementStatistics.tsx
index 28bc8736..71bf5c3a 100644
--- a/frontend/src/components/MeasurementStatistics.tsx
+++ b/frontend/src/components/MeasurementStatistics.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {memo} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {Grid, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
@@ -8,83 +8,78 @@ type MyProps = {
     s: measurement_statistics,
 };
 
-type MyState = {};
+function MeasurementStatistics({s}: MyProps) {
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 550, width: '100%' }}>
+        <Grid container spacing={0}>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <br/><strong>Measurement statistics</strong><br/><br/>
 
-class MeasurementStatistics extends Component<MyProps, MyState> {
- 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 550, width: '100%' }}>
-            <Grid container spacing={0}>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <br/><strong>Measurement statistics</strong><br/><br/>
+                <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
+                    <Table size="small" aria-label="simple table">
+                        <TableBody>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> File prefix: </TableCell>
+                                <TableCell align="right">{(s.file_prefix !== undefined) ? s.file_prefix : "(images not written)"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Run number: </TableCell>
+                                <TableCell align="right">{(s.run_number !== undefined) ? s.run_number : "(not set)"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Experiment group: </TableCell>
+                                <TableCell align="right">{s.experiment_group}</TableCell>
+                            </TableRow>
 
-                    <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
-                        <Table size="small" aria-label="simple table">
-                            <TableBody>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> File prefix: </TableCell>
-                                    <TableCell align="right">{(this.props.s.file_prefix !== undefined) ? this.props.s.file_prefix : "(images not written)"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Run number: </TableCell>
-                                    <TableCell align="right">{(this.props.s.run_number !== undefined) ? this.props.s.run_number : "(not set)"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Experiment group: </TableCell>
-                                    <TableCell align="right">{this.props.s.experiment_group}</TableCell>
-                                </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Images expected: </TableCell>
+                                <TableCell align="right">{s.images_expected}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Images collected: </TableCell>
+                                <TableCell align="right">{s.images_collected}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Images sent to writer: </TableCell>
+                                <TableCell align="right">{s.images_sent}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Images discarded by lossy compression: </TableCell>
+                                <TableCell align="right">{s.images_discarded_lossy_compression}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Compression ratio: </TableCell>
+                                <TableCell align="right">{(s.compression_ratio !== undefined)
+                                    ? (s.compression_ratio.toFixed(1)) + "x" : "-" } </TableCell>
 
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Images expected: </TableCell>
-                                    <TableCell align="right">{this.props.s.images_expected}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Images collected: </TableCell>
-                                    <TableCell align="right">{this.props.s.images_collected}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Images sent to writer: </TableCell>
-                                    <TableCell align="right">{this.props.s.images_sent}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Images discarded by lossy compression: </TableCell>
-                                    <TableCell align="right">{this.props.s.images_discarded_lossy_compression}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Compression ratio: </TableCell>
-                                    <TableCell align="right">{(this.props.s.compression_ratio !== undefined)
-                                        ? (this.props.s.compression_ratio.toFixed(1)) + "x" : "-" } </TableCell>
-
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Data acquisition efficiency: </TableCell>
-                                    <TableCell align="right">{(this.props.s.collection_efficiency !== undefined)
-                                        ? (Math.floor(this.props.s.collection_efficiency * 1000.0) / 1000.0).toFixed(3) : "-"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Indexing rate: </TableCell>
-                                    <TableCell align="right">{(this.props.s.indexing_rate !== undefined)
-                                        ? this.props.s.indexing_rate.toFixed(2) : "-"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Background estimate: </TableCell>
-                                    <TableCell align="right">{(this.props.s.bkg_estimate !== undefined)
-                                        ? this.props.s.bkg_estimate.toPrecision(7) : "-"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Unit cell: </TableCell>
-                                    <TableCell align="right">{this.props.s.unit_cell}</TableCell>
-                                </TableRow>
-                            </TableBody>
-                        </Table>
-                    </TableContainer>
-                    <br/>
-                </Grid>
-                <Grid item xs={1}/>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Data acquisition efficiency: </TableCell>
+                                <TableCell align="right">{(s.collection_efficiency !== undefined)
+                                    ? (Math.floor(s.collection_efficiency * 1000.0) / 1000.0).toFixed(3) : "-"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Indexing rate: </TableCell>
+                                <TableCell align="right">{(s.indexing_rate !== undefined)
+                                    ? s.indexing_rate.toFixed(2) : "-"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Background estimate: </TableCell>
+                                <TableCell align="right">{(s.bkg_estimate !== undefined)
+                                    ? s.bkg_estimate.toPrecision(7) : "-"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Unit cell: </TableCell>
+                                <TableCell align="right">{s.unit_cell}</TableCell>
+                            </TableRow>
+                        </TableBody>
+                    </Table>
+                </TableContainer>
+                <br/>
             </Grid>
-        </Paper>
-    }
+            <Grid item xs={1}/>
+        </Grid>
+    </Paper>
 }
 
-export default MeasurementStatistics;
\ No newline at end of file
+export default memo(MeasurementStatistics);
diff --git a/frontend/src/components/NumberTextField.tsx b/frontend/src/components/NumberTextField.tsx
index 35ec5e70..663ac939 100644
--- a/frontend/src/components/NumberTextField.tsx
+++ b/frontend/src/components/NumberTextField.tsx
@@ -1,10 +1,9 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, ReactNode, useEffect, useState} from 'react';
 
 import {
     InputAdornment, SxProps,
     TextField, Theme
 } from "@mui/material";
-import { ReactNode } from "react";
 
 type MyProps = {
     start_val?: number,
@@ -21,94 +20,76 @@ type MyProps = {
     float?: boolean
 }
 
-type MyState = {
-    text: string,
-    err: boolean,
-    val: number
+function unitsNode(str: string | undefined): ReactNode | null {
+    if (str === undefined)
+        return null;
+    else if (str === "us")
+        return <InputAdornment position="end">&micro;s</InputAdornment>;
+    else if (str === "A-1")
+        return <InputAdornment position="end">
+            <span>&#8491;<sup>-1</sup></span>
+        </InputAdornment>;
+    else
+        return <InputAdornment position="end">{str}</InputAdornment>;
 }
 
-class NumberTextField extends Component<MyProps, MyState> {
-    state : MyState = {
-        text: ".",
-        err: true,
-        val: 0
-    }
+function NumberTextField({start_val, default: defaultValue, label, callback, counter, min, max, sx, units, disabled, float}: MyProps) {
+    const [text, setText] = useState(".");
+    const [err, setErr] = useState(true);
+    const [val, setVal] = useState(0);
 
-    setup() {
-        let val : number = 0;
-        if (this.props.start_val !== undefined)
-            val = this.props.start_val;
-        else if (this.props.default !== undefined)
-            val = this.props.default;
+    // Something has to change in parent to trigger setup => otherwise this makes infinite loop.
+    // In case of error state start_val could stay same, but we want to return to "safe" set
+    // so there is external counter that if changed reset is triggered.
+    useEffect(() => {
+        let v : number = 0;
+        if (start_val !== undefined)
+            v = start_val;
+        else if (defaultValue !== undefined)
+            v = defaultValue;
 
-        if (this.props.float !== true)
-            val = Math.round(val);
+        if (float !== true)
+            v = Math.round(v);
         else
-            val = Math.round(val * 1000.0) / 1000.0
+            v = Math.round(v * 1000.0) / 1000.0
 
-        this.setState({
-            err: false,
-            val: val,
-            text: val.toString()
-        });
-    }
+        setErr(false);
+        setVal(v);
+        setText(v.toString());
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [counter, start_val]);
 
-    componentDidMount() {
-        this.setup();
-    }
+    const updateValue = (event: ChangeEvent<HTMLInputElement>) => {
+        let new_text = event.target.value;
+        if (!new_text) new_text = "0";
 
-    componentDidUpdate(prevProps: Readonly<MyProps>, prevState: Readonly<MyState>, snapshot?: any) {
-        // Something has to change in parent function to trigger setup => otherwise this makes infinite loop
-        // In case of error state start_val could stay same, but we want to return to "safe" set
-        // so there is external counter that if changed reset is triggered
-        if ((prevProps.counter !== this.props.counter) || (prevProps.start_val !== this.props.start_val))
-            this.setup();
-    }
+        let num_val : number = Number(new_text);
 
-    updateValue = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let text = event.target.value;
-        if (!text) text = "0";
-
-        let num_val : number = Number(text);
-
-        let err : boolean = !Number.isFinite(num_val)
-            || (!this.props.float && !Number.isInteger(num_val))
-            || ((this.props.min !== undefined) && (num_val < this.props.min))
-            || ((this.props.max !== undefined) && (num_val > this.props.max));
+        let new_err : boolean = !Number.isFinite(num_val)
+            || (!float && !Number.isInteger(num_val))
+            || ((min !== undefined) && (num_val < min))
+            || ((max !== undefined) && (num_val > max));
 
         // If error I keep old numeric value to return (so there is always a proper value kept)
-        let new_val : number = err ? this.state.val : num_val;
-        this.setState({err: err, val: new_val, text: text});
-        this.props.callback(new_val, err);
-    }
+        let new_val : number = new_err ? val : num_val;
+        setErr(new_err);
+        setVal(new_val);
+        setText(new_text);
+        callback(new_val, new_err);
+    };
 
-    units(str: string | undefined): ReactNode | null {
-        if (str === undefined)
-            return null;
-        else if (str === "us")
-            return <InputAdornment position="end">&micro;s</InputAdornment>;
-        else if (str === "A-1")
-            return <InputAdornment position="end">
-                <span>&#8491;<sup>-1</sup></span>
-            </InputAdornment>;
-        else
-            return <InputAdornment position="end">{str}</InputAdornment>;
-    }
-
-    render() {
-        return <TextField id="frame_time" label={this.props.label} variant="outlined"
-                          sx = {this.props.sx}
-                          error={this.state.err}
-                          onChange={this.updateValue}
-                          value={this.state.text}
-                          disabled={this.props.disabled}
-                          InputProps={{
-                              inputProps: {
-                                  style: {textAlign: 'right'}
-                              },
-                              endAdornment: this.units(this.props.units)
-                          }}/>
-    }
+    return <TextField id="frame_time" label={label} variant="outlined"
+                      sx = {sx}
+                      error={err}
+                      onChange={updateValue}
+                      value={text}
+                      disabled={disabled}
+                      InputProps={{
+                          inputProps: {
+                              style: {textAlign: 'right'}
+                          },
+                          endAdornment: unitsNode(units)
+                      }}/>
 }
 
-export default NumberTextField;
\ No newline at end of file
+export default memo(NumberTextField);
diff --git a/frontend/src/components/PixelMask.tsx b/frontend/src/components/PixelMask.tsx
index 7130fabd..d10a6df8 100644
--- a/frontend/src/components/PixelMask.tsx
+++ b/frontend/src/components/PixelMask.tsx
@@ -1,4 +1,4 @@
-import React from 'react';
+import {ChangeEvent, memo, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {
@@ -16,67 +16,61 @@ type MyProps = {
     s?: pixel_mask_statistics
 };
 
-type MyState = {
-    file?: File
-};
+function PixelMask({s}: MyProps) {
+    const [file, setFile] = useState<File>();
 
-class PixelMask extends React.Component<MyProps, MyState> {
-    state: MyState = {};
-
-    handleUpload = () => {
-        if (this.state.file)
-            putConfigUserMaskTiff({ body: this.state.file });
+    const handleUpload = () => {
+        if (file)
+            putConfigUserMaskTiff({ body: file });
     };
 
-    handleFileChange = (event: React.ChangeEvent<HTMLInputElement>) => {
+    const handleFileChange = (event: ChangeEvent<HTMLInputElement>) => {
         if (event.target.files && event.target.files[0]) {
-            this.setState({file: event.target.files[0]});
+            setFile(event.target.files[0]);
         }
     };
 
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/><strong>Pixel mask</strong><br/><br/>
-            <Grid container spacing={0}>
-                <Grid item xs={1}/>
-                <Grid item xs={10}>
-                    <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
-                        <Table size="small" aria-label="simple table">
-                            <TableBody>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> User mask: </TableCell>
-                                    <TableCell align="right">{this.props.s?.user_mask ?? "N/A"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Error pixels: </TableCell>
-                                    <TableCell align="right">{this.props.s?.wrong_gain ?? "N/A"}</TableCell>
-                                </TableRow>
-                                <TableRow>
-                                    <TableCell component="th" scope="row"> Noisy pixels: </TableCell>
-                                    <TableCell align="right">{this.props.s?.too_high_pedestal_rms ?? "N/A"}</TableCell>
-                                </TableRow>
-                            </TableBody>
-                        </Table>
-                    </TableContainer>
-                </Grid>
-                <Grid item xs={1}/>
+    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
+        <br/><strong>Pixel mask</strong><br/><br/>
+        <Grid container spacing={0}>
+            <Grid item xs={1}/>
+            <Grid item xs={10}>
+                <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
+                    <Table size="small" aria-label="simple table">
+                        <TableBody>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> User mask: </TableCell>
+                                <TableCell align="right">{s?.user_mask ?? "N/A"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Error pixels: </TableCell>
+                                <TableCell align="right">{s?.wrong_gain ?? "N/A"}</TableCell>
+                            </TableRow>
+                            <TableRow>
+                                <TableCell component="th" scope="row"> Noisy pixels: </TableCell>
+                                <TableCell align="right">{s?.too_high_pedestal_rms ?? "N/A"}</TableCell>
+                            </TableRow>
+                        </TableBody>
+                    </Table>
+                </TableContainer>
             </Grid>
-            <br/>
-            <a href="/config/mask.tiff">Download pixel mask</a><br/>
-            <a href="/config/user_mask.tiff">Download user pixel mask</a><br/><br/>
-            <TextField
-                type="file"
-                inputProps={{accept: '.tiff'}}
-                onChange={this.handleFileChange}
-            /><br/><br/>
-            <Button onClick={this.handleUpload}
-                    variant="contained"
-                    disableElevation
-                    disabled={!this.state.file}
-                    color={"primary"}>Upload</Button>
-            <br/><br/>
-        </Paper>
-    }
+            <Grid item xs={1}/>
+        </Grid>
+        <br/>
+        <a href="/config/mask.tiff">Download pixel mask</a><br/>
+        <a href="/config/user_mask.tiff">Download user pixel mask</a><br/><br/>
+        <TextField
+            type="file"
+            inputProps={{accept: '.tiff'}}
+            onChange={handleFileChange}
+        /><br/><br/>
+        <Button onClick={handleUpload}
+                variant="contained"
+                disableElevation
+                disabled={!file}
+                color={"primary"}>Upload</Button>
+        <br/><br/>
+    </Paper>
 }
 
-export default PixelMask;
\ No newline at end of file
+export default memo(PixelMask);
diff --git a/frontend/src/components/PreviewImage.tsx b/frontend/src/components/PreviewImage.tsx
index 11d193bb..bb84605d 100644
--- a/frontend/src/components/PreviewImage.tsx
+++ b/frontend/src/components/PreviewImage.tsx
@@ -1,4 +1,4 @@
-import React, {Component} from 'react';
+import {ChangeEvent, memo, useEffect, useRef, useState} from 'react';
 import Paper from "@mui/material/Paper";
 import {
     Checkbox,
@@ -37,16 +37,6 @@ type MyProps = {
     max_image_number: number | undefined
 }
 
-type MyState = {
-    settings: preview_settings,
-    s: Blob | null,
-    s_url: string | null,
-    update: boolean,
-    connection_error: boolean,
-    image_id_mode: string,
-    image_id: number
-}
-
 function handleErrors(response: Response): Response {
     if (!response.ok) {
         throw Error(response.statusText);
@@ -63,197 +53,35 @@ function stringToEnum(value: string): color_scale {
     return enumValue || color_scale.INDIGO;
 }
 
-class PreviewImage extends Component<MyProps, MyState> {
-    interval: ReturnType<typeof setInterval> | undefined;
+const default_preview_settings: preview_settings = {
+    saturation: 10,
+    jpeg_quality: 90,
+    show_spots: true,
+    show_roi: false,
+    show_user_mask: false,
+    show_beam_center: true,
+    resolution_ring: 0.5,
+    scale: color_scale.INDIGO,
+    image_id: -1,
+    auto_contrast: true,
+    res_estimate: true
+};
 
-    state : MyState = {
-        s: null,
-        settings: {
-            saturation: 10,
-            jpeg_quality: 90,
-            show_spots: true,
-            show_roi: false,
-            show_user_mask: false,
-            show_beam_center: true,
-            resolution_ring: 0.5,
-            scale: color_scale.INDIGO,
-            image_id: -1,
-            auto_contrast: true,
-            res_estimate: true
-        },
-        s_url: null,
-        update: true,
-        connection_error: true,
-        image_id_mode: 'last',
-        image_id: 0
-    }
+function PreviewImage({measuring, min_image_number, max_image_number}: MyProps) {
+    const [settings, setSettings] = useState<preview_settings>(default_preview_settings);
+    const [sUrl, setSUrl] = useState<string | null>(null);
+    const [update, setUpdate] = useState(true);
+    const [connectionError, setConnectionError] = useState(true);
+    const [imageIdMode, setImageIdMode] = useState('last');
+    const [imageId, setImageId] = useState(0);
 
-    update_image_id_mode = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let image_id : number;
-        switch (event.target.value) {
-            case "last":
-                image_id = -1;
-                break;
-            case "last_indexed":
-                image_id = -2;
-                break;
-            case "select":
-                image_id = this.state.image_id;
-                break;
-            default:
-                return;
-        }
+    // Refs let the polling interval read the latest settings without being
+    // re-created on every settings change, and let cleanup revoke the live URL.
+    const sUrlRef = useRef<string | null>(null);
+    const settingsRef = useRef(settings);
+    settingsRef.current = settings;
 
-        let s : preview_settings = {...this.state.settings, image_id};
-        this.setState({settings: s, image_id_mode: event.target.value});
-        this.getValues(s);
-    }
-
-    updateToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        this.setState({
-            update: event.target.checked
-        });
-        if (event.target.checked)
-            this.getValues();
-    }
-
-    setSaturation = (event: Event, newValue: number | number[]) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            saturation: newValue as number
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    setSaturationText = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let newValue = 0;
-        if (event.target.value)
-            newValue = Number(event.target.value);
-        if (newValue < 0)
-            newValue = 0;
-
-        let s : preview_settings = {
-            ...this.state.settings,
-            saturation: newValue as number
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    };
-
-    showSpotsToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            show_spots: event.target.checked
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    resEstToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s: preview_settings = {
-            ...this.state.settings,
-            res_estimate: event.target.checked
-        }
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    autoContrastToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s: preview_settings = {
-            ...this.state.settings,
-            auto_contrast: event.target.checked
-        }
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    showROIToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            show_roi: event.target.checked
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    showBeamCenterToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            show_beam_center: event.target.checked
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    setResolutionRing = (event: Event, newValue: number | number[]) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            resolution_ring: newValue as number
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    setResolutionRingText = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let newValue = 0.5;
-        if (event.target.value)
-            newValue = Number(event.target.value);
-        if (newValue < 0.5)
-            newValue = 0.5;
-        if (newValue > 50.0)
-            newValue = 50.0;
-
-        let s : preview_settings = {
-            ...this.state.settings,
-            resolution_ring: newValue as number
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    };
-
-    setImageID = (event: Event, newValue: number | number[]) => {
-        if (this.state.image_id_mode == "select") {
-            let s : preview_settings = {
-                ...this.state.settings,
-                image_id: newValue as number
-            };
-            this.setState({settings: s, image_id: newValue as number});
-            this.getValues(s);
-        } else {
-            this.setState({image_id: newValue as number});
-        }
-    }
-
-    setImageIdText = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let newValue = 0;
-        if (event.target.value)
-            newValue = Number(event.target.value);
-        if (newValue < 0)
-            newValue = 0;
-
-        if (this.state.image_id_mode == "select") {
-            let s : preview_settings = {
-                ...this.state.settings,
-                image_id: newValue as number
-            };
-            this.setState({settings: s, image_id: newValue as number});
-            this.getValues(s);
-        } else {
-            this.setState({image_id: newValue as number});
-        }
-    };
-
-    showUserMaskToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
-        let s : preview_settings = {
-            ...this.state.settings,
-            show_user_mask: event.target.checked
-        };
-        this.setState({settings: s});
-        this.getValues(s);
-    }
-
-    getImage(s: preview_settings,) {
+    const getImage = (s: preview_settings) => {
         let url =  `/image_buffer/image.jpeg`;
         url += `?id=${s.image_id}`;
         if (!s.auto_contrast)
@@ -273,190 +101,321 @@ class PreviewImage extends Component<MyProps, MyState> {
             .then(handleErrors)
             .then(data => data.blob())
             .then(data => {
-                const url = URL.createObjectURL(data);
-                let tmp = this.state.s_url;
-                this.setState({s: data, s_url: url, connection_error: false});
+                const objectUrl = URL.createObjectURL(data);
+                const tmp = sUrlRef.current;
+                sUrlRef.current = objectUrl;
+                setSUrl(objectUrl);
+                setConnectionError(false);
                 if (tmp !== null)
                     URL.revokeObjectURL(tmp);
             }).catch(error => {
-            this.setState({connection_error: true});
+            setConnectionError(true);
         })
-    }
+    };
 
-    getValues(s: preview_settings = this.state.settings) {
-        this.getImage(s);
-    }
+    const getValues = (s: preview_settings = settings) => {
+        getImage(s);
+    };
 
-    componentDidMount() {
-        this.getValues();
-        this.interval = setInterval(() => {
-            if (this.state.update && this.props.measuring)
-                this.getValues()
+    // Initial fetch + revoke the live object URL on unmount.
+    useEffect(() => {
+        getImage(settingsRef.current);
+        return () => {
+            if (sUrlRef.current !== null)
+                URL.revokeObjectURL(sUrlRef.current);
+        };
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, []);
+
+    // Auto-update poll; reads the latest settings via ref.
+    useEffect(() => {
+        const id = setInterval(() => {
+            if (update && measuring)
+                getImage(settingsRef.current);
         }, 2000);
-    }
+        return () => clearInterval(id);
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [update, measuring]);
 
-    componentWillUnmount() {
-        clearInterval(this.interval);
-        let tmp = this.state.s_url;
-        if (tmp !== null)
-            URL.revokeObjectURL(tmp);
-    }
+    const update_image_id_mode = (event: ChangeEvent<HTMLInputElement>) => {
+        let image_id : number;
+        switch (event.target.value) {
+            case "last":
+                image_id = -1;
+                break;
+            case "last_indexed":
+                image_id = -2;
+                break;
+            case "select":
+                image_id = imageId;
+                break;
+            default:
+                return;
+        }
 
-    render() {
-        return <div>
+        let s : preview_settings = {...settings, image_id};
+        setSettings(s);
+        setImageIdMode(event.target.value);
+        getValues(s);
+    };
 
-            <Grid container spacing={3}>
+    const updateToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        setUpdate(event.target.checked);
+        if (event.target.checked)
+            getValues();
+    };
 
-                <Grid item xs={8}>
-                    <Paper sx={{height: 1250, minWidth: 1200} }>
-                        {(!this.state.connection_error && (this.state.s_url !== null)) ?
-                            <Stack
-                                direction="row"
-                                justifyContent="center"
-                                alignItems="center"
-                            >
-                                <TransformWrapper maxScale={32}>
-                                    <TransformComponent>
-                                        <img src={this.state.s_url} alt="Live preview"
-                                             style={{maxWidth: "100%", maxHeight: 900}}/>
-                                    </TransformComponent>
-                                </TransformWrapper>
-                            </Stack> : <div>Preview image not available</div>
-                        }
-                    </Paper>
-                </Grid>
-                <Grid item xs={4}>
-                    <Paper sx={{width: "100%", height: "100%"}}>
-                        <br/>
-                        <Stack spacing={2} direction="column" sx={{
-                            justifyContent: "center",
-                            alignItems: "center"}} alignItems="center">
-                            <div><strong>Preview image selection </strong></div>
-                            <FormControl sx={{width:"83%"}}>
-                                <RadioGroup value={this.state.image_id_mode} onChange={this.update_image_id_mode}>
-                                    <FormControlLabel value="last" control={<Radio />} label="Last image" />
-                                    <FormControlLabel value="last_indexed" control={<Radio />} label="Last indexed image" />
-                                    <FormControlLabel value="select" control={<Radio />} label="Choose image" />
-                                </RadioGroup>
-                            </FormControl>
-                            <Stack spacing={3} direction="row" sx={{width:"83%"}}>
-                                <Slider
-                                    value={this.state.image_id}
-                                    min={this.props.min_image_number ?? 0}
-                                    max={this.props.max_image_number ?? 0}
-                                    step={1}
-                                    onChange={this.setImageID}
-                                    disabled={this.state.image_id_mode !== "select"}
-                                    valueLabelDisplay="auto"/>
-                                <Input
-                                    value={this.state.image_id}
-                                    onChange={this.setImageIdText}
-                                    disabled={this.state.image_id_mode !== "select"}
-                                    inputProps={{
-                                        step: 1,
-                                        min: this.props.min_image_number ?? 0,
-                                        max: this.props.max_image_number ?? 0,
-                                        type: 'number',
-                                    }}
-                                />
-                            </Stack>
-                            <div><strong>Preview image settings </strong></div>
-                            <FormControl sx = {{width: "83%"}}>
+    const setSaturation = (event: Event, newValue: number | number[]) => {
+        let s : preview_settings = {...settings, saturation: newValue as number};
+        setSettings(s);
+        getValues(s);
+    };
 
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.update} onChange={this.updateToggle} name="Update"/>
-                                } label="Auto-update image"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.auto_contrast} onChange={this.autoContrastToggle} name="Auto-contrast"/>
-                                } label="Auto-contrast"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.show_spots} onChange={this.showSpotsToggle} name="Show spots"/>
-                                } label="Show spots"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.show_roi} onChange={this.showROIToggle} name="Show ROI"/>
-                                } label="Show ROI"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.res_estimate} onChange={this.resEstToggle} name="Show resolution estimation (auto ring)"/>
-                                } label="Show resolution estimate (auto ring)"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.show_beam_center} onChange={this.showBeamCenterToggle} name="Show beam center"/>
-                                } label="Show beam center"/>
-                                <FormControlLabel control={
-                                    <Checkbox checked={this.state.settings.show_user_mask} onChange={this.showUserMaskToggle} name="Show user mask"/>
-                                } label="Show user mask"/>
-                            </FormControl>
-                            <FormControl sx = {{width: "83%"}}>
-                                <InputLabel id="color-map">Color map</InputLabel>
-                                <Select
-                                    value={this.state.settings.scale}
-                                    variant="outlined"
-                                    label="Color map"
-                                    onChange={(event) => {
-                                        let s : preview_settings = {
-                                            ...this.state.settings,
-                                            scale: stringToEnum(event.target.value)
-                                        };
-                                        this.setState({settings: s});
-                                        this.getValues(s);
-                                    }}
-                                    fullWidth
-                                >
-                                    <MenuItem value={color_scale.INDIGO}>Indigo/white</MenuItem>
-                                    <MenuItem value={color_scale.HEAT}>Heat</MenuItem>
-                                    <MenuItem value={color_scale.VIRIDIS}>Viridis</MenuItem>
-                                    <MenuItem value={color_scale.MAGMA}>Magma</MenuItem>
-                                    <MenuItem value={color_scale.INFERNO}>Inferno</MenuItem>
-                                    <MenuItem value={color_scale.BW}>Black/white</MenuItem>
-                                    <MenuItem value={color_scale.WB}>White/black</MenuItem>
-                                    <MenuItem value={color_scale.GREEN}>Green</MenuItem>
-                                </Select>
-                            </FormControl>
-                            <Stack spacing={3} direction="row" sx={{width:"83%"}}>
-                                <Slider value={Number(this.state.settings.saturation)} min={1} max={200}
-                                        onChange={this.setSaturation}
-                                        disabled={this.state.settings.auto_contrast}
-                                        valueLabelDisplay="auto"/>
+    const setSaturationText = (event: ChangeEvent<HTMLInputElement>) => {
+        let newValue = 0;
+        if (event.target.value)
+            newValue = Number(event.target.value);
+        if (newValue < 0)
+            newValue = 0;
 
-                                <Input
-                                    value={this.state.settings.saturation}
-                                    onChange={this.setSaturationText}
-                                    disabled={this.state.settings.auto_contrast}
-                                    inputProps={{
-                                        step: 1,
-                                        min: 0,
-                                        max: 200,
-                                        type: 'number',
-                                    }}
-                                />
-                            </Stack><br/>Saturation level
+        let s : preview_settings = {...settings, saturation: newValue as number};
+        setSettings(s);
+        getValues(s);
+    };
 
-                            <Stack spacing={3} direction="row" sx={{width:"83%"}}>
-                            <Slider
-                                    value={(this.state.settings.resolution_ring === undefined) ? 0.5 : Number(this.state.settings.resolution_ring)}
-                                    min={0.5} max={10.0} step={0.1}
-                                    onChange={this.setResolutionRing} valueLabelDisplay="auto"
-                                    disabled={this.state.settings.res_estimate}/>
-                                <Input
-                                    value={this.state.settings.resolution_ring}
-                                    disabled={this.state.settings.res_estimate}
-                                    onChange={this.setResolutionRingText}
-                                    endAdornment="&nbsp;&nbsp;Å"
-                                    inputProps={{
-                                        step: 0.1,
-                                        min: 0.5,
-                                        max: 50.0,
-                                        type: 'number',
-                                    }}
-                                />
-                            </Stack>
-                            <br/>Resolution Ring
-                        </Stack>
-                    </Paper>
-                </Grid>
+    const showSpotsToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s : preview_settings = {...settings, show_spots: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const resEstToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s: preview_settings = {...settings, res_estimate: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const autoContrastToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s: preview_settings = {...settings, auto_contrast: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const showROIToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s : preview_settings = {...settings, show_roi: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const showBeamCenterToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s : preview_settings = {...settings, show_beam_center: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const setResolutionRing = (event: Event, newValue: number | number[]) => {
+        let s : preview_settings = {...settings, resolution_ring: newValue as number};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const setResolutionRingText = (event: ChangeEvent<HTMLInputElement>) => {
+        let newValue = 0.5;
+        if (event.target.value)
+            newValue = Number(event.target.value);
+        if (newValue < 0.5)
+            newValue = 0.5;
+        if (newValue > 50.0)
+            newValue = 50.0;
+
+        let s : preview_settings = {...settings, resolution_ring: newValue as number};
+        setSettings(s);
+        getValues(s);
+    };
+
+    const setImageIDSlider = (event: Event, newValue: number | number[]) => {
+        if (imageIdMode == "select") {
+            let s : preview_settings = {...settings, image_id: newValue as number};
+            setSettings(s);
+            setImageId(newValue as number);
+            getValues(s);
+        } else {
+            setImageId(newValue as number);
+        }
+    };
+
+    const setImageIdText = (event: ChangeEvent<HTMLInputElement>) => {
+        let newValue = 0;
+        if (event.target.value)
+            newValue = Number(event.target.value);
+        if (newValue < 0)
+            newValue = 0;
+
+        if (imageIdMode == "select") {
+            let s : preview_settings = {...settings, image_id: newValue as number};
+            setSettings(s);
+            setImageId(newValue as number);
+            getValues(s);
+        } else {
+            setImageId(newValue as number);
+        }
+    };
+
+    const showUserMaskToggle = (event: ChangeEvent<HTMLInputElement>) => {
+        let s : preview_settings = {...settings, show_user_mask: event.target.checked};
+        setSettings(s);
+        getValues(s);
+    };
+
+    return <div>
+
+        <Grid container spacing={3}>
+
+            <Grid item xs={8}>
+                <Paper sx={{height: 1250, minWidth: 1200} }>
+                    {(!connectionError && (sUrl !== null)) ?
+                        <Stack
+                            direction="row"
+                            justifyContent="center"
+                            alignItems="center"
+                        >
+                            <TransformWrapper maxScale={32}>
+                                <TransformComponent>
+                                    <img src={sUrl} alt="Live preview"
+                                         style={{maxWidth: "100%", maxHeight: 900}}/>
+                                </TransformComponent>
+                            </TransformWrapper>
+                        </Stack> : <div>Preview image not available</div>
+                    }
+                </Paper>
             </Grid>
-        </div>
+            <Grid item xs={4}>
+                <Paper sx={{width: "100%", height: "100%"}}>
+                    <br/>
+                    <Stack spacing={2} direction="column" sx={{
+                        justifyContent: "center",
+                        alignItems: "center"}} alignItems="center">
+                        <div><strong>Preview image selection </strong></div>
+                        <FormControl sx={{width:"83%"}}>
+                            <RadioGroup value={imageIdMode} onChange={update_image_id_mode}>
+                                <FormControlLabel value="last" control={<Radio />} label="Last image" />
+                                <FormControlLabel value="last_indexed" control={<Radio />} label="Last indexed image" />
+                                <FormControlLabel value="select" control={<Radio />} label="Choose image" />
+                            </RadioGroup>
+                        </FormControl>
+                        <Stack spacing={3} direction="row" sx={{width:"83%"}}>
+                            <Slider
+                                value={imageId}
+                                min={min_image_number ?? 0}
+                                max={max_image_number ?? 0}
+                                step={1}
+                                onChange={setImageIDSlider}
+                                disabled={imageIdMode !== "select"}
+                                valueLabelDisplay="auto"/>
+                            <Input
+                                value={imageId}
+                                onChange={setImageIdText}
+                                disabled={imageIdMode !== "select"}
+                                inputProps={{
+                                    step: 1,
+                                    min: min_image_number ?? 0,
+                                    max: max_image_number ?? 0,
+                                    type: 'number',
+                                }}
+                            />
+                        </Stack>
+                        <div><strong>Preview image settings </strong></div>
+                        <FormControl sx = {{width: "83%"}}>
 
-    }
+                            <FormControlLabel control={
+                                <Checkbox checked={update} onChange={updateToggle} name="Update"/>
+                            } label="Auto-update image"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.auto_contrast} onChange={autoContrastToggle} name="Auto-contrast"/>
+                            } label="Auto-contrast"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.show_spots} onChange={showSpotsToggle} name="Show spots"/>
+                            } label="Show spots"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.show_roi} onChange={showROIToggle} name="Show ROI"/>
+                            } label="Show ROI"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.res_estimate} onChange={resEstToggle} name="Show resolution estimation (auto ring)"/>
+                            } label="Show resolution estimate (auto ring)"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.show_beam_center} onChange={showBeamCenterToggle} name="Show beam center"/>
+                            } label="Show beam center"/>
+                            <FormControlLabel control={
+                                <Checkbox checked={settings.show_user_mask} onChange={showUserMaskToggle} name="Show user mask"/>
+                            } label="Show user mask"/>
+                        </FormControl>
+                        <FormControl sx = {{width: "83%"}}>
+                            <InputLabel id="color-map">Color map</InputLabel>
+                            <Select
+                                value={settings.scale}
+                                variant="outlined"
+                                label="Color map"
+                                onChange={(event) => {
+                                    let s : preview_settings = {...settings, scale: stringToEnum(event.target.value)};
+                                    setSettings(s);
+                                    getValues(s);
+                                }}
+                                fullWidth
+                            >
+                                <MenuItem value={color_scale.INDIGO}>Indigo/white</MenuItem>
+                                <MenuItem value={color_scale.HEAT}>Heat</MenuItem>
+                                <MenuItem value={color_scale.VIRIDIS}>Viridis</MenuItem>
+                                <MenuItem value={color_scale.MAGMA}>Magma</MenuItem>
+                                <MenuItem value={color_scale.INFERNO}>Inferno</MenuItem>
+                                <MenuItem value={color_scale.BW}>Black/white</MenuItem>
+                                <MenuItem value={color_scale.WB}>White/black</MenuItem>
+                                <MenuItem value={color_scale.GREEN}>Green</MenuItem>
+                            </Select>
+                        </FormControl>
+                        <Stack spacing={3} direction="row" sx={{width:"83%"}}>
+                            <Slider value={Number(settings.saturation)} min={1} max={200}
+                                    onChange={setSaturation}
+                                    disabled={settings.auto_contrast}
+                                    valueLabelDisplay="auto"/>
+
+                            <Input
+                                value={settings.saturation}
+                                onChange={setSaturationText}
+                                disabled={settings.auto_contrast}
+                                inputProps={{
+                                    step: 1,
+                                    min: 0,
+                                    max: 200,
+                                    type: 'number',
+                                }}
+                            />
+                        </Stack><br/>Saturation level
+
+                        <Stack spacing={3} direction="row" sx={{width:"83%"}}>
+                        <Slider
+                                value={(settings.resolution_ring === undefined) ? 0.5 : Number(settings.resolution_ring)}
+                                min={0.5} max={10.0} step={0.1}
+                                onChange={setResolutionRing} valueLabelDisplay="auto"
+                                disabled={settings.res_estimate}/>
+                            <Input
+                                value={settings.resolution_ring}
+                                disabled={settings.res_estimate}
+                                onChange={setResolutionRingText}
+                                endAdornment="&nbsp;&nbsp;Å"
+                                inputProps={{
+                                    step: 0.1,
+                                    min: 0.5,
+                                    max: 50.0,
+                                    type: 'number',
+                                }}
+                            />
+                        </Stack>
+                        <br/>Resolution Ring
+                    </Stack>
+                </Paper>
+            </Grid>
+        </Grid>
+    </div>
 }
 
-export default PreviewImage;
+export default memo(PreviewImage);
diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index 76c7b754..882257a2 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -1,10 +1,8 @@
-import React from 'react';
+import {memo, ReactNode, useEffect, useRef, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {
-    putConfigRoi,
-    instrument_metadata,
-    pixel_mask_statistics, roi_azimuthal,
+    roi_azimuthal,
     roi_box,
     roi_circle,
     roi_definitions
@@ -16,7 +14,6 @@ import DeleteIcon from '@mui/icons-material/DeleteOutlined';
 import ErrorIcon from '@mui/icons-material/Error';
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import _ from "lodash";
-import { ReactNode } from "react";
 
 type MyProps = {
     s?: roi_definitions
@@ -26,247 +23,214 @@ type BoxWrapper = roi_box & {id: number};
 type CircleWrapper = roi_circle & {id: number};
 type AzimWrapper = roi_azimuthal & {id: number};
 
-type MyState = {
-    last_downloaded_s: roi_definitions;
-    box: BoxWrapper[];
-    circle: CircleWrapper[];
-    azim: AzimWrapper[];
-    box_err?: string;
-    circle_err?: string;
-    azim_err?: string | ReactNode;
-};
-
 function getRandomInt(max : number) {
     return Math.floor(Math.random() * max);
 }
 
-class ROI extends React.Component<MyProps, MyState> {
-    counter: number = 0;
+function render_err(msg?: string | ReactNode) : ReactNode {
+    if (msg === undefined)
+        return <div><br/><br/></div>
+    return <div><br/><Typography color="error"><ErrorIcon color="error"/>&nbsp;{msg}</Typography><br/></div>;
+}
 
-    state : MyState = {
-        last_downloaded_s: {
-            box: {rois: []},
-            circle: {rois: []},
-            azim: {rois: []}
-        },
-        box: [],
-        circle: [],
-        azim: []
-    }
+const default_roi_definitions: roi_definitions = {
+    box: {rois: []},
+    circle: {rois: []},
+    azim: {rois: []}
+};
 
-    getValues () {
-        if (this.props.s !== undefined) {
-            let tmp: roi_definitions = this.props.s;
-            if (!_.isEqual(tmp, this.state.last_downloaded_s))
-                this.setState({
-                    circle_err: undefined,
-                    circle: (this.props.s.circle.rois === undefined) ? [] :
-                        this.props.s.circle.rois.map(
-                            (elem) : CircleWrapper => {return {id: this.counter++, ...elem}}
-                        ),
-                    box_err: undefined,
-                    box: (this.props.s.box.rois === undefined) ? [] :
-                        this.props.s.box.rois.map(
-                            (elem) : BoxWrapper => {return {id: this.counter++, ...elem}}
-                        ),
-                    azim: (this.props.s.azim.rois === undefined) ? [] :
-                        this.props.s.azim.rois.map(
-                            (elem) : AzimWrapper => {return {id: this.counter++, ...elem}}
-                        ),
-                    azim_err: undefined,
-                    last_downloaded_s: tmp
-                });
+function ROI({s: serverS}: MyProps) {
+    const counter = useRef(0);
+
+    const [lastDownloadedS, setLastDownloadedS] = useState<roi_definitions>(default_roi_definitions);
+    const [box, setBox] = useState<BoxWrapper[]>([]);
+    const [circle, setCircle] = useState<CircleWrapper[]>([]);
+    const [azim, setAzim] = useState<AzimWrapper[]>([]);
+    const [boxErr, setBoxErr] = useState<string>();
+    const [circleErr, setCircleErr] = useState<string>();
+    const [azimErr, setAzimErr] = useState<string | ReactNode>();
+
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            setCircleErr(undefined);
+            setCircle((serverS.circle.rois === undefined) ? [] :
+                serverS.circle.rois.map((elem) : CircleWrapper => ({id: counter.current++, ...elem})));
+            setBoxErr(undefined);
+            setBox((serverS.box.rois === undefined) ? [] :
+                serverS.box.rois.map((elem) : BoxWrapper => ({id: counter.current++, ...elem})));
+            setAzim((serverS.azim.rois === undefined) ? [] :
+                serverS.azim.rois.map((elem) : AzimWrapper => ({id: counter.current++, ...elem})));
+            setAzimErr(undefined);
+            setLastDownloadedS(serverS);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
-
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    checkDuplicatesBox(input : BoxWrapper[]) {
+    const checkDuplicatesBox = (input : BoxWrapper[]) => {
         let roi_names : string[] = [];
         input.map(element => roi_names.push(element.name));
-        this.state.circle.map(element => roi_names.push(element.name));
-        this.state.azim.map(element => roi_names.push(element.name));
+        circle.map(element => roi_names.push(element.name));
+        azim.map(element => roi_names.push(element.name));
         const duplicates = roi_names.filter((item, index) => roi_names.indexOf(item) !== index);
         return (duplicates.length !== 0);
-    }
+    };
 
-    checkDuplicatesCircle(input : CircleWrapper[]) {
+    const checkDuplicatesCircle = (input : CircleWrapper[]) => {
         let roi_names : string[] = [];
         input.map(element => roi_names.push(element.name));
-        this.state.box.map(element => roi_names.push(element.name));
-        this.state.azim.map(element => roi_names.push(element.name));
+        box.map(element => roi_names.push(element.name));
+        azim.map(element => roi_names.push(element.name));
         const duplicates = roi_names.filter((item, index) => roi_names.indexOf(item) !== index);
         return (duplicates.length !== 0);
-    }
+    };
 
-    checkDuplicatesAzim(input : AzimWrapper[]) {
+    const checkDuplicatesAzim = (input : AzimWrapper[]) => {
         let roi_names : string[] = [];
         input.map(element => roi_names.push(element.name));
-        this.state.box?.map(element => roi_names.push(element.name));
-        this.state.circle.map(element => roi_names.push(element.name));
+        box?.map(element => roi_names.push(element.name));
+        circle.map(element => roi_names.push(element.name));
         const duplicates = roi_names.filter((item, index) => roi_names.indexOf(item) !== index);
         return (duplicates.length !== 0);
-    }
+    };
 
-    validateBoxInteger(input: BoxWrapper[]) {
-        return input.every((x) : boolean =>
+    const validateBoxInteger = (input: BoxWrapper[]) =>
+        input.every((x) : boolean =>
             Number.isInteger(x.min_x_pxl) && Number.isInteger(x.max_x_pxl) &&
             Number.isInteger(x.min_y_pxl) && Number.isInteger(x.max_y_pxl));
-    }
 
-    validateBoxBounds(input: BoxWrapper[]) {
-        return input.every((x) : boolean =>
+    const validateBoxBounds = (input: BoxWrapper[]) =>
+        input.every((x) : boolean =>
             (x.min_x_pxl >= 0) && (x.max_x_pxl >= x.min_x_pxl) &&
             (x.min_y_pxl >= 0) && (x.max_y_pxl >= x.min_y_pxl));
-    }
 
-    validateCircleValues(input: CircleWrapper[]) {
-        return input.every((x) : boolean => x.radius_pxl >= 0);
-    }
+    const validateCircleValues = (input: CircleWrapper[]) =>
+        input.every((x) : boolean => x.radius_pxl >= 0);
 
-    validateAzimValues(input: AzimWrapper[]) {
-        return input.every((x) : boolean => x.q_min_recipA >= 0 && x.q_max_recipA > x.q_min_recipA);
-    }
+    const validateAzimValues = (input: AzimWrapper[]) =>
+        input.every((x) : boolean => x.q_min_recipA >= 0 && x.q_max_recipA > x.q_min_recipA);
 
-    validateBox (input:BoxWrapper[]) : undefined | string {
-        if (this.checkDuplicatesBox(input))
+    const validateBox = (input:BoxWrapper[]) : undefined | string => {
+        if (checkDuplicatesBox(input))
             return "Duplicate ROI names.";
-        if (!this.validateBoxInteger(input))
+        if (!validateBoxInteger(input))
             return "Box bounds are not integer values.";
-        if (!this.validateBoxBounds(input))
+        if (!validateBoxBounds(input))
             return "Box bounds are not correct (0 <= min <= max)";
         return undefined;
-    }
+    };
 
-    validateCircle (input:CircleWrapper[]) : undefined | string {
-        if (this.checkDuplicatesCircle(input))
+    const validateCircle = (input:CircleWrapper[]) : undefined | string => {
+        if (checkDuplicatesCircle(input))
             return "Duplicate ROI names.";
-        if (!this.validateCircleValues(input))
+        if (!validateCircleValues(input))
             return "Circle ROI radius must be positive.";
         return undefined;
-    }
+    };
 
-    validateAzim (input:AzimWrapper[]) : undefined | string | ReactNode {
-        if (this.checkDuplicatesAzim(input))
+    const validateAzim = (input:AzimWrapper[]) : undefined | string | ReactNode => {
+        if (checkDuplicatesAzim(input))
             return "Duplicate ROI names.";
-        if (!this.validateAzimValues(input))
+        if (!validateAzimValues(input))
             return <div>Azimuthal integration parameters must be 0 &lt; Q<sub>min</sub> &lt; Q<sub>max</sub>.</div>;
         return undefined;
-    }
+    };
 
-    uploadButton = () => { this.putValues(); }
-    downloadButton = () => { this.getValues(); }
-
-    addBoxButton = () => {
-        this.setState({
-            box: [...this.state.box,
-                {
-                    id: this.counter++,
-                    name: "roi" + getRandomInt(99999),
-                    min_x_pxl: 0,
-                    max_x_pxl: 0,
-                    min_y_pxl: 0,
-                    max_y_pxl: 0
-                }
-            ]
-        });
-    }
-
-    addCircleButton = () => {
-        this.setState({
-            circle: [
-                ...this.state.circle,
-                {
-                    id: this.counter++,
-                    name: "roi" + getRandomInt(65536),
-                    center_x_pxl: 0,
-                    center_y_pxl: 0,
-                    radius_pxl: 10
-                }
-            ]
-        });
-    }
-
-
-    addAzimButton = () => {
-        this.setState({
-            azim: [
-                ...this.state.azim,
-                {
-                    id: this.counter++,
-                    name: "roi" + getRandomInt(65536),
-                    q_min_recipA: 1,
-                    q_max_recipA: 3
-                }
-            ]
-        });
-    }
-    roiStruct = () : roi_definitions => {
-        return {
-            box: {
-                rois: this.state.box.map((elem): roi_box => elem)
-            },
-            circle: {
-                rois: this.state.circle.map((elem): roi_circle => elem)
-            },
-            azim: {
-                rois: this.state.azim.map((elem): roi_azimuthal => elem)
+    const addBoxButton = () => {
+        setBox([...box,
+            {
+                id: counter.current++,
+                name: "roi" + getRandomInt(99999),
+                min_x_pxl: 0,
+                max_x_pxl: 0,
+                min_y_pxl: 0,
+                max_y_pxl: 0
             }
+        ]);
+    };
+
+    const addCircleButton = () => {
+        setCircle([
+            ...circle,
+            {
+                id: counter.current++,
+                name: "roi" + getRandomInt(65536),
+                center_x_pxl: 0,
+                center_y_pxl: 0,
+                radius_pxl: 10
+            }
+        ]);
+    };
+
+    const addAzimButton = () => {
+        setAzim([
+            ...azim,
+            {
+                id: counter.current++,
+                name: "roi" + getRandomInt(65536),
+                q_min_recipA: 1,
+                q_max_recipA: 3
+            }
+        ]);
+    };
+
+    const roiStruct = () : roi_definitions => ({
+        box: {
+            rois: box.map((elem): roi_box => elem)
+        },
+        circle: {
+            rois: circle.map((elem): roi_circle => elem)
+        },
+        azim: {
+            rois: azim.map((elem): roi_azimuthal => elem)
         }
-    }
+    });
 
-    putValues = () => {
-        putConfigRoi({ body: this.roiStruct(), throwOnError: true }).catch(error => {} );
-    }
-
-
-
-    handleDeleteBoxROIClick = (id: GridRowModel) => () => {
-        let new_state : BoxWrapper[] = this.state.box.filter((row) => row.id !== id.id);
-        let err = this.validateBox(new_state);
-        this.setState({box_err: err, box: new_state});
+    const handleDeleteBoxROIClick = (id: GridRowModel) => () => {
+        let new_state : BoxWrapper[] = box.filter((row) => row.id !== id.id);
+        let err = validateBox(new_state);
+        setBoxErr(err);
+        setBox(new_state);
     };
 
-    handleDeleteCircleROIClick = (id: GridRowModel) => () => {
-        let new_state : CircleWrapper[] = this.state.circle.filter((row) => row.id !== id.id);
-        let err = this.validateCircle(new_state);
-        this.setState({circle_err: err, circle: new_state});
+    const handleDeleteCircleROIClick = (id: GridRowModel) => () => {
+        let new_state : CircleWrapper[] = circle.filter((row) => row.id !== id.id);
+        let err = validateCircle(new_state);
+        setCircleErr(err);
+        setCircle(new_state);
     };
 
-    handleDeleteAzimROIClick = (id: GridRowModel) => () => {
-        let new_state : AzimWrapper[] = this.state.azim.filter((row) => row.id !== id.id);
-        let err = this.validateAzim(new_state);
-        this.setState({azim_err: err, azim: new_state});
+    const handleDeleteAzimROIClick = (id: GridRowModel) => () => {
+        let new_state : AzimWrapper[] = azim.filter((row) => row.id !== id.id);
+        let err = validateAzim(new_state);
+        setAzimErr(err);
+        setAzim(new_state);
     };
 
-    processRowBoxUpdate = (newRow: BoxWrapper, oldRow: BoxWrapper) => {
-        let new_state = this.state.box.map((item) => item.id === oldRow.id ? newRow : item);
-        let err = this.validateBox(new_state);
-        this.setState({ box_err: err, box: new_state });
+    const processRowBoxUpdate = (newRow: BoxWrapper, oldRow: BoxWrapper) => {
+        let new_state = box.map((item) => item.id === oldRow.id ? newRow : item);
+        let err = validateBox(new_state);
+        setBoxErr(err);
+        setBox(new_state);
         return newRow;
     };
 
-    processRowCircleUpdate = (newRow: CircleWrapper, oldRow: CircleWrapper) => {
-        let new_state = this.state.circle.map((item) => item === oldRow ? newRow : item);
-        let err = this.validateCircle(new_state);
-        this.setState({ circle_err: err, circle: new_state });
+    const processRowCircleUpdate = (newRow: CircleWrapper, oldRow: CircleWrapper) => {
+        let new_state = circle.map((item) => item === oldRow ? newRow : item);
+        let err = validateCircle(new_state);
+        setCircleErr(err);
+        setCircle(new_state);
         return newRow;
     };
 
-    processRowAzimUpdate = (newRow: AzimWrapper, oldRow: AzimWrapper) => {
-        let new_state = this.state.azim.map((item) => item === oldRow ? newRow : item);
-        let err = this.validateAzim(new_state);
-        this.setState({ azim_err: err, azim: new_state });
+    const processRowAzimUpdate = (newRow: AzimWrapper, oldRow: AzimWrapper) => {
+        let new_state = azim.map((item) => item === oldRow ? newRow : item);
+        let err = validateAzim(new_state);
+        setAzimErr(err);
+        setAzim(new_state);
         return newRow;
     };
 
-    columns_box : GridColDef[] = [
+    const columns_box : GridColDef[] = [
         { field: 'name', type: 'string', headerName: 'Name' , editable: true, width: 200},
         { field: 'min_x_pxl', type: 'number', headerName: 'Min X', editable: true},
         { field: 'max_x_pxl', type: 'number', headerName: 'Max X', editable: true},
@@ -278,14 +242,14 @@ class ROI extends React.Component<MyProps, MyState> {
                     <GridActionsCellItem
                         icon={<DeleteIcon />}
                         label="Delete"
-                        onClick={this.handleDeleteBoxROIClick(id)}
+                        onClick={handleDeleteBoxROIClick(id)}
                         color="inherit"
                     />,
                 ];
             }}
     ];
 
-    columns_circle : GridColDef[] = [
+    const columns_circle : GridColDef[] = [
         { field: 'name', type: 'string', headerName: 'Name' , editable: true, width: 200},
         { field: 'center_x_pxl', type: 'number', headerName: 'X [pxl]', editable: true},
         { field: 'center_y_pxl', type: 'number', headerName: 'Y [pxl]', editable: true},
@@ -296,14 +260,14 @@ class ROI extends React.Component<MyProps, MyState> {
                     <GridActionsCellItem
                         icon={<DeleteIcon />}
                         label="Delete"
-                        onClick={this.handleDeleteCircleROIClick(id)}
+                        onClick={handleDeleteCircleROIClick(id)}
                         color="inherit"
                     />,
                 ];
             }}
     ];
 
-    columns_azim : GridColDef[] = [
+    const columns_azim : GridColDef[] = [
         { field: 'name', type: 'string', headerName: 'Name' , editable: true, width: 200},
         { field: 'q_min_recipA', type: 'number', editable: true,
             renderHeader: () => (<div>Q<sub>min</sub> [Å⁻¹]</div>) },
@@ -357,94 +321,85 @@ class ROI extends React.Component<MyProps, MyState> {
                     <GridActionsCellItem
                         icon={<DeleteIcon />}
                         label="Delete"
-                        onClick={this.handleDeleteAzimROIClick(id)}
+                        onClick={handleDeleteAzimROIClick(id)}
                         color="inherit"
                     />,
                 ];
             }}
     ];
 
-
-    render_err(msg?: string | ReactNode) : ReactNode {
-        if (msg === undefined)
-            return <div><br/><br/></div>
-        return <div><br/><Typography color="error"><ErrorIcon color="error"/>&nbsp;{msg}</Typography><br/></div>;
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 530, width: '100%' }}>
-            <br/>
-            <Grid container spacing={0}>
-                <Grid item xs={0.25}/>
-                <Grid item xs={3.5} >
-                    <strong>Box ROI</strong>
-                    <br/><br/><br/>
-                    <Paper sx={{height: 300, width: '100%'}} elevation={0}>
-                        <DataGrid
-                            getRowId={row => row.id}
-                            rows={this.state.box}
-                            columns={this.columns_box}
-                            editMode={"row"}
-                            processRowUpdate={this.processRowBoxUpdate}
-                        />
-                        {this.render_err(this.state.box_err)}
-                    </Paper>
-                </Grid>
-                <Grid item xs={0.5}/>
-                <Grid item xs={3.5}>
-                    <strong>Radial ROI</strong>
-                    <br/><br/><br/>
-
-                    <Paper sx={{height: 300, width: '100%'}} elevation={0}>
-                        <DataGrid
-                            getRowId={row => row.id}
-                            rows={this.state.circle}
-                            columns={this.columns_circle}
-                            editMode={"row"}
-                            processRowUpdate={this.processRowCircleUpdate}
-                        />{this.render_err(this.state.circle_err)}
-                    </Paper>
-                </Grid>
-                <Grid item xs={0.5}/>
-                <Grid item xs={3.5}>
-                    <strong>Azimuthal ROI</strong>
-                    <br/><br/><br/>
-
-                    <Paper sx={{height: 300, width: '100%'}} elevation={0}>
-                        <DataGrid
-                            getRowId={row => row.id}
-                            rows={this.state.azim}
-                            columns={this.columns_azim}
-                            editMode={"row"}
-                            processRowUpdate={this.processRowAzimUpdate}
-                        />{this.render_err(this.state.azim_err)}
-                    </Paper>
-                </Grid>
-
-                <Grid item xs={0.25}/>
-                <Grid item xs={1}/>
-                <Grid item xs={10}><br/><br/><br/>
-                    <Button color="secondary" onClick={this.addBoxButton} variant="contained"
-                            disableElevation>Add Box ROI</Button>&nbsp;&nbsp;
-                    <Button color="secondary" onClick={this.addCircleButton} variant="contained"
-                            disableElevation>Add Circle ROI</Button>&nbsp;&nbsp;
-                    <Button color="secondary" onClick={this.addAzimButton} variant="contained"
-                            disableElevation>Add Azimuthal ROI</Button>&nbsp;&nbsp;
-                    <ButtonWithSnackbar
-                        path={"/config/roi"}
-                        color={"primary"}
-                        method={"PUT"}
-                        disabled={(this.state.box_err !== undefined) || (this.state.circle_err !== undefined)}
-                        text={"Upload"}
-                        input={JSON.stringify(this.roiStruct())}
+    return <Paper style={{textAlign: 'center'}} sx={{ height: 530, width: '100%' }}>
+        <br/>
+        <Grid container spacing={0}>
+            <Grid item xs={0.25}/>
+            <Grid item xs={3.5} >
+                <strong>Box ROI</strong>
+                <br/><br/><br/>
+                <Paper sx={{height: 300, width: '100%'}} elevation={0}>
+                    <DataGrid
+                        getRowId={row => row.id}
+                        rows={box}
+                        columns={columns_box}
+                        editMode={"row"}
+                        processRowUpdate={processRowBoxUpdate}
                     />
-                    <br/><br/>
-
-                </Grid>
-                <Grid item xs={1}/>
+                    {render_err(boxErr)}
+                </Paper>
             </Grid>
-        </Paper>
-    }
+            <Grid item xs={0.5}/>
+            <Grid item xs={3.5}>
+                <strong>Radial ROI</strong>
+                <br/><br/><br/>
+
+                <Paper sx={{height: 300, width: '100%'}} elevation={0}>
+                    <DataGrid
+                        getRowId={row => row.id}
+                        rows={circle}
+                        columns={columns_circle}
+                        editMode={"row"}
+                        processRowUpdate={processRowCircleUpdate}
+                    />{render_err(circleErr)}
+                </Paper>
+            </Grid>
+            <Grid item xs={0.5}/>
+            <Grid item xs={3.5}>
+                <strong>Azimuthal ROI</strong>
+                <br/><br/><br/>
+
+                <Paper sx={{height: 300, width: '100%'}} elevation={0}>
+                    <DataGrid
+                        getRowId={row => row.id}
+                        rows={azim}
+                        columns={columns_azim}
+                        editMode={"row"}
+                        processRowUpdate={processRowAzimUpdate}
+                    />{render_err(azimErr)}
+                </Paper>
+            </Grid>
+
+            <Grid item xs={0.25}/>
+            <Grid item xs={1}/>
+            <Grid item xs={10}><br/><br/><br/>
+                <Button color="secondary" onClick={addBoxButton} variant="contained"
+                        disableElevation>Add Box ROI</Button>&nbsp;&nbsp;
+                <Button color="secondary" onClick={addCircleButton} variant="contained"
+                        disableElevation>Add Circle ROI</Button>&nbsp;&nbsp;
+                <Button color="secondary" onClick={addAzimButton} variant="contained"
+                        disableElevation>Add Azimuthal ROI</Button>&nbsp;&nbsp;
+                <ButtonWithSnackbar
+                    path={"/config/roi"}
+                    color={"primary"}
+                    method={"PUT"}
+                    disabled={(boxErr !== undefined) || (circleErr !== undefined)}
+                    text={"Upload"}
+                    input={JSON.stringify(roiStruct())}
+                />
+                <br/><br/>
+
+            </Grid>
+            <Grid item xs={1}/>
+        </Grid>
+    </Paper>
 }
 
-export default ROI;
+export default memo(ROI);
diff --git a/frontend/src/components/StatusBar.tsx b/frontend/src/components/StatusBar.tsx
index fd651bfc..79249eef 100644
--- a/frontend/src/components/StatusBar.tsx
+++ b/frontend/src/components/StatusBar.tsx
@@ -1,18 +1,15 @@
-import React, {Component} from 'react';
+import {memo, ReactNode} from 'react';
 
 import AppBar from '@mui/material/AppBar';
 import Toolbar from '@mui/material/Toolbar';
 import Typography from '@mui/material/Typography';
 import {broker_status} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
-import { ReactNode } from "react";
 
 type MyProps = {
     s?: broker_status
 }
 
-type MyState = {}
-
 function FormatNumber(x: number) : string {
     if (x === undefined)
         return "";
@@ -22,50 +19,47 @@ function FormatNumber(x: number) : string {
         return x.toFixed(1);
 }
 
-class StatusBar extends Component<MyProps, MyState> {
-
-    statusDescription() : ReactNode {
-        if (this.props.s === undefined)
+function StatusBar({s}: MyProps) {
+    const statusDescription = (): ReactNode => {
+        if (s === undefined)
             return <>Not connected</>;
         else
             return <div>
-                State: {this.props.s.state.toString()}
-                {(this.props.s.progress !== undefined) ? " (" + FormatNumber(this.props.s.progress * 100.0) + " %)" : ""}
+                State: {s.state.toString()}
+                {(s.progress !== undefined) ? " (" + FormatNumber(s.progress * 100.0) + " %)" : ""}
             </div>
-    }
+    };
 
-    render() {
-        return <AppBar>
-            <Toolbar>
-                <Typography variant="h6" style={{flexGrow: 0.5}}>
-                    PSI Jungfraujoch
-                </Typography>
+    return <AppBar>
+        <Toolbar>
+            <Typography variant="h6" style={{flexGrow: 0.5}}>
+                PSI Jungfraujoch
+            </Typography>
 
-                <Typography variant="h6" style={{flexGrow: 2.0}}>
-                    {this.statusDescription()}
-                </Typography>
+            <Typography variant="h6" style={{flexGrow: 2.0}}>
+                {statusDescription()}
+            </Typography>
 
-                <Typography variant="h6" style={{flexGrow: 2.0}}>
-                </Typography>
-                <ButtonWithSnackbar
-                    text={"Pedestal"}
-                    path={"/pedestal"}
-                    color={"secondary"}
-                    disabled={(this.props.s === undefined) || (this.props.s.state !== 'Idle')}
-                />&nbsp;&nbsp;
-                <ButtonWithSnackbar
-                    text={"Cancel"}
-                    path={"/cancel"}
-                    color={"secondary"}
-                />&nbsp;&nbsp;
-                <ButtonWithSnackbar
-                    text={"Initialize"}
-                    path={"/initialize"}
-                    color={"secondary"}
-                />
-            </Toolbar>
-        </AppBar>
-    }
+            <Typography variant="h6" style={{flexGrow: 2.0}}>
+            </Typography>
+            <ButtonWithSnackbar
+                text={"Pedestal"}
+                path={"/pedestal"}
+                color={"secondary"}
+                disabled={(s === undefined) || (s.state !== 'Idle')}
+            />&nbsp;&nbsp;
+            <ButtonWithSnackbar
+                text={"Cancel"}
+                path={"/cancel"}
+                color={"secondary"}
+            />&nbsp;&nbsp;
+            <ButtonWithSnackbar
+                text={"Initialize"}
+                path={"/initialize"}
+                color={"secondary"}
+            />
+        </Toolbar>
+    </AppBar>
 }
 
-export default StatusBar;
+export default memo(StatusBar);
diff --git a/frontend/src/components/ZeroMQPreview.tsx b/frontend/src/components/ZeroMQPreview.tsx
index 268011e7..c5cc1642 100644
--- a/frontend/src/components/ZeroMQPreview.tsx
+++ b/frontend/src/components/ZeroMQPreview.tsx
@@ -1,4 +1,4 @@
-import React from 'react';
+import {memo, useEffect, useState} from 'react';
 
 import Paper from '@mui/material/Paper';
 import {FormControlLabel, Radio, RadioGroup, Stack} from "@mui/material";
@@ -12,142 +12,108 @@ type MyProps = {
    s?: zeromq_preview_settings
 };
 
-type MyState = {
-    s: zeromq_preview_settings,
-    last_downloaded_s: zeromq_preview_settings,
-    period_err: boolean,
-    download_counter: number,
-    freq_choice: string,
-    period_ms: number
-};
-
 const default_zeromq_preview_settings : zeromq_preview_settings = {
     socket_address: "",
     enabled: true,
     period_ms: 1000
 }
 
-class ZeroMQPreview extends React.Component<MyProps, MyState> {
-    state : MyState = {
-        s: default_zeromq_preview_settings,
-        last_downloaded_s: default_zeromq_preview_settings,
-        period_err: false,
-        download_counter: 0,
-        freq_choice: "custom",
-        period_ms: default_zeromq_preview_settings.period_ms
-    }
+function ZeroMQPreview({s: serverS}: MyProps) {
+    const [s, setS] = useState<zeromq_preview_settings>(default_zeromq_preview_settings);
+    const [lastDownloadedS, setLastDownloadedS] = useState<zeromq_preview_settings>(default_zeromq_preview_settings);
+    const [periodErr, setPeriodErr] = useState(false);
+    const [downloadCounter, setDownloadCounter] = useState(0);
+    const [freqChoice, setFreqChoice] = useState("custom");
+    const [periodMs, setPeriodMs] = useState(default_zeromq_preview_settings.period_ms);
 
-    update_freq = (freq_choice: string) => {
-        switch (freq_choice) {
+    const update_freq = (choice: string) => {
+        switch (choice) {
             case "custom":
-                this.setState(prevState => ({
-                    s: {...prevState.s, enabled: true, period_ms: this.state.period_ms},
-                    freq_choice: "custom"
-                }));
+                setS(prev => ({...prev, enabled: true, period_ms: periodMs}));
+                setFreqChoice("custom");
                 break;
             case "all":
-                this.setState(prevState => ({
-                    s: {...prevState.s, enabled: true, period_ms: 0},
-                    freq_choice: "all"
-                }));
+                setS(prev => ({...prev, enabled: true, period_ms: 0}));
+                setFreqChoice("all");
                 break;
             default:
-                this.setState(prevState => ({
-                    s: {...prevState.s, enabled: false},
-                    freq_choice: "none"
-                }));
+                setS(prev => ({...prev, enabled: false}));
+                setFreqChoice("none");
                 break;
         }
-    }
+    };
 
-    getValues = () => {
-        if (this.props.s !== undefined) {
-            let format_set: zeromq_preview_settings = this.props.s;
-            if (!_.isEqual(format_set, this.state.last_downloaded_s)) {
-                let x : number = this.state.period_ms;
-                let choice : string = "none";
-                if (this.props.s.enabled) {
-                    if (this.props.s.period_ms === 0)
-                        choice = "all";
-                    else {
-                        choice = "custom";
-                        x = this.props.s.period_ms;
-                    }
+    useEffect(() => {
+        if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
+            let x : number = periodMs;
+            let choice : string = "none";
+            if (serverS.enabled) {
+                if (serverS.period_ms === 0)
+                    choice = "all";
+                else {
+                    choice = "custom";
+                    x = serverS.period_ms;
                 }
-
-                this.setState(prevState => ({
-                    s: format_set,
-                    last_downloaded_s: format_set,
-                    download_counter: prevState.download_counter + 1,
-                    period_err: false,
-                    freq_choice: choice,
-                    period_ms: x
-                }));
             }
+
+            setS(serverS);
+            setLastDownloadedS(serverS);
+            setDownloadCounter(c => c + 1);
+            setPeriodErr(false);
+            setFreqChoice(choice);
+            setPeriodMs(x);
         }
-    }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [serverS]);
 
-    componentDidMount() {
-        this.getValues();
-    }
+    const empty = () : boolean =>
+        (s.socket_address === undefined) || (s.socket_address === "");
 
-    componentDidUpdate() {
-        this.getValues();
-    }
-
-    empty() : boolean {
-        return (this.state.s.socket_address === undefined) || (this.state.s.socket_address === "");
-    }
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-            <br/>
-            <Stack spacing={3} sx={{
-                justifyContent: "center",
-                alignItems: "center",
-            }}>
-                <div><strong>ZeroMQ preview settings </strong></div>
-                    <div>
-                        {this.empty() ? "No preview available" : `ZeroMQ socket: ${this.state.s.socket_address}`}
-                    </div>
-                <FormControl>
-                    <RadioGroup
-                        value={this.state.freq_choice}
-                        onChange={(event) => {this.update_freq(event.target.value)}}
-                    >
-                        <FormControlLabel value="none" control={<Radio />} label="None" />
-                        <FormControlLabel value="all" control={<Radio />} label="All images" />
-                        <FormControlLabel value="custom" control={<Radio />} label="Frequency" />
-                    </RadioGroup>
-                </FormControl>
-                <NumberTextField
-                    default={1000}
-                    start_val={this.state.period_ms}
-                    label={"Period"}
-                    min={0}
-                    units={"ms"}
-                    counter={this.state.download_counter}
-                    callback={(val: number, err: boolean) => {
-                        this.setState(prevState => ({
-                            s: {...prevState.s, period_ms: val},
-                            period_err: err,
-                            period_ms: val
-                        }));
-                    }}
-                    disabled={this.state.freq_choice != "custom"}
-                    fullWidth/>
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/zeromq_preview"}
-                    input={JSON.stringify(this.state.s)}
-                    method={"PUT"}
-                    text={"Upload"}
-                    disabled={((this.state.freq_choice == "custom") && this.state.period_err)}
-                />
-            </Stack>
-            <br/>
-        </Paper>
-    }
+    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
+        <br/>
+        <Stack spacing={3} sx={{
+            justifyContent: "center",
+            alignItems: "center",
+        }}>
+            <div><strong>ZeroMQ preview settings </strong></div>
+                <div>
+                    {empty() ? "No preview available" : `ZeroMQ socket: ${s.socket_address}`}
+                </div>
+            <FormControl>
+                <RadioGroup
+                    value={freqChoice}
+                    onChange={(event) => {update_freq(event.target.value)}}
+                >
+                    <FormControlLabel value="none" control={<Radio />} label="None" />
+                    <FormControlLabel value="all" control={<Radio />} label="All images" />
+                    <FormControlLabel value="custom" control={<Radio />} label="Frequency" />
+                </RadioGroup>
+            </FormControl>
+            <NumberTextField
+                default={1000}
+                start_val={periodMs}
+                label={"Period"}
+                min={0}
+                units={"ms"}
+                counter={downloadCounter}
+                callback={(val: number, err: boolean) => {
+                    setS(prev => ({...prev, period_ms: val}));
+                    setPeriodErr(err);
+                    setPeriodMs(val);
+                }}
+                disabled={freqChoice != "custom"}
+                fullWidth/>
+            <ButtonWithSnackbar
+                color={"primary"}
+                path={"/config/zeromq_preview"}
+                input={JSON.stringify(s)}
+                method={"PUT"}
+                text={"Upload"}
+                disabled={((freqChoice == "custom") && periodErr)}
+            />
+        </Stack>
+        <br/>
+    </Paper>
 }
 
-export default ZeroMQPreview;
+export default memo(ZeroMQPreview);
diff --git a/frontend/src/index.tsx b/frontend/src/index.tsx
index e9a5c1ea..ced52314 100644
--- a/frontend/src/index.tsx
+++ b/frontend/src/index.tsx
@@ -1,6 +1,17 @@
 import { StrictMode } from "react";
 import { createRoot } from "react-dom/client";
+import { QueryClient, QueryClientProvider } from "@tanstack/react-query";
 import App from "./App";
+import { client } from "./client/client.gen";
+
+// Talk to the same origin that serves the frontend (was OpenAPI.BASE='').
+client.setConfig({ baseUrl: '' });
+
+const queryClient = new QueryClient({
+    defaultOptions: {
+        queries: { retry: false, refetchOnWindowFocus: false },
+    },
+});
 
 const rootElement = document.getElementById("root");
 
@@ -9,6 +20,8 @@ const root = createRoot(rootElement!);
 
 root.render(
     <StrictMode>
-        <App />
+        <QueryClientProvider client={queryClient}>
+            <App />
+        </QueryClientProvider>
     </StrictMode>
 );
-- 
2.52.0


From c000b872bbdd582599fc02182d3e1c7e0d947e9b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 21:36:50 +0200
Subject: [PATCH 094/228] jfjoch_viewer: Fix status_bar, it looks nicer now

---
 viewer/JFJochViewerStatusBar.cpp | 54 ++++++--------------------------
 viewer/JFJochViewerStatusBar.h   |  5 ---
 2 files changed, 10 insertions(+), 49 deletions(-)

diff --git a/viewer/JFJochViewerStatusBar.cpp b/viewer/JFJochViewerStatusBar.cpp
index 680f7ede..64ba1ed4 100644
--- a/viewer/JFJochViewerStatusBar.cpp
+++ b/viewer/JFJochViewerStatusBar.cpp
@@ -6,11 +6,10 @@
 #include <algorithm>
 
 JFJochViewerStatusBar::JFJochViewerStatusBar(QWidget *parent) : QStatusBar(parent) {
-    // Added left-to-right within the permanent (right-aligned) area.
-    conn_label = new QLabel(this);
-    conn_label->setFixedWidth(100);
-    conn_label->setAlignment(Qt::AlignCenter);
-    addPermanentWidget(conn_label);
+    rate_label = new QLabel(this);
+    rate_label->setFixedWidth(60);
+    rate_label->setAlignment(Qt::AlignCenter);
+    addPermanentWidget(rate_label);
 
     state_box = new QProgressBar(this);
     state_box->setFixedWidth(110);
@@ -20,16 +19,6 @@ JFJochViewerStatusBar::JFJochViewerStatusBar(QWidget *parent) : QStatusBar(paren
     state_box->setAlignment(Qt::AlignCenter);
     state_box->setFormat("");
     addPermanentWidget(state_box);
-
-    new_label = new QLabel(this);
-    new_label->setFixedWidth(70);
-    new_label->setAlignment(Qt::AlignCenter);
-    addPermanentWidget(new_label);
-
-    rate_label = new QLabel(this);
-    rate_label->setFixedWidth(60);
-    rate_label->setAlignment(Qt::AlignCenter);
-    addPermanentWidget(rate_label);
 }
 
 void JFJochViewerStatusBar::display(QString input) {
@@ -51,7 +40,7 @@ void JFJochViewerStatusBar::setBrokerStatus(BrokerStatus status) {
     if (status.progress.has_value())
         state_box->setValue(std::clamp(static_cast<int>(status.progress.value() * 1000.0f), 0, 1000));
     else
-        state_box->setValue(0);
+        state_box->setValue(1000.0);
 
     const QString chunk = (status.state == JFJochState::Error) ? "#d9534f" : "#5cb85c";
     state_box->setStyleSheet(QString(
@@ -67,44 +56,33 @@ void JFJochViewerStatusBar::setBrokerStatus(BrokerStatus status) {
 void JFJochViewerStatusBar::setHttpConnection(bool connected, QString addr) {
     if (addr.isEmpty()) {
         // No detector session at all -> blank the whole cluster (but keep the reserved space).
-        conn_label->setText("");
-        conn_label->setToolTip("");
-        conn_label->setStyleSheet("");
         state_box->setFormat("");
         state_box->setValue(0);
         state_box->setStyleSheet("");
         state_box->setToolTip("");
         rate_label->setText("");
-        new_label->setText("");
-        new_label->setStyleSheet("");
         return;
     }
 
-    conn_label->setToolTip(addr);
-    if (connected) {
-        conn_label->setText("Live");
-        conn_label->setStyleSheet("color: white; background-color: #5cb85c; border-radius: 3px;");
-    } else {
-        conn_label->setText("Disconnected");
-        conn_label->setStyleSheet("color: white; background-color: #d9534f; border-radius: 3px;");
+    if (!connected)  {
         // Connection lost: clear live readouts but keep the badge so the user sees why.
-        state_box->setFormat("");
+        state_box->setStyleSheet(QString(
+       "QProgressBar { border: 1px solid #aaa; border-radius: 2px; background: transparent; }"
+       "QProgressBar::chunk { background-color: #888888; }"));
+        state_box->setFormat("Disconnected");
         state_box->setValue(0);
         state_box->setToolTip("");
         rate_label->setText("");
-        new_label->setText("");
     }
 }
 
 void JFJochViewerStatusBar::setAutoloadMode(JFJochImageReadingWorker::AutoloadMode mode) {
     autoload_mode = mode;
-    UpdateNewLabel();
 }
 
 void JFJochViewerStatusBar::setImageNumber(int64_t in_total_images, int64_t in_current_image) {
     total_images = in_total_images;
     current_image = in_current_image;
-    UpdateNewLabel();
 }
 
 void JFJochViewerStatusBar::setLiveRate(double hz) {
@@ -114,15 +92,3 @@ void JFJochViewerStatusBar::setLiveRate(double hz) {
         rate_label->setText("");
 }
 
-void JFJochViewerStatusBar::UpdateNewLabel() {
-    if (autoload_mode == JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset) {
-        const int64_t n = total_images - 1 - current_image;
-        if (n > 0) {
-            new_label->setText(QString("+%1 new").arg(n));
-            new_label->setStyleSheet("color: #f0ad4e; font-weight: bold;");
-            return;
-        }
-    }
-    new_label->setText("");
-    new_label->setStyleSheet("");
-}
diff --git a/viewer/JFJochViewerStatusBar.h b/viewer/JFJochViewerStatusBar.h
index 7592f523..528050bd 100644
--- a/viewer/JFJochViewerStatusBar.h
+++ b/viewer/JFJochViewerStatusBar.h
@@ -15,17 +15,12 @@ class JFJochViewerStatusBar : public QStatusBar {
 
     // Permanent (right-side) widgets. These are created once and never shown/hidden or resized,
     // so the status bar never reflows; when not applicable they are just blanked in place.
-    QLabel *conn_label;       // "Live" / "Disconnected" (host:port in tooltip)
     QProgressBar *state_box;  // Jungfraujoch state text, progress drawn as the bar fill
-    QLabel *new_label;        // "+N new" when following the dataset with a frozen image
     QLabel *rate_label;       // effective live update rate
 
     JFJochImageReadingWorker::AutoloadMode autoload_mode = JFJochImageReadingWorker::AutoloadMode::None;
     int64_t total_images = 0;
     int64_t current_image = 0;
-
-    void UpdateNewLabel();
-
 public:
     explicit JFJochViewerStatusBar(QWidget *parent = nullptr);
 
-- 
2.52.0


From 59da040e30659a065918ca1e066caa23ee46bb1e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 22:04:55 +0200
Subject: [PATCH 095/228] frontend: shared SettingsPanel + typed upload with
 error display

Generalize the expert-panel boilerplate (container + title + widgets +
upload button) and surface real upload errors via hey-api.

- SettingsPanel: consistent padded Paper + Typography title (one place to
  size it) + optional Upload button + result snackbar; PanelTitle and
  UploadSnackbarView exported for panels with bespoke layouts (DetectorSettings
  grid, ROI)
- useUpload(mutation): wraps a generated hey-api mutation, shows the server's
  error message on failure (errorMessage handles 400 string / 500 error_message)
- "unsaved changes" dot on panel titles, derived from the existing
  last-downloaded snapshot (dirty = !isEqual(value, lastDownloaded))
- fix PixelMask: TIFF upload was swallowing errors; now shows them
- config panels (FileWriter, ImageFormat, Detector, AzInt, DarkMask, Indexing,
  Instrument, ZeroMQ, ROI, DetectorSelection) upload through the typed SDK
  instead of ButtonWithSnackbar's raw fetch; status/display panels share the
  same shell for consistent spacing
- ButtonWithSnackbar now only powers bodyless action buttons (pedestal/cancel/
  initialize, start/trigger, deactivate)

Build (tsc + vite) passes; dev server transforms all modules.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/components/AzIntSettings.tsx     | 40 +++-----
 frontend/src/components/DarkMaskSettings.tsx  | 32 ++-----
 .../src/components/DataProcessingSettings.tsx |  9 +-
 frontend/src/components/DetectorSelection.tsx | 35 +++----
 frontend/src/components/DetectorSettings.tsx  | 38 ++++----
 frontend/src/components/DetectorStatus.tsx    | 18 ++--
 .../src/components/FileWriterSettings.tsx     | 32 +++----
 .../src/components/ImageFormatSettings.tsx    | 32 +++----
 frontend/src/components/ImagePusherStatus.tsx | 12 +--
 frontend/src/components/IndexingSettings.tsx  | 32 +++----
 .../src/components/InstrumentMetadata.tsx     | 32 ++-----
 .../src/components/MeasurementStatistics.tsx  | 18 ++--
 frontend/src/components/PixelMask.tsx         | 91 +++++++++----------
 frontend/src/components/ROI.tsx               | 17 ++--
 frontend/src/components/SettingsPanel.tsx     | 81 +++++++++++++++++
 frontend/src/components/ZeroMQPreview.tsx     | 35 +++----
 frontend/src/components/useUpload.ts          | 41 +++++++++
 17 files changed, 311 insertions(+), 284 deletions(-)
 create mode 100644 frontend/src/components/SettingsPanel.tsx
 create mode 100644 frontend/src/components/useUpload.ts

diff --git a/frontend/src/components/AzIntSettings.tsx b/frontend/src/components/AzIntSettings.tsx
index af00ab69..83a29157 100644
--- a/frontend/src/components/AzIntSettings.tsx
+++ b/frontend/src/components/AzIntSettings.tsx
@@ -1,12 +1,13 @@
 import {ChangeEvent, memo, useEffect, useState} from 'react';
 
-import Paper from '@mui/material/Paper';
 import {FormControlLabel, Checkbox, Stack, Radio, RadioGroup, Typography} from "@mui/material";
 import NumberTextField from "./NumberTextField";
 import {azim_int_settings} from "../client";
+import {putConfigAzimIntMutation} from "../client/@tanstack/react-query.gen";
 import _ from "lodash";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import FormControl from "@mui/material/FormControl";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: azim_int_settings
@@ -29,6 +30,7 @@ function AzIntSettings({s: serverS}: MyProps) {
     const [lowQError, setLowQError] = useState(false);
     const [highQError, setHighQError] = useState(false);
     const [qSpacingError, setQSpacingError] = useState(false);
+    const { submit, pending, snackbar } = useUpload(putConfigAzimIntMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -39,15 +41,13 @@ function AzIntSettings({s: serverS}: MyProps) {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [serverS]);
 
-    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-            marginLeft: '8%',
-            marginRight: '8%',
-        }}>
-            <div><strong>Azimuthal integration settings </strong></div>
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
+    return (
+        <SettingsPanel title="Azimuthal integration" dirty={dirty}
+                       onUpload={() => submit(s)}
+                       uploadDisabled={pending || (s.high_q_recipA <= s.low_q_recipA) || highQError || lowQError || qSpacingError}
+                       snackbar={snackbar}>
             <Stack spacing={2} direction="row">
                 <NumberTextField
                     default={1.0}
@@ -139,22 +139,8 @@ function AzIntSettings({s: serverS}: MyProps) {
                 </RadioGroup>
             </FormControl>
 
-            <ButtonWithSnackbar
-                color={"primary"}
-                path={"/config/azim_int"}
-                input={JSON.stringify(s)}
-                method={"PUT"}
-                text={"Upload"}
-                disabled={
-                    (s.high_q_recipA <= s.low_q_recipA)
-                    || highQError
-                    || lowQError
-                    || qSpacingError
-                }
-            />
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(AzIntSettings);
diff --git a/frontend/src/components/DarkMaskSettings.tsx b/frontend/src/components/DarkMaskSettings.tsx
index 9dac096c..5e59c1f4 100644
--- a/frontend/src/components/DarkMaskSettings.tsx
+++ b/frontend/src/components/DarkMaskSettings.tsx
@@ -1,10 +1,11 @@
 import {memo, useEffect, useState} from 'react';
-import Paper from '@mui/material/Paper';
 import {Checkbox, FormControlLabel, Stack} from '@mui/material';
 import _ from 'lodash';
 import NumberTextField from './NumberTextField';
-import ButtonWithSnackbar from './ButtonWithSnackbar';
 import { dark_mask_settings } from '../client';
+import { putConfigDarkMaskMutation } from '../client/@tanstack/react-query.gen';
+import SettingsPanel from './SettingsPanel';
+import { useUpload } from './useUpload';
 
 type MyProps = {
     s?: dark_mask_settings;
@@ -28,6 +29,7 @@ function DarkMaskSettings({s: serverS}: MyProps) {
     const [numberOfFramesOld, setNumberOfFramesOld] = useState(1000);
     const [maxPixelCountErr, setMaxPixelCountErr] = useState(false);
     const [maxFramesWithSignalErr, setMaxFramesWithSignalErr] = useState(false);
+    const { submit, pending, snackbar } = useUpload(putConfigDarkMaskMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -51,17 +53,11 @@ function DarkMaskSettings({s: serverS}: MyProps) {
         maxPixelCountErr ||
         maxFramesWithSignalErr;
 
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
     return (
-        <Paper style={{ textAlign: 'center' }} sx={{ width: '100%' }}>
-            <br />
-            <Stack
-                spacing={3}
-                sx={{
-                    justifyContent: 'center',
-                    alignItems: 'center',
-                }}
-            >
-                <strong>Dark data collection settings for mask</strong>
+        <SettingsPanel title="Dark mask" dirty={dirty}
+                       onUpload={() => submit(s)} uploadDisabled={pending || hasError()} snackbar={snackbar}>
                 <div>(DECTRIS detectors only)</div>
 
                 <FormControlLabel
@@ -161,17 +157,7 @@ function DarkMaskSettings({s: serverS}: MyProps) {
                         }}
                     />
                 </Stack>
-                <ButtonWithSnackbar
-                    path={'/config/dark_mask'}
-                    color={'primary'}
-                    method={'PUT'}
-                    disabled={hasError()}
-                    text={'Upload'}
-                    input={JSON.stringify(s)}
-                />
-            </Stack>
-            <br />
-        </Paper>
+        </SettingsPanel>
     );
 }
 
diff --git a/frontend/src/components/DataProcessingSettings.tsx b/frontend/src/components/DataProcessingSettings.tsx
index 9a73519f..47a6183b 100644
--- a/frontend/src/components/DataProcessingSettings.tsx
+++ b/frontend/src/components/DataProcessingSettings.tsx
@@ -1,8 +1,8 @@
 import {ChangeEvent, memo, useEffect, useState} from 'react';
 
-import Paper from '@mui/material/Paper';
 import {Grid, Slider, Switch, Typography} from "@mui/material";
 import {putConfigSpotFinding, spot_finding_settings} from "../client";
+import SettingsPanel from "./SettingsPanel";
 import _ from "lodash";
 
 type MyProps = {
@@ -91,12 +91,12 @@ function DataProcessingSettings({s: serverS, update}: MyProps) {
         apply({...s, high_res_gap_Q_recipA: v});
     };
 
-    return <Paper style={{textAlign: 'center'}} sx={{ height: 800, width: '100%' }}>
+    return (
+        <SettingsPanel title="Spot finding parameters" sx={{ height: 800 }}>
                 <Grid container spacing={0}>
 
                     <Grid item xs={1}/>
                     <Grid item xs={10}>
-                        <br/><strong>Spot finding parameters</strong><br/><br/>
                         <Switch onChange={enableSpotFindingToggle} checked={s.enable}/>
                         Spot finding
                         <br/><br/>
@@ -183,7 +183,8 @@ function DataProcessingSettings({s: serverS, update}: MyProps) {
                     </Grid>
                     <Grid item xs={1}/>
                 </Grid>
-            </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(DataProcessingSettings);
diff --git a/frontend/src/components/DetectorSelection.tsx b/frontend/src/components/DetectorSelection.tsx
index 9d7426fd..f3a771ab 100644
--- a/frontend/src/components/DetectorSelection.tsx
+++ b/frontend/src/components/DetectorSelection.tsx
@@ -1,13 +1,15 @@
 import {memo, ReactNode, useEffect, useState} from 'react';
 
 import Select, { SelectChangeEvent } from '@mui/material/Select';
-import {Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
+import {Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
 import Paper from "@mui/material/Paper";
 import InputLabel from '@mui/material/InputLabel';
 import MenuItem from '@mui/material/MenuItem';
 import FormControl from '@mui/material/FormControl';
 import {detector_list, detector_list_element} from "../client";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import {putConfigSelectDetectorMutation} from "../client/@tanstack/react-query.gen";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: detector_list
@@ -39,6 +41,7 @@ const default_detector_element: detector_list_element = {
 
 function DetectorSelection({s}: MyProps) {
     const [choice, setChoice] = useState("0");
+    const { submit, pending, snackbar } = useUpload(putConfigSelectDetectorMutation());
 
     useEffect(() => {
         if (s !== undefined)
@@ -105,13 +108,14 @@ function DetectorSelection({s}: MyProps) {
         return v;
     };
 
-    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center"
-        }}>
-            <strong>Detector selection </strong>
+    const dirty = s !== undefined && Number(choice) !== s.current_id;
+
+    return (
+        <SettingsPanel title="Detector selection" dirty={dirty}
+                       uploadText="Select detector"
+                       onUpload={() => submit({ id: Number(choice) })}
+                       uploadDisabled={pending || s === undefined}
+                       snackbar={snackbar}>
 
             {detector_info()}
 
@@ -128,17 +132,8 @@ function DetectorSelection({s}: MyProps) {
                     {detector_options().map(d => (<MenuItem value={d.id}> {d.name} </MenuItem>))}
                 </Select>
             </FormControl>
-            <ButtonWithSnackbar
-                color={"primary"}
-                path={"/config/select_detector"}
-                input={JSON.stringify({id: Number(choice)})}
-                method={"PUT"}
-                text={"Select detector"}
-                disabled={s === undefined}
-            />
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(DetectorSelection);
diff --git a/frontend/src/components/DetectorSettings.tsx b/frontend/src/components/DetectorSettings.tsx
index 8685d1b0..66cb92e9 100644
--- a/frontend/src/components/DetectorSettings.tsx
+++ b/frontend/src/components/DetectorSettings.tsx
@@ -7,9 +7,13 @@ import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
 import {detector_settings, detector_timing} from "../client";
+import {putConfigDetectorMutation} from "../client/@tanstack/react-query.gen";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import Button from "@mui/material/Button";
+import {PanelTitle, UploadSnackbarView} from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: detector_settings
@@ -46,6 +50,7 @@ function DetectorSettings({s: serverS}: MyProps) {
     const [eigerThresholdErr, setEigerThresholdErr] = useState(false);
     const [eigerThresholdKeVOld, setEigerThresholdKeVOld] = useState(6.0);
     const [downloadCounter, setDownloadCounter] = useState(0);
+    const { submit, pending, snackbar } = useUpload(putConfigDetectorMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -139,13 +144,15 @@ function DetectorSettings({s: serverS}: MyProps) {
         setS(prev => ({...prev, jungfrau_storage_cell_count: Number(event.target.value)}));
     };
 
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
     return <Paper style={{textAlign: 'center'}} sx={{ height: 1150, width: '100%' }}>
 
         <Grid container>
 
             <Grid item xs={1}/>
             <Grid item xs={10}>
-                <br/><strong>Detector settings </strong>
+                <br/><PanelTitle title="Detector settings" dirty={dirty}/>
                 <br/><br/><br/>
                 <NumberTextField start_val={s.frame_time_us}
                                  label={"Internal frame time"}
@@ -410,22 +417,18 @@ function DetectorSettings({s: serverS}: MyProps) {
             <Grid item xs={1}/>
             <Grid item xs={1}/>
             <Grid item xs={10}>
-                <ButtonWithSnackbar
-                    color={"primary"}
-                    path={"/config/detector"}
-                    disabled={countTimeErr
-                        || frameTimeErr
-                        || internalFrameGeneratorImagesErr
-                        || detectorTriggerDelayErr
-                        || storageCellDelayErr
-                        || pedestalG0FramesErr
-                        || pedestalG1FramesErr
-                        || pedestalG2FramesErr
-                        || pedestalMinImageCountErr}
-                    text={"Upload"}
-                    input={JSON.stringify(s)}
-                    method={"PUT"}
-                />&nbsp;&nbsp;
+                <Button color="primary" variant="contained" disableElevation
+                        onClick={() => submit(s)}
+                        disabled={pending
+                            || countTimeErr
+                            || frameTimeErr
+                            || internalFrameGeneratorImagesErr
+                            || detectorTriggerDelayErr
+                            || storageCellDelayErr
+                            || pedestalG0FramesErr
+                            || pedestalG1FramesErr
+                            || pedestalG2FramesErr
+                            || pedestalMinImageCountErr}>Upload</Button>&nbsp;&nbsp;
                 <ButtonWithSnackbar
                     color={"primary"}
                     path={"/deactivate"}
@@ -435,6 +438,7 @@ function DetectorSettings({s: serverS}: MyProps) {
             </Grid>
             <Grid item xs={1}/>
         </Grid>
+        <UploadSnackbarView snackbar={snackbar}/>
     </Paper>
 }
 
diff --git a/frontend/src/components/DetectorStatus.tsx b/frontend/src/components/DetectorStatus.tsx
index 1c4e84e7..f01622d3 100644
--- a/frontend/src/components/DetectorStatus.tsx
+++ b/frontend/src/components/DetectorStatus.tsx
@@ -1,8 +1,9 @@
 import {memo} from 'react';
 
 import Paper from '@mui/material/Paper';
-import {Stack, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
+import {Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
 import {detector_status, detector_state, detector_power_state} from "../client";
+import SettingsPanel from "./SettingsPanel";
 
 type MyProps = {
     s?: detector_status
@@ -42,14 +43,8 @@ function DetectorStatus({s}: MyProps) {
         high_voltage_V: []
     };
 
-    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center"
-        }}>
-
-            <strong>Detector status</strong>
+    return (
+        <SettingsPanel title="Detector status">
 
             <TableContainer component={Paper}
                             style={{marginLeft: "auto", marginRight: "auto"}}
@@ -85,9 +80,8 @@ function DetectorStatus({s}: MyProps) {
                 </Table>
             </TableContainer>
 
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(DetectorStatus);
diff --git a/frontend/src/components/FileWriterSettings.tsx b/frontend/src/components/FileWriterSettings.tsx
index de07c66a..ba1b5340 100644
--- a/frontend/src/components/FileWriterSettings.tsx
+++ b/frontend/src/components/FileWriterSettings.tsx
@@ -1,13 +1,14 @@
 import {memo, useEffect, useState} from 'react';
 
-import Paper from '@mui/material/Paper';
-import {Checkbox, FormControlLabel, FormGroup, Select, Stack} from "@mui/material";
+import {Checkbox, FormControlLabel, FormGroup, Select} from "@mui/material";
 import {file_writer_format, file_writer_settings} from "../client";
+import {putConfigFileWriterMutation} from "../client/@tanstack/react-query.gen";
 import _ from "lodash";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
 import MenuItem from "@mui/material/MenuItem";
 import InputLabel from "@mui/material/InputLabel";
 import FormControl from "@mui/material/FormControl";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: file_writer_settings
@@ -31,6 +32,7 @@ function stringToEnum(value: string): file_writer_format {
 function FileWriterSettings({s: serverS}: MyProps) {
     const [s, setS] = useState<file_writer_settings>(default_file_writer_settings);
     const [lastDownloadedS, setLastDownloadedS] = useState<file_writer_settings>(default_file_writer_settings);
+    const { submit, pending, snackbar } = useUpload(putConfigFileWriterMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -40,13 +42,11 @@ function FileWriterSettings({s: serverS}: MyProps) {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [serverS]);
 
-    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-        }}>
-            <div><strong>File Writer settings </strong></div>
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
+    return (
+        <SettingsPanel title="File writer" dirty={dirty}
+                       onUpload={() => submit(s)} uploadDisabled={pending} snackbar={snackbar}>
             <FormGroup>
                 <FormControlLabel
                     control={
@@ -80,16 +80,8 @@ function FileWriterSettings({s: serverS}: MyProps) {
                     <MenuItem value={file_writer_format.NO_FILE_WRITTEN}>No files saved</MenuItem>
                 </Select>
             </FormControl>
-            <ButtonWithSnackbar
-                color={"primary"}
-                path={"/config/file_writer"}
-                input={JSON.stringify(s)}
-                method={"PUT"}
-                text={"Upload"}
-            />
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(FileWriterSettings);
diff --git a/frontend/src/components/ImageFormatSettings.tsx b/frontend/src/components/ImageFormatSettings.tsx
index 1c4eebef..9fa0753d 100644
--- a/frontend/src/components/ImageFormatSettings.tsx
+++ b/frontend/src/components/ImageFormatSettings.tsx
@@ -1,15 +1,16 @@
 import {ChangeEvent, memo, useEffect, useState} from 'react';
 
 import {Checkbox, FormControlLabel, FormGroup, List, ListItem, Stack, Tooltip} from "@mui/material";
-import Paper from "@mui/material/Paper";
 import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
 import {image_format_settings} from "../client";
+import {putConfigImageFormatMutation} from "../client/@tanstack/react-query.gen";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: image_format_settings
@@ -59,6 +60,7 @@ function ImageFormatSettings({s: serverS}: MyProps) {
     const [jungfrauConversionFactorErr, setJungfrauConversionFactorErr] = useState(false);
     const [jungfrauConversionFactorOld, setJungfrauConversionFactorOld] = useState(12.4);
     const [downloadCounter, setDownloadCounter] = useState(0);
+    const { submit, pending, snackbar } = useUpload(putConfigImageFormatMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -103,13 +105,11 @@ function ImageFormatSettings({s: serverS}: MyProps) {
         setS(prev => ({...prev, signed_output: val}));
     };
 
-    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-        }}>
-            <strong>Output image format settings </strong>
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
+    return (
+        <SettingsPanel title="Output image format" dirty={dirty}
+                       onUpload={() => submit(s)} uploadDisabled={pending || jungfrauConversionFactorErr} snackbar={snackbar}>
             <FormGroup>
                 <FormControlLabel control={
                     <Checkbox checked={s.geometry_transform}
@@ -254,18 +254,8 @@ function ImageFormatSettings({s: serverS}: MyProps) {
                                  }}
                 />
 
-            <ButtonWithSnackbar
-                path={"/config/image_format"}
-                color={"primary"}
-                method={"PUT"}
-                disabled={jungfrauConversionFactorErr}
-                text={"Upload"}
-                input={JSON.stringify(s)}
-            />
-
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(ImageFormatSettings);
diff --git a/frontend/src/components/ImagePusherStatus.tsx b/frontend/src/components/ImagePusherStatus.tsx
index 0a21e00a..71014d68 100644
--- a/frontend/src/components/ImagePusherStatus.tsx
+++ b/frontend/src/components/ImagePusherStatus.tsx
@@ -5,8 +5,9 @@
 
 import {memo} from 'react';
 import Paper from '@mui/material/Paper';
-import {Stack, Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
+import {Table, TableBody, TableCell, TableContainer, TableRow} from "@mui/material";
 import {image_pusher_status, image_pusher_type} from "../client";
+import SettingsPanel from "./SettingsPanel";
 
 type MyProps = {
     s?: image_pusher_status
@@ -34,10 +35,7 @@ function renderPusherType(type?: image_pusher_type): string {
 
 function ImagePusherStatus({s}: MyProps) {
     return (
-        <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-            <br/>
-            <Stack spacing={2} sx={{justifyContent: "center", alignItems: "center"}}>
-                <strong>Image pusher status</strong>
+        <SettingsPanel title="Image pusher status" spacing={2}>
                 <TableContainer component={Paper} sx={{width: '90%'}} style={{marginLeft: "auto", marginRight: "auto"}}>
                     <Table size="small">
                         <TableBody>
@@ -60,9 +58,7 @@ function ImagePusherStatus({s}: MyProps) {
                         </TableBody>
                     </Table>
                 </TableContainer>
-            </Stack>
-            <br/>
-        </Paper>
+        </SettingsPanel>
     );
 }
 
diff --git a/frontend/src/components/IndexingSettings.tsx b/frontend/src/components/IndexingSettings.tsx
index 3e0c9b3b..cc8e45cb 100644
--- a/frontend/src/components/IndexingSettings.tsx
+++ b/frontend/src/components/IndexingSettings.tsx
@@ -1,15 +1,16 @@
 import {memo, useEffect, useState} from 'react';
 
 import {Stack, Typography, FormControlLabel, Checkbox} from "@mui/material";
-import Paper from "@mui/material/Paper";
 import FormControl from "@mui/material/FormControl";
 import InputLabel from "@mui/material/InputLabel";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 import MenuItem from "@mui/material/MenuItem";
 import {broker_status, geom_refinement_algorithm, indexing_algorithm, indexing_settings} from "../client";
+import {putConfigIndexingMutation} from "../client/@tanstack/react-query.gen";
 import NumberTextField from "./NumberTextField";
 import _ from "lodash";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: indexing_settings
@@ -48,6 +49,7 @@ function IndexingSettings({s: serverS, status}: MyProps) {
     const [unitCellDistToleranceError, setUnitCellDistToleranceError] = useState(false);
     const [rotationIndexingMinAngularRangeDegError, setRotationIndexingMinAngularRangeDegError] = useState(false);
     const [rotationIndexingAngularStrideDegError, setRotationIndexingAngularStrideDegError] = useState(false);
+    const { submit, pending, snackbar } = useUpload(putConfigIndexingMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -86,13 +88,11 @@ function IndexingSettings({s: serverS, status}: MyProps) {
         || rotationIndexingAngularStrideDegError
         || rotationIndexingMinAngularRangeDegError;
 
-    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-        }}>
-            <strong>Indexing settings </strong>
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
+    return (
+        <SettingsPanel title="Indexing" dirty={dirty}
+                       onUpload={() => submit(s)} uploadDisabled={pending || isError()} snackbar={snackbar}>
 
             <b>Algorithm</b>
                 <FormControl sx = {{width: "80%"}}>
@@ -290,18 +290,8 @@ function IndexingSettings({s: serverS, status}: MyProps) {
                              }}
                              sx={{width: '80%'}}/>
 
-                <ButtonWithSnackbar
-                path={"/config/indexing"}
-                color={"primary"}
-                method={"PUT"}
-                disabled={isError()}
-                text={"Upload"}
-                input={JSON.stringify(s)}
-            />
-
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(IndexingSettings);
diff --git a/frontend/src/components/InstrumentMetadata.tsx b/frontend/src/components/InstrumentMetadata.tsx
index 0d91a1fd..36c24607 100644
--- a/frontend/src/components/InstrumentMetadata.tsx
+++ b/frontend/src/components/InstrumentMetadata.tsx
@@ -4,13 +4,13 @@ import {
     Autocomplete,
     Checkbox,
     FormControlLabel, FormGroup,
-    Stack,
     TextField
 } from "@mui/material";
-import Paper from "@mui/material/Paper";
 import {instrument_metadata} from "../client";
+import {putConfigInstrumentMutation} from "../client/@tanstack/react-query.gen";
 import _ from "lodash";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: instrument_metadata
@@ -37,6 +37,7 @@ const source_types : string[] = [
 function InstrumentMetadata({s: serverS}: MyProps) {
     const [s, setS] = useState<instrument_metadata>(default_instrument_metadata);
     const [lastDownloadedS, setLastDownloadedS] = useState<instrument_metadata>(default_instrument_metadata);
+    const { submit, pending, snackbar } = useUpload(putConfigInstrumentMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -46,16 +47,11 @@ function InstrumentMetadata({s: serverS}: MyProps) {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [serverS]);
 
-    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%' }}>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-            marginLeft: '8%',
-            marginRight: '8%',
-        }}>
+    const dirty = !_.isEqual(s, lastDownloadedS);
 
-
-            <div><strong>Source and instrument metadata</strong></div>
+    return (
+        <SettingsPanel title="Source and instrument metadata" dirty={dirty}
+                       onUpload={() => submit(s)} uploadDisabled={pending} snackbar={snackbar}>
                 <TextField id="source_name" label="Source name" variant="outlined"
                            fullWidth
                            onChange={(event: ChangeEvent<HTMLInputElement>) => {
@@ -104,16 +100,8 @@ function InstrumentMetadata({s: serverS}: MyProps) {
                                       }}/>
                     } label="Electron source"/>
                 </FormGroup>
-            <ButtonWithSnackbar
-                color={"primary"}
-                path={"/config/instrument"}
-                input={JSON.stringify(s)}
-                method={"PUT"}
-                text={"Upload"}
-            />
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(InstrumentMetadata);
diff --git a/frontend/src/components/MeasurementStatistics.tsx b/frontend/src/components/MeasurementStatistics.tsx
index 71bf5c3a..be41c2b7 100644
--- a/frontend/src/components/MeasurementStatistics.tsx
+++ b/frontend/src/components/MeasurementStatistics.tsx
@@ -1,20 +1,17 @@
 import {memo} from 'react';
 
 import Paper from '@mui/material/Paper';
-import {Grid, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
+import {Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
 import {measurement_statistics} from "../client";
+import SettingsPanel from "./SettingsPanel";
 
 type MyProps = {
     s: measurement_statistics,
 };
 
 function MeasurementStatistics({s}: MyProps) {
-    return <Paper style={{textAlign: 'center'}} sx={{ height: 550, width: '100%' }}>
-        <Grid container spacing={0}>
-            <Grid item xs={1}/>
-            <Grid item xs={10}>
-                <br/><strong>Measurement statistics</strong><br/><br/>
-
+    return (
+        <SettingsPanel title="Measurement statistics" sx={{ height: 550 }}>
                 <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
                     <Table size="small" aria-label="simple table">
                         <TableBody>
@@ -75,11 +72,8 @@ function MeasurementStatistics({s}: MyProps) {
                         </TableBody>
                     </Table>
                 </TableContainer>
-                <br/>
-            </Grid>
-            <Grid item xs={1}/>
-        </Grid>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(MeasurementStatistics);
diff --git a/frontend/src/components/PixelMask.tsx b/frontend/src/components/PixelMask.tsx
index d10a6df8..ee7dcfb0 100644
--- a/frontend/src/components/PixelMask.tsx
+++ b/frontend/src/components/PixelMask.tsx
@@ -9,8 +9,10 @@ import {
     TableContainer,
     TableRow, TextField
 } from "@mui/material";
-import {putConfigUserMaskTiff, pixel_mask_statistics} from "../client";
-import Button from "@mui/material/Button";
+import {pixel_mask_statistics} from "../client";
+import {putConfigUserMaskTiffMutation} from "../client/@tanstack/react-query.gen";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
     s?: pixel_mask_statistics
@@ -18,11 +20,7 @@ type MyProps = {
 
 function PixelMask({s}: MyProps) {
     const [file, setFile] = useState<File>();
-
-    const handleUpload = () => {
-        if (file)
-            putConfigUserMaskTiff({ body: file });
-    };
+    const { submit, pending, snackbar } = useUpload(putConfigUserMaskTiffMutation());
 
     const handleFileChange = (event: ChangeEvent<HTMLInputElement>) => {
         if (event.target.files && event.target.files[0]) {
@@ -30,47 +28,46 @@ function PixelMask({s}: MyProps) {
         }
     };
 
-    return <Paper style={{textAlign: 'center'}} sx={{width: '100%'}}>
-        <br/><strong>Pixel mask</strong><br/><br/>
-        <Grid container spacing={0}>
-            <Grid item xs={1}/>
-            <Grid item xs={10}>
-                <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
-                    <Table size="small" aria-label="simple table">
-                        <TableBody>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> User mask: </TableCell>
-                                <TableCell align="right">{s?.user_mask ?? "N/A"}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Error pixels: </TableCell>
-                                <TableCell align="right">{s?.wrong_gain ?? "N/A"}</TableCell>
-                            </TableRow>
-                            <TableRow>
-                                <TableCell component="th" scope="row"> Noisy pixels: </TableCell>
-                                <TableCell align="right">{s?.too_high_pedestal_rms ?? "N/A"}</TableCell>
-                            </TableRow>
-                        </TableBody>
-                    </Table>
-                </TableContainer>
+    return (
+        <SettingsPanel title="Pixel mask"
+                       onUpload={() => file && submit(file)}
+                       uploadDisabled={!file || pending}
+                       snackbar={snackbar}>
+            <Grid container spacing={0}>
+                <Grid item xs={1}/>
+                <Grid item xs={10}>
+                    <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
+                        <Table size="small" aria-label="simple table">
+                            <TableBody>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> User mask: </TableCell>
+                                    <TableCell align="right">{s?.user_mask ?? "N/A"}</TableCell>
+                                </TableRow>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> Error pixels: </TableCell>
+                                    <TableCell align="right">{s?.wrong_gain ?? "N/A"}</TableCell>
+                                </TableRow>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> Noisy pixels: </TableCell>
+                                    <TableCell align="right">{s?.too_high_pedestal_rms ?? "N/A"}</TableCell>
+                                </TableRow>
+                            </TableBody>
+                        </Table>
+                    </TableContainer>
+                </Grid>
+                <Grid item xs={1}/>
             </Grid>
-            <Grid item xs={1}/>
-        </Grid>
-        <br/>
-        <a href="/config/mask.tiff">Download pixel mask</a><br/>
-        <a href="/config/user_mask.tiff">Download user pixel mask</a><br/><br/>
-        <TextField
-            type="file"
-            inputProps={{accept: '.tiff'}}
-            onChange={handleFileChange}
-        /><br/><br/>
-        <Button onClick={handleUpload}
-                variant="contained"
-                disableElevation
-                disabled={!file}
-                color={"primary"}>Upload</Button>
-        <br/><br/>
-    </Paper>
+            <div>
+                <a href="/config/mask.tiff">Download pixel mask</a><br/>
+                <a href="/config/user_mask.tiff">Download user pixel mask</a>
+            </div>
+            <TextField
+                type="file"
+                inputProps={{accept: '.tiff'}}
+                onChange={handleFileChange}
+            />
+        </SettingsPanel>
+    );
 }
 
 export default memo(PixelMask);
diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index 882257a2..379ccad4 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -12,7 +12,9 @@ import Button from "@mui/material/Button";
 import {DataGrid, GridActionsCellItem, GridColDef, GridRowModel} from "@mui/x-data-grid";
 import DeleteIcon from '@mui/icons-material/DeleteOutlined';
 import ErrorIcon from '@mui/icons-material/Error';
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import {putConfigRoiMutation} from "../client/@tanstack/react-query.gen";
+import {UploadSnackbarView} from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 import _ from "lodash";
 
 type MyProps = {
@@ -49,6 +51,7 @@ function ROI({s: serverS}: MyProps) {
     const [boxErr, setBoxErr] = useState<string>();
     const [circleErr, setCircleErr] = useState<string>();
     const [azimErr, setAzimErr] = useState<string | ReactNode>();
+    const { submit, pending, snackbar } = useUpload(putConfigRoiMutation());
 
     useEffect(() => {
         if ((serverS !== undefined) && !_.isEqual(serverS, lastDownloadedS)) {
@@ -386,19 +389,15 @@ function ROI({s: serverS}: MyProps) {
                         disableElevation>Add Circle ROI</Button>&nbsp;&nbsp;
                 <Button color="secondary" onClick={addAzimButton} variant="contained"
                         disableElevation>Add Azimuthal ROI</Button>&nbsp;&nbsp;
-                <ButtonWithSnackbar
-                    path={"/config/roi"}
-                    color={"primary"}
-                    method={"PUT"}
-                    disabled={(boxErr !== undefined) || (circleErr !== undefined)}
-                    text={"Upload"}
-                    input={JSON.stringify(roiStruct())}
-                />
+                <Button color="primary" variant="contained" disableElevation
+                        onClick={() => submit(roiStruct())}
+                        disabled={pending || (boxErr !== undefined) || (circleErr !== undefined)}>Upload</Button>
                 <br/><br/>
 
             </Grid>
             <Grid item xs={1}/>
         </Grid>
+        <UploadSnackbarView snackbar={snackbar}/>
     </Paper>
 }
 
diff --git a/frontend/src/components/SettingsPanel.tsx b/frontend/src/components/SettingsPanel.tsx
new file mode 100644
index 00000000..c9d93404
--- /dev/null
+++ b/frontend/src/components/SettingsPanel.tsx
@@ -0,0 +1,81 @@
+import { ReactNode } from "react";
+import { Alert, Box, Button, Paper, Snackbar, Stack, Tooltip, Typography } from "@mui/material";
+import { SxProps, Theme } from "@mui/material/styles";
+import { TypographyProps } from "@mui/material/Typography";
+import { UploadSnackbar } from "./useUpload";
+
+/** The upload-result snackbar, usable on its own by panels that don't use SettingsPanel. */
+export function UploadSnackbarView({ snackbar }: { snackbar?: UploadSnackbar }) {
+    if (!snackbar) return null;
+    return (
+        <Snackbar open={snackbar.open} autoHideDuration={5000} onClose={snackbar.onClose}>
+            <Alert onClose={snackbar.onClose} variant="filled"
+                   severity={snackbar.success ? "success" : "error"} sx={{ width: "100%" }}>
+                {snackbar.success ? "Ok!" : snackbar.message}
+            </Alert>
+        </Snackbar>
+    );
+}
+
+/** A title with an optional "unsaved changes" marker. */
+export function PanelTitle({ title, variant = "h6", dirty }: { title: string; variant?: TypographyProps["variant"]; dirty?: boolean }) {
+    return (
+        <Typography variant={variant} component="div">
+            {title}
+            {dirty && (
+                <Tooltip title="Unsaved changes — upload to apply">
+                    <Box component="span" sx={{ color: "warning.main", ml: 0.5 }}>●</Box>
+                </Tooltip>
+            )}
+        </Typography>
+    );
+}
+
+type SettingsPanelProps = {
+    title?: string;
+    titleVariant?: TypographyProps["variant"];
+    dirty?: boolean;
+    onUpload?: () => void;
+    uploadText?: string;
+    uploadDisabled?: boolean;
+    snackbar?: UploadSnackbar;
+    sx?: SxProps<Theme>;
+    spacing?: number;
+    children: ReactNode;
+};
+
+/**
+ * Consistent shell for the expert configuration panels: a padded Paper, a title
+ * (with an optional "unsaved changes" marker), the panel widgets, an optional
+ * Upload button, and the upload result snackbar.
+ */
+function SettingsPanel({
+    title,
+    titleVariant = "h6",
+    dirty,
+    onUpload,
+    uploadText = "Upload",
+    uploadDisabled,
+    snackbar,
+    sx,
+    spacing = 3,
+    children,
+}: SettingsPanelProps) {
+    return (
+        <Paper sx={[{ width: "100%", p: 3, textAlign: "center" }, ...(Array.isArray(sx) ? sx : [sx])]}>
+            <Stack spacing={spacing} alignItems="center">
+                {title !== undefined && <PanelTitle title={title} variant={titleVariant} dirty={dirty} />}
+                {children}
+                {onUpload && (
+                    <Button variant="contained" color="primary" disableElevation
+                            onClick={onUpload} disabled={uploadDisabled}>
+                        {uploadText}
+                    </Button>
+                )}
+            </Stack>
+            <UploadSnackbarView snackbar={snackbar} />
+        </Paper>
+    );
+}
+
+export default SettingsPanel;
diff --git a/frontend/src/components/ZeroMQPreview.tsx b/frontend/src/components/ZeroMQPreview.tsx
index c5cc1642..bc9dfb5c 100644
--- a/frontend/src/components/ZeroMQPreview.tsx
+++ b/frontend/src/components/ZeroMQPreview.tsx
@@ -1,12 +1,13 @@
 import {memo, useEffect, useState} from 'react';
 
-import Paper from '@mui/material/Paper';
-import {FormControlLabel, Radio, RadioGroup, Stack} from "@mui/material";
+import {FormControlLabel, Radio, RadioGroup} from "@mui/material";
 import NumberTextField from "./NumberTextField";
 import {zeromq_preview_settings} from "../client";
+import {putConfigZeromqPreviewMutation} from "../client/@tanstack/react-query.gen";
 import _ from "lodash";
 import FormControl from "@mui/material/FormControl";
-import ButtonWithSnackbar from "./ButtonWithSnackbar";
+import SettingsPanel from "./SettingsPanel";
+import {useUpload} from "./useUpload";
 
 type MyProps = {
    s?: zeromq_preview_settings
@@ -25,6 +26,7 @@ function ZeroMQPreview({s: serverS}: MyProps) {
     const [downloadCounter, setDownloadCounter] = useState(0);
     const [freqChoice, setFreqChoice] = useState("custom");
     const [periodMs, setPeriodMs] = useState(default_zeromq_preview_settings.period_ms);
+    const { submit, pending, snackbar } = useUpload(putConfigZeromqPreviewMutation());
 
     const update_freq = (choice: string) => {
         switch (choice) {
@@ -69,13 +71,13 @@ function ZeroMQPreview({s: serverS}: MyProps) {
     const empty = () : boolean =>
         (s.socket_address === undefined) || (s.socket_address === "");
 
-    return <Paper style={{textAlign: 'center'}} sx={{ width: '100%'}}>
-        <br/>
-        <Stack spacing={3} sx={{
-            justifyContent: "center",
-            alignItems: "center",
-        }}>
-            <div><strong>ZeroMQ preview settings </strong></div>
+    const dirty = !_.isEqual(s, lastDownloadedS);
+
+    return (
+        <SettingsPanel title="ZeroMQ preview" dirty={dirty}
+                       onUpload={() => submit(s)}
+                       uploadDisabled={pending || ((freqChoice == "custom") && periodErr)}
+                       snackbar={snackbar}>
                 <div>
                     {empty() ? "No preview available" : `ZeroMQ socket: ${s.socket_address}`}
                 </div>
@@ -103,17 +105,8 @@ function ZeroMQPreview({s: serverS}: MyProps) {
                 }}
                 disabled={freqChoice != "custom"}
                 fullWidth/>
-            <ButtonWithSnackbar
-                color={"primary"}
-                path={"/config/zeromq_preview"}
-                input={JSON.stringify(s)}
-                method={"PUT"}
-                text={"Upload"}
-                disabled={((freqChoice == "custom") && periodErr)}
-            />
-        </Stack>
-        <br/>
-    </Paper>
+        </SettingsPanel>
+    );
 }
 
 export default memo(ZeroMQPreview);
diff --git a/frontend/src/components/useUpload.ts b/frontend/src/components/useUpload.ts
new file mode 100644
index 00000000..ce4c1877
--- /dev/null
+++ b/frontend/src/components/useUpload.ts
@@ -0,0 +1,41 @@
+import { useState } from "react";
+import { useMutation, UseMutationOptions } from "@tanstack/react-query";
+
+/** Pull a human-readable message out of a hey-api error (400 = string, 500 = error_message). */
+export function errorMessage(error: unknown): string {
+    if (typeof error === "string") return error;
+    if (error && typeof error === "object" && "msg" in error)
+        return String((error as { msg?: unknown }).msg ?? "Unknown error");
+    return "Upload failed";
+}
+
+export type UploadSnackbar = {
+    open: boolean;
+    success: boolean;
+    message: string;
+    onClose: () => void;
+};
+
+/**
+ * Wraps a generated hey-api mutation (e.g. putConfigFileWriterMutation()) and
+ * surfaces the result as a snackbar. submit(body) sends the typed body; on
+ * failure the server's error message is shown.
+ */
+export function useUpload<TError, TVars extends { body?: unknown }>(
+    mutationOptions: UseMutationOptions<unknown, TError, TVars>,
+) {
+    const mutation = useMutation(mutationOptions);
+    const [open, setOpen] = useState(false);
+
+    const submit = (body: TVars["body"]) =>
+        mutation.mutate({ body } as TVars, { onSettled: () => setOpen(true) });
+
+    const snackbar: UploadSnackbar = {
+        open,
+        success: mutation.isSuccess,
+        message: mutation.error ? errorMessage(mutation.error) : "",
+        onClose: () => setOpen(false),
+    };
+
+    return { submit, pending: mutation.isPending, snackbar };
+}
-- 
2.52.0


From 5d8e33d52c321cfd1e1a7499c215c1ec6e6b075c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Thu, 18 Jun 2026 22:14:10 +0200
Subject: [PATCH 096/228] frontend: orange Upload button when panel is dirty

Match the unsaved-changes dot: the Upload button uses the warning color
while the panel has unedited changes, primary otherwise.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/components/DetectorSettings.tsx | 2 +-
 frontend/src/components/SettingsPanel.tsx    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/frontend/src/components/DetectorSettings.tsx b/frontend/src/components/DetectorSettings.tsx
index 66cb92e9..9709d983 100644
--- a/frontend/src/components/DetectorSettings.tsx
+++ b/frontend/src/components/DetectorSettings.tsx
@@ -417,7 +417,7 @@ function DetectorSettings({s: serverS}: MyProps) {
             <Grid item xs={1}/>
             <Grid item xs={1}/>
             <Grid item xs={10}>
-                <Button color="primary" variant="contained" disableElevation
+                <Button color={dirty ? "warning" : "primary"} variant="contained" disableElevation
                         onClick={() => submit(s)}
                         disabled={pending
                             || countTimeErr
diff --git a/frontend/src/components/SettingsPanel.tsx b/frontend/src/components/SettingsPanel.tsx
index c9d93404..620527ec 100644
--- a/frontend/src/components/SettingsPanel.tsx
+++ b/frontend/src/components/SettingsPanel.tsx
@@ -67,7 +67,7 @@ function SettingsPanel({
                 {title !== undefined && <PanelTitle title={title} variant={titleVariant} dirty={dirty} />}
                 {children}
                 {onUpload && (
-                    <Button variant="contained" color="primary" disableElevation
+                    <Button variant="contained" color={dirty ? "warning" : "primary"} disableElevation
                             onClick={onUpload} disabled={uploadDisabled}>
                         {uploadText}
                     </Button>
-- 
2.52.0


From 9fc971c1d26ebcc17d58a16f591d73d594deec02 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 07:24:52 +0200
Subject: [PATCH 097/228] frontend: add zod plugin to hey-api openapi-ts

Generate Zod schemas alongside the typed client (src/client/zod.gen.ts),
picking up the OpenAPI field defaults. Enables runtime validation and
default-filling for form payloads.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/openapi-ts.config.ts  |    1 +
 frontend/package-lock.json     |   12 +-
 frontend/package.json          |    3 +-
 frontend/src/client/zod.gen.ts | 1214 ++++++++++++++++++++++++++++++++
 4 files changed, 1228 insertions(+), 2 deletions(-)
 create mode 100644 frontend/src/client/zod.gen.ts

diff --git a/frontend/openapi-ts.config.ts b/frontend/openapi-ts.config.ts
index ed71a8a9..9fe84523 100644
--- a/frontend/openapi-ts.config.ts
+++ b/frontend/openapi-ts.config.ts
@@ -14,5 +14,6 @@ export default defineConfig({
         },
         '@hey-api/sdk',
         '@tanstack/react-query',
+        'zod',
     ],
 });
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 4e746d46..ed73ab33 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -28,7 +28,8 @@
         "typescript": "^5.9.3",
         "vite": "^7.3.1",
         "vite-plugin-svgr": "^4.5.0",
-        "vite-tsconfig-paths": "^6.1.1"
+        "vite-tsconfig-paths": "^6.1.1",
+        "zod": "^4.4.3"
       },
       "devDependencies": {
         "@hey-api/openapi-ts": "^0.98.2",
@@ -9795,6 +9796,15 @@
       "engines": {
         "node": ">=10"
       }
+    },
+    "node_modules/zod": {
+      "version": "4.4.3",
+      "resolved": "https://registry.npmjs.org/zod/-/zod-4.4.3.tgz",
+      "integrity": "sha512-ytENFjIJFl2UwYglde2jchW2Hwm4GJFLDiSXWdTrJQBIN9Fcyp7n4DhxJEiWNAJMV1/BqWfW/kkg71UDcHJyTQ==",
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/sponsors/colinhacks"
+      }
     }
   }
 }
diff --git a/frontend/package.json b/frontend/package.json
index da894318..362fc4c6 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -25,7 +25,8 @@
     "typescript": "^5.9.3",
     "vite": "^7.3.1",
     "vite-plugin-svgr": "^4.5.0",
-    "vite-tsconfig-paths": "^6.1.1"
+    "vite-tsconfig-paths": "^6.1.1",
+    "zod": "^4.4.3"
   },
   "scripts": {
     "start": "vite",
diff --git a/frontend/src/client/zod.gen.ts b/frontend/src/client/zod.gen.ts
new file mode 100644
index 00000000..b3259a73
--- /dev/null
+++ b/frontend/src/client/zod.gen.ts
@@ -0,0 +1,1214 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+import * as z from 'zod';
+
+/**
+ * Definition of a grid scan (mutually exclusive with `rotation_axis`)
+ */
+export const zGridScan = z.object({
+    n_fast: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    step_x_um: z.number(),
+    step_y_um: z.number(),
+    vertical: z.boolean().optional().default(false),
+    snake: z.boolean().optional().default(false)
+});
+
+/**
+ * Definition of a crystal rotation axis
+ */
+export const zRotationAxis = z.object({
+    name: z.string().min(1).optional().default('omega'),
+    step: z.number(),
+    start: z.number().optional().default(0),
+    vector: z.tuple([
+        z.number(),
+        z.number(),
+        z.number()
+    ]),
+    helical_step_um: z.tuple([
+        z.number(),
+        z.number(),
+        z.number()
+    ]).optional(),
+    screening_wedge_deg: z.number().optional()
+});
+
+/**
+ * Selection of an indexing algorithm used by Jungfraujoch
+ *
+ */
+export const zIndexingAlgorithm = z.enum([
+    'FFBIDX',
+    'FFT',
+    'FFTW',
+    'Auto',
+    'None'
+]).default('FFBIDX');
+
+/**
+ * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
+ * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
+ * OrientationOnly - This option is refining only orientation of the lattice.
+ *
+ */
+export const zGeomRefinementAlgorithm = z.enum([
+    'BeamCenter',
+    'OrientationOnly',
+    'None'
+]);
+
+/**
+ * Real-space crystal lattice 3D vectors in Angstrom.
+ * Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)
+ *
+ */
+export const zCrystalLattice = z.tuple([
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number(),
+    z.number()
+]);
+
+/**
+ * Unit cell parameters. Necessary to run indexing. Units of angstrom and degree
+ */
+export const zUnitCell = z.object({
+    a: z.number().gte(0),
+    b: z.number().gte(0),
+    c: z.number().gte(0),
+    alpha: z.number().gte(0).lte(360),
+    beta: z.number().gte(0).lte(360),
+    gamma: z.number().gte(0).lte(360)
+});
+
+export const zDatasetSettings = z.object({
+    images_per_trigger: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(1)),
+    ntrigger: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(1)),
+    image_time_us: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    beam_x_pxl: z.number(),
+    beam_y_pxl: z.number(),
+    detector_distance_mm: z.number().gte(0),
+    incident_energy_keV: z.number().gte(0.001).lte(500),
+    file_prefix: z.string().optional().default(''),
+    images_per_file: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(1000)),
+    space_group_number: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(194)).optional(),
+    sample_name: z.string().optional().default(''),
+    compression: z.enum([
+        'bslz4',
+        'bszstd',
+        'bszstd_rle',
+        'none'
+    ]).optional().default('bslz4'),
+    total_flux: z.number().optional(),
+    transmission: z.number().gte(0).lte(1).optional(),
+    goniometer: zRotationAxis.optional(),
+    grid_scan: zGridScan.optional(),
+    header_appendix: z.unknown().optional(),
+    image_appendix: z.unknown().optional(),
+    data_reduction_factor_serialmx: z.number().gte(0).lte(1).optional().default(1),
+    pixel_value_low_threshold: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    run_number: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    run_name: z.string().optional(),
+    experiment_group: z.string().optional(),
+    poisson_compression: z.coerce.bigint().gte(BigInt(0)).lte(BigInt(16)).optional(),
+    write_nxmx_hdf5_master: z.boolean().optional().default(true),
+    save_calibration: z.boolean().optional(),
+    polarization_factor: z.number().gte(-1).lte(1).optional(),
+    ring_current_mA: z.number().gte(0).optional(),
+    sample_temperature_K: z.number().gte(0).optional(),
+    poni_rot1_rad: z.number().gte(-6.28318530718).lte(6.28318530718).optional().default(0),
+    poni_rot2_rad: z.number().gte(-6.28318530718).lte(6.28318530718).optional().default(0),
+    poni_rot3_rad: z.number().gte(-6.28318530718).lte(6.28318530718).optional().default(0),
+    unit_cell: zUnitCell.optional(),
+    spot_finding: z.boolean().optional().default(true),
+    max_spot_count: z.int().gte(10).lte(2000).optional().default(250),
+    detect_ice_rings: z.boolean().optional(),
+    async_start: z.boolean().optional().default(false),
+    xray_fluorescence_spectrum: z.object({
+        energy_eV: z.array(z.number()),
+        data: z.array(z.number())
+    }).optional()
+});
+
+/**
+ * NoFileWritten - no files are written at all
+ * NXmxOnlyData - only data files are written, no master file
+ * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
+ * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
+ * NXmxIntegrated - single HDF5 per dataset
+ * CBF - CBF format (limited metadata)
+ * TIFF - TIFF format (no metadata)
+ *
+ */
+export const zFileWriterFormat = z.enum([
+    'NXmxOnlyData',
+    'NXmxLegacy',
+    'NXmxVDS',
+    'NXmxIntegrated',
+    'CBF',
+    'TIFF',
+    'NoFileWritten'
+]).default('NXmxLegacy');
+
+export const zFileWriterSettings = z.object({
+    overwrite: z.boolean().optional().default(false),
+    format: zFileWriterFormat.optional()
+});
+
+export const zPixelMaskStatistics = z.object({
+    user_mask: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    too_high_pedestal_rms: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    wrong_gain: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional()
+});
+
+export const zImageBufferStatus = z.object({
+    min_image_number: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    max_image_number: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    image_numbers: z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })),
+    total_slots: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    available_slots: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    in_preparation_slots: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    in_sending_slots: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    current_counter: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional()
+});
+
+export const zImageFormatSettings = z.object({
+    summation: z.boolean(),
+    geometry_transform: z.boolean(),
+    jungfrau_conversion: z.boolean(),
+    jungfrau_conversion_factor_keV: z.number().gte(0.001).lte(500).optional(),
+    bit_depth_image: z.union([
+        z.literal(8),
+        z.literal(16),
+        z.literal(32)
+    ]).optional(),
+    signed_output: z.boolean().optional(),
+    mask_module_edges: z.boolean().default(true),
+    mask_chip_edges: z.boolean().default(true),
+    jungfrau_mask_pixels_without_g0: z.boolean().optional().default(true),
+    apply_mask: z.boolean().default(false),
+    jungfrau_pedestal_g0_rms_limit: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(100))
+});
+
+/**
+ * Power on of ASICs
+ */
+export const zDetectorPowerState = z.enum([
+    'PowerOn',
+    'PowerOff',
+    'Partial'
+]);
+
+/**
+ * Current state of the detector
+ */
+export const zDetectorState = z.enum([
+    'Idle',
+    'Waiting',
+    'Busy',
+    'Error',
+    'Not connected'
+]);
+
+export const zDetectorStatus = z.object({
+    state: zDetectorState,
+    powerchip: zDetectorPowerState,
+    server_version: z.string(),
+    number_of_triggers_left: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    fpga_temp_degC: z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })),
+    high_voltage_V: z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }))
+});
+
+export const zDetectorTiming = z.enum([
+    'auto',
+    'trigger',
+    'burst',
+    'gated'
+]).default('trigger');
+
+export const zDetectorSettings = z.object({
+    frame_time_us: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    count_time_us: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    internal_frame_generator: z.boolean().optional().default(false),
+    internal_frame_generator_images: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(64)).optional().default(BigInt(1)),
+    detector_trigger_delay_ns: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(0)),
+    timing: zDetectorTiming.optional(),
+    eiger_threshold_keV: z.number().gte(1).lte(100).optional(),
+    eiger_bit_depth: z.union([
+        z.literal(8),
+        z.literal(16),
+        z.literal(32)
+    ]).optional(),
+    jungfrau_pedestal_g0_frames: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(2000)),
+    jungfrau_pedestal_g1_frames: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(300)),
+    jungfrau_pedestal_g2_frames: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(300)),
+    jungfrau_pedestal_min_image_count: z.coerce.bigint().gte(BigInt(32)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(128)),
+    jungfrau_storage_cell_count: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(16)).optional().default(BigInt(1)),
+    jungfrau_storage_cell_delay_ns: z.coerce.bigint().gte(BigInt(2100)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(5000)),
+    jungfrau_fixed_gain_g1: z.boolean().optional().default(false),
+    jungfrau_use_gain_hg0: z.boolean().optional().default(false)
+});
+
+export const zSpotFindingSettings = z.object({
+    enable: z.boolean().default(true),
+    indexing: z.boolean().default(true),
+    signal_to_noise_threshold: z.number().gte(0),
+    photon_count_threshold: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    min_pix_per_spot: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    max_pix_per_spot: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    high_resolution_limit: z.number(),
+    low_resolution_limit: z.number(),
+    high_resolution_limit_for_spot_count_low_res: z.number().gte(2).lte(8),
+    quick_integration: z.boolean().default(false),
+    ice_ring_width_q_recipA: z.number().gte(0).lte(1).default(0.02),
+    high_res_gap_Q_recipA: z.number().gte(0.1).lte(5).optional().default(1.5)
+});
+
+export const zAzimIntSettings = z.object({
+    polarization_corr: z.boolean().default(true),
+    solid_angle_corr: z.boolean().default(true),
+    high_q_recipA: z.number().gte(0.00002).lte(10),
+    low_q_recipA: z.number().gte(0.00001).lte(10),
+    q_spacing: z.number().gte(0.00001),
+    azimuthal_bins: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(512)).optional().default(BigInt(1)),
+    force_cpu: z.boolean().optional().default(false)
+});
+
+export const zDetectorSelection = z.object({
+    id: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })
+});
+
+export const zMeasurementStatistics = z.object({
+    file_prefix: z.string().optional(),
+    run_number: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    experiment_group: z.string().optional(),
+    images_expected: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    images_collected: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    images_sent: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    images_written: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    images_discarded_lossy_compression: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    max_image_number_sent: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    collection_efficiency: z.number().gte(0).lte(1).optional(),
+    compression_ratio: z.number().gte(0).optional(),
+    cancelled: z.boolean().optional(),
+    max_receiver_delay: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    indexing_rate: z.number().optional(),
+    detector_width: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    detector_height: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    detector_pixel_depth: z.union([z.literal(2), z.literal(4)]).optional(),
+    bkg_estimate: z.number().optional(),
+    unit_cell: z.string().optional(),
+    error_pixels: z.number().optional(),
+    saturated_pixels: z.number().optional(),
+    roi_beam_pixels: z.number().optional(),
+    roi_beam_sum: z.number().optional()
+});
+
+export const zFpgaStatus = z.array(z.object({
+    pci_dev_id: z.string(),
+    serial_number: z.string(),
+    fw_version: z.string(),
+    base_mac_addr: z.string(),
+    eth_link_count: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    eth_link_status: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    power_usage_W: z.number(),
+    fpga_temp_C: z.number(),
+    hbm_temp_C: z.number(),
+    packets_udp: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    packets_sls: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    idle: z.boolean(),
+    pcie_link_speed: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    pcie_link_width: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })
+}));
+
+export const zBrokerStatus = z.object({
+    state: z.enum([
+        'Inactive',
+        'Idle',
+        'Busy',
+        'Measuring',
+        'Pedestal',
+        'Error'
+    ]),
+    progress: z.number().gte(0).lte(1).optional(),
+    message: z.string().optional(),
+    message_severity: z.enum([
+        'success',
+        'info',
+        'warning',
+        'error'
+    ]).optional().default('error'),
+    gpu_count: z.int().min(-2147483648, { error: 'Invalid value: Expected int32 to be >= -2147483648' }).max(2147483647, { error: 'Invalid value: Expected int32 to be <= 2147483647' }).optional(),
+    broker_version: z.string().optional()
+});
+
+/**
+ * x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly
+ */
+export const zPlot = z.object({
+    title: z.string().default(''),
+    x: z.array(z.number()),
+    y: z.array(z.number().nullable()),
+    z: z.array(z.number().nullable()).optional()
+});
+
+export const zPlotUnitX = z.enum([
+    'image_number',
+    'q_recipA',
+    'd_A',
+    'angle_deg',
+    'ADU',
+    'grid_um'
+]).default('image_number');
+
+export const zPlots = z.object({
+    title: z.string().optional(),
+    unit_x: zPlotUnitX,
+    size_x: z.number().optional(),
+    size_y: z.number().optional(),
+    plot: z.array(zPlot)
+});
+
+/**
+ * Results of a scan
+ */
+export const zScanResult = z.object({
+    file_prefix: z.string().optional(),
+    rotation_unit_cell: zUnitCell.optional(),
+    rotation_crystal_lattice: zCrystalLattice.optional(),
+    images: z.array(z.object({
+        efficiency: z.number(),
+        number: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+        nx: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        ny: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        angle: z.number().optional(),
+        bkg: z.number().optional(),
+        spots: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        spots_low_res: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        spots_indexed: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        spots_ice: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        index: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        latt_count: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        pr: z.number().optional(),
+        b: z.number().optional(),
+        uc: zUnitCell.optional(),
+        xfel_pulseid: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        pixel_sum: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        max: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        sat: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        err: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+        res: z.number().optional()
+    }))
+});
+
+export const zCalibrationStatistics = z.array(z.object({
+    module_number: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    storage_cell_number: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    pedestal_g0_mean: z.number(),
+    pedestal_g1_mean: z.number(),
+    pedestal_g2_mean: z.number(),
+    gain_g0_mean: z.number(),
+    gain_g1_mean: z.number(),
+    gain_g2_mean: z.number(),
+    masked_pixels: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })
+}));
+
+export const zErrorMessage = z.object({
+    msg: z.string(),
+    reason: z.enum(['WrongDAQState', 'Other'])
+});
+
+/**
+ * ROI as Q-range (or resolution range)
+ */
+export const zRoiAzimuthal = z.object({
+    name: z.string().min(1),
+    q_min_recipA: z.number().gte(0.00001),
+    q_max_recipA: z.number().gte(0.00001)
+});
+
+/**
+ * Circular ROI
+ */
+export const zRoiCircle = z.object({
+    name: z.string().min(1),
+    center_x_pxl: z.number(),
+    center_y_pxl: z.number(),
+    radius_pxl: z.number().gt(0)
+});
+
+/**
+ * Box ROI
+ */
+export const zRoiBox = z.object({
+    name: z.string().min(1),
+    min_x_pxl: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    max_x_pxl: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    min_y_pxl: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    max_y_pxl: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })
+});
+
+/**
+ * List of circular ROIs
+ */
+export const zRoiCircleList = z.object({
+    rois: z.array(zRoiCircle).max(12)
+});
+
+/**
+ * List of box ROIs
+ */
+export const zRoiBoxList = z.object({
+    rois: z.array(zRoiBox).max(12).optional()
+});
+
+/**
+ * List of azimuthal ROIs
+ */
+export const zRoiAzimList = z.object({
+    rois: z.array(zRoiAzimuthal).max(12).optional()
+});
+
+/**
+ * ROI defintions
+ */
+export const zRoiDefinitions = z.object({
+    box: zRoiBoxList,
+    circle: zRoiCircleList,
+    azim: zRoiAzimList
+});
+
+/**
+ * Settings for collection of dark images to be used for mask calculation
+ */
+export const zDarkMaskSettings = z.object({
+    detector_threshold_keV: z.number().gte(2.5).lte(100).default(3.5),
+    frame_time_us: z.coerce.bigint().gte(BigInt(500)).lte(BigInt(100000)).default(BigInt(10000)),
+    number_of_frames: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(1000)),
+    max_allowed_pixel_count: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(1)),
+    max_frames_with_signal: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(10))
+});
+
+/**
+ * Settings for crystallography indexing
+ */
+export const zIndexingSettings = z.object({
+    algorithm: zIndexingAlgorithm,
+    fft_max_unit_cell_A: z.number().gte(50).lte(500).default(250),
+    fft_min_unit_cell_A: z.number().gte(5).lte(40).default(10),
+    fft_high_resolution_A: z.number().gte(0.5).lte(6).default(2),
+    fft_num_vectors: z.coerce.bigint().gte(BigInt(128)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(16384)),
+    tolerance: z.number().gte(0).lte(0.5),
+    thread_count: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(64)),
+    geom_refinement_algorithm: zGeomRefinementAlgorithm,
+    unit_cell_dist_tolerance: z.number().gte(0.0001).lte(0.2001).default(0.05),
+    viable_cell_min_spots: z.coerce.bigint().gte(BigInt(5)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(10)),
+    index_ice_rings: z.boolean().default(false),
+    rotation_indexing: z.boolean().default(false),
+    rotation_indexing_min_angular_range_deg: z.number().gte(1).default(20),
+    rotation_indexing_angular_stride_deg: z.number().gte(0).default(0.5),
+    blocking: z.boolean().default(true)
+});
+
+/**
+ * Metadata for a measurement instrument
+ */
+export const zInstrumentMetadata = z.object({
+    source_name: z.string(),
+    source_type: z.string().optional().default(''),
+    instrument_name: z.string(),
+    pulsed_source: z.boolean().optional().default(false),
+    electron_source: z.boolean().optional().default(false)
+});
+
+export const zDetectorModuleDirection = z.enum([
+    'Xp',
+    'Xn',
+    'Yp',
+    'Yn'
+]);
+
+export const zDetectorType = z.enum([
+    'EIGER',
+    'JUNGFRAU',
+    'DECTRIS'
+]);
+
+export const zDetectorListElement = z.object({
+    id: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    description: z.string(),
+    serial_number: z.string(),
+    base_ipv4_addr: z.string(),
+    udp_interface_count: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    nmodules: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    width: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    height: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    pixel_size_mm: z.number().optional(),
+    readout_time_ns: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    min_frame_time_ns: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    min_count_time_ns: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    type: zDetectorType.optional()
+});
+
+export const zDetectorList = z.object({
+    detectors: z.array(zDetectorListElement),
+    current_id: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })
+});
+
+export const zImagePusherType = z.enum([
+    'ZeroMQ',
+    'HDF5',
+    'CBOR',
+    'TCP',
+    'None'
+]).default('None');
+
+/**
+ * Informs about status of the image pusher.
+ *
+ */
+export const zImagePusherStatus = z.object({
+    pusher_type: zImagePusherType,
+    addr: z.array(z.string()),
+    connected_writers: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    images_written: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    images_write_error: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    writer_fifo_utilization: z.array(z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })).optional()
+});
+
+/**
+ * Regular rectangular geometry, first module is in the bottom left corner of the detector
+ */
+export const zStandardDetectorGeometry = z.object({
+    nmodules: z.int().gte(1),
+    gap_x: z.int().gte(0).optional().default(8),
+    gap_y: z.int().gte(0).optional().default(36),
+    modules_in_row: z.int().gte(1).optional().default(1)
+});
+
+export const zDetectorModule = z.object({
+    x0: z.number(),
+    y0: z.number(),
+    fast_axis: zDetectorModuleDirection,
+    slow_axis: zDetectorModuleDirection
+});
+
+export const zDetector = z.object({
+    description: z.string().min(1),
+    serial_number: z.string().min(1).optional().default('Unknown'),
+    type: zDetectorType.optional(),
+    high_voltage_V: z.coerce.bigint().gte(BigInt(0)).lte(BigInt(200)).optional().default(BigInt(0)),
+    udp_interface_count: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(2)).optional().default(BigInt(1)),
+    module_sync: z.boolean().optional().default(true),
+    sensor_thickness_um: z.number().gte(0).optional().default(320),
+    readout_time_ns: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    min_count_time_ns: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    min_frame_time_ns: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    calibration_file: z.array(z.string()).optional(),
+    hostname: z.array(z.string()).optional(),
+    sensor_material: z.string().optional().default('Si'),
+    tx_delay: z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })).optional(),
+    base_data_ipv4_address: z.string().optional(),
+    standard_geometry: zStandardDetectorGeometry.optional(),
+    custom_geometry: z.array(zDetectorModule).optional(),
+    roi_mode: z.string().optional().default(''),
+    mirror_y: z.boolean().optional().default(true),
+    temp_thresold_degC: z.coerce.bigint().gte(BigInt(40)).lte(BigInt(70)).optional().default(BigInt(55)),
+    default_settings: zDetectorSettings.optional()
+});
+
+/**
+ * ZeroMQ configuration for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export const zZeromqSettings = z.object({
+    send_watermark: z.coerce.bigint().gte(BigInt(2)).lte(BigInt(16384)).optional().default(BigInt(100)),
+    send_buffer_size: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    image_socket: z.array(z.string()).optional(),
+    writer_notification_socket: z.string().optional()
+});
+
+/**
+ * TCP image stream configuration for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export const zTcpSettings = z.object({
+    send_buffer_size: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    image_socket: z.string().optional(),
+    nwriters: z.coerce.bigint().gte(BigInt(1)).lte(BigInt(100)).optional().default(BigInt(32))
+});
+
+export const zPcieDevices = z.array(z.object({
+    blk: z.string().optional(),
+    ipv4: z.string().optional()
+}));
+
+export const zZeromqMetadataSettings = z.object({
+    enabled: z.boolean().default(true),
+    period_ms: z.coerce.bigint().gte(BigInt(1)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(1000)),
+    socket_address: z.string().optional()
+});
+
+export const zZeromqPreviewSettings = z.object({
+    enabled: z.boolean().default(true),
+    period_ms: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(1000)),
+    socket_address: z.string().optional()
+});
+
+/**
+ * Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker
+ */
+export const zJfjochStatistics = z.object({
+    detector: zDetectorStatus.optional(),
+    detector_list: zDetectorList.optional(),
+    detector_settings: zDetectorSettings.optional(),
+    image_format_settings: zImageFormatSettings.optional(),
+    instrument_metadata: zInstrumentMetadata.optional(),
+    file_writer_settings: zFileWriterSettings.optional(),
+    data_processing_settings: zSpotFindingSettings.optional(),
+    measurement: zMeasurementStatistics.optional(),
+    broker: zBrokerStatus.optional(),
+    fpga: zFpgaStatus.optional(),
+    calibration: zCalibrationStatistics.optional(),
+    zeromq_preview: zZeromqPreviewSettings.optional(),
+    zeromq_metadata: zZeromqMetadataSettings.optional(),
+    dark_mask: zDarkMaskSettings.optional(),
+    pixel_mask: zPixelMaskStatistics.optional(),
+    roi: zRoiDefinitions.optional(),
+    az_int: zAzimIntSettings.optional(),
+    buffer: zImageBufferStatus.optional(),
+    indexing: zIndexingSettings.optional(),
+    image_pusher: zImagePusherStatus.optional()
+});
+
+/**
+ * Default settings for Jungfraujoch software.
+ * This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
+ *
+ */
+export const zJfjochSettings = z.object({
+    pcie: zPcieDevices.optional(),
+    zeromq: zZeromqSettings.optional(),
+    tcp: zTcpSettings.optional(),
+    instrument: zInstrumentMetadata.optional(),
+    file_writer: zFileWriterSettings.optional(),
+    detector: z.array(zDetector),
+    indexing: zIndexingSettings.optional(),
+    detector_settings: zDetectorSettings.optional(),
+    azim_int: zAzimIntSettings.optional(),
+    image_format: zImageFormatSettings.optional(),
+    image_buffer_MiB: z.int().gte(128).optional().default(2048),
+    verbose: z.boolean().optional().default(false),
+    receiver_threads: z.int().gte(1).lte(512).optional().default(64),
+    numa_policy: z.string().optional(),
+    frontend_directory: z.string(),
+    spot_finding: zSpotFindingSettings.optional(),
+    image_pusher: zImagePusherType,
+    zeromq_preview: zZeromqPreviewSettings.optional(),
+    zeromq_metadata: zZeromqMetadataSettings.optional(),
+    dark_mask: zDarkMaskSettings.optional()
+});
+
+/**
+ * Binning of frames for the plot (0 = default binning)
+ */
+export const zBinning = z.int().default(1);
+
+/**
+ * If measurement has goniometer axis defined, plot X-axis will represent rotation angle
+ * If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
+ * For still measurement the number is ignored
+ *
+ */
+export const zExperimentalCoord = z.boolean().default(false);
+
+/**
+ * Unit used for azim int.
+ *
+ */
+export const zAzintUnit = z.enum([
+    'Q_recipA',
+    'd_A',
+    'two_theta_deg'
+]).default('Q_recipA');
+
+/**
+ * Fill value for elements that were missed during data collection
+ *
+ */
+export const zFillValue = z.number();
+
+/**
+ * Type of requested plot
+ */
+export const zPlotType = z.enum([
+    'bkg_estimate',
+    'azint',
+    'azint_1d',
+    'spot_count',
+    'spot_count_low_res',
+    'spot_count_indexed',
+    'spot_count_ice',
+    'indexing_rate',
+    'indexing_lattice_count',
+    'indexing_unit_cell_length',
+    'indexing_unit_cell_angle',
+    'profile_radius',
+    'mosaicity',
+    'b_factor',
+    'error_pixels',
+    'saturated_pixels',
+    'image_collection_efficiency',
+    'receiver_delay',
+    'receiver_free_send_buf',
+    'strong_pixels',
+    'roi_sum',
+    'roi_mean',
+    'roi_max_count',
+    'roi_pixels',
+    'roi_weighted_x',
+    'roi_weighted_y',
+    'packets_received',
+    'max_pixel_value',
+    'resolution_estimate',
+    'pixel_sum',
+    'processing_time',
+    'beam_center_x',
+    'beam_center_y',
+    'integrated_reflections',
+    'image_scale_factor',
+    'image_scale_cc',
+    'image_scale_b',
+    'compression_ratio'
+]);
+
+/**
+ * Name of ROI for which plot is requested
+ */
+export const zRoi = z.string().min(1);
+
+/**
+ * Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer
+ */
+export const zImageId = z.coerce.bigint().gte(BigInt(-2)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).default(BigInt(-1));
+
+/**
+ * Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
+ */
+export const zSaturation = z.number().gte(-32767).lte(32767);
+
+/**
+ * Background value to set contrast in the preview image
+ */
+export const zBackground = z.number().gte(-32767).lte(32767).default(0);
+
+/**
+ * Show spot finding results on the image
+ */
+export const zShowSpots = z.boolean().default(true);
+
+/**
+ * Show beam center on the image
+ */
+export const zShowBeamCenter = z.boolean().default(true);
+
+/**
+ * Show ROI areas on the image
+ */
+export const zShowRoi = z.boolean().default(false);
+
+/**
+ * Quality of JPEG image (100 - highest; 0 - lowest)
+ */
+export const zJpegQuality = z.coerce.bigint().gte(BigInt(0)).lte(BigInt(100)).default(BigInt(100));
+
+/**
+ * Show user mask
+ */
+export const zShowUserMask = z.boolean().default(false);
+
+/**
+ * Show resolution ring, provided in Angstrom
+ */
+export const zResolutionRing = z.number().gte(0.1).lte(100).default(0.1);
+
+/**
+ * Show resolution estimation as a ring
+ */
+export const zResolutionEstimate = z.boolean().default(false);
+
+/**
+ * Color scale for preview image
+ */
+export const zColorScale = z.enum([
+    'indigo',
+    'viridis',
+    'bw',
+    'wb',
+    'green',
+    'heat',
+    'magma',
+    'inferno'
+]).default('indigo');
+
+export const zPostStartBody = zDatasetSettings;
+
+export const zPostWaitUntilRunningQuery = z.object({
+    timeout: z.int().gte(0).lte(3600).optional().default(60)
+});
+
+export const zPostWaitTillDoneQuery = z.object({
+    timeout: z.int().gte(0).lte(3600).optional().default(60)
+});
+
+/**
+ * Everything OK
+ */
+export const zGetConfigDetectorResponse = zDetectorSettings;
+
+export const zPutConfigDetectorBody = zDetectorSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigIndexingResponse = zIndexingSettings;
+
+export const zPutConfigIndexingBody = zIndexingSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigFileWriterResponse = zFileWriterSettings;
+
+export const zPutConfigFileWriterBody = zFileWriterSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigInstrumentResponse = zInstrumentMetadata;
+
+export const zPutConfigInstrumentBody = zInstrumentMetadata;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigImageFormatResponse = zImageFormatSettings;
+
+export const zPutConfigImageFormatBody = zImageFormatSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigSpotFindingResponse = zSpotFindingSettings;
+
+export const zPutConfigSpotFindingBody = zSpotFindingSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigAzimIntResponse = zAzimIntSettings;
+
+export const zPutConfigAzimIntBody = zAzimIntSettings;
+
+export const zPutConfigInternalGeneratorImageBody = z.string();
+
+export const zPutConfigInternalGeneratorImageQuery = z.object({
+    id: z.coerce.bigint().gte(BigInt(0)).lte(BigInt(127)).optional()
+});
+
+export const zPutConfigInternalGeneratorImageTiffBody = z.string();
+
+export const zPutConfigInternalGeneratorImageTiffQuery = z.object({
+    id: z.int().gte(0).lte(127).optional()
+});
+
+/**
+ * Everything OK
+ */
+export const zGetConfigSelectDetectorResponse = zDetectorList;
+
+export const zPutConfigSelectDetectorBody = zDetectorSelection;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigZeromqPreviewResponse = zZeromqPreviewSettings;
+
+export const zPutConfigZeromqPreviewBody = zZeromqPreviewSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigZeromqMetadataResponse = zZeromqMetadataSettings;
+
+export const zPutConfigZeromqMetadataBody = zZeromqMetadataSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetConfigDarkMaskResponse = zDarkMaskSettings;
+
+export const zPutConfigDarkMaskBody = zDarkMaskSettings;
+
+/**
+ * Everything OK
+ */
+export const zGetStatusResponse = zBrokerStatus;
+
+/**
+ * Everything OK
+ */
+export const zGetFpgaStatusResponse = zFpgaStatus;
+
+/**
+ * Pulse ID collected
+ */
+export const zGetXfelPulseIdResponse = z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }));
+
+/**
+ * Event codes collected
+ */
+export const zGetXfelEventCodeResponse = z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }));
+
+/**
+ * Everything OK
+ */
+export const zGetImagePusherStatusResponse = zImagePusherStatus;
+
+/**
+ * Everything OK
+ */
+export const zGetDetectorStatusResponse = zDetectorStatus;
+
+/**
+ * OK
+ */
+export const zGetConfigRoiResponse = zRoiDefinitions;
+
+export const zPutConfigRoiBody = zRoiDefinitions;
+
+/**
+ * Everything OK
+ */
+export const zGetStatisticsResponse = zJfjochStatistics;
+
+/**
+ * Everything OK
+ */
+export const zGetStatisticsDataCollectionResponse = zMeasurementStatistics;
+
+/**
+ * Everything OK
+ */
+export const zGetStatisticsCalibrationResponse = zCalibrationStatistics;
+
+/**
+ * Binary array (4 byte; unsigned)
+ */
+export const zGetConfigMaskResponse = z.string();
+
+/**
+ * User mask in binary format (4 byte; unsigned)
+ */
+export const zGetConfigUserMaskResponse = z.string();
+
+export const zPutConfigUserMaskBody = z.string();
+
+/**
+ * Pixel mask in TIFF format (4 byte; unsigned)
+ */
+export const zGetConfigMaskTiffResponse = z.string();
+
+/**
+ * User mask in TIFF format (4 byte; unsigned)
+ */
+export const zGetConfigUserMaskTiffResponse = z.string();
+
+export const zPutConfigUserMaskTiffBody = z.string();
+
+export const zGetPreviewPedestalTiffQuery = z.object({
+    gain_level: z.int(),
+    sc: z.int().optional()
+});
+
+/**
+ * Calibration image
+ */
+export const zGetPreviewPedestalTiffResponse = z.string();
+
+export const zGetPreviewPlotQuery = z.object({
+    binning: z.int().optional().default(1),
+    type: z.enum([
+        'bkg_estimate',
+        'azint',
+        'azint_1d',
+        'spot_count',
+        'spot_count_low_res',
+        'spot_count_indexed',
+        'spot_count_ice',
+        'indexing_rate',
+        'indexing_lattice_count',
+        'indexing_unit_cell_length',
+        'indexing_unit_cell_angle',
+        'profile_radius',
+        'mosaicity',
+        'b_factor',
+        'error_pixels',
+        'saturated_pixels',
+        'image_collection_efficiency',
+        'receiver_delay',
+        'receiver_free_send_buf',
+        'strong_pixels',
+        'roi_sum',
+        'roi_mean',
+        'roi_max_count',
+        'roi_pixels',
+        'roi_weighted_x',
+        'roi_weighted_y',
+        'packets_received',
+        'max_pixel_value',
+        'resolution_estimate',
+        'pixel_sum',
+        'processing_time',
+        'beam_center_x',
+        'beam_center_y',
+        'integrated_reflections',
+        'image_scale_factor',
+        'image_scale_cc',
+        'image_scale_b',
+        'compression_ratio'
+    ]),
+    fill: z.number().optional(),
+    experimental_coord: z.boolean().optional().default(false),
+    azint_unit: z.enum([
+        'Q_recipA',
+        'd_A',
+        'two_theta_deg'
+    ]).optional().default('Q_recipA')
+});
+
+/**
+ * Everything OK.
+ */
+export const zGetPreviewPlotResponse = zPlots;
+
+export const zGetPreviewPlotBinQuery = z.object({
+    type: z.enum([
+        'bkg_estimate',
+        'azint',
+        'azint_1d',
+        'spot_count',
+        'spot_count_low_res',
+        'spot_count_indexed',
+        'spot_count_ice',
+        'indexing_rate',
+        'indexing_lattice_count',
+        'indexing_unit_cell_length',
+        'indexing_unit_cell_angle',
+        'profile_radius',
+        'mosaicity',
+        'b_factor',
+        'error_pixels',
+        'saturated_pixels',
+        'image_collection_efficiency',
+        'receiver_delay',
+        'receiver_free_send_buf',
+        'strong_pixels',
+        'roi_sum',
+        'roi_mean',
+        'roi_max_count',
+        'roi_pixels',
+        'roi_weighted_x',
+        'roi_weighted_y',
+        'packets_received',
+        'max_pixel_value',
+        'resolution_estimate',
+        'pixel_sum',
+        'processing_time',
+        'beam_center_x',
+        'beam_center_y',
+        'integrated_reflections',
+        'image_scale_factor',
+        'image_scale_cc',
+        'image_scale_b',
+        'compression_ratio'
+    ]),
+    roi: z.string().min(1).optional()
+});
+
+/**
+ * Everything OK.
+ */
+export const zGetPreviewPlotBinResponse = z.string();
+
+/**
+ * Everything OK.
+ */
+export const zGetResultScanResponse = zScanResult;
+
+/**
+ * Return start message
+ */
+export const zGetImageBufferStartCborResponse = z.string();
+
+export const zGetImageBufferImageCborQuery = z.object({
+    id: z.coerce.bigint().gte(BigInt(-2)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(-1))
+});
+
+/**
+ * Return image message
+ */
+export const zGetImageBufferImageCborResponse = z.string();
+
+export const zGetImageBufferImageJpegQuery = z.object({
+    id: z.coerce.bigint().gte(BigInt(-2)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(-1)),
+    show_user_mask: z.boolean().optional().default(false),
+    show_roi: z.boolean().optional().default(false),
+    show_spots: z.boolean().optional().default(true),
+    show_beam_center: z.boolean().optional().default(true),
+    saturation: z.number().gte(-32767).lte(32767).optional(),
+    jpeg_quality: z.coerce.bigint().gte(BigInt(0)).lte(BigInt(100)).optional().default(BigInt(100)),
+    show_res_ring: z.number().gte(0.1).lte(100).optional().default(0.1),
+    color: z.enum([
+        'indigo',
+        'viridis',
+        'bw',
+        'wb',
+        'green',
+        'heat',
+        'magma',
+        'inferno'
+    ]).optional().default('indigo'),
+    show_res_est: z.boolean().optional().default(false)
+});
+
+/**
+ * Preview image
+ */
+export const zGetImageBufferImageJpegResponse = z.string();
+
+export const zGetImageBufferImageTiffQuery = z.object({
+    id: z.coerce.bigint().gte(BigInt(-2)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional().default(BigInt(-1))
+});
+
+/**
+ * Preview image
+ */
+export const zGetImageBufferImageTiffResponse = z.string();
+
+/**
+ * Done
+ */
+export const zGetImageBufferStatusResponse = zImageBufferStatus;
+
+/**
+ * Release number of Jungfraujoch
+ */
+export const zGetVersionResponse = z.string();
-- 
2.52.0


From 4f9452736a953ec8ba53747927418a8271f64366 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 07:57:57 +0200
Subject: [PATCH 098/228] frontend: drawer-based navigation shell

Replace the stack of toggle-revealed sections with a left navigation
drawer (collapsible, expanded by default) clipped under a persistent
status bar. Dashboard (plots + measurement statistics + spot-finding)
is the default view; every other panel is its own drawer entry, so one
thing shows at a time.

- Group entries under Acquisition / Expert / Reference subheaders;
  ROI folded into On-the-fly processing.
- Pale-indigo drawer with a lime accent on the selected entry.
- Gray out JUNGFRAU calibration / FPGA status when their data is empty.
- API reference and documentation open in-app via iframe.
- Fixed footer pinned to the page bottom.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/App.tsx                  | 371 +++++++++++++++-----------
 frontend/src/components/StatusBar.tsx |  14 +-
 2 files changed, 220 insertions(+), 165 deletions(-)

diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 97194c70..2b11076b 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -1,35 +1,61 @@
-import React, {useState} from 'react';
+import { ReactNode, useCallback, useState } from 'react';
 
-import {createTheme, CssBaseline, Grid, Stack, Switch, ThemeProvider, Typography} from "@mui/material";
-import {indigo, lime} from "@mui/material/colors";
-import {useQuery} from "@tanstack/react-query";
+import {
+    Box, createTheme, CssBaseline, Drawer, Grid, Link, List, ListItemButton,
+    ListItemIcon, ListItemText, ListSubheader, Stack, ThemeProvider, Toolbar,
+} from "@mui/material";
+import { indigo, lime } from "@mui/material/colors";
+import { useQuery } from "@tanstack/react-query";
+
+import DashboardIcon from "@mui/icons-material/Dashboard";
+import ImageIcon from "@mui/icons-material/Image";
+import VideocamIcon from "@mui/icons-material/Videocam";
+import MemoryIcon from "@mui/icons-material/Memory";
+import ChecklistIcon from "@mui/icons-material/Checklist";
+import GridOnIcon from "@mui/icons-material/GridOn";
+import BoltIcon from "@mui/icons-material/Bolt";
+import SaveIcon from "@mui/icons-material/Save";
+import HubIcon from "@mui/icons-material/Hub";
+import StraightenIcon from "@mui/icons-material/Straighten";
+import DeveloperBoardIcon from "@mui/icons-material/DeveloperBoard";
+import OpenInNewIcon from "@mui/icons-material/OpenInNew";
+import ApiIcon from "@mui/icons-material/Api";
+import MenuBookIcon from "@mui/icons-material/MenuBook";
+import _ from "lodash";
 
-import DataProcessingSettings from "./components/DataProcessingSettings";
-import DetectorSettings from "./components/DetectorSettings";
-import Calibration from "./components/Calibration";
 import StatusBar from "./components/StatusBar";
+import ErrorMessage from "./components/ErrorMessage";
 import DataProcessingPlots from "./components/DataProcessingPlots";
-import DetectorSelection from "./components/DetectorSelection";
 import MeasurementStatistics from "./components/MeasurementStatistics";
-import DetectorStatus from "./components/DetectorStatus";
-import Paper from "@mui/material/Paper";
+import DataProcessingSettings from "./components/DataProcessingSettings";
 import PreviewImage from "./components/PreviewImage";
+import DataCollection from "./components/DataCollection";
+import DetectorSettings from "./components/DetectorSettings";
+import DetectorSelection from "./components/DetectorSelection";
+import DetectorStatus from "./components/DetectorStatus";
+import PixelMask from "./components/PixelMask";
+import DarkMaskSettings from "./components/DarkMaskSettings";
+import IndexingSettings from "./components/IndexingSettings";
+import AzIntSettings from "./components/AzIntSettings";
 import ROI from "./components/ROI";
+import FileWriterSettings from "./components/FileWriterSettings";
 import ImageFormatSettings from "./components/ImageFormatSettings";
 import InstrumentMetadata from "./components/InstrumentMetadata";
-import {JFJOCH_VERSION} from "./version";
-import FpgaStatus from "./components/FpgaStatus";
-import {plot_type} from "./client";
-import {getStatisticsOptions} from "./client/@tanstack/react-query.gen";
-import DataCollection from "./components/DataCollection";
 import ZeroMQPreview from "./components/ZeroMQPreview";
-import PixelMask from "./components/PixelMask";
-import ErrorMessage from "./components/ErrorMessage";
-import FileWriterSettings from "./components/FileWriterSettings";
-import AzIntSettings from "./components/AzIntSettings";
-import IndexingSettings from "./components/IndexingSettings";
-import DarkMaskSettings from "./components/DarkMaskSettings";
 import ImagePusherStatus from "./components/ImagePusherStatus";
+import Calibration from "./components/Calibration";
+import FpgaStatus from "./components/FpgaStatus";
+
+import { plot_type } from "./client";
+import { getStatisticsOptions } from "./client/@tanstack/react-query.gen";
+import { JFJOCH_VERSION } from "./version";
+
+const drawerWidth = 240;
+
+// Pale indigo drawer that echoes the indigo top bar without repeating it, with a
+// lime accent on the selected entry (lime reads well small, garish large).
+const drawerBg = indigo[50];
+const drawerSelectedBg = indigo[100];
 
 const jfjoch_theme = createTheme({
     palette: {
@@ -38,161 +64,182 @@ const jfjoch_theme = createTheme({
     },
 });
 
-function renderTitleWithSwitch(name: string, checked: boolean, func: ((event: React.ChangeEvent<HTMLInputElement>) => void)) {
-    return <Grid item xs={12}>
-        <Paper style={{textAlign: 'center'}} sx={{height: 60, width: '100%'}} component={Stack}
-               direction="column" justifyContent="center">
-            <Grid container spacing={0}>
-                <Grid xs={1}/>
-                <Grid xs={10}>
-                    <Typography variant="h5"> {name} </Typography>
-                </Grid>
-                <Grid xs={1}>
-                    <Switch checked={checked}
-                            onChange={func}
-                            name="Show detector setup"/>
-                </Grid>
-            </Grid>
-        </Paper>
-    </Grid>
+type NavItem = { id: string; label: string; icon: ReactNode; disabled?: boolean; render: () => ReactNode };
+type NavSection = { subheader?: string; items: NavItem[] };
+
+/** Documentation / API reference shown inside the app area, with a new-tab escape hatch. */
+function DocFrame({ title, src }: { title: string; src: string }) {
+    return (
+        <Box>
+            <Box sx={{ mb: 1, textAlign: "right" }}>
+                <Link href={src} target="_blank" rel="noopener"
+                      sx={{ display: "inline-flex", alignItems: "center", gap: 0.5 }}>
+                    Open in new tab <OpenInNewIcon fontSize="small"/>
+                </Link>
+            </Box>
+            <Box component="iframe" title={title} src={src}
+                 sx={{ width: "100%", height: "calc(100vh - 220px)", border: "1px solid",
+                       borderColor: "divider", borderRadius: 1 }}/>
+        </Box>
+    );
 }
 
 function App() {
-    const [showDetectorSetup, setShowDetectorSetup] = useState(false);
-    const [showModuleCalibration, setShowModuleCalibration] = useState(false);
-    const [showPreview, setShowPreview] = useState(false);
-    const [showRoiSetup, setShowRoiSetup] = useState(false);
-    const [showFpgaStatus, setShowFpgaStatus] = useState(false);
-    const [showDataCollection, setShowDataCollection] = useState(false);
+    const [drawerOpen, setDrawerOpen] = useState(true);
+    const [view, setView] = useState('dashboard');
+
+    const toggleDrawer = useCallback(() => setDrawerOpen(o => !o), []);
 
     // Poll general statistics once per second; structural sharing keeps unchanged
-    // slices referentially stable so memoized children below only re-render when
-    // their own slice changes.
-    const {data, isError, refetch} = useQuery({
+    // slices referentially stable so memoized panels only re-render when their own
+    // slice changes.
+    const { data, isError, refetch } = useQuery({
         ...getStatisticsOptions(),
         refetchInterval: 1000,
     });
     const s = isError || data === undefined ? {} : data;
-
     const isMeasuring = s.broker?.state === 'Measuring';
 
+    // Every panel that used to live behind a toggle is now a single drawer entry;
+    // only the active one is mounted, so the screen shows one thing at a time.
+    const sections: NavSection[] = [
+        { items: [
+            { id: 'dashboard', label: 'Dashboard', icon: <DashboardIcon/>, render: () => (
+                <Grid container spacing={3} justifyContent="center" alignItems="flex-start">
+                    <Grid item xs={12} lg={8}>
+                        <DataProcessingPlots height={550} type={plot_type.BKG_ESTIMATE}/>
+                    </Grid>
+                    <Grid item xs={12} lg={4}>
+                        <MeasurementStatistics s={s.measurement ?? {}}/>
+                    </Grid>
+                    <Grid item xs={12} lg={8}>
+                        <DataProcessingPlots height={800} type={plot_type.INDEXING_RATE}/>
+                    </Grid>
+                    <Grid item xs={12} lg={4}>
+                        <DataProcessingSettings s={s.data_processing_settings} update={refetch}/>
+                    </Grid>
+                </Grid>
+            )},
+        ]},
+        { subheader: 'Acquisition', items: [
+            { id: 'preview', label: 'Live preview', icon: <ImageIcon/>, render: () => (
+                <PreviewImage measuring={isMeasuring}
+                              max_image_number={s.buffer?.max_image_number}
+                              min_image_number={s.buffer?.min_image_number}/>
+            )},
+            { id: 'data-collection', label: 'Data collection', icon: <VideocamIcon/>, render: () => (
+                <DataCollection frame_time_us={s.detector_settings?.frame_time_us ?? 500}/>
+            )},
+        ]},
+        { subheader: 'Expert', items: [
+            { id: 'detector', label: 'Detector', icon: <MemoryIcon/>, render: () => (
+                <Stack spacing={2}>
+                    <DetectorStatus s={s.detector}/>
+                    <DetectorSettings s={s.detector_settings}/>
+                </Stack>
+            )},
+            { id: 'detector-selection', label: 'Detector selection', icon: <ChecklistIcon/>, render: () => (
+                <DetectorSelection s={s.detector_list}/>
+            )},
+            { id: 'masks', label: 'Masks', icon: <GridOnIcon/>, render: () => (
+                <Stack spacing={2}>
+                    <PixelMask s={s.pixel_mask}/>
+                    <DarkMaskSettings s={s.dark_mask}/>
+                </Stack>
+            )},
+            { id: 'processing', label: 'On-the-fly processing', icon: <BoltIcon/>, render: () => (
+                <Stack spacing={2}>
+                    <IndexingSettings s={s.indexing} status={s.broker}/>
+                    <AzIntSettings s={s.az_int}/>
+                    <ROI s={s.roi}/>
+                </Stack>
+            )},
+            { id: 'output', label: 'Output', icon: <SaveIcon/>, render: () => (
+                <Stack spacing={2}>
+                    <FileWriterSettings s={s.file_writer_settings}/>
+                    <ImageFormatSettings s={s.image_format_settings}/>
+                    <InstrumentMetadata s={s.instrument_metadata}/>
+                </Stack>
+            )},
+            { id: 'streaming', label: 'Streaming', icon: <HubIcon/>, render: () => (
+                <Stack spacing={2}>
+                    <ZeroMQPreview s={s.zeromq_preview}/>
+                    <ImagePusherStatus s={s.image_pusher}/>
+                </Stack>
+            )},
+            { id: 'calibration', label: 'JUNGFRAU calibration', icon: <StraightenIcon/>,
+              disabled: _.isEmpty(s.calibration), render: () => (
+                <Calibration s={s.calibration}/>
+            )},
+            { id: 'fpga', label: 'FPGA status', icon: <DeveloperBoardIcon/>,
+              disabled: _.isEmpty(s.fpga), render: () => (
+                <FpgaStatus s={s.fpga}/>
+            )},
+        ]},
+        { subheader: 'Reference', items: [
+            { id: 'api-reference', label: 'API reference', icon: <ApiIcon/>, render: () => (
+                <DocFrame title="API reference" src="/frontend/openapi.html"/>
+            )},
+            { id: 'documentation', label: 'Documentation', icon: <MenuBookIcon/>, render: () => (
+                <DocFrame title="Documentation" src="https://jungfraujoch.readthedocs.io/"/>
+            )},
+        ]},
+    ];
+
+    const activeItem = sections.flatMap(sec => sec.items).find(it => it.id === view) ?? sections[0].items[0];
+
     return <ThemeProvider theme={jfjoch_theme}>
         <CssBaseline enableColorScheme/>
-        <StatusBar s={s.broker}/> <br/><br/><br/><br/>
-        <div style={{
-            display: 'flex',
-            alignItems: 'center',
-            justifyContent: 'center'
+        <Box sx={{ display: 'flex' }}>
+            <StatusBar s={s.broker} onMenuClick={toggleDrawer}/>
+            {drawerOpen && (
+                <Drawer variant="permanent"
+                        sx={{ width: drawerWidth, flexShrink: 0,
+                              '& .MuiDrawer-paper': { width: drawerWidth, boxSizing: 'border-box',
+                                                      bgcolor: drawerBg, borderRight: 'none' } }}>
+                    <Toolbar/>
+                    <Box sx={{ overflow: 'auto', pb: 6 }}>
+                        {sections.map((sec, i) => (
+                            <List key={i} subheader={sec.subheader
+                                ? <ListSubheader sx={{ bgcolor: 'transparent', color: 'primary.dark',
+                                                       fontWeight: 600 }}>{sec.subheader}</ListSubheader>
+                                : undefined}>
+                                {sec.items.map(it => (
+                                    <ListItemButton key={it.id} selected={view === it.id}
+                                                    disabled={it.disabled}
+                                                    onClick={() => setView(it.id)}
+                                                    sx={{ borderLeft: '4px solid transparent',
+                                                          '&.Mui-selected': { bgcolor: drawerSelectedBg,
+                                                              borderColor: 'secondary.main' },
+                                                          '&.Mui-selected:hover': { bgcolor: drawerSelectedBg } }}>
+                                        <ListItemIcon sx={{ minWidth: 40 }}>{it.icon}</ListItemIcon>
+                                        <ListItemText primary={it.label}/>
+                                    </ListItemButton>
+                                ))}
+                            </List>
+                        ))}
+                    </Box>
+                </Drawer>
+            )}
+            <Box component="main" sx={{ flexGrow: 1, p: 3, pb: '64px', minWidth: 0 }}>
+                <Toolbar/>
+                <ErrorMessage s={s.broker}/>
+                <Box sx={{ maxWidth: 1300, mx: 'auto', mt: 2 }}>
+                    {activeItem.render()}
+                </Box>
+            </Box>
+        </Box>
+        <Box component="footer" sx={{
+            position: 'fixed', bottom: 0, left: 0, right: 0,
+            zIndex: (t) => t.zIndex.drawer + 1,
+            bgcolor: 'background.paper', borderTop: '1px solid', borderColor: 'divider',
+            py: 0.5, px: 2, textAlign: 'center', fontSize: '0.8rem',
         }}>
-            <Grid container
-                  justifyContent="center"
-                  alignItems="center"
-                  spacing={3}
-                  sx={{width: "95%"}}>
-                <Grid item xs={2}/>
-                <Grid item xs={8}>
-                    <ErrorMessage s={s.broker}/>
-                </Grid>
-                <Grid item xs={2}/>
-                <Grid item xs={8}>
-                    <DataProcessingPlots height={550} type={plot_type.BKG_ESTIMATE}/>
-                </Grid>
-                <Grid item xs={4}>
-                    <MeasurementStatistics
-                        s={(s.measurement === undefined) ? {} : s.measurement}/>
-                </Grid>
-                <Grid item xs={8}>
-                    <DataProcessingPlots height={800} type={plot_type.INDEXING_RATE}/>
-                </Grid>
-                <Grid item xs={4}>
-                    <DataProcessingSettings s={s.data_processing_settings} update={refetch}/>
-                </Grid>
-                {
-                    renderTitleWithSwitch("Live image preview", showPreview, e => setShowPreview(e.target.checked))
-                }
-                <Grid item xs={12}>
-                    {showPreview ? <PreviewImage measuring={isMeasuring}
-                                                 max_image_number={s.buffer?.max_image_number}
-                                                 min_image_number={s.buffer?.min_image_number}/> : ""}
-                </Grid>
-                <br/><br/>
-                {
-                    renderTitleWithSwitch("Data collection",
-                        showDataCollection, e => setShowDataCollection(e.target.checked))
-                }
-                <Grid item xs={2}/>
-                <Grid item xs={8}>
-                    {showDataCollection ? <DataCollection frame_time_us={
-                        s.detector_settings?.frame_time_us ?? 500
-                    }/> : ""}
-                </Grid>
-                <Grid item xs={2}/>
-                <br/><br/>
-                {
-                    renderTitleWithSwitch("Jungfraujoch expert configuration",
-                        showDetectorSetup, e => setShowDetectorSetup(e.target.checked))
-                }
-                <Grid item xs={4}>
-                    {showDetectorSetup ? <Stack spacing={2}>
-                        <DetectorSettings s={s.detector_settings}/>
-                        <PixelMask s={s.pixel_mask}/>
-                        <DarkMaskSettings s={s.dark_mask}/>
-                        <FileWriterSettings s={s.file_writer_settings}/>
-                    </Stack>: ""}
-                </Grid>
-                <Grid item xs={4}>
-                    {showDetectorSetup ?
-                        <Stack spacing={2}>
-                            <DetectorSelection s={s.detector_list}/>
-                            <DetectorStatus s={s.detector}/>
-                            <ZeroMQPreview s={s.zeromq_preview}/>
-                            <IndexingSettings s={s.indexing} status={s.broker}/>
-                        </Stack> : ""}
-                </Grid>
-                <Grid item xs={4}>
-                    {showDetectorSetup ?
-                        <Stack spacing={2}>
-                            <ImageFormatSettings s={s.image_format_settings}/>
-                            <InstrumentMetadata s={s.instrument_metadata}/>
-                            <AzIntSettings s={s.az_int}/>
-                            <ImagePusherStatus s={s.image_pusher}/>
-                        </Stack> : ""}
-                </Grid>
-                <br/><br/>
-                {
-                    renderTitleWithSwitch("JUNGFRAU module calibration",
-                        showModuleCalibration, e => setShowModuleCalibration(e.target.checked))
-                }
-                <Grid item xs={12}>
-                    {showModuleCalibration ? <Calibration s={s.calibration}/> : ""}
-                </Grid>
-                <br/><br/>
-                {
-                    renderTitleWithSwitch("Region of interest (ROI)",
-                        showRoiSetup, e => setShowRoiSetup(e.target.checked))
-                }
-                <Grid item xs={12}>
-                    {showRoiSetup ? <ROI s={s.roi}/> : ""}
-                </Grid>
-                <br/><br/>
-                {
-                    renderTitleWithSwitch("FPGA status",
-                        showFpgaStatus, e => setShowFpgaStatus(e.target.checked))
-                }
-                <Grid item xs={12}>
-                    {showFpgaStatus ? <FpgaStatus s={s.fpga}/> : ""}
-                </Grid>
-            </Grid>
-        </div>
-        <br/>
-        <center>Developed at Paul Scherrer Institute (2019-2024). Main author: <a
-            href="mailto:filip.leonarski@psi.ch">Filip Leonarski</a> <br/>
-            For more information see <a href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron
-                Rad.</i> (2023). <b>30</b>, 227–234</a> <br/>
-            Version: {JFJOCH_VERSION}&nbsp;&nbsp;&nbsp;
-            <a href="/frontend/openapi.html">API reference</a>&nbsp;&nbsp;&nbsp;
-            <a href="https://jungfraujoch.readthedocs.io/">Documentation</a></center>
-        <br/>
+            Developed at Paul Scherrer Institute (2019–2026). Main author:{' '}
+            <Link href="mailto:filip.leonarski@psi.ch">Filip Leonarski</Link> ·{' '}
+            <Link href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron Rad.</i> (2023). <b>30</b>, 227–234</Link>
+            {' '}· Version: {JFJOCH_VERSION}
+        </Box>
     </ThemeProvider>
 }
 
diff --git a/frontend/src/components/StatusBar.tsx b/frontend/src/components/StatusBar.tsx
index 79249eef..90852b0a 100644
--- a/frontend/src/components/StatusBar.tsx
+++ b/frontend/src/components/StatusBar.tsx
@@ -3,11 +3,14 @@ import {memo, ReactNode} from 'react';
 import AppBar from '@mui/material/AppBar';
 import Toolbar from '@mui/material/Toolbar';
 import Typography from '@mui/material/Typography';
+import IconButton from '@mui/material/IconButton';
+import MenuIcon from '@mui/icons-material/Menu';
 import {broker_status} from "../client";
 import ButtonWithSnackbar from "./ButtonWithSnackbar";
 
 type MyProps = {
-    s?: broker_status
+    s?: broker_status;
+    onMenuClick?: () => void;
 }
 
 function FormatNumber(x: number) : string {
@@ -19,7 +22,7 @@ function FormatNumber(x: number) : string {
         return x.toFixed(1);
 }
 
-function StatusBar({s}: MyProps) {
+function StatusBar({s, onMenuClick}: MyProps) {
     const statusDescription = (): ReactNode => {
         if (s === undefined)
             return <>Not connected</>;
@@ -30,8 +33,13 @@ function StatusBar({s}: MyProps) {
             </div>
     };
 
-    return <AppBar>
+    return <AppBar sx={{zIndex: (theme) => theme.zIndex.drawer + 1}}>
         <Toolbar>
+            {onMenuClick && (
+                <IconButton color="inherit" edge="start" onClick={onMenuClick} sx={{mr: 2}}>
+                    <MenuIcon/>
+                </IconButton>
+            )}
             <Typography variant="h6" style={{flexGrow: 0.5}}>
                 PSI Jungfraujoch
             </Typography>
-- 
2.52.0


From a76aac65b7b9262b4605429a52e95954a9f27715 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 08:01:03 +0200
Subject: [PATCH 099/228] frontend: add missing React keys in DetectorSelection
 and ROI

DetectorSelection rendered the info-table rows and the detector-select
menu items without keys; ROI's grid action cells likewise. Add stable
keys to silence the warnings.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/components/DetectorSelection.tsx | 4 ++--
 frontend/src/components/ROI.tsx               | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/frontend/src/components/DetectorSelection.tsx b/frontend/src/components/DetectorSelection.tsx
index f3a771ab..d38b1f1e 100644
--- a/frontend/src/components/DetectorSelection.tsx
+++ b/frontend/src/components/DetectorSelection.tsx
@@ -83,7 +83,7 @@ function DetectorSelection({s}: MyProps) {
                 <TableBody>
                     {
                         arr.map(d => (
-                            <TableRow>
+                            <TableRow key={d.title}>
                                 <TableCell component="th" scope="row">{d.title}: </TableCell>
                                 <TableCell align="right">{d.val}</TableCell>
                             </TableRow>
@@ -129,7 +129,7 @@ function DetectorSelection({s}: MyProps) {
                     onChange={handleChange}
                     disabled={s === undefined}
                 >
-                    {detector_options().map(d => (<MenuItem value={d.id}> {d.name} </MenuItem>))}
+                    {detector_options().map(d => (<MenuItem key={d.id} value={d.id}> {d.name} </MenuItem>))}
                 </Select>
             </FormControl>
         </SettingsPanel>
diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index 379ccad4..5e0a43bc 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -243,6 +243,7 @@ function ROI({s: serverS}: MyProps) {
             getActions: (id : GridRowModel) => {
                 return [
                     <GridActionsCellItem
+                        key="delete"
                         icon={<DeleteIcon />}
                         label="Delete"
                         onClick={handleDeleteBoxROIClick(id)}
@@ -261,6 +262,7 @@ function ROI({s: serverS}: MyProps) {
             getActions: (id : GridRowModel) => {
                 return [
                     <GridActionsCellItem
+                        key="delete"
                         icon={<DeleteIcon />}
                         label="Delete"
                         onClick={handleDeleteCircleROIClick(id)}
@@ -322,6 +324,7 @@ function ROI({s: serverS}: MyProps) {
             getActions: (id : GridRowModel) => {
                 return [
                     <GridActionsCellItem
+                        key="delete"
                         icon={<DeleteIcon />}
                         label="Delete"
                         onClick={handleDeleteAzimROIClick(id)}
-- 
2.52.0


From 88f97fc19760348cc80aed0e480bc66072220c46 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 08:08:46 +0200
Subject: [PATCH 100/228] docs: add CLAUDE.md with build/test/architecture,
 code-style and portability guidance

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CLAUDE.md | 159 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100644 CLAUDE.md

diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 00000000..cc308d96
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,159 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## What this is
+
+Jungfraujoch is the data-acquisition and analysis system for the PSI JUNGFRAU and EIGER
+X-ray detectors. It receives detector data, runs it through an FPGA-accelerated pipeline
+(spot finding, azimuthal/ROI integration, compression), streams images out over ZeroMQ for
+writing to HDF5, and runs crystallographic analysis (indexing, integration, scaling/merging).
+Most authoritative documentation lives in `docs/` and on Read The Docs
+(https://jungfraujoch.readthedocs.io). When changing CLI behaviour, the program's own
+usage message is the source of truth, not the docs.
+
+## Build
+
+Out-of-source CMake build, C++20, heavy use of `FetchContent` (spdlog, zstd, HDF5,
+slsDetectorPackage, Catch2, cpp-httplib, libzmq, Ceres, fast-feedback-indexer are downloaded
+and statically linked — the **first configure needs network access** and is slow).
+
+```
+mkdir build && cd build
+cmake -DCMAKE_BUILD_TYPE=Release ..
+make -j$(nproc) jfjoch_broker      # the main service; build other targets by name
+```
+
+Key CMake options:
+- `JFJOCH_USE_CUDA` (default ON) — GPU path. Needs CUDA ≥ 12.8. Provides the `ffbidx` and `fft`
+  GPU indexers; without it only the CPU `fftw` indexer is available (requires FFTW at configure
+  time, auto-detected). CUDA absence is not a build error.
+- `JFJOCH_WRITER_ONLY` (default OFF) — builds only the HDF5 writer; skips broker, FPGA,
+  receiver, analysis, tests, frontend.
+- `JFJOCH_VIEWER_BUILD` (default OFF) — builds the Qt6 `jfjoch_viewer` desktop app.
+- `SLS9` (default OFF) — build against slsDetectorPackage 9.2.0 instead of 8.0.2.
+
+The frontend is a separate custom target: `make frontend` (runs `npm ci && npm run build` in
+`frontend/`). It is not built by default unless installing.
+
+## Test
+
+Tests use **Catch2** and are collected into a single binary `tests/jfjoch_test`.
+
+```
+make -j$(nproc) jfjoch_test
+cd tests
+./jfjoch_test                       # all tests
+./jfjoch_test "<test name>"         # one test case (exact name in TEST_CASE)
+./jfjoch_test "[tag]"               # by tag
+./jfjoch_test -r junit -o report.xml
+```
+
+`make jfjoch_hdf5_test` builds the HDF5 write-speed benchmark, also used by CI to produce files
+that are validated against XDS (Durin/Neggia) and CrystFEL.
+
+Lint config is `.clang-tidy` (broad `*` check set with many exceptions; namespaces lower_case,
+classes CamelCase, global constants UPPER_CASE).
+
+## Code style
+
+The overriding principle is **simple, readable code** — favour the smallest, most direct
+implementation that a reader can verify at a glance. Extra abstraction, speculative guards, and
+clever-but-dense constructs are treated as actively harmful, not as polish. When torn between a
+tidy abstraction and a flat, obvious version, pick the obvious one.
+
+This matters most in `image_analysis/pixel_refinement/` (e.g. `PixelRefine.cpp`), which is an
+experimental prototype where readability is how the physics gets verified — keep it especially
+plain. **Do not add defensive/unrequested code** (extra validation, rejection heuristics, "just in
+case" branches) without asking first; if a guard isn't clearly needed, leave it out.
+
+Match the surrounding code's idiom, naming, and comment density rather than importing a different
+style.
+
+## Local end-to-end run (no detector / no FPGA)
+
+The FPGA HLS logic can be simulated on the CPU (`HLSSimulatedDevice`), so the full software
+stack runs without hardware (slowly — fixed-point math on CPU). See
+`docs/JFJOCH_BROKER.md` for the canonical walkthrough.
+
+```
+cd build/broker
+./jfjoch_broker ../../etc/broker_local.json 5232      # config JSON + HTTP port
+# then, separately:
+cd tests/test_data && python jfjoch_broker_test.py     # feeds a test image, starts collection
+# observe at http://localhost:5232 ; HDF5 is written under build/broker
+```
+
+`etc/broker_local.json`, `broker_eiger.json`, `broker_crmx.json` are example broker configs
+(schema = `jfjoch_settings` in `broker/jfjoch_api.yaml`).
+
+## Architecture
+
+**Data flow (online):** detector → FPGA acquisition (`fpga/`, `acquisition_device/`) →
+`receiver/` builds full images from per-module FPGA output → `image_pusher/` streams CBOR-encoded
+images over ZeroMQ → `jfjoch_writer` (`writer/`) consumes the stream and writes NXmx HDF5. The
+broker also emits a low-rate preview stream and a metadata stream (`preview/`).
+
+**`jfjoch_broker`** (`broker/`) is the central online service: HTTP/REST + OpenAPI control plane,
+FPGA configuration, image building, ZeroMQ output. `JFJochStateMachine` drives acquisition state;
+`JFJochServices` wires the pieces; `OpenAPIConvert`/`JFJochBrokerParser` translate between the
+generated API model and internal types.
+
+**Three analysis frontends share one analysis library** (`image_analysis/`, built as
+`JFJochImageAnalysis`):
+- `jfjoch_broker` — online, real-time (FPGA + GPU).
+- `jfjoch_viewer` — interactive Qt desktop (`viewer/`), results not persisted.
+- `jfjoch_process` (`tools/jfjoch_process.cpp`) — offline batch over a stored HDF5; writes
+  `_process.h5` and `.mtz`/`.cif`/`.hkl`. `jfjoch_scale` re-scales/merges already-integrated data.
+
+**`image_analysis/` pipeline** (subdirs): `spot_finding`, `indexing` (`ffbidx`/`fft` GPU,
+`fftw` CPU), `lattice_search`, `geom_refinement`, `pixel_refinement`, `bragg_prediction`,
+`bragg_integration`, `rotation_indexer`, `azint`, `roi`, `scale_merge`. Least-squares refinement
+uses **Ceres** (fetched, built with miniglog, no MKL, CXX_THREADS). `ffbidx` needs a known cell
+(`-C`) and suits sparse serial stills; `fft`/`fftw` index de novo and suit strong rotation data.
+
+**FPGA** (`fpga/`): `hls/` is the Vitis HLS source (image-analysis kernels), `hls_simulation/`
+runs that same HLS on CPU for hardware-free testing, `host_library/` is the host-side driver,
+`pcie_driver/` is the kernel module. The HLS algorithms are documented in
+`docs/FPGA_DATA_ANALYSIS.md`.
+
+**Detector control** (`detector_control/`): wrappers for SLS (JUNGFRAU) and DECTRIS SIMPLON
+(EIGER). **`jungfrau/`**: JUNGFRAU ADU→energy gain/pedestal calibration.
+
+**Other libs:** `common/` (geometry, diffraction experiment, image buffer, CUDA wrappers — the
+shared core, linked nearly everywhere), `compression/` (zstd + bitshuffle + sqrt lossy),
+`frame_serialize/` (CBOR stream codec), `gemmi_gph/` (vendored GEMMI for MTZ/XDS_ASCII I/O),
+`xds-plugin/` (XDS HDF5 read plugin).
+
+## Portability (jfjoch_viewer)
+
+Cross-platform support is a goal **only for `jfjoch_viewer` and its dependency tree** — keep that
+code, and any shared library it transitively links (`common/`, `image_analysis/`, `reader/`,
+`gemmi_gph/`, etc.), **MSVC-compatible** so the viewer can build on Windows. The rest of the
+project (broker, receiver, FPGA host, detector control, …) is Linux-only and does not need to be
+portable; don't constrain it for portability's sake.
+
+- **Windows/MSVC** is the primary portability target (a Windows viewer build needs MSVC, since
+  CUDA on Windows requires it). Avoid GCC/Clang-only extensions, POSIX-only APIs, and other
+  non-MSVC constructs in viewer-reachable code.
+- **macOS** is a nice-to-have for the viewer. It rules out CUDA, so anything the viewer depends on
+  must also have a working CPU-only / non-CUDA path (the `JFJOCH_USE_CUDA=OFF`, `fftw`-indexer
+  configuration).
+
+## OpenAPI is the single source of truth
+
+`broker/jfjoch_api.yaml` defines the entire REST API **and the shared data schemas**. From it,
+`update_version.sh` regenerates three clients — **do not hand-edit generated code**:
+- C++ server model → `broker/gen/` (cpp-pistache-server generator; compiled as `JFJochAPI`).
+- Python client → `python-client/` (and `gen_python_client.sh`, published as PyPI `jfjoch-client`).
+- TypeScript frontend client → `frontend/src/client/` (hey-api `openapi-ts`, `npm run openapi`).
+
+When you change `jfjoch_api.yaml`, regenerate the relevant client(s); for a version bump run
+`update_version.sh` (also rewrites `VERSION`, `frontend/src/version.ts`, and the Redoc html).
+
+## Frontend
+
+React 19 + TypeScript + MUI + Vite (`frontend/`). Data layer is generated from the OpenAPI spec
+(`@hey-api/openapi-ts` → fetch client + TanStack Query hooks + zod schemas). Scripts:
+`npm start` (dev server), `npm run build` (tsc + vite), `npm run openapi` (regen client),
+`npm run redocly4broker` (regen `broker/redoc-static.html`).
-- 
2.52.0


From 9e57219b3124e5c8bcf6d11afe719e3113f0760b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 09:21:39 +0200
Subject: [PATCH 101/228] common: add azimuthal-angle (phi) sectors to
 ROIAzimuthal

ROIAzimuthal can now be restricted to an azimuthal-angle sector in
addition to its Q/d range, enabling STXM-style directional ROIs. phi
bounds are optional (both-or-neither); absent means a full 360 ring, so
existing Q-only azimuthal ROIs are unchanged.

- ROIElement::CheckROI gains a phi_deg argument; box/circle ignore it.
- MarkROI gains an optional phi_map; ROIMap builds it from Phi_rad
  alongside the resolution map only when azimuthal ROIs are present.
- phi bounds are normalized to [0,360) and wrap-around sectors are
  supported (phi_min > phi_max).
- ROIConfigAzim carries phi_min/phi_max (kept trivially copyable for the
  union; phi_min == phi_max means full ring).

No phi crosses the wire yet (CBOR/API wiring follows separately).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/JFJochMessages.h             |  2 +
 common/ROIAzimuthal.cpp             | 45 +++++++++++++++++++--
 common/ROIAzimuthal.h               | 16 +++++---
 common/ROIBox.cpp                   |  2 +-
 common/ROIBox.h                     |  2 +-
 common/ROICircle.cpp                |  2 +-
 common/ROICircle.h                  |  2 +-
 common/ROIElement.cpp               | 10 +++--
 common/ROIElement.h                 |  4 +-
 common/ROIMap.cpp                   | 12 ++++--
 tests/ROIMapTest.cpp                | 62 +++++++++++++++++++++++++++++
 viewer/JFJochImageReadingWorker.cpp |  4 +-
 12 files changed, 139 insertions(+), 24 deletions(-)

diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index 067f938c..eee16f6e 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -48,6 +48,8 @@ struct ROIConfigCircle {
 
 struct ROIConfigAzim {
     double qmin, qmax;
+    // Azimuthal-angle sector in degrees; phi_min == phi_max means full ring.
+    float phi_min, phi_max;
 };
 
 struct ROIConfig {
diff --git a/common/ROIAzimuthal.cpp b/common/ROIAzimuthal.cpp
index d9321b68..3e716c19 100644
--- a/common/ROIAzimuthal.cpp
+++ b/common/ROIAzimuthal.cpp
@@ -1,11 +1,20 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include <cmath>
 #include "JFJochMath.h"
 #include "ROIAzimuthal.h"
 #include "JFJochException.h"
 
-ROIAzimuthal::ROIAzimuthal(const std::string &in_name, float in_d_min_A, float in_d_max_A)
+static float NormalizePhi_deg(float phi) {
+    phi = std::fmod(phi, 360.0f);
+    if (phi < 0)
+        phi += 360.0f;
+    return phi;
+}
+
+ROIAzimuthal::ROIAzimuthal(const std::string &in_name, float in_d_min_A, float in_d_max_A,
+                           std::optional<float> in_phi_min_deg, std::optional<float> in_phi_max_deg)
         : ROIElement(in_name) {
     if ((in_d_min_A <= 0) || (in_d_max_A <= 0))
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
@@ -17,6 +26,12 @@ ROIAzimuthal::ROIAzimuthal(const std::string &in_name, float in_d_min_A, float i
         d_max_A = in_d_max_A;
         d_min_A = in_d_min_A;
     }
+
+    if (in_phi_min_deg && in_phi_max_deg) {
+        has_phi = true;
+        phi_min_deg = NormalizePhi_deg(in_phi_min_deg.value());
+        phi_max_deg = NormalizePhi_deg(in_phi_max_deg.value());
+    }
 }
 
 float ROIAzimuthal::GetDMin_A() const {
@@ -27,8 +42,28 @@ float ROIAzimuthal::GetDMax_A() const {
     return d_max_A;
 }
 
-bool ROIAzimuthal::CheckROI(int64_t x, int64_t y, float resolution) const {
-    return (resolution >= d_min_A && resolution <= d_max_A);
+bool ROIAzimuthal::HasPhi() const {
+    return has_phi;
+}
+
+float ROIAzimuthal::GetPhiMin_deg() const {
+    return phi_min_deg;
+}
+
+float ROIAzimuthal::GetPhiMax_deg() const {
+    return phi_max_deg;
+}
+
+bool ROIAzimuthal::CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const {
+    if (resolution < d_min_A || resolution > d_max_A)
+        return false;
+    if (!has_phi)
+        return true;
+    // A sector with phi_min > phi_max wraps across 0 degrees.
+    if (phi_min_deg <= phi_max_deg)
+        return (phi_deg >= phi_min_deg) && (phi_deg <= phi_max_deg);
+    else
+        return (phi_deg >= phi_min_deg) || (phi_deg <= phi_max_deg);
 }
 
 float ROIAzimuthal::GetQMax_recipA() const {
@@ -45,6 +80,8 @@ ROIConfig ROIAzimuthal::ExportMetadata() const {
     return ROIConfig{
         .type = ROIConfig::ROIType::Azim,
         .name = name,
-        .azim = ROIConfigAzim{.qmin = qmin, .qmax = qmax}
+        .azim = ROIConfigAzim{.qmin = qmin, .qmax = qmax,
+                              .phi_min = has_phi ? phi_min_deg : 0.0f,
+                              .phi_max = has_phi ? phi_max_deg : 0.0f}
     };
 }
diff --git a/common/ROIAzimuthal.h b/common/ROIAzimuthal.h
index 3934df9a..d51271b6 100644
--- a/common/ROIAzimuthal.h
+++ b/common/ROIAzimuthal.h
@@ -3,21 +3,27 @@
 
 #pragma once
 
+#include <optional>
 #include "ROIElement.h"
 
 class ROIAzimuthal : public ROIElement {
     float d_min_A, d_max_A;
+    bool has_phi = false;
+    float phi_min_deg = 0;   // normalized to [0, 360), used only when has_phi
+    float phi_max_deg = 0;
 public:
-    ROIAzimuthal(const std::string &name, float d_min_A, float d_max_A);
+    ROIAzimuthal(const std::string &name, float d_min_A, float d_max_A,
+                 std::optional<float> phi_min_deg = std::nullopt,
+                 std::optional<float> phi_max_deg = std::nullopt);
     ~ROIAzimuthal() override = default;
     [[nodiscard]] float GetDMin_A() const;
     [[nodiscard]] float GetDMax_A() const;
     [[nodiscard]] float GetQMin_recipA() const;
     [[nodiscard]] float GetQMax_recipA() const;
+    [[nodiscard]] bool HasPhi() const;
+    [[nodiscard]] float GetPhiMin_deg() const;
+    [[nodiscard]] float GetPhiMax_deg() const;
 
-    bool CheckROI(int64_t x, int64_t y, float resolution) const override;
+    bool CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const override;
     ROIConfig ExportMetadata() const override;
 };
-
-
-
diff --git a/common/ROIBox.cpp b/common/ROIBox.cpp
index 0d8cbc7e..26ff3b33 100644
--- a/common/ROIBox.cpp
+++ b/common/ROIBox.cpp
@@ -65,7 +65,7 @@ int64_t ROIBox::GetArea() const {
     return GetWidth() * GetHeight();
 }
 
-bool ROIBox::CheckROI(int64_t x, int64_t y, float resolution) const {
+bool ROIBox::CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const {
     return ((x >= x_min) && (x <= x_max) && (y >= y_min) && (y <= y_max));
 }
 
diff --git a/common/ROIBox.h b/common/ROIBox.h
index 35bc2952..ee3df420 100644
--- a/common/ROIBox.h
+++ b/common/ROIBox.h
@@ -21,6 +21,6 @@ public:
     [[nodiscard]] int64_t GetHeight() const;
     [[nodiscard]] int64_t GetArea() const;
 
-    bool CheckROI(int64_t x, int64_t y, float resolution) const override;
+    bool CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const override;
     ROIConfig ExportMetadata() const override;
 };
diff --git a/common/ROICircle.cpp b/common/ROICircle.cpp
index f237e93a..4fd72ec4 100644
--- a/common/ROICircle.cpp
+++ b/common/ROICircle.cpp
@@ -31,7 +31,7 @@ ROIConfig ROICircle::ExportMetadata() const {
     };
 }
 
-bool ROICircle::CheckROI(int64_t x, int64_t y, float resolution) const {
+bool ROICircle::CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const {
     float x_fl = static_cast<float>(x) - center_x;
     float y_fl = static_cast<float>(y) - center_y;
     float dist_from_center_sq = x_fl * x_fl + y_fl * y_fl;
diff --git a/common/ROICircle.h b/common/ROICircle.h
index 63b192ee..6a252e86 100644
--- a/common/ROICircle.h
+++ b/common/ROICircle.h
@@ -17,6 +17,6 @@ public:
     [[nodiscard]] float GetX() const;
     [[nodiscard]] float GetY() const;
     [[nodiscard]] float GetRadius_pxl() const;
-    bool CheckROI(int64_t x, int64_t y, float resolution) const override;
+    bool CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const override;
     ROIConfig ExportMetadata() const override;
 };
diff --git a/common/ROIElement.cpp b/common/ROIElement.cpp
index deb4f9dd..45cdc90a 100644
--- a/common/ROIElement.cpp
+++ b/common/ROIElement.cpp
@@ -12,7 +12,7 @@ std::string ROIElement::GetName() const {
 }
 
 void ROIElement::MarkROI(std::vector<uint16_t> &v, uint16_t value_to_mark, int64_t xpixel, int64_t ypixel,
-                         const std::vector<float> &resolution_map) const {
+                         const std::vector<float> &resolution_map, const std::vector<float> &phi_map) const {
 
     if (resolution_map.size() != xpixel * ypixel)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
@@ -26,10 +26,14 @@ void ROIElement::MarkROI(std::vector<uint16_t> &v, uint16_t value_to_mark, int64
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "ROICircle: Only 16 selections available for ROI");
 
+    // phi_map is only supplied (and only consulted by azimuthal ROIs) when an
+    // azimuthal ROI is present; an empty map means the angle is unconstrained.
     for (int64_t y = 0; y < ypixel; y++) {
         for (int64_t x = 0; x < xpixel; x++) {
-            if (CheckROI(x, y, resolution_map[y * xpixel + x]))
-                v[y * xpixel + x] |= (1<<value_to_mark);
+            int64_t idx = y * xpixel + x;
+            float phi = phi_map.empty() ? 0.0f : phi_map[idx];
+            if (CheckROI(x, y, resolution_map[idx], phi))
+                v[idx] |= (1<<value_to_mark);
         }
     }
 }
\ No newline at end of file
diff --git a/common/ROIElement.h b/common/ROIElement.h
index 432f72a6..097df834 100644
--- a/common/ROIElement.h
+++ b/common/ROIElement.h
@@ -17,7 +17,7 @@ public:
 
     [[nodiscard]] std::string GetName() const;
     [[nodiscard]] virtual ROIConfig ExportMetadata() const = 0;
-    [[nodiscard]] virtual bool CheckROI(int64_t x, int64_t y, float resolution) const = 0;
+    [[nodiscard]] virtual bool CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const = 0;
     void MarkROI(std::vector<uint16_t> &v, uint16_t value_to_mark, int64_t xpixel, int64_t ypixel,
-                 const std::vector<float> &resolution_map) const;
+                 const std::vector<float> &resolution_map, const std::vector<float> &phi_map = {}) const;
 };
diff --git a/common/ROIMap.cpp b/common/ROIMap.cpp
index 97b0f1e0..adb97ab5 100644
--- a/common/ROIMap.cpp
+++ b/common/ROIMap.cpp
@@ -1,17 +1,21 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include "JFJochMath.h"
 #include "ROIMap.h"
 #include "JFJochException.h"
 
 std::vector<uint16_t> ROIMap::GetROIMap(const DiffractionGeometry &geom, size_t xpixel, size_t ypixel) const {
     std::vector<uint16_t> map(xpixel * ypixel, 0);
     std::vector<float> resolution_map(xpixel * ypixel, 0);
+    std::vector<float> phi_map;
     if (!rois.azimuthal.empty()) {
-
+        phi_map.resize(xpixel * ypixel, 0);
         for (int y = 0; y < ypixel; y++) {
             for (int x = 0; x < xpixel; x++) {
                 resolution_map[y * xpixel + x] = geom.PxlToRes(static_cast<float>(x), static_cast<float>(y));
+                phi_map[y * xpixel + x] = geom.Phi_rad(static_cast<float>(x), static_cast<float>(y))
+                                          * 180.0f / static_cast<float>(PI);
             }
         }
     }
@@ -19,17 +23,17 @@ std::vector<uint16_t> ROIMap::GetROIMap(const DiffractionGeometry &geom, size_t
     uint16_t roi_id = 0;
 
     for (const auto & box : rois.boxes) {
-        box.MarkROI(map, roi_id, xpixel, ypixel, resolution_map);
+        box.MarkROI(map, roi_id, xpixel, ypixel, resolution_map, phi_map);
         roi_id++;
     }
 
     for (const auto & circle : rois.circles) {
-        circle.MarkROI(map, roi_id, xpixel, ypixel, resolution_map);
+        circle.MarkROI(map, roi_id, xpixel, ypixel, resolution_map, phi_map);
         roi_id++;
     }
 
     for (const auto &az : rois.azimuthal) {
-        az.MarkROI(map, roi_id, xpixel, ypixel, resolution_map);
+        az.MarkROI(map, roi_id, xpixel, ypixel, resolution_map, phi_map);
         roi_id++;
     }
 
diff --git a/tests/ROIMapTest.cpp b/tests/ROIMapTest.cpp
index ca4291c6..578064e6 100644
--- a/tests/ROIMapTest.cpp
+++ b/tests/ROIMapTest.cpp
@@ -189,6 +189,68 @@ TEST_CASE("ROIAzimuthal_ROImark", "[ROIMap]") {
     }
 }
 
+TEST_CASE("ROIAzimuthal_Phi", "[ROIMap]") {
+    ROIAzimuthal full("roi1", 2.0, 4.0);
+    REQUIRE_FALSE(full.HasPhi());
+    // Full ring: phi is ignored, only d-range matters
+    REQUIRE(full.CheckROI(0, 0, 3.0, 123.0));
+    REQUIRE(full.CheckROI(0, 0, 3.0, 0.0));
+    REQUIRE_FALSE(full.CheckROI(0, 0, 1.0, 123.0));
+
+    ROIAzimuthal sector("roi2", 2.0, 4.0, 30.0f, 90.0f);
+    REQUIRE(sector.HasPhi());
+    REQUIRE(sector.GetPhiMin_deg() == 30.0f);
+    REQUIRE(sector.GetPhiMax_deg() == 90.0f);
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 60.0));
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 30.0));   // inclusive bounds
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 90.0));
+    REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 120.0));
+    REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 0.0));
+    REQUIRE_FALSE(sector.CheckROI(0, 0, 1.0, 60.0)); // outside d-range
+}
+
+TEST_CASE("ROIAzimuthal_Phi_Wrap", "[ROIMap]") {
+    // Sector wrapping across 0 deg: 350 .. 10
+    ROIAzimuthal sector("roi1", 2.0, 4.0, 350.0f, 10.0f);
+    REQUIRE(sector.HasPhi());
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 355.0));
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 5.0));
+    REQUIRE(sector.CheckROI(0, 0, 3.0, 0.0));
+    REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 180.0));
+    REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 11.0));
+}
+
+TEST_CASE("ROIAzimuthal_Phi_Normalize", "[ROIMap]") {
+    // Out-of-range inputs are normalized to [0, 360)
+    ROIAzimuthal sector("roi1", 2.0, 4.0, -30.0f, 400.0f);
+    REQUIRE(sector.GetPhiMin_deg() == 330.0f);
+    REQUIRE(sector.GetPhiMax_deg() == 40.0f);
+
+    // Only one phi bound provided -> treated as full ring
+    ROIAzimuthal one_bound("roi2", 2.0, 4.0, 30.0f);
+    REQUIRE_FALSE(one_bound.HasPhi());
+}
+
+TEST_CASE("ROIAzimuthal_Phi_MarkROI", "[ROIMap]") {
+    DiffractionExperiment x(DetJF(1));
+    std::vector<float> resolution_map(x.GetPixelsNum(), 3.0);
+    std::vector<float> phi_map(x.GetPixelsNum(), 0.0);
+    phi_map[0] = 45.0;
+    phi_map[1] = 200.0;
+    phi_map[2] = 45.0;
+    resolution_map[2] = 1.0; // outside d-range
+
+    ROIAzimuthal sector("roi1", 2.0, 4.0, 30.0f, 90.0f);
+    std::vector<uint16_t> mask(x.GetPixelsNum(), 0);
+    REQUIRE_NOTHROW(sector.MarkROI(mask, 3, x.GetXPixelsNum(), x.GetYPixelsNum(), resolution_map, phi_map));
+
+    REQUIRE(mask[0] == (1<<3)); // d in range, phi 45 in [30, 90]
+    REQUIRE(mask[1] == 0);      // phi 200 outside sector
+    REQUIRE(mask[2] == 0);      // d outside range
+    for (int i = 3; i < x.GetPixelsNum(); i++)
+        REQUIRE(mask[i] == 0);  // phi 0 outside sector
+}
+
 TEST_CASE("ROIMap") {
     DiffractionExperiment x(DetJF(1));
 
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index f6aaedef..a86e4619 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -619,7 +619,7 @@ void JFJochImageReadingWorker::AddROIToUserMask() {
     const auto res = azint_mapping->Resolution();
     for (int y = 0; y < height; y++) {
         for (int x = 0; x < width; x++) {
-            if (roi->CheckROI(x, y, 0))
+            if (roi->CheckROI(x, y, 0, 0))
                 user_mask[x + y * width] = 1;
         }
     }
@@ -639,7 +639,7 @@ void JFJochImageReadingWorker::SubtractROIFromUserMask() {
 
     for (int y = 0; y < height; y++) {
         for (int x = 0; x < width; x++) {
-            if (roi->CheckROI(x, y, 0))
+            if (roi->CheckROI(x, y, 0, 0))
                 user_mask[x + y * width] = 0;
         }
     }
-- 
2.52.0


From 1d04656dc8bbd660c3dd7abad5d19fe1e0d97559 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 09:28:25 +0200
Subject: [PATCH 102/228] api: serialize azimuthal ROI phi sector over OpenAPI
 and CBOR

Expose the optional phi_min_deg / phi_max_deg azimuthal-sector bounds
added to ROIAzimuthal through the wire formats. Both are optional, so
older clients and streams (Q-only ROIs) remain valid.

- jfjoch_api.yaml: optional phi_min_deg / phi_max_deg on roi_azimuthal;
  regenerated the cpp-pistache server model and the TS frontend client.
- OpenAPIConvert: map phi both directions (set only when present).
- CBOR start message: emit phi_min/phi_max only for a sector; on decode,
  absent phi means a full ring.
- Documented the new optional CBOR fields; extended the CBOR round-trip
  test with a sector and a full-ring azimuthal ROI.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/OpenAPIConvert.cpp                   | 15 +++++-
 broker/gen/model/Roi_azimuthal.cpp          | 60 ++++++++++++++++++++-
 broker/gen/model/Roi_azimuthal.h            | 22 +++++++-
 broker/jfjoch_api.yaml                      | 14 ++++-
 docs/CBOR.md                                |  2 +-
 frame_serialize/CBORStream2Deserializer.cpp |  3 ++
 frame_serialize/CBORStream2Serializer.cpp   |  5 ++
 frontend/src/client/types.gen.ts            | 12 ++++-
 frontend/src/client/zod.gen.ts              |  6 ++-
 tests/CBORTest.cpp                          | 23 ++++++--
 10 files changed, 149 insertions(+), 13 deletions(-)

diff --git a/broker/OpenAPIConvert.cpp b/broker/OpenAPIConvert.cpp
index 87bf76e3..4dc07646 100644
--- a/broker/OpenAPIConvert.cpp
+++ b/broker/OpenAPIConvert.cpp
@@ -461,10 +461,17 @@ ROIDefinition Convert(const org::openapitools::server::model::Roi_definitions& i
         output.boxes.emplace_back(ROIBox(i.getName(), i.getMinXPxl(), i.getMaxXPxl(), i.getMinYPxl(), i.getMaxYPxl()));
     for (const auto &i: input.getCircle().getRois())
         output.circles.emplace_back(ROICircle(i.getName(), i.getCenterXPxl(), i.getCenterYPxl(), i.getRadiusPxl()));
-    for (const auto &i: input.getAzim().getRois())
+    for (const auto &i: input.getAzim().getRois()) {
+        std::optional<float> phi_min, phi_max;
+        if (i.phiMinDegIsSet())
+            phi_min = i.getPhiMinDeg();
+        if (i.phiMaxDegIsSet())
+            phi_max = i.getPhiMaxDeg();
         output.azimuthal.emplace_back(ROIAzimuthal(i.getName(),
                                                    (i.getQMaxRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMaxRecipA(),
-                                                   (i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMinRecipA()));
+                                                   (i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMinRecipA(),
+                                                   phi_min, phi_max));
+    }
     return output;
 }
 
@@ -491,6 +498,10 @@ org::openapitools::server::model::Roi_azim_list Convert(const std::vector<ROIAzi
         elem.setName(i.GetName());
         elem.setQMinRecipA(i.GetQMin_recipA());
         elem.setQMaxRecipA(i.GetQMax_recipA());
+        if (i.HasPhi()) {
+            elem.setPhiMinDeg(i.GetPhiMin_deg());
+            elem.setPhiMaxDeg(i.GetPhiMax_deg());
+        }
         tmp.emplace_back(elem);
     }
     ret.setRois(tmp);
diff --git a/broker/gen/model/Roi_azimuthal.cpp b/broker/gen/model/Roi_azimuthal.cpp
index dfed1827..d6c4aa5d 100644
--- a/broker/gen/model/Roi_azimuthal.cpp
+++ b/broker/gen/model/Roi_azimuthal.cpp
@@ -24,6 +24,10 @@ Roi_azimuthal::Roi_azimuthal()
     m_Name = "";
     m_Q_min_recipA = 0.0f;
     m_Q_max_recipA = 0.0f;
+    m_Phi_min_deg = 0.0f;
+    m_Phi_min_degIsSet = false;
+    m_Phi_max_deg = 0.0f;
+    m_Phi_max_degIsSet = false;
     
 }
 
@@ -88,7 +92,7 @@ bool Roi_azimuthal::validate(std::stringstream& msg, const std::string& pathPref
         }
 
     }
-    
+            
     return success;
 }
 
@@ -104,8 +108,14 @@ bool Roi_azimuthal::operator==(const Roi_azimuthal& rhs) const
      &&
     
     (getQMaxRecipA() == rhs.getQMaxRecipA())
+     &&
     
     
+    ((!phiMinDegIsSet() && !rhs.phiMinDegIsSet()) || (phiMinDegIsSet() && rhs.phiMinDegIsSet() && getPhiMinDeg() == rhs.getPhiMinDeg())) &&
+    
+    
+    ((!phiMaxDegIsSet() && !rhs.phiMaxDegIsSet()) || (phiMaxDegIsSet() && rhs.phiMaxDegIsSet() && getPhiMaxDeg() == rhs.getPhiMaxDeg()))
+    
     ;
 }
 
@@ -120,6 +130,10 @@ void to_json(nlohmann::json& j, const Roi_azimuthal& o)
     j["name"] = o.m_Name;
     j["q_min_recipA"] = o.m_Q_min_recipA;
     j["q_max_recipA"] = o.m_Q_max_recipA;
+    if(o.phiMinDegIsSet())
+        j["phi_min_deg"] = o.m_Phi_min_deg;
+    if(o.phiMaxDegIsSet())
+        j["phi_max_deg"] = o.m_Phi_max_deg;
     
 }
 
@@ -128,6 +142,16 @@ void from_json(const nlohmann::json& j, Roi_azimuthal& o)
     j.at("name").get_to(o.m_Name);
     j.at("q_min_recipA").get_to(o.m_Q_min_recipA);
     j.at("q_max_recipA").get_to(o.m_Q_max_recipA);
+    if(j.find("phi_min_deg") != j.end())
+    {
+        j.at("phi_min_deg").get_to(o.m_Phi_min_deg);
+        o.m_Phi_min_degIsSet = true;
+    } 
+    if(j.find("phi_max_deg") != j.end())
+    {
+        j.at("phi_max_deg").get_to(o.m_Phi_max_deg);
+        o.m_Phi_max_degIsSet = true;
+    } 
     
 }
 
@@ -155,6 +179,40 @@ void Roi_azimuthal::setQMaxRecipA(float const value)
 {
     m_Q_max_recipA = value;
 }
+float Roi_azimuthal::getPhiMinDeg() const
+{
+    return m_Phi_min_deg;
+}
+void Roi_azimuthal::setPhiMinDeg(float const value)
+{
+    m_Phi_min_deg = value;
+    m_Phi_min_degIsSet = true;
+}
+bool Roi_azimuthal::phiMinDegIsSet() const
+{
+    return m_Phi_min_degIsSet;
+}
+void Roi_azimuthal::unsetPhi_min_deg()
+{
+    m_Phi_min_degIsSet = false;
+}
+float Roi_azimuthal::getPhiMaxDeg() const
+{
+    return m_Phi_max_deg;
+}
+void Roi_azimuthal::setPhiMaxDeg(float const value)
+{
+    m_Phi_max_deg = value;
+    m_Phi_max_degIsSet = true;
+}
+bool Roi_azimuthal::phiMaxDegIsSet() const
+{
+    return m_Phi_max_degIsSet;
+}
+void Roi_azimuthal::unsetPhi_max_deg()
+{
+    m_Phi_max_degIsSet = false;
+}
 
 
 } // namespace org::openapitools::server::model
diff --git a/broker/gen/model/Roi_azimuthal.h b/broker/gen/model/Roi_azimuthal.h
index 8913039b..7f938c2d 100644
--- a/broker/gen/model/Roi_azimuthal.h
+++ b/broker/gen/model/Roi_azimuthal.h
@@ -12,7 +12,7 @@
 /*
  * Roi_azimuthal.h
  *
- * ROI as Q-range (or resolution range)
+ * ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
  */
 
 #ifndef Roi_azimuthal_H_
@@ -26,7 +26,7 @@ namespace org::openapitools::server::model
 {
 
 /// <summary>
-/// ROI as Q-range (or resolution range)
+/// ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
 /// </summary>
 class  Roi_azimuthal
 {
@@ -73,6 +73,20 @@ public:
     /// </summary>
     float getQMaxRecipA() const;
     void setQMaxRecipA(float const value);
+    /// <summary>
+    /// Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit both for a full ring. A sector with phi_min_deg &gt; phi_max_deg wraps across 0. 
+    /// </summary>
+    float getPhiMinDeg() const;
+    void setPhiMinDeg(float const value);
+    bool phiMinDegIsSet() const;
+    void unsetPhi_min_deg();
+    /// <summary>
+    /// Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg. 
+    /// </summary>
+    float getPhiMaxDeg() const;
+    void setPhiMaxDeg(float const value);
+    bool phiMaxDegIsSet() const;
+    void unsetPhi_max_deg();
 
     friend  void to_json(nlohmann::json& j, const Roi_azimuthal& o);
     friend  void from_json(const nlohmann::json& j, Roi_azimuthal& o);
@@ -83,6 +97,10 @@ protected:
 
     float m_Q_max_recipA;
 
+    float m_Phi_min_deg;
+    bool m_Phi_min_degIsSet;
+    float m_Phi_max_deg;
+    bool m_Phi_max_degIsSet;
     
 };
 
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 573288da..31a53a89 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -1682,7 +1682,7 @@ components:
           enum: ["WrongDAQState", "Other"]
     roi_azimuthal:
       type: object
-      description: "ROI as Q-range (or resolution range)"
+      description: "ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector"
       required:
         - name
         - q_min_recipA
@@ -1702,6 +1702,18 @@ components:
           format: float
           minimum: 0.00001
           description: "Maximum Q-range for the ROI"
+        phi_min_deg:
+          type: number
+          format: float
+          description: >
+            Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both
+            phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit
+            both for a full ring. A sector with phi_min_deg > phi_max_deg wraps across 0.
+        phi_max_deg:
+          type: number
+          format: float
+          description: >
+            Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.
     roi_circle:
       type: object
       description: "Circular ROI"
diff --git a/docs/CBOR.md b/docs/CBOR.md
index a82af4bc..cf25bc8c 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -96,7 +96,7 @@ There are minor differences at the moment:
 | - roi                            | Array(object)        | ROI configurations; each element is one of:                                                                                                    |                           |
 |                                  |                      | type "box": xmin, xmax, ymin, ymax (numbers)                                                                                                   |                           |
 |                                  |                      | type "circle": r, x, y (numbers)                                                                                                               |                           |
-|                                  |                      | type "azim": qmin, qmax (numbers)                                                                                                              |                           |
+|                                  |                      | type "azim": qmin, qmax (numbers); optional phi_min, phi_max (numbers, deg) for an angular sector                                              |                           |
 | - gain_file_names                | Array(string)        | Names of JUNGFRAU gain files used for the current detector                                                                                     |                           |
 | - write_master_file              | bool                 | With multiple sockets, it selects which socket will provide master file                                                                        |                           |
 | - write_images                   | bool                 | Write images in the HDF5 file (if false, will only write metadata)                                                                             |                           |
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index 06241be0..4c01990c 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -1000,6 +1000,9 @@ namespace {
                     cfg.type = ROIConfig::ROIType::Azim;
                     cfg.azim.qmin = jr["qmin"];
                     cfg.azim.qmax = jr["qmax"];
+                    // Absent phi (older streams) means a full ring.
+                    cfg.azim.phi_min = jr.value("phi_min", 0.0f);
+                    cfg.azim.phi_max = jr.value("phi_max", 0.0f);
                     message.rois.emplace_back(std::move(cfg));
                 } else
                     continue;
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index dee8591f..3e361ef3 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -504,6 +504,11 @@ inline nlohmann::json CBOR_ENC_ROI_CONFIG(const std::vector<ROIConfig> &roi) {
                 jr["type"] = "azim";
                 jr["qmin"] = r.azim.qmin;
                 jr["qmax"] = r.azim.qmax;
+                // phi_min == phi_max means a full ring; only emit a sector.
+                if (r.azim.phi_min != r.azim.phi_max) {
+                    jr["phi_min"] = r.azim.phi_min;
+                    jr["phi_max"] = r.azim.phi_max;
+                }
                 break;
         }
         j.push_back(jr);
diff --git a/frontend/src/client/types.gen.ts b/frontend/src/client/types.gen.ts
index e7b33b4f..a8b818e8 100644
--- a/frontend/src/client/types.gen.ts
+++ b/frontend/src/client/types.gen.ts
@@ -1073,7 +1073,7 @@ export type error_message = {
 };
 
 /**
- * ROI as Q-range (or resolution range)
+ * ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
  */
 export type roi_azimuthal = {
     /**
@@ -1088,6 +1088,16 @@ export type roi_azimuthal = {
      * Maximum Q-range for the ROI
      */
     q_max_recipA: number;
+    /**
+     * Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit both for a full ring. A sector with phi_min_deg > phi_max_deg wraps across 0.
+     *
+     */
+    phi_min_deg?: number;
+    /**
+     * Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.
+     *
+     */
+    phi_max_deg?: number;
 };
 
 /**
diff --git a/frontend/src/client/zod.gen.ts b/frontend/src/client/zod.gen.ts
index b3259a73..c6095998 100644
--- a/frontend/src/client/zod.gen.ts
+++ b/frontend/src/client/zod.gen.ts
@@ -424,12 +424,14 @@ export const zErrorMessage = z.object({
 });
 
 /**
- * ROI as Q-range (or resolution range)
+ * ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
  */
 export const zRoiAzimuthal = z.object({
     name: z.string().min(1),
     q_min_recipA: z.number().gte(0.00001),
-    q_max_recipA: z.number().gte(0.00001)
+    q_max_recipA: z.number().gte(0.00001),
+    phi_min_deg: z.number().optional(),
+    phi_max_deg: z.number().optional()
 });
 
 /**
diff --git a/tests/CBORTest.cpp b/tests/CBORTest.cpp
index da3ecd21..35bbed6f 100644
--- a/tests/CBORTest.cpp
+++ b/tests/CBORTest.cpp
@@ -290,7 +290,19 @@ TEST_CASE("CBORSerialize_ROI", "[CBOR]") {
                 .name = "roi3",
                 .azim = ROIConfigAzim{
                     .qmin = 4.0,
-                    .qmax = 5.0
+                    .qmax = 5.0,
+                    .phi_min = 30.0f,
+                    .phi_max = 90.0f
+                }
+            },
+            ROIConfig{
+                .type = ROIConfig::ROIType::Azim,
+                .name = "roi4",
+                .azim = ROIConfigAzim{
+                    .qmin = 1.0,
+                    .qmax = 2.0,
+                    .phi_min = 0.0f,
+                    .phi_max = 0.0f
                 }
             }
         }
@@ -304,8 +316,8 @@ TEST_CASE("CBORSerialize_ROI", "[CBOR]") {
     REQUIRE(deserialized->start_message);
     StartMessage &output_message = *deserialized->start_message;
 
-    REQUIRE(output_message.rois.size() == 3);
-    for (int i = 0; i < 3; i++) {
+    REQUIRE(output_message.rois.size() == 4);
+    for (int i = 0; i < 4; i++) {
         CHECK(output_message.rois[i].name == message.rois[i].name);
         CHECK(output_message.rois[i].type == message.rois[i].type);
     }
@@ -320,6 +332,11 @@ TEST_CASE("CBORSerialize_ROI", "[CBOR]") {
 
     CHECK(output_message.rois[2].azim.qmin == message.rois[2].azim.qmin);
     CHECK(output_message.rois[2].azim.qmax == message.rois[2].azim.qmax);
+    CHECK(output_message.rois[2].azim.phi_min == 30.0f);
+    CHECK(output_message.rois[2].azim.phi_max == 90.0f);
+
+    // Full ring: phi_min == phi_max round-trips (no sector emitted)
+    CHECK(output_message.rois[3].azim.phi_min == output_message.rois[3].azim.phi_max);
 }
 
 TEST_CASE("CBORSerialize_Start_EmptyString", "[CBOR]") {
-- 
2.52.0


From 03814b142568794e32d5695a5f271999aa0e1647 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 09:41:26 +0200
Subject: [PATCH 103/228] writer: save ROI bitmap and definitions in the master
 file

Persist regions of interest so an acquisition's ROI layout can be
recovered from the master (_master.h5 / _process.h5):

- /entry/roi/roi_map: uint16 per-pixel bitmask (bit i == ROI i).
- /entry/roi/<name>: logical definition (type + geometry params, incl.
  azimuthal phi sector) plus bit_index tying it to the bitmap plane.

The bitmap rides along in the StartMessage (CBOR, mirroring az_int_map)
and is filled both online (JFJochReceiver::SendStartMessage) and offline
(jfjoch_process). Definitions come from the already-transmitted rois.
Both are dataset-wide metadata, so they are written by the NXmx master
writer (new NXmx::ROI), not the per-image data-file plugin.

Documented the /entry/roi layout in docs/HDF5.md and the master-vs-data
writer convention in CLAUDE.md; added a CBOR roi_map round-trip test.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CLAUDE.md                                   |  7 +++
 common/JFJochMessages.h                     |  3 ++
 docs/HDF5.md                                | 20 +++++++-
 frame_serialize/CBORStream2Deserializer.cpp | 10 ++++
 frame_serialize/CBORStream2Serializer.cpp   | 18 +++++++
 receiver/JFJochReceiver.cpp                 |  2 +
 tests/CBORTest.cpp                          | 23 +++++++++
 tools/jfjoch_process.cpp                    |  3 ++
 writer/HDF5NXmx.cpp                         | 52 +++++++++++++++++++++
 writer/HDF5NXmx.h                           |  1 +
 10 files changed, 137 insertions(+), 2 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index cc308d96..48e59478 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -94,6 +94,13 @@ cd tests/test_data && python jfjoch_broker_test.py     # feeds a test image, sta
 images over ZeroMQ → `jfjoch_writer` (`writer/`) consumes the stream and writes NXmx HDF5. The
 broker also emits a low-rate preview stream and a metadata stream (`preview/`).
 
+**Writer file split:** one acquisition produces one `_master.h5` plus many `_data_NNNNNN.h5`
+files. Dataset-wide metadata (geometry, detector config, ROI/azimuthal definitions — anything
+fixed for the whole run) is written to the **master** file in `writer/HDF5NXmx.cpp` (the `NXmx`
+class). Per-image arrays (one entry per frame) are written to the **data** files by the
+`HDF5DataFilePlugin` subclasses in `writer/`. Put shared metadata in `NXmx`, not in a data-file
+plugin.
+
 **`jfjoch_broker`** (`broker/`) is the central online service: HTTP/REST + OpenAPI control plane,
 FPGA configuration, image building, ZeroMQ output. `JFJochStateMachine` drives acquisition state;
 `JFJochServices` wires the pieces; `OpenAPIConvert`/`JFJochBrokerParser` translate between the
diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index eee16f6e..11a29806 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -270,6 +270,9 @@ struct StartMessage {
 
     std::map<std::string, std::vector<uint32_t>> pixel_mask;
 
+    // Per-pixel ROI bitmask (converted geometry), bit i set for ROI i in rois.
+    std::vector<uint16_t> roi_map;
+
     std::map<std::string, float> threshold_energy;
 
     std::optional<float> total_flux;
diff --git a/docs/HDF5.md b/docs/HDF5.md
index 49e72cbd..0b6d38cf 100644
--- a/docs/HDF5.md
+++ b/docs/HDF5.md
@@ -319,9 +319,10 @@ In the master file these per-image groups are exposed through `/entry/reflection
 | `image_count` | `[n_images, φ_bins, q_bins]` | | pixels contributing per bin |
 | `map` | `[y, x]` | | pixel→bin mapping (master file only) |
 
-### 4.4 `/entry/roi/<roi_name>` — regions of interest
+### 4.4 `/entry/roi` — regions of interest
 
-One sub-group per configured ROI, each with `[n_images]` vectors:
+`/entry/roi/<roi_name>` has one sub-group per configured ROI. The **per-image result
+vectors** `[n_images]` live in the data files:
 
 | Dataset | Meaning |
 |---------|---------|
@@ -331,6 +332,21 @@ One sub-group per configured ROI, each with `[n_images]` vectors:
 | `npixel` | number of valid pixels |
 | `x`, `y` | intensity-weighted centroid |
 
+The **dataset-wide ROI definition** (geometry, fixed for the whole acquisition) lives in the
+master file in the same sub-group:
+
+| Dataset | Meaning |
+|---------|---------|
+| `bit_index` | which bit of `roi_map` (below) marks this ROI |
+| `type` | `box`, `circle` or `azim` |
+| `min_x_pxl`, `max_x_pxl`, `min_y_pxl`, `max_y_pxl` | box bounds (type `box`) |
+| `center_x_pxl`, `center_y_pxl`, `radius_pxl` | circle (type `circle`) |
+| `q_min_recipA`, `q_max_recipA` | Q range (type `azim`) |
+| `phi_min_deg`, `phi_max_deg` | azimuthal-angle sector (type `azim`, omitted for a full ring) |
+
+`/entry/roi/roi_map` `[y, x]` (master file only) is a `uint16` per-pixel bitmask: bit `bit_index`
+is set for every pixel belonging to that ROI, so an ROI's footprint can be recovered exactly.
+
 ### 4.5 `/entry/image` — per-image pixel statistics
 
 `[n_images]` vectors: `max_value`, `min_value` (viable min/max, excluding error/saturated pixels),
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index 4c01990c..b61e9c67 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -1056,6 +1056,14 @@ namespace {
                          image.GetWidth() * image.GetHeight());
     }
 
+    void ProcessROIMapElement(StartMessage &message, CborValue &value) {
+        CompressedImage image = GetCBORMultidimTypedArray(value);
+        if (image.GetMode() == CompressedImageMode::Uint16)
+            JFJochDecompress(message.roi_map, image.GetCompressionAlgorithm(),
+                         image.GetCompressed(), image.GetCompressedSize(),
+                         image.GetWidth() * image.GetHeight());
+    }
+
     std::optional<FileWriterFormat> ProcessHDF5Format(int input) {
         auto tmp = static_cast<FileWriterFormat>(input);
         switch (tmp) {
@@ -1221,6 +1229,8 @@ namespace {
                 ProcessPixelMaskElement(message, value);
             else if (key == "az_int_map")
                 ProcessAzintMapElement(message, value);
+            else if (key == "roi_map")
+                ProcessROIMapElement(message, value);
             else if (key == "channels")
                 GetCBORStringArray(value, message.channels);
             else if (key == "detector_translation")
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index 3e361ef3..0cf19abd 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -446,6 +446,23 @@ inline void CBOR_ENC_AZINT_MAP(CborEncoder &encoder, const StartMessage &msg) {
     CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
 }
 
+inline void CBOR_ENC_ROI_MAP(CborEncoder &encoder, const StartMessage &msg) {
+    if (msg.roi_map.empty())
+        return;
+
+    if (msg.roi_map.size() != msg.image_size_x * msg.image_size_y)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Mismatch in size of ROI map");
+
+    JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
+    auto mask_compressed = compressor.Compress(msg.roi_map);
+    CompressedImage image(mask_compressed.data(), mask_compressed.size(),
+                          msg.image_size_x, msg.image_size_y,
+                          CompressedImageMode::Uint16,
+                          CompressionAlgorithm::BSHUF_LZ4, "roi_map");
+    CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
+}
+
 inline void CBOR_ENC(CborEncoder &encoder, const char* key, const UnitCell &val) {
     CborEncoder mapEncoder;
 
@@ -667,6 +684,7 @@ void CBORStream2Serializer::SerializeSequenceStart(const StartMessage& message)
 
     CBOR_ENC_PIXEL_MASK(mapEncoder, message);
     CBOR_ENC_AZINT_MAP(mapEncoder, message);
+    CBOR_ENC_ROI_MAP(mapEncoder, message);
 
     CBOR_ENC(mapEncoder, "channels", message.channels);
     CBOR_ENC(mapEncoder, "max_spot_count", message.max_spot_count);
diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp
index 752013ff..666cc16a 100644
--- a/receiver/JFJochReceiver.cpp
+++ b/receiver/JFJochReceiver.cpp
@@ -119,6 +119,8 @@ void JFJochReceiver::SendStartMessage() {
     }
     message.writer_notification_zmq_addr = image_pusher.GetWriterNotificationSocketAddress();
     message.rois = experiment.ROI().ExportMetadata();
+    if (!experiment.ROI().empty())
+        message.roi_map = experiment.ExportROIMap();
     message.max_spot_count = experiment.GetMaxSpotCount();
 
 
diff --git a/tests/CBORTest.cpp b/tests/CBORTest.cpp
index 35bbed6f..347aef50 100644
--- a/tests/CBORTest.cpp
+++ b/tests/CBORTest.cpp
@@ -870,6 +870,29 @@ TEST_CASE("CBORSerialize_Start_AzintMap", "[CBOR]") {
     CHECK(deserialized->start_message->az_int_map == azint_map);
 }
 
+TEST_CASE("CBORSerialize_Start_ROIMap", "[CBOR]") {
+    std::vector<uint8_t> buffer(8 * 1024 * 1024);
+    CBORStream2Serializer serializer(buffer.data(), buffer.size());
+
+    std::vector<uint16_t> roi_map(32 * 15, 0);
+    roi_map[0] = (1 << 0) | (1 << 3);
+    roi_map[32 * 14] = (1 << 2);
+
+    StartMessage msg{
+        .image_size_x = 32,
+        .image_size_y = 15,
+        .roi_map = roi_map
+    };
+
+    REQUIRE_NOTHROW(serializer.SerializeSequenceStart(msg));
+
+    auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
+    REQUIRE(deserialized);
+    REQUIRE(deserialized->msg_type == CBORImageType::START);
+    REQUIRE(deserialized->start_message);
+    CHECK(deserialized->start_message->roi_map == roi_map);
+}
+
 
 TEST_CASE("CBORSerialize_Image_Spots", "[CBOR]") {
     std::vector<uint8_t> buffer(8 * 1024 * 1024);
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index ffb707bc..79702b50 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -760,6 +760,9 @@ int main(int argc, char **argv) {
         start_message.az_int_bin_to_phi = mapping.GetBinToPhi();
 
     start_message.pixel_mask["default"] = pixel_mask.GetMask(experiment);
+    start_message.rois = experiment.ROI().ExportMetadata();
+    if (!experiment.ROI().empty())
+        start_message.roi_map = experiment.ExportROIMap();
     start_message.max_spot_count = experiment.GetMaxSpotCount();
     start_message.master_suffix = "process";
 
diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index 252e83f6..d666c390 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -51,6 +51,7 @@ NXmx::NXmx(const StartMessage &start)
     Attenuator(start);
     UserData(start);
     MX(start);
+    ROI(start);
     Fluorescence(start);
 }
 
@@ -444,6 +445,57 @@ void NXmx::MX(const StartMessage &start) {
     }
 }
 
+static void WriteROIDefinition(const HDF5Object &group, const ROIConfig &def) {
+    switch (def.type) {
+        case ROIConfig::ROIType::Box:
+            SaveScalar(group, "type", "box");
+            SaveScalar(group, "min_x_pxl", def.box.xmin);
+            SaveScalar(group, "max_x_pxl", def.box.xmax);
+            SaveScalar(group, "min_y_pxl", def.box.ymin);
+            SaveScalar(group, "max_y_pxl", def.box.ymax);
+            break;
+        case ROIConfig::ROIType::Circle:
+            SaveScalar(group, "type", "circle");
+            SaveScalar(group, "center_x_pxl", def.circle.x);
+            SaveScalar(group, "center_y_pxl", def.circle.y);
+            SaveScalar(group, "radius_pxl", def.circle.r);
+            break;
+        case ROIConfig::ROIType::Azim:
+            SaveScalar(group, "type", "azim");
+            SaveScalar(group, "q_min_recipA", def.azim.qmin);
+            SaveScalar(group, "q_max_recipA", def.azim.qmax);
+            // phi_min == phi_max means a full ring; only record a sector.
+            if (def.azim.phi_min != def.azim.phi_max) {
+                SaveScalar(group, "phi_min_deg", def.azim.phi_min);
+                SaveScalar(group, "phi_max_deg", def.azim.phi_max);
+            }
+            break;
+    }
+}
+
+void NXmx::ROI(const StartMessage &start) {
+    if (start.rois.empty())
+        return;
+
+    HDF5Group roi_group(*hdf5_file, "/entry/roi");
+    roi_group.NXClass("NXcollection");
+
+    if (!start.roi_map.empty()) {
+        // Per-pixel ROI bitmask: bit i (the bit_index below) marks pixels in ROI i.
+        CompressionAlgorithm roi_alg = (start.file_format == FileWriterFormat::NXmxLegacy)
+                                       ? CompressionAlgorithm::NO_COMPRESSION
+                                       : CompressionAlgorithm::BSHUF_LZ4;
+        std::vector<hsize_t> dims = {start.image_size_y, start.image_size_x};
+        roi_group.SaveVector("roi_map", start.roi_map, dims, roi_alg);
+    }
+
+    for (size_t i = 0; i < start.rois.size(); i++) {
+        HDF5Group g(roi_group, start.rois[i].name);
+        SaveScalar(g, "bit_index", static_cast<uint16_t>(i));
+        WriteROIDefinition(g, start.rois[i]);
+    }
+}
+
 void NXmx::DetectorModule(const std::string &name, const std::vector<int32_t> &origin, const std::vector<int32_t> &size,
                           const std::vector<double> &fast_axis, const std::vector<double> &slow_axis,
                           const std::string &nx_axis, double pixel_size_mm) {
diff --git a/writer/HDF5NXmx.h b/writer/HDF5NXmx.h
index 30612dc0..427f1895 100644
--- a/writer/HDF5NXmx.h
+++ b/writer/HDF5NXmx.h
@@ -54,6 +54,7 @@ class NXmx {
     void EndResultVectors(const EndMessage &end);
     void UserData(const StartMessage &start);
     void MX(const StartMessage &start);
+    void ROI(const StartMessage &start);
     void Fluorescence(const StartMessage &start);
 
 public:
-- 
2.52.0


From 2bd276ae1b2347022b5cb93e285065a5cec14aed Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 09:44:57 +0200
Subject: [PATCH 104/228] preview: draw azimuthal ROIs

AddROI now renders azimuthal ROIs in addition to box and circle ROIs:
inner/outer arcs at the Q (d) bounds and, for a sector, the two radial
edges at the phi bounds. The per-pixel phi comes from the same
DiffractionGeometry::Phi_rad used to assign ROIs, so the overlay matches
the ROI footprint exactly (including wrap-around sectors). Full-ring
azimuthal ROIs draw as two concentric arcs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 preview/PreviewImage.cpp | 44 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/preview/PreviewImage.cpp b/preview/PreviewImage.cpp
index 9d820bb7..37076154 100644
--- a/preview/PreviewImage.cpp
+++ b/preview/PreviewImage.cpp
@@ -36,6 +36,20 @@ constexpr const static rgb plotly[] = {{0x1f, 0x77, 0xb4},
 
 constexpr const static rgb gray = {.r = 0xbe, .g = 0xbe, .b = 0xbe};
 
+// Smallest difference between two angles in degrees, accounting for wrap-around.
+static float AngularDistance_deg(float a, float b) {
+    float d = std::fabs(a - b);
+    if (d > 180.0f)
+        d = 360.0f - d;
+    return d;
+}
+
+static bool InPhiSector(float phi_deg, float phi_min, float phi_max) {
+    if (phi_min <= phi_max)
+        return phi_deg >= phi_min && phi_deg <= phi_max;
+    return phi_deg >= phi_min || phi_deg <= phi_max;   // sector wraps across 0
+}
+
 void PreviewImage::color_pixel(std::vector<rgb> &ret, int64_t in_xpixel, int64_t in_ypixel,const rgb &color) const {
     if ((in_xpixel >= 0) && (in_xpixel < xpixel) && (in_ypixel >= 0) && (in_ypixel < ypixel))
         ret[(in_ypixel * xpixel + in_xpixel)] = color;
@@ -198,6 +212,36 @@ void PreviewImage::AddROI(std::vector<rgb> &rgb_image) const {
         }
         roi_counter++;
     }
+
+    DiffractionGeometry geom = experiment.GetDiffractionGeometry();
+    for (const auto &az: experiment.ROI().GetROIDefinition().azimuthal) {
+        const int width = 5;
+        const float r_inner = geom.ResToPxl(az.GetDMax_A());   // larger d -> smaller radius
+        const float r_outer = geom.ResToPxl(az.GetDMin_A());
+        const bool has_phi = az.HasPhi();
+
+        for (int64_t y = 0; y <= ypixel; y++) {
+            for (int64_t x = 0; x <= xpixel; x++) {
+                const float dx = x - beam_x;
+                const float dy = y - beam_y;
+                const float dist = sqrtf(dx * dx + dy * dy);
+                const float phi_deg = geom.Phi_rad(x, y) * 180.0f / static_cast<float>(PI);
+
+                const bool in_sector = !has_phi || InPhiSector(phi_deg, az.GetPhiMin_deg(), az.GetPhiMax_deg());
+                const bool on_arc = (std::fabs(dist - r_inner) < width) || (std::fabs(dist - r_outer) < width);
+
+                // Radial edges of a sector: angular tolerance scaled to keep ~constant pixel width.
+                const float tol_deg = (dist > 1.0f) ? width / dist * 180.0f / static_cast<float>(PI) : 180.0f;
+                const bool on_edge = has_phi && (dist >= r_inner) && (dist <= r_outer)
+                    && (AngularDistance_deg(phi_deg, az.GetPhiMin_deg()) < tol_deg
+                        || AngularDistance_deg(phi_deg, az.GetPhiMax_deg()) < tol_deg);
+
+                if ((on_arc && in_sector) || on_edge)
+                    roi(rgb_image, x, y, roi_counter);
+            }
+        }
+        roi_counter++;
+    }
 }
 
 void PreviewImage::AddResolutionRing(std::vector<rgb> &rgb_image, float d) const {
-- 
2.52.0


From c6e7f8aa15997596d0153ec1c193812421b7c2c1 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 10:35:18 +0200
Subject: [PATCH 105/228] writer/reader: move ROI definitions to
 /entry/roi_defs and read them back

Relocate the ROI definitions and the roi_map bitmap from /entry/roi to a
separate /entry/roi_defs group in the master file. /entry/roi keeps its
original meaning (per-image ROI results only), so an older reader that
iterates /entry/roi is not disturbed by the bitmap/definition entries
(which would otherwise make it try to read /entry/roi/roi_map/max and
fail to open the file at all). Back-compatibility for already-deployed
viewers is the reason for the split.

JFJochHDF5Reader now reads the logical definitions into experiment.ROI()
and the roi_map bitmask (+ a name->bit index) into the dataset, for all
file formats (the master always carries them). Reading both lets a later
viewer either re-derive ROIs with the current geometry (logical) or show
the exact written footprint (bitmap).

Added a write/read round-trip test over VDS and integrated formats.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/HDF5.md                 | 18 ++++++----
 reader/JFJochHDF5Reader.cpp  | 51 +++++++++++++++++++++++++++
 reader/JFJochHDF5Reader.h    |  4 +++
 reader/JFJochReaderDataset.h |  8 +++++
 tests/JFJochReaderTest.cpp   | 68 ++++++++++++++++++++++++++++++++++++
 writer/HDF5NXmx.cpp          |  5 ++-
 6 files changed, 146 insertions(+), 8 deletions(-)

diff --git a/docs/HDF5.md b/docs/HDF5.md
index 0b6d38cf..b0e285c5 100644
--- a/docs/HDF5.md
+++ b/docs/HDF5.md
@@ -319,10 +319,10 @@ In the master file these per-image groups are exposed through `/entry/reflection
 | `image_count` | `[n_images, φ_bins, q_bins]` | | pixels contributing per bin |
 | `map` | `[y, x]` | | pixel→bin mapping (master file only) |
 
-### 4.4 `/entry/roi` — regions of interest
+### 4.4 `/entry/roi` — regions of interest (per-image results)
 
-`/entry/roi/<roi_name>` has one sub-group per configured ROI. The **per-image result
-vectors** `[n_images]` live in the data files:
+`/entry/roi/<roi_name>` has one sub-group per configured ROI, holding the **per-image result
+vectors** `[n_images]` (in the data files):
 
 | Dataset | Meaning |
 |---------|---------|
@@ -332,8 +332,12 @@ vectors** `[n_images]` live in the data files:
 | `npixel` | number of valid pixels |
 | `x`, `y` | intensity-weighted centroid |
 
-The **dataset-wide ROI definition** (geometry, fixed for the whole acquisition) lives in the
-master file in the same sub-group:
+### 4.4.1 `/entry/roi_defs` — ROI definitions (master file)
+
+The **dataset-wide ROI definitions** (geometry, fixed for the whole acquisition) live in the
+master file under a *separate* `/entry/roi_defs` group — kept apart from `/entry/roi` above so
+that older readers, which iterate `/entry/roi`, are unaffected by these entries. One sub-group
+`/entry/roi_defs/<roi_name>` per ROI:
 
 | Dataset | Meaning |
 |---------|---------|
@@ -344,8 +348,8 @@ master file in the same sub-group:
 | `q_min_recipA`, `q_max_recipA` | Q range (type `azim`) |
 | `phi_min_deg`, `phi_max_deg` | azimuthal-angle sector (type `azim`, omitted for a full ring) |
 
-`/entry/roi/roi_map` `[y, x]` (master file only) is a `uint16` per-pixel bitmask: bit `bit_index`
-is set for every pixel belonging to that ROI, so an ROI's footprint can be recovered exactly.
+`/entry/roi_defs/roi_map` `[y, x]` is a `uint16` per-pixel bitmask: bit `bit_index` is set for
+every pixel belonging to that ROI, so an ROI's footprint can be recovered exactly.
 
 ### 4.5 `/entry/image` — per-image pixel statistics
 
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index e6d639c8..30b14b8a 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -9,6 +9,8 @@
 #include "../image_analysis/bragg_integration/CalcISigma.h"
 #include "../image_analysis/spot_finding/SpotUtils.h"
 #include "../common/GridScanSettings.h"
+#include "../common/JFJochMath.h"
+#include "../common/ROIDefinition.h"
 
 inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
     if (val.empty())
@@ -239,6 +241,52 @@ std::vector<T> ReadVectorMasterFirst(HDF5Object &master_file,
     return {};
 }
 
+void JFJochHDF5Reader::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const {
+    // ROI definitions live in /entry/roi_defs (kept separate from the per-image ROI
+    // results in /entry/roi so that older readers, which iterate /entry/roi, are not
+    // disturbed by the bitmap and definition subgroups).
+    if (!file.Exists("/entry/roi_defs"))
+        return;
+
+    if (file.Exists("/entry/roi_defs/roi_map")) {
+        auto dim = file.GetDimension("/entry/roi_defs/roi_map");   // [y, x]
+        if (dim.size() == 2)
+            dataset.roi_map = file.ReadOptVector<uint16_t>("/entry/roi_defs/roi_map",
+                                                           {0, 0}, {dim[0], dim[1]});
+    }
+
+    ROIDefinition defs;
+    for (const auto &name: file.FindLeafs("/entry/roi_defs")) {
+        const std::string base = "/entry/roi_defs/" + name;
+        // Skip the roi_map bitmask; only named ROI subgroups carry a definition.
+        if (name == "roi_map" || !file.Exists(base + "/type"))
+            continue;
+
+        dataset.roi_bit_index[name] = static_cast<uint16_t>(file.GetInt(base + "/bit_index"));
+
+        const std::string type = file.GetString(base + "/type");
+        if (type == "box")
+            defs.boxes.emplace_back(name, file.GetInt(base + "/min_x_pxl"), file.GetInt(base + "/max_x_pxl"),
+                                          file.GetInt(base + "/min_y_pxl"), file.GetInt(base + "/max_y_pxl"));
+        else if (type == "circle")
+            defs.circles.emplace_back(name, file.GetFloat(base + "/center_x_pxl"), file.GetFloat(base + "/center_y_pxl"),
+                                            file.GetFloat(base + "/radius_pxl"));
+        else if (type == "azim") {
+            const float qmin = file.GetFloat(base + "/q_min_recipA");
+            const float qmax = file.GetFloat(base + "/q_max_recipA");
+            std::optional<float> phi_min, phi_max;
+            if (file.Exists(base + "/phi_min_deg")) phi_min = file.GetFloat(base + "/phi_min_deg");
+            if (file.Exists(base + "/phi_max_deg")) phi_max = file.GetFloat(base + "/phi_max_deg");
+            const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
+            const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
+            defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
+        }
+    }
+
+    if (!defs.boxes.empty() || !defs.circles.empty() || !defs.azimuthal.empty())
+        dataset.experiment.ROI().SetROI(defs);
+}
+
 void JFJochHDF5Reader::ReadFile(const std::string &filename) {
     std::unique_lock ul(hdf5_mutex);
     try {
@@ -631,6 +679,9 @@ void JFJochHDF5Reader::ReadFile(const std::string &filename) {
                 mask_tmp = std::vector<uint32_t>(image_size_x * image_size_y);
             dataset->pixel_mask = PixelMask(mask_tmp);
         }
+
+        ReadROIMetadata(*master_file, *dataset);
+
         dataset->experiment.ImagesPerTrigger(number_of_images);
         cached_geom = dataset->experiment.GetDiffractionGeometry();
         SetStartMessage(dataset);
diff --git a/reader/JFJochHDF5Reader.h b/reader/JFJochHDF5Reader.h
index 25f59255..137f2ad6 100644
--- a/reader/JFJochHDF5Reader.h
+++ b/reader/JFJochHDF5Reader.h
@@ -41,6 +41,10 @@ class JFJochHDF5Reader : public JFJochReader {
 
     std::pair<std::shared_ptr<HDF5ReadOnlyFile>, uint32_t> GetImageLocation(int64_t image_number);
     std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
+
+    // Read the master-file ROI definitions: logical definitions into experiment.ROI()
+    // and the roi_map bitmask (+ bit index) into the dataset. Present for all formats.
+    void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
 public:
     ~JFJochHDF5Reader() override = default;
 
diff --git a/reader/JFJochReaderDataset.h b/reader/JFJochReaderDataset.h
index 654dd73b..d4dc7d44 100644
--- a/reader/JFJochReaderDataset.h
+++ b/reader/JFJochReaderDataset.h
@@ -6,6 +6,7 @@
 #include <string>
 #include <optional>
 #include <vector>
+#include <map>
 
 #include "../common/DiffractionGeometry.h"
 #include "../common/DiffractionExperiment.h"
@@ -54,6 +55,13 @@ struct JFJochReaderDataset {
     std::vector<std::vector<float>> roi_x;
     std::vector<std::vector<float>> roi_y;
 
+    // ROI definitions stored in the master file. The logical definitions populate
+    // experiment.ROI() (they re-derive with the current geometry); roi_map is the
+    // per-pixel bitmask as written (constant footprint), with roi_bit_index mapping
+    // each ROI name to its bit.
+    std::vector<uint16_t> roi_map;
+    std::map<std::string, uint16_t> roi_bit_index;
+
     std::vector<std::string> calibration_data;
 
     JFJochReaderDataset() = default;
diff --git a/tests/JFJochReaderTest.cpp b/tests/JFJochReaderTest.cpp
index 8c865ad4..92d750d3 100644
--- a/tests/JFJochReaderTest.cpp
+++ b/tests/JFJochReaderTest.cpp
@@ -257,6 +257,74 @@ TEST_CASE("JFJochReader_PixelMask", "[HDF5][Full]") {
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+TEST_CASE("JFJochReader_ROIDefinitions", "[HDF5][Full]") {
+    RegisterHDF5Filter();
+
+    // ROI definitions and the bitmap live in the master file for every format.
+    auto format = GENERATE(FileWriterFormat::NXmxVDS, FileWriterFormat::NXmxIntegrated);
+
+    DiffractionExperiment x(DetJF(1));
+    x.FilePrefix("test_roi").ImagesPerTrigger(950).OverwriteExistingFiles(true)
+            .SetFileWriterFormat(format);
+    x.BeamX_pxl(100).BeamY_pxl(200).DetectorDistance_mm(150)
+            .IncidentEnergy_keV(WVL_1A_IN_KEV).PixelSigned(false).BitDepthImage(16)
+            .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
+
+    ROIDefinition defs;
+    defs.boxes.emplace_back("mybox", 10, 20, 30, 40);
+    defs.circles.emplace_back("mycircle", 100, 200, 15);
+    defs.azimuthal.emplace_back("mywedge", 2.0f, 4.0f, 30.0f, 90.0f);
+    x.ROI().SetROI(defs);
+
+    ScanResultGenerator generator(x);
+    std::vector<uint16_t> image(x.GetPixelsNum(), 0);
+    {
+        StartMessage start_message;
+        x.FillMessage(start_message);
+        start_message.rois = x.ROI().ExportMetadata();
+        start_message.roi_map = x.ExportROIMap();
+
+        FileWriter file_set(start_message);
+        DataMessage message{};
+        message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+        message.number = 0;
+        REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+        generator.Add(message);
+
+        EndMessage end_message;
+        end_message.max_image_number = 1;
+        generator.FillEndMessage(end_message);
+        file_set.WriteHDF5(end_message);
+        file_set.Finalize();
+    }
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("test_roi_master.h5"));
+        auto dataset = reader.GetDataset();
+
+        const auto &rd = dataset->experiment.ROI().GetROIDefinition();
+        REQUIRE(rd.boxes.size() == 1);
+        REQUIRE(rd.circles.size() == 1);
+        REQUIRE(rd.azimuthal.size() == 1);
+        CHECK(rd.boxes[0].GetName() == "mybox");
+        CHECK(rd.boxes[0].GetXMin() == 10);
+        CHECK(rd.boxes[0].GetXMax() == 20);
+        CHECK(rd.circles[0].GetName() == "mycircle");
+        CHECK(rd.circles[0].GetRadius_pxl() == 15.0f);
+        CHECK(rd.azimuthal[0].GetName() == "mywedge");
+        CHECK(rd.azimuthal[0].HasPhi());
+        CHECK(rd.azimuthal[0].GetPhiMin_deg() == 30.0f);
+
+        // bitmap read back with the per-pixel footprint and the name->bit index
+        CHECK(dataset->roi_map.size() == x.GetXPixelsNumConv() * x.GetYPixelsNumConv());
+        CHECK(dataset->roi_bit_index.size() == 3);
+        CHECK(dataset->roi_bit_index.at("mybox") == 0);
+    }
+    remove("test_roi_master.h5");
+    remove("test_roi_data_000001.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
 TEST_CASE("JFJochReader_Goniometer", "[HDF5][Full]") {
     DiffractionExperiment x(DetJF(1));
 
diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index d666c390..fc776102 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -477,7 +477,10 @@ void NXmx::ROI(const StartMessage &start) {
     if (start.rois.empty())
         return;
 
-    HDF5Group roi_group(*hdf5_file, "/entry/roi");
+    // ROI definitions go in /entry/roi_defs, kept separate from the per-image ROI
+    // results (/entry/roi, written by the data-file plugin) so that older readers
+    // iterating /entry/roi are not disturbed by the bitmap and definition subgroups.
+    HDF5Group roi_group(*hdf5_file, "/entry/roi_defs");
     roi_group.NXClass("NXcollection");
 
     if (!start.roi_map.empty()) {
-- 
2.52.0


From 6b95600260d5e82db51ca252eb043d6ed07b0338 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 10:38:24 +0200
Subject: [PATCH 106/228] writer: link ROI results into the VDS master file

In VDS mode the per-image ROI results (max/sum/sum_sq/npixel/x/y) are
written into the data files but were not exposed in the master, so a VDS
master surfaced no ROI statistics. Add virtual datasets under
/entry/roi/<name> in LinkToData_VDS, one group per ROI, mirroring how the
spot-finding and azimuthal-integration arrays are linked. Integrated and
legacy formats are unaffected (the results are already reachable there).

Extended the reader round-trip test to write real ROI results and check
they read back from the master for both VDS and integrated formats.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/HDF5.md               |  4 +++-
 tests/JFJochReaderTest.cpp | 10 ++++++++++
 writer/HDF5NXmx.cpp        | 16 ++++++++++++++++
 3 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/docs/HDF5.md b/docs/HDF5.md
index b0e285c5..ddfc52b2 100644
--- a/docs/HDF5.md
+++ b/docs/HDF5.md
@@ -322,7 +322,9 @@ In the master file these per-image groups are exposed through `/entry/reflection
 ### 4.4 `/entry/roi` — regions of interest (per-image results)
 
 `/entry/roi/<roi_name>` has one sub-group per configured ROI, holding the **per-image result
-vectors** `[n_images]` (in the data files):
+vectors** `[n_images]`. These are written into the data files; in VDS mode they are exposed from
+the master file through virtual datasets, and in integrated mode they are in the single file.
+(In legacy mode they remain only in the data files.)
 
 | Dataset | Meaning |
 |---------|---------|
diff --git a/tests/JFJochReaderTest.cpp b/tests/JFJochReaderTest.cpp
index 92d750d3..91dc0bf3 100644
--- a/tests/JFJochReaderTest.cpp
+++ b/tests/JFJochReaderTest.cpp
@@ -288,6 +288,9 @@ TEST_CASE("JFJochReader_ROIDefinitions", "[HDF5][Full]") {
         DataMessage message{};
         message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
         message.number = 0;
+        for (const auto &name : {"mybox", "mycircle", "mywedge"})
+            message.roi[name] = ROIMessage{.sum = 100, .sum_square = 1000, .max_count = 50,
+                                           .pixels = 10, .x_weighted = 500, .y_weighted = 600};
         REQUIRE_NOTHROW(file_set.WriteHDF5(message));
         generator.Add(message);
 
@@ -319,6 +322,13 @@ TEST_CASE("JFJochReader_ROIDefinitions", "[HDF5][Full]") {
         CHECK(dataset->roi_map.size() == x.GetXPixelsNumConv() * x.GetYPixelsNumConv());
         CHECK(dataset->roi_bit_index.size() == 3);
         CHECK(dataset->roi_bit_index.at("mybox") == 0);
+
+        // per-image ROI results surface from the master (VDS-linked for VDS format)
+        REQUIRE(dataset->roi.size() == 3);
+        auto it = std::find(dataset->roi.begin(), dataset->roi.end(), "mybox");
+        REQUIRE(it != dataset->roi.end());
+        const size_t idx = std::distance(dataset->roi.begin(), it);
+        CHECK(dataset->roi_sum.at(idx).at(0) == 100);
     }
     remove("test_roi_master.h5");
     remove("test_roi_data_000001.h5");
diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index fc776102..1da5057f 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -160,6 +160,22 @@ void NXmx::LinkToData_VDS(const StartMessage &start, const EndMessage &end) {
             }
         }
 
+        if (!start.rois.empty()) {
+            // Per-image ROI results live in the data files; expose them in the master
+            // through virtual datasets, one /entry/roi/<name> group per ROI.
+            HDF5Group(*hdf5_file, "/entry/roi").NXClass("NXcollection");
+            for (const auto &r: start.rois) {
+                const std::string base = "/entry/roi/" + r.name;
+                HDF5Group(*hdf5_file, base);
+                VDS(start, base + "/max",    {total_images}, HDF5DataType((int64_t) 0));
+                VDS(start, base + "/sum",    {total_images}, HDF5DataType((int64_t) 0));
+                VDS(start, base + "/sum_sq", {total_images}, HDF5DataType((int64_t) 0));
+                VDS(start, base + "/npixel", {total_images}, HDF5DataType((int64_t) 0));
+                VDS(start, base + "/x",      {total_images}, HDF5DataType((float) 0));
+                VDS(start, base + "/y",      {total_images}, HDF5DataType((float) 0));
+            }
+        }
+
         if (start.xfel_pulse_id.value_or(false)) {
             HDF5Group(*hdf5_file, "/entry/xfel").NXClass("NXcollection");
             VDS(start, "/entry/xfel/pulseID", {total_images}, HDF5DataType((uint64_t) 0));
-- 
2.52.0


From eadbce51bd207346b0bc4905ed512dcf7a06c72d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 11:03:40 +0200
Subject: [PATCH 107/228] common: take ROIAzimuthal phi as plain floats, not
 optionals

The phi bounds were stored as plain floats internally but passed through
std::optional in the constructor, which obscured the intent. Take them
as float arguments defaulting to 0 instead. The convention is explicit:
phi_min == phi_max means the full ring (all angles), a sector wraps
across 0 when phi_min > phi_max, and otherwise phi_min <= phi_max. The
"both bounds or none" rule belongs at the API/file boundary
(OpenAPIConvert, reader), not in the core class, so it lives there now.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/OpenAPIConvert.cpp   |  7 ++++---
 common/ROIAzimuthal.cpp     | 25 +++++++++----------------
 common/ROIAzimuthal.h       | 11 +++++------
 reader/JFJochHDF5Reader.cpp |  8 +++++---
 tests/ROIMapTest.cpp        |  8 +++++---
 5 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/broker/OpenAPIConvert.cpp b/broker/OpenAPIConvert.cpp
index 4dc07646..d137c2e1 100644
--- a/broker/OpenAPIConvert.cpp
+++ b/broker/OpenAPIConvert.cpp
@@ -462,11 +462,12 @@ ROIDefinition Convert(const org::openapitools::server::model::Roi_definitions& i
     for (const auto &i: input.getCircle().getRois())
         output.circles.emplace_back(ROICircle(i.getName(), i.getCenterXPxl(), i.getCenterYPxl(), i.getRadiusPxl()));
     for (const auto &i: input.getAzim().getRois()) {
-        std::optional<float> phi_min, phi_max;
-        if (i.phiMinDegIsSet())
+        // A sector needs both bounds; if only one is given, treat it as a full ring.
+        float phi_min = 0, phi_max = 0;
+        if (i.phiMinDegIsSet() && i.phiMaxDegIsSet()) {
             phi_min = i.getPhiMinDeg();
-        if (i.phiMaxDegIsSet())
             phi_max = i.getPhiMaxDeg();
+        }
         output.azimuthal.emplace_back(ROIAzimuthal(i.getName(),
                                                    (i.getQMaxRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMaxRecipA(),
                                                    (i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMinRecipA(),
diff --git a/common/ROIAzimuthal.cpp b/common/ROIAzimuthal.cpp
index 3e716c19..4c0d2103 100644
--- a/common/ROIAzimuthal.cpp
+++ b/common/ROIAzimuthal.cpp
@@ -14,8 +14,10 @@ static float NormalizePhi_deg(float phi) {
 }
 
 ROIAzimuthal::ROIAzimuthal(const std::string &in_name, float in_d_min_A, float in_d_max_A,
-                           std::optional<float> in_phi_min_deg, std::optional<float> in_phi_max_deg)
-        : ROIElement(in_name) {
+                           float in_phi_min_deg, float in_phi_max_deg)
+        : ROIElement(in_name),
+          phi_min_deg(NormalizePhi_deg(in_phi_min_deg)),
+          phi_max_deg(NormalizePhi_deg(in_phi_max_deg)) {
     if ((in_d_min_A <= 0) || (in_d_max_A <= 0))
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Resolution cannot be zero or negative");
@@ -26,12 +28,6 @@ ROIAzimuthal::ROIAzimuthal(const std::string &in_name, float in_d_min_A, float i
         d_max_A = in_d_max_A;
         d_min_A = in_d_min_A;
     }
-
-    if (in_phi_min_deg && in_phi_max_deg) {
-        has_phi = true;
-        phi_min_deg = NormalizePhi_deg(in_phi_min_deg.value());
-        phi_max_deg = NormalizePhi_deg(in_phi_max_deg.value());
-    }
 }
 
 float ROIAzimuthal::GetDMin_A() const {
@@ -43,7 +39,7 @@ float ROIAzimuthal::GetDMax_A() const {
 }
 
 bool ROIAzimuthal::HasPhi() const {
-    return has_phi;
+    return phi_min_deg != phi_max_deg;
 }
 
 float ROIAzimuthal::GetPhiMin_deg() const {
@@ -57,13 +53,11 @@ float ROIAzimuthal::GetPhiMax_deg() const {
 bool ROIAzimuthal::CheckROI(int64_t x, int64_t y, float resolution, float phi_deg) const {
     if (resolution < d_min_A || resolution > d_max_A)
         return false;
-    if (!has_phi)
-        return true;
-    // A sector with phi_min > phi_max wraps across 0 degrees.
+    if (phi_min_deg == phi_max_deg)
+        return true;                          // full ring: all angles
     if (phi_min_deg <= phi_max_deg)
         return (phi_deg >= phi_min_deg) && (phi_deg <= phi_max_deg);
-    else
-        return (phi_deg >= phi_min_deg) || (phi_deg <= phi_max_deg);
+    return (phi_deg >= phi_min_deg) || (phi_deg <= phi_max_deg);   // sector wraps across 0
 }
 
 float ROIAzimuthal::GetQMax_recipA() const {
@@ -81,7 +75,6 @@ ROIConfig ROIAzimuthal::ExportMetadata() const {
         .type = ROIConfig::ROIType::Azim,
         .name = name,
         .azim = ROIConfigAzim{.qmin = qmin, .qmax = qmax,
-                              .phi_min = has_phi ? phi_min_deg : 0.0f,
-                              .phi_max = has_phi ? phi_max_deg : 0.0f}
+                              .phi_min = phi_min_deg, .phi_max = phi_max_deg}
     };
 }
diff --git a/common/ROIAzimuthal.h b/common/ROIAzimuthal.h
index d51271b6..23cbe7e3 100644
--- a/common/ROIAzimuthal.h
+++ b/common/ROIAzimuthal.h
@@ -3,24 +3,23 @@
 
 #pragma once
 
-#include <optional>
 #include "ROIElement.h"
 
 class ROIAzimuthal : public ROIElement {
     float d_min_A, d_max_A;
-    bool has_phi = false;
-    float phi_min_deg = 0;   // normalized to [0, 360), used only when has_phi
+    // Azimuthal-angle sector, normalized to [0, 360). phi_min_deg == phi_max_deg means
+    // the full ring (all angles); a sector with phi_min_deg > phi_max_deg wraps across 0.
+    float phi_min_deg = 0;
     float phi_max_deg = 0;
 public:
     ROIAzimuthal(const std::string &name, float d_min_A, float d_max_A,
-                 std::optional<float> phi_min_deg = std::nullopt,
-                 std::optional<float> phi_max_deg = std::nullopt);
+                 float phi_min_deg = 0, float phi_max_deg = 0);
     ~ROIAzimuthal() override = default;
     [[nodiscard]] float GetDMin_A() const;
     [[nodiscard]] float GetDMax_A() const;
     [[nodiscard]] float GetQMin_recipA() const;
     [[nodiscard]] float GetQMax_recipA() const;
-    [[nodiscard]] bool HasPhi() const;
+    [[nodiscard]] bool HasPhi() const;   // a sector is set (phi_min_deg != phi_max_deg)
     [[nodiscard]] float GetPhiMin_deg() const;
     [[nodiscard]] float GetPhiMax_deg() const;
 
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 30b14b8a..212aa29a 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -274,9 +274,11 @@ void JFJochHDF5Reader::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDatas
         else if (type == "azim") {
             const float qmin = file.GetFloat(base + "/q_min_recipA");
             const float qmax = file.GetFloat(base + "/q_max_recipA");
-            std::optional<float> phi_min, phi_max;
-            if (file.Exists(base + "/phi_min_deg")) phi_min = file.GetFloat(base + "/phi_min_deg");
-            if (file.Exists(base + "/phi_max_deg")) phi_max = file.GetFloat(base + "/phi_max_deg");
+            float phi_min = 0, phi_max = 0;
+            if (file.Exists(base + "/phi_min_deg") && file.Exists(base + "/phi_max_deg")) {
+                phi_min = file.GetFloat(base + "/phi_min_deg");
+                phi_max = file.GetFloat(base + "/phi_max_deg");
+            }
             const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
             const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
             defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
diff --git a/tests/ROIMapTest.cpp b/tests/ROIMapTest.cpp
index 578064e6..1c4b52c8 100644
--- a/tests/ROIMapTest.cpp
+++ b/tests/ROIMapTest.cpp
@@ -226,9 +226,11 @@ TEST_CASE("ROIAzimuthal_Phi_Normalize", "[ROIMap]") {
     REQUIRE(sector.GetPhiMin_deg() == 330.0f);
     REQUIRE(sector.GetPhiMax_deg() == 40.0f);
 
-    // Only one phi bound provided -> treated as full ring
-    ROIAzimuthal one_bound("roi2", 2.0, 4.0, 30.0f);
-    REQUIRE_FALSE(one_bound.HasPhi());
+    // Default (no phi bounds) and equal bounds are both the full ring
+    ROIAzimuthal full("roi2", 2.0, 4.0);
+    REQUIRE_FALSE(full.HasPhi());
+    ROIAzimuthal equal_bounds("roi3", 2.0, 4.0, 45.0f, 45.0f);
+    REQUIRE_FALSE(equal_bounds.HasPhi());
 }
 
 TEST_CASE("ROIAzimuthal_Phi_MarkROI", "[ROIMap]") {
-- 
2.52.0


From cee4739221f456ccf8ff32c5aee29c5811e4ade8 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 12:44:00 +0200
Subject: [PATCH 108/228] frontend: bundle Sphinx docs locally instead of
 linking readthedocs

The Documentation tab pointed at jungfraujoch.readthedocs.io, which lags
behind the installed version. Build the Sphinx docs into frontend/dist/docs
and serve them at /frontend/docs so they always match the package.

- make_doc.sh: accept an output dir (default public), absolutize it, run
  from the script dir, and allow $PYTHON override
- package.json: add "docs" script building into dist/docs
- CMakeLists: run "npm run docs" in the frontend target so CPack packs the
  docs via the existing dist/ install
- App.tsx: point the Documentation DocFrame at /frontend/docs/index.html

Also clean up the Sphinx build (911 -> 0 warnings):
- fix typo myst_heading_anchor -> myst_heading_anchors so cross-doc
  #anchor links actually resolve
- suppress myst.header/myst.xref_missing (auto-generated OpenAPI client
  docs only) and the harmless sphinx_material config.cache note
- drop a dangling "---" transition at the end of CPU_DATA_ANALYSIS.md
- add REPOSITORIES and the generated python_client model pages to toctrees

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 CMakeLists.txt            |  1 +
 docs/CPU_DATA_ANALYSIS.md |  2 --
 docs/conf.py              | 10 +++++++++-
 docs/index.rst            | 12 +++++++++++-
 frontend/package.json     |  1 +
 frontend/src/App.tsx      |  2 +-
 make_doc.sh               | 23 +++++++++++++++++++++--
 7 files changed, 44 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f81c5ea0..34983c02 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -195,6 +195,7 @@ IF (NOT JFJOCH_WRITER_ONLY)
             COMMAND npm ci
             COMMAND npm run build
             COMMAND npm run redocly
+            COMMAND npm run docs            # bundle Sphinx docs into dist/docs (served at /frontend/docs)
             WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend)
     ADD_CUSTOM_TARGET(frontend DEPENDS frontend/dist/index.html)
 
diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md
index 620a5339..e7ff6a34 100644
--- a/docs/CPU_DATA_ANALYSIS.md
+++ b/docs/CPU_DATA_ANALYSIS.md
@@ -609,5 +609,3 @@ Numerical quadrature over a scaled intensity variable is used to compute posteri
 - **Space-group symmetry** beyond centering absences is not necessarily enforced during prediction/integration unless the space group is supplied and used downstream.
 - **Resolution masking and ice rings** are controllable; including ice-ring spots in indexing can improve robustness for some samples but may bias refinement in others.
 - **Rotation vs still modes** differ substantially in prediction and scaling because partiality is angle-driven in rotation data and excitation-error-driven in still data.
-
----
diff --git a/docs/conf.py b/docs/conf.py
index 029de2d0..d5b883ba 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -29,7 +29,15 @@ myst_enable_extensions = [
     'amsmath',
 ]
 
-myst_heading_anchor = 3
+myst_heading_anchors = 3
+
+# The OpenAPI Python-client pages under docs/python_client/ are generated by the
+# openapi-generator and contain header-level jumps and intra-page anchors that MyST
+# cannot resolve. We do not hand-edit generated files, so silence that noise here;
+# the hand-written docs are anchor-clean once myst_heading_anchors is set above.
+# 'config.cache' fires only because the sphinx_material theme stores a function in
+# html_context, which is harmless for our single-shot builds.
+suppress_warnings = ['myst.header', 'myst.xref_missing', 'config.cache']
 
 # Render LaTeX-style math nicely in HTML and support AMS-style equation numbering.
 mathjax3_config = {
diff --git a/docs/index.rst b/docs/index.rst
index c6016839..52e95c02 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -22,6 +22,7 @@ Jungfraujoch is distributed under the GPLv3 license.
    SOFTWARE
    VERSIONING
    DEPLOYMENT
+   REPOSITORIES
    CHANGELOG
 
 .. toctree::
@@ -67,4 +68,13 @@ Jungfraujoch is distributed under the GPLv3 license.
    :caption: OpenAPI Python client
 
    python_client/README
-   python_client/docs/DefaultApi
\ No newline at end of file
+   python_client/docs/DefaultApi
+
+.. The remaining python_client/docs/*.md pages are generated per-model reference
+   files linked from the client README/DefaultApi; include them in a hidden glob
+   toctree so they are built without each one warning about being orphaned.
+.. toctree::
+   :hidden:
+   :glob:
+
+   python_client/docs/*
diff --git a/frontend/package.json b/frontend/package.json
index 362fc4c6..ca8ef706 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -33,6 +33,7 @@
     "build": "tsc && vite build",
     "serve": "vite preview",
     "redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=dist/openapi.html",
+    "docs": "bash ../make_doc.sh dist/docs",
     "redocly4broker": "redocly build-docs ../broker/jfjoch_api.yaml --output=../broker/redoc-static.html",
     "openapi": "openapi-ts"
   },
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 2b11076b..f0746031 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -181,7 +181,7 @@ function App() {
                 <DocFrame title="API reference" src="/frontend/openapi.html"/>
             )},
             { id: 'documentation', label: 'Documentation', icon: <MenuBookIcon/>, render: () => (
-                <DocFrame title="Documentation" src="https://jungfraujoch.readthedocs.io/"/>
+                <DocFrame title="Documentation" src="/frontend/docs/index.html"/>
             )},
         ]},
     ];
diff --git a/make_doc.sh b/make_doc.sh
index 6af1d0c1..7853ad44 100644
--- a/make_doc.sh
+++ b/make_doc.sh
@@ -2,11 +2,30 @@
 
 set -euo pipefail
 
-python3.11 -m venv tmp_venv/
+# Build the Sphinx HTML documentation.
+#
+# Usage: make_doc.sh [output_dir]
+#   output_dir   where the rendered HTML is written (default: ./public).
+#                Relative paths are resolved against the caller's working
+#                directory, so the frontend build can point this at frontend/dist/docs.
+#
+# The Python interpreter can be overridden with $PYTHON (default: python3.11).
+
+OUT="${1:-public}"
+PYTHON="${PYTHON:-python3.11}"
+
+# Resolve the output directory to an absolute path before we change directories.
+mkdir -p "$OUT"
+OUT="$(cd "$OUT" && pwd)"
+
+# Run from the repository root regardless of where the script was invoked from.
+cd "$(dirname "$0")"
+
+"$PYTHON" -m venv tmp_venv/
 source tmp_venv/bin/activate
 
 pip install -r docs/requirements.txt
 
-sphinx-build -b html docs public
+sphinx-build -b html docs "$OUT"
 
 rm -rf tmp_venv/
-- 
2.52.0


From 6962a61489799adfd33899740444d62beee0911c Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:21:19 +0200
Subject: [PATCH 109/228] frontend: render Changelog inline instead of in a
 Sphinx iframe

The framed Sphinx changelog reused MUI with the same colours, so it read as
a picture-in-picture. Bundle docs/CHANGELOG.md at build time (?raw) and render
it with react-markdown, themed to match the app, for a quick frame-less view.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 frontend/package-lock.json | 1469 ++++++++++++++++++++++++++++++++++++
 frontend/package.json      |    2 +
 frontend/src/App.tsx       |   27 +
 3 files changed, 1498 insertions(+)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index ed73ab33..214fd4a3 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -23,8 +23,10 @@
         "plotly.js-cartesian-dist-min": "^3.3.1",
         "react": "^19.2.4",
         "react-dom": "^19.2.4",
+        "react-markdown": "^10.1.0",
         "react-plotly.js": "^2.6.0",
         "react-zoom-pan-pinch": "^3.4.3",
+        "remark-gfm": "^4.0.1",
         "typescript": "^5.9.3",
         "vite": "^7.3.1",
         "vite-plugin-svgr": "^4.5.0",
@@ -3591,12 +3593,30 @@
         "url": "https://opencollective.com/turf"
       }
     },
+    "node_modules/@types/debug": {
+      "version": "4.1.13",
+      "resolved": "https://registry.npmjs.org/@types/debug/-/debug-4.1.13.tgz",
+      "integrity": "sha512-KSVgmQmzMwPlmtljOomayoR89W4FynCAi3E8PPs7vmDVPe84hT+vGPKkJfThkmXs0x0jAaa9U8uW8bbfyS2fWw==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/ms": "*"
+      }
+    },
     "node_modules/@types/estree": {
       "version": "1.0.8",
       "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.8.tgz",
       "integrity": "sha512-dWHzHa2WqEXI/O1E9OjrocMTKJl2mSrEolh1Iomrv6U+JuNwaHXsXx9bLu5gG7BUWFIN0skIQJQ/L1rIex4X6w==",
       "license": "MIT"
     },
+    "node_modules/@types/estree-jsx": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/@types/estree-jsx/-/estree-jsx-1.0.5.tgz",
+      "integrity": "sha512-52CcUVNFyfb1A2ALocQw/Dd1BQFNmSdkuC3BkZ6iqhdMfQz7JWOFRuJFloOzjk+6WijU56m9oKXFAXc7o3Towg==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/estree": "*"
+      }
+    },
     "node_modules/@types/geojson": {
       "version": "7946.0.16",
       "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.16.tgz",
@@ -3612,6 +3632,15 @@
         "@types/geojson": "*"
       }
     },
+    "node_modules/@types/hast": {
+      "version": "3.0.4",
+      "resolved": "https://registry.npmjs.org/@types/hast/-/hast-3.0.4.tgz",
+      "integrity": "sha512-WPs+bbQw5aCj+x6laNGWLH3wviHtoCv/P3+otBhbOhJgG8qtpdAMlTCxLtsTWA7LH1Oh/bFCHsBn0TPS5m30EQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "*"
+      }
+    },
     "node_modules/@types/json-schema": {
       "version": "7.0.15",
       "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.15.tgz",
@@ -3647,6 +3676,21 @@
         "@types/pbf": "*"
       }
     },
+    "node_modules/@types/mdast": {
+      "version": "4.0.4",
+      "resolved": "https://registry.npmjs.org/@types/mdast/-/mdast-4.0.4.tgz",
+      "integrity": "sha512-kGaNbPh1k7AFzgpud/gMdvIm5xuECykRR+JnWKQno9TAXVa6WIVCGTPvYGekIDL4uwCZQSYbUxNBSb1aUo79oA==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "*"
+      }
+    },
+    "node_modules/@types/ms": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/@types/ms/-/ms-2.1.0.tgz",
+      "integrity": "sha512-GsCCIZDE/p3i96vtEqx+7dBUGXrc7zeSK3wwPHIaRThS+9OhWIXRqzs4d6k1SVU8g91DrNRWxWUGhp5KXQb2VA==",
+      "license": "MIT"
+    },
     "node_modules/@types/node": {
       "version": "25.2.3",
       "resolved": "https://registry.npmjs.org/@types/node/-/node-25.2.3.tgz",
@@ -3750,6 +3794,18 @@
       "license": "MIT",
       "optional": true
     },
+    "node_modules/@types/unist": {
+      "version": "3.0.3",
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+      "license": "MIT",
+      "dependencies": {
+        "@types/hast": "^3.0.0",
+        "@types/mdast": "^4.0.0",
+        "mdast-util-to-hast": "^13.0.0",
+        "unified": "^11.0.0",
+        "vfile": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/remark-stringify": {
+      "version": "11.0.0",
+      "resolved": "https://registry.npmjs.org/remark-stringify/-/remark-stringify-11.0.0.tgz",
+      "integrity": "sha512-1OSmLd3awB/t8qdoEOMazZkNsfVTeY4fTsgzcQFdXNq8ToTN4ZGwrMnlda4K6smTFKD+GRV6O48i6Z4iKgPPpw==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/mdast": "^4.0.0",
+        "mdast-util-to-markdown": "^2.0.0",
+        "unified": "^11.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
     "node_modules/require-directory": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -8707,6 +9977,16 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/space-separated-tokens": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/space-separated-tokens/-/space-separated-tokens-2.0.2.tgz",
+      "integrity": "sha512-PEGlAwrG8yXGXRjW32fGbg66JAlOAwbObuqVoJpv/mRgoWDQfgH1wDPvtzWyUSNAXBGSk8h755YDbbcEy3SH2Q==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
     "node_modules/stack-trace": {
       "version": "0.0.9",
       "resolved": "https://registry.npmjs.org/stack-trace/-/stack-trace-0.0.9.tgz",
@@ -8815,6 +10095,20 @@
         "node": ">=8"
       }
     },
+    "node_modules/stringify-entities": {
+      "version": "4.0.4",
+      "resolved": "https://registry.npmjs.org/stringify-entities/-/stringify-entities-4.0.4.tgz",
+      "integrity": "sha512-IwfBptatlO+QCJUo19AqvrPNqlVMpW9YEL2LIVY+Rpv2qsjCGxaDLNRgeGsQWJhfItebuJhsGSLjaBbNSQ+ieg==",
+      "license": "MIT",
+      "dependencies": {
+        "character-entities-html4": "^2.0.0",
+        "character-entities-legacy": "^3.0.0"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
     "node_modules/strip-ansi": {
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
@@ -8859,6 +10153,24 @@
       "integrity": "sha512-i0TFx4wPcO0FwX+4RkLJi1MxmcTv90jNZgxMu9XRnMXMeFUY1VJlIoXpZunPUvUUqbCT1pg5PEkFqqpcaElNaA==",
       "peer": true
     },
+    "node_modules/style-to-js": {
+      "version": "1.1.21",
+      "resolved": "https://registry.npmjs.org/style-to-js/-/style-to-js-1.1.21.tgz",
+      "integrity": "sha512-RjQetxJrrUJLQPHbLku6U/ocGtzyjbJMP9lCNK7Ag0CNh690nSH8woqWH9u16nMjYBAok+i7JO1NP2pOy8IsPQ==",
+      "license": "MIT",
+      "dependencies": {
+        "style-to-object": "1.0.14"
+      }
+    },
+    "node_modules/style-to-object": {
+      "version": "1.0.14",
+      "resolved": "https://registry.npmjs.org/style-to-object/-/style-to-object-1.0.14.tgz",
+      "integrity": "sha512-LIN7rULI0jBscWQYaSswptyderlarFkjQ+t79nzty8tcIAceVomEVlLzH5VP4Cmsv6MtKhs7qaAiwlcp+Mgaxw==",
+      "license": "MIT",
+      "dependencies": {
+        "inline-style-parser": "0.2.7"
+      }
+    },
     "node_modules/styled-components": {
       "version": "5.3.11",
       "resolved": "https://registry.npmjs.org/styled-components/-/styled-components-5.3.11.tgz",
@@ -9250,6 +10562,26 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/trim-lines": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/trim-lines/-/trim-lines-3.0.1.tgz",
+      "integrity": "sha512-kRj8B+YHZCc9kQYdWfJB2/oUl9rA99qbowYYBtr4ui4mZyAQ2JpvVBd/6U2YloATfqBhBTSMhTpgBHtU0Mf3Rg==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
+    "node_modules/trough": {
+      "version": "2.2.0",
+      "resolved": "https://registry.npmjs.org/trough/-/trough-2.2.0.tgz",
+      "integrity": "sha512-tmMpK00BjZiUyVyvrBK7knerNgmgvcV/KLVyuma/SC+TQN167GrMRciANTz09+k3zW8L8t60jWO1GpfkZdjTaw==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
     "node_modules/ts-algebra": {
       "version": "1.2.2",
       "resolved": "https://registry.npmjs.org/ts-algebra/-/ts-algebra-1.2.2.tgz",
@@ -9355,6 +10687,105 @@
       "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==",
       "license": "MIT"
     },
+    "node_modules/unified": {
+      "version": "11.0.5",
+      "resolved": "https://registry.npmjs.org/unified/-/unified-11.0.5.tgz",
+      "integrity": "sha512-xKvGhPWw3k84Qjh8bI3ZeJjqnyadK+GEFtazSfZv/rKeTkTjOJho6mFqh2SM96iIcZokxiOpg78GazTSg8+KHA==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "bail": "^2.0.0",
+        "devlop": "^1.0.0",
+        "extend": "^3.0.0",
+        "is-plain-obj": "^4.0.0",
+        "trough": "^2.0.0",
+        "vfile": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unified/node_modules/is-plain-obj": {
+      "version": "4.1.0",
+      "resolved": "https://registry.npmjs.org/is-plain-obj/-/is-plain-obj-4.1.0.tgz",
+      "integrity": "sha512-+Pgi+vMuUNkJyExiMBt5IlFoMyKnr5zhJ4Uspz58WOhBF5QoIZkFyNHIbBAtHwzVAgk5RtndVNsDRN61/mmDqg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/unist-util-is": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/unist-util-is/-/unist-util-is-6.0.1.tgz",
+      "integrity": "sha512-LsiILbtBETkDz8I9p1dQ0uyRUWuaQzd/cuEeS1hoRSyW5E5XGmTzlwY1OrNzzakGowI9Dr/I8HVaw4hTtnxy8g==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-position": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/unist-util-position/-/unist-util-position-5.0.0.tgz",
+      "integrity": "sha512-fucsC7HjXvkB5R3kTCO7kUjRdrS0BJt3M/FPxmHMBOm8JQi2BsHAHFsy27E0EolP8rp0NzXsJ+jNPyDWvOJZPA==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-stringify-position": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/unist-util-stringify-position/-/unist-util-stringify-position-4.0.0.tgz",
+      "integrity": "sha512-0ASV06AAoKCDkS2+xw5RXJywruurpbC4JZSm7nr7MOt1ojAzvyyaO+UxZf18j8FCF6kmzCZKcAgN/yu2gm2XgQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-visit": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/unist-util-visit/-/unist-util-visit-5.1.0.tgz",
+      "integrity": "sha512-m+vIdyeCOpdr/QeQCu2EzxX/ohgS8KbnPDgFni4dQsfSCtpz8UqDyY5GjRru8PDKuYn7Fq19j1CQ+nJSsGKOzg==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-is": "^6.0.0",
+        "unist-util-visit-parents": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-visit-parents": {
+      "version": "6.0.2",
+      "resolved": "https://registry.npmjs.org/unist-util-visit-parents/-/unist-util-visit-parents-6.0.2.tgz",
+      "integrity": "sha512-goh1s1TBrqSqukSc8wrjwWhL0hiJxgA8m4kFxGlQ+8FYQ3C/m11FcTs4YYem7V664AhHVvgoQLk890Ssdsr2IQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-is": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
     "node_modules/unquote": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/unquote/-/unquote-1.1.1.tgz",
@@ -9417,6 +10848,34 @@
       "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
       "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw=="
     },
+    "node_modules/vfile": {
+      "version": "6.0.3",
+      "resolved": "https://registry.npmjs.org/vfile/-/vfile-6.0.3.tgz",
+      "integrity": "sha512-KzIbH/9tXat2u30jf+smMwFCsno4wHVdNmzFyL+T/L3UGqqk6JKfVqOFOZEpZSHADH1k40ab6NUIXZq422ov3Q==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "vfile-message": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/vfile-message": {
+      "version": "4.0.3",
+      "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.3.tgz",
+      "integrity": "sha512-QTHzsGd1EhbZs4AsQ20JX1rC3cOlt/IWJruk893DfLRr57lcnOeMaWG4K0JrRta4mIJZKth2Au3mM3u03/JWKw==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-stringify-position": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
     "node_modules/vite": {
       "version": "7.3.2",
       "resolved": "https://registry.npmjs.org/vite/-/vite-7.3.2.tgz",
@@ -9805,6 +11264,16 @@
       "funding": {
         "url": "https://github.com/sponsors/colinhacks"
       }
+    },
+    "node_modules/zwitch": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
+      "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
     }
   }
 }
diff --git a/frontend/package.json b/frontend/package.json
index ca8ef706..77cfa144 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -20,8 +20,10 @@
     "plotly.js-cartesian-dist-min": "^3.3.1",
     "react": "^19.2.4",
     "react-dom": "^19.2.4",
+    "react-markdown": "^10.1.0",
     "react-plotly.js": "^2.6.0",
     "react-zoom-pan-pinch": "^3.4.3",
+    "remark-gfm": "^4.0.1",
     "typescript": "^5.9.3",
     "vite": "^7.3.1",
     "vite-plugin-svgr": "^4.5.0",
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index f0746031..98807bee 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -21,7 +21,10 @@ import DeveloperBoardIcon from "@mui/icons-material/DeveloperBoard";
 import OpenInNewIcon from "@mui/icons-material/OpenInNew";
 import ApiIcon from "@mui/icons-material/Api";
 import MenuBookIcon from "@mui/icons-material/MenuBook";
+import HistoryIcon from "@mui/icons-material/History";
 import _ from "lodash";
+import Markdown from "react-markdown";
+import remarkGfm from "remark-gfm";
 
 import StatusBar from "./components/StatusBar";
 import ErrorMessage from "./components/ErrorMessage";
@@ -49,6 +52,8 @@ import FpgaStatus from "./components/FpgaStatus";
 import { plot_type } from "./client";
 import { getStatisticsOptions } from "./client/@tanstack/react-query.gen";
 import { JFJOCH_VERSION } from "./version";
+// Bundled at build time, so it always matches the running release.
+import changelogMd from "../../docs/CHANGELOG.md?raw";
 
 const drawerWidth = 240;
 
@@ -84,6 +89,25 @@ function DocFrame({ title, src }: { title: string; src: string }) {
     );
 }
 
+/** Render the bundled CHANGELOG.md inline, styled with the app theme so it reads as
+ *  part of the frontend rather than the framed Sphinx documentation. */
+function Changelog() {
+    return (
+        <Box sx={{
+            maxWidth: 900, mx: "auto",
+            "& h1": { typography: "h4", mt: 0, mb: 2 },
+            "& h2": { typography: "h5", mt: 4, mb: 1, color: "primary.dark" },
+            "& h3": { typography: "h6", mt: 3, mb: 1 },
+            "& ul": { pl: 3, my: 1 },
+            "& li": { mb: 0.5 },
+            "& a": { color: "primary.main" },
+            "& code": { bgcolor: "grey.100", px: 0.5, borderRadius: 0.5, fontSize: "0.85em" },
+        }}>
+            <Markdown remarkPlugins={[remarkGfm]}>{changelogMd}</Markdown>
+        </Box>
+    );
+}
+
 function App() {
     const [drawerOpen, setDrawerOpen] = useState(true);
     const [view, setView] = useState('dashboard');
@@ -183,6 +207,9 @@ function App() {
             { id: 'documentation', label: 'Documentation', icon: <MenuBookIcon/>, render: () => (
                 <DocFrame title="Documentation" src="/frontend/docs/index.html"/>
             )},
+            { id: 'changelog', label: 'Changelog', icon: <HistoryIcon/>, render: () => (
+                <Changelog/>
+            )},
         ]},
     ];
 
-- 
2.52.0


From 332fd32224258f472286305bc61529a0f776375d Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:23:51 +0200
Subject: [PATCH 110/228] frontend: link PSI in footer, add Source code and
 License to References

- Footer "Paul Scherrer Institute" now links to https://www.psi.ch
- Reference drawer gains a "Source code" entry linking out to the Gitea
  repository (new nav-item href that opens in a new tab)
- Reference drawer gains a "License" entry rendering the nicely formatted
  docs/LICENSE.md inline (generalises the changelog renderer into MarkdownDoc)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 frontend/src/App.tsx | 39 ++++++++++++++++++++++++++++-----------
 1 file changed, 28 insertions(+), 11 deletions(-)

diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 98807bee..2a42dea1 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -22,6 +22,8 @@ import OpenInNewIcon from "@mui/icons-material/OpenInNew";
 import ApiIcon from "@mui/icons-material/Api";
 import MenuBookIcon from "@mui/icons-material/MenuBook";
 import HistoryIcon from "@mui/icons-material/History";
+import CodeIcon from "@mui/icons-material/Code";
+import GavelIcon from "@mui/icons-material/Gavel";
 import _ from "lodash";
 import Markdown from "react-markdown";
 import remarkGfm from "remark-gfm";
@@ -52,8 +54,9 @@ import FpgaStatus from "./components/FpgaStatus";
 import { plot_type } from "./client";
 import { getStatisticsOptions } from "./client/@tanstack/react-query.gen";
 import { JFJOCH_VERSION } from "./version";
-// Bundled at build time, so it always matches the running release.
+// Bundled at build time, so they always match the running release.
 import changelogMd from "../../docs/CHANGELOG.md?raw";
+import licenseMd from "../../docs/LICENSE.md?raw";
 
 const drawerWidth = 240;
 
@@ -69,7 +72,10 @@ const jfjoch_theme = createTheme({
     },
 });
 
-type NavItem = { id: string; label: string; icon: ReactNode; disabled?: boolean; render: () => ReactNode };
+// An item either renders a panel inside the app (render) or links out to an
+// external page in a new tab (href), e.g. the source repository.
+type NavItem = { id: string; label: string; icon: ReactNode; disabled?: boolean;
+                 href?: string; render?: () => ReactNode };
 type NavSection = { subheader?: string; items: NavItem[] };
 
 /** Documentation / API reference shown inside the app area, with a new-tab escape hatch. */
@@ -89,9 +95,9 @@ function DocFrame({ title, src }: { title: string; src: string }) {
     );
 }
 
-/** Render the bundled CHANGELOG.md inline, styled with the app theme so it reads as
- *  part of the frontend rather than the framed Sphinx documentation. */
-function Changelog() {
+/** Render bundled Markdown inline, styled with the app theme so it reads as part of
+ *  the frontend rather than the framed Sphinx documentation. */
+function MarkdownDoc({ md }: { md: string }) {
     return (
         <Box sx={{
             maxWidth: 900, mx: "auto",
@@ -103,7 +109,7 @@ function Changelog() {
             "& a": { color: "primary.main" },
             "& code": { bgcolor: "grey.100", px: 0.5, borderRadius: 0.5, fontSize: "0.85em" },
         }}>
-            <Markdown remarkPlugins={[remarkGfm]}>{changelogMd}</Markdown>
+            <Markdown remarkPlugins={[remarkGfm]}>{md}</Markdown>
         </Box>
     );
 }
@@ -208,8 +214,13 @@ function App() {
                 <DocFrame title="Documentation" src="/frontend/docs/index.html"/>
             )},
             { id: 'changelog', label: 'Changelog', icon: <HistoryIcon/>, render: () => (
-                <Changelog/>
+                <MarkdownDoc md={changelogMd}/>
             )},
+            { id: 'license', label: 'License', icon: <GavelIcon/>, render: () => (
+                <MarkdownDoc md={licenseMd}/>
+            )},
+            { id: 'source-code', label: 'Source code', icon: <CodeIcon/>,
+              href: 'https://gitea.psi.ch/mx/jungfraujoch' },
         ]},
     ];
 
@@ -232,9 +243,13 @@ function App() {
                                                        fontWeight: 600 }}>{sec.subheader}</ListSubheader>
                                 : undefined}>
                                 {sec.items.map(it => (
-                                    <ListItemButton key={it.id} selected={view === it.id}
+                                    <ListItemButton key={it.id}
                                                     disabled={it.disabled}
-                                                    onClick={() => setView(it.id)}
+                                                    {...(it.href
+                                                        ? { component: 'a', href: it.href,
+                                                            target: '_blank', rel: 'noopener' }
+                                                        : { selected: view === it.id,
+                                                            onClick: () => setView(it.id) })}
                                                     sx={{ borderLeft: '4px solid transparent',
                                                           '&.Mui-selected': { bgcolor: drawerSelectedBg,
                                                               borderColor: 'secondary.main' },
@@ -252,7 +267,7 @@ function App() {
                 <Toolbar/>
                 <ErrorMessage s={s.broker}/>
                 <Box sx={{ maxWidth: 1300, mx: 'auto', mt: 2 }}>
-                    {activeItem.render()}
+                    {activeItem.render?.()}
                 </Box>
             </Box>
         </Box>
@@ -262,7 +277,9 @@ function App() {
             bgcolor: 'background.paper', borderTop: '1px solid', borderColor: 'divider',
             py: 0.5, px: 2, textAlign: 'center', fontSize: '0.8rem',
         }}>
-            Developed at Paul Scherrer Institute (2019–2026). Main author:{' '}
+            Developed at{' '}
+            <Link href="https://www.psi.ch" target="_blank" rel="noopener">Paul Scherrer Institute</Link>
+            {' '}(2019–2026). Main author:{' '}
             <Link href="mailto:filip.leonarski@psi.ch">Filip Leonarski</Link> ·{' '}
             <Link href="https://doi.org/10.1107/S1600577522010268"><i>J. Synchrotron Rad.</i> (2023). <b>30</b>, 227–234</Link>
             {' '}· Version: {JFJOCH_VERSION}
-- 
2.52.0


From 35f6ffdde980cdc54ac73973043c628b5b8e1aef Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 11:15:59 +0200
Subject: [PATCH 111/228] viewer: draw loaded ROIs on the diffraction image

When a file with ROI definitions is opened (read into experiment.ROI()
by the HDF5 reader), the diffraction image now overlays the configured
box and circle ROIs as distinct colour-coded outlines, alongside the
existing resolution rings and spots. This is the first step of the
ROI-map-based multi-ROI canvas: showing the ROIs loaded from a file.

Azimuthal ROIs (wedge rendering) and per-ROI statistics from the bitmap
follow in subsequent steps.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../image_viewer/JFJochDiffractionImage.cpp   | 33 +++++++++++++++++++
 viewer/image_viewer/JFJochDiffractionImage.h  |  1 +
 2 files changed, 34 insertions(+)

diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 9b744348..435cfceb 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -313,6 +313,7 @@ void JFJochDiffractionImage::DrawTopPixels() {
 
 void JFJochDiffractionImage::addCustomOverlay() {
     DrawResolutionRings();
+    DrawROIs();
     DrawTopPixels();
 
     DrawBeamCenter();
@@ -326,6 +327,38 @@ void JFJochDiffractionImage::addCustomOverlay() {
     DrawResolutionText();
 }
 
+void JFJochDiffractionImage::DrawROIs() {
+    if (!image)
+        return;
+
+    const auto &rois = image->Dataset().experiment.ROI().GetROIDefinition();
+
+    // Distinct colours per ROI; loaded ROIs use solid lines (the interactively
+    // drawn scratch ROI keeps its dashed feature_color).
+    static const QColor palette[] = {Qt::cyan, Qt::yellow, QColor(0xff, 0x57, 0x22),
+                                     Qt::green, Qt::magenta, QColor(0x21, 0x96, 0xf3)};
+    const int palette_size = sizeof(palette) / sizeof(palette[0]);
+    int color_index = 0;
+    auto roi_pen = [&]() {
+        QPen pen(palette[color_index % palette_size], 2);
+        pen.setCosmetic(true);
+        color_index++;
+        return pen;
+    };
+
+    for (const auto &b : rois.boxes) {
+        auto *rect = scene()->addRect(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight(), roi_pen());
+        addOverlayItem(rect);
+    }
+
+    for (const auto &c : rois.circles) {
+        const float r = c.GetRadius_pxl();
+        auto *ell = scene()->addEllipse(c.GetX() - r, c.GetY() - r, 2 * r, 2 * r, roi_pen());
+        addOverlayItem(ell);
+    }
+    // Azimuthal ROIs are drawn as wedges in a later step.
+}
+
 
 void JFJochDiffractionImage::UpdateForeground() {
     if (!image || !auto_fg)
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 80e7871e..49ba0172 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -25,6 +25,7 @@ private:
     void addCustomOverlay() override;
     void LoadImageInternal();
     void DrawResolutionRings();
+    void DrawROIs();
     void DrawSpots();
     void DrawPredictions();
     void DrawBeamCenter();
-- 
2.52.0


From 7d6f79a1dab821a38a33cfa7dca04823bc4802b2 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 11:40:24 +0200
Subject: [PATCH 112/228] viewer: draw azimuthal ROI wedges, with optional fill
 and labels

Azimuthal ROIs now render on the diffraction image as annular sectors
(or full-ring annuli), sampled through DiffractionGeometry::ResPhiToPxl
so the outline follows the ROI footprint, including wrap-around sectors.

Add two side-panel toggles (both default off): a translucent fill for
every ROI (helpful when outline colours clash with the image colour map,
and with many ROIs) and ROI name labels (constant on-screen size). Wired
side panel -> window -> diffraction image like the existing feature
toggles.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerSidePanel.cpp              |  10 ++
 viewer/JFJochViewerSidePanel.h                |   2 +
 viewer/JFJochViewerWindow.cpp                 |   4 +
 .../image_viewer/JFJochDiffractionImage.cpp   | 112 ++++++++++++++++--
 viewer/image_viewer/JFJochDiffractionImage.h  |  10 ++
 5 files changed, 126 insertions(+), 12 deletions(-)

diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index 40677d48..70c94acf 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -113,6 +113,16 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
 
     layout->addWidget(new TitleLabel("ROI", this));
 
+    auto roiLabelsCheckBox = new QCheckBox("Show ROI labels", this);
+    roiLabelsCheckBox->setCheckState(Qt::CheckState::Unchecked);
+    connect(roiLabelsCheckBox, &QCheckBox::toggled, this, &JFJochViewerSidePanel::showROILabels);
+    layout->addWidget(roiLabelsCheckBox);
+
+    auto roiFillCheckBox = new QCheckBox("Translucent ROI fill", this);
+    roiFillCheckBox->setCheckState(Qt::CheckState::Unchecked);
+    connect(roiFillCheckBox, &QCheckBox::toggled, this, &JFJochViewerSidePanel::showROIFill);
+    layout->addWidget(roiFillCheckBox);
+
     roi = new JFJochViewerImageROIStatistics(this);
     layout->addWidget(roi);
 
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 6eabf1bd..f4652fa0 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -29,6 +29,8 @@ signals:
     void showSaturatedPixels(bool input);
     void showPredictions(bool input);
     void highlightIceRings(bool input);
+    void showROILabels(bool input);
+    void showROIFill(bool input);
     void findBeamCenter(const UnitCell &input, bool guess);
     void analyze();
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 7763b9e1..c49599be 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -281,6 +281,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             viewer, &JFJochDiffractionImage::showSpots);
     connect(side_panel, &JFJochViewerSidePanel::showPredictions,
             viewer, &JFJochDiffractionImage::showPredictions);
+    connect(side_panel, &JFJochViewerSidePanel::showROILabels,
+            viewer, &JFJochDiffractionImage::showROILabels);
+    connect(side_panel, &JFJochViewerSidePanel::showROIFill,
+            viewer, &JFJochDiffractionImage::showROIFill);
 
     connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
             viewer, &JFJochDiffractionImage::setFeatureColor);
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 435cfceb..f82efa42 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -4,7 +4,10 @@
 #include "JFJochDiffractionImage.h"
 #include "../../common/DiffractionGeometry.h"
 #include "../../common/JFJochMath.h"
+#include "../../common/ROIAzimuthal.h"
 
+#include <QPainterPath>
+#include <QBrush>
 #include <QGraphicsPixmapItem>
 #include <QGraphicsSimpleTextItem>
 #include <QGraphicsScene>
@@ -332,31 +335,116 @@ void JFJochDiffractionImage::DrawROIs() {
         return;
 
     const auto &rois = image->Dataset().experiment.ROI().GetROIDefinition();
+    auto geom = image->Dataset().experiment.GetDiffractionGeometry();
 
     // Distinct colours per ROI; loaded ROIs use solid lines (the interactively
     // drawn scratch ROI keeps its dashed feature_color).
+    // TODO: align this palette with the ROI colours in the bottom-panel plots.
     static const QColor palette[] = {Qt::cyan, Qt::yellow, QColor(0xff, 0x57, 0x22),
                                      Qt::green, Qt::magenta, QColor(0x21, 0x96, 0xf3)};
     const int palette_size = sizeof(palette) / sizeof(palette[0]);
     int color_index = 0;
-    auto roi_pen = [&]() {
-        QPen pen(palette[color_index % palette_size], 2);
-        pen.setCosmetic(true);
-        color_index++;
-        return pen;
+
+    auto fill_brush = [&](const QColor &c) {
+        return show_roi_fill ? QBrush(QColor(c.red(), c.green(), c.blue(), 60)) : QBrush(Qt::NoBrush);
+    };
+    auto label = [&](const std::string &name, const QColor &c, float px, float py) {
+        if (!show_roi_labels)
+            return;
+        auto *text = scene()->addText(QString::fromStdString(name));
+        text->setDefaultTextColor(c);
+        text->setFlag(QGraphicsItem::ItemIgnoresTransformations);   // constant on-screen size
+        text->setPos(px, py);
+        addOverlayItem(text);
     };
 
     for (const auto &b : rois.boxes) {
-        auto *rect = scene()->addRect(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight(), roi_pen());
-        addOverlayItem(rect);
+        QColor c = palette[color_index++ % palette_size];
+        QPen pen(c, 2); pen.setCosmetic(true);
+        addOverlayItem(scene()->addRect(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight(), pen, fill_brush(c)));
+        label(b.GetName(), c, b.GetXMin(), b.GetYMin());
     }
 
-    for (const auto &c : rois.circles) {
-        const float r = c.GetRadius_pxl();
-        auto *ell = scene()->addEllipse(c.GetX() - r, c.GetY() - r, 2 * r, 2 * r, roi_pen());
-        addOverlayItem(ell);
+    for (const auto &c_roi : rois.circles) {
+        QColor c = palette[color_index++ % palette_size];
+        QPen pen(c, 2); pen.setCosmetic(true);
+        const float r = c_roi.GetRadius_pxl();
+        addOverlayItem(scene()->addEllipse(c_roi.GetX() - r, c_roi.GetY() - r, 2 * r, 2 * r, pen, fill_brush(c)));
+        label(c_roi.GetName(), c, c_roi.GetX(), c_roi.GetY());
     }
-    // Azimuthal ROIs are drawn as wedges in a later step.
+
+    for (const auto &az : rois.azimuthal)
+        DrawAzimuthalROI(az, palette[color_index++ % palette_size], geom);
+}
+
+void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color,
+                                              const DiffractionGeometry &geom) {
+    QPen pen(color, 2); pen.setCosmetic(true);
+    QBrush brush = show_roi_fill ? QBrush(QColor(color.red(), color.green(), color.blue(), 60))
+                                 : QBrush(Qt::NoBrush);
+
+    const float d_inner = az.GetDMax_A();   // larger d -> smaller radius
+    const float d_outer = az.GetDMin_A();
+    auto deg2rad = [](float d) { return d * static_cast<float>(PI) / 180.0f; };
+
+    // Sample the boundary through the geometry so the wedge matches the ROI footprint.
+    // ResPhiToPxl throws when the resolution is too high for the wavelength; skip such ROIs.
+    auto add_arc = [&](QPainterPath &path, float d, float phi_a, float phi_b, int steps) -> bool {
+        for (int i = 0; i <= steps; i++) {
+            float phi = phi_a + (phi_b - phi_a) * static_cast<float>(i) / static_cast<float>(steps);
+            try {
+                auto [px, py] = geom.ResPhiToPxl(d, phi);
+                if (path.elementCount() == 0)
+                    path.moveTo(px, py);
+                else
+                    path.lineTo(px, py);
+            } catch (...) { return false; }
+        }
+        return true;
+    };
+
+    QPainterPath path;
+    if (az.HasPhi()) {
+        float phi0 = deg2rad(az.GetPhiMin_deg());
+        float phi1 = deg2rad(az.GetPhiMax_deg());
+        if (phi1 < phi0) phi1 += 2.0f * static_cast<float>(PI);   // unwrap the sector
+        int steps = std::max(8, static_cast<int>((phi1 - phi0) * 180.0f / static_cast<float>(PI) / 2.0f));
+        if (!add_arc(path, d_outer, phi0, phi1, steps)) return;   // outer arc
+        if (!add_arc(path, d_inner, phi1, phi0, steps)) return;   // inner arc back
+        path.closeSubpath();
+    } else {
+        path.setFillRule(Qt::OddEvenFill);                        // annulus
+        const float two_pi = 2.0f * static_cast<float>(PI);
+        if (!add_arc(path, d_outer, 0, two_pi, 180)) return;
+        path.closeSubpath();
+        QPainterPath inner;
+        if (!add_arc(inner, d_inner, 0, two_pi, 180)) return;
+        inner.closeSubpath();
+        path.addPath(inner);
+    }
+
+    addOverlayItem(scene()->addPath(path, pen, brush));
+
+    if (show_roi_labels) {
+        try {
+            auto [px, py] = geom.ResPhiToPxl(d_outer, az.HasPhi() ? deg2rad(az.GetPhiMin_deg()) : 0.0f);
+            auto *text = scene()->addText(QString::fromStdString(az.GetName()));
+            text->setDefaultTextColor(color);
+            text->setFlag(QGraphicsItem::ItemIgnoresTransformations);
+            text->setPos(px, py);
+            addOverlayItem(text);
+        } catch (...) {}
+    }
+}
+
+void JFJochDiffractionImage::showROILabels(bool input) {
+    show_roi_labels = input;
+    updateOverlay();
+}
+
+void JFJochDiffractionImage::showROIFill(bool input) {
+    show_roi_fill = input;
+    updateOverlay();
 }
 
 
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 49ba0172..612f8058 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -6,6 +6,9 @@
 #include "JFJochImage.h"
 #include "../../reader/JFJochReaderImage.h"
 
+class ROIAzimuthal;
+class DiffractionGeometry;
+
 class JFJochDiffractionImage : public JFJochImage {
 Q_OBJECT
 
@@ -26,6 +29,7 @@ private:
     void LoadImageInternal();
     void DrawResolutionRings();
     void DrawROIs();
+    void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
     void DrawSpots();
     void DrawPredictions();
     void DrawBeamCenter();
@@ -49,6 +53,9 @@ private:
     bool show_spots = false;
     bool show_predictions = false;
 
+    bool show_roi_labels = false;
+    bool show_roi_fill = false;
+
     bool highlight_ice_rings = true;
 
     float ice_ring_width_Q_recipA = 0.01;
@@ -64,6 +71,9 @@ public slots:
     void showSpots(bool input);
     void showPredictions(bool input);
 
+    void showROILabels(bool input);
+    void showROIFill(bool input);
+
     void setSpotColor(QColor input);
     void setPredictionColor(QColor input);
 
-- 
2.52.0


From 33118ebe8b0911ca08dde6f9151bff7cf7735573 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 11:44:42 +0200
Subject: [PATCH 113/228] viewer: fix stray line from origin on full-ring
 azimuthal ROI

The full-ring annulus built the inner ring as a separate QPainterPath and
merged it with addPath, which stitched a spurious segment from (0,0) to
the ring. Build both concentric rings as subpaths of one path, each begun
with an explicit moveTo, so there is no connecting segment.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../image_viewer/JFJochDiffractionImage.cpp   | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index f82efa42..412845d0 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -389,12 +389,14 @@ void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QCol
 
     // Sample the boundary through the geometry so the wedge matches the ROI footprint.
     // ResPhiToPxl throws when the resolution is too high for the wavelength; skip such ROIs.
-    auto add_arc = [&](QPainterPath &path, float d, float phi_a, float phi_b, int steps) -> bool {
+    // move_to_start == true begins a new subpath (no connecting line); false continues
+    // the current one (used for the radial edge between a sector's outer and inner arc).
+    auto add_arc = [&](QPainterPath &path, float d, float phi_a, float phi_b, int steps, bool move_to_start) -> bool {
         for (int i = 0; i <= steps; i++) {
             float phi = phi_a + (phi_b - phi_a) * static_cast<float>(i) / static_cast<float>(steps);
             try {
                 auto [px, py] = geom.ResPhiToPxl(d, phi);
-                if (path.elementCount() == 0)
+                if (move_to_start && i == 0)
                     path.moveTo(px, py);
                 else
                     path.lineTo(px, py);
@@ -409,18 +411,16 @@ void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QCol
         float phi1 = deg2rad(az.GetPhiMax_deg());
         if (phi1 < phi0) phi1 += 2.0f * static_cast<float>(PI);   // unwrap the sector
         int steps = std::max(8, static_cast<int>((phi1 - phi0) * 180.0f / static_cast<float>(PI) / 2.0f));
-        if (!add_arc(path, d_outer, phi0, phi1, steps)) return;   // outer arc
-        if (!add_arc(path, d_inner, phi1, phi0, steps)) return;   // inner arc back
+        if (!add_arc(path, d_outer, phi0, phi1, steps, true)) return;    // outer arc
+        if (!add_arc(path, d_inner, phi1, phi0, steps, false)) return;   // inner arc; radial edges close it
         path.closeSubpath();
     } else {
-        path.setFillRule(Qt::OddEvenFill);                        // annulus
+        path.setFillRule(Qt::OddEvenFill);                        // annulus: two concentric rings
         const float two_pi = 2.0f * static_cast<float>(PI);
-        if (!add_arc(path, d_outer, 0, two_pi, 180)) return;
+        if (!add_arc(path, d_outer, 0, two_pi, 180, true)) return;
+        path.closeSubpath();
+        if (!add_arc(path, d_inner, 0, two_pi, 180, true)) return;
         path.closeSubpath();
-        QPainterPath inner;
-        if (!add_arc(inner, d_inner, 0, two_pi, 180)) return;
-        inner.closeSubpath();
-        path.addPath(inner);
     }
 
     addOverlayItem(scene()->addPath(path, pen, brush));
-- 
2.52.0


From 39965956060b32558bcd4d85baa0c3a1d104df77 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 12:01:43 +0200
Subject: [PATCH 114/228] viewer: per-ROI statistics on the diffraction image
 via the CPU ROI engine

When ROI labels are shown, each ROI's label now also reports its sum,
max and pixel count for the current image. Rather than reimplementing the
accumulation, this reuses the existing ROIIntegrationCPU engine (the
software counterpart of the FPGA roi_calc), built from the experiment and
cached per dataset. A small adapter folds the viewer's gap sentinel
(INT32_MIN+1) onto the engine's masked sentinel (INT32_MIN) so masked and
saturated pixels are handled correctly.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../image_viewer/JFJochDiffractionImage.cpp   | 76 +++++++++++++++----
 viewer/image_viewer/JFJochDiffractionImage.h  | 14 ++++
 2 files changed, 74 insertions(+), 16 deletions(-)

diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 412845d0..861647a6 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -5,6 +5,7 @@
 #include "../../common/DiffractionGeometry.h"
 #include "../../common/JFJochMath.h"
 #include "../../common/ROIAzimuthal.h"
+#include "../../image_analysis/roi/ROIIntegrationCPU.h"
 
 #include <QPainterPath>
 #include <QBrush>
@@ -22,6 +23,8 @@
 // Constructor
 JFJochDiffractionImage::JFJochDiffractionImage(QWidget *parent) : JFJochImage(parent) {}
 
+JFJochDiffractionImage::~JFJochDiffractionImage() = default;
+
 void JFJochDiffractionImage::mouseHover(QMouseEvent *event) {
     auto coord = mapToScene(event->pos());
 
@@ -348,21 +351,12 @@ void JFJochDiffractionImage::DrawROIs() {
     auto fill_brush = [&](const QColor &c) {
         return show_roi_fill ? QBrush(QColor(c.red(), c.green(), c.blue(), 60)) : QBrush(Qt::NoBrush);
     };
-    auto label = [&](const std::string &name, const QColor &c, float px, float py) {
-        if (!show_roi_labels)
-            return;
-        auto *text = scene()->addText(QString::fromStdString(name));
-        text->setDefaultTextColor(c);
-        text->setFlag(QGraphicsItem::ItemIgnoresTransformations);   // constant on-screen size
-        text->setPos(px, py);
-        addOverlayItem(text);
-    };
 
     for (const auto &b : rois.boxes) {
         QColor c = palette[color_index++ % palette_size];
         QPen pen(c, 2); pen.setCosmetic(true);
         addOverlayItem(scene()->addRect(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight(), pen, fill_brush(c)));
-        label(b.GetName(), c, b.GetXMin(), b.GetYMin());
+        AddROILabel(b.GetName(), c, b.GetXMin(), b.GetYMin());
     }
 
     for (const auto &c_roi : rois.circles) {
@@ -370,13 +364,66 @@ void JFJochDiffractionImage::DrawROIs() {
         QPen pen(c, 2); pen.setCosmetic(true);
         const float r = c_roi.GetRadius_pxl();
         addOverlayItem(scene()->addEllipse(c_roi.GetX() - r, c_roi.GetY() - r, 2 * r, 2 * r, pen, fill_brush(c)));
-        label(c_roi.GetName(), c, c_roi.GetX(), c_roi.GetY());
+        AddROILabel(c_roi.GetName(), c, c_roi.GetX(), c_roi.GetY());
     }
 
     for (const auto &az : rois.azimuthal)
         DrawAzimuthalROI(az, palette[color_index++ % palette_size], geom);
 }
 
+namespace {
+// Adapts the viewer image for ROIIntegrationCPU, whose masking convention is
+// "min() == masked, max() == saturated". The reader uses two masked sentinels
+// (ERROR_PXL_VALUE == INT32_MIN and GAP_PXL_VALUE == INT32_MIN+1), so fold the
+// gap value onto the error value; saturated already maps to INT32_MAX.
+struct MaskedImageView {
+    const std::vector<int32_t> &img;
+    [[nodiscard]] size_t size() const { return img.size(); }
+    int32_t operator[](size_t i) const {
+        const int32_t v = img[i];
+        return (v == GAP_PXL_VALUE) ? ERROR_PXL_VALUE : v;
+    }
+};
+}
+
+void JFJochDiffractionImage::ComputeROIStats() {
+    roi_stats_.clear();
+    if (!image || image->Dataset().experiment.ROI().empty())
+        return;
+
+    // Rebuild the engine only when the dataset changes (it rasterizes the bitmap).
+    if (roi_integration_dataset_ != &image->Dataset()) {
+        roi_integration_ = std::make_unique<ROIIntegrationCPU>(image->Dataset().experiment);
+        roi_integration_dataset_ = &image->Dataset();
+    }
+    if (roi_integration_->empty())
+        return;
+
+    try {
+        roi_integration_->RunROI(MaskedImageView{image->Image()}, roi_stats_);
+    } catch (const std::exception &) {
+        roi_stats_.clear();   // e.g. image/bitmap size mismatch
+    }
+}
+
+void JFJochDiffractionImage::AddROILabel(const std::string &name, const QColor &color, float px, float py) {
+    if (!show_roi_labels)
+        return;
+
+    QString text_str = QString::fromStdString(name);
+    auto it = roi_stats_.find(name);
+    if (it != roi_stats_.end() && it->second.pixels > 0) {
+        const auto &m = it->second;
+        text_str += QString("  Σ=%1  max=%2  n=%3").arg(m.sum).arg(m.max_count).arg(m.pixels);
+    }
+
+    auto *text = scene()->addText(text_str);
+    text->setDefaultTextColor(color);
+    text->setFlag(QGraphicsItem::ItemIgnoresTransformations);   // constant on-screen size
+    text->setPos(px, py);
+    addOverlayItem(text);
+}
+
 void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color,
                                               const DiffractionGeometry &geom) {
     QPen pen(color, 2); pen.setCosmetic(true);
@@ -428,11 +475,7 @@ void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QCol
     if (show_roi_labels) {
         try {
             auto [px, py] = geom.ResPhiToPxl(d_outer, az.HasPhi() ? deg2rad(az.GetPhiMin_deg()) : 0.0f);
-            auto *text = scene()->addText(QString::fromStdString(az.GetName()));
-            text->setDefaultTextColor(color);
-            text->setFlag(QGraphicsItem::ItemIgnoresTransformations);
-            text->setPos(px, py);
-            addOverlayItem(text);
+            AddROILabel(az.GetName(), color, px, py);
         } catch (...) {}
     }
 }
@@ -473,6 +516,7 @@ void JFJochDiffractionImage::loadImage(std::shared_ptr<const JFJochReaderImage>
         image = in_image;
         UpdateForeground();
         LoadImageInternal();
+        ComputeROIStats();
         GeneratePixmap();
         Redraw();
         CalcROI();
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 612f8058..98943738 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -3,11 +3,15 @@
 
 #pragma once
 
+#include <map>
+#include <memory>
+
 #include "JFJochImage.h"
 #include "../../reader/JFJochReaderImage.h"
 
 class ROIAzimuthal;
 class DiffractionGeometry;
+class ROIIntegrationCPU;
 
 class JFJochDiffractionImage : public JFJochImage {
 Q_OBJECT
@@ -23,6 +27,7 @@ public:
     Q_ENUM(RingMode)
 
     JFJochDiffractionImage(QWidget *parent = nullptr);
+    ~JFJochDiffractionImage() override;   // out-of-line for the unique_ptr to an incomplete type
 private:
 
     void addCustomOverlay() override;
@@ -30,6 +35,8 @@ private:
     void DrawResolutionRings();
     void DrawROIs();
     void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
+    void ComputeROIStats();
+    void AddROILabel(const std::string &name, const QColor &color, float px, float py);
     void DrawSpots();
     void DrawPredictions();
     void DrawBeamCenter();
@@ -56,6 +63,13 @@ private:
     bool show_roi_labels = false;
     bool show_roi_fill = false;
 
+    // Per-ROI statistics for the current image, computed with the shared CPU ROI
+    // engine (the software counterpart of the FPGA roi_calc). The engine is rebuilt
+    // only when the dataset changes, as it rasterizes the ROI bitmap on construction.
+    std::map<std::string, ROIMessage> roi_stats_;
+    std::unique_ptr<ROIIntegrationCPU> roi_integration_;
+    const JFJochReaderDataset *roi_integration_dataset_ = nullptr;
+
     bool highlight_ice_rings = true;
 
     float ice_ring_width_Q_recipA = 0.01;
-- 
2.52.0


From a433399106a3804e79e09b72f67f61815b00997d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 12:23:19 +0200
Subject: [PATCH 115/228] image_analysis: surgical ROI-only entry points in
 MXAnalysisWithoutFPGA

Add three entry points so ROI statistics can be (re)computed without a
full re-analysis, in support of interactive ROI editing in the viewer:

- RebuildROI(): recreate the ROI engine after the ROI set changes (the
  CudaStream is now kept as a member so the GPU engine can be rebuilt).
- AnalyzeROIOnly(): decompress + preprocess + ROI, skipping azimuthal
  integration, spot finding and indexing (a new image when re-analysis
  is off).
- RunROIOnly(): rerun only the ROI integration on the already-preprocessed
  image (an interactive ROI move). A full Analyze() still computes ROIs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/MXAnalysisWithoutFPGA.cpp | 33 +++++++++++++++++++++++-
 image_analysis/MXAnalysisWithoutFPGA.h   | 13 ++++++++++
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index cbe26e6a..2adcf932 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -48,7 +48,7 @@ MXAnalysisWithoutFPGA::MXAnalysisWithoutFPGA(const DiffractionExperiment &in_exp
             roi = std::make_unique<ROIIntegrationCPU>(experiment);
 #ifdef JFJOCH_USE_CUDA
     } else {
-        auto stream = std::make_shared<CudaStream>();
+        stream = std::make_shared<CudaStream>();
         preprocessor_buffer = std::make_unique<ImagePreprocessorBufferGPU>(experiment.GetPixelsNum());
         preprocessor = std::make_unique<ImagePreprocessorGPU>(in_experiment, in_mask, stream);
         spotFinder = std::make_unique<ImageSpotFinderGPU>(experiment.GetXPixelsNum(), experiment.GetYPixelsNum(), stream);
@@ -115,6 +115,37 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
     output.bkg_estimate = profile.GetBkgEstimate(integration.Settings());
 }
 
+void MXAnalysisWithoutFPGA::RebuildROI() {
+    if (experiment.ROI().empty()) {
+        roi.reset();
+        return;
+    }
+#ifdef JFJOCH_USE_CUDA
+    if (stream) {
+        roi = std::make_unique<ROIIntegrationGPU>(experiment, stream);
+        return;
+    }
+#endif
+    roi = std::make_unique<ROIIntegrationCPU>(experiment);
+}
+
+void MXAnalysisWithoutFPGA::AnalyzeROIOnly(DataMessage &output) {
+    if ((output.image.GetWidth() != xpixels)
+        || (output.image.GetWidth() * output.image.GetHeight() != npixels))
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Mismatch in pixel size");
+
+    const uint8_t *image_ptr = output.image.GetUncompressedPtr(decompression_buffer);
+    preprocessor->Analyze(*preprocessor_buffer, image_ptr, output.image.GetMode());
+    RunROIOnly(output);
+}
+
+void MXAnalysisWithoutFPGA::RunROIOnly(DataMessage &output) {
+    output.roi.clear();
+    if (roi)
+        roi->Run(*preprocessor_buffer, output.roi);
+}
+
 void MXAnalysisWithoutFPGA::UpdateMaskResolution(const SpotFindingSettings &settings) {
     mask_low_res = settings.low_resolution_limit;
     mask_high_res = settings.high_resolution_limit;
diff --git a/image_analysis/MXAnalysisWithoutFPGA.h b/image_analysis/MXAnalysisWithoutFPGA.h
index 9d6bd0a9..b14d5f6f 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.h
+++ b/image_analysis/MXAnalysisWithoutFPGA.h
@@ -19,6 +19,8 @@
 #include "image_preprocessing/ImagePreprocessor.h"
 #include "image_preprocessing/ImagePreprocessorBuffer.h"
 
+class CudaStream;
+
 // MXAnalysisWithoutFPGA is not thread safe - it has to owned by a single thread
 class MXAnalysisWithoutFPGA {
     const DiffractionExperiment &experiment;
@@ -43,10 +45,21 @@ class MXAnalysisWithoutFPGA {
     float mask_high_res;
     float mask_low_res;
     void UpdateMaskResolution(const SpotFindingSettings& settings);
+#ifdef JFJOCH_USE_CUDA
+    std::shared_ptr<CudaStream> stream;   // kept so RebuildROI() can recreate the GPU ROI engine
+#endif
 public:
     MXAnalysisWithoutFPGA(const DiffractionExperiment &experiment, const AzimuthalIntegrationMapping &integration,
                      const PixelMask &mask, IndexAndRefine &indexer);
     void Analyze(DataMessage &output, AzimuthalIntegrationProfile &profile, const SpotFindingSettings &spot_finding_settings);
+
+    // Surgical ROI-only paths used when a full re-analysis is not wanted: rebuild the
+    // ROI engine after the ROI set changes, recompute ROIs after preprocessing a new
+    // image (reanalyze off), or just rerun ROIs on the current preprocessed image (an
+    // interactive ROI move). A full Analyze() already computes ROIs, so needs nothing.
+    void RebuildROI();
+    void AnalyzeROIOnly(DataMessage &output);
+    void RunROIOnly(DataMessage &output);
 };
 
 
-- 
2.52.0


From 4e45680e969debf212ab7826502111a93d3c3b26 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:02:03 +0200
Subject: [PATCH 116/228] viewer: worker can update ROIs and recompute them
 without full re-analysis

The reading worker's experiment is the source of truth for ROIs. Add a
SetROIDefinition slot that updates curr_experiment.ROI(), rebuilds the
analysis ROI engine, mutates the dataset (so the canvas reflects the new
ROIs) and recomputes only the ROIs for the current image via RunROIOnly.
On image load when full re-analysis is off, ROIs are still computed via
AnalyzeROIOnly so the statistics stay current.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp | 45 ++++++++++++++++++++++++++++-
 viewer/JFJochImageReadingWorker.h   |  4 +++
 2 files changed, 48 insertions(+), 1 deletion(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index a86e4619..0e8de2c5 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -90,6 +90,7 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
       azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
     qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
     qRegisterMetaType<BrokerStatus>("BrokerStatus");
+    qRegisterMetaType<ROIDefinition>("ROIDefinition");
     spot_finding_settings = settings;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
@@ -382,8 +383,16 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
 
         auto end = std::chrono::high_resolution_clock::now();
 
-        if (auto_reanalyze)
+        if (auto_reanalyze) {
             ReanalyzeImage_i();
+        } else if (image_analysis && !curr_experiment.ROI().empty()) {
+            // ROIs are wanted even when a full re-analysis is not; compute only those.
+            try {
+                image_analysis->AnalyzeROIOnly(current_image_ptr->ImageData());
+            } catch (const std::exception &e) {
+                logger.Error("ROI-only analysis failed: {}", e.what());
+            }
+        }
 
         auto end_analysis = std::chrono::high_resolution_clock::now();
 
@@ -580,6 +589,40 @@ void JFJochImageReadingWorker::UpdateAzintSettings(const AzimuthalIntegrationSet
     UpdateDataset_i(std::nullopt);
 }
 
+void JFJochImageReadingWorker::SetROIDefinition(const ROIDefinition &rois) {
+    QMutexLocker locker(&m);
+    SetROIDefinition_i(rois);
+}
+
+void JFJochImageReadingWorker::SetROIDefinition_i(const ROIDefinition &rois) {
+    // The worker experiment is the source of truth; the analysis ROI engine is rebuilt
+    // for it so newly loaded images pick up the change automatically.
+    curr_experiment.ROI().SetROI(rois);
+    if (image_analysis)
+        image_analysis->RebuildROI();
+
+    if (!current_image_ptr)
+        return;
+
+    // Mutate the dataset too, so the canvas (which draws image->Dataset().experiment.ROI())
+    // reflects the edit, then recompute only the ROIs for the current image.
+    auto mutable_dataset = current_image_ptr->CreateMutableDataset();
+    mutable_dataset->experiment.ROI().SetROI(rois);
+    std::shared_ptr<const JFJochReaderDataset> dataset = mutable_dataset;
+    current_image_ptr = std::make_shared<JFJochReaderImage>(current_image_ptr->ImageData(), dataset);
+
+    if (image_analysis) {
+        try {
+            image_analysis->RunROIOnly(current_image_ptr->ImageData());
+        } catch (const std::exception &e) {
+            logger.Error("ROI-only analysis failed: {}", e.what());
+        }
+    }
+
+    emit datasetLoaded(dataset);
+    emit imageLoaded(current_image_ptr);
+}
+
 void JFJochImageReadingWorker::UpdateUserMask_i(const std::vector<uint32_t> &mask) {
     std::shared_ptr<const JFJochReaderDataset> dataset;
     if (http_mode) {
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 07144f52..3db9e495 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -31,6 +31,7 @@ Q_DECLARE_METATYPE(AzimuthalIntegrationSettings)
 Q_DECLARE_METATYPE(UnitCell)
 Q_DECLARE_METATYPE(std::shared_ptr<const SimpleImage>)
 Q_DECLARE_METATYPE(BrokerStatus)
+Q_DECLARE_METATYPE(ROIDefinition)
 
 class JFJochImageReadingWorker : public QObject {
     Q_OBJECT
@@ -117,6 +118,7 @@ private:
     void UpdateDataset_i(const std::optional<DiffractionExperiment>& experiment);
     void UpdateAzint_i(const JFJochReaderDataset *dataset);
     void UpdateUserMask_i(const std::vector<uint32_t> &mask);
+    void SetROIDefinition_i(const ROIDefinition &rois);
     void setAutoLoadMode_i(AutoloadMode mode);
 
 signals:
@@ -164,6 +166,8 @@ public slots:
     void AddROIToUserMask();
     void SubtractROIFromUserMask();
 
+    void SetROIDefinition(const ROIDefinition &rois);
+
     void SaveUserMaskTIFF(QString filename);
     void UploadUserMask();
     void ClearUserMask();
-- 
2.52.0


From 2f8d486b51fbea3385d8e63dcfcdd180a1db8f14 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:02:17 +0200
Subject: [PATCH 117/228] =?UTF-8?q?viewer:=20ROI=20list=20panel=20?=
 =?UTF-8?q?=E2=80=94=20select,=20add,=20rename,=20delete,=20per-ROI=20resu?=
 =?UTF-8?q?lts?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Add JFJochViewerROIList to the side panel: a list of the dataset's ROIs
with selection, add (box/circle/azimuthal), rename and delete, plus a
statistics readout (sum/mean/std/max/valid/masked/centre-of-mass) for the
selected ROI, taken from the analysis output for the current image. Edits
emit a full ROIDefinition, routed to the worker's SetROIDefinition.

Per-ROI statistics now live in this panel rather than the canvas labels;
the diffraction image's labels show only the ROI name, and the ad-hoc
ROIIntegrationCPU computation there is removed in favour of the analysis
pipeline. The result widget now reports std dev instead of variance.

The single-ROI scratch panel remains for now and will be retired once the
interactive canvas editing replaces it.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         |   2 +
 viewer/JFJochViewerSidePanel.cpp              |   6 +
 viewer/JFJochViewerSidePanel.h                |   4 +
 viewer/JFJochViewerWindow.cpp                 |   3 +
 .../image_viewer/JFJochDiffractionImage.cpp   |  49 +----
 viewer/image_viewer/JFJochDiffractionImage.h  |  13 --
 viewer/widgets/JFJochViewerROIList.cpp        | 173 ++++++++++++++++++
 viewer/widgets/JFJochViewerROIList.h          |  47 +++++
 viewer/widgets/JFJochViewerROIResult.cpp      |   4 +-
 9 files changed, 240 insertions(+), 61 deletions(-)
 create mode 100644 viewer/widgets/JFJochViewerROIList.cpp
 create mode 100644 viewer/widgets/JFJochViewerROIList.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index b8a54837..2a7d4c49 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -87,6 +87,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJoch2DAzintImageWindow.h
         widgets/JFJochViewerROIResult.cpp
         widgets/JFJochViewerROIResult.h
+        widgets/JFJochViewerROIList.cpp
+        widgets/JFJochViewerROIList.h
         widgets/ResolutionRingWidget.cpp
         widgets/ResolutionRingWidget.h
         image_viewer/JFJochGridScanImage.cpp
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index 70c94acf..bb260d64 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -123,6 +123,12 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     connect(roiFillCheckBox, &QCheckBox::toggled, this, &JFJochViewerSidePanel::showROIFill);
     layout->addWidget(roiFillCheckBox);
 
+    roi_list = new JFJochViewerROIList(this);
+    layout->addWidget(roi_list);
+    connect(this, &JFJochViewerSidePanel::imageLoaded, roi_list, &JFJochViewerROIList::loadImage);
+    connect(roi_list, &JFJochViewerROIList::roisChanged, this, &JFJochViewerSidePanel::roisChanged);
+    connect(roi_list, &JFJochViewerROIList::selectedROIChanged, this, &JFJochViewerSidePanel::selectedROIChanged);
+
     roi = new JFJochViewerImageROIStatistics(this);
     layout->addWidget(roi);
 
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index f4652fa0..0af1f790 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -9,6 +9,7 @@
 #include <QCheckBox>
 
 #include "widgets/JFJochViewerImageROIStatistics.h"
+#include "widgets/JFJochViewerROIList.h"
 #include "../reader/JFJochReader.h"
 #include "charts/JFJochSimpleChartView.h"
 #include "widgets/JFJochViewerSidePanelChart.h"
@@ -19,6 +20,7 @@ class JFJochViewerSidePanel : public QWidget {
 
     JFJochViewerSidePanelChart *chart = nullptr;
     JFJochViewerImageROIStatistics *roi = nullptr;
+    JFJochViewerROIList *roi_list = nullptr;
     ResolutionRingWidget *res_rings = nullptr;
 
 signals:
@@ -31,6 +33,8 @@ signals:
     void highlightIceRings(bool input);
     void showROILabels(bool input);
     void showROIFill(bool input);
+    void roisChanged(ROIDefinition rois);
+    void selectedROIChanged(QString name);
     void findBeamCenter(const UnitCell &input, bool guess);
     void analyze();
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index c49599be..42b905cc 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -204,6 +204,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(viewer, &JFJochDiffractionImage::roiCalculated,
             side_panel, &JFJochViewerSidePanel::SetROIResult);
 
+    connect(side_panel, &JFJochViewerSidePanel::roisChanged,
+            reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
+
     connect(side_panel, &JFJochViewerSidePanel::ROIBoxConfigured,
             reading_worker, &JFJochImageReadingWorker::SetROIBox);
 
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 861647a6..93889186 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -5,7 +5,6 @@
 #include "../../common/DiffractionGeometry.h"
 #include "../../common/JFJochMath.h"
 #include "../../common/ROIAzimuthal.h"
-#include "../../image_analysis/roi/ROIIntegrationCPU.h"
 
 #include <QPainterPath>
 #include <QBrush>
@@ -23,8 +22,6 @@
 // Constructor
 JFJochDiffractionImage::JFJochDiffractionImage(QWidget *parent) : JFJochImage(parent) {}
 
-JFJochDiffractionImage::~JFJochDiffractionImage() = default;
-
 void JFJochDiffractionImage::mouseHover(QMouseEvent *event) {
     auto coord = mapToScene(event->pos());
 
@@ -371,53 +368,12 @@ void JFJochDiffractionImage::DrawROIs() {
         DrawAzimuthalROI(az, palette[color_index++ % palette_size], geom);
 }
 
-namespace {
-// Adapts the viewer image for ROIIntegrationCPU, whose masking convention is
-// "min() == masked, max() == saturated". The reader uses two masked sentinels
-// (ERROR_PXL_VALUE == INT32_MIN and GAP_PXL_VALUE == INT32_MIN+1), so fold the
-// gap value onto the error value; saturated already maps to INT32_MAX.
-struct MaskedImageView {
-    const std::vector<int32_t> &img;
-    [[nodiscard]] size_t size() const { return img.size(); }
-    int32_t operator[](size_t i) const {
-        const int32_t v = img[i];
-        return (v == GAP_PXL_VALUE) ? ERROR_PXL_VALUE : v;
-    }
-};
-}
-
-void JFJochDiffractionImage::ComputeROIStats() {
-    roi_stats_.clear();
-    if (!image || image->Dataset().experiment.ROI().empty())
-        return;
-
-    // Rebuild the engine only when the dataset changes (it rasterizes the bitmap).
-    if (roi_integration_dataset_ != &image->Dataset()) {
-        roi_integration_ = std::make_unique<ROIIntegrationCPU>(image->Dataset().experiment);
-        roi_integration_dataset_ = &image->Dataset();
-    }
-    if (roi_integration_->empty())
-        return;
-
-    try {
-        roi_integration_->RunROI(MaskedImageView{image->Image()}, roi_stats_);
-    } catch (const std::exception &) {
-        roi_stats_.clear();   // e.g. image/bitmap size mismatch
-    }
-}
-
 void JFJochDiffractionImage::AddROILabel(const std::string &name, const QColor &color, float px, float py) {
     if (!show_roi_labels)
         return;
 
-    QString text_str = QString::fromStdString(name);
-    auto it = roi_stats_.find(name);
-    if (it != roi_stats_.end() && it->second.pixels > 0) {
-        const auto &m = it->second;
-        text_str += QString("  Σ=%1  max=%2  n=%3").arg(m.sum).arg(m.max_count).arg(m.pixels);
-    }
-
-    auto *text = scene()->addText(text_str);
+    // Just the name; per-ROI statistics are shown in the side-panel ROI list.
+    auto *text = scene()->addText(QString::fromStdString(name));
     text->setDefaultTextColor(color);
     text->setFlag(QGraphicsItem::ItemIgnoresTransformations);   // constant on-screen size
     text->setPos(px, py);
@@ -516,7 +472,6 @@ void JFJochDiffractionImage::loadImage(std::shared_ptr<const JFJochReaderImage>
         image = in_image;
         UpdateForeground();
         LoadImageInternal();
-        ComputeROIStats();
         GeneratePixmap();
         Redraw();
         CalcROI();
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 98943738..14917fdc 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -3,15 +3,11 @@
 
 #pragma once
 
-#include <map>
-#include <memory>
-
 #include "JFJochImage.h"
 #include "../../reader/JFJochReaderImage.h"
 
 class ROIAzimuthal;
 class DiffractionGeometry;
-class ROIIntegrationCPU;
 
 class JFJochDiffractionImage : public JFJochImage {
 Q_OBJECT
@@ -27,7 +23,6 @@ public:
     Q_ENUM(RingMode)
 
     JFJochDiffractionImage(QWidget *parent = nullptr);
-    ~JFJochDiffractionImage() override;   // out-of-line for the unique_ptr to an incomplete type
 private:
 
     void addCustomOverlay() override;
@@ -35,7 +30,6 @@ private:
     void DrawResolutionRings();
     void DrawROIs();
     void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
-    void ComputeROIStats();
     void AddROILabel(const std::string &name, const QColor &color, float px, float py);
     void DrawSpots();
     void DrawPredictions();
@@ -63,13 +57,6 @@ private:
     bool show_roi_labels = false;
     bool show_roi_fill = false;
 
-    // Per-ROI statistics for the current image, computed with the shared CPU ROI
-    // engine (the software counterpart of the FPGA roi_calc). The engine is rebuilt
-    // only when the dataset changes, as it rasterizes the ROI bitmap on construction.
-    std::map<std::string, ROIMessage> roi_stats_;
-    std::unique_ptr<ROIIntegrationCPU> roi_integration_;
-    const JFJochReaderDataset *roi_integration_dataset_ = nullptr;
-
     bool highlight_ice_rings = true;
 
     float ice_ring_width_Q_recipA = 0.01;
diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
new file mode 100644
index 00000000..24c5bbde
--- /dev/null
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -0,0 +1,173 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochViewerROIList.h"
+
+#include <set>
+
+#include <QVBoxLayout>
+#include <QHBoxLayout>
+#include <QPushButton>
+#include <QInputDialog>
+#include <QListWidgetItem>
+
+JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
+    auto *layout = new QVBoxLayout(this);
+
+    list_ = new QListWidget(this);
+    list_->setMaximumHeight(120);
+    layout->addWidget(list_);
+    connect(list_, &QListWidget::itemSelectionChanged, this, &JFJochViewerROIList::OnSelectionChanged);
+
+    auto *buttons = new QHBoxLayout();
+    type_combo_ = new QComboBox(this);
+    type_combo_->addItems({"Box", "Circle", "Azimuthal"});
+    buttons->addWidget(type_combo_);
+    auto *add = new QPushButton("+", this);
+    auto *ren = new QPushButton("Rename", this);
+    auto *del = new QPushButton("Delete", this);
+    buttons->addWidget(add);
+    buttons->addWidget(ren);
+    buttons->addWidget(del);
+    layout->addLayout(buttons);
+    connect(add, &QPushButton::clicked, this, &JFJochViewerROIList::OnAdd);
+    connect(ren, &QPushButton::clicked, this, &JFJochViewerROIList::OnRename);
+    connect(del, &QPushButton::clicked, this, &JFJochViewerROIList::OnDelete);
+
+    result_ = new JFJochViewerROIResult(this);
+    layout->addWidget(result_);
+}
+
+void JFJochViewerROIList::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
+    image_ = image;
+    const QString keep = SelectedName();
+    rois_ = image_ ? image_->Dataset().experiment.ROI().GetROIDefinition() : ROIDefinition{};
+    RebuildList(keep);
+    ShowSelectedResult();
+}
+
+void JFJochViewerROIList::RebuildList(const QString &keep_selected) {
+    rebuilding_ = true;
+    list_->clear();
+
+    auto add_item = [&](const std::string &name, const char *type) {
+        auto *item = new QListWidgetItem(QString("%1  ·  %2").arg(QString::fromStdString(name), type));
+        item->setData(Qt::UserRole, QString::fromStdString(name));   // name independent of display text
+        list_->addItem(item);
+    };
+    for (const auto &b : rois_.boxes) add_item(b.GetName(), "box");
+    for (const auto &c : rois_.circles) add_item(c.GetName(), "circle");
+    for (const auto &a : rois_.azimuthal) add_item(a.GetName(), "azim");
+
+    if (!keep_selected.isEmpty()) {
+        for (int i = 0; i < list_->count(); i++)
+            if (list_->item(i)->data(Qt::UserRole).toString() == keep_selected) {
+                list_->setCurrentRow(i);
+                break;
+            }
+    }
+    rebuilding_ = false;
+}
+
+QString JFJochViewerROIList::SelectedName() const {
+    auto *item = list_->currentItem();
+    return item ? item->data(Qt::UserRole).toString() : QString();
+}
+
+void JFJochViewerROIList::ShowSelectedResult() {
+    const QString name = SelectedName();
+    if (image_ && !name.isEmpty()) {
+        const auto &roi = image_->ImageData().roi;
+        auto it = roi.find(name.toStdString());
+        if (it != roi.end()) {
+            result_->SetROIResult(it->second);
+            return;
+        }
+    }
+    result_->SetROIResult(ROIMessage{});   // clears the display
+}
+
+std::string JFJochViewerROIList::UniqueName() const {
+    std::set<std::string> used;
+    for (const auto &b : rois_.boxes) used.insert(b.GetName());
+    for (const auto &c : rois_.circles) used.insert(c.GetName());
+    for (const auto &a : rois_.azimuthal) used.insert(a.GetName());
+    for (int i = 1; ; i++) {
+        std::string n = "roi" + std::to_string(i);
+        if (!used.count(n)) return n;
+    }
+}
+
+void JFJochViewerROIList::OnSelectionChanged() {
+    if (rebuilding_)
+        return;
+    ShowSelectedResult();
+    emit selectedROIChanged(SelectedName());
+}
+
+void JFJochViewerROIList::OnAdd() {
+    if (rois_.boxes.size() + rois_.circles.size() + rois_.azimuthal.size() >= 16)
+        return;   // bitmap allows at most 16 ROIs
+
+    const std::string name = UniqueName();
+    int64_t cx = 100, cy = 100;
+    if (image_) {
+        cx = image_->Dataset().experiment.GetXPixelsNum() / 2;
+        cy = image_->Dataset().experiment.GetYPixelsNum() / 2;
+    }
+    switch (type_combo_->currentIndex()) {
+        case 0:  rois_.boxes.emplace_back(name, cx - 100, cx + 100, cy - 100, cy + 100); break;
+        case 1:  rois_.circles.emplace_back(name, cx, cy, 100); break;
+        default: rois_.azimuthal.emplace_back(name, 2.0f, 4.0f); break;
+    }
+    emit roisChanged(rois_);
+    RebuildList(QString::fromStdString(name));
+    ShowSelectedResult();
+}
+
+void JFJochViewerROIList::OnDelete() {
+    const std::string name = SelectedName().toStdString();
+    if (name.empty())
+        return;
+
+    auto erase_by_name = [&name](auto &vec) {
+        for (auto it = vec.begin(); it != vec.end(); ++it)
+            if (it->GetName() == name) { vec.erase(it); return true; }
+        return false;
+    };
+    if (erase_by_name(rois_.boxes) || erase_by_name(rois_.circles) || erase_by_name(rois_.azimuthal)) {
+        emit roisChanged(rois_);
+        RebuildList(QString());
+        ShowSelectedResult();
+    }
+}
+
+void JFJochViewerROIList::OnRename() {
+    const QString old_name = SelectedName();
+    if (old_name.isEmpty())
+        return;
+
+    bool ok = false;
+    const QString new_name = QInputDialog::getText(this, "Rename ROI", "New name:",
+                                                   QLineEdit::Normal, old_name, &ok);
+    if (!ok || new_name.isEmpty() || new_name == old_name)
+        return;
+
+    const std::string oldn = old_name.toStdString();
+    const std::string newn = new_name.toStdString();
+
+    for (auto &b : rois_.boxes)
+        if (b.GetName() == oldn) { b = ROIBox(newn, b.GetXMin(), b.GetXMax(), b.GetYMin(), b.GetYMax()); break; }
+    for (auto &c : rois_.circles)
+        if (c.GetName() == oldn) { c = ROICircle(newn, c.GetX(), c.GetY(), c.GetRadius_pxl()); break; }
+    for (auto &a : rois_.azimuthal)
+        if (a.GetName() == oldn) {
+            a = a.HasPhi() ? ROIAzimuthal(newn, a.GetDMin_A(), a.GetDMax_A(), a.GetPhiMin_deg(), a.GetPhiMax_deg())
+                           : ROIAzimuthal(newn, a.GetDMin_A(), a.GetDMax_A());
+            break;
+        }
+
+    emit roisChanged(rois_);
+    RebuildList(new_name);
+    ShowSelectedResult();
+}
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
new file mode 100644
index 00000000..675c5721
--- /dev/null
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -0,0 +1,47 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <memory>
+
+#include <QWidget>
+#include <QListWidget>
+#include <QComboBox>
+
+#include "JFJochViewerROIResult.h"
+#include "../../common/ROIDefinition.h"
+#include "../../reader/JFJochReaderImage.h"
+
+// Manages the dataset's ROI list: select one, add (box/circle/azimuthal), rename or
+// delete, and show the selected ROI's statistics for the current image. Edits are
+// emitted as a complete ROIDefinition; the reading worker is the source of truth and
+// recomputes the per-image ROI results, which arrive back via loadImage().
+class JFJochViewerROIList : public QWidget {
+    Q_OBJECT
+
+    QListWidget *list_;
+    QComboBox *type_combo_;
+    JFJochViewerROIResult *result_;
+
+    ROIDefinition rois_;
+    std::shared_ptr<const JFJochReaderImage> image_;
+    bool rebuilding_ = false;
+
+    void RebuildList(const QString &keep_selected);
+    void ShowSelectedResult();
+    [[nodiscard]] QString SelectedName() const;
+    [[nodiscard]] std::string UniqueName() const;
+public:
+    explicit JFJochViewerROIList(QWidget *parent = nullptr);
+public slots:
+    void loadImage(std::shared_ptr<const JFJochReaderImage> image);
+private slots:
+    void OnSelectionChanged();
+    void OnAdd();
+    void OnDelete();
+    void OnRename();
+signals:
+    void roisChanged(ROIDefinition rois);
+    void selectedROIChanged(QString name);
+};
diff --git a/viewer/widgets/JFJochViewerROIResult.cpp b/viewer/widgets/JFJochViewerROIResult.cpp
index d5f766e4..c6915fc0 100644
--- a/viewer/widgets/JFJochViewerROIResult.cpp
+++ b/viewer/widgets/JFJochViewerROIResult.cpp
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include "JFJochViewerROIResult.h"
+#include <cmath>
 #include <QGridLayout>
 
 JFJochViewerROIResult::JFJochViewerROIResult(QWidget *parent) : QWidget(parent) {
@@ -40,10 +41,11 @@ void JFJochViewerROIResult::SetROIResult(ROIMessage roi) {
         auto roi_npixel_val = static_cast<double>(roi.pixels);
         double roi_mean_val = static_cast<double>(roi.sum) / roi_npixel_val;
         double variance = static_cast<double>(roi.sum_square) / roi_npixel_val - roi_mean_val * roi_mean_val;
+        double std_dev = std::sqrt(std::max(0.0, variance));
 
         roi_sum->setText(QString("Sum <b>%1</b>").arg(roi.sum));
         roi_mean->setText(QString("Mean <b>%1</b>").arg(QString::number(roi_mean_val, 'f', 3)));
-        roi_var->setText(QString("Var <b>%1</b>").arg(QString::number(variance, 'f', 3)));
+        roi_var->setText(QString("Std <b>%1</b>").arg(QString::number(std_dev, 'f', 3)));
         roi_max->setText(QString("Max <b>%1</b>").arg(roi.max_count));
         roi_npixel->setText(QString("Valid <b>%1</b>").arg(roi.pixels));
         roi_masked->setText(QString("Masked <b>%1</b>").arg(roi.pixels_masked));
-- 
2.52.0


From e49a9088625f6fb4fa15ac5968dfb9606ecf49f0 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:16:16 +0200
Subject: [PATCH 118/228] =?UTF-8?q?viewer:=20ROI=20panel=20refinements=20?=
 =?UTF-8?q?=E2=80=94=20persist=20edits,=20combobox,=20compact=20toggles?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Edited ROIs now override the file's for every subsequently loaded image
  and survive settings changes, until a new file is opened (previously a
  delete/add was lost on the next image). Tracked via an roi_override_ that
  is re-applied to curr_experiment and to each loaded image's dataset.
- The ROI selector is a compact combobox instead of a list widget.
- "Show labels" and "Translucent fill" share one row to save space.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp    | 19 ++++++++++++-
 viewer/JFJochImageReadingWorker.h      |  4 +++
 viewer/JFJochViewerSidePanel.cpp       | 11 +++++---
 viewer/widgets/JFJochViewerROIList.cpp | 37 +++++++++++---------------
 viewer/widgets/JFJochViewerROIList.h   |  5 ++--
 5 files changed, 47 insertions(+), 29 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 0e8de2c5..a6ba76b2 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -271,6 +271,7 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
         current_file = filename;
         if (dataset) {
             curr_experiment = dataset->experiment;
+            roi_override_.reset();   // new file: use its ROIs, forget any earlier edits
             curr_experiment.ImportIndexingSettings(indexing_settings);
             curr_experiment.ImportAzimuthalIntegrationSettings(azint_settings);
             UpdateAzint_i(dataset.get());
@@ -378,6 +379,8 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
             return;
         }
 
+        ApplyROIOverrideToImage_i();   // edited ROIs win over the file's for every image
+
         current_image = current_image_ptr->ImageData().number;
         current_summation = summation;
 
@@ -466,6 +469,8 @@ void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionEx
     }
 
     curr_experiment = dataset->experiment;
+    if (roi_override_)
+        curr_experiment.ROI().SetROI(*roi_override_);   // keep edited ROIs across settings changes
     curr_experiment.ImportIndexingSettings(indexing_settings);
     curr_experiment.ImportAzimuthalIntegrationSettings(azint_settings);
     UpdateAzint_i(dataset.get());
@@ -473,6 +478,7 @@ void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionEx
     emit datasetLoaded(dataset);
 
     current_image_ptr = std::make_shared<JFJochReaderImage>(current_image_ptr->ImageData(), dataset);
+    ApplyROIOverrideToImage_i();
 
     if (auto_reanalyze)
         ReanalyzeImage_i();
@@ -596,7 +602,9 @@ void JFJochImageReadingWorker::SetROIDefinition(const ROIDefinition &rois) {
 
 void JFJochImageReadingWorker::SetROIDefinition_i(const ROIDefinition &rois) {
     // The worker experiment is the source of truth; the analysis ROI engine is rebuilt
-    // for it so newly loaded images pick up the change automatically.
+    // for it so newly loaded images pick up the change automatically. From now on the
+    // edited ROIs override whatever the file carried.
+    roi_override_ = rois;
     curr_experiment.ROI().SetROI(rois);
     if (image_analysis)
         image_analysis->RebuildROI();
@@ -623,6 +631,15 @@ void JFJochImageReadingWorker::SetROIDefinition_i(const ROIDefinition &rois) {
     emit imageLoaded(current_image_ptr);
 }
 
+void JFJochImageReadingWorker::ApplyROIOverrideToImage_i() {
+    if (!roi_override_ || !current_image_ptr)
+        return;
+    auto md = current_image_ptr->CreateMutableDataset();
+    md->experiment.ROI().SetROI(*roi_override_);
+    current_image_ptr = std::make_shared<JFJochReaderImage>(
+        current_image_ptr->ImageData(), std::shared_ptr<const JFJochReaderDataset>(md));
+}
+
 void JFJochImageReadingWorker::UpdateUserMask_i(const std::vector<uint32_t> &mask) {
     std::shared_ptr<const JFJochReaderDataset> dataset;
     if (http_mode) {
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 3db9e495..b9e546a0 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -53,6 +53,9 @@ private:
     QString current_file;
 
     DiffractionExperiment curr_experiment;
+    // Once the user edits ROIs they override whatever the file carried, for this and
+    // every subsequently loaded image, until a new file is opened.
+    std::optional<ROIDefinition> roi_override_;
     IndexingSettings indexing_settings;
     AzimuthalIntegrationSettings azint_settings;
     std::unique_ptr<IndexerThreadPool> indexing;
@@ -119,6 +122,7 @@ private:
     void UpdateAzint_i(const JFJochReaderDataset *dataset);
     void UpdateUserMask_i(const std::vector<uint32_t> &mask);
     void SetROIDefinition_i(const ROIDefinition &rois);
+    void ApplyROIOverrideToImage_i();   // rewrite current_image_ptr's dataset with roi_override_
     void setAutoLoadMode_i(AutoloadMode mode);
 
 signals:
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index bb260d64..c78fec8a 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -113,15 +113,18 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
 
     layout->addWidget(new TitleLabel("ROI", this));
 
-    auto roiLabelsCheckBox = new QCheckBox("Show ROI labels", this);
+    auto roiLabelsCheckBox = new QCheckBox("Show labels", this);
     roiLabelsCheckBox->setCheckState(Qt::CheckState::Unchecked);
     connect(roiLabelsCheckBox, &QCheckBox::toggled, this, &JFJochViewerSidePanel::showROILabels);
-    layout->addWidget(roiLabelsCheckBox);
 
-    auto roiFillCheckBox = new QCheckBox("Translucent ROI fill", this);
+    auto roiFillCheckBox = new QCheckBox("Translucent fill", this);
     roiFillCheckBox->setCheckState(Qt::CheckState::Unchecked);
     connect(roiFillCheckBox, &QCheckBox::toggled, this, &JFJochViewerSidePanel::showROIFill);
-    layout->addWidget(roiFillCheckBox);
+
+    auto roiToggleRow = new QHBoxLayout();
+    roiToggleRow->addWidget(roiLabelsCheckBox);
+    roiToggleRow->addWidget(roiFillCheckBox);
+    layout->addLayout(roiToggleRow);
 
     roi_list = new JFJochViewerROIList(this);
     layout->addWidget(roi_list);
diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index 24c5bbde..250da1b8 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -9,15 +9,13 @@
 #include <QHBoxLayout>
 #include <QPushButton>
 #include <QInputDialog>
-#include <QListWidgetItem>
 
 JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
     auto *layout = new QVBoxLayout(this);
 
-    list_ = new QListWidget(this);
-    list_->setMaximumHeight(120);
-    layout->addWidget(list_);
-    connect(list_, &QListWidget::itemSelectionChanged, this, &JFJochViewerROIList::OnSelectionChanged);
+    combo_ = new QComboBox(this);
+    layout->addWidget(combo_);
+    connect(combo_, &QComboBox::currentIndexChanged, this, &JFJochViewerROIList::OnSelectionChanged);
 
     auto *buttons = new QHBoxLayout();
     type_combo_ = new QComboBox(this);
@@ -42,36 +40,33 @@ void JFJochViewerROIList::loadImage(std::shared_ptr<const JFJochReaderImage> ima
     image_ = image;
     const QString keep = SelectedName();
     rois_ = image_ ? image_->Dataset().experiment.ROI().GetROIDefinition() : ROIDefinition{};
-    RebuildList(keep);
+    RebuildCombo(keep);
     ShowSelectedResult();
 }
 
-void JFJochViewerROIList::RebuildList(const QString &keep_selected) {
+void JFJochViewerROIList::RebuildCombo(const QString &keep_selected) {
     rebuilding_ = true;
-    list_->clear();
+    combo_->clear();
 
     auto add_item = [&](const std::string &name, const char *type) {
-        auto *item = new QListWidgetItem(QString("%1  ·  %2").arg(QString::fromStdString(name), type));
-        item->setData(Qt::UserRole, QString::fromStdString(name));   // name independent of display text
-        list_->addItem(item);
+        // display "name · type", with the bare name kept as item data for lookups
+        combo_->addItem(QString("%1  ·  %2").arg(QString::fromStdString(name), type),
+                        QString::fromStdString(name));
     };
     for (const auto &b : rois_.boxes) add_item(b.GetName(), "box");
     for (const auto &c : rois_.circles) add_item(c.GetName(), "circle");
     for (const auto &a : rois_.azimuthal) add_item(a.GetName(), "azim");
 
     if (!keep_selected.isEmpty()) {
-        for (int i = 0; i < list_->count(); i++)
-            if (list_->item(i)->data(Qt::UserRole).toString() == keep_selected) {
-                list_->setCurrentRow(i);
-                break;
-            }
+        const int idx = combo_->findData(keep_selected);
+        if (idx >= 0)
+            combo_->setCurrentIndex(idx);
     }
     rebuilding_ = false;
 }
 
 QString JFJochViewerROIList::SelectedName() const {
-    auto *item = list_->currentItem();
-    return item ? item->data(Qt::UserRole).toString() : QString();
+    return combo_->currentData().toString();
 }
 
 void JFJochViewerROIList::ShowSelectedResult() {
@@ -121,7 +116,7 @@ void JFJochViewerROIList::OnAdd() {
         default: rois_.azimuthal.emplace_back(name, 2.0f, 4.0f); break;
     }
     emit roisChanged(rois_);
-    RebuildList(QString::fromStdString(name));
+    RebuildCombo(QString::fromStdString(name));
     ShowSelectedResult();
 }
 
@@ -137,7 +132,7 @@ void JFJochViewerROIList::OnDelete() {
     };
     if (erase_by_name(rois_.boxes) || erase_by_name(rois_.circles) || erase_by_name(rois_.azimuthal)) {
         emit roisChanged(rois_);
-        RebuildList(QString());
+        RebuildCombo(QString());
         ShowSelectedResult();
     }
 }
@@ -168,6 +163,6 @@ void JFJochViewerROIList::OnRename() {
         }
 
     emit roisChanged(rois_);
-    RebuildList(new_name);
+    RebuildCombo(new_name);
     ShowSelectedResult();
 }
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
index 675c5721..b8332062 100644
--- a/viewer/widgets/JFJochViewerROIList.h
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -6,7 +6,6 @@
 #include <memory>
 
 #include <QWidget>
-#include <QListWidget>
 #include <QComboBox>
 
 #include "JFJochViewerROIResult.h"
@@ -20,7 +19,7 @@
 class JFJochViewerROIList : public QWidget {
     Q_OBJECT
 
-    QListWidget *list_;
+    QComboBox *combo_;
     QComboBox *type_combo_;
     JFJochViewerROIResult *result_;
 
@@ -28,7 +27,7 @@ class JFJochViewerROIList : public QWidget {
     std::shared_ptr<const JFJochReaderImage> image_;
     bool rebuilding_ = false;
 
-    void RebuildList(const QString &keep_selected);
+    void RebuildCombo(const QString &keep_selected);
     void ShowSelectedResult();
     [[nodiscard]] QString SelectedName() const;
     [[nodiscard]] std::string UniqueName() const;
-- 
2.52.0


From 0c780a5cbbc0dec8b2d7520550a6e0f1bce08791 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:22:25 +0200
Subject: [PATCH 119/228] Harmonize licsense files

---
 LICENSE         | 5 ++++-
 docs/LICENSE.md | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/LICENSE b/LICENSE
index 383abbd4..7dbd24cd 100644
--- a/LICENSE
+++ b/LICENSE
@@ -679,7 +679,10 @@ Public License instead of this License.  But first, please read
 
 ================
 
-As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries.
+As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries and Intel MKL.
 
 We also permit to link Jungfraujoch software (GPLv3) with Jungfraujoch high-level synthesis code (CERN OHL 2.0) for the purpose
 of simulating FPGA design on CPU.
+
+If OpenAPI definition file (jfjoch_api.yaml) is solely used to generate client code or to interact with the Jungfraujoch
+API it may be distributed under terms of your choosing without being subject to GPL requirements.
diff --git a/docs/LICENSE.md b/docs/LICENSE.md
index 8b19c24c..222b84ba 100644
--- a/docs/LICENSE.md
+++ b/docs/LICENSE.md
@@ -681,7 +681,7 @@ Public License instead of this License.  But first, please read
 
 ## Jungfraujoch exceptions to GPL
 
-As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries.
+As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries and Intel MKL.
 
 We also permit to link Jungfraujoch software (GPLv3) with Jungfraujoch high-level synthesis code (CERN OHL 2.0) for the purpose
 of simulating FPGA design on CPU.
-- 
2.52.0


From 308265c7b1584ed77d5be3c4f81877e66b3f8eba Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:23:03 +0200
Subject: [PATCH 120/228] viewer: move the selected box/circle ROI on the
 canvas

Add base-class mouse hooks (roiEditPress/Move/Release) so the diffraction
image can edit the persistent ROI selected in the side-panel combobox.
The selected ROI is highlighted (dashed, thicker), and dragging its
interior moves a box or circle; on release the new geometry is committed
through SetROIDefinition, which recomputes only the ROIs. Resize,
azimuthal handles and delete-key follow.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp                 |   4 +
 .../image_viewer/JFJochDiffractionImage.cpp   | 102 ++++++++++++++++--
 viewer/image_viewer/JFJochDiffractionImage.h  |  19 ++++
 viewer/image_viewer/JFJochImage.cpp           |  19 +++-
 viewer/image_viewer/JFJochImage.h             |   9 +-
 5 files changed, 142 insertions(+), 11 deletions(-)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 42b905cc..57215cd6 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -206,6 +206,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     connect(side_panel, &JFJochViewerSidePanel::roisChanged,
             reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
+    connect(side_panel, &JFJochViewerSidePanel::selectedROIChanged,
+            viewer, &JFJochDiffractionImage::setSelectedROI);
+    connect(viewer, &JFJochDiffractionImage::roiGeometryEdited,
+            reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
 
     connect(side_panel, &JFJochViewerSidePanel::ROIBoxConfigured,
             reading_worker, &JFJochImageReadingWorker::SetROIBox);
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 93889186..ec1165cb 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -351,17 +351,31 @@ void JFJochDiffractionImage::DrawROIs() {
 
     for (const auto &b : rois.boxes) {
         QColor c = palette[color_index++ % palette_size];
-        QPen pen(c, 2); pen.setCosmetic(true);
-        addOverlayItem(scene()->addRect(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight(), pen, fill_brush(c)));
-        AddROILabel(b.GetName(), c, b.GetXMin(), b.GetYMin());
+        const bool selected = (QString::fromStdString(b.GetName()) == selected_roi_);
+        QPen pen(c, selected ? 3 : 2);
+        pen.setCosmetic(true);
+        if (selected) pen.setStyle(Qt::DashLine);   // highlight the editable ROI
+        const QRectF rect = (roi_edit_ == RoiEdit::MoveBox && b.GetName() == edit_name_.toStdString())
+                              ? edit_box_
+                              : QRectF(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight());
+        addOverlayItem(scene()->addRect(rect, pen, fill_brush(c)));
+        AddROILabel(b.GetName(), c, rect.left(), rect.top());
     }
 
     for (const auto &c_roi : rois.circles) {
         QColor c = palette[color_index++ % palette_size];
-        QPen pen(c, 2); pen.setCosmetic(true);
-        const float r = c_roi.GetRadius_pxl();
-        addOverlayItem(scene()->addEllipse(c_roi.GetX() - r, c_roi.GetY() - r, 2 * r, 2 * r, pen, fill_brush(c)));
-        AddROILabel(c_roi.GetName(), c, c_roi.GetX(), c_roi.GetY());
+        const bool selected = (QString::fromStdString(c_roi.GetName()) == selected_roi_);
+        QPen pen(c, selected ? 3 : 2);
+        pen.setCosmetic(true);
+        if (selected) pen.setStyle(Qt::DashLine);
+        QPointF center(c_roi.GetX(), c_roi.GetY());
+        double r = c_roi.GetRadius_pxl();
+        if (roi_edit_ == RoiEdit::MoveCircle && c_roi.GetName() == edit_name_.toStdString()) {
+            center = edit_center_;
+            r = edit_radius_;
+        }
+        addOverlayItem(scene()->addEllipse(center.x() - r, center.y() - r, 2 * r, 2 * r, pen, fill_brush(c)));
+        AddROILabel(c_roi.GetName(), c, center.x(), center.y());
     }
 
     for (const auto &az : rois.azimuthal)
@@ -446,6 +460,80 @@ void JFJochDiffractionImage::showROIFill(bool input) {
     updateOverlay();
 }
 
+void JFJochDiffractionImage::setSelectedROI(QString name) {
+    selected_roi_ = name;
+    updateOverlay();
+}
+
+bool JFJochDiffractionImage::roiEditPress(const QPointF &scenePos) {
+    if (!image || selected_roi_.isEmpty())
+        return false;
+
+    const auto &rois = image->Dataset().experiment.ROI().GetROIDefinition();
+    const std::string sel = selected_roi_.toStdString();
+
+    for (const auto &b : rois.boxes)
+        if (b.GetName() == sel) {
+            const QRectF r(QPointF(b.GetXMin(), b.GetYMin()), QPointF(b.GetXMax(), b.GetYMax()));
+            if (!r.contains(scenePos))
+                return false;
+            roi_edit_ = RoiEdit::MoveBox;
+            edit_name_ = selected_roi_;
+            edit_box_ = r;
+            move_last_ = scenePos;
+            return true;
+        }
+    for (const auto &c : rois.circles)
+        if (c.GetName() == sel) {
+            const QPointF center(c.GetX(), c.GetY());
+            if (QLineF(center, scenePos).length() > c.GetRadius_pxl())
+                return false;
+            roi_edit_ = RoiEdit::MoveCircle;
+            edit_name_ = selected_roi_;
+            edit_center_ = center;
+            edit_radius_ = c.GetRadius_pxl();
+            move_last_ = scenePos;
+            return true;
+        }
+    return false;   // azimuthal editing is not yet supported
+}
+
+void JFJochDiffractionImage::roiEditMove(const QPointF &scenePos) {
+    const QPointF delta = scenePos - move_last_;
+    move_last_ = scenePos;
+    if (roi_edit_ == RoiEdit::MoveBox)
+        edit_box_.translate(delta);
+    else if (roi_edit_ == RoiEdit::MoveCircle)
+        edit_center_ += delta;
+    updateOverlay();
+}
+
+void JFJochDiffractionImage::roiEditRelease() {
+    if (roi_edit_ == RoiEdit::None || !image) {
+        roi_edit_ = RoiEdit::None;
+        return;
+    }
+
+    ROIDefinition rois = image->Dataset().experiment.ROI().GetROIDefinition();
+    const std::string sel = edit_name_.toStdString();
+    if (roi_edit_ == RoiEdit::MoveBox) {
+        for (auto &b : rois.boxes)
+            if (b.GetName() == sel) {
+                b = ROIBox(sel, std::lround(edit_box_.left()), std::lround(edit_box_.right()),
+                                std::lround(edit_box_.top()), std::lround(edit_box_.bottom()));
+                break;
+            }
+    } else if (roi_edit_ == RoiEdit::MoveCircle) {
+        for (auto &c : rois.circles)
+            if (c.GetName() == sel) {
+                c = ROICircle(sel, edit_center_.x(), edit_center_.y(), edit_radius_);
+                break;
+            }
+    }
+    roi_edit_ = RoiEdit::None;
+    emit roiGeometryEdited(rois);
+}
+
 
 void JFJochDiffractionImage::UpdateForeground() {
     if (!image || !auto_fg)
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 14917fdc..dc068b00 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -5,6 +5,7 @@
 
 #include "JFJochImage.h"
 #include "../../reader/JFJochReaderImage.h"
+#include "../../common/ROIDefinition.h"
 
 class ROIAzimuthal;
 class DiffractionGeometry;
@@ -31,6 +32,21 @@ private:
     void DrawROIs();
     void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
     void AddROILabel(const std::string &name, const QColor &color, float px, float py);
+
+    // Interactive editing of the selected (named) ROI: move box/circle for now.
+    bool roiEditPress(const QPointF &scenePos) override;
+    void roiEditMove(const QPointF &scenePos) override;
+    void roiEditRelease() override;
+
+    QString selected_roi_;
+    enum class RoiEdit { None, MoveBox, MoveCircle };
+    RoiEdit roi_edit_ = RoiEdit::None;
+    QString edit_name_;
+    QRectF edit_box_;
+    QPointF edit_center_;
+    double edit_radius_ = 0;
+    QPointF move_last_;
+
     void DrawSpots();
     void DrawPredictions();
     void DrawBeamCenter();
@@ -63,7 +79,10 @@ private:
 
     void mouseHover(QMouseEvent* event) override;
 
+signals:
+    void roiGeometryEdited(ROIDefinition rois);
 public slots:
+    void setSelectedROI(QString name);
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
     void setAutoForeground(bool input);
     void setResolutionRing(QVector<float> v);
diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index 7f151a92..0dd1b6d3 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -157,6 +157,13 @@ void JFJochImage::mousePressEvent(QMouseEvent *event) {
 
     if (event->button() == Qt::LeftButton) {
         const QPointF scenePos = mapToScene(event->pos());
+
+        if (roiEditPress(scenePos)) {
+            mouse_event_type = MouseEventType::EditingExternalROI;
+            event->accept();
+            return;
+        }
+
         active_handle_ = hitTestROIHandle(scenePos, 4.0 / std::sqrt(std::max(1e-4, scale_factor)));
 
         if (active_handle_ != ResizeHandle::None && active_handle_ != ResizeHandle::Inside) {
@@ -193,6 +200,9 @@ void JFJochImage::mouseMoveEvent(QMouseEvent *event) {
     QPointF delta;
 
     switch (mouse_event_type) {
+        case MouseEventType::EditingExternalROI:
+            roiEditMove(scenePos);
+            return;
         case MouseEventType::Panning: {
             const QPoint viewDelta = event->pos() - lastMousePos;
             lastMousePos = event->pos();
@@ -284,10 +294,13 @@ void JFJochImage::mouseReleaseEvent(QMouseEvent *event) {
     if (!scene()) return;
 
     if (event->button() == Qt::LeftButton) {
-        if (mouse_event_type == MouseEventType::DrawingROI) {
-            roiEndPos = RoundPoint(mapToScene(event->pos()));
+        if (mouse_event_type == MouseEventType::EditingExternalROI) {
+            roiEditRelease();
+        } else {
+            if (mouse_event_type == MouseEventType::DrawingROI)
+                roiEndPos = RoundPoint(mapToScene(event->pos()));
+            updateROI();
         }
-        updateROI();
     }
 
     mouse_event_type = MouseEventType::None;
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index 5e98e599..cbdd3634 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -75,8 +75,15 @@ protected:
     // Helper: add an overlay item to the scene and track it for selective removal
     void addOverlayItem(QGraphicsItem *item);
 
-    enum class MouseEventType {None, Panning, DrawingROI, MovingROI, ResizingROI};
+    enum class MouseEventType {None, Panning, DrawingROI, MovingROI, ResizingROI, EditingExternalROI};
     MouseEventType mouse_event_type = MouseEventType::None;
+
+    // Hooks for editing a named, persistent ROI drawn by a subclass (the base only
+    // owns the mouse events; the subclass knows the loaded ROIs). roiEditPress returns
+    // true to claim the gesture for ROI editing.
+    virtual bool roiEditPress(const QPointF &scenePos) { return false; }
+    virtual void roiEditMove(const QPointF &scenePos) {}
+    virtual void roiEditRelease() {}
     QPoint lastMousePos;  // To track panning movement
 
     // Resizing which edge/corner
-- 
2.52.0


From d9dfd3641371f05e9dbf03681331d7f09a59a91a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 13:33:04 +0200
Subject: [PATCH 121/228] viewer: click to select an ROI, with live move and a
 hand cursor

Clicking a box/circle on the image now selects it (syncing the side-panel
combobox) and grabs it for moving, with a closed-hand cursor during the
drag. The move recomputes ROI statistics live rather than only on release,
throttled to at most one in-flight recompute so the worker is not flooded.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerSidePanel.cpp              |  4 ++
 viewer/JFJochViewerSidePanel.h                |  1 +
 viewer/JFJochViewerWindow.cpp                 |  2 +
 .../image_viewer/JFJochDiffractionImage.cpp   | 57 ++++++++++++-------
 viewer/image_viewer/JFJochDiffractionImage.h  |  3 +
 viewer/widgets/JFJochViewerROIList.cpp        |  6 ++
 viewer/widgets/JFJochViewerROIList.h          |  1 +
 7 files changed, 54 insertions(+), 20 deletions(-)

diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index c78fec8a..b1f61618 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -189,6 +189,10 @@ void JFJochViewerSidePanel::highlightIceRingsToggled(bool input) {
     emit highlightIceRings(input);
 }
 
+void JFJochViewerSidePanel::selectROIInList(QString name) {
+    roi_list->setSelected(name);
+}
+
 void JFJochViewerSidePanel::SetROIBox(QRect box) {
     roi->SetROIBox(box);
 }
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 0af1f790..8d95f257 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -56,6 +56,7 @@ public slots:
     void SetROICircle(double x, double y, double radius);
     void SetROIResult(ROIMessage msg);
     void SetRings(QVector<float> v);
+    void selectROIInList(QString name);
 
 private slots:
     void spotsToggled(bool input);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 57215cd6..0e3da6a2 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -210,6 +210,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             viewer, &JFJochDiffractionImage::setSelectedROI);
     connect(viewer, &JFJochDiffractionImage::roiGeometryEdited,
             reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
+    connect(viewer, &JFJochDiffractionImage::roiSelected,
+            side_panel, &JFJochViewerSidePanel::selectROIInList);
 
     connect(side_panel, &JFJochViewerSidePanel::ROIBoxConfigured,
             reading_worker, &JFJochImageReadingWorker::SetROIBox);
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index ec1165cb..6414de8f 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -466,35 +466,39 @@ void JFJochDiffractionImage::setSelectedROI(QString name) {
 }
 
 bool JFJochDiffractionImage::roiEditPress(const QPointF &scenePos) {
-    if (!image || selected_roi_.isEmpty())
+    if (!image)
         return false;
 
     const auto &rois = image->Dataset().experiment.ROI().GetROIDefinition();
-    const std::string sel = selected_roi_.toStdString();
 
-    for (const auto &b : rois.boxes)
-        if (b.GetName() == sel) {
-            const QRectF r(QPointF(b.GetXMin(), b.GetYMin()), QPointF(b.GetXMax(), b.GetYMax()));
-            if (!r.contains(scenePos))
-                return false;
+    // Pick the first box/circle under the cursor, so an ROI can be grabbed by clicking it.
+    for (const auto &b : rois.boxes) {
+        const QRectF r(QPointF(b.GetXMin(), b.GetYMin()), QPointF(b.GetXMax(), b.GetYMax()));
+        if (r.contains(scenePos)) {
             roi_edit_ = RoiEdit::MoveBox;
-            edit_name_ = selected_roi_;
+            edit_name_ = QString::fromStdString(b.GetName());
             edit_box_ = r;
             move_last_ = scenePos;
+            selected_roi_ = edit_name_;
+            emit roiSelected(edit_name_);
+            setCursor(Qt::ClosedHandCursor);
             return true;
         }
-    for (const auto &c : rois.circles)
-        if (c.GetName() == sel) {
-            const QPointF center(c.GetX(), c.GetY());
-            if (QLineF(center, scenePos).length() > c.GetRadius_pxl())
-                return false;
+    }
+    for (const auto &c : rois.circles) {
+        const QPointF center(c.GetX(), c.GetY());
+        if (QLineF(center, scenePos).length() <= c.GetRadius_pxl()) {
             roi_edit_ = RoiEdit::MoveCircle;
-            edit_name_ = selected_roi_;
+            edit_name_ = QString::fromStdString(c.GetName());
             edit_center_ = center;
             edit_radius_ = c.GetRadius_pxl();
             move_last_ = scenePos;
+            selected_roi_ = edit_name_;
+            emit roiSelected(edit_name_);
+            setCursor(Qt::ClosedHandCursor);
             return true;
         }
+    }
     return false;   // azimuthal editing is not yet supported
 }
 
@@ -506,15 +510,28 @@ void JFJochDiffractionImage::roiEditMove(const QPointF &scenePos) {
     else if (roi_edit_ == RoiEdit::MoveCircle)
         edit_center_ += delta;
     updateOverlay();
+
+    // Live recompute, but keep at most one in flight (cleared in loadImage) so the
+    // worker is not flooded with edits faster than it can recompute them.
+    if (!live_pending_) {
+        live_pending_ = true;
+        emit roiGeometryEdited(BuildEditedROIDefinition());
+    }
 }
 
 void JFJochDiffractionImage::roiEditRelease() {
-    if (roi_edit_ == RoiEdit::None || !image) {
-        roi_edit_ = RoiEdit::None;
+    if (roi_edit_ == RoiEdit::None)
         return;
-    }
+    const ROIDefinition rois = BuildEditedROIDefinition();
+    roi_edit_ = RoiEdit::None;
+    setCursor(Qt::ArrowCursor);
+    emit roiGeometryEdited(rois);   // final, exact position
+}
 
-    ROIDefinition rois = image->Dataset().experiment.ROI().GetROIDefinition();
+ROIDefinition JFJochDiffractionImage::BuildEditedROIDefinition() const {
+    ROIDefinition rois;
+    if (image)
+        rois = image->Dataset().experiment.ROI().GetROIDefinition();
     const std::string sel = edit_name_.toStdString();
     if (roi_edit_ == RoiEdit::MoveBox) {
         for (auto &b : rois.boxes)
@@ -530,8 +547,7 @@ void JFJochDiffractionImage::roiEditRelease() {
                 break;
             }
     }
-    roi_edit_ = RoiEdit::None;
-    emit roiGeometryEdited(rois);
+    return rois;
 }
 
 
@@ -556,6 +572,7 @@ void JFJochDiffractionImage::setHDRMode(bool input) {
 }
 
 void JFJochDiffractionImage::loadImage(std::shared_ptr<const JFJochReaderImage> in_image) {
+    live_pending_ = false;   // a live ROI edit (if any) has now been recomputed
     if (in_image) {
         image = in_image;
         UpdateForeground();
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index dc068b00..ab00c8ea 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -37,6 +37,7 @@ private:
     bool roiEditPress(const QPointF &scenePos) override;
     void roiEditMove(const QPointF &scenePos) override;
     void roiEditRelease() override;
+    [[nodiscard]] ROIDefinition BuildEditedROIDefinition() const;   // current ROIs with the edit applied
 
     QString selected_roi_;
     enum class RoiEdit { None, MoveBox, MoveCircle };
@@ -46,6 +47,7 @@ private:
     QPointF edit_center_;
     double edit_radius_ = 0;
     QPointF move_last_;
+    bool live_pending_ = false;   // a live edit is being recomputed; throttles emissions
 
     void DrawSpots();
     void DrawPredictions();
@@ -81,6 +83,7 @@ private:
 
 signals:
     void roiGeometryEdited(ROIDefinition rois);
+    void roiSelected(QString name);   // user picked an ROI by clicking it on the image
 public slots:
     void setSelectedROI(QString name);
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index 250da1b8..efaa8b13 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -69,6 +69,12 @@ QString JFJochViewerROIList::SelectedName() const {
     return combo_->currentData().toString();
 }
 
+void JFJochViewerROIList::setSelected(QString name) {
+    const int idx = combo_->findData(name);
+    if (idx >= 0 && idx != combo_->currentIndex())
+        combo_->setCurrentIndex(idx);   // updates the stats and selection highlight
+}
+
 void JFJochViewerROIList::ShowSelectedResult() {
     const QString name = SelectedName();
     if (image_ && !name.isEmpty()) {
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
index b8332062..f3b0650a 100644
--- a/viewer/widgets/JFJochViewerROIList.h
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -35,6 +35,7 @@ public:
     explicit JFJochViewerROIList(QWidget *parent = nullptr);
 public slots:
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
+    void setSelected(QString name);   // select an ROI by name (e.g. clicked on the canvas)
 private slots:
     void OnSelectionChanged();
     void OnAdd();
-- 
2.52.0


From 00b58cd42687aa7e772dc40e15bf78db871d53aa Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:07:16 +0200
Subject: [PATCH 122/228] viewer: resize box/circle/azimuthal ROIs and delete
 with the Delete key

Extend canvas ROI editing beyond move:
- Box: drag corners/edges to resize (handles shown on the selected ROI).
- Circle: drag the perimeter to resize, interior to move.
- Azimuthal: drag the inner/outer arc to change the Q/d range, or a radial
  edge to rotate a phi bound; sampled through the geometry so it tracks
  the conic.
- Delete removes the selected ROI (the view now takes keyboard focus).

All edits go through the same live, throttled SetROIDefinition path.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../image_viewer/JFJochDiffractionImage.cpp   | 301 ++++++++++++++----
 viewer/image_viewer/JFJochDiffractionImage.h  |   8 +-
 2 files changed, 254 insertions(+), 55 deletions(-)

diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 6414de8f..62cd60a2 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -8,6 +8,7 @@
 
 #include <QPainterPath>
 #include <QBrush>
+#include <QKeyEvent>
 #include <QGraphicsPixmapItem>
 #include <QGraphicsSimpleTextItem>
 #include <QGraphicsScene>
@@ -20,7 +21,38 @@
 #include "JFJochSimpleImage.h"
 
 // Constructor
-JFJochDiffractionImage::JFJochDiffractionImage(QWidget *parent) : JFJochImage(parent) {}
+static float AngularDistance_deg(float a, float b) {
+    float d = std::fabs(a - b);
+    return (d > 180.0f) ? 360.0f - d : d;
+}
+
+static bool InPhiSector(float phi, float phi_min, float phi_max) {
+    if (phi_min <= phi_max)
+        return phi >= phi_min && phi <= phi_max;
+    return phi >= phi_min || phi <= phi_max;
+}
+
+JFJochDiffractionImage::JFJochDiffractionImage(QWidget *parent) : JFJochImage(parent) {
+    setFocusPolicy(Qt::StrongFocus);   // so the Delete key reaches the view
+}
+
+JFJochImage::ResizeHandle JFJochDiffractionImage::hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const {
+    auto on = [&](qreal a, qreal b) { return std::abs(a - b) <= tol; };
+    const bool L = on(p.x(), r.left()),  R = on(p.x(), r.right());
+    const bool T = on(p.y(), r.top()),   B = on(p.y(), r.bottom());
+    const bool inX = p.x() >= r.left() - tol && p.x() <= r.right() + tol;
+    const bool inY = p.y() >= r.top() - tol && p.y() <= r.bottom() + tol;
+    if (L && T) return ResizeHandle::TopLeft;
+    if (R && T) return ResizeHandle::TopRight;
+    if (L && B) return ResizeHandle::BottomLeft;
+    if (R && B) return ResizeHandle::BottomRight;
+    if (L && inY) return ResizeHandle::Left;
+    if (R && inY) return ResizeHandle::Right;
+    if (T && inX) return ResizeHandle::Top;
+    if (B && inX) return ResizeHandle::Bottom;
+    if (r.contains(p)) return ResizeHandle::Inside;
+    return ResizeHandle::None;
+}
 
 void JFJochDiffractionImage::mouseHover(QMouseEvent *event) {
     auto coord = mapToScene(event->pos());
@@ -348,38 +380,67 @@ void JFJochDiffractionImage::DrawROIs() {
     auto fill_brush = [&](const QColor &c) {
         return show_roi_fill ? QBrush(QColor(c.red(), c.green(), c.blue(), 60)) : QBrush(Qt::NoBrush);
     };
+    auto draw_handle = [&](const QPointF &p, const QColor &c) {
+        const qreal s = 4.0 / std::sqrt(std::max(1e-4, scale_factor));
+        addOverlayItem(scene()->addRect(QRectF(p.x() - s, p.y() - s, 2 * s, 2 * s), QPen(c, 1), QBrush(c)));
+    };
 
     for (const auto &b : rois.boxes) {
         QColor c = palette[color_index++ % palette_size];
         const bool selected = (QString::fromStdString(b.GetName()) == selected_roi_);
+        const bool editing = b.GetName() == edit_name_.toStdString()
+                             && (roi_edit_ == RoiEdit::MoveBox || roi_edit_ == RoiEdit::ResizeBox);
         QPen pen(c, selected ? 3 : 2);
         pen.setCosmetic(true);
         if (selected) pen.setStyle(Qt::DashLine);   // highlight the editable ROI
-        const QRectF rect = (roi_edit_ == RoiEdit::MoveBox && b.GetName() == edit_name_.toStdString())
-                              ? edit_box_
-                              : QRectF(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight());
+        const QRectF rect = editing ? edit_box_
+                                    : QRectF(b.GetXMin(), b.GetYMin(), b.GetWidth(), b.GetHeight());
         addOverlayItem(scene()->addRect(rect, pen, fill_brush(c)));
         AddROILabel(b.GetName(), c, rect.left(), rect.top());
+        if (selected) {
+            draw_handle(rect.topLeft(), c);    draw_handle(rect.topRight(), c);
+            draw_handle(rect.bottomLeft(), c); draw_handle(rect.bottomRight(), c);
+            draw_handle({rect.center().x(), rect.top()}, c);
+            draw_handle({rect.center().x(), rect.bottom()}, c);
+            draw_handle({rect.left(), rect.center().y()}, c);
+            draw_handle({rect.right(), rect.center().y()}, c);
+        }
     }
 
     for (const auto &c_roi : rois.circles) {
         QColor c = palette[color_index++ % palette_size];
         const bool selected = (QString::fromStdString(c_roi.GetName()) == selected_roi_);
+        const bool editing = c_roi.GetName() == edit_name_.toStdString()
+                             && (roi_edit_ == RoiEdit::MoveCircle || roi_edit_ == RoiEdit::ResizeCircle);
         QPen pen(c, selected ? 3 : 2);
         pen.setCosmetic(true);
         if (selected) pen.setStyle(Qt::DashLine);
-        QPointF center(c_roi.GetX(), c_roi.GetY());
-        double r = c_roi.GetRadius_pxl();
-        if (roi_edit_ == RoiEdit::MoveCircle && c_roi.GetName() == edit_name_.toStdString()) {
-            center = edit_center_;
-            r = edit_radius_;
-        }
+        const QPointF center = editing ? edit_center_ : QPointF(c_roi.GetX(), c_roi.GetY());
+        const double r = editing ? edit_radius_ : c_roi.GetRadius_pxl();
         addOverlayItem(scene()->addEllipse(center.x() - r, center.y() - r, 2 * r, 2 * r, pen, fill_brush(c)));
         AddROILabel(c_roi.GetName(), c, center.x(), center.y());
+        if (selected) {
+            draw_handle({center.x() + r, center.y()}, c);
+            draw_handle({center.x() - r, center.y()}, c);
+            draw_handle({center.x(), center.y() + r}, c);
+            draw_handle({center.x(), center.y() - r}, c);
+        }
     }
 
-    for (const auto &az : rois.azimuthal)
-        DrawAzimuthalROI(az, palette[color_index++ % palette_size], geom);
+    for (const auto &az : rois.azimuthal) {
+        QColor c = palette[color_index++ % palette_size];
+        const bool editing = az.GetName() == edit_name_.toStdString()
+                             && (roi_edit_ == RoiEdit::AzimInner || roi_edit_ == RoiEdit::AzimOuter
+                                 || roi_edit_ == RoiEdit::RotatePhiMin || roi_edit_ == RoiEdit::RotatePhiMax);
+        if (editing) {
+            const ROIAzimuthal edited = edit_has_phi_
+                ? ROIAzimuthal(az.GetName(), edit_d_min_, edit_d_max_, edit_phi_min_, edit_phi_max_)
+                : ROIAzimuthal(az.GetName(), edit_d_min_, edit_d_max_);
+            DrawAzimuthalROI(edited, c, geom);
+        } else {
+            DrawAzimuthalROI(az, c, geom);
+        }
+    }
 }
 
 void JFJochDiffractionImage::AddROILabel(const std::string &name, const QColor &color, float px, float py) {
@@ -396,7 +457,9 @@ void JFJochDiffractionImage::AddROILabel(const std::string &name, const QColor &
 
 void JFJochDiffractionImage::DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color,
                                               const DiffractionGeometry &geom) {
-    QPen pen(color, 2); pen.setCosmetic(true);
+    const bool selected = (QString::fromStdString(az.GetName()) == selected_roi_);
+    QPen pen(color, selected ? 3 : 2); pen.setCosmetic(true);
+    if (selected) pen.setStyle(Qt::DashLine);
     QBrush brush = show_roi_fill ? QBrush(QColor(color.red(), color.green(), color.blue(), 60))
                                  : QBrush(Qt::NoBrush);
 
@@ -470,45 +533,137 @@ bool JFJochDiffractionImage::roiEditPress(const QPointF &scenePos) {
         return false;
 
     const auto &rois = image->Dataset().experiment.ROI().GetROIDefinition();
+    auto geom = image->Dataset().experiment.GetDiffractionGeometry();
+    const qreal tol = 6.0 / std::sqrt(std::max(1e-4, scale_factor));
 
-    // Pick the first box/circle under the cursor, so an ROI can be grabbed by clicking it.
+    auto start = [&](const std::string &name) {
+        edit_name_ = QString::fromStdString(name);
+        selected_roi_ = edit_name_;
+        move_last_ = scenePos;
+        emit roiSelected(edit_name_);
+        setCursor(Qt::ClosedHandCursor);
+    };
+
+    // Box: corners/edges resize, interior moves.
     for (const auto &b : rois.boxes) {
         const QRectF r(QPointF(b.GetXMin(), b.GetYMin()), QPointF(b.GetXMax(), b.GetYMax()));
-        if (r.contains(scenePos)) {
+        const ResizeHandle h = hitTestBoxHandle(r, scenePos, tol);
+        if (h == ResizeHandle::None)
+            continue;
+        start(b.GetName());
+        edit_box_ = r;
+        if (h == ResizeHandle::Inside) {
             roi_edit_ = RoiEdit::MoveBox;
-            edit_name_ = QString::fromStdString(b.GetName());
-            edit_box_ = r;
-            move_last_ = scenePos;
-            selected_roi_ = edit_name_;
-            emit roiSelected(edit_name_);
-            setCursor(Qt::ClosedHandCursor);
-            return true;
+        } else {
+            roi_edit_ = RoiEdit::ResizeBox;
+            box_handle_ = h;
         }
+        return true;
     }
+
+    // Circle: perimeter resizes, interior moves.
     for (const auto &c : rois.circles) {
         const QPointF center(c.GetX(), c.GetY());
-        if (QLineF(center, scenePos).length() <= c.GetRadius_pxl()) {
-            roi_edit_ = RoiEdit::MoveCircle;
-            edit_name_ = QString::fromStdString(c.GetName());
-            edit_center_ = center;
-            edit_radius_ = c.GetRadius_pxl();
-            move_last_ = scenePos;
-            selected_roi_ = edit_name_;
-            emit roiSelected(edit_name_);
-            setCursor(Qt::ClosedHandCursor);
-            return true;
-        }
+        const double dist = QLineF(center, scenePos).length();
+        if (dist > c.GetRadius_pxl() + tol)
+            continue;
+        start(c.GetName());
+        edit_center_ = center;
+        edit_radius_ = c.GetRadius_pxl();
+        roi_edit_ = (std::abs(dist - c.GetRadius_pxl()) <= tol) ? RoiEdit::ResizeCircle : RoiEdit::MoveCircle;
+        return true;
     }
-    return false;   // azimuthal editing is not yet supported
+
+    // Azimuthal: inner/outer arc resizes Q/d, radial edge rotates phi.
+    for (const auto &az : rois.azimuthal) {
+        const auto [bx, by] = geom.GetDirectBeam_pxl();
+        const double cursor_r = QLineF(QPointF(bx, by), scenePos).length();
+        const double r_inner = geom.ResToPxl(az.GetDMax_A());   // larger d -> smaller radius
+        const double r_outer = geom.ResToPxl(az.GetDMin_A());
+        const float phi = geom.Phi_rad(scenePos.x(), scenePos.y()) * 180.0f / static_cast<float>(PI);
+
+        if (az.HasPhi() && !InPhiSector(phi, az.GetPhiMin_deg(), az.GetPhiMax_deg()))
+            continue;
+        if (cursor_r < r_inner - tol || cursor_r > r_outer + tol)
+            continue;
+
+        start(az.GetName());
+        edit_d_min_ = az.GetDMin_A();
+        edit_d_max_ = az.GetDMax_A();
+        edit_has_phi_ = az.HasPhi();
+        edit_phi_min_ = az.GetPhiMin_deg();
+        edit_phi_max_ = az.GetPhiMax_deg();
+
+        if (std::abs(cursor_r - r_inner) <= tol) {
+            roi_edit_ = RoiEdit::AzimInner;
+        } else if (std::abs(cursor_r - r_outer) <= tol) {
+            roi_edit_ = RoiEdit::AzimOuter;
+        } else if (az.HasPhi()) {
+            const float tol_deg = (cursor_r > 1.0) ? tol / cursor_r * 180.0f / static_cast<float>(PI) : 180.0f;
+            if (AngularDistance_deg(phi, az.GetPhiMin_deg()) <= tol_deg)
+                roi_edit_ = RoiEdit::RotatePhiMin;
+            else if (AngularDistance_deg(phi, az.GetPhiMax_deg()) <= tol_deg)
+                roi_edit_ = RoiEdit::RotatePhiMax;
+            else
+                roi_edit_ = RoiEdit::None;   // interior: select only
+        } else {
+            roi_edit_ = RoiEdit::None;
+        }
+        return true;
+    }
+    return false;
 }
 
 void JFJochDiffractionImage::roiEditMove(const QPointF &scenePos) {
-    const QPointF delta = scenePos - move_last_;
-    move_last_ = scenePos;
-    if (roi_edit_ == RoiEdit::MoveBox)
-        edit_box_.translate(delta);
-    else if (roi_edit_ == RoiEdit::MoveCircle)
-        edit_center_ += delta;
+    if (!image)
+        return;
+    auto geom = image->Dataset().experiment.GetDiffractionGeometry();
+    const auto [bx, by] = geom.GetDirectBeam_pxl();
+    const float cursor_r = QLineF(QPointF(bx, by), scenePos).length();
+
+    switch (roi_edit_) {
+        case RoiEdit::MoveBox:
+            edit_box_.translate(scenePos - move_last_);
+            move_last_ = scenePos;
+            break;
+        case RoiEdit::ResizeBox: {
+            QRectF r = edit_box_;
+            switch (box_handle_) {
+                case ResizeHandle::Left:        r.setLeft(scenePos.x()); break;
+                case ResizeHandle::Right:       r.setRight(scenePos.x()); break;
+                case ResizeHandle::Top:         r.setTop(scenePos.y()); break;
+                case ResizeHandle::Bottom:      r.setBottom(scenePos.y()); break;
+                case ResizeHandle::TopLeft:     r.setTopLeft(scenePos); break;
+                case ResizeHandle::TopRight:    r.setTopRight(scenePos); break;
+                case ResizeHandle::BottomLeft:  r.setBottomLeft(scenePos); break;
+                case ResizeHandle::BottomRight: r.setBottomRight(scenePos); break;
+                default: break;
+            }
+            edit_box_ = r.normalized();
+            break;
+        }
+        case RoiEdit::MoveCircle:
+            edit_center_ += (scenePos - move_last_);
+            move_last_ = scenePos;
+            break;
+        case RoiEdit::ResizeCircle:
+            edit_radius_ = std::max(1.0, QLineF(edit_center_, scenePos).length());
+            break;
+        case RoiEdit::AzimInner:
+            edit_d_max_ = geom.PxlToRes(cursor_r);
+            break;
+        case RoiEdit::AzimOuter:
+            edit_d_min_ = geom.PxlToRes(cursor_r);
+            break;
+        case RoiEdit::RotatePhiMin:
+            edit_phi_min_ = geom.Phi_rad(scenePos.x(), scenePos.y()) * 180.0f / static_cast<float>(PI);
+            break;
+        case RoiEdit::RotatePhiMax:
+            edit_phi_max_ = geom.Phi_rad(scenePos.x(), scenePos.y()) * 180.0f / static_cast<float>(PI);
+            break;
+        default:
+            return;   // None: select only, nothing to drag
+    }
     updateOverlay();
 
     // Live recompute, but keep at most one in flight (cleared in loadImage) so the
@@ -525,7 +680,7 @@ void JFJochDiffractionImage::roiEditRelease() {
     const ROIDefinition rois = BuildEditedROIDefinition();
     roi_edit_ = RoiEdit::None;
     setCursor(Qt::ArrowCursor);
-    emit roiGeometryEdited(rois);   // final, exact position
+    emit roiGeometryEdited(rois);   // final, exact geometry
 }
 
 ROIDefinition JFJochDiffractionImage::BuildEditedROIDefinition() const {
@@ -533,23 +688,61 @@ ROIDefinition JFJochDiffractionImage::BuildEditedROIDefinition() const {
     if (image)
         rois = image->Dataset().experiment.ROI().GetROIDefinition();
     const std::string sel = edit_name_.toStdString();
-    if (roi_edit_ == RoiEdit::MoveBox) {
-        for (auto &b : rois.boxes)
-            if (b.GetName() == sel) {
-                b = ROIBox(sel, std::lround(edit_box_.left()), std::lround(edit_box_.right()),
-                                std::lround(edit_box_.top()), std::lround(edit_box_.bottom()));
-                break;
-            }
-    } else if (roi_edit_ == RoiEdit::MoveCircle) {
-        for (auto &c : rois.circles)
-            if (c.GetName() == sel) {
-                c = ROICircle(sel, edit_center_.x(), edit_center_.y(), edit_radius_);
-                break;
-            }
+    switch (roi_edit_) {
+        case RoiEdit::MoveBox:
+        case RoiEdit::ResizeBox:
+            for (auto &b : rois.boxes)
+                if (b.GetName() == sel) {
+                    b = ROIBox(sel, std::lround(edit_box_.left()), std::lround(edit_box_.right()),
+                                    std::lround(edit_box_.top()), std::lround(edit_box_.bottom()));
+                    break;
+                }
+            break;
+        case RoiEdit::MoveCircle:
+        case RoiEdit::ResizeCircle:
+            for (auto &c : rois.circles)
+                if (c.GetName() == sel) {
+                    c = ROICircle(sel, edit_center_.x(), edit_center_.y(), edit_radius_);
+                    break;
+                }
+            break;
+        case RoiEdit::AzimInner:
+        case RoiEdit::AzimOuter:
+        case RoiEdit::RotatePhiMin:
+        case RoiEdit::RotatePhiMax:
+            for (auto &a : rois.azimuthal)
+                if (a.GetName() == sel) {
+                    a = edit_has_phi_
+                          ? ROIAzimuthal(sel, edit_d_min_, edit_d_max_, edit_phi_min_, edit_phi_max_)
+                          : ROIAzimuthal(sel, edit_d_min_, edit_d_max_);
+                    break;
+                }
+            break;
+        default:
+            break;
     }
     return rois;
 }
 
+void JFJochDiffractionImage::keyPressEvent(QKeyEvent *event) {
+    if (event->key() == Qt::Key_Delete && image && !selected_roi_.isEmpty()) {
+        ROIDefinition rois = image->Dataset().experiment.ROI().GetROIDefinition();
+        const std::string sel = selected_roi_.toStdString();
+        auto erase = [&sel](auto &vec) {
+            for (auto it = vec.begin(); it != vec.end(); ++it)
+                if (it->GetName() == sel) { vec.erase(it); return true; }
+            return false;
+        };
+        if (erase(rois.boxes) || erase(rois.circles) || erase(rois.azimuthal)) {
+            selected_roi_.clear();
+            emit roiGeometryEdited(rois);
+        }
+        event->accept();
+        return;
+    }
+    QGraphicsView::keyPressEvent(event);
+}
+
 
 void JFJochDiffractionImage::UpdateForeground() {
     if (!image || !auto_fg)
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index ab00c8ea..41d9b610 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -37,15 +37,21 @@ private:
     bool roiEditPress(const QPointF &scenePos) override;
     void roiEditMove(const QPointF &scenePos) override;
     void roiEditRelease() override;
+    void keyPressEvent(QKeyEvent *event) override;   // Delete removes the selected ROI
     [[nodiscard]] ROIDefinition BuildEditedROIDefinition() const;   // current ROIs with the edit applied
+    [[nodiscard]] ResizeHandle hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const;
 
     QString selected_roi_;
-    enum class RoiEdit { None, MoveBox, MoveCircle };
+    enum class RoiEdit { None, MoveBox, ResizeBox, MoveCircle, ResizeCircle,
+                         AzimInner, AzimOuter, RotatePhiMin, RotatePhiMax };
     RoiEdit roi_edit_ = RoiEdit::None;
+    ResizeHandle box_handle_ = ResizeHandle::None;
     QString edit_name_;
     QRectF edit_box_;
     QPointF edit_center_;
     double edit_radius_ = 0;
+    float edit_d_min_ = 0, edit_d_max_ = 0, edit_phi_min_ = 0, edit_phi_max_ = 0;   // azimuthal edit state
+    bool edit_has_phi_ = false;
     QPointF move_last_;
     bool live_pending_ = false;   // a live edit is being recomputed; throttles emissions
 
-- 
2.52.0


From d413af0e9228e1fab3a3d7fbbf9999ab00e756dd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:21:23 +0200
Subject: [PATCH 123/228] viewer: azimuthal ROI handles, and keep panning
 inside the ROI

Azimuthal ROIs now show discrete grab handles on the selected ROI: the
inner/outer arc (resize Q/d) and, for a sector, the two phi edges
(rotate). Editing is by clicking a handle, with a generous tolerance,
which fixes the previously near-impossible phi-edge grab. Clicking the
(large) interior of an azimuthal ROI now only selects it and lets the
view pan, instead of capturing the gesture.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../image_viewer/JFJochDiffractionImage.cpp   | 109 +++++++++++-------
 viewer/image_viewer/JFJochDiffractionImage.h  |   4 +
 2 files changed, 74 insertions(+), 39 deletions(-)

diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 62cd60a2..85917787 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -21,11 +21,6 @@
 #include "JFJochSimpleImage.h"
 
 // Constructor
-static float AngularDistance_deg(float a, float b) {
-    float d = std::fabs(a - b);
-    return (d > 180.0f) ? 360.0f - d : d;
-}
-
 static bool InPhiSector(float phi, float phi_min, float phi_max) {
     if (phi_min <= phi_max)
         return phi >= phi_min && phi <= phi_max;
@@ -54,6 +49,31 @@ JFJochImage::ResizeHandle JFJochDiffractionImage::hitTestBoxHandle(const QRectF
     return ResizeHandle::None;
 }
 
+void JFJochDiffractionImage::azimuthalHandles(const ROIAzimuthal &az, const DiffractionGeometry &geom,
+        QPointF &inner, QPointF &outer, QPointF &phimin, QPointF &phimax) const {
+    const float d2r = static_cast<float>(PI) / 180.0f;
+    const float phi0 = az.GetPhiMin_deg();
+    const float phi1 = az.GetPhiMax_deg();
+    const float mid_phi = az.HasPhi()
+        ? (phi1 >= phi0 ? (phi0 + phi1) / 2.0f : std::fmod((phi0 + phi1 + 360.0f) / 2.0f, 360.0f))
+        : 0.0f;
+    const float r_inner = geom.ResToPxl(az.GetDMax_A());
+    const float r_outer = geom.ResToPxl(az.GetDMin_A());
+    const float d_mid = geom.PxlToRes((r_inner + r_outer) / 2.0f);
+    auto pt = [&](float d, float phi_deg) -> QPointF {
+        try {
+            auto [x, y] = geom.ResPhiToPxl(d, phi_deg * d2r);
+            return QPointF(x, y);
+        } catch (...) {
+            return QPointF(-1e9, -1e9);   // off-image: never matches a handle hit-test
+        }
+    };
+    inner  = pt(az.GetDMax_A(), mid_phi);
+    outer  = pt(az.GetDMin_A(), mid_phi);
+    phimin = pt(d_mid, phi0);
+    phimax = pt(d_mid, phi1);
+}
+
 void JFJochDiffractionImage::mouseHover(QMouseEvent *event) {
     auto coord = mapToScene(event->pos());
 
@@ -427,18 +447,26 @@ void JFJochDiffractionImage::DrawROIs() {
         }
     }
 
-    for (const auto &az : rois.azimuthal) {
+    for (const auto &az_committed : rois.azimuthal) {
         QColor c = palette[color_index++ % palette_size];
-        const bool editing = az.GetName() == edit_name_.toStdString()
+        const bool selected = (QString::fromStdString(az_committed.GetName()) == selected_roi_);
+        const bool editing = az_committed.GetName() == edit_name_.toStdString()
                              && (roi_edit_ == RoiEdit::AzimInner || roi_edit_ == RoiEdit::AzimOuter
                                  || roi_edit_ == RoiEdit::RotatePhiMin || roi_edit_ == RoiEdit::RotatePhiMax);
-        if (editing) {
-            const ROIAzimuthal edited = edit_has_phi_
-                ? ROIAzimuthal(az.GetName(), edit_d_min_, edit_d_max_, edit_phi_min_, edit_phi_max_)
-                : ROIAzimuthal(az.GetName(), edit_d_min_, edit_d_max_);
-            DrawAzimuthalROI(edited, c, geom);
-        } else {
-            DrawAzimuthalROI(az, c, geom);
+        const ROIAzimuthal az = editing
+            ? (edit_has_phi_ ? ROIAzimuthal(az_committed.GetName(), edit_d_min_, edit_d_max_, edit_phi_min_, edit_phi_max_)
+                             : ROIAzimuthal(az_committed.GetName(), edit_d_min_, edit_d_max_))
+            : az_committed;
+        DrawAzimuthalROI(az, c, geom);
+        if (selected) {
+            QPointF inner, outer, pmin, pmax;
+            azimuthalHandles(az, geom, inner, outer, pmin, pmax);
+            draw_handle(inner, c);
+            draw_handle(outer, c);
+            if (az.HasPhi()) {
+                draw_handle(pmin, c);
+                draw_handle(pmax, c);
+            }
         }
     }
 }
@@ -574,17 +602,20 @@ bool JFJochDiffractionImage::roiEditPress(const QPointF &scenePos) {
         return true;
     }
 
-    // Azimuthal: inner/outer arc resizes Q/d, radial edge rotates phi.
+    // Azimuthal: grab one of the discrete handles to resize Q/d (inner/outer arc) or
+    // rotate a phi edge. Larger tolerance than the thin arcs would give.
+    const qreal tol_h = 9.0 / std::sqrt(std::max(1e-4, scale_factor));
     for (const auto &az : rois.azimuthal) {
-        const auto [bx, by] = geom.GetDirectBeam_pxl();
-        const double cursor_r = QLineF(QPointF(bx, by), scenePos).length();
-        const double r_inner = geom.ResToPxl(az.GetDMax_A());   // larger d -> smaller radius
-        const double r_outer = geom.ResToPxl(az.GetDMin_A());
-        const float phi = geom.Phi_rad(scenePos.x(), scenePos.y()) * 180.0f / static_cast<float>(PI);
+        QPointF inner, outer, pmin, pmax;
+        azimuthalHandles(az, geom, inner, outer, pmin, pmax);
+        auto grab = [&](const QPointF &h) { return QLineF(h, scenePos).length() <= tol_h; };
 
-        if (az.HasPhi() && !InPhiSector(phi, az.GetPhiMin_deg(), az.GetPhiMax_deg()))
-            continue;
-        if (cursor_r < r_inner - tol || cursor_r > r_outer + tol)
+        RoiEdit mode = RoiEdit::None;
+        if (grab(inner))                       mode = RoiEdit::AzimInner;
+        else if (grab(outer))                  mode = RoiEdit::AzimOuter;
+        else if (az.HasPhi() && grab(pmin))    mode = RoiEdit::RotatePhiMin;
+        else if (az.HasPhi() && grab(pmax))    mode = RoiEdit::RotatePhiMax;
+        if (mode == RoiEdit::None)
             continue;
 
         start(az.GetName());
@@ -593,24 +624,24 @@ bool JFJochDiffractionImage::roiEditPress(const QPointF &scenePos) {
         edit_has_phi_ = az.HasPhi();
         edit_phi_min_ = az.GetPhiMin_deg();
         edit_phi_max_ = az.GetPhiMax_deg();
-
-        if (std::abs(cursor_r - r_inner) <= tol) {
-            roi_edit_ = RoiEdit::AzimInner;
-        } else if (std::abs(cursor_r - r_outer) <= tol) {
-            roi_edit_ = RoiEdit::AzimOuter;
-        } else if (az.HasPhi()) {
-            const float tol_deg = (cursor_r > 1.0) ? tol / cursor_r * 180.0f / static_cast<float>(PI) : 180.0f;
-            if (AngularDistance_deg(phi, az.GetPhiMin_deg()) <= tol_deg)
-                roi_edit_ = RoiEdit::RotatePhiMin;
-            else if (AngularDistance_deg(phi, az.GetPhiMax_deg()) <= tol_deg)
-                roi_edit_ = RoiEdit::RotatePhiMax;
-            else
-                roi_edit_ = RoiEdit::None;   // interior: select only
-        } else {
-            roi_edit_ = RoiEdit::None;
-        }
+        roi_edit_ = mode;
         return true;
     }
+
+    // Inside an azimuthal ROI but not on a handle: select it and let the base pan
+    // (these ROIs are large and should not capture the panning gesture).
+    for (const auto &az : rois.azimuthal) {
+        const auto [bx, by] = geom.GetDirectBeam_pxl();
+        const double cursor_r = QLineF(QPointF(bx, by), scenePos).length();
+        const float phi = geom.Phi_rad(scenePos.x(), scenePos.y()) * 180.0f / static_cast<float>(PI);
+        if (cursor_r < geom.ResToPxl(az.GetDMax_A()) || cursor_r > geom.ResToPxl(az.GetDMin_A()))
+            continue;
+        if (az.HasPhi() && !InPhiSector(phi, az.GetPhiMin_deg(), az.GetPhiMax_deg()))
+            continue;
+        selected_roi_ = QString::fromStdString(az.GetName());
+        emit roiSelected(selected_roi_);
+        break;
+    }
     return false;
 }
 
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index 41d9b610..d9e6dd04 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -40,6 +40,10 @@ private:
     void keyPressEvent(QKeyEvent *event) override;   // Delete removes the selected ROI
     [[nodiscard]] ROIDefinition BuildEditedROIDefinition() const;   // current ROIs with the edit applied
     [[nodiscard]] ResizeHandle hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const;
+    // Grab points for an azimuthal ROI: inner/outer arc (resize Q/d) and the two phi
+    // edges (rotate). The phi handles are only meaningful for a sector (HasPhi()).
+    void azimuthalHandles(const ROIAzimuthal &az, const DiffractionGeometry &geom,
+                          QPointF &inner, QPointF &outer, QPointF &phimin, QPointF &phimax) const;
 
     QString selected_roi_;
     enum class RoiEdit { None, MoveBox, ResizeBox, MoveCircle, ResizeCircle,
-- 
2.52.0


From 1d015145a413588b1978c1231bf2b5e08e78f3ea Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:24:57 +0200
Subject: [PATCH 124/228] viewer: numeric editing of the selected ROI's bounds

The ROI panel now shows editable numeric fields for the selected ROI,
labelled by type: box min/max X/Y, circle centre/radius, or azimuthal
Q-range and phi sector. Editing a field rebuilds that ROI and commits it
through the same SetROIDefinition path, so all three types can be created
(via +) and dialled in by typing, not only by dragging.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/widgets/JFJochViewerROIList.cpp | 82 ++++++++++++++++++++++++++
 viewer/widgets/JFJochViewerROIList.h   |  6 ++
 2 files changed, 88 insertions(+)

diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index efaa8b13..8edbb706 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -4,9 +4,13 @@
 #include "JFJochViewerROIList.h"
 
 #include <set>
+#include <cmath>
+
+#include "../../common/JFJochMath.h"
 
 #include <QVBoxLayout>
 #include <QHBoxLayout>
+#include <QGridLayout>
 #include <QPushButton>
 #include <QInputDialog>
 
@@ -32,16 +36,93 @@ JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
     connect(ren, &QPushButton::clicked, this, &JFJochViewerROIList::OnRename);
     connect(del, &QPushButton::clicked, this, &JFJochViewerROIList::OnDelete);
 
+    auto *grid = new QGridLayout();
+    for (int i = 0; i < 4; i++) {
+        flabel_[i] = new QLabel("", this);
+        fedit_[i] = new QLineEdit(this);
+        grid->addWidget(flabel_[i], i, 0);
+        grid->addWidget(fedit_[i], i, 1);
+        connect(fedit_[i], &QLineEdit::editingFinished, this, &JFJochViewerROIList::ApplyEditor);
+    }
+    layout->addLayout(grid);
+
     result_ = new JFJochViewerROIResult(this);
     layout->addWidget(result_);
 }
 
+void JFJochViewerROIList::UpdateEditor() {
+    const std::string sel = SelectedName().toStdString();
+    auto set = [&](int i, const QString &label, double val, bool integer) {
+        flabel_[i]->setText(label);
+        flabel_[i]->setVisible(!label.isEmpty());
+        fedit_[i]->setVisible(!label.isEmpty());
+        if (!label.isEmpty())
+            fedit_[i]->setText(integer ? QString::number(std::lround(val)) : QString::number(val, 'g', 6));
+    };
+    for (int i = 0; i < 4; i++)
+        set(i, "", 0, false);
+
+    for (const auto &b : rois_.boxes)
+        if (b.GetName() == sel) {
+            set(0, "Min X", b.GetXMin(), true);  set(1, "Max X", b.GetXMax(), true);
+            set(2, "Min Y", b.GetYMin(), true);  set(3, "Max Y", b.GetYMax(), true);
+            return;
+        }
+    for (const auto &c : rois_.circles)
+        if (c.GetName() == sel) {
+            set(0, "Center X", c.GetX(), false); set(1, "Center Y", c.GetY(), false);
+            set(2, "Radius", c.GetRadius_pxl(), false); set(3, "", 0, false);
+            return;
+        }
+    for (const auto &a : rois_.azimuthal)
+        if (a.GetName() == sel) {
+            set(0, "Q min [1/A]", a.GetQMin_recipA(), false); set(1, "Q max [1/A]", a.GetQMax_recipA(), false);
+            set(2, "phi min [deg]", a.GetPhiMin_deg(), false); set(3, "phi max [deg]", a.GetPhiMax_deg(), false);
+            return;
+        }
+}
+
+void JFJochViewerROIList::ApplyEditor() {
+    if (rebuilding_)
+        return;
+    const std::string sel = SelectedName().toStdString();
+    bool changed = false;
+
+    for (auto &b : rois_.boxes)
+        if (b.GetName() == sel) {
+            b = ROIBox(sel, fedit_[0]->text().toLongLong(), fedit_[1]->text().toLongLong(),
+                            fedit_[2]->text().toLongLong(), fedit_[3]->text().toLongLong());
+            changed = true; break;
+        }
+    for (auto &c : rois_.circles)
+        if (c.GetName() == sel) {
+            c = ROICircle(sel, fedit_[0]->text().toDouble(), fedit_[1]->text().toDouble(),
+                               std::max(0.1, fedit_[2]->text().toDouble()));
+            changed = true; break;
+        }
+    for (auto &a : rois_.azimuthal)
+        if (a.GetName() == sel) {
+            const float qmin = fedit_[0]->text().toFloat();
+            const float qmax = fedit_[1]->text().toFloat();
+            const float phimin = fedit_[2]->text().toFloat();
+            const float phimax = fedit_[3]->text().toFloat();
+            const float d_min = (qmax > 0) ? 2.0f * static_cast<float>(PI) / qmax : a.GetDMin_A();
+            const float d_max = (qmin > 0) ? 2.0f * static_cast<float>(PI) / qmin : a.GetDMax_A();
+            a = ROIAzimuthal(sel, d_min, d_max, phimin, phimax);
+            changed = true; break;
+        }
+
+    if (changed)
+        emit roisChanged(rois_);
+}
+
 void JFJochViewerROIList::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
     image_ = image;
     const QString keep = SelectedName();
     rois_ = image_ ? image_->Dataset().experiment.ROI().GetROIDefinition() : ROIDefinition{};
     RebuildCombo(keep);
     ShowSelectedResult();
+    UpdateEditor();
 }
 
 void JFJochViewerROIList::RebuildCombo(const QString &keep_selected) {
@@ -103,6 +184,7 @@ void JFJochViewerROIList::OnSelectionChanged() {
     if (rebuilding_)
         return;
     ShowSelectedResult();
+    UpdateEditor();
     emit selectedROIChanged(SelectedName());
 }
 
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
index f3b0650a..5a6afe41 100644
--- a/viewer/widgets/JFJochViewerROIList.h
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -7,6 +7,8 @@
 
 #include <QWidget>
 #include <QComboBox>
+#include <QLineEdit>
+#include <QLabel>
 
 #include "JFJochViewerROIResult.h"
 #include "../../common/ROIDefinition.h"
@@ -21,6 +23,8 @@ class JFJochViewerROIList : public QWidget {
 
     QComboBox *combo_;
     QComboBox *type_combo_;
+    QLabel *flabel_[4];
+    QLineEdit *fedit_[4];
     JFJochViewerROIResult *result_;
 
     ROIDefinition rois_;
@@ -28,6 +32,8 @@ class JFJochViewerROIList : public QWidget {
     bool rebuilding_ = false;
 
     void RebuildCombo(const QString &keep_selected);
+    void UpdateEditor();   // populate the numeric fields for the selected ROI
+    void ApplyEditor();    // rebuild the selected ROI from the numeric fields
     void ShowSelectedResult();
     [[nodiscard]] QString SelectedName() const;
     [[nodiscard]] std::string UniqueName() const;
-- 
2.52.0


From 142cb88aa821a4f738feff24b57f4b368128cbbf Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:31:23 +0200
Subject: [PATCH 125/228] viewer: shift/ctrl-drag creates list ROIs; remove the
 old scratch panel

The interactive shift-drag (box) / shift+ctrl-drag (circle) now creates a
new persistent ROI in the list instead of feeding the old single-ROI
scratch panel. The base emits a roiScratchDrawn hook on release; the
diffraction image turns the drawn shape into a named ROI committed via
SetROIDefinition.

The old JFJochViewerImageROIStatistics scratch panel and all its wiring
(box/circle configuration, single-ROI result, add/subtract user mask) are
removed from the side panel and window; the ROI list is now the single
source.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerSidePanel.cpp              | 26 -------------
 viewer/JFJochViewerSidePanel.h                |  9 -----
 viewer/JFJochViewerWindow.cpp                 | 33 ----------------
 .../image_viewer/JFJochDiffractionImage.cpp   | 38 +++++++++++++++++++
 viewer/image_viewer/JFJochDiffractionImage.h  |  1 +
 viewer/image_viewer/JFJochImage.cpp           |  5 ++-
 viewer/image_viewer/JFJochImage.h             |  1 +
 7 files changed, 44 insertions(+), 69 deletions(-)

diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index b1f61618..c944549c 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -132,20 +132,6 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     connect(roi_list, &JFJochViewerROIList::roisChanged, this, &JFJochViewerSidePanel::roisChanged);
     connect(roi_list, &JFJochViewerROIList::selectedROIChanged, this, &JFJochViewerSidePanel::selectedROIChanged);
 
-    roi = new JFJochViewerImageROIStatistics(this);
-    layout->addWidget(roi);
-
-    connect(roi, &JFJochViewerImageROIStatistics::ROIBoxConfigured, [this] (QRect box) {
-        emit ROIBoxConfigured(box);
-    });
-
-    connect(roi, &JFJochViewerImageROIStatistics::ROICircleConfigured, [this] (double x, double y, double radius) {
-        emit ROICircleConfigured(x, y, radius);
-    });
-
-    connect(roi, &JFJochViewerImageROIStatistics::AddROIToUserMask, [this]() { emit AddROIToUserMask(); });
-    connect(roi, &JFJochViewerImageROIStatistics::SubtractROIFromUserMask, [this]() { emit SubtractROIFromUserMask(); });
-
     layout->addWidget(new TitleLabel("Data analysis", this));
 
     auto analyzeButton = new QPushButton("Full analysis", this);
@@ -193,18 +179,6 @@ void JFJochViewerSidePanel::selectROIInList(QString name) {
     roi_list->setSelected(name);
 }
 
-void JFJochViewerSidePanel::SetROIBox(QRect box) {
-    roi->SetROIBox(box);
-}
-
-void JFJochViewerSidePanel::SetROICircle(double x, double y, double radius) {
-    roi->SetROICircle(x, y, radius);
-}
-
-void JFJochViewerSidePanel::SetROIResult(ROIMessage msg) {
-    roi->SetROIResult(msg);
-}
-
 void JFJochViewerSidePanel::SetRings(QVector<float> v) {
     res_rings->setRings(v);
 }
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 8d95f257..1886ba1a 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -8,7 +8,6 @@
 #include <QLineEdit>
 #include <QCheckBox>
 
-#include "widgets/JFJochViewerImageROIStatistics.h"
 #include "widgets/JFJochViewerROIList.h"
 #include "../reader/JFJochReader.h"
 #include "charts/JFJochSimpleChartView.h"
@@ -19,7 +18,6 @@ class JFJochViewerSidePanel : public QWidget {
     Q_OBJECT
 
     JFJochViewerSidePanelChart *chart = nullptr;
-    JFJochViewerImageROIStatistics *roi = nullptr;
     JFJochViewerROIList *roi_list = nullptr;
     ResolutionRingWidget *res_rings = nullptr;
 
@@ -40,10 +38,6 @@ signals:
 
     void imageLoaded(std::shared_ptr<const JFJochReaderImage> image);
 
-    void ROIBoxConfigured(QRect box);
-    void ROICircleConfigured(double center_x, double center_y, double radius);
-    void AddROIToUserMask();
-    void SubtractROIFromUserMask();
     void writeStatusBar(QString string, int timeout_ms = 0);
 
     void ringModeSet(JFJochDiffractionImage::RingMode mode);
@@ -52,9 +46,6 @@ public:
     JFJochViewerSidePanel(QWidget *parent);
 public slots:
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
-    void SetROIBox(QRect box);
-    void SetROICircle(double x, double y, double radius);
-    void SetROIResult(ROIMessage msg);
     void SetRings(QVector<float> v);
     void selectROIInList(QString name);
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 0e3da6a2..885d3183 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -189,21 +189,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(viewer, &JFJochDiffractionImage::foregroundChanged,
             toolBarDisplay, &JFJochViewerToolbarDisplay::updateForeground);
 
-    connect(viewer, &JFJochDiffractionImage::roiBoxUpdated,
-            reading_worker, &JFJochImageReadingWorker::SetROIBox);
-
-    connect(viewer, &JFJochDiffractionImage::roiCircleUpdated,
-            reading_worker, &JFJochImageReadingWorker::SetROICircle);
-
-    connect(viewer, &JFJochDiffractionImage::roiBoxUpdated,
-            side_panel, &JFJochViewerSidePanel::SetROIBox);
-
-    connect(viewer, &JFJochDiffractionImage::roiCircleUpdated,
-            side_panel, &JFJochViewerSidePanel::SetROICircle);
-
-    connect(viewer, &JFJochDiffractionImage::roiCalculated,
-            side_panel, &JFJochViewerSidePanel::SetROIResult);
-
     connect(side_panel, &JFJochViewerSidePanel::roisChanged,
             reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
     connect(side_panel, &JFJochViewerSidePanel::selectedROIChanged,
@@ -213,24 +198,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(viewer, &JFJochDiffractionImage::roiSelected,
             side_panel, &JFJochViewerSidePanel::selectROIInList);
 
-    connect(side_panel, &JFJochViewerSidePanel::ROIBoxConfigured,
-            reading_worker, &JFJochImageReadingWorker::SetROIBox);
-
-    connect(side_panel, &JFJochViewerSidePanel::ROICircleConfigured,
-            reading_worker, &JFJochImageReadingWorker::SetROICircle);
-
-    connect(side_panel, &JFJochViewerSidePanel::ROIBoxConfigured,
-            viewer, &JFJochDiffractionImage::SetROIBox);
-
-    connect(side_panel, &JFJochViewerSidePanel::ROICircleConfigured,
-            viewer, &JFJochDiffractionImage::SetROICircle);
-
-    connect(side_panel, &JFJochViewerSidePanel::AddROIToUserMask,
-            reading_worker, &JFJochImageReadingWorker::AddROIToUserMask);
-
-    connect(side_panel, &JFJochViewerSidePanel::SubtractROIFromUserMask,
-            reading_worker, &JFJochImageReadingWorker::SubtractROIFromUserMask);
-
     connect(menuBar, &JFJochViewerMenu::clearUserMaskSelected,
             reading_worker, &JFJochImageReadingWorker::ClearUserMask);
 
diff --git a/viewer/image_viewer/JFJochDiffractionImage.cpp b/viewer/image_viewer/JFJochDiffractionImage.cpp
index 85917787..9864a268 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.cpp
+++ b/viewer/image_viewer/JFJochDiffractionImage.cpp
@@ -1,6 +1,8 @@
 // SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include <set>
+
 #include "JFJochDiffractionImage.h"
 #include "../../common/DiffractionGeometry.h"
 #include "../../common/JFJochMath.h"
@@ -755,6 +757,42 @@ ROIDefinition JFJochDiffractionImage::BuildEditedROIDefinition() const {
     return rois;
 }
 
+void JFJochDiffractionImage::roiScratchDrawn() {
+    // The base just drew a scratch box/circle (roiBox/roi_type, in pixel coords);
+    // turn it into a new persistent ROI in the list.
+    if (!image || roiBox.isNull() || roiBox.width() <= 0 || roiBox.height() <= 0)
+        return;
+
+    ROIDefinition rois = image->Dataset().experiment.ROI().GetROIDefinition();
+    if (rois.boxes.size() + rois.circles.size() + rois.azimuthal.size() >= 16)
+        return;
+
+    std::set<std::string> used;
+    for (const auto &b : rois.boxes) used.insert(b.GetName());
+    for (const auto &c : rois.circles) used.insert(c.GetName());
+    for (const auto &a : rois.azimuthal) used.insert(a.GetName());
+    std::string name;
+    for (int i = 1; ; i++) {
+        name = "roi" + std::to_string(i);
+        if (!used.count(name)) break;
+    }
+
+    if (roi_type == RoiType::RoiBox) {
+        const QRectF r = roiBox.normalized();
+        rois.boxes.emplace_back(name, std::lround(r.left()), std::lround(r.right()),
+                                      std::lround(r.top()), std::lround(r.bottom()));
+    } else {
+        const QPointF c = roiBox.center();
+        const double rad = 0.5 * std::min(roiBox.width(), roiBox.height());
+        rois.circles.emplace_back(name, c.x(), c.y(), std::max(0.1, rad));
+    }
+
+    roiBox = QRectF();   // clear the scratch overlay
+    selected_roi_ = QString::fromStdString(name);
+    emit roiSelected(selected_roi_);
+    emit roiGeometryEdited(rois);
+}
+
 void JFJochDiffractionImage::keyPressEvent(QKeyEvent *event) {
     if (event->key() == Qt::Key_Delete && image && !selected_roi_.isEmpty()) {
         ROIDefinition rois = image->Dataset().experiment.ROI().GetROIDefinition();
diff --git a/viewer/image_viewer/JFJochDiffractionImage.h b/viewer/image_viewer/JFJochDiffractionImage.h
index d9e6dd04..a9606b57 100644
--- a/viewer/image_viewer/JFJochDiffractionImage.h
+++ b/viewer/image_viewer/JFJochDiffractionImage.h
@@ -37,6 +37,7 @@ private:
     bool roiEditPress(const QPointF &scenePos) override;
     void roiEditMove(const QPointF &scenePos) override;
     void roiEditRelease() override;
+    void roiScratchDrawn() override;
     void keyPressEvent(QKeyEvent *event) override;   // Delete removes the selected ROI
     [[nodiscard]] ROIDefinition BuildEditedROIDefinition() const;   // current ROIs with the edit applied
     [[nodiscard]] ResizeHandle hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const;
diff --git a/viewer/image_viewer/JFJochImage.cpp b/viewer/image_viewer/JFJochImage.cpp
index 0dd1b6d3..af7d14a5 100644
--- a/viewer/image_viewer/JFJochImage.cpp
+++ b/viewer/image_viewer/JFJochImage.cpp
@@ -297,9 +297,12 @@ void JFJochImage::mouseReleaseEvent(QMouseEvent *event) {
         if (mouse_event_type == MouseEventType::EditingExternalROI) {
             roiEditRelease();
         } else {
-            if (mouse_event_type == MouseEventType::DrawingROI)
+            const bool drawn = (mouse_event_type == MouseEventType::DrawingROI);
+            if (drawn)
                 roiEndPos = RoundPoint(mapToScene(event->pos()));
             updateROI();
+            if (drawn)
+                roiScratchDrawn();   // turn the drawn scratch box/circle into a persistent ROI
         }
     }
 
diff --git a/viewer/image_viewer/JFJochImage.h b/viewer/image_viewer/JFJochImage.h
index cbdd3634..a318da82 100644
--- a/viewer/image_viewer/JFJochImage.h
+++ b/viewer/image_viewer/JFJochImage.h
@@ -84,6 +84,7 @@ protected:
     virtual bool roiEditPress(const QPointF &scenePos) { return false; }
     virtual void roiEditMove(const QPointF &scenePos) {}
     virtual void roiEditRelease() {}
+    virtual void roiScratchDrawn() {}   // a shift/ctrl-drag finished drawing a new box/circle
     QPoint lastMousePos;  // To track panning movement
 
     // Resizing which edge/corner
-- 
2.52.0


From b2c60dfbd0888b0aff038a02fdb38b97998a1d76 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:47:10 +0200
Subject: [PATCH 126/228] viewer: download/upload ROIs to the broker

Add Download and "Upload to server" buttons to the ROI panel. The HTTP
reader gains GetROIDefinitions (GET /config/roi) and UploadROIDefinitions
(PUT /config/roi), converting between ROIDefinition and the generated
Roi_definitions model (including the optional azimuthal phi sector), the
same shapes OpenAPIConvert uses on the server. Download applies the
fetched ROIs through SetROIDefinition; upload pushes the current ones.
Both are no-ops unless the viewer is connected to a broker.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHttpReader.cpp            | 89 ++++++++++++++++++++++++++
 reader/JFJochHttpReader.h              |  4 ++
 viewer/JFJochImageReadingWorker.cpp    | 22 +++++++
 viewer/JFJochImageReadingWorker.h      |  2 +
 viewer/JFJochViewerSidePanel.cpp       |  2 +
 viewer/JFJochViewerSidePanel.h         |  2 +
 viewer/JFJochViewerWindow.cpp          |  4 ++
 viewer/widgets/JFJochViewerROIList.cpp |  9 +++
 viewer/widgets/JFJochViewerROIList.h   |  2 +
 9 files changed, 136 insertions(+)

diff --git a/reader/JFJochHttpReader.cpp b/reader/JFJochHttpReader.cpp
index dd383d27..fe1a1f6d 100644
--- a/reader/JFJochHttpReader.cpp
+++ b/reader/JFJochHttpReader.cpp
@@ -9,6 +9,8 @@
 #include "../broker/gen/model/Image_buffer_status.h"
 #include "../broker/gen/model/Plots.h"
 #include "../broker/gen/model/Broker_status.h"
+#include "../broker/gen/model/Roi_definitions.h"
+#include "../common/JFJochMath.h"
 #include "../image_analysis/bragg_integration/CalcISigma.h"
 
 void JFJochHttpReader::Close() {
@@ -402,6 +404,93 @@ void JFJochHttpReader::UploadUserMask(const std::vector<uint32_t>& mask) {
                               "Server rejected user mask upload");
 }
 
+ROIDefinition JFJochHttpReader::GetROIDefinitions() const {
+    std::unique_lock ul(http_mutex);
+    if (addr.empty())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "HTTP address not set");
+
+    httplib::Client cli_cmd(addr);
+    auto res = cli_cmd.Get("/config/roi");
+    if (!res || res->status != httplib::StatusCode::OK_200)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Could not get ROI definitions");
+
+    org::openapitools::server::model::Roi_definitions input = nlohmann::json::parse(res->body);
+    ROIDefinition out;
+    for (const auto &i : input.getBox().getRois())
+        out.boxes.emplace_back(i.getName(), i.getMinXPxl(), i.getMaxXPxl(), i.getMinYPxl(), i.getMaxYPxl());
+    for (const auto &i : input.getCircle().getRois())
+        out.circles.emplace_back(i.getName(), i.getCenterXPxl(), i.getCenterYPxl(), i.getRadiusPxl());
+    for (const auto &i : input.getAzim().getRois()) {
+        float phi_min = 0, phi_max = 0;
+        if (i.phiMinDegIsSet() && i.phiMaxDegIsSet()) {
+            phi_min = i.getPhiMinDeg();
+            phi_max = i.getPhiMaxDeg();
+        }
+        const float d_min = (i.getQMaxRecipA() == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / i.getQMaxRecipA();
+        const float d_max = (i.getQMinRecipA() == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / i.getQMinRecipA();
+        out.azimuthal.emplace_back(i.getName(), d_min, d_max, phi_min, phi_max);
+    }
+    return out;
+}
+
+void JFJochHttpReader::UploadROIDefinitions(const ROIDefinition &rois) const {
+    std::unique_lock ul(http_mutex);
+    if (addr.empty())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "HTTP address not set");
+
+    namespace model = org::openapitools::server::model;
+    model::Roi_definitions out;
+
+    model::Roi_box_list bl;
+    std::vector<model::Roi_box> boxes;
+    for (const auto &b : rois.boxes) {
+        model::Roi_box e;
+        e.setName(b.GetName());
+        e.setMinXPxl(b.GetXMin()); e.setMaxXPxl(b.GetXMax());
+        e.setMinYPxl(b.GetYMin()); e.setMaxYPxl(b.GetYMax());
+        boxes.push_back(e);
+    }
+    bl.setRois(boxes);
+    out.setBox(bl);
+
+    model::Roi_circle_list cl;
+    std::vector<model::Roi_circle> circles;
+    for (const auto &c : rois.circles) {
+        model::Roi_circle e;
+        e.setName(c.GetName());
+        e.setCenterXPxl(c.GetX()); e.setCenterYPxl(c.GetY());
+        e.setRadiusPxl(c.GetRadius_pxl());
+        circles.push_back(e);
+    }
+    cl.setRois(circles);
+    out.setCircle(cl);
+
+    model::Roi_azim_list al;
+    std::vector<model::Roi_azimuthal> azim;
+    for (const auto &a : rois.azimuthal) {
+        model::Roi_azimuthal e;
+        e.setName(a.GetName());
+        e.setQMinRecipA(a.GetQMin_recipA());
+        e.setQMaxRecipA(a.GetQMax_recipA());
+        if (a.HasPhi()) {
+            e.setPhiMinDeg(a.GetPhiMin_deg());
+            e.setPhiMaxDeg(a.GetPhiMax_deg());
+        }
+        azim.push_back(e);
+    }
+    al.setRois(azim);
+    out.setAzim(al);
+
+    nlohmann::json j = out;
+    httplib::Client cli_cmd(addr);
+    auto res = cli_cmd.Put("/config/roi", j.dump(), "application/json");
+    if (!res)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Failed to connect to server to upload ROIs");
+    if (res->status != httplib::StatusCode::OK_200)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Server rejected ROI upload");
+}
+
 std::vector<SpotToSave> JFJochHttpReader::ReadSpots(int64_t image) const {
     std::unique_lock ul(http_mutex);
 
diff --git a/reader/JFJochHttpReader.h b/reader/JFJochHttpReader.h
index e558d98a..84b8876c 100644
--- a/reader/JFJochHttpReader.h
+++ b/reader/JFJochHttpReader.h
@@ -6,6 +6,7 @@
 #include "JFJochReader.h"
 #include "../common/BrokerStatus.h"
 #include "../common/ImageBuffer.h"
+#include "../common/ROIDefinition.h"
 
 class JFJochHttpReader : public JFJochReader {
     mutable std::mutex http_mutex;
@@ -36,6 +37,9 @@ public:
 
     void UploadUserMask(const std::vector<uint32_t>& mask);
 
+    [[nodiscard]] ROIDefinition GetROIDefinitions() const;          // GET  /config/roi
+    void UploadROIDefinitions(const ROIDefinition &rois) const;     // PUT  /config/roi
+
     BrokerStatus GetBrokerStatus() const;
 
     std::shared_ptr<JFJochReaderRawImage> GetRawImage(int64_t image_number) override;
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index a6ba76b2..015f47b3 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -600,6 +600,28 @@ void JFJochImageReadingWorker::SetROIDefinition(const ROIDefinition &rois) {
     SetROIDefinition_i(rois);
 }
 
+void JFJochImageReadingWorker::DownloadROIsFromServer() {
+    QMutexLocker locker(&m);
+    if (!http_mode)
+        return;
+    try {
+        SetROIDefinition_i(http_reader.GetROIDefinitions());
+    } catch (const std::exception &e) {
+        logger.Error("Download ROIs from server failed: {}", e.what());
+    }
+}
+
+void JFJochImageReadingWorker::UploadROIsToServer() {
+    QMutexLocker locker(&m);
+    if (!http_mode)
+        return;
+    try {
+        http_reader.UploadROIDefinitions(curr_experiment.ROI().GetROIDefinition());
+    } catch (const std::exception &e) {
+        logger.Error("Upload ROIs to server failed: {}", e.what());
+    }
+}
+
 void JFJochImageReadingWorker::SetROIDefinition_i(const ROIDefinition &rois) {
     // The worker experiment is the source of truth; the analysis ROI engine is rebuilt
     // for it so newly loaded images pick up the change automatically. From now on the
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index b9e546a0..e4857d49 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -171,6 +171,8 @@ public slots:
     void SubtractROIFromUserMask();
 
     void SetROIDefinition(const ROIDefinition &rois);
+    void DownloadROIsFromServer();
+    void UploadROIsToServer();
 
     void SaveUserMaskTIFF(QString filename);
     void UploadUserMask();
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index c944549c..e4e34f77 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -131,6 +131,8 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     connect(this, &JFJochViewerSidePanel::imageLoaded, roi_list, &JFJochViewerROIList::loadImage);
     connect(roi_list, &JFJochViewerROIList::roisChanged, this, &JFJochViewerSidePanel::roisChanged);
     connect(roi_list, &JFJochViewerROIList::selectedROIChanged, this, &JFJochViewerSidePanel::selectedROIChanged);
+    connect(roi_list, &JFJochViewerROIList::downloadROIs, this, &JFJochViewerSidePanel::downloadROIs);
+    connect(roi_list, &JFJochViewerROIList::uploadROIs, this, &JFJochViewerSidePanel::uploadROIs);
 
     layout->addWidget(new TitleLabel("Data analysis", this));
 
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 1886ba1a..549d9d8a 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -33,6 +33,8 @@ signals:
     void showROIFill(bool input);
     void roisChanged(ROIDefinition rois);
     void selectedROIChanged(QString name);
+    void downloadROIs();
+    void uploadROIs();
     void findBeamCenter(const UnitCell &input, bool guess);
     void analyze();
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 885d3183..0f2f04f5 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -197,6 +197,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
     connect(viewer, &JFJochDiffractionImage::roiSelected,
             side_panel, &JFJochViewerSidePanel::selectROIInList);
+    connect(side_panel, &JFJochViewerSidePanel::downloadROIs,
+            reading_worker, &JFJochImageReadingWorker::DownloadROIsFromServer);
+    connect(side_panel, &JFJochViewerSidePanel::uploadROIs,
+            reading_worker, &JFJochImageReadingWorker::UploadROIsToServer);
 
     connect(menuBar, &JFJochViewerMenu::clearUserMaskSelected,
             reading_worker, &JFJochImageReadingWorker::ClearUserMask);
diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index 8edbb706..178e0b95 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -36,6 +36,15 @@ JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
     connect(ren, &QPushButton::clicked, this, &JFJochViewerROIList::OnRename);
     connect(del, &QPushButton::clicked, this, &JFJochViewerROIList::OnDelete);
 
+    auto *server = new QHBoxLayout();
+    auto *download = new QPushButton("Download", this);
+    auto *upload = new QPushButton("Upload to server", this);
+    server->addWidget(download);
+    server->addWidget(upload);
+    layout->addLayout(server);
+    connect(download, &QPushButton::clicked, this, &JFJochViewerROIList::downloadROIs);
+    connect(upload, &QPushButton::clicked, this, &JFJochViewerROIList::uploadROIs);
+
     auto *grid = new QGridLayout();
     for (int i = 0; i < 4; i++) {
         flabel_[i] = new QLabel("", this);
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
index 5a6afe41..ae468ae2 100644
--- a/viewer/widgets/JFJochViewerROIList.h
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -50,4 +50,6 @@ private slots:
 signals:
     void roisChanged(ROIDefinition rois);
     void selectedROIChanged(QString name);
+    void downloadROIs();   // fetch ROIs from the connected broker
+    void uploadROIs();     // push ROIs to the connected broker
 };
-- 
2.52.0


From fef9c2f4c346d5f73255081bc6b4bfd83d7d5b6c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:52:21 +0200
Subject: [PATCH 127/228] viewer: load user mask from TIFF (replace or add)

Two Mask-menu entries read a 16-bit TIFF (via ReadTIFFFromString16) and
apply it as the user mask: "replace" overwrites the current mask, "add"
unions the TIFF into it. The TIFF must match the detector dimensions; any
non-zero pixel masks. Both go through UpdateUserMask_i like the other
mask edits.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp | 36 +++++++++++++++++++++++++++++
 viewer/JFJochImageReadingWorker.h   |  1 +
 viewer/JFJochViewerMenu.cpp         | 17 ++++++++++++++
 viewer/JFJochViewerMenu.h           |  4 ++++
 viewer/JFJochViewerWindow.cpp       |  3 +++
 5 files changed, 61 insertions(+)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 015f47b3..a3a3bdd4 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -3,6 +3,8 @@
 
 #include <cerrno>
 #include <cstring>
+#include <fstream>
+#include <iterator>
 #include "../common/JFJochMath.h"
 #ifndef _WIN32
 #include <sys/stat.h>
@@ -747,6 +749,40 @@ void JFJochImageReadingWorker::SaveUserMaskTIFF(QString filename) {
     WriteTIFFToFile(filename.toStdString(), mask_image);
 }
 
+void JFJochImageReadingWorker::LoadUserMaskTIFF(QString filename, bool replace) {
+    QMutexLocker locker(&m);
+    if (!current_image_ptr)
+        return;
+
+    std::ifstream f(filename.toStdString(), std::ios::binary);
+    const std::string content((std::istreambuf_iterator<char>(f)), std::istreambuf_iterator<char>());
+
+    uint32_t cols = 0, lines = 0;
+    std::vector<uint16_t> tiff;
+    try {
+        tiff = ReadTIFFFromString16(content, cols, lines);
+    } catch (const std::exception &e) {
+        logger.Error("Could not read mask TIFF {}: {}", filename.toStdString(), e.what());
+        return;
+    }
+
+    const int64_t width = current_image_ptr->Dataset().experiment.GetXPixelsNum();
+    const int64_t height = current_image_ptr->Dataset().experiment.GetYPixelsNum();
+    if (static_cast<int64_t>(cols) != width || static_cast<int64_t>(lines) != height) {
+        logger.Error("Mask TIFF is {}x{} but the detector is {}x{}", cols, lines, width, height);
+        return;
+    }
+
+    // replace: start from an empty mask; add: keep the current one. A non-zero TIFF pixel masks.
+    auto user_mask = replace ? std::vector<uint32_t>(width * height, 0)
+                             : current_image_ptr->Dataset().pixel_mask.GetUserMask();
+    for (size_t i = 0; i < tiff.size(); i++)
+        if (tiff[i] != 0)
+            user_mask[i] = 1;
+
+    UpdateUserMask_i(user_mask);
+}
+
 void JFJochImageReadingWorker::UploadUserMask() {
     QMutexLocker locker(&m);
     if (!current_image_ptr)
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index e4857d49..87b26843 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -175,6 +175,7 @@ public slots:
     void UploadROIsToServer();
 
     void SaveUserMaskTIFF(QString filename);
+    void LoadUserMaskTIFF(QString filename, bool replace);
     void UploadUserMask();
     void ClearUserMask();
 
diff --git a/viewer/JFJochViewerMenu.cpp b/viewer/JFJochViewerMenu.cpp
index ff630a4d..563aa54a 100644
--- a/viewer/JFJochViewerMenu.cpp
+++ b/viewer/JFJochViewerMenu.cpp
@@ -44,6 +44,12 @@ JFJochViewerMenu::JFJochViewerMenu(QWidget *parent) : QMenuBar(parent) {
     const QAction *saveMaskTiff = maskMenu->addAction("Save User Mask as TIFF...");
     connect(saveMaskTiff, &QAction::triggered, this, &JFJochViewerMenu::saveUserMaskAsTiffSelected);
 
+    const QAction *loadMaskReplace = maskMenu->addAction("Load User Mask from TIFF (replace)...");
+    connect(loadMaskReplace, &QAction::triggered, [this] { openLoadUserMaskTiff(true); });
+
+    const QAction *loadMaskAdd = maskMenu->addAction("Load User Mask from TIFF (add)...");
+    connect(loadMaskAdd, &QAction::triggered, [this] { openLoadUserMaskTiff(false); });
+
     const QAction *uploadMask = maskMenu->addAction("&Upload User Mask");
     connect(uploadMask, &QAction::triggered, this, &JFJochViewerMenu::uploadUserMaskAction);
 
@@ -185,6 +191,17 @@ void JFJochViewerMenu::saveUserMaskAsTiffSelected() {
     }
 }
 
+void JFJochViewerMenu::openLoadUserMaskTiff(bool replace) {
+    QString filename = QFileDialog::getOpenFileName(
+        this,
+        replace ? "Load User Mask from TIFF (replace)" : "Load User Mask from TIFF (add)",
+        "",
+        "TIFF Images (*.tif *.tiff);;All Files (*)"
+    );
+    if (!filename.isEmpty())
+        emit loadUserMaskTiffSelected(filename, replace);
+}
+
 void JFJochViewerMenu::uploadUserMaskAction() {
     auto reply = QMessageBox::question(
         this,
diff --git a/viewer/JFJochViewerMenu.h b/viewer/JFJochViewerMenu.h
index 1bed4966..6d64a674 100644
--- a/viewer/JFJochViewerMenu.h
+++ b/viewer/JFJochViewerMenu.h
@@ -28,6 +28,7 @@ signals:
     void fileCloseSelected();
 
     void saveUserMaskTiffSelected(const QString &filename);
+    void loadUserMaskTiffSelected(const QString &filename, bool replace);
     void uploadUserMaskSelected();
     void clearUserMaskSelected();
     void openDatasetInfo();
@@ -41,4 +42,7 @@ private slots:
 
     void saveUserMaskAsTiffSelected();
     void uploadUserMaskAction();
+
+private:
+    void openLoadUserMaskTiff(bool replace);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 0f2f04f5..90f04c95 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -208,6 +208,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(menuBar, &JFJochViewerMenu::saveUserMaskTiffSelected,
             reading_worker, &JFJochImageReadingWorker::SaveUserMaskTIFF);
 
+    connect(menuBar, &JFJochViewerMenu::loadUserMaskTiffSelected,
+            reading_worker, &JFJochImageReadingWorker::LoadUserMaskTIFF);
+
     connect(menuBar, &JFJochViewerMenu::uploadUserMaskSelected,
             reading_worker, &JFJochImageReadingWorker::UploadUserMask);
 
-- 
2.52.0


From d4c96d48fca6f801fe17afc4ab2589c34370c821 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:52:40 +0200
Subject: [PATCH 128/228] make_doc.sh: Use default python

---
 make_doc.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/make_doc.sh b/make_doc.sh
index 7853ad44..b1441e26 100644
--- a/make_doc.sh
+++ b/make_doc.sh
@@ -9,10 +9,10 @@ set -euo pipefail
 #                Relative paths are resolved against the caller's working
 #                directory, so the frontend build can point this at frontend/dist/docs.
 #
-# The Python interpreter can be overridden with $PYTHON (default: python3.11).
+# The Python interpreter can be overridden with $PYTHON (default: python).
 
 OUT="${1:-public}"
-PYTHON="${PYTHON:-python3.11}"
+PYTHON="${PYTHON:-python}"
 
 # Resolve the output directory to an absolute path before we change directories.
 mkdir -p "$OUT"
-- 
2.52.0


From 52aca9a4a9bc521c1bd16cf3f2df365f680cb4f6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:55:01 +0200
Subject: [PATCH 129/228] docs: ROIs/azimuthal apply to both FPGA and DECTRIS
 workflows

Clarify in FPGA_DATA_ANALYSIS.md that the ROI and azimuthal definitions
are also evaluated on CPU via the shared image_analysis library, so they
apply to the DECTRIS SIMPLON (EIGER) path that has no FPGA, not only the
FPGA-accelerated JUNGFRAU/PSI path. Document the three NXmx writer formats
(Legacy/VDS/Integrated) and the two acquisition workflows in CLAUDE.md.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CLAUDE.md                  | 12 ++++++++++++
 docs/FPGA_DATA_ANALYSIS.md |  8 ++++++++
 2 files changed, 20 insertions(+)

diff --git a/CLAUDE.md b/CLAUDE.md
index 48e59478..acc50bcf 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -101,6 +101,18 @@ class). Per-image arrays (one entry per frame) are written to the **data** files
 `HDF5DataFilePlugin` subclasses in `writer/`. Put shared metadata in `NXmx`, not in a data-file
 plugin.
 
+The HDF5 master/data layout is one of three `FileWriterFormat`s (`common/JFJochMessages.h`),
+all NXmx: **`NXmxLegacy`** (master + `_data_NNNNNN.h5` joined by external links),
+**`NXmxVDS`** (master + data joined by HDF5 virtual datasets — the default), and
+**`NXmxIntegrated`** (a single self-contained file, no separate data files). Per-image plugins
+must work for all three; with `NXmxIntegrated` "master" and "data" are the same file.
+
+**Two acquisition workflows:** the FPGA-accelerated path (JUNGFRAU at PSI; FPGA does masking,
+summation, spot finding, ROI/azimuthal integration, compression) and the DECTRIS SIMPLON path
+(EIGER), which has no FPGA — masking/ROI/azimuthal analysis then runs on CPU through the shared
+`image_analysis/` library. Treat ROI and azimuthal features as available in **both** workflows,
+not FPGA-only.
+
 **`jfjoch_broker`** (`broker/`) is the central online service: HTTP/REST + OpenAPI control plane,
 FPGA configuration, image building, ZeroMQ output. `JFJochStateMachine` drives acquisition state;
 `JFJochServices` wires the pieces; `OpenAPIConvert`/`JFJochBrokerParser` translate between the
diff --git a/docs/FPGA_DATA_ANALYSIS.md b/docs/FPGA_DATA_ANALYSIS.md
index 493ca232..772fd84f 100644
--- a/docs/FPGA_DATA_ANALYSIS.md
+++ b/docs/FPGA_DATA_ANALYSIS.md
@@ -36,6 +36,9 @@ This way 2D azimuthal integration, as needed for example by SAS-TT, cannot be cu
 One needs to be careful with per-pixel corrections - their acceptable range is constrained by 16-bit pixed point integer implementation
 and is tuned for standard SAXS/WAXS range.
 
+As with ROIs, azimuthal integration is also available on CPU through the shared analysis library,
+so it applies to both the FPGA-accelerated (JUNGFRAU/PSI) and the DECTRIS-driven (EIGER) workflows.
+
 ## Spot finding
 Jungfraujoch FPGA implements a built-in spot finder. Spot finder allows to apply the following criteria for finding strong pixels:
 1. Resolution criterion - pixels only within a provided resolution range can be considered as strong pixels (calculating resolution map needs to happen on CPU before data collection run).
@@ -58,6 +61,11 @@ Given very large box size, approximation are made, for example that `N ≈ N-1`
 Each pixel in a module can be assigned to one of 64 ROIs. For each ROIs, sum, sum of squares, max count, and number of valid pixels will be calculated.
 Jungfraujoch also calculates X and Y values weighted by pixel values, though this feature is not properly tested at the moment and not integrated in downstream analysis.
 
+ROIs are not specific to the FPGA path. The same ROI definitions — box, circle, and azimuthal
+(Q-range with an optional φ-sector) — are also evaluated on CPU by the shared `image_analysis/roi/`
+engine, so ROI statistics are produced both for the FPGA-accelerated JUNGFRAU/PSI workflow and for
+detectors driven through DECTRIS SIMPLON (e.g. EIGER), which have no FPGA acquisition path.
+
 ## Pixel statisitics
 The following statistics are collected for each module:
 * Number of masked pixels
-- 
2.52.0


From 81b48febcf08b4a4044f7384a293c4409969b8ef Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 14:58:33 +0200
Subject: [PATCH 130/228] viewer: remove the dead scratch-ROI widgets and
 worker methods

With the scratch ROI panel gone, delete the now-orphaned
JFJochViewerImageROIStatistics(_Box/_Circle) widgets and the worker's
unused scratch-ROI plumbing (SetROIBox/SetROICircle, the ROIElement
member, AddROIToUserMask/SubtractROIFromUserMask). ROI-to-mask, if wanted
later, should act on the selected list ROI.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         |  6 --
 viewer/JFJochImageReadingWorker.cpp           | 59 ------------
 viewer/JFJochImageReadingWorker.h             |  7 --
 viewer/JFJochViewerSidePanel.cpp              |  1 -
 .../JFJochViewerImageROIStatistics.cpp        | 91 -------------------
 .../widgets/JFJochViewerImageROIStatistics.h  | 46 ----------
 .../JFJochViewerImageROIStatistics_Box.cpp    | 71 ---------------
 .../JFJochViewerImageROIStatistics_Box.h      | 30 ------
 .../JFJochViewerImageROIStatistics_Circle.cpp | 55 -----------
 .../JFJochViewerImageROIStatistics_Circle.h   | 31 -------
 10 files changed, 397 deletions(-)
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics.cpp
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics.h
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics_Box.cpp
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics_Box.h
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics_Circle.cpp
 delete mode 100644 viewer/widgets/JFJochViewerImageROIStatistics_Circle.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 2a7d4c49..58fc4a8a 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -64,12 +64,6 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         image_viewer/JFJochAzIntImage.h
         windows/JFJochViewerReflectionListWindow.cpp
         windows/JFJochViewerReflectionListWindow.h
-        widgets/JFJochViewerImageROIStatistics.cpp
-        widgets/JFJochViewerImageROIStatistics.h
-        widgets/JFJochViewerImageROIStatistics_Box.cpp
-        widgets/JFJochViewerImageROIStatistics_Box.h
-        widgets/JFJochViewerImageROIStatistics_Circle.cpp
-        widgets/JFJochViewerImageROIStatistics_Circle.h
         toolbar/JFJochViewerToolbarImage.cpp
         toolbar/JFJochViewerToolbarImage.h
         toolbar/JFJochViewerToolbarDisplay.cpp
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index a3a3bdd4..75aae6f8 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -432,24 +432,6 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
     }
 }
 
-void JFJochImageReadingWorker::SetROIBox(QRect box) {
-    QMutexLocker ul(&m);
-
-    if (box.width() * box.height() == 0)
-        roi.reset();
-
-    roi = std::make_unique<ROIBox>("roi1", box.left(), box.right(), box.bottom(), box.top());
-}
-
-void JFJochImageReadingWorker::SetROICircle(double x, double y, double radius) {
-    QMutexLocker ul(&m);
-
-    if (radius <= 0)
-        roi.reset();
-    else
-        roi = std::make_unique<ROICircle>("roi1", x, y, radius);
-}
-
 void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionExperiment> &experiment) {
     if (!current_image_ptr)
         return;
@@ -690,47 +672,6 @@ void JFJochImageReadingWorker::UpdateUserMask_i(const std::vector<uint32_t> &mas
 }
 
 
-void JFJochImageReadingWorker::AddROIToUserMask() {
-    QMutexLocker locker(&m);
-
-    if (!roi || !current_image_ptr)
-        return;
-
-    auto user_mask = current_image_ptr->Dataset().pixel_mask.GetUserMask();
-
-    int64_t width = current_image_ptr->Dataset().experiment.GetXPixelsNum();
-    int64_t height = current_image_ptr->Dataset().experiment.GetYPixelsNum();
-    const auto res = azint_mapping->Resolution();
-    for (int y = 0; y < height; y++) {
-        for (int x = 0; x < width; x++) {
-            if (roi->CheckROI(x, y, 0, 0))
-                user_mask[x + y * width] = 1;
-        }
-    }
-
-    UpdateUserMask_i(user_mask);
-}
-
-void JFJochImageReadingWorker::SubtractROIFromUserMask() {
-    QMutexLocker locker(&m);
-    if (!roi || !current_image_ptr)
-        return;
-
-    auto user_mask = current_image_ptr->Dataset().pixel_mask.GetUserMask();
-
-    int64_t width = current_image_ptr->Dataset().experiment.GetXPixelsNum();
-    int64_t height = current_image_ptr->Dataset().experiment.GetYPixelsNum();
-
-    for (int y = 0; y < height; y++) {
-        for (int x = 0; x < width; x++) {
-            if (roi->CheckROI(x, y, 0, 0))
-                user_mask[x + y * width] = 0;
-        }
-    }
-
-    UpdateUserMask_i(user_mask);
-}
-
 void JFJochImageReadingWorker::ClearUserMask() {
     QMutexLocker locker(&m);
     if (!current_image_ptr)
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 87b26843..85d2f8dd 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -68,8 +68,6 @@ private:
     // Azimuthal profile buffer of the most recently analyzed image (filled by Analyze).
     std::unique_ptr<AzimuthalIntegrationProfile> last_profile_;
 
-    std::unique_ptr<ROIElement> roi;
-
     SpotFindingSettings spot_finding_settings;
 
     std::optional<int64_t> current_image;
@@ -155,9 +153,6 @@ public slots:
     void LoadImage(int64_t image_number, int64_t summation);
     void LoadSpots(int64_t start_image, int64_t end_image, int64_t stride);
 
-    void SetROIBox(QRect box);
-    void SetROICircle(double x, double y, double radius);
-
     void UpdateDataset(const DiffractionExperiment& experiment);
 
     void FindCenter(const UnitCell& calibrant, bool guess);
@@ -167,8 +162,6 @@ public slots:
     void UpdateSpotFindingSettings(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
     void ReanalyzeImages(bool input);
     void UpdateAzintSettings(const AzimuthalIntegrationSettings& settings);
-    void AddROIToUserMask();
-    void SubtractROIFromUserMask();
 
     void SetROIDefinition(const ROIDefinition &rois);
     void DownloadROIsFromServer();
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index e4e34f77..2426a6cb 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -7,7 +7,6 @@
 
 #include "JFJochViewerSidePanel.h"
 
-#include "widgets/JFJochViewerImageROIStatistics.h"
 #include "widgets/TitleLabel.h"
 #include "widgets/JFJochViewerImageStatistics.h"
 #include "widgets/PowderCalibrationWidget.h"
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics.cpp b/viewer/widgets/JFJochViewerImageROIStatistics.cpp
deleted file mode 100644
index 66ea26a0..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics.cpp
+++ /dev/null
@@ -1,91 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "JFJochViewerImageROIStatistics.h"
-
-#include <QPushButton>
-#include <QVBoxLayout>
-#include <QHBoxLayout>
-
-JFJochViewerImageROIStatistics::JFJochViewerImageROIStatistics(QWidget *parent)
-    : QWidget(parent) {
-    QVBoxLayout *layout = new QVBoxLayout(this);
-
-    box_radio = new QRadioButton("Box", this);
-    box_settings = new JFJochViewerImageROIStatistics_Box(this);
-    QHBoxLayout *box_row = new QHBoxLayout();
-    box_row->addWidget(box_radio);
-    box_row->addWidget(box_settings);
-    layout->addLayout(box_row);
-
-    circle_radio = new QRadioButton("Circle", this);
-    circle_settings = new JFJochViewerImageROIStatistics_Circle(this);
-    QHBoxLayout *circle_row = new QHBoxLayout();
-    circle_row->addWidget(circle_radio);
-    circle_row->addWidget(circle_settings);
-    layout->addLayout(circle_row);
-
-    radio_group = new QButtonGroup(this);
-    radio_group->addButton(box_radio, 1);
-    radio_group->addButton(circle_radio, 2);
-
-    connect(box_radio, &QRadioButton::clicked, this, &JFJochViewerImageROIStatistics::BoxButtonClicked);
-    connect(circle_radio, &QRadioButton::clicked, this, &JFJochViewerImageROIStatistics::CircleButtonClicked);
-    connect(box_settings, &JFJochViewerImageROIStatistics_Box::Updated, this,
-            &JFJochViewerImageROIStatistics::BoxButtonClicked);
-    connect(circle_settings, &JFJochViewerImageROIStatistics_Circle::Updated, this,
-            &JFJochViewerImageROIStatistics::CircleButtonClicked);
-
-    circle_settings->Disable();
-    box_radio->setChecked(true);
-
-    roi_result = new JFJochViewerROIResult(this);
-    layout->addWidget(roi_result);
-
-    QPushButton *add_button = new QPushButton("Add ROI to user mask", this);
-    connect(add_button, &QPushButton::clicked, [this]() { emit AddROIToUserMask(); });
-
-    QPushButton *sub_button = new QPushButton("Subtract ROI from user mask", this);
-    connect(sub_button, &QPushButton::clicked, [this]() { emit SubtractROIFromUserMask(); });
-
-    QHBoxLayout *buttons_row = new QHBoxLayout();
-    buttons_row->setSpacing(12);
-    buttons_row->addWidget(add_button);
-    buttons_row->addWidget(sub_button);
-
-    layout->addLayout(buttons_row);
-
-}
-
-void JFJochViewerImageROIStatistics::SetROIResult(ROIMessage roi) {
-   roi_result->SetROIResult(roi);
-}
-
-
-void JFJochViewerImageROIStatistics::SetROIBox(QRect box) {
-    box_radio->setChecked(true);
-    box_settings->ROIBoxConfigured(box);
-    circle_settings->Disable();
-}
-
-void JFJochViewerImageROIStatistics::SetROICircle(double x, double y, double radius) {
-    circle_radio->setChecked(true);
-    circle_settings->SetROICircle(CircleSettings{.x = x, .y = y, .r = radius});
-    box_settings->Disable();
-}
-
-void JFJochViewerImageROIStatistics::BoxButtonClicked() {
-    box_radio->setChecked(true);
-    box_settings->Enable();
-    circle_settings->Disable();
-
-    emit ROIBoxConfigured(box_settings->GetROIBox());
-}
-
-void JFJochViewerImageROIStatistics::CircleButtonClicked() {
-    circle_settings->Enable();
-    box_settings->Disable();
-    circle_radio->setChecked(true);
-    auto tmp = circle_settings->GetROICircle();
-    emit ROICircleConfigured(tmp.x, tmp.y, tmp.r);
-}
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics.h b/viewer/widgets/JFJochViewerImageROIStatistics.h
deleted file mode 100644
index 2d2a0118..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics.h
+++ /dev/null
@@ -1,46 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-
-#pragma once
-
-#include <QLabel>
-#include <QRadioButton>
-#include <QButtonGroup>
-
-#include "../JFJochImageReadingWorker.h"
-#include "JFJochViewerImageROIStatistics_Box.h"
-#include "JFJochViewerImageROIStatistics_Circle.h"
-#include "JFJochViewerROIResult.h"
-#include "../../reader/JFJochReaderImage.h"
-
-class JFJochViewerImageROIStatistics : public QWidget {
-    Q_OBJECT
-
-    QRadioButton *box_radio;
-    QRadioButton *circle_radio;
-    QRadioButton *azim_radio;
-    QButtonGroup *radio_group;
-
-    JFJochViewerImageROIStatistics_Box *box_settings;
-    JFJochViewerImageROIStatistics_Circle *circle_settings;
-
-    JFJochViewerROIResult *roi_result;
-
-public:
-    JFJochViewerImageROIStatistics(QWidget *parent);
-private slots:
-    void BoxButtonClicked();
-    void CircleButtonClicked();
-public slots:
-    void SetROIBox(QRect box);
-    void SetROICircle(double x, double y, double radius);
-    void SetROIResult(ROIMessage msg);
-signals:
-    void ROIBoxConfigured(QRect box);  // Signal emitted when Box ROI is set
-    void ROICircleConfigured(double center_x, double center_y, double radius);  // Signal emitted when Circle ROI is set
-    void AddROIToUserMask();
-    void SubtractROIFromUserMask();
-};
-
-
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics_Box.cpp b/viewer/widgets/JFJochViewerImageROIStatistics_Box.cpp
deleted file mode 100644
index dc49a4be..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics_Box.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include <QHBoxLayout>
-#include "JFJochViewerImageROIStatistics_Box.h"
-
-#include <QLabel>
-
-JFJochViewerImageROIStatistics_Box::JFJochViewerImageROIStatistics_Box(QWidget *parent)
-    : QWidget(parent) {
-    auto layout = new QHBoxLayout(this);
-
-    setFixedWidth(300);
-    layout->addWidget(new QLabel("x:"));
-
-    x0 = new NumberLineEdit(0, 10000, 0, 0, "", this);
-    x0->setFixedWidth(50);
-    layout->addWidget(x0);
-
-    layout->addWidget(new QLabel(" - "));
-
-    x1 = new NumberLineEdit(0, 10000, 0, 0, "", this);
-    x1->setFixedWidth(50);
-    layout->addWidget(x1);
-
-    layout->addWidget(new QLabel("  y:"));
-    y0 = new NumberLineEdit(0, 10000, 0, 0, "", this);
-    y0->setFixedWidth(50);
-    layout->addWidget(y0);
-    layout->addWidget(new QLabel(" - "));
-
-    y1 = new NumberLineEdit(0, 10000, 0, 0, "", this);
-    y1->setFixedWidth(50);
-    layout->addWidget(y1);
-
-    connect(x0, &NumberLineEdit::newValue, [this] (float) { emit Updated(); } );
-    connect(y0, &NumberLineEdit::newValue, [this] (float) { emit Updated(); } );
-    connect(x1, &NumberLineEdit::newValue, [this] (float) { emit Updated(); } );
-    connect(y1, &NumberLineEdit::newValue, [this] (float) { emit Updated(); } );
-}
-
-void JFJochViewerImageROIStatistics_Box::ROIBoxConfigured(QRect box) {
-    Enable();
-    x0->setValue(box.left());
-    x1->setValue(box.right());
-    y0->setValue(box.top());
-    y1->setValue(box.bottom());
-}
-
-void JFJochViewerImageROIStatistics_Box::Disable() {
-    x0->setEnabled(false);
-    x1->setEnabled(false);
-    y0->setEnabled(false);
-    y1->setEnabled(false);
-}
-
-void JFJochViewerImageROIStatistics_Box::Enable() {
-    x0->setEnabled(true);
-    x1->setEnabled(true);
-    y0->setEnabled(true);
-    y1->setEnabled(true);
-}
-
-QRect JFJochViewerImageROIStatistics_Box::GetROIBox() {
-    int64_t out_x0 = std::lround(x0->value());
-    int64_t out_x1 = std::lround(x1->value());
-    int64_t out_y0 = std::lround(y0->value());
-    int64_t out_y1 = std::lround(y1->value());
-
-    return QRect(out_x0, out_y0, out_x1 - out_x0, out_y1 - out_y0).normalized();
-}
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics_Box.h b/viewer/widgets/JFJochViewerImageROIStatistics_Box.h
deleted file mode 100644
index 80cc72cd..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics_Box.h
+++ /dev/null
@@ -1,30 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include <QWidget>
-
-#include "NumberLineEdit.h"
-
-class JFJochViewerImageROIStatistics_Box : public QWidget {
-    Q_OBJECT
-
-    NumberLineEdit *x0 = nullptr;
-    NumberLineEdit *x1 = nullptr;
-    NumberLineEdit *y0 = nullptr;
-    NumberLineEdit *y1 = nullptr;
-
-public:
-    JFJochViewerImageROIStatistics_Box(QWidget *parent = nullptr);
-    QRect GetROIBox();
-signals:
-    void Updated();  // Signal emitted when Box ROI is set
-
-public slots:
-    void ROIBoxConfigured(QRect box);  // Signal emitted when Box ROI is set
-    void Disable();
-    void Enable();
-};
-
-
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics_Circle.cpp b/viewer/widgets/JFJochViewerImageROIStatistics_Circle.cpp
deleted file mode 100644
index d6442f5b..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics_Circle.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include <QHBoxLayout>
-#include <QLabel>
-
-#include "JFJochViewerImageROIStatistics_Circle.h"
-
-JFJochViewerImageROIStatistics_Circle::JFJochViewerImageROIStatistics_Circle(QWidget *parent)
-    :QWidget(parent) {
-    auto layout = new QHBoxLayout(this);
-
-    setFixedWidth(300);
-
-    layout->addWidget(new QLabel("x: "));
-    x = new NumberLineEdit(0, 10000, 0, 1, "", this);
-    layout->addWidget(x);
-
-    layout->addWidget(new QLabel(" y: "));
-    y = new NumberLineEdit(0, 10000, 0, 1, "", this);
-    layout->addWidget(y);
-
-
-    layout->addWidget(new QLabel(" r: "));
-    r = new NumberLineEdit(0, 10000, 0, 1, "", this);
-    layout->addWidget(r);
-
-    connect(x, &NumberLineEdit::newValue, [this] (float) {emit Updated();});
-    connect(y, &NumberLineEdit::newValue, [this] (float) {emit Updated();});
-    connect(r, &NumberLineEdit::newValue, [this] (float) {emit Updated();});
-}
-
-void JFJochViewerImageROIStatistics_Circle::SetROICircle(const CircleSettings& input) {
-    Enable();
-    x->setValue(input.x);
-    y->setValue(input.y);
-    r->setValue(input.r);
-}
-
-void JFJochViewerImageROIStatistics_Circle::Disable() {
-    x->setEnabled(false);
-    y->setEnabled(false);
-    r->setEnabled(false);
-}
-
-void JFJochViewerImageROIStatistics_Circle::Enable() {
-    x->setEnabled(true);
-    y->setEnabled(true);
-    r->setEnabled(true);
-}
-
-CircleSettings JFJochViewerImageROIStatistics_Circle::GetROICircle() {
-    return CircleSettings{.x = x->value(), .y = y->value(), .r = r->value()};
-}
-
diff --git a/viewer/widgets/JFJochViewerImageROIStatistics_Circle.h b/viewer/widgets/JFJochViewerImageROIStatistics_Circle.h
deleted file mode 100644
index dc7808b2..00000000
--- a/viewer/widgets/JFJochViewerImageROIStatistics_Circle.h
+++ /dev/null
@@ -1,31 +0,0 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#pragma once
-
-#include <QWidget>
-
-#include "NumberLineEdit.h"
-
-struct CircleSettings {
-    double x, y, r;
-};
-
-class JFJochViewerImageROIStatistics_Circle : public QWidget {
-    Q_OBJECT
-
-    NumberLineEdit *x = nullptr;
-    NumberLineEdit *y = nullptr;
-    NumberLineEdit *r = nullptr;
-public:
-    JFJochViewerImageROIStatistics_Circle(QWidget *parent = nullptr);
-    void SetROICircle(const CircleSettings &input);
-    CircleSettings GetROICircle();
-
-    void Disable();
-    void Enable();
-signals:
-    void Updated();
-};
-
-
-- 
2.52.0


From abc1d1c079cf4a001360eeb7017a4cd013e2b8ff Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 15:08:59 +0200
Subject: [PATCH 131/228] viewer: add/subtract the selected ROI to/from the
 user mask

Restore the ROI-to-mask action on the new list: "Add to mask" and
"Subtract from mask" buttons rasterise the selected ROI into the user
mask (set or clear), through the same UpdateUserMask_i path. The ROI is
evaluated with per-pixel resolution and phi from the geometry, so box,
circle and azimuthal (sector) ROIs all map correctly.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp    | 31 ++++++++++++++++++++++++++
 viewer/JFJochImageReadingWorker.h      |  1 +
 viewer/JFJochViewerSidePanel.cpp       |  1 +
 viewer/JFJochViewerSidePanel.h         |  1 +
 viewer/JFJochViewerWindow.cpp          |  2 ++
 viewer/widgets/JFJochViewerROIList.cpp | 13 +++++++++++
 viewer/widgets/JFJochViewerROIList.h   |  1 +
 7 files changed, 50 insertions(+)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 75aae6f8..d9cca04b 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -584,6 +584,37 @@ void JFJochImageReadingWorker::SetROIDefinition(const ROIDefinition &rois) {
     SetROIDefinition_i(rois);
 }
 
+void JFJochImageReadingWorker::MaskFromSelectedROI(QString name, bool add) {
+    QMutexLocker locker(&m);
+    if (!current_image_ptr)
+        return;
+
+    const auto &exp = current_image_ptr->Dataset().experiment;
+    const auto rois = exp.ROI().GetROIDefinition();
+    const std::string n = name.toStdString();
+
+    const ROIElement *elem = nullptr;
+    for (const auto &b : rois.boxes)     if (b.GetName() == n) { elem = &b; break; }
+    if (!elem) for (const auto &c : rois.circles)   if (c.GetName() == n) { elem = &c; break; }
+    if (!elem) for (const auto &a : rois.azimuthal) if (a.GetName() == n) { elem = &a; break; }
+    if (!elem)
+        return;
+
+    auto user_mask = current_image_ptr->Dataset().pixel_mask.GetUserMask();
+    auto geom = exp.GetDiffractionGeometry();
+    const int64_t width = exp.GetXPixelsNum();
+    const int64_t height = exp.GetYPixelsNum();
+    for (int64_t y = 0; y < height; y++) {
+        for (int64_t x = 0; x < width; x++) {
+            const float res = geom.PxlToRes(x, y);
+            const float phi = geom.Phi_rad(x, y) * 180.0f / static_cast<float>(PI);
+            if (elem->CheckROI(x, y, res, phi))
+                user_mask[x + y * width] = add ? 1 : 0;
+        }
+    }
+    UpdateUserMask_i(user_mask);
+}
+
 void JFJochImageReadingWorker::DownloadROIsFromServer() {
     QMutexLocker locker(&m);
     if (!http_mode)
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 85d2f8dd..6ab4e7e4 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -166,6 +166,7 @@ public slots:
     void SetROIDefinition(const ROIDefinition &rois);
     void DownloadROIsFromServer();
     void UploadROIsToServer();
+    void MaskFromSelectedROI(QString name, bool add);   // rasterise an ROI into the user mask
 
     void SaveUserMaskTIFF(QString filename);
     void LoadUserMaskTIFF(QString filename, bool replace);
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index 2426a6cb..85220768 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -132,6 +132,7 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     connect(roi_list, &JFJochViewerROIList::selectedROIChanged, this, &JFJochViewerSidePanel::selectedROIChanged);
     connect(roi_list, &JFJochViewerROIList::downloadROIs, this, &JFJochViewerSidePanel::downloadROIs);
     connect(roi_list, &JFJochViewerROIList::uploadROIs, this, &JFJochViewerSidePanel::uploadROIs);
+    connect(roi_list, &JFJochViewerROIList::maskFromROI, this, &JFJochViewerSidePanel::maskFromROI);
 
     layout->addWidget(new TitleLabel("Data analysis", this));
 
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 549d9d8a..4aec0662 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -35,6 +35,7 @@ signals:
     void selectedROIChanged(QString name);
     void downloadROIs();
     void uploadROIs();
+    void maskFromROI(QString name, bool add);
     void findBeamCenter(const UnitCell &input, bool guess);
     void analyze();
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 90f04c95..7ec2f070 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -201,6 +201,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::DownloadROIsFromServer);
     connect(side_panel, &JFJochViewerSidePanel::uploadROIs,
             reading_worker, &JFJochImageReadingWorker::UploadROIsToServer);
+    connect(side_panel, &JFJochViewerSidePanel::maskFromROI,
+            reading_worker, &JFJochImageReadingWorker::MaskFromSelectedROI);
 
     connect(menuBar, &JFJochViewerMenu::clearUserMaskSelected,
             reading_worker, &JFJochImageReadingWorker::ClearUserMask);
diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index 178e0b95..1b648995 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -55,6 +55,19 @@ JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
     }
     layout->addLayout(grid);
 
+    auto *mask = new QHBoxLayout();
+    auto *mask_add = new QPushButton("Add to mask", this);
+    auto *mask_sub = new QPushButton("Subtract from mask", this);
+    mask->addWidget(mask_add);
+    mask->addWidget(mask_sub);
+    layout->addLayout(mask);
+    connect(mask_add, &QPushButton::clicked, [this] {
+        if (!SelectedName().isEmpty()) emit maskFromROI(SelectedName(), true);
+    });
+    connect(mask_sub, &QPushButton::clicked, [this] {
+        if (!SelectedName().isEmpty()) emit maskFromROI(SelectedName(), false);
+    });
+
     result_ = new JFJochViewerROIResult(this);
     layout->addWidget(result_);
 }
diff --git a/viewer/widgets/JFJochViewerROIList.h b/viewer/widgets/JFJochViewerROIList.h
index ae468ae2..c1138b13 100644
--- a/viewer/widgets/JFJochViewerROIList.h
+++ b/viewer/widgets/JFJochViewerROIList.h
@@ -52,4 +52,5 @@ signals:
     void selectedROIChanged(QString name);
     void downloadROIs();   // fetch ROIs from the connected broker
     void uploadROIs();     // push ROIs to the connected broker
+    void maskFromROI(QString name, bool add);   // add/subtract the selected ROI to/from the user mask
 };
-- 
2.52.0


From e60b42ea8311a0efe293a6b6b9e6c09d54bb28af Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 16:01:13 +0200
Subject: [PATCH 132/228] viewer: white, compact, right-aligned ROI numeric
 fields

The ROI bound editors now have a white background, a capped width and
right-aligned text, which reads better for numeric entry.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/widgets/JFJochViewerROIList.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/viewer/widgets/JFJochViewerROIList.cpp b/viewer/widgets/JFJochViewerROIList.cpp
index 1b648995..1a9c2bc3 100644
--- a/viewer/widgets/JFJochViewerROIList.cpp
+++ b/viewer/widgets/JFJochViewerROIList.cpp
@@ -49,8 +49,11 @@ JFJochViewerROIList::JFJochViewerROIList(QWidget *parent) : QWidget(parent) {
     for (int i = 0; i < 4; i++) {
         flabel_[i] = new QLabel("", this);
         fedit_[i] = new QLineEdit(this);
+        fedit_[i]->setAlignment(Qt::AlignRight);
+        fedit_[i]->setMaximumWidth(90);
+        fedit_[i]->setStyleSheet("background-color: white; color: black;");
         grid->addWidget(flabel_[i], i, 0);
-        grid->addWidget(fedit_[i], i, 1);
+        grid->addWidget(fedit_[i], i, 1, Qt::AlignRight);
         connect(fedit_[i], &QLineEdit::editingFinished, this, &JFJochViewerROIList::ApplyEditor);
     }
     layout->addLayout(grid);
-- 
2.52.0


From e9e5ec79cdb8ec143277c1db644735680ff542c1 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 16:01:13 +0200
Subject: [PATCH 133/228] frontend: phi_min/phi_max columns in the azimuthal
 ROI table

Surface the optional azimuthal phi-sector bounds (phi_min_deg/phi_max_deg)
as editable columns, so a sector can be set from the web UI, not only the
viewer. Also fix the Q_max row's d header, which read d_max but is d_min.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/components/ROI.tsx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index 5e0a43bc..59be05a7 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -318,8 +318,12 @@ function ROI({s: serverS}: MyProps) {
                 } else
                     return row;
             },
-            renderHeader: () => (<div>d<sub>max</sub> [Å]</div>)
+            renderHeader: () => (<div>d<sub>min</sub> [Å]</div>)
         },
+        { field: 'phi_min_deg', type: 'number', editable: true,
+            renderHeader: () => (<div>φ<sub>min</sub> [°]</div>) },
+        { field: 'phi_max_deg', type: 'number', editable: true,
+            renderHeader: () => (<div>φ<sub>max</sub> [°]</div>) },
         { field: 'actions', type: 'actions', width: 50, cellClassName: 'actions',
             getActions: (id : GridRowModel) => {
                 return [
-- 
2.52.0


From a34a033c992bd259087ab4b9392d02630d2878f6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 16:05:15 +0200
Subject: [PATCH 134/228] frontend: auto-fill the missing phi bound for a
 sector

When only one azimuthal phi bound is entered, fill the other so the
sector is well-defined and the server accepts it: a missing phi_min
becomes 0 and a missing phi_max becomes 360. Leaving both empty still
means a full ring.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 frontend/src/components/ROI.tsx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/frontend/src/components/ROI.tsx b/frontend/src/components/ROI.tsx
index 59be05a7..9060ac8f 100644
--- a/frontend/src/components/ROI.tsx
+++ b/frontend/src/components/ROI.tsx
@@ -226,6 +226,12 @@ function ROI({s: serverS}: MyProps) {
     };
 
     const processRowAzimUpdate = (newRow: AzimWrapper, oldRow: AzimWrapper) => {
+        // A phi sector needs both bounds; if only one is given, fill the other (min -> 0, max -> 360).
+        const phiSet = (v?: number | null) => v !== undefined && v !== null && !Number.isNaN(v);
+        if (phiSet(newRow.phi_min_deg) && !phiSet(newRow.phi_max_deg))
+            newRow = {...newRow, phi_max_deg: 360};
+        else if (phiSet(newRow.phi_max_deg) && !phiSet(newRow.phi_min_deg))
+            newRow = {...newRow, phi_min_deg: 0};
         let new_state = azim.map((item) => item === oldRow ? newRow : item);
         let err = validateAzim(new_state);
         setAzimErr(err);
-- 
2.52.0


From 4e9505e6bb38a3003ab9512984520d38562d5bc5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 16:06:49 +0200
Subject: [PATCH 135/228] make_doc.sh: Use python3

---
 make_doc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/make_doc.sh b/make_doc.sh
index b1441e26..c2e11ab4 100644
--- a/make_doc.sh
+++ b/make_doc.sh
@@ -12,7 +12,7 @@ set -euo pipefail
 # The Python interpreter can be overridden with $PYTHON (default: python).
 
 OUT="${1:-public}"
-PYTHON="${PYTHON:-python}"
+PYTHON="${PYTHON:-python3}"
 
 # Resolve the output directory to an absolute path before we change directories.
 mkdir -p "$OUT"
-- 
2.52.0


From 3ce7666738a9cf6ce582b5b88cef133d53039bfa Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 16:37:32 +0200
Subject: [PATCH 136/228] make_doc.sh: prefer the newest available python3.x

The bare python3 is often too old for the Sphinx build. Auto-select the
newest python3.13/3.12/3.11/3 found on PATH, still allowing $PYTHON to
override.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 make_doc.sh | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/make_doc.sh b/make_doc.sh
index c2e11ab4..68b33144 100644
--- a/make_doc.sh
+++ b/make_doc.sh
@@ -9,10 +9,24 @@ set -euo pipefail
 #                Relative paths are resolved against the caller's working
 #                directory, so the frontend build can point this at frontend/dist/docs.
 #
-# The Python interpreter can be overridden with $PYTHON (default: python).
+# The Python interpreter can be overridden with $PYTHON. Otherwise the newest
+# available python3.x is used (the bare "python3" is often too old).
 
 OUT="${1:-public}"
-PYTHON="${PYTHON:-python3}"
+
+if [ -z "${PYTHON:-}" ]; then
+    for candidate in python3.13 python3.12 python3.11 python3; do
+        if command -v "$candidate" >/dev/null 2>&1; then
+            PYTHON="$candidate"
+            break
+        fi
+    done
+fi
+if [ -z "${PYTHON:-}" ]; then
+    echo "No python3 interpreter found" >&2
+    exit 1
+fi
+echo "Using $PYTHON ($("$PYTHON" --version 2>&1))"
 
 # Resolve the output directory to an absolute path before we change directories.
 mkdir -p "$OUT"
-- 
2.52.0


From 1e53db8f649715fa5615d938f108366911c0a905 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 20:55:32 +0200
Subject: [PATCH 137/228] Docker: Update 2606 to support python3.12/3.13

---
 docker/rocky9/Dockerfile     | 69 +++++-------------------------------
 docker/ubuntu2204/Dockerfile |  3 ++
 docker/ubuntu2404/Dockerfile |  5 ++-
 3 files changed, 15 insertions(+), 62 deletions(-)

diff --git a/docker/rocky9/Dockerfile b/docker/rocky9/Dockerfile
index 24e65d44..a39ae69d 100644
--- a/docker/rocky9/Dockerfile
+++ b/docker/rocky9/Dockerfile
@@ -1,8 +1,8 @@
-FROM nvidia/cuda:13.0.1-devel-rockylinux9
+FROM nvidia/cuda:13.3.0-devel-rockylinux9
 LABEL authors="leonarski_f"
 
 ARG OPENSSL_VERSION=3.5.4
-ARG QT_VERSION=6.9.0
+ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
 ARG EIGEN_TAG=3.4.0
 ARG LIBJPEG_TURBO_VERSION=3.1.2
@@ -38,11 +38,13 @@ RUN dnf -y update && \
       redhat-rpm-config \
       ninja-build \
       python3 \
+      python3.12 \
       perl \
       nasm \
       pkgconf-pkg-config \
       libxcb-devel \
       xcb-util-*-devel \
+      libxcb-devel \
       libxkbcommon-devel \
       libxkbcommon-x11-devel \
       libX11-devel \
@@ -61,6 +63,10 @@ RUN dnf -y update && \
       glib2-devel \
       fftw-static \
       fftw-devel \
+      libtiff \
+      libtiff-devel \
+      libjpeg-turbo \
+      libjpeg-turbo-devel \
       eigen3-devel \
       zlib-static \
       fontconfig-devel \
@@ -93,65 +99,6 @@ RUN curl -fsSL https://rpm.nodesource.com/setup_${NODE_MAJOR}.x | bash - && \
     dnf clean all && rm -rf /var/cache/dnf && \
     node --version && npm --version && (corepack enable || true)
 
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBJPEG_TURBO_VERSION} https://github.com/libjpeg-turbo/libjpeg-turbo.git /tmp/libjpeg-turbo-src; \
-    mkdir /tmp/libjpeg-turbo-src/build; \
-    cd /tmp/libjpeg-turbo-src/build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DENABLE_SHARED=FALSE \
-      -DENABLE_STATIC=TRUE \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libjpeg-turbo-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBTIFF_VERSION} https://gitlab.com/libtiff/libtiff.git /tmp/libtiff-src; \
-    mkdir /tmp/libtiff-src/build.cm; \
-    cd /tmp/libtiff-src/build.cm; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DBUILD_SHARED_LIBS=OFF \
-      -Dtools=OFF \
-      -Dtests=OFF \
-      -Ddocs=OFF \
-      -Dlzma=OFF \
-      -Djbig=OFF \
-      -Dwebp=OFF \
-      -Djpeg=OFF \
-      -Dold-jpeg=OFF \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libtiff-${LIBTIFF_VERSION}-static \
-      ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libtiff-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${HDF5_TAG} https://github.com/HDFGroup/hdf5 /tmp/hdf5-src; \
-    cd /tmp/hdf5-src; \
-    mkdir build && cd build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DHDF5_BUILD_SHARED_LIBS=OFF \
-      -DBUILD_TESTING=OFF \
-      -DHDF5_BUILD_TOOLS=OFF \
-      -DHDF5_BUILD_EXAMPLES=OFF \
-      -DHDF5_ENABLE_SZIP_SUPPORT=OFF \
-      -DHDF5_ENABLE_SZIP_ENCODING=OFF \
-      -DHDF5_BUILD_CPP_LIB=OFF \
-      -DHDF5_ENABLE_Z_LIB_SUPPORT=OFF \
-      -DCMAKE_INSTALL_PREFIX=/opt/hdf5-${HDF5_TAG}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/hdf5-src
-
-ENV CMAKE_PREFIX_PATH=/opt/libtiff-${LIBTIFF_VERSION}-static:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static
-ENV PKG_CONFIG_PATH=/opt/hdf5-${HDF5_TAG}-static/lib/pkgconfig:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static/lib/pkgconfig:/opt/libtiff-${LIBTIFF_VERSION}-static/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
-
 # Make GCC/G++ 13 the default for builds
 ENV GCC_TOOLSET_ROOT=/opt/rh/gcc-toolset-13/root
 ENV PATH=${GCC_TOOLSET_ROOT}/usr/bin:${PATH}
diff --git a/docker/ubuntu2204/Dockerfile b/docker/ubuntu2204/Dockerfile
index e357dfba..d127c769 100644
--- a/docker/ubuntu2204/Dockerfile
+++ b/docker/ubuntu2204/Dockerfile
@@ -29,12 +29,15 @@ RUN set -eux; \
       build-essential \
       ninja-build \
       python3 \
+      python3-venv \
       python3-requests \
       perl \
       pkg-config \
       gdb \
       file \
       nasm \
+      python3.11 \
+      python3.11-venv \
       dpkg-dev \
       fakeroot \
       libnuma-dev \
diff --git a/docker/ubuntu2404/Dockerfile b/docker/ubuntu2404/Dockerfile
index f1e7c2d8..b4046668 100644
--- a/docker/ubuntu2404/Dockerfile
+++ b/docker/ubuntu2404/Dockerfile
@@ -1,5 +1,5 @@
 # Ubuntu 24.04 (Noble) base with CUDA 13 devel toolchain
-FROM nvidia/cuda:13.0.1-devel-ubuntu24.04
+FROM nvidia/cuda:13.3.0-devel-ubuntu24.04
 LABEL authors="leonarski_f"
 
 ENV DEBIAN_FRONTEND=noninteractive
@@ -24,7 +24,10 @@ RUN set -eux; \
       cmake \
       ninja-build \
       python3 \
+      python3-venv \
       python3-requests \
+      python3.12 \
+      python3.12-venv \
       perl \
       pkg-config \
       gdb \
-- 
2.52.0


From 74c2c808de9167ddc74fdbe0cc8de43b661e1f5e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 19:33:47 +0200
Subject: [PATCH 138/228] cmake: drop GCC-only hardcoded flags, bump CUDA to
 C++20

Make the build less hostile to MSVC (needed for the viewer port) and
align the CUDA standard with C++.

- Remove the CMAKE_C/CXX_FLAGS_RELEASE overrides: -O3/-DNDEBUG only
  duplicate CMake's own GCC/Clang Release defaults, and the SET()
  clobbered the MSVC defaults. The lone meaningful flag,
  -Wno-deprecated-enum-enum-conversion, merely silenced warnings from
  the vendored Xilinx ap_private.h in the FPGA path; with no -Werror
  it is just log noise, so drop it.
- CMAKE_CUDA_STANDARD 17 -> 20 (+ STANDARD_REQUIRED); CUDA >= 12.8
  already supports C++20.
- Drop the file-scoped -Ofast on JFPedestalCalc.cpp /
  JFConversionFloatingPoint.cpp: it is GCC-only and reaches the MSVC
  viewer via JFJochCommon -> JFCalibration. Those files now build at
  plain -O3.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt          | 6 ++----
 jungfrau/CMakeLists.txt | 2 --
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 34983c02..11606e64 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,9 +8,6 @@ SET(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
 SET(CMAKE_CXX_STANDARD 20)
 SET(CMAKE_CXX_STANDARD_REQUIRED True)
 
-SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wno-deprecated-enum-enum-conversion -DNDEBUG")
-SET(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG")
-
 SET(JFJOCH_WRITER_ONLY           OFF CACHE BOOL "Compile HDF5 writer only")
 SET(JFJOCH_INSTALL_DRIVER_SOURCE OFF CACHE BOOL "Install kernel driver source (ignored if building writer only; necessary for RPM building)")
 SET(JFJOCH_USE_CUDA              ON CACHE BOOL "Compile Jungfraujoch with CUDA")
@@ -42,7 +39,8 @@ INCLUDE(CheckIncludeFile)
 CHECK_LANGUAGE(CUDA)
 
 SET(CMAKE_CUDA_ARCHITECTURES 75 80 86 89 90 100 120) # T4, A100, RTX A4000, L4
-SET(CMAKE_CUDA_STANDARD 17)
+SET(CMAKE_CUDA_STANDARD 20)
+SET(CMAKE_CUDA_STANDARD_REQUIRED True)
 SET(CMAKE_CUDA_FLAGS_RELEASE "-O3 -lineinfo")
 SET(CMAKE_CUDA_RUNTIME_LIBRARY Static)
 
diff --git a/jungfrau/CMakeLists.txt b/jungfrau/CMakeLists.txt
index adc83356..2986d404 100644
--- a/jungfrau/CMakeLists.txt
+++ b/jungfrau/CMakeLists.txt
@@ -6,5 +6,3 @@ ADD_LIBRARY(JFCalibration STATIC
         JFPedestalCalc.cpp JFPedestalCalc.h)
 
 TARGET_LINK_LIBRARIES(JFCalibration JFJochCommon)
-
-SET_SOURCE_FILES_PROPERTIES(JFPedestalCalc.cpp JFConversionFloatingPoint.cpp PROPERTIES COMPILE_FLAGS -Ofast)
-- 
2.52.0


From f21c22d4531822c5c7debebb483c616f60e42874 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 19:47:45 +0200
Subject: [PATCH 139/228] cmake: add JFJOCH_VIEWER_ONLY to build the viewer
 standalone

New option (default OFF) that compiles only jfjoch_viewer and the
libraries it transitively links -- common, image_analysis, writer,
reader, preview, image_puller, frame_serialize, gemmi_gph, compression,
jungfrau, and the OpenAPI model (JFJochAPI) -- skipping the Linux-only
online stack (broker service, receiver, fpga, acquisition_device,
detector_control, image_pusher, xds-plugin, tests, tools) and the
frontend. This is the standalone build path for the cross-platform
viewer.

JFJochAPI is the only piece the viewer needs from broker/, so the broker
service library and executable are gated behind NOT JFJOCH_VIEWER_ONLY.
The full build and JFJOCH_VIEWER_BUILD (viewer on top of the full build)
are unchanged -- that path is the verbatim ELSE() branch.

Verified on Linux: cmake -DJFJOCH_VIEWER_ONLY=ON configures and
`make jfjoch_viewer` links cleanly with the online stack absent.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt        | 70 +++++++++++++++++++++++++++----------------
 broker/CMakeLists.txt | 26 +++++++++-------
 2 files changed, 59 insertions(+), 37 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 11606e64..be6e490c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,6 +12,7 @@ SET(JFJOCH_WRITER_ONLY           OFF CACHE BOOL "Compile HDF5 writer only")
 SET(JFJOCH_INSTALL_DRIVER_SOURCE OFF CACHE BOOL "Install kernel driver source (ignored if building writer only; necessary for RPM building)")
 SET(JFJOCH_USE_CUDA              ON CACHE BOOL "Compile Jungfraujoch with CUDA")
 SET(JFJOCH_VIEWER_BUILD          OFF CACHE BOOL "Compile Jungfraujoch viewer")
+SET(JFJOCH_VIEWER_ONLY           OFF CACHE BOOL "Compile only jfjoch_viewer and its dependencies")
 
 FIND_PACKAGE(ZLIB REQUIRED)
 
@@ -159,36 +160,53 @@ FetchContent_Declare(
 FetchContent_MakeAvailable(libzmq)
 FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
 
-ADD_SUBDIRECTORY(jungfrau)
-ADD_SUBDIRECTORY(compression)
-ADD_SUBDIRECTORY(common)
-ADD_SUBDIRECTORY(writer)
-ADD_SUBDIRECTORY(frame_serialize)
-ADD_SUBDIRECTORY(reader)
-ADD_SUBDIRECTORY(detector_control)
-ADD_SUBDIRECTORY(image_puller)
-ADD_SUBDIRECTORY(preview)
-ADD_SUBDIRECTORY(gemmi_gph)
-ADD_SUBDIRECTORY(xds-plugin)
-
-IF (JFJOCH_WRITER_ONLY)
-    MESSAGE(STATUS "Compiling HDF5 writer only")
-ELSE()
-    ADD_SUBDIRECTORY(image_pusher)
-    ADD_SUBDIRECTORY(broker)
-    ADD_SUBDIRECTORY(fpga)
-    ADD_SUBDIRECTORY(acquisition_device)
-    ADD_SUBDIRECTORY(receiver)
+IF (JFJOCH_VIEWER_ONLY)
+    # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
+    # (broker here provides JFJochAPI only; its service targets are gated out.)
+    ADD_SUBDIRECTORY(jungfrau)
+    ADD_SUBDIRECTORY(compression)
+    ADD_SUBDIRECTORY(common)
+    ADD_SUBDIRECTORY(gemmi_gph)
+    ADD_SUBDIRECTORY(frame_serialize)
+    ADD_SUBDIRECTORY(image_puller)
+    ADD_SUBDIRECTORY(preview)
+    ADD_SUBDIRECTORY(writer)
     ADD_SUBDIRECTORY(image_analysis)
-    ADD_SUBDIRECTORY(tests)
-    ADD_SUBDIRECTORY(tools)
-ENDIF()
-
-IF (JFJOCH_VIEWER_BUILD)
+    ADD_SUBDIRECTORY(broker)
+    ADD_SUBDIRECTORY(reader)
     ADD_SUBDIRECTORY(viewer)
+ELSE()
+    ADD_SUBDIRECTORY(jungfrau)
+    ADD_SUBDIRECTORY(compression)
+    ADD_SUBDIRECTORY(common)
+    ADD_SUBDIRECTORY(writer)
+    ADD_SUBDIRECTORY(frame_serialize)
+    ADD_SUBDIRECTORY(reader)
+    ADD_SUBDIRECTORY(detector_control)
+    ADD_SUBDIRECTORY(image_puller)
+    ADD_SUBDIRECTORY(preview)
+    ADD_SUBDIRECTORY(gemmi_gph)
+    ADD_SUBDIRECTORY(xds-plugin)
+
+    IF (JFJOCH_WRITER_ONLY)
+        MESSAGE(STATUS "Compiling HDF5 writer only")
+    ELSE()
+        ADD_SUBDIRECTORY(image_pusher)
+        ADD_SUBDIRECTORY(broker)
+        ADD_SUBDIRECTORY(fpga)
+        ADD_SUBDIRECTORY(acquisition_device)
+        ADD_SUBDIRECTORY(receiver)
+        ADD_SUBDIRECTORY(image_analysis)
+        ADD_SUBDIRECTORY(tests)
+        ADD_SUBDIRECTORY(tools)
+    ENDIF()
+
+    IF (JFJOCH_VIEWER_BUILD)
+        ADD_SUBDIRECTORY(viewer)
+    ENDIF()
 ENDIF()
 
-IF (NOT JFJOCH_WRITER_ONLY)
+IF (NOT JFJOCH_WRITER_ONLY AND NOT JFJOCH_VIEWER_ONLY)
     ADD_CUSTOM_COMMAND(OUTPUT frontend/dist/index.html
             COMMAND npm ci
             COMMAND npm run build
diff --git a/broker/CMakeLists.txt b/broker/CMakeLists.txt
index 8a87b41a..6921a7ce 100644
--- a/broker/CMakeLists.txt
+++ b/broker/CMakeLists.txt
@@ -6,17 +6,21 @@ AUX_SOURCE_DIRECTORY(gen/model MODEL_SOURCES)
 ADD_LIBRARY(JFJochAPI STATIC ${MODEL_SOURCES})
 TARGET_INCLUDE_DIRECTORIES(JFJochAPI PUBLIC gen/model)
 
-# Jungfraujoch Broker (abstract from HTTP service)
-ADD_LIBRARY(JFJochBroker STATIC
-        JFJochStateMachine.cpp JFJochStateMachine.h
-        JFJochServices.cpp JFJochServices.h
-        JFJochBrokerParser.cpp JFJochBrokerParser.h
-        OpenAPIConvert.h OpenAPIConvert.cpp)
+# The broker service pulls in the receiver/detector stack. A viewer-only build
+# needs JFJochAPI (the shared OpenAPI model, above) but none of this machinery.
+IF (NOT JFJOCH_VIEWER_ONLY)
+    # Jungfraujoch Broker (abstract from HTTP service)
+    ADD_LIBRARY(JFJochBroker STATIC
+            JFJochStateMachine.cpp JFJochStateMachine.h
+            JFJochServices.cpp JFJochServices.h
+            JFJochBrokerParser.cpp JFJochBrokerParser.h
+            OpenAPIConvert.h OpenAPIConvert.cpp)
 
-TARGET_LINK_LIBRARIES(JFJochBroker JFJochReceiver JFJochDetector JFJochCommon JFJochAPI JFJochPreview)
+    TARGET_LINK_LIBRARIES(JFJochBroker JFJochReceiver JFJochDetector JFJochCommon JFJochAPI JFJochPreview)
 
-ADD_EXECUTABLE(jfjoch_broker jfjoch_broker.cpp JFJochBrokerHttp.cpp JFJochBrokerHttp.h)
+    ADD_EXECUTABLE(jfjoch_broker jfjoch_broker.cpp JFJochBrokerHttp.cpp JFJochBrokerHttp.h)
 
-TARGET_LINK_LIBRARIES(jfjoch_broker JFJochBroker httplib::httplib ${CMAKE_DL_LIBS})
-TARGET_INCLUDE_DIRECTORIES(jfjoch_broker PUBLIC gen/api)
-INSTALL(TARGETS jfjoch_broker RUNTIME COMPONENT jfjoch)
+    TARGET_LINK_LIBRARIES(jfjoch_broker JFJochBroker httplib::httplib ${CMAKE_DL_LIBS})
+    TARGET_INCLUDE_DIRECTORIES(jfjoch_broker PUBLIC gen/api)
+    INSTALL(TARGETS jfjoch_broker RUNTIME COMPONENT jfjoch)
+ENDIF()
-- 
2.52.0


From 3c6439530dedaeec60fc09a4a43eaf01e5040f22 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 20:03:18 +0200
Subject: [PATCH 140/228] cmake: raise policy floor to 3.5 for FetchContent
 deps (CMake 4.x)

CMake >= 4.0 (4.3.1 ships bundled with Visual Studio 2026) makes any
cmake_minimum_required(VERSION < 3.5) a fatal error. The fetched libzmq
still declares VERSION 3.0.2, which aborts configuration before our own
CMakeLists gets a say. Set CMAKE_POLICY_VERSION_MINIMUM=3.5 before the
FetchContent_MakeAvailable calls so those subprojects configure; the
variable is simply unused (harmless) on CMake < 3.30.

Verified against CMake 4.3.1: the real libzmq source fails without it and
configures with it, and an in-file SET() propagates into the
add_subdirectory child exactly as a -D cache entry does.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index be6e490c..d90e1341 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -156,6 +156,12 @@ FetchContent_Declare(
         EXCLUDE_FROM_ALL
 )
 
+# CMake >= 4.0 (e.g. the 4.x bundled with Visual Studio 2026) makes any
+# cmake_minimum_required(VERSION < 3.5) a fatal error. Some fetched dependencies still
+# declare such old floors (libzmq: 3.0.2), so raise the policy-version floor for the
+# FetchContent subprojects. Ignored (harmless) on CMake < 3.30, which lacks this variable.
+SET(CMAKE_POLICY_VERSION_MINIMUM 3.5)
+
 # libzmq must be made available BEFORE sls_detector_package for the override above to take effect.
 FetchContent_MakeAvailable(libzmq)
 FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
-- 
2.52.0


From 0585fab9bfad4f8146a916431968d4ab3216c1d4 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 20:17:31 +0200
Subject: [PATCH 141/228] cmake: don't fetch sls/catch2 in a viewer-only build

Under JFJOCH_VIEWER_ONLY, only the viewer's transitive deps are built, so
sls_detector_package (detector_control/receiver) and catch2 (tests) are
never used -- and sls does not configure under MSVC, which is the whole
point of the viewer-only mode. Skip fetching just those two; zstd, hdf5,
spdlog, libzmq and httplib are still required (JFJochReader links httplib).

Verified: cmake -DJFJOCH_VIEWER_ONLY=ON configures with sls/catch2 absent
and `make jfjoch_viewer` still links.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d90e1341..c8828ad7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -164,7 +164,14 @@ SET(CMAKE_POLICY_VERSION_MINIMUM 3.5)
 
 # libzmq must be made available BEFORE sls_detector_package for the override above to take effect.
 FetchContent_MakeAvailable(libzmq)
-FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
+IF (JFJOCH_VIEWER_ONLY)
+    # A viewer-only build still needs zstd/hdf5/spdlog/httplib (JFJochReader uses httplib).
+    # Only sls_detector_package (detector) and catch2 (tests) are not built here -- and sls
+    # in particular does not configure under MSVC -- so skip just those two.
+    FetchContent_MakeAvailable(zstd hdf5 spdlog httplib)
+ELSE()
+    FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
+ENDIF()
 
 IF (JFJOCH_VIEWER_ONLY)
     # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
-- 
2.52.0


From fcbe19103d173f74613f24d8410532b923403c7c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 22:02:19 +0200
Subject: [PATCH 142/228] Update to most recent bitshuffle version

---
 compression/bitshuffle/bitshuffle.c           |  19 ++-
 compression/bitshuffle/bitshuffle.h           |  12 +-
 compression/bitshuffle/bitshuffle_core.c      | 123 ++++++++++++------
 compression/bitshuffle/bitshuffle_core.h      |   2 +-
 compression/bitshuffle/bitshuffle_internals.h |  10 +-
 compression/bitshuffle/bshuf_h5filter.c       |  34 ++---
 compression/bitshuffle/bshuf_h5filter.h       |   6 +-
 compression/bitshuffle/iochain.c              |   5 +-
 compression/bitshuffle/iochain.h              |   7 +-
 9 files changed, 127 insertions(+), 91 deletions(-)

diff --git a/compression/bitshuffle/bitshuffle.c b/compression/bitshuffle/bitshuffle.c
index 4fdb25db..dc61bdc7 100644
--- a/compression/bitshuffle/bitshuffle.c
+++ b/compression/bitshuffle/bitshuffle.c
@@ -2,7 +2,7 @@
  * Bitshuffle - Filter for improving compression of typed binary data.
  *
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -23,12 +23,17 @@
 
 
 // Macros.
-#define CHECK_ERR_FREE_LZ(count, buf) if (count < 0) {                      \
-    free(buf); return count - 1000; }
+#define CHECK_ERR_FREE_LZ(count, buf)   \
+        do {                            \
+            if ((count) < 0) {          \
+                free(buf);              \
+                return (count) - 1000;  \
+            }                           \
+        } while (0)
 
 
 /* Bitshuffle and compress a single block. */
-int64_t bshuf_compress_lz4_block(ioc_chain *C_ptr, \
+int64_t bshuf_compress_lz4_block(ioc_chain *C_ptr,
         const size_t size, const size_t elem_size, const int option) {
 
     int64_t nbytes, count;
@@ -115,7 +120,7 @@ int64_t bshuf_decompress_lz4_block(ioc_chain *C_ptr,
 
 #ifdef ZSTD_SUPPORT
 /* Bitshuffle and compress a single block. */
-int64_t bshuf_compress_zstd_block(ioc_chain *C_ptr, \
+int64_t bshuf_compress_zstd_block(ioc_chain *C_ptr,
         const size_t size, const size_t elem_size, const int comp_lvl) {
 
     int64_t nbytes, count;
@@ -182,14 +187,14 @@ int64_t bshuf_decompress_zstd_block(ioc_chain *C_ptr,
     tmp_buf = malloc(size * elem_size);
     if (tmp_buf == NULL) return -1;
 
-    nbytes = ZSTD_decompress(tmp_buf, size * elem_size, in + 4, nbytes_from_header);
+    nbytes = ZSTD_decompress(tmp_buf, size * elem_size, (void *)((char *) in + 4), nbytes_from_header);
     CHECK_ERR_FREE_LZ(nbytes, tmp_buf);
     if (nbytes != size * elem_size) {
         free(tmp_buf);
         return -91;
     }
-    nbytes = nbytes_from_header;
 
+    nbytes = nbytes_from_header;
     count = bshuf_untrans_bit_elem(tmp_buf, out, size, elem_size);
     CHECK_ERR_FREE(count, tmp_buf);
     nbytes += 4;
diff --git a/compression/bitshuffle/bitshuffle.h b/compression/bitshuffle/bitshuffle.h
index b273a3e0..f8e5b8f2 100644
--- a/compression/bitshuffle/bitshuffle.h
+++ b/compression/bitshuffle/bitshuffle.h
@@ -3,7 +3,7 @@
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -98,11 +98,6 @@ int64_t bshuf_compress_lz4(const void* in, void* out, const size_t size, const s
  * To properly unshuffle bitshuffled data, *size*, *elem_size* and *block_size*
  * must patch the parameters used to compress the data.
  *
- * NOT TO BE USED WITH UNTRUSTED DATA: This routine uses the function
- * LZ4_decompress_fast from LZ4, which does not protect against maliciously
- * formed datasets. By modifying the compressed data, this function could be
- * coerced into leaving the boundaries of the input buffer.
- *
  * Parameters
  * ----------
  *  in : input buffer
@@ -184,11 +179,6 @@ int64_t bshuf_compress_zstd(const void* in, void* out, const size_t size, const
  * To properly unshuffle bitshuffled data, *size*, *elem_size* and *block_size*
  * must patch the parameters used to compress the data.
  *
- * NOT TO BE USED WITH UNTRUSTED DATA: This routine uses the function
- * ZSTD_decompress_fast from ZSTD, which does not protect against maliciously
- * formed datasets. By modifying the compressed data, this function could be
- * coerced into leaving the boundaries of the input buffer.
- *
  * Parameters
  * ----------
  *  in : input buffer
diff --git a/compression/bitshuffle/bitshuffle_core.c b/compression/bitshuffle/bitshuffle_core.c
index ba41473f..24621627 100644
--- a/compression/bitshuffle/bitshuffle_core.c
+++ b/compression/bitshuffle/bitshuffle_core.c
@@ -2,7 +2,7 @@
  * Bitshuffle - Filter for improving compression of typed binary data.
  *
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -49,8 +49,14 @@ typedef int64_t omp_size_t;
 typedef size_t omp_size_t;
 #endif
 
+#if defined(_MSC_VER)
+  typedef uint16_t alias_uint16_t;
+#else
+  typedef uint16_t alias_uint16_t __attribute__((may_alias));
+#endif
+
 // Macros.
-#define CHECK_MULT_EIGHT(n) if (n % 8) return -80;
+#define CHECK_MULT_EIGHT(n) do { if ((n) % 8) return -80; } while (0)
 #define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
 
 
@@ -309,7 +315,7 @@ int64_t bshuf_trans_byte_bitrow_scal(const void* in, void* out, const size_t siz
     for (jj = 0; jj < elem_size; jj++) {
         for (ii = 0; ii < nbyte_row; ii++) {
             for (kk = 0; kk < 8; kk++) {
-                out_b[ii * 8 * elem_size + jj * 8 + kk] = \
+                out_b[ii * 8 * elem_size + jj * 8 + kk] =
                         in_b[(jj * 8 + kk) * nbyte_row + ii];
             }
         }
@@ -319,7 +325,7 @@ int64_t bshuf_trans_byte_bitrow_scal(const void* in, void* out, const size_t siz
 
 
 /* Shuffle bits within the bytes of eight element blocks. */
-int64_t bshuf_shuffle_bit_eightelem_scal(const void* in, void* out, \
+int64_t bshuf_shuffle_bit_eightelem_scal(const void* in, void* out,
         const size_t size, const size_t elem_size) {
 
     const char *in_b;
@@ -605,44 +611,59 @@ int64_t bshuf_trans_byte_elem_NEON(const void* in, void* out, const size_t size,
     }
 }
 
-
-/* Creates a mask made up of the most significant
- * bit of each byte of 'input'
- */
-int32_t move_byte_mask_neon(uint8x16_t input) {
-
-    return (  ((input[0] & 0x80) >> 7)          | (((input[1] & 0x80) >> 7) << 1)   | (((input[2] & 0x80) >> 7) << 2)   | (((input[3] & 0x80) >> 7) << 3)
-            | (((input[4] & 0x80) >> 7) << 4)   | (((input[5] & 0x80) >> 7) << 5)   | (((input[6] & 0x80) >> 7) << 6)   | (((input[7] & 0x80) >> 7) << 7)
-            | (((input[8] & 0x80) >> 7) << 8)   | (((input[9] & 0x80) >> 7) << 9)   | (((input[10] & 0x80) >> 7) << 10) | (((input[11] & 0x80) >> 7) << 11)
-            | (((input[12] & 0x80) >> 7) << 12) | (((input[13] & 0x80) >> 7) << 13) | (((input[14] & 0x80) >> 7) << 14) | (((input[15] & 0x80) >> 7) << 15)
-           );
+uint64_t neonmovemask_bulk(uint8x16_t p0, uint8x16_t p1, uint8x16_t p2, uint8x16_t p3) {
+  const uint8x16_t bitmask = { 0x01, 0x02, 0x4, 0x8, 0x10, 0x20, 0x40, 0x80,
+                               0x01, 0x02, 0x4, 0x8, 0x10, 0x20, 0x40, 0x80};
+  uint8x16_t t0 = vandq_u8(p0, bitmask);
+  uint8x16_t t1 = vandq_u8(p1, bitmask);
+  uint8x16_t t2 = vandq_u8(p2, bitmask);
+  uint8x16_t t3 = vandq_u8(p3, bitmask);
+  uint8x16_t sum0 = vpaddq_u8(t0, t1);
+  uint8x16_t sum1 = vpaddq_u8(t2, t3);
+  sum0 = vpaddq_u8(sum0, sum1);
+  sum0 = vpaddq_u8(sum0, sum0);
+  return vgetq_lane_u64(vreinterpretq_u64_u8(sum0), 0);
 }
 
 /* Transpose bits within bytes. */
 int64_t bshuf_trans_bit_byte_NEON(const void* in, void* out, const size_t size,
          const size_t elem_size) {
 
-    size_t ii, kk;
+    size_t ii;
     const char* in_b = (const char*) in;
     char* out_b = (char*) out;
-    uint16_t* out_ui16;
-
     int64_t count;
-
     size_t nbyte = elem_size * size;
 
     CHECK_MULT_EIGHT(nbyte);
 
-    int16x8_t xmm;
-    int32_t bt;
+    const uint8x16_t a0 = vdupq_n_u8(0x80);
+    const uint8x16_t a1 = vdupq_n_u8(0x40);
+    const uint8x16_t a2 = vdupq_n_u8(0x20);
+    const uint8x16_t a3 = vdupq_n_u8(0x10);
+    const uint8x16_t a4 = vdupq_n_u8(0x8);
+    const uint8x16_t a5 = vdupq_n_u8(0x4);
+    const uint8x16_t a6 = vdupq_n_u8(0x2);
+    const uint8x16_t a7 = vdupq_n_u8(0x1);
 
     for (ii = 0; ii + 15 < nbyte; ii += 16) {
-        xmm = vld1q_s16((int16_t *) (in_b + ii));
+        uint8x16_t x = vld1q_u8((uint8_t *) (in_b + ii));
+        uint8x16_t x0 = vceqq_u8(a0, vandq_u8(x, a0));
+        uint8x16_t x1 = vceqq_u8(a1, vandq_u8(x, a1));
+        uint8x16_t x2 = vceqq_u8(a2, vandq_u8(x, a2));
+        uint8x16_t x3 = vceqq_u8(a3, vandq_u8(x, a3));
+        uint8x16_t x4 = vceqq_u8(a4, vandq_u8(x, a4));
+        uint8x16_t x5 = vceqq_u8(a5, vandq_u8(x, a5));
+        uint8x16_t x6 = vceqq_u8(a6, vandq_u8(x, a6));
+        uint8x16_t x7 = vceqq_u8(a7, vandq_u8(x, a7));
+
+        uint64_t out[2];
+        out[0] = neonmovemask_bulk(x0, x1, x2, x3);
+        out[1] = neonmovemask_bulk(x4, x5, x6, x7);
+        int kk;
         for (kk = 0; kk < 8; kk++) {
-            bt = move_byte_mask_neon((uint8x16_t) xmm);
-            xmm = vshlq_n_s16(xmm, 1);
-            out_ui16 = (uint16_t*) &out_b[((7 - kk) * nbyte + ii) / 8];
-            *out_ui16 = bt;
+            alias_uint16_t *out_ui16 = (uint16_t*) &out_b[((7 - kk) * nbyte + ii) / 8];
+            *out_ui16 = ((alias_uint16_t*)out)[kk];
         }
     }
     count = bshuf_trans_bit_byte_remainder(in, out, size, elem_size,
@@ -780,26 +801,42 @@ int64_t bshuf_shuffle_bit_eightelem_NEON(const void* in, void* out, const size_t
     // With a bit of care, this could be written such that such that it is
     // in_buf = out_buf safe.
     const char* in_b = (const char*) in;
-    uint16_t* out_ui16 = (uint16_t*) out;
+    alias_uint16_t* out_ui16 = (alias_uint16_t*) out;
 
     size_t ii, jj, kk;
     size_t nbyte = elem_size * size;
 
-    int16x8_t xmm;
-    int32_t bt;
-
     if (elem_size % 2) {
         bshuf_shuffle_bit_eightelem_scal(in, out, size, elem_size);
     } else {
+        const uint8x16_t a0 = vdupq_n_u8(0x80);
+        const uint8x16_t a1 = vdupq_n_u8(0x40);
+        const uint8x16_t a2 = vdupq_n_u8(0x20);
+        const uint8x16_t a3 = vdupq_n_u8(0x10);
+        const uint8x16_t a4 = vdupq_n_u8(0x8);
+        const uint8x16_t a5 = vdupq_n_u8(0x4);
+        const uint8x16_t a6 = vdupq_n_u8(0x2);
+        const uint8x16_t a7 = vdupq_n_u8(0x1);
         for (ii = 0; ii + 8 * elem_size - 1 < nbyte;
                 ii += 8 * elem_size) {
             for (jj = 0; jj + 15 < 8 * elem_size; jj += 16) {
-                xmm = vld1q_s16((int16_t *) &in_b[ii + jj]);
+                uint8x16_t x = vld1q_u8((uint8_t *) &in_b[ii + jj]);
+                uint8x16_t x0 = vceqq_u8(a0, vandq_u8(x, a0));
+                uint8x16_t x1 = vceqq_u8(a1, vandq_u8(x, a1));
+                uint8x16_t x2 = vceqq_u8(a2, vandq_u8(x, a2));
+                uint8x16_t x3 = vceqq_u8(a3, vandq_u8(x, a3));
+                uint8x16_t x4 = vceqq_u8(a4, vandq_u8(x, a4));
+                uint8x16_t x5 = vceqq_u8(a5, vandq_u8(x, a5));
+                uint8x16_t x6 = vceqq_u8(a6, vandq_u8(x, a6));
+                uint8x16_t x7 = vceqq_u8(a7, vandq_u8(x, a7));
+
+                uint64_t out[2];
+                out[0] = neonmovemask_bulk(x0, x1, x2, x3);
+                out[1] = neonmovemask_bulk(x4, x5, x6, x7);
+
                 for (kk = 0; kk < 8; kk++) {
-                    bt = move_byte_mask_neon((uint8x16_t) xmm);
-                    xmm = vshlq_n_s16(xmm, 1);
                     size_t ind = (ii + jj / 8 + (7 - kk) * elem_size);
-                    out_ui16[ind / 2] = bt;
+                    out_ui16[ind / 2] = ((alias_uint16_t *)out)[kk];
                 }
             }
         }
@@ -890,7 +927,7 @@ int64_t bshuf_shuffle_bit_eightelem_NEON(const void* in, void* out, const size_t
 /* ---- Worker code that uses SSE2 ----
  *
  * The following code makes use of the SSE2 instruction set and specialized
- * 16 byte registers. The SSE2 instructions are present on modern x86 
+ * 16 byte registers. The SSE2 instructions are present on modern x86
  * processors. The first Intel processor microarchitecture supporting SSE2 was
  * Pentium 4 (2000).
  *
@@ -1114,7 +1151,7 @@ int64_t bshuf_trans_bit_byte_SSE(const void* in, void* out, const size_t size,
     size_t ii, kk;
     const char* in_b = (const char*) in;
     char* out_b = (char*) out;
-    uint16_t* out_ui16;
+    alias_uint16_t* out_ui16;
 
     int64_t count;
 
@@ -1130,7 +1167,7 @@ int64_t bshuf_trans_bit_byte_SSE(const void* in, void* out, const size_t size,
         for (kk = 0; kk < 8; kk++) {
             bt = _mm_movemask_epi8(xmm);
             xmm = _mm_slli_epi16(xmm, 1);
-            out_ui16 = (uint16_t*) &out_b[((7 - kk) * nbyte + ii) / 8];
+            out_ui16 = (alias_uint16_t*) &out_b[((7 - kk) * nbyte + ii) / 8];
             *out_ui16 = bt;
         }
     }
@@ -1795,7 +1832,7 @@ int64_t bshuf_untrans_bit_elem_AVX512(const void* in, void* out, const size_t si
 
 /* ---- Drivers selecting best instruction set at compile time. ---- */
 
-int64_t bshuf_trans_bit_elem(const void* in, void* out, const size_t size, 
+int64_t bshuf_trans_bit_elem(const void* in, void* out, const size_t size,
         const size_t elem_size) {
 
     int64_t count;
@@ -1814,7 +1851,7 @@ int64_t bshuf_trans_bit_elem(const void* in, void* out, const size_t size,
 }
 
 
-int64_t bshuf_untrans_bit_elem(const void* in, void* out, const size_t size, 
+int64_t bshuf_untrans_bit_elem(const void* in, void* out, const size_t size,
         const size_t elem_size) {
 
     int64_t count;
@@ -1837,7 +1874,7 @@ int64_t bshuf_untrans_bit_elem(const void* in, void* out, const size_t size,
 
 /* Wrap a function for processing a single block to process an entire buffer in
  * parallel. */
-int64_t bshuf_blocked_wrap_fun(bshufBlockFunDef fun, const void* in, void* out, \
+int64_t bshuf_blocked_wrap_fun(bshufBlockFunDef fun, const void* in, void* out,
         const size_t size, const size_t elem_size, size_t block_size, const int option) {
 
     omp_size_t ii = 0;
@@ -1895,7 +1932,7 @@ int64_t bshuf_blocked_wrap_fun(bshufBlockFunDef fun, const void* in, void* out,
 
 
 /* Bitshuffle a single block. */
-int64_t bshuf_bitshuffle_block(ioc_chain *C_ptr, \
+int64_t bshuf_bitshuffle_block(ioc_chain *C_ptr,
         const size_t size, const size_t elem_size, const int option) {
 
     size_t this_iter;
@@ -1904,7 +1941,7 @@ int64_t bshuf_bitshuffle_block(ioc_chain *C_ptr, \
     int64_t count;
 
 
-    
+
     in = ioc_get_in(C_ptr, &this_iter);
     ioc_set_next_in(C_ptr, &this_iter,
             (void*) ((char*) in + size * elem_size));
@@ -1918,7 +1955,7 @@ int64_t bshuf_bitshuffle_block(ioc_chain *C_ptr, \
 
 
 /* Bitunshuffle a single block. */
-int64_t bshuf_bitunshuffle_block(ioc_chain* C_ptr, \
+int64_t bshuf_bitunshuffle_block(ioc_chain* C_ptr,
         const size_t size, const size_t elem_size, const int option) {
 
 
diff --git a/compression/bitshuffle/bitshuffle_core.h b/compression/bitshuffle/bitshuffle_core.h
index af09b1c4..13630225 100644
--- a/compression/bitshuffle/bitshuffle_core.h
+++ b/compression/bitshuffle/bitshuffle_core.h
@@ -3,7 +3,7 @@
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
diff --git a/compression/bitshuffle/bitshuffle_internals.h b/compression/bitshuffle/bitshuffle_internals.h
index 59356f10..74e05676 100644
--- a/compression/bitshuffle/bitshuffle_internals.h
+++ b/compression/bitshuffle/bitshuffle_internals.h
@@ -3,7 +3,7 @@
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -38,7 +38,13 @@
 
 
 // Macros.
-#define CHECK_ERR_FREE(count, buf) if (count < 0) { free(buf); return count; }
+#define CHECK_ERR_FREE(count, buf) \
+        do {                       \
+            if ((count) < 0) {     \
+                free(buf);         \
+                return (count);    \
+            }                      \
+        } while (0)
 
 
 #ifdef __cplusplus
diff --git a/compression/bitshuffle/bshuf_h5filter.c b/compression/bitshuffle/bshuf_h5filter.c
index acb86e55..7a5e68ae 100644
--- a/compression/bitshuffle/bshuf_h5filter.c
+++ b/compression/bitshuffle/bshuf_h5filter.c
@@ -3,7 +3,7 @@
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -25,7 +25,7 @@ void bshuf_write_uint32_BE(void* buf, uint32_t num);
 uint32_t bshuf_read_uint32_BE(const void* buf);
 
 
-// Only called on compresion, not on reverse.
+// Only called on compression, not on reverse.
 herr_t bshuf_h5_set_local(hid_t dcpl, hid_t type, hid_t space){
 
     herr_t r;
@@ -56,7 +56,7 @@ herr_t bshuf_h5_set_local(hid_t dcpl, hid_t type, hid_t space){
 
     elem_size = H5Tget_size(type);
     if(elem_size <= 0) {
-        PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK, 
+        PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK,
                 "Invalid element size.");
         return -1;
     }
@@ -83,7 +83,7 @@ herr_t bshuf_h5_set_local(hid_t dcpl, hid_t type, hid_t space){
                 break;
             #endif
             default:
-                PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK, 
+                PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK,
                          "Invalid bitshuffle compression.");
         }
     }
@@ -108,23 +108,23 @@ size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
     void *out_buf;
 
     if (cd_nelmts < 3) {
-        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK,
                 "Not enough parameters.");
         return 0;
     }
     elem_size = cd_values[2];
 #ifdef ZSTD_SUPPORT
-    const unsigned int comp_lvl = (cd_nelmts > 5) ? cd_values[5] : 0;
+    const int comp_lvl = cd_values[5];
 #endif
 
     // User specified block size.
     if (cd_nelmts > 3) block_size = cd_values[3];
 
     if (block_size == 0) block_size = bshuf_default_block_size(elem_size);
-    
+
 #ifndef ZSTD_SUPPORT
     if (cd_nelmts > 4 && (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD)) {
-        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK,
                 "ZSTD compression filter chosen but ZSTD support not installed.");
         return 0;
     }
@@ -145,12 +145,12 @@ size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
             nbytes_uncomp = nbytes;
             // Pick which compressions library to use
             if(cd_values[4] == BSHUF_H5_COMPRESS_LZ4) {
-              buf_size_out = bshuf_compress_lz4_bound(nbytes_uncomp / elem_size, 
+              buf_size_out = bshuf_compress_lz4_bound(nbytes_uncomp / elem_size,
                   elem_size, block_size) + 12;
             }
 #ifdef ZSTD_SUPPORT
             else if (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD) {
-              buf_size_out = bshuf_compress_zstd_bound(nbytes_uncomp / elem_size, 
+              buf_size_out = bshuf_compress_zstd_bound(nbytes_uncomp / elem_size,
                   elem_size, block_size) + 12;
             }
 #endif
@@ -162,7 +162,7 @@ size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
 
     // TODO, remove this restriction by memcopying the extra.
     if (nbytes_uncomp % elem_size) {
-        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK,
                 "Non integer number of elements.");
         return 0;
     }
@@ -170,7 +170,7 @@ size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
 
     out_buf = malloc(buf_size_out);
     if (out_buf == NULL) {
-        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK,
                 "Could not allocate output buffer.");
         return 0;
     }
@@ -191,24 +191,24 @@ size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
         } else {
             // Bit shuffle/compress.
             // Write the header, described in
-            // http://www.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
-            // Techincally we should be using signed integers instead of
+            // https://support.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
+            // Technically we should be using signed integers instead of
             // unsigned ones, however for valid inputs (positive numbers) these
             // have the same representation.
             bshuf_write_uint64_BE(out_buf, nbytes_uncomp);
             bshuf_write_uint32_BE((char*) out_buf + 8, block_size * elem_size);
             if(cd_values[4] == BSHUF_H5_COMPRESS_LZ4) {
                 err = bshuf_compress_lz4(in_buf, (char*) out_buf + 12, size,
-                        elem_size, block_size); 
+                        elem_size, block_size);
             }
 #ifdef ZSTD_SUPPORT
             else if (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD) {
                 err = bshuf_compress_zstd(in_buf, (char*) out_buf + 12, size,
-                        elem_size, block_size, comp_lvl); 
+                        elem_size, block_size, comp_lvl);
             }
 #endif
             nbytes_out = err + 12;
-        } 
+        }
     } else {
             if (flags & H5Z_FLAG_REVERSE) {
             // Bit unshuffle.
diff --git a/compression/bitshuffle/bshuf_h5filter.h b/compression/bitshuffle/bshuf_h5filter.h
index 54ee6775..69a64ccf 100644
--- a/compression/bitshuffle/bshuf_h5filter.h
+++ b/compression/bitshuffle/bshuf_h5filter.h
@@ -3,7 +3,7 @@
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -13,7 +13,7 @@
  *
  * Filter Options
  * --------------
- *  block_size (option slot 0) : interger (optional)
+ *  block_size (option slot 0) : integer (optional)
  *      What block size to use (in elements not bytes). Default is 0,
  *      for which bitshuffle will pick a block size with a target of 8kb.
  *  Compression (option slot 1) : 0 or BSHUF_H5_COMPRESS_LZ4
@@ -24,7 +24,7 @@
  *
  *      For LZ4 compression, the compressed format of the data is the same as
  *      for the normal LZ4 filter described in
- *      http://www.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
+ *      https://support.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
  *
  */
 
diff --git a/compression/bitshuffle/iochain.c b/compression/bitshuffle/iochain.c
index baa97296..1822c439 100644
--- a/compression/bitshuffle/iochain.c
+++ b/compression/bitshuffle/iochain.c
@@ -1,9 +1,9 @@
 /*
- * IOchain - Distribute a chain of dependant IO events amoung threads.
+ * IOchain - Distribute a chain of dependent IO events among threads.
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -87,4 +87,3 @@ void ioc_set_next_out(ioc_chain *C, size_t *this_iter, void* out_ptr) {
     omp_unset_lock(&(C->in_pl[(*this_iter) % IOC_SIZE].lock));
 #endif
 }
-
diff --git a/compression/bitshuffle/iochain.h b/compression/bitshuffle/iochain.h
index 4e225d1b..d6923f89 100644
--- a/compression/bitshuffle/iochain.h
+++ b/compression/bitshuffle/iochain.h
@@ -1,9 +1,9 @@
 /*
- * IOchain - Distribute a chain of dependant IO events amoung threads.
+ * IOchain - Distribute a chain of dependent IO events among threads.
  *
  * This file is part of Bitshuffle
  * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
- * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Website: https://www.github.com/kiyo-masui/bitshuffle
  * Created: 2014
  *
  * See LICENSE file for details about copyright and rights to use.
@@ -25,7 +25,7 @@
  * Usage
  * -----
  *  - Call `ioc_init` in serial block.
- *  - Each thread should create a local variable *size_t this_iter* and 
+ *  - Each thread should create a local variable *size_t this_iter* and
  *    pass its address to all function calls. Its value will be set
  *    inside the functions and is used to identify the thread.
  *  - Each thread must call each of the `ioc_get*` and `ioc_set*` methods
@@ -91,4 +91,3 @@ void * ioc_get_out(ioc_chain *C, size_t *this_iter);
 void ioc_set_next_out(ioc_chain *C, size_t *this_iter, void* out_ptr);
 
 #endif  // IOCHAIN_H
-
-- 
2.52.0


From 0220c6376dfe425f8e0cd6c606cf369e336b6544 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 22:16:05 +0200
Subject: [PATCH 143/228] cmake: fetch libtiff and FFTW instead of relying on
 system libs

Both are leaf deps (JFJochPreview / JFJochIndexing) that only our own code
looks for, so building them ourselves removes the system-package lottery and
gives a reproducible, statically-linked build on every platform.

- libtiff: FetchContent, library only (jbig/zstd/lzma/jpeg/old-jpeg/tools/
  tests off). The C++ binding (TIFF::CXX / libtiffxx) is packaged
  inconsistently across distros -- missing on Rocky 9 -- and absent on
  Windows, so find_package(TIFF COMPONENTS CXX) was unreliable; that call is
  removed and JFJochPreview links the tiff/tiffxx targets directly. GitHub
  mirror because upstream (gitlab) is unreachable from some restricted hosts.
- FFTW: FetchContent single precision (ENABLE_FLOAT) from the release tarball
  -- the git repo ships no pre-generated codelets (needs OCaml genfft). It's
  now always available, so the CPU FFT indexer is always built and
  JFJOCH_USE_FFTW always defined; the "FFTW disabled" path is gone. Static
  (libfftw3f.a) via the global BUILD_SHARED_LIBS OFF.

Verified on Linux: jfjoch_viewer builds and links libfftw3f.a + libtiff*.a,
all static.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                         | 37 ++++++++++++++++++++------
 image_analysis/indexing/CMakeLists.txt | 10 +++----
 preview/CMakeLists.txt                 |  3 +--
 viewer/CMakeLists.txt                  |  7 +----
 4 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c8828ad7..8a8fd1b2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -63,14 +63,6 @@ IF (CMAKE_CUDA_COMPILER)
     ENDIF()
 ENDIF()
 
-FIND_LIBRARY(FFTWF_LIBRARY NAMES libfftw3f.a libfftw3f.so fftw3f DOC "FFTW single-precision library"
-        PATHS /usr/lib /usr/lib64 /usr/lib/x86_64-linux-gnu/)
-CHECK_INCLUDE_FILE(fftw3.h HAS_FFTW3_H)
-
-IF(HAS_FFTW3_H AND FFTWF_LIBRARY)
-    ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
-ENDIF()
-
 INCLUDE_DIRECTORIES(include)
 
 include(FetchContent)
@@ -173,6 +165,35 @@ ELSE()
     FetchContent_MakeAvailable(zstd sls_detector_package catch2 hdf5 spdlog httplib)
 ENDIF()
 
+# libtiff (used by JFJochPreview in every build mode): build it ourselves. Its C++ binding
+# (tiffxx) is packaged inconsistently across distros (missing on Rocky 9) and absent on
+# Windows. Library only; the SET()s below are libtiff's own codec/tool switches. The GitHub
+# mirror is used because upstream (gitlab) is unreachable from some restricted build hosts.
+SET(jbig OFF)
+SET(zstd OFF)
+SET(lzma OFF)
+SET(jpeg OFF)
+SET(old-jpeg OFF)
+SET(tiff-tools OFF)
+SET(tiff-tests OFF)
+FetchContent_Declare(tiff
+        GIT_REPOSITORY https://github.com/fleon-psi/libtiff
+        GIT_TAG v4.6.0
+        EXCLUDE_FROM_ALL)
+FetchContent_MakeAvailable(tiff)
+
+# FFTW single precision (target fftw3f): the CPU fallback indexer, enables JFJOCH_USE_FFTW.
+# Built from the release tarball -- the git repo ships no pre-generated codelets (needs the
+# OCaml genfft). It's a fallback, so no aggressive SIMD tuning (plain scalar build is fine).
+SET(ENABLE_FLOAT ON  CACHE BOOL "" FORCE)
+SET(BUILD_TESTS  OFF CACHE BOOL "" FORCE)
+FetchContent_Declare(fftw
+        URL https://www.fftw.org/fftw-3.3.10.tar.gz
+        URL_HASH SHA256=56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467
+        EXCLUDE_FROM_ALL)
+FetchContent_MakeAvailable(fftw)
+ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
+
 IF (JFJOCH_VIEWER_ONLY)
     # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
     # (broker here provides JFJochAPI only; its service targets are gated out.)
diff --git a/image_analysis/indexing/CMakeLists.txt b/image_analysis/indexing/CMakeLists.txt
index f40c1492..159ac0b8 100644
--- a/image_analysis/indexing/CMakeLists.txt
+++ b/image_analysis/indexing/CMakeLists.txt
@@ -39,10 +39,6 @@ ELSE()
     TARGET_LINK_LIBRARIES(JFJochIndexing Eigen3::Eigen)
 ENDIF()
 
-IF(HAS_FFTW3_H AND FFTWF_LIBRARY)
-    TARGET_SOURCES(JFJochIndexing PRIVATE FFTIndexerCPU.cpp FFTIndexerCPU.h)
-    TARGET_LINK_LIBRARIES(JFJochIndexing ${FFTWF_LIBRARY})
-    MESSAGE(STATUS "FFT single-precision library found: ${FFTWF_LIBRARY}")
-ELSE()
-    MESSAGE(WARNING "FFTW disabled")
-ENDIF()
+# FFTW (fftw3f) is always available via FetchContent -> the CPU FFT indexer is always built.
+TARGET_SOURCES(JFJochIndexing PRIVATE FFTIndexerCPU.cpp FFTIndexerCPU.h)
+TARGET_LINK_LIBRARIES(JFJochIndexing fftw3f)
diff --git a/preview/CMakeLists.txt b/preview/CMakeLists.txt
index d73e4379..08477371 100644
--- a/preview/CMakeLists.txt
+++ b/preview/CMakeLists.txt
@@ -2,7 +2,6 @@ include(ExternalProject)
 
 find_package(ZLIB REQUIRED)
 find_package(JPEG REQUIRED)
-find_package(TIFF REQUIRED COMPONENTS CXX)
 
 ADD_LIBRARY(JFJochPreview STATIC
         JFJochTIFF.cpp JFJochTIFF.h
@@ -16,5 +15,5 @@ ADD_LIBRARY(JFJochPreview STATIC
 )
 
 TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JFJochZMQ JFJochCommon CBORStream2FrameSerialize)
-TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JPEG::JPEG TIFF::TIFF TIFF::CXX ZLIB::ZLIB)
+TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JPEG::JPEG tiff tiffxx ZLIB::ZLIB)
 
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 58fc4a8a..b7f0a20e 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -133,9 +133,4 @@ ELSE()
     qt_import_plugins(jfjoch_viewer INCLUDE Qt::QXcbIntegrationPlugin)
 ENDIF()
 
-IF(HAS_FFTW3_H AND FFTWF_LIBRARY)
-    TARGET_LINK_LIBRARIES(jfjoch_viewer ${FFTWF_LIBRARY})
-    MESSAGE(STATUS "FFT single-precision library found: ${FFTWF_LIBRARY}")
-ELSE()
-    MESSAGE(WARNING "FFTW disabled")
-ENDIF()
\ No newline at end of file
+TARGET_LINK_LIBRARIES(jfjoch_viewer fftw3f)
\ No newline at end of file
-- 
2.52.0


From 53645434be32f1c8060c36eed5d0e5c603308353 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 22:37:09 +0200
Subject: [PATCH 144/228] cmake: enable FFTW SSE2/AVX/AVX2 codelets (x86,
 runtime-dispatched)

FFTW selects SIMD codelets at runtime via cpuid, so enabling AVX2 does not
require an AVX2 CPU -- it just speeds up the CPU FFT fallback indexer on
capable hardware and falls back to SSE2/scalar otherwise. Arch-guarded to
x86_64/AMD64 (ARM would need ENABLE_NEON). AVX-512 left off on purpose:
it's x86-64-v4 (not our v3 target), the FFT gain over AVX2 is marginal,
older Intel downclocks on it, and it's the riskiest to build under MSVC.

Verified on Linux: SSE2/AVX/AVX2 codelets compile, libfftw3f.a stays a
single static archive, jfjoch_viewer relinks cleanly.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8a8fd1b2..14e95f43 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -184,9 +184,16 @@ FetchContent_MakeAvailable(tiff)
 
 # FFTW single precision (target fftw3f): the CPU fallback indexer, enables JFJOCH_USE_FFTW.
 # Built from the release tarball -- the git repo ships no pre-generated codelets (needs the
-# OCaml genfft). It's a fallback, so no aggressive SIMD tuning (plain scalar build is fine).
+# OCaml genfft).
 SET(ENABLE_FLOAT ON  CACHE BOOL "" FORCE)
 SET(BUILD_TESTS  OFF CACHE BOOL "" FORCE)
+# SIMD codelets are runtime-dispatched (cpuid), so enabling AVX2 does NOT require an AVX2 CPU
+# -- FFTW falls back at runtime. x86-only, so guard by arch (ARM would use ENABLE_NEON instead).
+IF (CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64|amd64")
+    SET(ENABLE_SSE2 ON CACHE BOOL "" FORCE)
+    SET(ENABLE_AVX  ON CACHE BOOL "" FORCE)
+    SET(ENABLE_AVX2 ON CACHE BOOL "" FORCE)
+ENDIF()
 FetchContent_Declare(fftw
         URL https://www.fftw.org/fftw-3.3.10.tar.gz
         URL_HASH SHA256=56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467
-- 
2.52.0


From 5a6485da3a43401ddde9c5df840867c4e1a3adc0 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 22:47:36 +0200
Subject: [PATCH 145/228] cmake: use upstream libtiff (gitlab) at v4.7.1

Switch the libtiff FetchContent from the personal GitHub mirror to the
upstream gitlab repo and bump v4.6.0 -> v4.7.1 -- cleaner provenance; the
mirror was only ever a network-reachability workaround.

Verified on Linux: fetches, builds static (libtiff.a/libtiffxx.a), and
jfjoch_viewer links cleanly.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 14e95f43..cffdedb7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -167,8 +167,7 @@ ENDIF()
 
 # libtiff (used by JFJochPreview in every build mode): build it ourselves. Its C++ binding
 # (tiffxx) is packaged inconsistently across distros (missing on Rocky 9) and absent on
-# Windows. Library only; the SET()s below are libtiff's own codec/tool switches. The GitHub
-# mirror is used because upstream (gitlab) is unreachable from some restricted build hosts.
+# Windows. Library only; the SET()s below are libtiff's own codec/tool switches.
 SET(jbig OFF)
 SET(zstd OFF)
 SET(lzma OFF)
@@ -177,8 +176,8 @@ SET(old-jpeg OFF)
 SET(tiff-tools OFF)
 SET(tiff-tests OFF)
 FetchContent_Declare(tiff
-        GIT_REPOSITORY https://github.com/fleon-psi/libtiff
-        GIT_TAG v4.6.0
+        GIT_REPOSITORY https://gitlab.com/libtiff/libtiff.git
+        GIT_TAG v4.7.1
         EXCLUDE_FROM_ALL)
 FetchContent_MakeAvailable(tiff)
 
-- 
2.52.0


From c9803ccbfdd67ecbffd45ea186cc64586658cf23 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 22:56:11 +0200
Subject: [PATCH 146/228] Separate JFJochWriter and JFJochStreamWriter

---
 tests/CMakeLists.txt  | 2 +-
 writer/CMakeLists.txt | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index bc6539d3..eb32e313 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -76,7 +76,7 @@ ADD_EXECUTABLE(jfjoch_test
         LatticeReductionTest.cpp
 )
 
-target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochWriter
+target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochStreamWriter
                       JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
                       jfjoch_xds_plugin)
 target_include_directories(jfjoch_test PRIVATE .)
diff --git a/writer/CMakeLists.txt b/writer/CMakeLists.txt
index 95215a06..851b81c5 100644
--- a/writer/CMakeLists.txt
+++ b/writer/CMakeLists.txt
@@ -35,8 +35,11 @@ ADD_LIBRARY(JFJochWriter STATIC
         CBFWriter.h
 )
 
-TARGET_LINK_LIBRARIES(JFJochWriter JFJochPreview JFJochImagePuller JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
+TARGET_LINK_LIBRARIES(JFJochWriter JFJochPreview JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
+
+ADD_LIBRARY(JFJochStreamWriter StreamWriter.cpp StreamWriter.h)
+TARGET_LINK_LIBRARIES(JFJochStreamWriter JFJochWriter JFJochImagePuller)
 
 ADD_EXECUTABLE(jfjoch_writer jfjoch_writer.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_writer JFJochWriter)
+TARGET_LINK_LIBRARIES(jfjoch_writer JFJochStreamWriter)
 INSTALL(TARGETS jfjoch_writer RUNTIME COMPONENT writer)
-- 
2.52.0


From 07ce8b785aa7be74faa9447436ee5ea22bc88eb6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 23:03:07 +0200
Subject: [PATCH 147/228] CMake: Remove image_puller dependency from the
 jfjoch_viewer

---
 CMakeLists.txt              | 1 -
 image_puller/CMakeLists.txt | 2 +-
 viewer/CMakeLists.txt       | 6 +++---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index cffdedb7..649734ff 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -208,7 +208,6 @@ IF (JFJOCH_VIEWER_ONLY)
     ADD_SUBDIRECTORY(common)
     ADD_SUBDIRECTORY(gemmi_gph)
     ADD_SUBDIRECTORY(frame_serialize)
-    ADD_SUBDIRECTORY(image_puller)
     ADD_SUBDIRECTORY(preview)
     ADD_SUBDIRECTORY(writer)
     ADD_SUBDIRECTORY(image_analysis)
diff --git a/image_puller/CMakeLists.txt b/image_puller/CMakeLists.txt
index 24d01ab1..2ac60e68 100644
--- a/image_puller/CMakeLists.txt
+++ b/image_puller/CMakeLists.txt
@@ -5,4 +5,4 @@ ADD_LIBRARY(JFJochImagePuller ZMQImagePuller.cpp ZMQImagePuller.h
         TestImagePuller.h
         TCPImagePuller.cpp
         TCPImagePuller.h)
-TARGET_LINK_LIBRARIES(JFJochImagePuller JFJochCommon JFJochZMQ JFJochLogger)
+TARGET_LINK_LIBRARIES(JFJochImagePuller JFJochCommon JFJochZMQ JFJochLogger CBORStream2FrameSerialize)
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index b7f0a20e..20690708 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -98,7 +98,9 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::Concurrent
         Qt6::OpenGL Qt6::OpenGLWidgets
-        JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis)
+        JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis
+        fftw3f)
+
 INSTALL(TARGETS jfjoch_viewer RUNTIME COMPONENT viewer)
 
 IF(JFJOCH_VIEWER_DBUS)
@@ -132,5 +134,3 @@ ELSEIF(APPLE)
 ELSE()
     qt_import_plugins(jfjoch_viewer INCLUDE Qt::QXcbIntegrationPlugin)
 ENDIF()
-
-TARGET_LINK_LIBRARIES(jfjoch_viewer fftw3f)
\ No newline at end of file
-- 
2.52.0


From ebc28744e2cf40af9de7437003e00ade34d01ba7 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 23:15:27 +0200
Subject: [PATCH 148/228] viewer: fix MSVC compatibility in viewer-reachable
 code

Address portability issues found building jfjoch_viewer with MSVC:

- common/{ADUHistogram,AzimuthalIntegrationProfile}.h and
  image_analysis/spot_finding/StrongPixelSet.h only need DeviceOutput,
  so include fpga/pcie_driver/jfjoch_fpga.h (plain-C, self-contained)
  directly instead of acquisition_device/AcquisitionDevice.h, which
  dragged <unistd.h> into the viewer tree.
- common/time_utc.h: guard gmtime_r/timegm/localtime_r with the MSVC
  equivalents (gmtime_s/_mkgmtime/localtime_s) under _WIN32; drop the
  duplicated includes and add the headers used directly.
- gemmi_gph/gemmi/utf.hpp: vendor the upstream gemmi header; fileutil.hpp
  includes it on Windows for UTF8_to_wchar but it was never vendored.
- writer/HDF5Objects.cpp: ExtractFilename returns path.filename().string()
  (std::filesystem::path has no implicit conversion to std::string on
  Windows, where it is wchar_t-based).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/ADUHistogram.h                        |  2 +-
 common/AzimuthalIntegrationProfile.h         |  2 +-
 common/time_utc.h                            | 22 ++++--
 gemmi_gph/gemmi/utf.hpp                      | 78 ++++++++++++++++++++
 image_analysis/spot_finding/StrongPixelSet.h |  2 +-
 writer/HDF5Objects.cpp                       |  2 +-
 6 files changed, 99 insertions(+), 9 deletions(-)
 create mode 100644 gemmi_gph/gemmi/utf.hpp

diff --git a/common/ADUHistogram.h b/common/ADUHistogram.h
index 2e30d90b..6a42913d 100644
--- a/common/ADUHistogram.h
+++ b/common/ADUHistogram.h
@@ -5,7 +5,7 @@
 
 #include <mutex>
 #include "MultiLinePlot.h"
-#include "../acquisition_device/AcquisitionDevice.h"
+#include "../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 
 class ADUHistogram {
     mutable std::mutex m;
diff --git a/common/AzimuthalIntegrationProfile.h b/common/AzimuthalIntegrationProfile.h
index 90000efb..0fd41524 100644
--- a/common/AzimuthalIntegrationProfile.h
+++ b/common/AzimuthalIntegrationProfile.h
@@ -8,7 +8,7 @@
 #include "MultiLinePlot.h"
 
 #include "AzimuthalIntegrationMapping.h"
-#include "../acquisition_device/AcquisitionDevice.h"
+#include "../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 
 class AzimuthalIntegrationProfile {
     mutable std::mutex m;
diff --git a/common/time_utc.h b/common/time_utc.h
index 4d925929..4a1067ab 100644
--- a/common/time_utc.h
+++ b/common/time_utc.h
@@ -7,10 +7,10 @@
 #include <chrono>
 #include <regex>
 #include <iomanip>
-#include <string>
-#include <chrono>
-#include <regex>
-#include <iomanip>
+#include <sstream>
+#include <stdexcept>
+#include <ctime>
+#include <cstdio>
 
 inline std::string time_UTC(const std::chrono::time_point<std::chrono::system_clock> &input) {
     auto time_ms = std::chrono::duration_cast<std::chrono::milliseconds>(input.time_since_epoch()).count();
@@ -19,8 +19,12 @@ inline std::string time_UTC(const std::chrono::time_point<std::chrono::system_cl
     time_t time = time_ms / (1000);
 
     std::tm tm_utc{};
+#ifdef _WIN32
+    if (gmtime_s(&tm_utc, &time) != 0)
+#else
     if (gmtime_r(&time, &tm_utc) == nullptr)
-        throw std::runtime_error("gmtime_r failed");
+#endif
+        throw std::runtime_error("gmtime failed");
 
     strftime(buf1, sizeof(buf1), "%FT%T", &tm_utc);
     snprintf(buf2, sizeof(buf2), ".%03ld", time_ms % 1000);
@@ -58,7 +62,11 @@ inline uint64_t parse_UTC_to_ms(const std::string& utc_string) {
         milliseconds = std::stoi(frac);
     }
 
+#ifdef _WIN32
+    time_t t = _mkgmtime(&tm);
+#else
     time_t t = timegm(&tm);
+#endif
     return static_cast<uint64_t>(t) * 1000ULL + milliseconds;
 }
 
@@ -71,7 +79,11 @@ inline std::string utc_to_local_human_readable(const std::string& utc_string) {
         time_t t = system_clock::to_time_t(tp);
 
         std::tm tm_local{};
+#ifdef _WIN32
+        if (localtime_s(&tm_local, &t) != 0)
+#else
         if (localtime_r(&t, &tm_local) == nullptr)
+#endif
             return "";
 
         static const char* months[] = {
diff --git a/gemmi_gph/gemmi/utf.hpp b/gemmi_gph/gemmi/utf.hpp
new file mode 100644
index 00000000..2b407419
--- /dev/null
+++ b/gemmi_gph/gemmi/utf.hpp
@@ -0,0 +1,78 @@
+// Copyright 2017 Global Phasing Ltd.
+//
+// Conversion between UTF-8 and wchar. Used only for file names on Windows.
+
+#ifndef GEMMI_UTF_HPP_
+#define GEMMI_UTF_HPP_
+
+#include <string>
+
+namespace gemmi {
+
+// from Mark Ransom's answer
+// https://stackoverflow.com/questions/148403/utf8-to-from-wide-char-conversion-in-stl/148766#148766
+inline std::wstring UTF8_to_wchar(const char* in) {
+  std::wstring out;
+  unsigned int codepoint = 0;
+  while (*in != 0) {
+    unsigned char ch = static_cast<unsigned char>(*in);
+    if (ch <= 0x7f)
+      codepoint = ch;
+    else if (ch <= 0xbf)
+      codepoint = (codepoint << 6) | (ch & 0x3f);
+    else if (ch <= 0xdf)
+      codepoint = ch & 0x1f;
+    else if (ch <= 0xef)
+      codepoint = ch & 0x0f;
+    else
+      codepoint = ch & 0x07;
+    ++in;
+    if ((*in & 0xc0) != 0x80 && codepoint <= 0x10ffff) {
+      if (sizeof(wchar_t) > 2) {
+        out.append(1, static_cast<wchar_t>(codepoint));
+      } else if (codepoint > 0xffff) {
+        out.append(1, static_cast<wchar_t>(0xd800 + (codepoint >> 10)));
+        out.append(1, static_cast<wchar_t>(0xdc00 + (codepoint & 0x03ff)));
+      } else if (codepoint < 0xd800 || codepoint >= 0xe000) {
+        out.append(1, static_cast<wchar_t>(codepoint));
+      }
+    }
+  }
+  return out;
+}
+
+inline std::string wchar_to_UTF8(const wchar_t* in) {
+  std::string out;
+  unsigned int codepoint = 0;
+  while (*in != 0) {
+    if (*in >= 0xd800 && *in <= 0xdbff) {
+      codepoint = ((*in - 0xd800) << 10) + 0x10000;
+    } else {
+      if (*in >= 0xdc00 && *in <= 0xdfff)
+        codepoint |= *in - 0xdc00;
+      else
+        codepoint = *in;
+      if (codepoint <= 0x7f) {
+        out += static_cast<char>(codepoint);
+      } else if (codepoint <= 0x7ff) {
+        out += static_cast<char>(0xc0 | ((codepoint >> 6) & 0x1f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      } else if (codepoint <= 0xffff) {
+        out += static_cast<char>(0xe0 | ((codepoint >> 12) & 0x0f));
+        out += static_cast<char>(0x80 | ((codepoint >> 6) & 0x3f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      } else {
+        out += static_cast<char>(0xf0 | ((codepoint >> 18) & 0x07));
+        out += static_cast<char>(0x80 | ((codepoint >> 12) & 0x3f));
+        out += static_cast<char>(0x80 | ((codepoint >> 6) & 0x3f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      }
+      codepoint = 0;
+    }
+    ++in;
+  }
+  return out;
+}
+
+} // namespace gemmi
+#endif
diff --git a/image_analysis/spot_finding/StrongPixelSet.h b/image_analysis/spot_finding/StrongPixelSet.h
index cbc322da..be242cec 100644
--- a/image_analysis/spot_finding/StrongPixelSet.h
+++ b/image_analysis/spot_finding/StrongPixelSet.h
@@ -5,7 +5,7 @@
 
 #include "../../common/DiffractionExperiment.h"
 #include "../../common/DiffractionSpot.h"
-#include "../../acquisition_device/AcquisitionDevice.h"
+#include "../../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 #include "SpotFindingSettings.h"
 
 struct strong_pixel {
diff --git a/writer/HDF5Objects.cpp b/writer/HDF5Objects.cpp
index e596398e..dc8329ec 100644
--- a/writer/HDF5Objects.cpp
+++ b/writer/HDF5Objects.cpp
@@ -1014,7 +1014,7 @@ CompressionAlgorithm HDF5Dcpl::GetCompression() {
 std::string ExtractFilename(const std::string& str) {
     std::filesystem::path path(str);
     // if (std::filesystem::is_regular_file(path))
-    return path.filename();
+    return path.filename().string();
 }
 
 bool HDF5Object::GetBool(const std::string &name) const {
-- 
2.52.0


From bcd588b400a50c7164e5ace00113f81dcb58266a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 19 Jun 2026 23:15:49 +0200
Subject: [PATCH 149/228] CMake: build StreamWriter only into
 JFJochStreamWriter

StreamWriter.cpp was compiled into both JFJochWriter and JFJochStreamWriter,
so JFJochWriter still transitively pulled in image_puller headers via
StreamWriter.h. Compile it only into JFJochStreamWriter (which already
links JFJochImagePuller); targets needing the streaming writer (jfjoch_writer,
jfjoch_test) link that lib, while JFJochWriter consumers (viewer, tools,
ImagePusher) no longer drag in the puller. Also drop a stray duplicate
HDF5DataFile source listing.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 writer/CMakeLists.txt | 2 --
 1 file changed, 2 deletions(-)

diff --git a/writer/CMakeLists.txt b/writer/CMakeLists.txt
index 851b81c5..94eb4499 100644
--- a/writer/CMakeLists.txt
+++ b/writer/CMakeLists.txt
@@ -11,8 +11,6 @@ ADD_LIBRARY(JFJochWriter STATIC
         HDF5DataFile.h  HDF5DataFile.cpp
         HDF5NXmx.cpp      HDF5NXmx.h
         FileWriter.cpp FileWriter.h
-        StreamWriter.cpp StreamWriter.h
-        HDF5DataFile.h  HDF5DataFile.cpp
         HDF5DataFilePlugin.cpp
         HDF5DataFilePlugin.h
         HDF5DataFilePluginROI.cpp
-- 
2.52.0


From a872b68d6fcebb5bd737c0d7d220206e20a220a5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 06:14:15 +0200
Subject: [PATCH 150/228] ADUHistogram: Fix missing exception header

---
 common/ADUHistogram.cpp | 1 +
 common/ADUHistogram.h   | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/common/ADUHistogram.cpp b/common/ADUHistogram.cpp
index e74d1493..1fa29b5e 100644
--- a/common/ADUHistogram.cpp
+++ b/common/ADUHistogram.cpp
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include "ADUHistogram.h"
+#include "JFJochException.h"
 
 ADUHistogram::ADUHistogram() : histogram(ADU_HISTO_BIN_COUNT) {
 
diff --git a/common/ADUHistogram.h b/common/ADUHistogram.h
index 6a42913d..addb29dc 100644
--- a/common/ADUHistogram.h
+++ b/common/ADUHistogram.h
@@ -3,6 +3,8 @@
 
 #pragma once
 
+#include <cstdint>
+#include <vector>
 #include <mutex>
 #include "MultiLinePlot.h"
 #include "../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
-- 
2.52.0


From b888c535093260e550f1862c44e8433de979840a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:10:04 +0200
Subject: [PATCH 151/228] CMake: stop libtiff/httplib pulling in webp,
 sharpyuv, brotli

libtiff's webp and lerc codec options default ON whenever their library is
found on the build host, dragging in libwebp + libsharpyuv (webp) and libLerc.
We only need DEFLATE (zlib) + the internal LZW codec, so turn both OFF.

httplib likewise auto-enables Brotli content-encoding when system Brotli is
present; gzip/zlib is enough for the broker, so disable it.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 649734ff..4e68e465 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -129,6 +129,9 @@ FetchContent_Declare(
         GIT_TAG v0.39.0
         EXCLUDE_FROM_ALL
 )
+# httplib enables Brotli content-encoding whenever it finds system Brotli; we don't use it
+# (gzip/zlib is enough for the broker), so disable it to avoid linking libbrotli.
+SET(HTTPLIB_USE_BROTLI_IF_AVAILABLE OFF CACHE BOOL "" FORCE)
 
 # ZeroMQ (libzmq): fetch it here, at the top level, so that THIS project - not
 # slsDetectorPackage - controls the version. slsDetectorPackage bundles its own libzmq
@@ -168,11 +171,17 @@ ENDIF()
 # libtiff (used by JFJochPreview in every build mode): build it ourselves. Its C++ binding
 # (tiffxx) is packaged inconsistently across distros (missing on Rocky 9) and absent on
 # Windows. Library only; the SET()s below are libtiff's own codec/tool switches.
+# We only need DEFLATE (zlib) + the internal LZW codec, matching what Python tifffile writes
+# by default. The remaining codecs default to ON whenever their library is found on the build
+# host, so each must be explicitly turned OFF to keep the dependency set minimal -- otherwise
+# webp pulls in libwebp + libsharpyuv and lerc pulls in libLerc.
 SET(jbig OFF)
 SET(zstd OFF)
 SET(lzma OFF)
 SET(jpeg OFF)
 SET(old-jpeg OFF)
+SET(webp OFF)
+SET(lerc OFF)
 SET(tiff-tools OFF)
 SET(tiff-tests OFF)
 FetchContent_Declare(tiff
-- 
2.52.0


From 4a39f2cfcf4260b97436cef6bb7e731989403607 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:15:47 +0200
Subject: [PATCH 152/228] Fix FFTW build-tree header wiring and two MSVC
 warnings

FFTW exposes fftw3.h only via $<INSTALL_INTERFACE:include>, so consuming
fftw3f from the build tree (FetchContent) leaves FFTIndexerCPU.h unable to
find the header. A system-installed fftw3.h masks this on Linux, so it only
bit on Windows; add the source-tree api/ dir to fftw3f's interface includes.

Also two viewer-reachable warnings:
- time_utc.h (C4477): %03ld was fed a chrono milliseconds::rep (64-bit), not
  a long; cast the 0-999 value to int and use %03d.
- HDF5Objects.h (C4700): value-initialize the scalar read buffer.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt       | 4 ++++
 common/time_utc.h    | 2 +-
 writer/HDF5Objects.h | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4e68e465..92702d72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -207,6 +207,10 @@ FetchContent_Declare(fftw
         URL_HASH SHA256=56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467
         EXCLUDE_FROM_ALL)
 FetchContent_MakeAvailable(fftw)
+# FFTW exposes fftw3.h only via $<INSTALL_INTERFACE:include>, so consuming fftw3f straight from
+# the build tree (FetchContent) leaves the header unreachable. On Linux a system-installed
+# fftw3.h masks this; on Windows it does not. Add the source-tree api/ dir for build-tree use.
+TARGET_INCLUDE_DIRECTORIES(fftw3f INTERFACE $<BUILD_INTERFACE:${fftw_SOURCE_DIR}/api>)
 ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 
 IF (JFJOCH_VIEWER_ONLY)
diff --git a/common/time_utc.h b/common/time_utc.h
index 4a1067ab..bec55fd7 100644
--- a/common/time_utc.h
+++ b/common/time_utc.h
@@ -27,7 +27,7 @@ inline std::string time_UTC(const std::chrono::time_point<std::chrono::system_cl
         throw std::runtime_error("gmtime failed");
 
     strftime(buf1, sizeof(buf1), "%FT%T", &tm_utc);
-    snprintf(buf2, sizeof(buf2), ".%03ld", time_ms % 1000);
+    snprintf(buf2, sizeof(buf2), ".%03d", static_cast<int>(time_ms % 1000));
     return std::string(buf1) + std::string(buf2) + "Z";
 }
 
diff --git a/writer/HDF5Objects.h b/writer/HDF5Objects.h
index d4945359..ba085b45 100644
--- a/writer/HDF5Objects.h
+++ b/writer/HDF5Objects.h
@@ -264,7 +264,7 @@ public:
         if (file_space.GetNumOfDimensions() != 0)
             throw JFJochException(JFJochExceptionCategory::HDF5, "Dataset tries to read scalar from vector dataset");;
 
-        T output;
+        T output{};
         if (H5Dread(id, HDF5DataType(output).GetID(), mem_space.GetID(), H5S_ALL, H5P_DEFAULT, &output) < 0)
             throw JFJochException(JFJochExceptionCategory::HDF5, dataset_name + ": read unsuccessful");
         return output;
-- 
2.52.0


From 025c6394b698ea26ec55e7369a1967f40ab13951 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:23:07 +0200
Subject: [PATCH 153/228] reader: fix Windows path handling in JFJochHDF5Reader

Two spots used POSIX-only path logic that breaks on Windows:

- dataset_name() located the basename with rfind('/'), which misses
  backslash separators, so a C:\...\foo_master.h5 file prefix kept the
  whole directory. Use std::filesystem::path::filename() instead.
- Legacy-format data-file resolution joined paths with
  fmt::format("{}/{}", ...), producing mixed \/ separators and prepending
  the master directory even to absolute link targets. Reuse the existing
  ResolveRelativeToMaster() helper, which joins via std::filesystem and
  leaves absolute targets untouched.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHDF5Reader.cpp | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 212aa29a..590d2100 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -125,10 +125,7 @@ std::string removeSuffix(const std::string &s, const std::string &suffix) {
 }
 
 std::string dataset_name(const std::string &path) {
-    std::string file = path;
-    int pos = file.rfind('/');
-    if (pos != std::string::npos)
-        file = file.substr(pos + 1);
+    std::string file = std::filesystem::path(path).filename().string();
     file = removeSuffix(file, "_master.h5");
     // If previous suffix was not found, try removing this one
     file = removeSuffix(file, ".h5");
@@ -400,10 +397,8 @@ void JFJochHDF5Reader::ReadFile(const std::string &filename) {
                 size_t fimages = 0;
 
                 try {
-                    auto fname = master_file->GetLinkedFileName(dname);
-
-                    if (!directory.empty())
-                        fname = fmt::format("{}/{}", directory.string(), fname);
+                    auto fname = ResolveRelativeToMaster(directory.string(),
+                                                         master_file->GetLinkedFileName(dname));
 
                     HDF5ReadOnlyFile data_file(fname);
 
-- 
2.52.0


From 1ae2e6869da75ab1892eacc966d6f07292be3590 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:38:06 +0200
Subject: [PATCH 154/228] CLAUDE.md: record Windows viewer goal of MSVC + CUDA,
 and unbundled deps

The recurring goal is a Windows jfjoch_viewer built with MSVC *and* CUDA ON
(GPU processing is wanted, not a CPU-only fallback); the non-CUDA path is the
macOS fallback. Also note the three deps a self-contained Windows build still
needs but FetchContent does not auto-provide: ZLIB (bundle zlib-ng as
ZLIB::ZLIB), libjpeg-turbo (ExternalProject), and Eigen (header-only, also
needed by Ceres) -- each guarded so the Linux build is unchanged.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CLAUDE.md | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index acc50bcf..f57bc197 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -152,12 +152,26 @@ code, and any shared library it transitively links (`common/`, `image_analysis/`
 project (broker, receiver, FPGA host, detector control, …) is Linux-only and does not need to be
 portable; don't constrain it for portability's sake.
 
-- **Windows/MSVC** is the primary portability target (a Windows viewer build needs MSVC, since
-  CUDA on Windows requires it). Avoid GCC/Clang-only extensions, POSIX-only APIs, and other
-  non-MSVC constructs in viewer-reachable code.
+- **Windows/MSVC** is the primary portability target. The end goal is a Windows viewer built
+  with **MSVC *and* CUDA** (`JFJOCH_USE_CUDA=ON`): GPU processing is a wanted feature, not
+  optional, so the intended Windows config is the full GPU path (`ffbidx`, GPU `fft`), not a
+  CPU-only fallback. MSVC is required regardless, because CUDA on Windows requires it. Avoid
+  GCC/Clang-only extensions, POSIX-only APIs, and other non-MSVC constructs in viewer-reachable
+  code, and keep CUDA-reachable viewer code (`ffbidx`, GPU indexers) MSVC-buildable too.
 - **macOS** is a nice-to-have for the viewer. It rules out CUDA, so anything the viewer depends on
   must also have a working CPU-only / non-CUDA path (the `JFJOCH_USE_CUDA=OFF`, `fftw`-indexer
-  configuration).
+  configuration). This non-CUDA path must keep working, but it is the macOS fallback — *not* the
+  intended Windows configuration.
+
+A self-contained Windows build still needs a few dependencies that the Linux build picks up from
+the system and that are **not** auto-provided via `FetchContent` (besides Qt, supplied
+externally): **ZLIB** (pulled by hdf5/libtiff/gemmi/libzmq — a bundled zlib-ng in `ZLIB_COMPAT`
+mode is the intended fix, presented as the `ZLIB::ZLIB` target so the scattered
+`find_package(ZLIB)` calls resolve), **libjpeg-turbo** (used by `preview/`; upstream discourages
+`add_subdirectory`, so bring it in via `ExternalProject`), and **Eigen** (header-only; needed by
+Ceres, by the analysis libs directly, and by `ffbidx` under CUDA — fetch it and point Ceres'
+internal `find_package(Eigen3)` at it). Wire each guarded so the Linux build, which finds these on
+the system, stays unchanged.
 
 ## OpenAPI is the single source of truth
 
-- 
2.52.0


From 7eb927e82f815eae019bece4f7ac321944614793 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:40:56 +0200
Subject: [PATCH 155/228] CMake: Ensure static ZLIB (must be before
 FIND_PACKAGE)

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 92702d72..4da0a03a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,10 +14,10 @@ SET(JFJOCH_USE_CUDA              ON CACHE BOOL "Compile Jungfraujoch with CUDA")
 SET(JFJOCH_VIEWER_BUILD          OFF CACHE BOOL "Compile Jungfraujoch viewer")
 SET(JFJOCH_VIEWER_ONLY           OFF CACHE BOOL "Compile only jfjoch_viewer and its dependencies")
 
-FIND_PACKAGE(ZLIB REQUIRED)
-
 SET (ZLIB_USE_STATIC_LIBS TRUE)
 
+FIND_PACKAGE(ZLIB REQUIRED)
+
 OPTION(SLS9 "Build with sls_detector_package v9.2.0" OFF)
 
 SET(BUILD_SHARED_LIBS OFF)
-- 
2.52.0


From 4737eff1a97cd168303fedcdfa881c2cfd344d67 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:44:50 +0200
Subject: [PATCH 156/228] jfjoch_process: Missing include <set>

---
 tools/jfjoch_process.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 79702b50..54e32e84 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -15,6 +15,7 @@
 #include <algorithm>
 #include <numeric>
 #include <cmath>
+#include <set>
 
 #include "../reader/JFJochHDF5Reader.h"
 #include "../common/Logger.h"
-- 
2.52.0


From cd394c5249b41fbc210d5aba16751e54c3bce72a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 07:55:56 +0200
Subject: [PATCH 157/228] CMake: vendor Eigen (5.0.1) and libjpeg-turbo so the
 build is self-contained

Two deps the Linux build picked up from the system were absent on Windows.
Bundle both, unconditionally (matching how libtiff/FFTW are vendored), so the
tree builds without system Eigen/JPEG:

- Eigen 5.0.1 via FetchContent with OVERRIDE_FIND_PACKAGE, so every
  find_package(Eigen3) -- ours, Ceres', and ffbidx' -- resolves to this copy and
  the requested 3.4 version is satisfied by the newer major. ffbidx's bundled
  eigen submodule is disabled (GIT_SUBMODULES "" on fast-indexer) so it no longer
  creates a duplicate Eigen3::Eigen target. Verified on a CUDA build: Ceres 2.3.0,
  the analysis libs, and ffbidx's CUDA code all compile against 5.0.1.

- libjpeg-turbo 3.0.4 via ExternalProject (upstream discourages add_subdirectory);
  built+installed static and imported as JPEG::JPEG, replacing find_package(JPEG)
  in preview/. SIMD is lazy: WITH_SIMD=ON + REQUIRE_SIMD=OFF means NASM-accelerated
  when nasm is present, otherwise a warning and a scalar build (no hard failure).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                         | 15 ++++++++
 image_analysis/indexing/CMakeLists.txt |  4 +++
 preview/CMakeLists.txt                 | 47 +++++++++++++++++++++++++-
 3 files changed, 65 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4da0a03a..366e86f9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -213,6 +213,21 @@ FetchContent_MakeAvailable(fftw)
 TARGET_INCLUDE_DIRECTORIES(fftw3f INTERFACE $<BUILD_INTERFACE:${fftw_SOURCE_DIR}/api>)
 ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 
+# Eigen (header-only): consumed by Ceres and by the analysis libs directly, and by ffbidx under
+# CUDA. Not auto-provided by FetchContent and absent on Windows, so vendor it here. OVERRIDE_FIND_PACKAGE
+# routes every find_package(Eigen3) -- ours, Ceres', ffbidx' -- to this copy and bypasses the version
+# request (they ask for 3.4; this is a newer major). ffbidx's own bundled eigen is disabled below
+# (GIT_SUBMODULES "" on fast-indexer) so it does not create a duplicate Eigen3::Eigen target.
+SET(EIGEN_BUILD_DOC OFF CACHE BOOL "" FORCE)
+SET(EIGEN_BUILD_TESTING OFF CACHE BOOL "" FORCE)
+SET(EIGEN_BUILD_PKGCONFIG OFF CACHE BOOL "" FORCE)
+FetchContent_Declare(Eigen3
+        GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+        GIT_TAG 5.0.1
+        GIT_SHALLOW TRUE
+        EXCLUDE_FROM_ALL
+        OVERRIDE_FIND_PACKAGE)
+
 IF (JFJOCH_VIEWER_ONLY)
     # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
     # (broker here provides JFJochAPI only; its service targets are gated out.)
diff --git a/image_analysis/indexing/CMakeLists.txt b/image_analysis/indexing/CMakeLists.txt
index 159ac0b8..6b8dc312 100644
--- a/image_analysis/indexing/CMakeLists.txt
+++ b/image_analysis/indexing/CMakeLists.txt
@@ -19,10 +19,14 @@ ADD_LIBRARY(JFJochIndexing STATIC
 TARGET_LINK_LIBRARIES(JFJochIndexing JFJochCommon JFJochLatticeSearch)
 
 IF (JFJOCH_CUDA_AVAILABLE)
+    # GIT_SUBMODULES "" -> do not fetch ffbidx's bundled eigen submodule; it would add_subdirectory
+    # a second Eigen3::Eigen target. ffbidx instead resolves Eigen via the project-level Eigen3
+    # (OVERRIDE_FIND_PACKAGE in the top-level CMakeLists).
     FetchContent_Declare(
             fast-indexer
             GIT_REPOSITORY https://github.com/paulscherrerinstitute/fast-feedback-indexer/
             GIT_TAG ca9e17486a1eb96319a738acef33cc24c9cd8845
+            GIT_SUBMODULES ""
     )
 
     FetchContent_MakeAvailable(fast-indexer)
diff --git a/preview/CMakeLists.txt b/preview/CMakeLists.txt
index 08477371..20d8f11c 100644
--- a/preview/CMakeLists.txt
+++ b/preview/CMakeLists.txt
@@ -1,7 +1,48 @@
 include(ExternalProject)
 
 find_package(ZLIB REQUIRED)
-find_package(JPEG REQUIRED)
+
+# libjpeg-turbo: upstream does NOT support add_subdirectory/FetchContent inclusion, so build and
+# install it out-of-line and import the static lib. (Adapted from aseprite's FindJpegTurbo.cmake.)
+# The static lib is `jpeg-static.lib` on MSVC and `libjpeg.a` elsewhere.
+IF (MSVC)
+    SET(LIBJPEG_TURBO_STATIC_SUFFIX "-static")
+ELSE()
+    SET(LIBJPEG_TURBO_STATIC_SUFFIX "")
+ENDIF()
+SET(LIBJPEG_TURBO_DIR "${CMAKE_CURRENT_BINARY_DIR}/libjpeg-turbo")
+SET(LIBJPEG_TURBO_LIBRARY "${LIBJPEG_TURBO_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}jpeg${LIBJPEG_TURBO_STATIC_SUFFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
+SET(LIBJPEG_TURBO_INCLUDE_DIRS "${LIBJPEG_TURBO_DIR}/include")
+
+ExternalProject_Add(libjpeg-turbo-project
+        GIT_REPOSITORY https://github.com/libjpeg-turbo/libjpeg-turbo
+        GIT_TAG 3.0.4
+        PREFIX "${LIBJPEG_TURBO_DIR}"
+        INSTALL_DIR "${LIBJPEG_TURBO_DIR}"
+        BUILD_BYPRODUCTS "${LIBJPEG_TURBO_LIBRARY}"
+        CMAKE_CACHE_ARGS
+        -DENABLE_SHARED:BOOL=OFF
+        -DENABLE_STATIC:BOOL=ON
+        -DWITH_ARITH_DEC:BOOL=ON
+        -DWITH_ARITH_ENC:BOOL=ON
+        -DWITH_JPEG8:BOOL=OFF
+        -DWITH_JPEG7:BOOL=OFF
+        -DWITH_TURBOJPEG:BOOL=OFF
+        # Lazy SIMD: use NASM-accelerated SIMD when nasm is present, otherwise warn and build a
+        # scalar libjpeg (REQUIRE_SIMD=OFF is libjpeg-turbo's default; pinned here to be explicit).
+        -DWITH_SIMD:BOOL=ON
+        -DREQUIRE_SIMD:BOOL=OFF
+        -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+        -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
+        -DCMAKE_INSTALL_LIBDIR:PATH=<INSTALL_DIR>/lib)
+
+# Create the include dir up front so setting INTERFACE_INCLUDE_DIRECTORIES below does not fail.
+FILE(MAKE_DIRECTORY ${LIBJPEG_TURBO_INCLUDE_DIRS})
+
+ADD_LIBRARY(JPEG::JPEG STATIC IMPORTED GLOBAL)
+SET_TARGET_PROPERTIES(JPEG::JPEG PROPERTIES
+        IMPORTED_LOCATION "${LIBJPEG_TURBO_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${LIBJPEG_TURBO_INCLUDE_DIRS}")
 
 ADD_LIBRARY(JFJochPreview STATIC
         JFJochTIFF.cpp JFJochTIFF.h
@@ -14,6 +55,10 @@ ADD_LIBRARY(JFJochPreview STATIC
         ZMQMetadataSocket.h
 )
 
+# JPEG::JPEG is an IMPORTED target, so the build-order dependency on the ExternalProject must be
+# attached to the consuming target instead.
+ADD_DEPENDENCIES(JFJochPreview libjpeg-turbo-project)
+
 TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JFJochZMQ JFJochCommon CBORStream2FrameSerialize)
 TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JPEG::JPEG tiff tiffxx ZLIB::ZLIB)
 
-- 
2.52.0


From d4d2d0d8ade27224e0777b6bf2b659ab2973c6ed Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 13:38:46 +0200
Subject: [PATCH 158/228] CMake: fix CI -- export vendored Eigen so Ceres'
 install(EXPORT) resolves

A clean configure failed at generation:
  install(EXPORT "CeresExport" ...) includes target "ceres" which requires
  target "eigen" that is not in any export set.

Ceres' install(EXPORT CeresExport) is unconditional, and its ceres target
transitively links the eigen target. As a FetchContent subproject Eigen leaves
EIGEN_BUILD_CMAKE_PACKAGE OFF (it defaults to PROJECT_IS_TOP_LEVEL), so its
install(EXPORT Eigen3Targets) never runs and eigen ends up in no installed
export set. Force EIGEN_BUILD_CMAKE_PACKAGE ON so eigen is exported and Ceres'
export validates. Install/export-only change; the build is unaffected.

Verified with a clean configure (fresh CMakeCache): configure + generate now
succeed where they previously errored.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 366e86f9..fdaa5546 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -221,6 +221,11 @@ ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 SET(EIGEN_BUILD_DOC OFF CACHE BOOL "" FORCE)
 SET(EIGEN_BUILD_TESTING OFF CACHE BOOL "" FORCE)
 SET(EIGEN_BUILD_PKGCONFIG OFF CACHE BOOL "" FORCE)
+# Ceres' install(EXPORT CeresExport) is unconditional and its ceres target transitively links the
+# eigen target, so eigen must live in an installed export set or generation fails ("eigen is not in
+# any export set"). As a subproject Eigen defaults EIGEN_BUILD_CMAKE_PACKAGE OFF, which skips its
+# install(EXPORT Eigen3Targets); force it ON so eigen is exported and Ceres' export resolves.
+SET(EIGEN_BUILD_CMAKE_PACKAGE ON CACHE BOOL "" FORCE)
 FetchContent_Declare(Eigen3
         GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
         GIT_TAG 5.0.1
-- 
2.52.0


From 31630c20a1433707c1484cd55e5b9c8af853f5b7 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 15:05:40 +0200
Subject: [PATCH 159/228] viewer: macOS .app / Windows GUI packaging + Qt
 deploy + CPack generators

Add the platform packaging the viewer was missing so it can ship as a .dmg
(macOS) or installer (Windows):

- viewer: set MACOSX_BUNDLE (a .app bundle on macOS) and WIN32_EXECUTABLE
  (GUI subsystem, no console window) -- both ignored where they don't apply;
  install with BUNDLE/RUNTIME destinations.
- viewer: qt_generate_deploy_app_script + install(SCRIPT) to bundle the Qt
  runtime at install time (windeployqt on Windows, macdeployqt on macOS).
  Gated on Qt >= 6.5, which is where the OUTPUT_SCRIPT signature and the Linux
  deploy path landed; with a static Qt (our Linux builds) it is a no-op.
- CPack: select DragNDrop (.dmg) on macOS and NSIS on Windows, ahead of the
  Linux-only /etc/* probes; DEB/RPM path unchanged.

Verified: configures + generates cleanly on Linux with the viewer enabled
(Qt 6.4.2 -> deploy step correctly skipped).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt        | 11 +++++++++--
 viewer/CMakeLists.txt | 24 +++++++++++++++++++++++-
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fdaa5546..b1efaa97 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -332,8 +332,15 @@ set(CPACK_PACKAGE_CONTACT "Filip Leonarski <filip.leonarski@psi.ch>")
 set(CPACK_PACKAGE_VENDOR "Paul Scherrer Institut")
 set(CPACK_PACKAGE_VERSION ${JFJOCH_VERSION})
 
-# OS-aware packaging: DEB on Debian/Ubuntu, RPM on RHEL/Rocky
-if (EXISTS "/etc/debian_version")
+# OS-aware packaging: DragNDrop (.dmg) on macOS, NSIS installer on Windows, DEB on Debian/Ubuntu,
+# RPM on RHEL/Rocky. macOS/Windows are checked first because the /etc/* probes below are Linux-only.
+if (APPLE)
+    # .dmg containing jfjoch_viewer.app (Qt runtime already deployed into the bundle).
+    set(CPACK_GENERATOR "DragNDrop")
+elseif (WIN32)
+    # NSIS installer .exe (Qt runtime deployed next to the binary by windeployqt).
+    set(CPACK_GENERATOR "NSIS")
+elseif (EXISTS "/etc/debian_version")
     set(CPACK_PACKAGE_LICENSE "GPL-3.0-only")
     set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
 
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 20690708..f3909025 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -101,7 +101,15 @@ TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts
         JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis
         fftw3f)
 
-INSTALL(TARGETS jfjoch_viewer RUNTIME COMPONENT viewer)
+# Native GUI app per platform: a .app bundle on macOS, GUI subsystem (no console window) on
+# Windows. Each property is ignored on the platforms it does not apply to, so set both always.
+SET_TARGET_PROPERTIES(jfjoch_viewer PROPERTIES
+        MACOSX_BUNDLE    ON
+        WIN32_EXECUTABLE ON)
+
+INSTALL(TARGETS jfjoch_viewer
+        BUNDLE  DESTINATION .   COMPONENT viewer   # macOS .app bundle
+        RUNTIME DESTINATION bin COMPONENT viewer)  # Windows .exe / Linux binary
 
 IF(JFJOCH_VIEWER_DBUS)
     TARGET_SOURCES(jfjoch_viewer PRIVATE dbus/JFJochViewerAdaptor.cpp dbus/JFJochViewerAdaptor.h)
@@ -134,3 +142,17 @@ ELSEIF(APPLE)
 ELSE()
     qt_import_plugins(jfjoch_viewer INCLUDE Qt::QXcbIntegrationPlugin)
 ENDIF()
+
+# Bundle the Qt runtime into the install tree at install time: this drives windeployqt on Windows
+# and macdeployqt on macOS, copying the Qt shared libraries + plugins next to the app. With a
+# static Qt (e.g. our Linux build) there is nothing to copy, so it is a no-op. Requires Qt >= 6.5,
+# which is when the OUTPUT_SCRIPT signature and the Linux deploy path landed (6.3/6.4 used the older
+# FILENAME_VARIABLE and had no Linux support); skipped on older Qt. NO_UNSUPPORTED_PLATFORM_ERROR
+# keeps it from hard-failing on configurations it does not handle.
+IF(Qt6_VERSION VERSION_GREATER_EQUAL "6.5")
+    qt_generate_deploy_app_script(
+            TARGET jfjoch_viewer
+            OUTPUT_SCRIPT jfjoch_viewer_deploy_script
+            NO_UNSUPPORTED_PLATFORM_ERROR)
+    INSTALL(SCRIPT ${jfjoch_viewer_deploy_script} COMPONENT viewer)
+ENDIF()
-- 
2.52.0


From da5fff71a90389327416c325a47e560b92459cb5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 15:28:29 +0200
Subject: [PATCH 160/228] docker: unify static Qt 6.9.1 on all 4 Linux images,
 drop dead prebuilds

The jungfraujoch CMake now builds HDF5 + libtiff (FetchContent) and
libjpeg-turbo + Eigen (ExternalProject / OVERRIDE_FIND_PACKAGE) itself, so the
per-image pre-builds and system -dev packages for those were dead weight (the
app rebuilt its own copies regardless). Consolidate dependency management into
the one CMakeLists at the cost of longer build time (build env has network).

- Qt: pin static 6.9.1 everywhere. ubuntu2204 was on 6.10.0 and ubuntu2404 used
  the OS Qt (~6.4, dynamic) -- the latter is now a static 6.9.1 build like the
  others, so every image ships a self-contained, identical-Qt viewer.
- Remove the HDF5/libtiff/libjpeg-turbo/Eigen source builds + their system -dev
  packages + the stale /opt/* CMAKE_PREFIX_PATH/PKG_CONFIG_PATH entries.
- nasm: now needed by the project's libjpeg-turbo ExternalProject; added to
  ubuntu2404 (the others already had it).
- Standardize the Qt configure flags across all four (xcb, xcb_xlib=OFF,
  no Wayland -- the qtwayland module was never built, so wayland_client=ON on
  ubuntu2204 was a no-op).

Untested here (no Docker on this host) -- needs a build in each image; the
ubuntu2404 static-Qt dep list in particular should be sanity-checked.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docker/rocky8/Dockerfile     | 77 +++-------------------------------
 docker/rocky9/Dockerfile     | 15 ++-----
 docker/ubuntu2204/Dockerfile | 80 ++++--------------------------------
 docker/ubuntu2404/Dockerfile | 78 ++++++++++++++++++++++-------------
 4 files changed, 66 insertions(+), 184 deletions(-)

diff --git a/docker/rocky8/Dockerfile b/docker/rocky8/Dockerfile
index 2173bab7..b98d7058 100644
--- a/docker/rocky8/Dockerfile
+++ b/docker/rocky8/Dockerfile
@@ -2,12 +2,10 @@ FROM nvidia/cuda:12.9.1-devel-rockylinux8
 LABEL authors="leonarski_f"
 
 ARG OPENSSL_VERSION=3.5.4
-ARG QT_VERSION=6.9.0
+ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-ARG EIGEN_TAG=3.4.0
-ARG LIBJPEG_TURBO_VERSION=3.1.2
-ARG LIBTIFF_VERSION=v4.7.1
-ARG HDF5_TAG="hdf5_1.14.6"
+# HDF5, libtiff, libjpeg-turbo and Eigen are now built by the jungfraujoch CMake itself
+# (FetchContent / ExternalProject), so they are no longer pre-built here.
 
 # Update base and install common utilities
 RUN dnf -y update && \
@@ -92,78 +90,13 @@ RUN curl -fsSL https://rpm.nodesource.com/setup_${NODE_MAJOR}.x | bash - && \
     dnf clean all && rm -rf /var/cache/dnf && \
     node --version && npm --version && (corepack enable || true)
 
-RUN git clone --depth 1 --branch ${EIGEN_TAG} https://gitlab.com/libeigen/eigen.git /tmp/eigen && \
-    cd /tmp/eigen && \
-    mkdir build && \
-    cd build && \
-    cmake .. -DCMAKE_INSTALL_PREFIX=/opt/eigen && \
-    make install && \
-    rm -rf /tmp/eigen
-
 # Make GCC/G++ 13 the default for builds
 ENV GCC_TOOLSET_ROOT=/opt/rh/gcc-toolset-13/root
 ENV PATH=${GCC_TOOLSET_ROOT}/usr/bin:${PATH}
 ENV CC=${GCC_TOOLSET_ROOT}/usr/bin/gcc
 ENV CXX=${GCC_TOOLSET_ROOT}/usr/bin/g++
 
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBJPEG_TURBO_VERSION} https://github.com/libjpeg-turbo/libjpeg-turbo.git /tmp/libjpeg-turbo-src; \
-    mkdir /tmp/libjpeg-turbo-src/build; \
-    cd /tmp/libjpeg-turbo-src/build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DENABLE_SHARED=FALSE \
-      -DENABLE_STATIC=TRUE \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libjpeg-turbo-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBTIFF_VERSION} https://gitlab.com/libtiff/libtiff.git /tmp/libtiff-src; \
-    mkdir /tmp/libtiff-src/build.cm; \
-    cd /tmp/libtiff-src/build.cm; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DBUILD_SHARED_LIBS=OFF \
-      -Dtools=OFF \
-      -Dtests=OFF \
-      -Ddocs=OFF \
-      -Dlzma=OFF \
-      -Djbig=OFF \
-      -Dwebp=OFF \
-      -Djpeg=OFF \
-      -Dold-jpeg=OFF \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libtiff-${LIBTIFF_VERSION}-static \
-      ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libtiff-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${HDF5_TAG} https://github.com/HDFGroup/hdf5 /tmp/hdf5-src; \
-    cd /tmp/hdf5-src; \
-    mkdir build && cd build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DHDF5_BUILD_SHARED_LIBS=OFF \
-      -DBUILD_TESTING=OFF \
-      -DHDF5_BUILD_TOOLS=OFF \
-      -DHDF5_BUILD_EXAMPLES=OFF \
-      -DHDF5_ENABLE_SZIP_SUPPORT=OFF \
-      -DHDF5_ENABLE_SZIP_ENCODING=OFF \
-      -DHDF5_BUILD_CPP_LIB=OFF \
-      -DHDF5_ENABLE_Z_LIB_SUPPORT=OFF \
-      -DCMAKE_INSTALL_PREFIX=/opt/hdf5-${HDF5_TAG}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/hdf5-src
-
-ENV CMAKE_PREFIX_PATH=/opt/libtiff-${LIBTIFF_VERSION}-static:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static
-ENV PKG_CONFIG_PATH=/opt/hdf5-${HDF5_TAG}-static/lib/pkgconfig:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static/lib/pkgconfig:/opt/libtiff-${LIBTIFF_VERSION}-static/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
+ENV PKG_CONFIG_PATH=${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
 
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
@@ -196,7 +129,7 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-ENV CMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}:/opt/hdf5-${HDF5_TAG}-static:/opt/qt-${QT_VERSION}-static:/opt/eigen
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
 
 # Set workdir for your project
 WORKDIR /workspace
diff --git a/docker/rocky9/Dockerfile b/docker/rocky9/Dockerfile
index a39ae69d..59f24886 100644
--- a/docker/rocky9/Dockerfile
+++ b/docker/rocky9/Dockerfile
@@ -4,10 +4,8 @@ LABEL authors="leonarski_f"
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-ARG EIGEN_TAG=3.4.0
-ARG LIBJPEG_TURBO_VERSION=3.1.2
-ARG LIBTIFF_VERSION=v4.7.1
-ARG HDF5_TAG="hdf5_1.14.6"
+# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
+# (FetchContent / ExternalProject), so they are not provided here.
 ARG DIALS_VERSION=3.27.0
 ARG DIALS_TARBALL_URL=https://github.com/dials/dials/releases/download/v3.27.0/dials-v3-27-0-linux-x86_64.tar.xz
 ARG DIALS_PREFIX=/opt
@@ -63,11 +61,6 @@ RUN dnf -y update && \
       glib2-devel \
       fftw-static \
       fftw-devel \
-      libtiff \
-      libtiff-devel \
-      libjpeg-turbo \
-      libjpeg-turbo-devel \
-      eigen3-devel \
       zlib-static \
       fontconfig-devel \
       mesa-dri-drivers \
@@ -172,8 +165,8 @@ RUN set -eux; \
           -O /opt/xds/durin-plugin.so \
           https://gitea.psi.ch/mx/durin/releases/download/1.0.0/libdurin-plugin.so.1.0.0
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}:/opt/hdf5-${HDF5_TAG}-static:/opt/qt-${QT_VERSION}-static
+# Make Qt discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
 
 ENV LANG=en_US.UTF-8
 ENV LANGUAGE=en_US:en
diff --git a/docker/ubuntu2204/Dockerfile b/docker/ubuntu2204/Dockerfile
index d127c769..0802d749 100644
--- a/docker/ubuntu2204/Dockerfile
+++ b/docker/ubuntu2204/Dockerfile
@@ -5,12 +5,10 @@ LABEL authors="leonarski_f"
 ENV DEBIAN_FRONTEND=noninteractive
 
 ARG OPENSSL_VERSION=3.5.4
-ARG QT_VERSION=6.10.0
+ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-ARG EIGEN_TAG=3.4.0
-ARG LIBJPEG_TURBO_VERSION=3.1.2
-ARG LIBTIFF_VERSION=v4.7.1
-ARG HDF5_TAG="hdf5_1.14.6"
+# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
+# (FetchContent / ExternalProject), so they are not pre-built here.
 
 # Update base and install toolchain + Qt dependencies
 # Notes:
@@ -75,7 +73,6 @@ RUN set -eux; \
       libglib2.0-dev \
       libfontconfig1-dev \
       libfftw3-dev \
-      libeigen3-dev \
       libdrm-dev \
       mesa-utils \
       libassimp-dev \
@@ -124,71 +121,11 @@ RUN set -eux; \
     rm -rf /var/lib/apt/lists/*; \
     node --version; npm --version; (corepack enable || true)
 
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBJPEG_TURBO_VERSION} https://github.com/libjpeg-turbo/libjpeg-turbo.git /tmp/libjpeg-turbo-src; \
-    mkdir /tmp/libjpeg-turbo-src/build; \
-    cd /tmp/libjpeg-turbo-src/build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DENABLE_SHARED=FALSE \
-      -DENABLE_STATIC=TRUE \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libjpeg-turbo-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${LIBTIFF_VERSION} https://gitlab.com/libtiff/libtiff.git /tmp/libtiff-src; \
-    mkdir /tmp/libtiff-src/build.cm; \
-    cd /tmp/libtiff-src/build.cm; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DBUILD_SHARED_LIBS=OFF \
-      -Dtools=OFF \
-      -Dtests=OFF \
-      -Ddocs=OFF \
-      -Dlzma=OFF \
-      -Djbig=OFF \
-      -Dwebp=OFF \
-      -Djpeg=OFF \
-      -Dold-jpeg=OFF \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DCMAKE_INSTALL_PREFIX=/opt/libtiff-${LIBTIFF_VERSION}-static \
-      ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/libtiff-src
-
-RUN set -eux; \
-    git clone --depth 1 --branch ${HDF5_TAG} https://github.com/HDFGroup/hdf5 /tmp/hdf5-src; \
-    cd /tmp/hdf5-src; \
-    mkdir build && cd build; \
-    cmake -G Ninja \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DHDF5_BUILD_SHARED_LIBS=OFF \
-      -DBUILD_TESTING=OFF \
-      -DHDF5_BUILD_TOOLS=OFF \
-      -DHDF5_BUILD_EXAMPLES=OFF \
-      -DHDF5_ENABLE_SZIP_SUPPORT=OFF \
-      -DHDF5_ENABLE_SZIP_ENCODING=OFF \
-      -DHDF5_BUILD_CPP_LIB=OFF \
-      -DHDF5_ENABLE_Z_LIB_SUPPORT=OFF \
-      -DCMAKE_INSTALL_PREFIX=/opt/hdf5-${HDF5_TAG}-static ..; \
-    cmake --build . -j"$(nproc)"; \
-    cmake --install .; \
-    rm -rf /tmp/hdf5-src
-
-
-ENV CMAKE_PREFIX_PATH=/opt/libtiff-${LIBTIFF_VERSION}-static:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static
-ENV PKG_CONFIG_PATH=/opt/hdf5-${HDF5_TAG}-static/lib/pkgconfig:/opt/libjpeg-turbo-${LIBJPEG_TURBO_VERSION}-static/lib/pkgconfig:/opt/libtiff-${LIBTIFF_VERSION}-static/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
-
-# Build and install static Qt 6.9 with Core, Gui, Widgets, Charts, DBus
+# Build and install static Qt with Core, Gui, Widgets, Charts, DBus
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
     cd /tmp; \
-    curl -LO https://download.qt.io/official_releases/qt/6.10/${QT_VERSION}/single/qt-everywhere-src-${QT_VERSION}.tar.xz; \
+    curl -LO https://download.qt.io/official_releases/qt/6.9/${QT_VERSION}/single/qt-everywhere-src-${QT_VERSION}.tar.xz; \
     tar -xf qt-everywhere-src-${QT_VERSION}.tar.xz; \
     mkdir -p qt-everywhere-src-${QT_VERSION}/build && cd qt-everywhere-src-${QT_VERSION}/build; \
     cmake -G Ninja \
@@ -198,9 +135,8 @@ RUN set -eux; \
       -DQT_BUILD_EXAMPLES=OFF \
       -DQT_FEATURE_dbus=ON \
       -DQT_FEATURE_xcb=ON \
-      -DQT_FEATURE_xcb_xlib=ON \
+      -DQT_FEATURE_xcb_xlib=OFF \
       -DQT_FEATURE_xkbcommon_x11=ON \
-      -DQT_FEATURE_wayland_client=ON \
       -DQT_FEATURE_opengl=ON \
       -DQT_FEATURE_opengl_desktop=ON \
       -DQT_FEATURE_opengl_dynamic=OFF \
@@ -217,8 +153,8 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}:/opt/hdf5-${HDF5_TAG}-static:/opt/qt-${QT_VERSION}-static
+# Make Qt discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
 
 # Set workdir for your project
 WORKDIR /workspace
diff --git a/docker/ubuntu2404/Dockerfile b/docker/ubuntu2404/Dockerfile
index b4046668..432469e7 100644
--- a/docker/ubuntu2404/Dockerfile
+++ b/docker/ubuntu2404/Dockerfile
@@ -5,11 +5,14 @@ LABEL authors="leonarski_f"
 ENV DEBIAN_FRONTEND=noninteractive
 
 ARG OPENSSL_VERSION=3.5.4
+ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-ARG EIGEN_TAG=3.4.0
-ARG HDF5_TAG="hdf5_1.14.6"
+# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
+# (FetchContent / ExternalProject), so they are not provided here. nasm is required by the
+# project's libjpeg-turbo ExternalProject for SIMD-accelerated JPEG.
 
-# Update base and install toolchain + Qt dependencies
+# Update base and install toolchain + static-Qt build dependencies
+# (XCB/X11/OpenGL/EGL/DBus/fontconfig/freetype/zlib headers needed to build static Qt).
 RUN set -eux; \
     apt-get update; \
     apt-get install -y --no-install-recommends \
@@ -32,6 +35,7 @@ RUN set -eux; \
       pkg-config \
       gdb \
       file \
+      nasm \
       dpkg-dev \
       fakeroot \
       libnuma-dev \
@@ -60,24 +64,26 @@ RUN set -eux; \
       libxcb-shm0-dev \
       libxcb-cursor0 \
       libxcb-cursor-dev \
+      libxcb-glx0-dev \
       libgl1-mesa-dev \
+      libglx-dev \
       libegl1-mesa-dev \
       libdbus-1-dev \
-      libtiff-dev \
-      libjpeg-turbo8-dev \
       zlib1g-dev \
       libglib2.0-dev \
       libfontconfig1-dev \
       libfftw3-dev \
-      qt6-base-dev \
-      qt6-charts-dev \
-      qt6-tools-dev \
-      qt6-3d-dev \
-      libeigen3-dev \
+      libdrm-dev \
+      libglvnd-dev \
+      libassimp-dev \
       libfreetype6-dev; \
     apt-get clean; \
     rm -rf /var/lib/apt/lists/*
 
+# Use the default GCC/G++ (gcc-13 on Noble, supported by CUDA 13.3)
+ENV CC=/usr/bin/gcc
+ENV CXX=/usr/bin/g++
+
 # Build a static OpenSSL
 RUN set -eux; \
     cd /tmp; \
@@ -89,7 +95,11 @@ RUN set -eux; \
     make install_sw; \
     cd /; rm -rf /tmp/openssl-${OPENSSL_VERSION} /tmp/openssl-${OPENSSL_VERSION}.tar.gz
 
-# Install Node.js 22 (NodeSource)
+# Expose static OpenSSL to CMake/pkg-config
+ENV OPENSSL_ROOT_DIR=/opt/openssl-${OPENSSL_VERSION}
+ENV PKG_CONFIG_PATH=${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
+
+# Install Node.js (NodeSource)
 RUN set -eux; \
     curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash -; \
     apt-get update; \
@@ -98,30 +108,40 @@ RUN set -eux; \
     rm -rf /var/lib/apt/lists/*; \
     node --version; npm --version; (corepack enable || true)
 
+# Build and install static Qt with Core, Gui, Widgets, Charts, DBus
+ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
-    git clone --depth 1 --branch ${HDF5_TAG} https://github.com/HDFGroup/hdf5 /tmp/hdf5-src; \
-    cd /tmp/hdf5-src; \
-    mkdir build && cd build; \
+    cd /tmp; \
+    curl -LO https://download.qt.io/official_releases/qt/6.9/${QT_VERSION}/single/qt-everywhere-src-${QT_VERSION}.tar.xz; \
+    tar -xf qt-everywhere-src-${QT_VERSION}.tar.xz; \
+    mkdir -p qt-everywhere-src-${QT_VERSION}/build && cd qt-everywhere-src-${QT_VERSION}/build; \
     cmake -G Ninja \
+      -DQT_BUILD_SUBMODULES="qtbase;qtshadertools;qtdeclarative;qtcharts;qt3d" \
+      -DBUILD_SHARED_LIBS=OFF \
+      -DQT_BUILD_TESTS=OFF \
+      -DQT_BUILD_EXAMPLES=OFF \
+      -DQT_FEATURE_dbus=ON \
+      -DQT_FEATURE_xcb=ON \
+      -DQT_FEATURE_xcb_xlib=OFF \
+      -DQT_FEATURE_xkbcommon_x11=ON \
+      -DQT_FEATURE_opengl=ON \
+      -DQT_FEATURE_opengl_desktop=ON \
+      -DQT_FEATURE_opengl_dynamic=OFF \
+      -DQT_FEATURE_vulkan=OFF \
       -DCMAKE_BUILD_TYPE=Release \
-      -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-      -DHDF5_BUILD_SHARED_LIBS=OFF \
-      -DBUILD_TESTING=OFF \
-      -DHDF5_BUILD_TOOLS=OFF \
-      -DHDF5_BUILD_EXAMPLES=OFF \
-      -DHDF5_ENABLE_SZIP_SUPPORT=OFF \
-      -DHDF5_ENABLE_SZIP_ENCODING=OFF \
-      -DHDF5_BUILD_CPP_LIB=OFF \
-      -DHDF5_ENABLE_Z_LIB_SUPPORT=OFF \
-      -DCMAKE_INSTALL_PREFIX=/opt/hdf5-${HDF5_TAG}-static ..; \
+      -DCMAKE_INSTALL_PREFIX=${QT_PREFIX} \
+      -DCMAKE_C_COMPILER=${CC} \
+      -DCMAKE_CXX_COMPILER=${CXX} \
+      -DQT_FEATURE_openssl=ON \
+      -DQT_FEATURE_openssl_linked=ON \
+      -DOPENSSL_USE_STATIC_LIBS=TRUE \
+      ..; \
     cmake --build . -j"$(nproc)"; \
     cmake --install .; \
-    rm -rf /tmp/hdf5-src
+    cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-# Expose static OpenSSL to CMake/pkg-config
-ENV OPENSSL_ROOT_DIR=/opt/openssl-${OPENSSL_VERSION}
-ENV CMAKE_PREFIX_PATH=/opt/hdf5-${HDF5_TAG}-static:${OPENSSL_ROOT_DIR}
-ENV PKG_CONFIG_PATH=${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig:/opt/hdf5-${HDF5_TAG}-static/lib/pkgconfig
+# Make Qt discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
 
 # Set workdir for your project
 WORKDIR /workspace
-- 
2.52.0


From 8cd46751f97e72641dda244a0e83fb357501b636 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 15:32:05 +0200
Subject: [PATCH 161/228] docker: drop fftw too -- the project builds FFTW
 itself

FFTW is fetched and built by the jungfraujoch CMake (single-precision, from the
release tarball), so the system fftw packages (fftw-static/fftw-devel on Rocky,
libfftw3-dev on Ubuntu) were unused. Remove them from all four images.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docker/rocky8/Dockerfile     | 2 --
 docker/rocky9/Dockerfile     | 2 --
 docker/ubuntu2204/Dockerfile | 1 -
 docker/ubuntu2404/Dockerfile | 1 -
 4 files changed, 6 deletions(-)

diff --git a/docker/rocky8/Dockerfile b/docker/rocky8/Dockerfile
index b98d7058..53561969 100644
--- a/docker/rocky8/Dockerfile
+++ b/docker/rocky8/Dockerfile
@@ -52,8 +52,6 @@ RUN dnf -y update && \
       zlib-devel \
       zlib-static \
       glib2-devel \
-      fftw-static \
-      fftw-devel \
       fontconfig-devel \
       zlib-static \
       java-21-openjdk-headless \
diff --git a/docker/rocky9/Dockerfile b/docker/rocky9/Dockerfile
index 59f24886..dbc1a9b4 100644
--- a/docker/rocky9/Dockerfile
+++ b/docker/rocky9/Dockerfile
@@ -59,8 +59,6 @@ RUN dnf -y update && \
       zlib-devel \
       zlib-static \
       glib2-devel \
-      fftw-static \
-      fftw-devel \
       zlib-static \
       fontconfig-devel \
       mesa-dri-drivers \
diff --git a/docker/ubuntu2204/Dockerfile b/docker/ubuntu2204/Dockerfile
index 0802d749..c139ed8b 100644
--- a/docker/ubuntu2204/Dockerfile
+++ b/docker/ubuntu2204/Dockerfile
@@ -72,7 +72,6 @@ RUN set -eux; \
       zlib1g-dev \
       libglib2.0-dev \
       libfontconfig1-dev \
-      libfftw3-dev \
       libdrm-dev \
       mesa-utils \
       libassimp-dev \
diff --git a/docker/ubuntu2404/Dockerfile b/docker/ubuntu2404/Dockerfile
index 432469e7..7449e9b1 100644
--- a/docker/ubuntu2404/Dockerfile
+++ b/docker/ubuntu2404/Dockerfile
@@ -72,7 +72,6 @@ RUN set -eux; \
       zlib1g-dev \
       libglib2.0-dev \
       libfontconfig1-dev \
-      libfftw3-dev \
       libdrm-dev \
       libglvnd-dev \
       libassimp-dev \
-- 
2.52.0


From 9c9f818ea6dca046d1781ee0d31978b6795be176 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 15:42:00 +0200
Subject: [PATCH 162/228] CMake: support DGX Spark (Blackwell GB10 sm_121 +
 aarch64 FFTW NEON)

- CUDA: append sm_121 (Blackwell GB10 / DGX Spark) to CMAKE_CUDA_ARCHITECTURES
  when nvcc >= 12.9 knows it. The static list tops out at sm_120 and embeds no
  PTX, so without this a build would fail to launch on Spark ("no kernel image
  available"); guarded so CUDA 12.8 (which predates sm_121) is unaffected.
- FFTW: enable NEON codelets on aarch64 (Grace), mirroring the x86 SSE2/AVX/AVX2
  branch, so single-precision FFT is SIMD-accelerated instead of scalar on ARM.

Both are inert on x86 / CUDA 12.8; verified configure still succeeds there.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b1efaa97..a5626d04 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,6 +55,11 @@ IF (CMAKE_CUDA_COMPILER)
             FIND_PACKAGE(CUDAToolkit REQUIRED)
             ADD_COMPILE_DEFINITIONS(JFJOCH_USE_CUDA)
             SET(JFJOCH_CUDA_AVAILABLE ON)
+            # Blackwell GB10 (DGX Spark) is sm_121, only known to nvcc >= 12.9; add it there so the
+            # binary launches natively on Spark (the list above tops out at sm_120 and embeds no PTX).
+            IF (CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL "12.9")
+                LIST(APPEND CMAKE_CUDA_ARCHITECTURES 121)
+            ENDIF()
         ELSE()
             MESSAGE(WARNING "CUDA older than 12.8 not supported")
         ENDIF()
@@ -196,11 +201,14 @@ FetchContent_MakeAvailable(tiff)
 SET(ENABLE_FLOAT ON  CACHE BOOL "" FORCE)
 SET(BUILD_TESTS  OFF CACHE BOOL "" FORCE)
 # SIMD codelets are runtime-dispatched (cpuid), so enabling AVX2 does NOT require an AVX2 CPU
-# -- FFTW falls back at runtime. x86-only, so guard by arch (ARM would use ENABLE_NEON instead).
+# -- FFTW falls back at runtime. The codelet sets are arch-specific, so guard by processor:
+# x86 gets SSE2/AVX/AVX2, aarch64 (e.g. Grace on DGX Spark) gets NEON; other arches build scalar.
 IF (CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64|amd64")
     SET(ENABLE_SSE2 ON CACHE BOOL "" FORCE)
     SET(ENABLE_AVX  ON CACHE BOOL "" FORCE)
     SET(ENABLE_AVX2 ON CACHE BOOL "" FORCE)
+ELSEIF (CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64|arm64|ARM64")
+    SET(ENABLE_NEON ON CACHE BOOL "" FORCE)
 ENDIF()
 FetchContent_Declare(fftw
         URL https://www.fftw.org/fftw-3.3.10.tar.gz
-- 
2.52.0


From a89a4c5beb1e4e1c8286e2038416bb7eeb5fd35e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 16:08:13 +0200
Subject: [PATCH 163/228] jfjoch_viewer: Show detected GPUs in the about box

---
 viewer/JFJochViewerMenu.cpp | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/viewer/JFJochViewerMenu.cpp b/viewer/JFJochViewerMenu.cpp
index 563aa54a..fa39e87a 100644
--- a/viewer/JFJochViewerMenu.cpp
+++ b/viewer/JFJochViewerMenu.cpp
@@ -15,6 +15,7 @@
 
 #include "JFJochViewerWindow.h"
 #include "../common/GitInfo.h"
+#include "../common/CUDAWrapper.h"
 
 JFJochViewerMenu::JFJochViewerMenu(QWidget *parent) : QMenuBar(parent) {
     // Create "File" menu
@@ -85,15 +86,21 @@ void JFJochViewerMenu::aboutSelected() {
     QMessageBox aboutBox(this);
     aboutBox.setWindowTitle("About");
 
-    // Set detailed text with proper spacing and structure
-    aboutBox.setText(
-        "<h3>Jungfraujoch Image Viewer</h3>" // Use HTML for improved style
+    QString about_text = "<h3>Jungfraujoch Image Viewer</h3>" // Use HTML for improved style
         "<p><b>Version:</b> " + version + "</p>"
         "<p><b>Copyright:</b> 2019-2025 Paul Scherrer Institute</p>"
         "<p><b>Author:</b> Filip Leonarski &lt;filip.leonarski@psi.ch&gt;</p>"
         "<p><b>Links:</b> <a href='https://jungfraujoch.readthedocs.io'>Documentation</a>, "
-       "<a href='https://gitea.psi.ch/mx/jungfraujoch'>Repository</a></p>"
-    );
+       "<a href='https://gitea.psi.ch/mx/jungfraujoch'>Repository</a></p>";
+
+#ifdef JFJOCH_USE_CUDA
+    about_text += QString("<p>Compiled with CUDA support. %1 GPU(s) detected</p>")
+    .arg(QString::number(get_gpu_count()));
+#else
+    about_text += "<p><b>Note:</b> CUDA is not available on this system.</p>";
+#endif
+    // Set detailed text with proper spacing and structure
+    aboutBox.setText(about_text);
 
     // Optional: Add a larger informative text, if needed
     aboutBox.setInformativeText(
-- 
2.52.0


From 5064b5ba47df4e9d14f1a9f41bc85d247aa6421f Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 16:08:38 +0200
Subject: [PATCH 164/228] image_analysis: force Ceres to build without CUDA

USE_CUDA is a Ceres cache STRING (default "default" = auto-detect), not an
option(), so a plain SET was shadowed by the cache default and CUDA got
enabled on MSVC. Force it OFF in the cache instead.

Also drop two dead settings: MINIGLOG (Ceres uses abseil logging now, no
longer referenced) and EIGENSPARSE ON (already Ceres' default).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/CMakeLists.txt | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 00996187..6b656767 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -1,7 +1,5 @@
-SET(MINIGLOG ON)
 SET(PROVIDE_UNINSTALL_TARGET OFF)
-SET(USE_CUDA OFF)
-SET(EIGENSPARSE ON)
+SET(USE_CUDA OFF CACHE BOOL "Force Ceres to build without CUDA" FORCE)
 
 # Prevent MKL from being found (guarantees no MKL)
 SET(CMAKE_DISABLE_FIND_PACKAGE_MKL TRUE)
-- 
2.52.0


From 5247acc07e7375a6bf5dea26e384f0de29b7e497 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 16:13:24 +0200
Subject: [PATCH 165/228] CMake: package the viewer component in
 JFJOCH_VIEWER_ONLY builds

A viewer-only build builds jfjoch_viewer but the CPack block hard-coded
CPACK_COMPONENTS_ALL to "jfjoch writer" and only appended "viewer" when
JFJOCH_VIEWER_BUILD was set -- which a pure viewer-only build does not set.
cpack then tried to package the empty jfjoch/writer components and failed,
requiring a manual -D CPACK_COMPONENTS_ALL=viewer.

Branch the component list on build mode: viewer-only packages just "viewer";
other modes keep "jfjoch writer" plus driver-dkms/viewer when their flags are
set. Also drops the redundant re-set of the default list.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a5626d04..34dbf94d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -319,20 +319,19 @@ IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 
 # Set Package Name
-# Initialize CPACK_COMPONENTS_ALL with common components
-set(CPACK_COMPONENTS_ALL jfjoch writer)
-
 SET(CPACK_PACKAGE_NAME "jfjoch")
 
-# Add optional components
-if (JFJOCH_INSTALL_DRIVER_SOURCE)
-    list(APPEND CPACK_COMPONENTS_ALL driver-dkms)
+# Select the components to package based on build mode
+if (JFJOCH_VIEWER_ONLY)
+    set(CPACK_COMPONENTS_ALL viewer)
 else()
     set(CPACK_COMPONENTS_ALL jfjoch writer)
-endif()
-
-if (JFJOCH_VIEWER_BUILD)
-    list(APPEND CPACK_COMPONENTS_ALL viewer)
+    if (JFJOCH_INSTALL_DRIVER_SOURCE)
+        list(APPEND CPACK_COMPONENTS_ALL driver-dkms)
+    endif()
+    if (JFJOCH_VIEWER_BUILD)
+        list(APPEND CPACK_COMPONENTS_ALL viewer)
+    endif()
 endif()
 
 # Common metadata
-- 
2.52.0


From e6c6536e3a28ebe70254459a5df54ad65b803f21 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 16:26:11 +0200
Subject: [PATCH 166/228] JFJochReceiverPlots: Move to common/, so it can be
 linked without bringing JFJochReceiver HW dependencies

---
 common/CMakeLists.txt                        |  2 ++
 {receiver => common}/JFJochReceiverPlots.cpp |  0
 {receiver => common}/JFJochReceiverPlots.h   | 18 +++++++++---------
 receiver/CMakeLists.txt                      |  3 ---
 receiver/JFJochReceiver.h                    |  2 +-
 receiver/JFJochReceiverFPGA.h                |  2 +-
 receiver/JFJochReceiverLite.h                |  2 +-
 receiver/JFJochReceiverOutput.h              |  2 +-
 tests/JFJochReceiverPlotsTest.cpp            |  2 +-
 tools/jfjoch_azint.cpp                       |  2 +-
 tools/jfjoch_process.cpp                     |  2 +-
 tools/jfjoch_scale.cpp                       |  2 +-
 12 files changed, 19 insertions(+), 20 deletions(-)
 rename {receiver => common}/JFJochReceiverPlots.cpp (100%)
 rename {receiver => common}/JFJochReceiverPlots.h (92%)

diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt
index 06a365c2..43eafcec 100644
--- a/common/CMakeLists.txt
+++ b/common/CMakeLists.txt
@@ -136,6 +136,8 @@ ADD_LIBRARY(JFJochCommon STATIC
         UnitCell.h
         CorrelationCoefficient.cpp
         CorrelationCoefficient.h
+        JFJochReceiverPlots.cpp
+        JFJochReceiverPlots.h
 )
 
 # librt is Linux/glibc-only (older glibc keeps clock_gettime/timer_*/sem_* there, and some
diff --git a/receiver/JFJochReceiverPlots.cpp b/common/JFJochReceiverPlots.cpp
similarity index 100%
rename from receiver/JFJochReceiverPlots.cpp
rename to common/JFJochReceiverPlots.cpp
diff --git a/receiver/JFJochReceiverPlots.h b/common/JFJochReceiverPlots.h
similarity index 92%
rename from receiver/JFJochReceiverPlots.h
rename to common/JFJochReceiverPlots.h
index ab04602d..70f1cc91 100644
--- a/receiver/JFJochReceiverPlots.h
+++ b/common/JFJochReceiverPlots.h
@@ -7,15 +7,15 @@
 #include <shared_mutex>
 #include <string>
 
-#include "../common/StatusVector.h"
-#include "../common/Histogram.h"
-#include "../common/ADUHistogram.h"
-#include "../common/AutoIncrVector.h"
-#include "../common/DiffractionExperiment.h"
-#include "../common/AzimuthalIntegrationProfile.h"
-#include "../common/JFJochMessages.h"
-#include "../common/Plot.h"
-#include "../common/ScanResult.h"
+#include "StatusVector.h"
+#include "Histogram.h"
+#include "ADUHistogram.h"
+#include "AutoIncrVector.h"
+#include "DiffractionExperiment.h"
+#include "AzimuthalIntegrationProfile.h"
+#include "JFJochMessages.h"
+#include "Plot.h"
+#include "ScanResult.h"
 
 struct MeanProcessingTime {
     float compression;
diff --git a/receiver/CMakeLists.txt b/receiver/CMakeLists.txt
index ad1285af..228f4959 100644
--- a/receiver/CMakeLists.txt
+++ b/receiver/CMakeLists.txt
@@ -3,9 +3,6 @@ ADD_LIBRARY(JFJochReceiver STATIC
         JFJochReceiverService.cpp JFJochReceiverService.h
         JFJochReceiverTest.cpp JFJochReceiverTest.h
         JFJochReceiverFPGA.cpp JFJochReceiverFPGA.h
-        JFJochReceiverPlots.cpp
-        JFJochReceiverPlots.cpp
-        JFJochReceiverPlots.h
         ImageMetadata.cpp
         ImageMetadata.h
         LossyFilter.cpp
diff --git a/receiver/JFJochReceiver.h b/receiver/JFJochReceiver.h
index 8c2a1362..ea234d28 100644
--- a/receiver/JFJochReceiver.h
+++ b/receiver/JFJochReceiver.h
@@ -16,7 +16,7 @@
 #include "../preview/ZMQPreviewSocket.h"
 #include "../preview/ZMQMetadataSocket.h"
 #include "../preview/PreviewImage.h"
-#include "JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "LossyFilter.h"
 #include "../common/MovingAverage.h"
 #include "../common/ScanResultGenerator.h"
diff --git a/receiver/JFJochReceiverFPGA.h b/receiver/JFJochReceiverFPGA.h
index a34af2c0..d4bcdf3d 100644
--- a/receiver/JFJochReceiverFPGA.h
+++ b/receiver/JFJochReceiverFPGA.h
@@ -28,7 +28,7 @@
 #include "../jungfrau/JFCalibration.h"
 #include "../common/ADUHistogram.h"
 #include "../common/Plot.h"
-#include "JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "../preview/PreviewImage.h"
 #include "LossyFilter.h"
 #include "JFJochReceiverCurrentStatus.h"
diff --git a/receiver/JFJochReceiverLite.h b/receiver/JFJochReceiverLite.h
index 33a0d0aa..1ceae605 100644
--- a/receiver/JFJochReceiverLite.h
+++ b/receiver/JFJochReceiverLite.h
@@ -18,7 +18,7 @@
 #include "LossyFilter.h"
 #include "../common/MovingAverage.h"
 #include "JFJochReceiverCurrentStatus.h"
-#include "JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "JFJochReceiverOutput.h"
 #include "../image_puller/ZMQImagePuller.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
diff --git a/receiver/JFJochReceiverOutput.h b/receiver/JFJochReceiverOutput.h
index ec755538..edf086d8 100644
--- a/receiver/JFJochReceiverOutput.h
+++ b/receiver/JFJochReceiverOutput.h
@@ -8,7 +8,7 @@
 
 #include "../jungfrau/JFModulePedestal.h"
 #include "JFJochReceiverCurrentStatus.h"
-#include "JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "../common/ScanResult.h"
 
 struct JFJochReceiverOutput {
diff --git a/tests/JFJochReceiverPlotsTest.cpp b/tests/JFJochReceiverPlotsTest.cpp
index 6848eeac..b371ef9b 100644
--- a/tests/JFJochReceiverPlotsTest.cpp
+++ b/tests/JFJochReceiverPlotsTest.cpp
@@ -2,7 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include <catch2/catch_all.hpp>
-#include "../receiver/JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 
 TEST_CASE("JFJochReceiverPlots") {
     DiffractionExperiment experiment;
diff --git a/tools/jfjoch_azint.cpp b/tools/jfjoch_azint.cpp
index 4d46a1e2..cdc1d7bd 100644
--- a/tools/jfjoch_azint.cpp
+++ b/tools/jfjoch_azint.cpp
@@ -23,7 +23,7 @@
 #include "../image_analysis/azint/AzIntEngineCPU.h"
 #include "../image_analysis/image_preprocessing/ImagePreprocessorCPU.h"
 #include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
-#include "../receiver/JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "../writer/FileWriter.h"
 
 void print_usage() {
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 54e32e84..9657294e 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -29,7 +29,7 @@
 #include "../common/CUDAWrapper.h"
 #include "../writer/FileWriter.h"
 #include "../image_analysis/IndexAndRefine.h"
-#include "../receiver/JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "../compression/JFJochCompressor.h"
 #include "../image_analysis/LoadFCalcFromMtz.h"
 #include "../image_analysis/scale_merge/Merge.h"
diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index bb04f64a..b438a0af 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -17,7 +17,7 @@
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
 #include "../writer/FileWriter.h"
 #include "../image_analysis/IndexAndRefine.h"
-#include "../receiver/JFJochReceiverPlots.h"
+#include "../common/JFJochReceiverPlots.h"
 #include "../compression/JFJochCompressor.h"
 #include "../image_analysis/LoadFCalcFromMtz.h"
 #include "../image_analysis/scale_merge/Merge.h"
-- 
2.52.0


From f9396e01e7e5206746417b2713cdbb2750022541 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 16:40:46 +0200
Subject: [PATCH 167/228] viewer: Windows NSIS / macOS installer polish +
 bundle analysis CLIs

NSIS installer was missing several things on Windows:
- License: show the repo GPLv3 LICENSE as the click-through license page
  (CPACK_RESOURCE_FILE_LICENSE).
- Start Menu: no shortcut was created -- add CPACK_PACKAGE_EXECUTABLES for
  jfjoch_viewer, and embed an app icon so the shortcut is not generic. The
  icon is a new multi-size jfjoch.ico (256 PNG + 48/32/16) compiled into the
  .exe via resources/jfjoch.rc; macOS gets the matching jfjoch.icns copied
  into the .app bundle (MACOSX_BUNDLE_ICON_FILE). Both derived from
  resources/jfjoch.png, padded square with transparent bands.
- Naming: install folder, Start Menu group and Add/Remove Programs entry are
  now "Jungfraujoch" instead of "jfjoch <version>".

Also ship the offline analysis CLIs (jfjoch_process/scale/azint/extract_hkl)
in viewer-only / Windows packages: JFJochReceiverPlots now lives in
JFJochCommon, so their stale JFJochReceiver link is dropped, leaving only the
portable libs (reader/image_analysis/writer/common). tools/CMakeLists.txt is
split so those four build everywhere while the hardware tools stay gated
behind NOT JFJOCH_VIEWER_ONLY, and the viewer-only branch now adds tools/.
They install into the "viewer" CPack component.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt               |  15 +++++++
 tools/CMakeLists.txt         |  79 +++++++++++++++++++----------------
 viewer/CMakeLists.txt        |  11 +++++
 viewer/resources/jfjoch.icns | Bin 0 -> 95472 bytes
 viewer/resources/jfjoch.ico  | Bin 0 -> 86899 bytes
 viewer/resources/jfjoch.rc   |   3 ++
 6 files changed, 72 insertions(+), 36 deletions(-)
 create mode 100644 viewer/resources/jfjoch.icns
 create mode 100644 viewer/resources/jfjoch.ico
 create mode 100644 viewer/resources/jfjoch.rc

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 34dbf94d..5cb48fbc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -255,6 +255,7 @@ IF (JFJOCH_VIEWER_ONLY)
     ADD_SUBDIRECTORY(broker)
     ADD_SUBDIRECTORY(reader)
     ADD_SUBDIRECTORY(viewer)
+    ADD_SUBDIRECTORY(tools)   # builds only the portable analysis tools (process/scale/azint/extract_hkl)
 ELSE()
     ADD_SUBDIRECTORY(jungfrau)
     ADD_SUBDIRECTORY(compression)
@@ -347,6 +348,20 @@ if (APPLE)
 elseif (WIN32)
     # NSIS installer .exe (Qt runtime deployed next to the binary by windeployqt).
     set(CPACK_GENERATOR "NSIS")
+
+    # GPLv3 text shown as the click-through license page of the installer.
+    set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
+
+    # Name the install folder and Start Menu group "Jungfraujoch". CPack uses this single
+    # variable for both; without it they default to "jfjoch <version>".
+    set(CPACK_PACKAGE_INSTALL_DIRECTORY "Jungfraujoch")
+    set(CPACK_NSIS_DISPLAY_NAME "Jungfraujoch")
+    set(CPACK_NSIS_PACKAGE_NAME "Jungfraujoch")
+
+    # Start Menu shortcut for the viewer ("<exe basename>;<label>"). The shortcut and the
+    # Add/Remove Programs entry both use the .exe's embedded icon.
+    set(CPACK_PACKAGE_EXECUTABLES "jfjoch_viewer;Jungfraujoch Viewer")
+    set(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\jfjoch_viewer.exe")
 elseif (EXISTS "/etc/debian_version")
     set(CPACK_PACKAGE_LICENSE "GPL-3.0-only")
     set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index c31e6f00..499a4045 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -1,36 +1,7 @@
 
-ADD_EXECUTABLE(jfjoch_udp_simulator jfjoch_udp_simulator.cpp UDPSimulator.cpp UDPSimulator.h)
-TARGET_LINK_LIBRARIES(jfjoch_udp_simulator JFJochCommon)
-INSTALL(TARGETS jfjoch_udp_simulator RUNTIME COMPONENT jfjoch)
-
-ADD_EXECUTABLE(jfjoch_hdf5_test jfjoch_hdf5_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_hdf5_test JFJochWriter JFJochReceiver JFJochCommon)
-INSTALL(TARGETS jfjoch_hdf5_test RUNTIME COMPONENT jfjoch)
-
-ADD_EXECUTABLE(jfjoch_pcie_status jfjoch_pcie_status.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_pcie_status JFJochDevice JFJochCommon)
-INSTALL(TARGETS jfjoch_pcie_status RUNTIME COMPONENT jfjoch)
-
-ADD_EXECUTABLE(jfjoch_pcie_net_cfg jfjoch_pcie_net_cfg.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_pcie_net_cfg JFJochDevice JFJochCommon)
-INSTALL(TARGETS jfjoch_pcie_net_cfg RUNTIME COMPONENT jfjoch )
-
-ADD_EXECUTABLE(jfjoch_pcie_clear_net_counters jfjoch_pcie_clear_net_counters.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_pcie_clear_net_counters JFJochDevice JFJochCommon)
-INSTALL(TARGETS jfjoch_pcie_clear_net_counters RUNTIME COMPONENT jfjoch )
-
-ADD_EXECUTABLE(jfjoch_fpga_test jfjoch_fpga_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_fpga_test JFJochReceiver)
-INSTALL(TARGETS jfjoch_fpga_test RUNTIME COMPONENT jfjoch)
-
-ADD_EXECUTABLE(jfjoch_simplon_test jfjoch_simplon_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_simplon_test JFJochDetector JFJochPreview)
-INSTALL(TARGETS jfjoch_simplon_test RUNTIME COMPONENT jfjoch)
-
-ADD_EXECUTABLE(jfjoch_lite_perf_test jfjoch_lite_perf_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_lite_perf_test JFJochReceiver JFJochWriter)
-INSTALL(TARGETS jfjoch_lite_perf_test RUNTIME COMPONENT jfjoch)
-
+# Offline analysis CLI tools. These link only the portable libraries (reader,
+# image_analysis, writer, common), so they build in viewer-only / Windows packages too
+# and install into the "viewer" component.
 ADD_EXECUTABLE(jfjoch_extract_hkl jfjoch_extract_hkl.cpp
         XdsIntegrateParser.cpp
         XdsIntegrateParser.h)
@@ -38,15 +9,51 @@ TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
 INSTALL(TARGETS jfjoch_extract_hkl RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_process jfjoch_process.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_process JFJochReader JFJochImageAnalysis JFJochWriter JFJochReceiver)
+TARGET_LINK_LIBRARIES(jfjoch_process JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_process RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_scale jfjoch_scale.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_scale JFJochReader JFJochImageAnalysis JFJochWriter JFJochReceiver)
+TARGET_LINK_LIBRARIES(jfjoch_scale JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_scale RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_azint jfjoch_azint.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_azint JFJochReader JFJochImageAnalysis JFJochWriter JFJochReceiver)
+TARGET_LINK_LIBRARIES(jfjoch_azint JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_azint RUNTIME COMPONENT viewer)
 
-ADD_SUBDIRECTORY(xbflash.qspi)
+# Online / hardware tools (broker, FPGA, receiver, detector). They link the non-portable
+# libraries and are Linux-only, so they are skipped in a viewer-only build.
+IF(NOT JFJOCH_VIEWER_ONLY)
+    ADD_EXECUTABLE(jfjoch_udp_simulator jfjoch_udp_simulator.cpp UDPSimulator.cpp UDPSimulator.h)
+    TARGET_LINK_LIBRARIES(jfjoch_udp_simulator JFJochCommon)
+    INSTALL(TARGETS jfjoch_udp_simulator RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_hdf5_test jfjoch_hdf5_test.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_hdf5_test JFJochWriter JFJochReceiver JFJochCommon)
+    INSTALL(TARGETS jfjoch_hdf5_test RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_pcie_status jfjoch_pcie_status.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_pcie_status JFJochDevice JFJochCommon)
+    INSTALL(TARGETS jfjoch_pcie_status RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_pcie_net_cfg jfjoch_pcie_net_cfg.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_pcie_net_cfg JFJochDevice JFJochCommon)
+    INSTALL(TARGETS jfjoch_pcie_net_cfg RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_pcie_clear_net_counters jfjoch_pcie_clear_net_counters.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_pcie_clear_net_counters JFJochDevice JFJochCommon)
+    INSTALL(TARGETS jfjoch_pcie_clear_net_counters RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_fpga_test jfjoch_fpga_test.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_fpga_test JFJochReceiver)
+    INSTALL(TARGETS jfjoch_fpga_test RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_simplon_test jfjoch_simplon_test.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_simplon_test JFJochDetector JFJochPreview)
+    INSTALL(TARGETS jfjoch_simplon_test RUNTIME COMPONENT jfjoch)
+
+    ADD_EXECUTABLE(jfjoch_lite_perf_test jfjoch_lite_perf_test.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_lite_perf_test JFJochReceiver JFJochWriter)
+    INSTALL(TARGETS jfjoch_lite_perf_test RUNTIME COMPONENT jfjoch)
+
+    ADD_SUBDIRECTORY(xbflash.qspi)
+ENDIF()
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index f3909025..ecf1b3ed 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -107,6 +107,17 @@ SET_TARGET_PROPERTIES(jfjoch_viewer PROPERTIES
         MACOSX_BUNDLE    ON
         WIN32_EXECUTABLE ON)
 
+# Application icon: embedded into the .exe via a Windows resource script, and copied into
+# the macOS .app bundle (referenced from Info.plist through MACOSX_BUNDLE_ICON_FILE).
+IF(WIN32)
+    TARGET_SOURCES(jfjoch_viewer PRIVATE resources/jfjoch.rc)
+ELSEIF(APPLE)
+    SET(_viewer_icns ${CMAKE_CURRENT_SOURCE_DIR}/resources/jfjoch.icns)
+    TARGET_SOURCES(jfjoch_viewer PRIVATE ${_viewer_icns})
+    SET_SOURCE_FILES_PROPERTIES(${_viewer_icns} PROPERTIES MACOSX_PACKAGE_LOCATION Resources)
+    SET_TARGET_PROPERTIES(jfjoch_viewer PROPERTIES MACOSX_BUNDLE_ICON_FILE jfjoch.icns)
+ENDIF()
+
 INSTALL(TARGETS jfjoch_viewer
         BUNDLE  DESTINATION .   COMPONENT viewer   # macOS .app bundle
         RUNTIME DESTINATION bin COMPONENT viewer)  # Windows .exe / Linux binary
diff --git a/viewer/resources/jfjoch.icns b/viewer/resources/jfjoch.icns
new file mode 100644
index 0000000000000000000000000000000000000000..dac5ef7a155a796ab79ccebcfc539dbb9e8947f9
GIT binary patch
literal 95472
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zkJ><*oeZd{au@C+>mhs}_^#+Tlh6=z2smI<oi}Y|`*wo$a5Vb|-eTOj^VZRKjeBuz
zzmDilfX`X8UJP0S9tQ_|;ZH<GC(?q2tGNfDE$Qf*lYzk?(GMlT8DoCVdy?0Mg#~mp
zlzR&j&axkTlm-|KrQyTP1W&;~`@9!b@|(}^c<zlGA9D=HnSKkb9XOX^$}vH{;L%?h
z_bvbaXBU6xE%W8uBS%iWwXj(A*4^FXEk3LHz5jbZgYUn%m>x4Y)|%nt6EuTkzZv}d
PUwj9@tDz3Q`tAP%S}@nc

literal 0
HcmV?d00001

diff --git a/viewer/resources/jfjoch.rc b/viewer/resources/jfjoch.rc
new file mode 100644
index 00000000..d47ff003
--- /dev/null
+++ b/viewer/resources/jfjoch.rc
@@ -0,0 +1,3 @@
+// Windows resource script: embeds the application icon into jfjoch_viewer.exe.
+// The lowest integer resource ID is the icon Explorer and the Start Menu shortcut use.
+1 ICON "jfjoch.ico"
-- 
2.52.0


From e035f7c3035587d755af14906493b09c267ce4b6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 17:22:48 +0200
Subject: [PATCH 168/228] viewer: drop unused CMAKE_AUTORCC

The viewer's only .qrc is compiled explicitly via QT_ADD_RESOURCES into
APP_RESOURCES; no .qrc is added directly as a target source, so AUTORCC never
acted on anything. Remove the dead flag.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index ecf1b3ed..fcd99edc 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -2,7 +2,6 @@
 # SPDX-License-Identifier: GPL-3.0-only
 
 SET(CMAKE_AUTOMOC ON)
-SET(CMAKE_AUTORCC ON)
 SET(CMAKE_AUTOUIC ON)
 
 # D-Bus (single-instance / remote control) is Linux-only: Qt6::DBus does not
-- 
2.52.0


From e5034d0a2c9b8ee273f4b14940d9235f3b09bfe5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 18:35:50 +0200
Subject: [PATCH 169/228] licenses: add third-party notices, attribution texts,
 and viewer license window

Acknowledge all bundled third-party software and satisfy attribution/notice
requirements, while keeping it maintainable:

- THIRD_PARTY_NOTICES.md: human-readable manifest (component, copyright, SPDX
  license, link) for fetched, vendored, and runtime/SDK dependencies.
- licenses/: verbatim license texts; COLLECT.sh regenerates them from the
  build trees and system SDK locations.
- Bundle the verbatim Qt LGPL-3.0 text and the CUDA Toolkit 12.8 EULA.
- frontend: self-contained npm attribution generator (`npm run licenses` ->
  dist/THIRD_PARTY_LICENSES.txt), wired into the frontend build target.
- Install LICENSE + notices + licenses/ into share/doc/jfjoch for every
  packaged component.
- viewer: Help > "Third-party Licenses" window (QTextBrowser) showing a
  generated, self-contained HTML built from licenses/.
- docs/SOFTWARE.md: drop the stale hand-kept dependency lists; point at the
  manifest.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                                |   15 +
 THIRD_PARTY_NOTICES.md                        |   84 +
 docs/SOFTWARE.md                              |   34 +-
 frontend/package.json                         |    1 +
 .../scripts/generate-third-party-licenses.mjs |  121 +
 licenses/COLLECT.sh                           |   80 +
 licenses/NVIDIA-CUDA-EULA.txt                 | 1632 +++++
 licenses/NVIDIA-CUDA-NOTICE.txt               |   19 +
 licenses/Qt6-LGPL-3.0.txt                     |  165 +
 licenses/Qt6-NOTICE.txt                       |   24 +
 licenses/base64-macaron.txt                   |   24 +
 licenses/bitshuffle-hperf.txt                 |  202 +
 licenses/bitshuffle.txt                       |   21 +
 licenses/catch2.txt                           |   23 +
 licenses/ceres-solver.txt                     |  257 +
 licenses/cpp-httplib.txt                      |   22 +
 licenses/eigen-README.txt                     |    6 +
 licenses/eigen.txt                            |  373 ++
 licenses/fast-feedback-indexer.txt            |   22 +
 licenses/fftw.txt                             |  340 +
 licenses/gemmi.txt                            |  373 ++
 licenses/hdf5.txt                             |  111 +
 licenses/libjpeg-turbo.txt                    |  135 +
 licenses/libtiff.txt                          |   49 +
 licenses/libzmq.txt                           |  373 ++
 licenses/lz4.txt                              |   24 +
 licenses/nlohmann-json.txt                    |   21 +
 licenses/slsDetectorPackage-GPL-3.0.txt       |  688 ++
 licenses/slsDetectorPackage-LGPL-3.0.txt      |  179 +
 licenses/spdlog.txt                           |   25 +
 licenses/tinycbor.txt                         |   21 +
 licenses/xbflash-qspi.txt                     |  517 ++
 licenses/xilinx-hls-headers.txt               |   18 +
 licenses/zlib.txt                             |   19 +
 licenses/zstd.txt                             |   30 +
 viewer/CMakeLists.txt                         |    2 +
 viewer/JFJochViewerMenu.cpp                   |   13 +
 viewer/JFJochViewerMenu.h                     |    4 +
 viewer/resources/generate_licenses_html.mjs   |   71 +
 viewer/resources/resources.qrc                |    1 +
 viewer/resources/third_party_licenses.html    | 5812 +++++++++++++++++
 viewer/windows/JFJochLicenseWindow.cpp        |   23 +
 viewer/windows/JFJochLicenseWindow.h          |   13 +
 43 files changed, 11962 insertions(+), 25 deletions(-)
 create mode 100644 THIRD_PARTY_NOTICES.md
 create mode 100644 frontend/scripts/generate-third-party-licenses.mjs
 create mode 100644 licenses/COLLECT.sh
 create mode 100644 licenses/NVIDIA-CUDA-EULA.txt
 create mode 100644 licenses/NVIDIA-CUDA-NOTICE.txt
 create mode 100644 licenses/Qt6-LGPL-3.0.txt
 create mode 100644 licenses/Qt6-NOTICE.txt
 create mode 100644 licenses/base64-macaron.txt
 create mode 100644 licenses/bitshuffle-hperf.txt
 create mode 100644 licenses/bitshuffle.txt
 create mode 100644 licenses/catch2.txt
 create mode 100644 licenses/ceres-solver.txt
 create mode 100644 licenses/cpp-httplib.txt
 create mode 100644 licenses/eigen-README.txt
 create mode 100644 licenses/eigen.txt
 create mode 100644 licenses/fast-feedback-indexer.txt
 create mode 100644 licenses/fftw.txt
 create mode 100644 licenses/gemmi.txt
 create mode 100644 licenses/hdf5.txt
 create mode 100644 licenses/libjpeg-turbo.txt
 create mode 100644 licenses/libtiff.txt
 create mode 100644 licenses/libzmq.txt
 create mode 100644 licenses/lz4.txt
 create mode 100644 licenses/nlohmann-json.txt
 create mode 100644 licenses/slsDetectorPackage-GPL-3.0.txt
 create mode 100644 licenses/slsDetectorPackage-LGPL-3.0.txt
 create mode 100644 licenses/spdlog.txt
 create mode 100644 licenses/tinycbor.txt
 create mode 100644 licenses/xbflash-qspi.txt
 create mode 100644 licenses/xilinx-hls-headers.txt
 create mode 100644 licenses/zlib.txt
 create mode 100644 licenses/zstd.txt
 create mode 100644 viewer/resources/generate_licenses_html.mjs
 create mode 100644 viewer/resources/third_party_licenses.html
 create mode 100644 viewer/windows/JFJochLicenseWindow.cpp
 create mode 100644 viewer/windows/JFJochLicenseWindow.h

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5cb48fbc..fd16f609 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -291,6 +291,7 @@ IF (NOT JFJOCH_WRITER_ONLY AND NOT JFJOCH_VIEWER_ONLY)
     ADD_CUSTOM_COMMAND(OUTPUT frontend/dist/index.html
             COMMAND npm ci
             COMMAND npm run build
+            COMMAND npm run licenses        # write dist/THIRD_PARTY_LICENSES.txt (npm deps attribution)
             COMMAND npm run redocly
             COMMAND npm run docs            # bundle Sphinx docs into dist/docs (served at /frontend/docs)
             WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend)
@@ -428,4 +429,18 @@ else()
 endif()
 
 
+# Ship the license notices (top-level LICENSE, the third-party manifest, and the verbatim
+# license texts) with every package variant, under share/doc/jfjoch. Installed per component so
+# the file lands in whichever component package(s) the current build mode produces.
+SET(JFJOCH_NOTICE_FILES
+        ${CMAKE_SOURCE_DIR}/LICENSE
+        ${CMAKE_SOURCE_DIR}/THIRD_PARTY_NOTICES.md)
+FOREACH(_component IN LISTS CPACK_COMPONENTS_ALL)
+    INSTALL(FILES ${JFJOCH_NOTICE_FILES}
+            DESTINATION share/doc/jfjoch COMPONENT ${_component})
+    INSTALL(DIRECTORY ${CMAKE_SOURCE_DIR}/licenses/
+            DESTINATION share/doc/jfjoch/licenses COMPONENT ${_component}
+            PATTERN "COLLECT.sh" EXCLUDE)
+ENDFOREACH()
+
 INCLUDE(CPack)
diff --git a/THIRD_PARTY_NOTICES.md b/THIRD_PARTY_NOTICES.md
new file mode 100644
index 00000000..06d156c8
--- /dev/null
+++ b/THIRD_PARTY_NOTICES.md
@@ -0,0 +1,84 @@
+# Third-party software notices
+
+Jungfraujoch is licensed under **GPL-3.0** (see [`LICENSE`](LICENSE)); the FPGA design is
+licensed under **CERN-OHL-S-2.0** (see [`fpga/LICENSE`](fpga/LICENSE)). It builds on a number of
+third-party components, acknowledged below as required by their licenses.
+
+This file is the human-readable manifest. The verbatim license texts live in the
+[`licenses/`](licenses/) directory (regenerate with `bash licenses/COLLECT.sh`). The frontend's
+bundled JavaScript dependencies are listed separately in
+`frontend/dist/THIRD_PARTY_LICENSES.txt`, generated at build time (`npm run licenses`).
+
+All licenses below are GPL-3.0-compatible.
+
+## Fetched at build time and statically linked into the C++ binaries
+
+These are downloaded by CMake (`FetchContent` / `ExternalProject`) during the first configure and
+linked into the Jungfraujoch executables.
+
+| Component | Version | Copyright | License (SPDX) | License text |
+|---|---|---|---|---|
+| [spdlog](https://github.com/gabime/spdlog) | 1.17.0 | Gabi Melman | MIT | [spdlog.txt](licenses/spdlog.txt) |
+| [Zstandard](https://github.com/facebook/zstd) | (pinned) | Meta Platforms, Inc. | BSD-3-Clause | [zstd.txt](licenses/zstd.txt) |
+| [HDF5](https://github.com/HDFGroup/hdf5) | 2.1.0 | The HDF Group; UIUC | BSD-3-Clause-style | [hdf5.txt](licenses/hdf5.txt) |
+| [slsDetectorPackage](https://github.com/slsdetectorgroup/slsDetectorPackage) | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | [LGPL](licenses/slsDetectorPackage-LGPL-3.0.txt), [GPL](licenses/slsDetectorPackage-GPL-3.0.txt) |
+| [cpp-httplib](https://github.com/yhirose/cpp-httplib) | 0.39.0 | Yuji Hirose | MIT | [cpp-httplib.txt](licenses/cpp-httplib.txt) |
+| [libzmq (ZeroMQ)](https://github.com/zeromq/libzmq) | 4.3.5 | iMatix and contributors | MPL-2.0 | [libzmq.txt](licenses/libzmq.txt) |
+| [libtiff](https://gitlab.com/libtiff/libtiff) | 4.7.1 | Sam Leffler; SGI | libtiff (BSD-like) | [libtiff.txt](licenses/libtiff.txt) |
+| [FFTW](https://www.fftw.org/) | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | [fftw.txt](licenses/fftw.txt) |
+| [Eigen](https://gitlab.com/libeigen/eigen) | 5.0.1 | Eigen contributors | MPL-2.0 (+ BSD parts) | [eigen.txt](licenses/eigen.txt), [README](licenses/eigen-README.txt) |
+| [Ceres Solver](https://github.com/ceres-solver/ceres-solver) | (pinned) | Google Inc. and contributors | BSD-3-Clause | [ceres-solver.txt](licenses/ceres-solver.txt) |
+| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) | (pinned) | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](licenses/fast-feedback-indexer.txt) |
+| [libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) | (pinned) | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | [libjpeg-turbo.txt](licenses/libjpeg-turbo.txt) |
+| [Catch2](https://github.com/catchorg/Catch2) | 3.13.0 | Catch2 Authors | BSL-1.0 | [catch2.txt](licenses/catch2.txt) |
+
+Catch2 is used only to build the test binary (`jfjoch_test`) and is not part of any shipped
+artifact; it is listed here for completeness.
+
+## Vendored directly in the repository
+
+These are copied into the source tree (see the path) rather than fetched.
+
+| Component | Path | Copyright | License (SPDX) | License text |
+|---|---|---|---|---|
+| [nlohmann/json](https://github.com/nlohmann/json) | `include/nlohmann/` | Niels Lohmann | MIT | [nlohmann-json.txt](licenses/nlohmann-json.txt) |
+| [Macaron Base64](https://gist.github.com/tomykaira/f0fd86b6c73063283afe550bc5d77594) | `include/base64/` | tomykaira | MIT | [base64-macaron.txt](licenses/base64-macaron.txt) |
+| [TinyCBOR](https://github.com/intel/tinycbor) | `frame_serialize/tinycbor/` | Intel Corporation | MIT | [tinycbor.txt](licenses/tinycbor.txt) |
+| [Bitshuffle](https://github.com/kiyo-masui/bitshuffle) | `compression/bitshuffle/` | Kiyoshi Masui | MIT | [bitshuffle.txt](licenses/bitshuffle.txt) |
+| [Bitshuffle (h-perf)](https://github.com/kalcutter/bitshuffle) | `compression/bitshuffle_hperf/` | Kal Cutter (DECTRIS) | Apache-2.0 | [bitshuffle-hperf.txt](licenses/bitshuffle-hperf.txt) |
+| [LZ4](https://github.com/lz4/lz4) | `compression/lz4/` | Yann Collet | BSD-2-Clause | [lz4.txt](licenses/lz4.txt) |
+| [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](licenses/xilinx-hls-headers.txt) |
+| [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](licenses/gemmi.txt) |
+| [xbflash.qspi](https://github.com/Xilinx/XRT) | `tools/xbflash.qspi/` | Xilinx / AMD | Apache-2.0 | [xbflash-qspi.txt](licenses/xbflash-qspi.txt) |
+
+## Runtime libraries and SDKs (shipped in binaries, not in the source tree)
+
+| Component | Used by | License | Notice |
+|---|---|---|---|
+| [Qt 6](https://www.qt.io/) | `jfjoch_viewer` | LGPL-3.0 | [notice](licenses/Qt6-NOTICE.txt), [LGPL-3.0](licenses/Qt6-LGPL-3.0.txt) |
+| [NVIDIA CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit) (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | [notice](licenses/NVIDIA-CUDA-NOTICE.txt), [EULA](licenses/NVIDIA-CUDA-EULA.txt) |
+| [zlib](https://zlib.net/) | everywhere (compression) | Zlib | [zlib.txt](licenses/zlib.txt) |
+
+## Frontend (npm) dependencies
+
+The React/TypeScript frontend (`frontend/`) bundles a large transitive tree of npm packages,
+overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:
+
+```
+cd frontend && npm run licenses     # writes dist/THIRD_PARTY_LICENSES.txt
+```
+
+The generated file is produced as part of the `frontend` build target and installed alongside the
+served frontend, so the shipped web UI carries its own attribution.
+
+## Notes on weak-copyleft and attribution-sensitive components
+
+* **MPL-2.0** (Eigen, GEMMI, libzmq): file-level copyleft. The corresponding source is available as
+  part of this GPL-3.0 source distribution; GEMMI is vendored in `gemmi_gph/` in trimmed form.
+* **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
+* **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the
+  corresponding `licenses/` text.
+* **Qt (LGPL-3.0)** and **NVIDIA CUDA (EULA)** carry redistribution conditions beyond a copyright
+  notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
+  (`licenses/Qt6-LGPL-3.0.txt`, `licenses/NVIDIA-CUDA-EULA.txt`); the CUDA EULA is the one shipped
+  with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index 8b144dbe..6357695e 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -19,30 +19,14 @@ Required:
 * JPEG library (preferably jpeg-turbo) - see [github.com/libjpeg-turbo/libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo)
 
 Optional:
-* CUDA compiler version 12.7 or newer - required for MX fast feedback indexer
-* FFTW library - for indexing if GPU/CUDA is absent
-* Node.js - to make frontend
+* CUDA compiler version 12.8 or newer - required for the MX fast feedback indexer and GPU analysis
+* FFTW library - for indexing if GPU/CUDA is absent (also auto-downloaded by CMake)
+* Node.js - to build the frontend
 * Qt version 6 (for jfjoch_viewer)
 
-Automatically downloaded by CMake and statically linked:
-* SLS Detector Package - see [github.com/slsdetectorgroup/slsDetectorPackage](https://github.com/slsdetectorgroup/slsDetectorPackage)
-* Zstandard (Facebook) - see [github.com/facebook/zstd](https://github.com/facebook/zstd)
-* Cpp-http library for HTTP server and client - see [github.com/yhirose/cpp-httplib](https://github.com/yhirose/cpp-httplib)
-* Fast feedback indexer (Hans-Christian Stadler, PSI) - see [github.com/paulscherrerinstitute/fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer)
-* Catch2 testing library - see [github.com/catchorg/Catch2](https://github.com/catchorg/Catch2)
-* Ceres Solver library for least square optimization - see [http://ceres-solver.org/]
-* Spdlog logging library - see [github.com/gabime/spdlog](https://github.com/gabime/spdlog)
-Please follow the link provided above to check for LICENSE file. Building code with dependencies above requires access from the build system to github.com.
-
-Directly included in the repository:
-* JSON parser/writer from N. Lohmann - see [github.com/nlohmann/json](https://github.com/nlohmann/json)
-* Xilinx arbitrary precision arithmetic headers - see [github.com/Xilinx/HLS_arbitrary_Precision_Types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types)
-* Bitshuffle filter from K. Masui - see [github.com/kiyo-masui/bitshuffle](https://github.com/kiyo-masui/bitshuffle)
-* Fast replacement for Bitshuffle pre-compression filter (Kal Cutter, DECTRIS)  - see [github.com/kalcutter/bitshuffle](https://github.com/kalcutter/bitshuffle)
-* Tinycbor (Intel) - see [github.com/intel/tinycbor](https://github.com/intel/tinycbor)
-* LZ4 compression by Y.Collet - see [github.com/lz4/lz4](https://github.com/lz4/lz4)
-* ZeroMQ library (through slsDetectorPackage) - see [github.com/zeromq/libzmq](https://github.com/zeromq/libzmq)
-* Base64 decoder/encoder - see [gist.github.com/tomykaira](https://gist.github.com/tomykaira/f0fd86b6c73063283afe550bc5d77594)
-* GEMMI library by Global Phasing - see [github.com/project-gemmi/gemmi](https://github.com/project-gemmi/gemmi)
- 
-For license check LICENSE file in respective directory
+Many further dependencies (spdlog, Zstandard, HDF5, slsDetectorPackage, libzmq, libtiff,
+libjpeg-turbo, Eigen, Ceres, the fast feedback indexer, Catch2, ...) are downloaded automatically
+by CMake and statically linked; building therefore requires network access on the first configure.
+Others are vendored directly in the source tree. The complete list of third-party components, with
+copyright holders, licenses and verbatim license texts, is in
+[THIRD_PARTY_NOTICES.md](../THIRD_PARTY_NOTICES.md) and the `licenses/` directory.
diff --git a/frontend/package.json b/frontend/package.json
index 77cfa144..8d5a3ec3 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -37,6 +37,7 @@
     "redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=dist/openapi.html",
     "docs": "bash ../make_doc.sh dist/docs",
     "redocly4broker": "redocly build-docs ../broker/jfjoch_api.yaml --output=../broker/redoc-static.html",
+    "licenses": "node scripts/generate-third-party-licenses.mjs",
     "openapi": "openapi-ts"
   },
   "overrides": {
diff --git a/frontend/scripts/generate-third-party-licenses.mjs b/frontend/scripts/generate-third-party-licenses.mjs
new file mode 100644
index 00000000..0cb6c9fc
--- /dev/null
+++ b/frontend/scripts/generate-third-party-licenses.mjs
@@ -0,0 +1,121 @@
+// Generate frontend/dist/THIRD_PARTY_LICENSES.txt: the third-party attribution file for the
+// npm packages bundled into the built frontend.
+//
+// Self-contained (no extra dependency): it asks npm for the *production* dependency tree, then
+// reads each package's own license file from node_modules and concatenates them. Run via
+// `npm run licenses` (also invoked by the CMake `frontend` build target).
+
+import { execFileSync } from "node:child_process";
+import { readFileSync, readdirSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
+import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
+
+const frontendDir = join(dirname(fileURLToPath(import.meta.url)), "..");
+const nodeModules = join(frontendDir, "node_modules");
+const outFile = join(frontendDir, "dist", "THIRD_PARTY_LICENSES.txt");
+
+const LICENSE_FILE = /^(licen[sc]e|copying|notice)([.-].*)?$/i;
+
+// Set of "name@version" strings that actually ship in production (excludes devDependencies).
+function productionPackages() {
+  const json = execFileSync("npm", ["ls", "--omit=dev", "--all", "--json"], {
+    cwd: frontendDir,
+    encoding: "utf8",
+    maxBuffer: 64 * 1024 * 1024,
+  });
+  const set = new Set();
+  const walk = (deps) => {
+    for (const [name, info] of Object.entries(deps || {})) {
+      if (info.version) set.add(`${name}@${info.version}`);
+      walk(info.dependencies);
+    }
+  };
+  walk(JSON.parse(json).dependencies);
+  return set;
+}
+
+// Map "name@version" -> package directory, by scanning every node_modules in the install tree.
+function installedPackages() {
+  const map = new Map();
+  const scan = (nm) => {
+    if (!existsSync(nm)) return;
+    for (const entry of readdirSync(nm)) {
+      if (entry.startsWith(".")) continue;
+      if (entry.startsWith("@")) {
+        for (const sub of readdirSync(join(nm, entry))) record(join(nm, entry, sub));
+      } else {
+        record(join(nm, entry));
+      }
+    }
+  };
+  const record = (dir) => {
+    const pkgJson = join(dir, "package.json");
+    if (!existsSync(pkgJson)) return;
+    try {
+      const pkg = JSON.parse(readFileSync(pkgJson, "utf8"));
+      if (pkg.name && pkg.version) map.set(`${pkg.name}@${pkg.version}`, { dir, pkg });
+    } catch { /* ignore unparseable package.json */ }
+    scan(join(dir, "node_modules"));
+  };
+  scan(nodeModules);
+  return map;
+}
+
+function findLicenseText(dir) {
+  const file = readdirSync(dir).find((f) => LICENSE_FILE.test(f));
+  if (!file) return null;
+  try {
+    return readFileSync(join(dir, file), "utf8").trimEnd();
+  } catch {
+    return null;
+  }
+}
+
+function licenseId(pkg) {
+  if (typeof pkg.license === "string") return pkg.license;
+  if (pkg.license?.type) return pkg.license.type;
+  if (Array.isArray(pkg.licenses)) return pkg.licenses.map((l) => l.type || l).join(" OR ");
+  return "UNKNOWN";
+}
+
+function repoUrl(pkg) {
+  const r = pkg.repository;
+  if (typeof r === "string") return r;
+  if (r?.url) return r.url.replace(/^git\+/, "").replace(/\.git$/, "");
+  return pkg.homepage || "";
+}
+
+const prod = productionPackages();
+const installed = installedPackages();
+
+const blocks = [];
+const missing = [];
+for (const id of [...prod].sort((a, b) => a.localeCompare(b))) {
+  const found = installed.get(id);
+  if (!found) continue; // present in tree report but not on disk (e.g. bundled) — skip
+  const { dir, pkg } = found;
+  const text = findLicenseText(dir);
+  if (!text) missing.push(`${id} (${licenseId(pkg)})`);
+  const url = repoUrl(pkg);
+  blocks.push(
+    `${"=".repeat(80)}\n` +
+      `${id}  —  ${licenseId(pkg)}\n` +
+      (url ? `${url}\n` : "") +
+      `${"=".repeat(80)}\n\n` +
+      (text || `License: ${licenseId(pkg)} (no license file shipped in this package)`),
+  );
+}
+
+const header =
+  "Third-party software bundled in the Jungfraujoch frontend\n" +
+  "=========================================================\n\n" +
+  "The Jungfraujoch frontend is licensed under GPL-3.0. It bundles the following npm packages\n" +
+  "(production dependencies). Each package's license and notice text follows.\n\n" +
+  `Generated by scripts/generate-third-party-licenses.mjs — ${prod.size} packages.\n` +
+  (missing.length
+    ? `\nPackages without a bundled license file (license field shown above):\n  ${missing.join("\n  ")}\n`
+    : "");
+
+mkdirSync(dirname(outFile), { recursive: true });
+writeFileSync(outFile, header + "\n" + blocks.join("\n\n") + "\n", "utf8");
+console.log(`Wrote ${outFile} (${blocks.length} packages, ${missing.length} without license file).`);
diff --git a/licenses/COLLECT.sh b/licenses/COLLECT.sh
new file mode 100644
index 00000000..b8dbb98f
--- /dev/null
+++ b/licenses/COLLECT.sh
@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+# Collect the verbatim license texts of all third-party components into this directory.
+#
+# This is the bulk reference material that accompanies THIRD_PARTY_NOTICES.md (the human-readable
+# manifest at the repo root). Run from the repo root after a configure/build has populated the
+# FetchContent source trees (build/_deps or cmake-build-*/_deps). Re-run when a dependency version
+# changes. The output (licenses/*.txt) is committed so a source checkout needs no build to ship the
+# notices.
+#
+#   bash licenses/COLLECT.sh
+#
+set -euo pipefail
+cd "$(dirname "$0")/.."
+OUT=licenses
+
+# Copy $1 to licenses/$2, trying each source path in $1 (space-separated) until one exists.
+copy_license() {
+    local dest="$1"; shift
+    local src
+    for src in "$@"; do
+        if [[ -f "$src" ]]; then
+            cp "$src" "$OUT/$dest"
+            echo "  $dest  <-  $src"
+            return 0
+        fi
+    done
+    echo "  !! MISSING: $dest (none of: $*)" >&2
+    return 0
+}
+
+# Search the populated dependency trees in order of preference.
+DEPS=(_deps cmake-build-release/_deps build/_deps cmake-build-debug/_deps)
+find_dep() { # find_dep <relative-path-under-a-deps-dir>
+    local d
+    for d in "${DEPS[@]}"; do [[ -f "$d/$1" ]] && { echo "$d/$1"; return; }; done
+}
+
+echo "Collecting third-party license texts into $OUT/ ..."
+
+# --- Fetched at build, statically linked into the C++ binaries -------------------------------
+copy_license spdlog.txt              "$(find_dep spdlog-src/LICENSE)"
+copy_license zstd.txt                "$(find_dep zstd-src/LICENSE)"
+copy_license hdf5.txt                "$(find_dep hdf5-src/LICENSE)"
+copy_license catch2.txt              "$(find_dep catch2-src/LICENSE.txt)"
+copy_license cpp-httplib.txt         "$(find_dep httplib-src/LICENSE)"
+copy_license libzmq.txt              "$(find_dep libzmq-src/LICENSE)"
+copy_license libtiff.txt             "$(find_dep tiff-src/LICENSE.md)"
+copy_license fftw.txt                "$(find_dep fftw-src/COPYING)"
+copy_license ceres-solver.txt        "$(find_dep ceres-src/LICENSE)"
+copy_license fast-feedback-indexer.txt "$(find_dep fast-indexer-src/LICENSE.md)"
+copy_license eigen.txt               "$(find_dep eigen3-src/COPYING.MPL2)"
+copy_license eigen-README.txt        "$(find_dep eigen3-src/COPYING.README)"
+copy_license zlib.txt                "$(find_dep zlib-src/LICENSE.md)"
+
+# slsDetectorPackage is LGPL-3.0-or-later: ship both the GPL-3.0 base and the LGPL-3.0 addendum.
+copy_license slsDetectorPackage-LGPL-3.0.txt "$(find_dep sls_detector_package-src/LICENSES/LGPL-3.0)"
+copy_license slsDetectorPackage-GPL-3.0.txt  "$(find_dep sls_detector_package-src/LICENSES/GPL-3.0)"
+
+# libjpeg-turbo is built out-of-line by preview/ (ExternalProject), not under _deps.
+copy_license libjpeg-turbo.txt \
+    cmake-build-release/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md \
+    build/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md
+
+# --- Vendored directly in the repository ----------------------------------------------------
+copy_license nlohmann-json.txt       include/nlohmann/LICENSE.MIT
+copy_license tinycbor.txt            frame_serialize/tinycbor/LICENSE
+copy_license bitshuffle.txt          compression/bitshuffle/LICENSE
+copy_license bitshuffle-hperf.txt    compression/bitshuffle_hperf/LICENSE-APACHE
+copy_license lz4.txt                 compression/lz4/LICENSE
+copy_license xilinx-hls-headers.txt  fpga/include/LICENSE.HLS_Headers
+copy_license gemmi.txt               gemmi_gph/LICENSE.txt
+copy_license xbflash-qspi.txt        tools/xbflash.qspi/LICENSE
+
+# --- Runtime SDK license texts, copied from their system install (best effort) ---------------
+# These come from outside the build tree; the committed copies are authoritative if absent here.
+copy_license Qt6-LGPL-3.0.txt /usr/share/common-licenses/LGPL-3
+copy_license NVIDIA-CUDA-EULA.txt \
+    /usr/local/cuda/EULA.txt /usr/local/cuda-12.8/EULA.txt
+
+echo "Done. base64-macaron.txt, Qt6-NOTICE.txt and NVIDIA-CUDA-NOTICE.txt are maintained by hand."
diff --git a/licenses/NVIDIA-CUDA-EULA.txt b/licenses/NVIDIA-CUDA-EULA.txt
new file mode 100644
index 00000000..6622367a
--- /dev/null
+++ b/licenses/NVIDIA-CUDA-EULA.txt
@@ -0,0 +1,1632 @@
+End User License Agreement
+--------------------------
+
+NVIDIA Software License Agreement and CUDA Supplement to
+Software License Agreement.
+
+The CUDA Toolkit End User License Agreement applies to the
+NVIDIA CUDA Toolkit, the NVIDIA CUDA Samples, the NVIDIA
+Display Driver, NVIDIA Nsight tools (Visual Studio Edition),
+and the associated documentation on CUDA APIs, programming
+model and development tools. If you do not agree with the
+terms and conditions of the license agreement, then do not
+download or use the software.
+
+Last updated: January 12, 2024.
+
+
+Preface
+-------
+
+The Software License Agreement in Chapter 1 and the Supplement
+in Chapter 2 contain license terms and conditions that govern
+the use of NVIDIA toolkit. By accepting this agreement, you
+agree to comply with all the terms and conditions applicable
+to the product(s) included herein.
+
+
+NVIDIA Driver
+
+
+Description
+
+This package contains the operating system driver and
+fundamental system software components for NVIDIA GPUs.
+
+
+NVIDIA CUDA Toolkit
+
+
+Description
+
+The NVIDIA CUDA Toolkit provides command-line and graphical
+tools for building, debugging and optimizing the performance
+of applications accelerated by NVIDIA GPUs, runtime and math
+libraries, and documentation including programming guides,
+user manuals, and API references.
+
+
+Default Install Location of CUDA Toolkit
+
+Windows platform:
+
+%ProgramFiles%\NVIDIA GPU Computing Toolkit\CUDA\v#.#
+
+Linux platform:
+
+/usr/local/cuda-#.#
+
+Mac platform:
+
+/Developer/NVIDIA/CUDA-#.#
+
+
+NVIDIA CUDA Samples
+
+
+Description
+
+CUDA Samples are now located in
+https://github.com/nvidia/cuda-samples, which includes
+instructions for obtaining, building, and running the samples.
+They are no longer included in the CUDA toolkit.
+
+
+NVIDIA Nsight Visual Studio Edition (Windows only)
+
+
+Description
+
+NVIDIA Nsight Development Platform, Visual Studio Edition is a
+development environment integrated into Microsoft Visual
+Studio that provides tools for debugging, profiling, analyzing
+and optimizing your GPU computing and graphics applications.
+
+
+Default Install Location of Nsight Visual Studio Edition
+
+Windows platform:
+
+%ProgramFiles(x86)%\NVIDIA Corporation\Nsight Visual Studio Edition #.#
+
+
+1. License Agreement for NVIDIA Software Development Kits
+---------------------------------------------------------
+
+
+Important Notice—Read before downloading, installing,
+copying or using the licensed software:
+-------------------------------------------------------
+
+This license agreement, including exhibits attached
+("Agreement”) is a legal agreement between you and NVIDIA
+Corporation ("NVIDIA") and governs your use of a NVIDIA
+software development kit (“SDK”).
+
+Each SDK has its own set of software and materials, but here
+is a description of the types of items that may be included in
+a SDK: source code, header files, APIs, data sets and assets
+(examples include images, textures, models, scenes, videos,
+native API input/output files), binary software, sample code,
+libraries, utility programs, programming code and
+documentation.
+
+This Agreement can be accepted only by an adult of legal age
+of majority in the country in which the SDK is used.
+
+If you are entering into this Agreement on behalf of a company
+or other legal entity, you represent that you have the legal
+authority to bind the entity to this Agreement, in which case
+“you” will mean the entity you represent.
+
+If you don’t have the required age or authority to accept
+this Agreement, or if you don’t accept all the terms and
+conditions of this Agreement, do not download, install or use
+the SDK.
+
+You agree to use the SDK only for purposes that are permitted
+by (a) this Agreement, and (b) any applicable law, regulation
+or generally accepted practices or guidelines in the relevant
+jurisdictions.
+
+
+1.1. License
+
+
+1.1.1. License Grant
+
+Subject to the terms of this Agreement, NVIDIA hereby grants
+you a non-exclusive, non-transferable license, without the
+right to sublicense (except as expressly provided in this
+Agreement) to:
+
+  1. Install and use the SDK,
+
+  2. Modify and create derivative works of sample source code
+    delivered in the SDK, and
+
+  3. Distribute those portions of the SDK that are identified
+    in this Agreement as distributable, as incorporated in
+    object code format into a software application that meets
+    the distribution requirements indicated in this Agreement.
+
+
+1.1.2. Distribution Requirements
+
+These are the distribution requirements for you to exercise
+the distribution grant:
+
+  1. Your application must have material additional
+    functionality, beyond the included portions of the SDK.
+
+  2. The distributable portions of the SDK shall only be
+    accessed by your application.
+
+  3. The following notice shall be included in modifications
+    and derivative works of sample source code distributed:
+    “This software contains source code provided by NVIDIA
+    Corporation.”
+
+  4. Unless a developer tool is identified in this Agreement
+    as distributable, it is delivered for your internal use
+    only.
+
+  5. The terms under which you distribute your application
+    must be consistent with the terms of this Agreement,
+    including (without limitation) terms relating to the
+    license grant and license restrictions and protection of
+    NVIDIA’s intellectual property rights. Additionally, you
+    agree that you will protect the privacy, security and
+    legal rights of your application users.
+
+  6. You agree to notify NVIDIA in writing of any known or
+    suspected distribution or use of the SDK not in compliance
+    with the requirements of this Agreement, and to enforce
+    the terms of your agreements with respect to distributed
+    SDK.
+
+
+1.1.3. Authorized Users
+
+You may allow employees and contractors of your entity or of
+your subsidiary(ies) to access and use the SDK from your
+secure network to perform work on your behalf.
+
+If you are an academic institution you may allow users
+enrolled or employed by the academic institution to access and
+use the SDK from your secure network.
+
+You are responsible for the compliance with the terms of this
+Agreement by your authorized users. If you become aware that
+your authorized users didn’t follow the terms of this
+Agreement, you agree to take reasonable steps to resolve the
+non-compliance and prevent new occurrences.
+
+
+1.1.4. Pre-Release SDK
+
+The SDK versions identified as alpha, beta, preview or
+otherwise as pre-release, may not be fully functional, may
+contain errors or design flaws, and may have reduced or
+different security, privacy, accessibility, availability, and
+reliability standards relative to commercial versions of
+NVIDIA software and materials. Use of a pre-release SDK may
+result in unexpected results, loss of data, project delays or
+other unpredictable damage or loss.
+
+You may use a pre-release SDK at your own risk, understanding
+that pre-release SDKs are not intended for use in production
+or business-critical systems.
+
+NVIDIA may choose not to make available a commercial version
+of any pre-release SDK. NVIDIA may also choose to abandon
+development and terminate the availability of a pre-release
+SDK at any time without liability.
+
+
+1.1.5. Updates
+
+NVIDIA may, at its option, make available patches, workarounds
+or other updates to this SDK. Unless the updates are provided
+with their separate governing terms, they are deemed part of
+the SDK licensed to you as provided in this Agreement. You
+agree that the form and content of the SDK that NVIDIA
+provides may change without prior notice to you. While NVIDIA
+generally maintains compatibility between versions, NVIDIA may
+in some cases make changes that introduce incompatibilities in
+future versions of the SDK.
+
+
+1.1.6. Components Under Other Licenses
+
+The SDK may come bundled with, or otherwise include or be
+distributed with, NVIDIA or third-party components with
+separate legal notices or terms as may be described in
+proprietary notices accompanying the SDK. If and to the extent
+there is a conflict between the terms in this Agreement and
+the license terms associated with the component, the license
+terms associated with the components control only to the
+extent necessary to resolve the conflict.
+
+Subject to the other terms of this Agreement, you may use the
+SDK to develop and test applications released under Open
+Source Initiative (OSI) approved open source software
+licenses.
+
+
+1.1.7. Reservation of Rights
+
+NVIDIA reserves all rights, title, and interest in and to the
+SDK, not expressly granted to you under this Agreement.
+
+
+1.2. Limitations
+
+The following license limitations apply to your use of the
+SDK:
+
+  1. You may not reverse engineer, decompile or disassemble,
+    or remove copyright or other proprietary notices from any
+    portion of the SDK or copies of the SDK.
+
+  2. Except as expressly provided in this Agreement, you may
+    not copy, sell, rent, sublicense, transfer, distribute,
+    modify, or create derivative works of any portion of the
+    SDK. For clarity, you may not distribute or sublicense the
+    SDK as a stand-alone product.
+
+  3. Unless you have an agreement with NVIDIA for this
+    purpose, you may not indicate that an application created
+    with the SDK is sponsored or endorsed by NVIDIA.
+
+  4. You may not bypass, disable, or circumvent any
+    encryption, security, digital rights management or
+    authentication mechanism in the SDK.
+
+  5. You may not use the SDK in any manner that would cause it
+    to become subject to an open source software license. As
+    examples, licenses that require as a condition of use,
+    modification, and/or distribution that the SDK be:
+
+      a. Disclosed or distributed in source code form;
+
+      b. Licensed for the purpose of making derivative works;
+        or
+
+      c. Redistributable at no charge.
+
+  6.  You acknowledge that the SDK as delivered is not tested
+    or certified by NVIDIA for use in connection with the
+    design, construction, maintenance, and/or operation of any
+    system where the use or failure of such system could
+    result in a situation that threatens the safety of human
+    life or results in catastrophic damages (each, a "Critical
+    Application"). Examples of Critical Applications include
+    use in avionics, navigation, autonomous vehicle
+    applications, ai solutions for automotive products,
+    military, medical, life support or other life critical
+    applications. NVIDIA shall not be liable to you or any
+    third party, in whole or in part, for any claims or
+    damages arising from such uses. You are solely responsible
+    for ensuring that any product or service developed with
+    the SDK as a whole includes sufficient features to comply
+    with all applicable legal and regulatory standards and
+    requirements.
+
+  7.  You agree to defend, indemnify and hold harmless NVIDIA
+    and its affiliates, and their respective employees,
+    contractors, agents, officers and directors, from and
+    against any and all claims, damages, obligations, losses,
+    liabilities, costs or debt, fines, restitutions and
+    expenses (including but not limited to attorney’s fees
+    and costs incident to establishing the right of
+    indemnification) arising out of or related to products or
+    services that use the SDK in or for Critical Applications,
+    and for use of the SDK outside of the scope of this
+    Agreement or not in compliance with its terms.
+
+  8. You may not reverse engineer, decompile or disassemble
+    any portion of the output generated using SDK elements for
+    the purpose of translating such output artifacts to target
+    a non-NVIDIA platform.
+
+
+1.3. Ownership
+
+  1.  NVIDIA or its licensors hold all rights, title and
+    interest in and to the SDK and its modifications and
+    derivative works, including their respective intellectual
+    property rights, subject to your rights under Section
+    1.3.2. This SDK may include software and materials from
+    NVIDIA’s licensors, and these licensors are intended
+    third party beneficiaries that may enforce this Agreement
+    with respect to their intellectual property rights.
+
+  2.  You hold all rights, title and interest in and to your
+    applications and your derivative works of the sample
+    source code delivered in the SDK, including their
+    respective intellectual property rights, subject to
+    NVIDIA’s rights under Section 1.3.1.
+
+  3. You may, but don’t have to, provide to NVIDIA
+    suggestions, feature requests or other feedback regarding
+    the SDK, including possible enhancements or modifications
+    to the SDK. For any feedback that you voluntarily provide,
+    you hereby grant NVIDIA and its affiliates a perpetual,
+    non-exclusive, worldwide, irrevocable license to use,
+    reproduce, modify, license, sublicense (through multiple
+    tiers of sublicensees), and distribute (through multiple
+    tiers of distributors) it without the payment of any
+    royalties or fees to you. NVIDIA will use feedback at its
+    choice. NVIDIA is constantly looking for ways to improve
+    its products, so you may send feedback to NVIDIA through
+    the developer portal at https://developer.nvidia.com.
+
+
+1.4. No Warranties
+
+THE SDK IS PROVIDED BY NVIDIA “AS IS” AND “WITH ALL
+FAULTS.” TO THE MAXIMUM EXTENT PERMITTED BY LAW, NVIDIA AND
+ITS AFFILIATES EXPRESSLY DISCLAIM ALL WARRANTIES OF ANY KIND
+OR NATURE, WHETHER EXPRESS, IMPLIED OR STATUTORY, INCLUDING,
+BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE, TITLE, NON-INFRINGEMENT, OR THE
+ABSENCE OF ANY DEFECTS THEREIN, WHETHER LATENT OR PATENT. NO
+WARRANTY IS MADE ON THE BASIS OF TRADE USAGE, COURSE OF
+DEALING OR COURSE OF TRADE.
+
+
+1.5. Limitation of Liability
+
+TO THE MAXIMUM EXTENT PERMITTED BY LAW, NVIDIA AND ITS
+AFFILIATES SHALL NOT BE LIABLE FOR ANY (I) SPECIAL, INCIDENTAL,
+PUNITIVE OR CONSEQUENTIAL DAMAGES, OR (II) DAMAGES FOR (A) ANY 
+LOST PROFITS, LOSS OF USE, LOSS OF DATA OR LOSS OF GOODWILL, 
+OR THE COSTS OF PROCURING SUBSTITUTE PRODUCTS, ARISING OUT OF 
+OR IN CONNECTION WITH THIS AGREEMENT OR THE USE OR PERFORMANCE 
+OF THE SDK, WHETHER SUCH LIABILITY ARISES FROM ANY CLAIM BASED 
+UPON BREACH OF CONTRACT, BREACH OF WARRANTY, TORT (INCLUDING 
+NEGLIGENCE), PRODUCT LIABILITY OR ANY OTHER CAUSE OF ACTION OR 
+THEORY OF LIABILITY. IN NO EVENT WILL NVIDIA’S AND ITS AFFILIATES
+TOTAL CUMULATIVE LIABILITY UNDER OR ARISING OUT OF THIS
+AGREEMENT EXCEED US$10.00. THE NATURE OF THE LIABILITY OR THE
+NUMBER OF CLAIMS OR SUITS SHALL NOT ENLARGE OR EXTEND THIS
+LIMIT.
+
+These exclusions and limitations of liability shall apply
+regardless if NVIDIA or its affiliates have been advised of
+the possibility of such damages, and regardless of whether a
+remedy fails its essential purpose. These exclusions and
+limitations of liability form an essential basis of the
+bargain between the parties, and, absent any of these
+exclusions or limitations of liability, the provisions of this
+Agreement, including, without limitation, the economic terms,
+would be substantially different.
+
+
+1.6. Termination
+
+  1. This Agreement will continue to apply until terminated by
+    either you or NVIDIA as described below.
+
+  2. If you want to terminate this Agreement, you may do so by
+    stopping to use the SDK.
+
+  3. NVIDIA may, at any time, terminate this Agreement if:
+
+      a. (i) you fail to comply with any term of this
+        Agreement and the non-compliance is not fixed within
+        thirty (30) days following notice from NVIDIA (or
+        immediately if you violate NVIDIA’s intellectual
+        property rights);
+
+      b. (ii) you commence or participate in any legal
+        proceeding against NVIDIA with respect to the SDK; or
+
+      c. (iii) NVIDIA decides to no longer provide the SDK in
+        a country or, in NVIDIA’s sole discretion, the
+        continued use of it is no longer commercially viable.
+
+  4. Upon any termination of this Agreement, you agree to
+    promptly discontinue use of the SDK and destroy all copies
+    in your possession or control. Your prior distributions in
+    accordance with this Agreement are not affected by the
+    termination of this Agreement. Upon written request, you
+    will certify in writing that you have complied with your
+    commitments under this section. Upon any termination of
+    this Agreement all provisions survive except for the
+    license grant provisions.
+
+
+1.7. General
+
+If you wish to assign this Agreement or your rights and
+obligations, including by merger, consolidation, dissolution
+or operation of law, contact NVIDIA to ask for permission. Any
+attempted assignment not approved by NVIDIA in writing shall
+be void and of no effect. NVIDIA may assign, delegate or
+transfer this Agreement and its rights and obligations, and if
+to a non-affiliate you will be notified.
+
+You agree to cooperate with NVIDIA and provide reasonably
+requested information to verify your compliance with this
+Agreement.
+
+This Agreement will be governed in all respects by the laws of
+the United States and of the State of Delaware, without regard to the
+conflicts of laws principles. The United Nations Convention on
+Contracts for the International Sale of Goods is specifically
+disclaimed. You agree to all terms of this Agreement in the
+English language.
+
+The state or federal courts residing in Santa Clara County,
+California shall have exclusive jurisdiction over any dispute
+or claim arising out of this Agreement. Notwithstanding this,
+you agree that NVIDIA shall still be allowed to apply for
+injunctive remedies or an equivalent type of urgent legal
+relief in any jurisdiction.
+
+If any court of competent jurisdiction determines that any
+provision of this Agreement is illegal, invalid or
+unenforceable, such provision will be construed as limited to
+the extent necessary to be consistent with and fully
+enforceable under the law and the remaining provisions will
+remain in full force and effect. Unless otherwise specified,
+remedies are cumulative.
+
+Each party acknowledges and agrees that the other is an
+independent contractor in the performance of this Agreement.
+
+The SDK has been developed entirely at private expense and is
+“commercial items” consisting of “commercial computer
+software” and “commercial computer software
+documentation” provided with RESTRICTED RIGHTS. Use,
+duplication or disclosure by the U.S. Government or a U.S.
+Government subcontractor is subject to the restrictions in
+this Agreement pursuant to DFARS 227.7202-3(a) or as set forth
+in subparagraphs (c)(1) and (2) of the Commercial Computer
+Software - Restricted Rights clause at FAR 52.227-19, as
+applicable. Contractor/manufacturer is NVIDIA, 2788 San Tomas
+Expressway, Santa Clara, CA 95051.
+
+The SDK is subject to United States export laws and
+regulations. You agree that you will not ship, transfer or
+export the SDK into any country, or use the SDK in any manner,
+prohibited by the United States Bureau of Industry and
+Security or economic sanctions regulations administered by the
+U.S. Department of Treasury’s Office of Foreign Assets
+Control (OFAC), or any applicable export laws, restrictions or
+regulations. These laws include restrictions on destinations,
+end users and end use. By accepting this Agreement, you
+confirm that you are not located in a country currently 
+embargoed by the U.S. or otherwise prohibited from receiving 
+the SDK under U.S. law.
+
+Any notice delivered by NVIDIA to you under this Agreement
+will be delivered via mail, email or fax. You agree that any
+notices that NVIDIA sends you electronically will satisfy any
+legal communication requirements. Please direct your legal
+notices or other correspondence to NVIDIA Corporation, 2788
+San Tomas Expressway, Santa Clara, California 95051, United
+States of America, Attention: Legal Department.
+
+This Agreement and any exhibits incorporated into this
+Agreement constitute the entire agreement of the parties with
+respect to the subject matter of this Agreement and supersede
+all prior negotiations or documentation exchanged between the
+parties relating to this SDK license. Any additional and/or
+conflicting terms on documents issued by you are null, void,
+and invalid. Any amendment or waiver under this Agreement
+shall be in writing and signed by representatives of both
+parties.
+
+
+2. CUDA Toolkit Supplement to Software License Agreement for
+NVIDIA Software Development Kits
+------------------------------------------------------------
+
+The terms in this supplement govern your use of the NVIDIA
+CUDA Toolkit SDK under the terms of your license agreement
+(“Agreement”) as modified by this supplement. Capitalized
+terms used but not defined below have the meaning assigned to
+them in the Agreement.
+
+This supplement is an exhibit to the Agreement and is
+incorporated as an integral part of the Agreement. In the
+event of conflict between the terms in this supplement and the
+terms in the Agreement, the terms in this supplement govern.
+
+
+2.1. License Scope
+
+The SDK is licensed for you to develop applications only for
+use in systems with NVIDIA GPUs.
+
+
+2.2. Distribution
+
+The portions of the SDK that are distributable under the
+Agreement are listed in Attachment A.
+
+
+2.3. Operating Systems
+
+Those portions of the SDK designed exclusively for use on the
+Linux or FreeBSD operating systems, or other operating systems
+derived from the source code to these operating systems, may
+be copied and redistributed for use in accordance with this
+Agreement, provided that the object code files are not
+modified in any way (except for unzipping of compressed
+files).
+
+
+2.4. Audio and Video Encoders and Decoders
+
+You acknowledge and agree that it is your sole responsibility
+to obtain any additional third-party licenses required to
+make, have made, use, have used, sell, import, and offer for
+sale your products or services that include or incorporate any
+third-party software and content relating to audio and/or
+video encoders and decoders from, including but not limited
+to, Microsoft, Thomson, Fraunhofer IIS, Sisvel S.p.A.,
+MPEG-LA, and Coding Technologies. NVIDIA does not grant to you
+under this Agreement any necessary patent or other rights with
+respect to any audio and/or video encoders and decoders.
+
+
+2.5. Licensing
+
+If the distribution terms in this Agreement are not suitable
+for your organization, or for any questions regarding this
+Agreement, please contact NVIDIA at
+nvidia-compute-license-questions@nvidia.com.
+
+
+2.6. Attachment A
+
+The following CUDA Toolkit files may be distributed with
+applications developed by you, including certain
+variations of these files that have version number or
+architecture specific information embedded in the file name -
+as an example only, for release version 9.0 of the 64-bit
+Windows software, the file cudart64_90.dll is redistributable.
+
+Component
+
+CUDA Runtime
+
+Windows
+
+cudart.dll, cudart_static.lib, cudadevrt.lib
+
+Mac OSX
+
+libcudart.dylib, libcudart_static.a, libcudadevrt.a
+
+Linux
+
+libcudart.so, libcudart_static.a, libcudadevrt.a
+
+Android
+
+libcudart.so, libcudart_static.a, libcudadevrt.a
+
+Component
+
+CUDA FFT Library
+
+Windows
+
+cufft.dll, cufftw.dll, cufft.lib, cufftw.lib
+
+Mac OSX
+
+libcufft.dylib, libcufft_static.a, libcufftw.dylib,
+libcufftw_static.a
+
+Linux
+
+libcufft.so, libcufft_static.a, libcufftw.so,
+libcufftw_static.a
+
+Android
+
+libcufft.so, libcufft_static.a, libcufftw.so,
+libcufftw_static.a
+
+Component
+
+CUDA BLAS Library
+
+Windows
+
+cublas.dll, cublasLt.dll
+
+Mac OSX
+
+libcublas.dylib, libcublasLt.dylib, libcublas_static.a,
+libcublasLt_static.a
+
+Linux
+
+libcublas.so, libcublasLt.so, libcublas_static.a,
+libcublasLt_static.a
+
+Android
+
+libcublas.so, libcublasLt.so, libcublas_static.a,
+libcublasLt_static.a
+
+Component
+
+NVIDIA "Drop-in" BLAS Library
+
+Windows
+
+nvblas.dll
+
+Mac OSX
+
+libnvblas.dylib
+
+Linux
+
+libnvblas.so
+
+Component
+
+CUDA Sparse Matrix Library
+
+Windows
+
+cusparse.dll, cusparse.lib
+
+Mac OSX
+
+libcusparse.dylib, libcusparse_static.a
+
+Linux
+
+libcusparse.so, libcusparse_static.a
+
+Android
+
+libcusparse.so, libcusparse_static.a
+
+Component
+
+CUDA Linear Solver Library
+
+Windows
+
+cusolver.dll, cusolver.lib
+
+Mac OSX
+
+libcusolver.dylib, libcusolver_static.a
+
+Linux
+
+libcusolver.so, libcusolver_static.a
+
+Android
+
+libcusolver.so, libcusolver_static.a
+
+Component
+
+CUDA Random Number Generation Library
+
+Windows
+
+curand.dll, curand.lib
+
+Mac OSX
+
+libcurand.dylib, libcurand_static.a
+
+Linux
+
+libcurand.so, libcurand_static.a
+
+Android
+
+libcurand.so, libcurand_static.a
+
+Component
+
+NVIDIA Performance Primitives Library
+
+Windows
+
+nppc.dll, nppc.lib, nppial.dll, nppial.lib, nppicc.dll,
+nppicc.lib, nppicom.dll, nppicom.lib, nppidei.dll,
+nppidei.lib, nppif.dll, nppif.lib, nppig.dll, nppig.lib,
+nppim.dll, nppim.lib, nppist.dll, nppist.lib, nppisu.dll,
+nppisu.lib, nppitc.dll, nppitc.lib, npps.dll, npps.lib
+
+Mac OSX
+
+libnppc.dylib, libnppc_static.a, libnppial.dylib,
+libnppial_static.a, libnppicc.dylib, libnppicc_static.a,
+libnppicom.dylib, libnppicom_static.a, libnppidei.dylib,
+libnppidei_static.a, libnppif.dylib, libnppif_static.a,
+libnppig.dylib, libnppig_static.a, libnppim.dylib,
+libnppisu_static.a, libnppitc.dylib, libnppitc_static.a,
+libnpps.dylib, libnpps_static.a
+
+Linux
+
+libnppc.so, libnppc_static.a, libnppial.so,
+libnppial_static.a, libnppicc.so, libnppicc_static.a,
+libnppicom.so, libnppicom_static.a, libnppidei.so,
+libnppidei_static.a, libnppif.so, libnppif_static.a
+libnppig.so, libnppig_static.a, libnppim.so,
+libnppim_static.a, libnppist.so, libnppist_static.a,
+libnppisu.so, libnppisu_static.a, libnppitc.so
+libnppitc_static.a, libnpps.so, libnpps_static.a
+
+Android
+
+libnppc.so, libnppc_static.a, libnppial.so,
+libnppial_static.a, libnppicc.so, libnppicc_static.a,
+libnppicom.so, libnppicom_static.a, libnppidei.so,
+libnppidei_static.a, libnppif.so, libnppif_static.a
+libnppig.so, libnppig_static.a, libnppim.so,
+libnppim_static.a, libnppist.so, libnppist_static.a,
+libnppisu.so, libnppisu_static.a, libnppitc.so
+libnppitc_static.a, libnpps.so, libnpps_static.a
+
+Component
+
+NVIDIA JPEG Library
+
+Windows
+
+nvjpeg.lib, nvjpeg.dll
+
+Linux
+
+libnvjpeg.so, libnvjpeg_static.a
+
+Component
+
+Internal common library required for statically linking to
+cuBLAS, cuSPARSE, cuFFT, cuRAND, nvJPEG and NPP
+
+Mac OSX
+
+libculibos.a
+
+Linux
+
+libculibos.a
+
+Component
+
+NVIDIA Runtime Compilation Library and Header
+
+All
+
+nvrtc.h
+
+Windows
+
+nvrtc.dll, nvrtc-builtins.dll
+
+Mac OSX
+
+libnvrtc.dylib, libnvrtc-builtins.dylib
+
+Linux
+
+libnvrtc.so, libnvrtc-builtins.so, libnvrtc_static.a, libnvrtx-builtins_static.a
+
+Component
+
+NVIDIA Optimizing Compiler Library
+
+Windows
+
+nvvm.dll
+
+Mac OSX
+
+libnvvm.dylib
+
+Linux
+
+libnvvm.so
+
+Component
+
+NVIDIA JIT Linking Library
+
+Windows
+
+libnvJitLink.dll, libnvJitLink.lib
+
+Linux
+
+libnvJitLink.so, libnvJitLink_static.a
+
+Component
+
+NVIDIA Common Device Math Functions Library
+
+Windows
+
+libdevice.10.bc
+
+Mac OSX
+
+libdevice.10.bc
+
+Linux
+
+libdevice.10.bc
+
+Component
+
+CUDA Occupancy Calculation Header Library
+
+All
+
+cuda_occupancy.h
+
+Component
+
+CUDA Half Precision Headers
+
+All
+
+cuda_fp16.h, cuda_fp16.hpp
+
+Component
+
+CUDA Profiling Tools Interface (CUPTI) Library
+
+Windows
+
+cupti.dll
+
+Mac OSX
+
+libcupti.dylib
+
+Linux
+
+libcupti.so
+
+Component
+
+NVIDIA Tools Extension Library
+
+Windows
+
+nvToolsExt.dll, nvToolsExt.lib
+
+Mac OSX
+
+libnvToolsExt.dylib
+
+Linux
+
+libnvToolsExt.so
+
+Component
+
+NVIDIA CUDA Driver Libraries
+
+Linux
+
+libcuda.so, libnvidia-ptxjitcompiler.so, libnvptxcompiler_static.a
+
+Component
+
+NVIDIA CUDA File IO Libraries and Header
+
+All
+
+cufile.h
+
+Linux
+
+libcufile.so, libcufile_rdma.so, libcufile_static.a,
+libcufile_rdma_static.a
+
+In addition to the rights above, for parties that are
+developing software intended solely for use on Jetson
+development kits or Jetson modules, and running Linux for
+Tegra software, the following shall apply:
+
+  * The SDK may be distributed in its entirety, as provided by
+    NVIDIA, and without separation of its components, for you
+    and/or your licensees to create software development kits
+    for use only on the Jetson platform and running Linux for
+    Tegra software.
+
+
+2.7. Attachment B
+
+
+Additional Licensing Obligations
+
+The following third party components included in the SOFTWARE
+are licensed to Licensee pursuant to the following terms and
+conditions:
+
+  1. Licensee's use of the GDB third party component is
+    subject to the terms and conditions of GNU GPL v3:
+
+    This product includes copyrighted third-party software licensed
+    under the terms of the GNU General Public License v3 ("GPL v3").
+    All third-party software packages are copyright by their respective
+    authors. GPL v3 terms and conditions are hereby incorporated into
+    the Agreement by this reference:     http://www.gnu.org/licenses/gpl.txt
+
+    Consistent with these licensing requirements, the software
+    listed below is provided under the terms of the specified
+    open source software licenses. To obtain source code for
+    software provided under licenses that require
+    redistribution of source code, including the GNU General
+    Public License (GPL) and GNU Lesser General Public License
+    (LGPL), contact oss-requests@nvidia.com. This offer is
+    valid for a period of three (3) years from the date of the
+    distribution of this product by NVIDIA CORPORATION.
+
+    Component          License
+    CUDA-GDB           GPL v3  
+
+  2. Licensee represents and warrants that any and all third
+    party licensing and/or royalty payment obligations in
+    connection with Licensee's use of the H.264 video codecs
+    are solely the responsibility of Licensee.
+
+  3. Licensee's use of the Thrust library is subject to the
+    terms and conditions of the Apache License Version 2.0.
+    All third-party software packages are copyright by their
+    respective authors. Apache License Version 2.0 terms and
+    conditions are hereby incorporated into the Agreement by
+    this reference.
+    http://www.apache.org/licenses/LICENSE-2.0.html
+
+    In addition, Licensee acknowledges the following notice:
+    Thrust includes source code from the Boost Iterator,
+    Tuple, System, and Random Number libraries.
+
+    Boost Software License - Version 1.0 - August 17th, 2003
+    . . . .
+    
+    Permission is hereby granted, free of charge, to any person or 
+    organization obtaining a copy of the software and accompanying 
+    documentation covered by this license (the "Software") to use, 
+    reproduce, display, distribute, execute, and transmit the Software, 
+    and to prepare derivative works of the Software, and to permit 
+    third-parties to whom the Software is furnished to do so, all 
+    subject to the following:
+    
+    The copyright notices in the Software and this entire statement, 
+    including the above license grant, this restriction and the following 
+    disclaimer, must be included in all copies of the Software, in whole 
+    or in part, and all derivative works of the Software, unless such 
+    copies or derivative works are solely in the form of machine-executable 
+    object code generated by a source language processor.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND 
+    NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR 
+    ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+    OTHER DEALINGS IN THE SOFTWARE.  
+
+  4. Licensee's use of the LLVM third party component is
+    subject to the following terms and conditions:
+
+    ======================================================
+    LLVM Release License
+    ======================================================
+    University of Illinois/NCSA
+    Open Source License
+    
+    Copyright (c) 2003-2010 University of Illinois at Urbana-Champaign.
+    All rights reserved.
+    
+    Developed by:
+    
+        LLVM Team
+    
+        University of Illinois at Urbana-Champaign
+    
+        http://llvm.org
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to 
+    deal with the Software without restriction, including without limitation the
+    rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+    sell copies of the Software, and to permit persons to whom the Software is 
+    furnished to do so, subject to the following conditions:
+    
+    *  Redistributions of source code must retain the above copyright notice, 
+       this list of conditions and the following disclaimers.
+    
+    *  Redistributions in binary form must reproduce the above copyright 
+       notice, this list of conditions and the following disclaimers in the 
+       documentation and/or other materials provided with the distribution.
+    
+    *  Neither the names of the LLVM Team, University of Illinois at Urbana-
+       Champaign, nor the names of its contributors may be used to endorse or
+       promote products derived from this Software without specific prior 
+       written permission.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL 
+    THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+    ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS WITH THE SOFTWARE.  
+
+  5. Licensee's use of the PCRE third party component is
+    subject to the following terms and conditions:
+
+    ------------
+    PCRE LICENCE
+    ------------
+    PCRE is a library of functions to support regular expressions whose syntax
+    and semantics are as close as possible to those of the Perl 5 language.
+    Release 8 of PCRE is distributed under the terms of the "BSD" licence, as
+    specified below. The documentation for PCRE, supplied in the "doc" 
+    directory, is distributed under the same terms as the software itself. The
+    basic library functions are written in C and are freestanding. Also 
+    included in the distribution is a set of C++ wrapper functions, and a just-
+    in-time compiler that can be used to optimize pattern matching. These are 
+    both optional features that can be omitted when the library is built.
+    
+    THE BASIC LIBRARY FUNCTIONS
+    ---------------------------
+    Written by:       Philip Hazel
+    Email local part: ph10
+    Email domain:     cam.ac.uk
+    University of Cambridge Computing Service,
+    Cambridge, England.
+    Copyright (c) 1997-2012 University of Cambridge
+    All rights reserved.
+    
+    PCRE JUST-IN-TIME COMPILATION SUPPORT
+    -------------------------------------
+    Written by:       Zoltan Herczeg
+    Email local part: hzmester
+    Emain domain:     freemail.hu
+    Copyright(c) 2010-2012 Zoltan Herczeg
+    All rights reserved.
+    
+    STACK-LESS JUST-IN-TIME COMPILER
+    --------------------------------
+    Written by:       Zoltan Herczeg
+    Email local part: hzmester
+    Emain domain:     freemail.hu
+    Copyright(c) 2009-2012 Zoltan Herczeg
+    All rights reserved.
+    
+    THE C++ WRAPPER FUNCTIONS
+    -------------------------
+    Contributed by:   Google Inc.
+    Copyright (c) 2007-2012, Google Inc.
+    All rights reserved.
+
+    THE "BSD" LICENCE
+    -----------------
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+      * Redistributions of source code must retain the above copyright notice, 
+        this list of conditions and the following disclaimer.
+    
+      * Redistributions in binary form must reproduce the above copyright 
+        notice, this list of conditions and the following disclaimer in the 
+        documentation and/or other materials provided with the distribution.
+    
+      * Neither the name of the University of Cambridge nor the name of Google 
+        Inc. nor the names of their contributors may be used to endorse or 
+        promote products derived from this software without specific prior 
+        written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+    ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  6. Some of the cuBLAS library routines were written by or
+    derived from code written by Vasily Volkov and are subject
+    to the Modified Berkeley Software Distribution License as
+    follows:
+
+    Copyright (c) 2007-2009, Regents of the University of California
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the University of California, Berkeley nor
+          the names of its contributors may be used to endorse or promote
+          products derived from this software without specific prior
+          written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+    STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  7. Some of the cuBLAS library routines were written by or
+    derived from code written by Davide Barbieri and are
+    subject to the Modified Berkeley Software Distribution
+    License as follows:
+
+    Copyright (c) 2008-2009 Davide Barbieri @ University of Rome Tor Vergata.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * The name of the author may not be used to endorse or promote
+          products derived from this software without specific prior
+          written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+    STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  8. Some of the cuBLAS library routines were derived from
+    code developed by the University of Tennessee and are
+    subject to the Modified Berkeley Software Distribution
+    License as follows:
+
+    Copyright (c) 2010 The University of Tennessee.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer listed in this license in the documentation and/or
+          other materials provided with the distribution.
+        * Neither the name of the copyright holders nor the names of its
+          contributors may be used to endorse or promote products derived
+          from this software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  9. Some of the cuBLAS library routines were written by or
+    derived from code written by Jonathan Hogg and are subject
+    to the Modified Berkeley Software Distribution License as
+    follows:
+
+    Copyright (c) 2012, The Science and Technology Facilities Council (STFC).
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the STFC nor the names of its contributors
+          may be used to endorse or promote products derived from this
+          software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE STFC BE
+    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+    BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+    WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+    OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+    IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  10. Some of the cuBLAS library routines were written by or
+    derived from code written by Ahmad M. Abdelfattah, David
+    Keyes, and Hatem Ltaief, and are subject to the Apache
+    License, Version 2.0, as follows:
+
+     -- (C) Copyright 2013 King Abdullah University of Science and Technology
+      Authors:
+      Ahmad Abdelfattah (ahmad.ahmad@kaust.edu.sa)
+      David Keyes (david.keyes@kaust.edu.sa)
+      Hatem Ltaief (hatem.ltaief@kaust.edu.sa)
+    
+      Redistribution  and  use  in  source and binary forms, with or without
+      modification,  are  permitted  provided  that the following conditions
+      are met:
+    
+      * Redistributions  of  source  code  must  retain  the above copyright
+        notice,  this  list  of  conditions  and  the  following  disclaimer.
+      * Redistributions  in  binary  form must reproduce the above copyright
+        notice,  this list of conditions and the following disclaimer in the
+        documentation  and/or other materials provided with the distribution.
+      * Neither  the  name of the King Abdullah University of Science and
+        Technology nor the names of its contributors may be used to endorse 
+        or promote products derived from this software without specific prior 
+        written permission.
+    
+      THIS  SOFTWARE  IS  PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+      ``AS IS''  AND  ANY  EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+      LIMITED  TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+      A  PARTICULAR  PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+      HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+      SPECIAL,  EXEMPLARY,  OR  CONSEQUENTIAL  DAMAGES  (INCLUDING,  BUT NOT
+      LIMITED  TO,  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+      DATA,  OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+      THEORY  OF  LIABILITY,  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+      (INCLUDING  NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+      OF  THIS  SOFTWARE,  EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE  
+
+  11. Some of the cuSPARSE library routines were written by or
+    derived from code written by Li-Wen Chang and are subject
+    to the NCSA Open Source License as follows:
+
+    Copyright (c) 2012, University of Illinois.
+    
+    All rights reserved.
+    
+    Developed by: IMPACT Group, University of Illinois, http://impact.crhc.illinois.edu
+    
+    Permission is hereby granted, free of charge, to any person obtaining
+    a copy of this software and associated documentation files (the
+    "Software"), to deal with the Software without restriction, including
+    without limitation the rights to use, copy, modify, merge, publish,
+    distribute, sublicense, and/or sell copies of the Software, and to
+    permit persons to whom the Software is furnished to do so, subject to
+    the following conditions:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimers in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the names of IMPACT Group, University of Illinois, nor
+          the names of its contributors may be used to endorse or promote
+          products derived from this Software without specific prior
+          written permission.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+    NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT
+    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+    IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+    IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE
+    SOFTWARE.  
+
+  12. Some of the cuRAND library routines were written by or
+    derived from code written by Mutsuo Saito and Makoto
+    Matsumoto and are subject to the following license:
+
+    Copyright (c) 2009, 2010 Mutsuo Saito, Makoto Matsumoto and Hiroshima
+    University. All rights reserved.
+    
+    Copyright (c) 2011 Mutsuo Saito, Makoto Matsumoto, Hiroshima
+    University and University of Tokyo.  All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the Hiroshima University nor the names of
+          its contributors may be used to endorse or promote products
+          derived from this software without specific prior written
+          permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  13. Some of the cuRAND library routines were derived from
+    code developed by D. E. Shaw Research and are subject to
+    the following license:
+
+    Copyright 2010-2011, D. E. Shaw Research.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions, and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions, and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of D. E. Shaw Research nor the names of its
+          contributors may be used to endorse or promote products derived
+          from this software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  14. Some of the Math library routines were written by or
+    derived from code developed by Norbert Juffa and are
+    subject to the following license:
+
+    Copyright (c) 2015-2017, Norbert Juffa
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without 
+    modification, are permitted provided that the following conditions
+    are met:
+    
+    1. Redistributions of source code must retain the above copyright 
+       notice, this list of conditions and the following disclaimer.
+    
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  15. Licensee's use of the lz4 third party component is
+    subject to the following terms and conditions:
+
+    Copyright (C) 2011-2013, Yann Collet.
+    BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+    
+        * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+    copyright notice, this list of conditions and the following disclaimer
+    in the documentation and/or other materials provided with the
+    distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  16. The NPP library uses code from the Boost Math Toolkit,
+    and is subject to the following license:
+
+    Boost Software License - Version 1.0 - August 17th, 2003
+    . . . .
+    
+    Permission is hereby granted, free of charge, to any person or 
+    organization obtaining a copy of the software and accompanying 
+    documentation covered by this license (the "Software") to use, 
+    reproduce, display, distribute, execute, and transmit the Software, 
+    and to prepare derivative works of the Software, and to permit 
+    third-parties to whom the Software is furnished to do so, all 
+    subject to the following:
+    
+    The copyright notices in the Software and this entire statement, 
+    including the above license grant, this restriction and the following 
+    disclaimer, must be included in all copies of the Software, in whole 
+    or in part, and all derivative works of the Software, unless such 
+    copies or derivative works are solely in the form of machine-executable 
+    object code generated by a source language processor.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND 
+    NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR 
+    ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+    OTHER DEALINGS IN THE SOFTWARE.  
+
+  17. Portions of the Nsight Eclipse Edition is subject to the
+    following license:
+
+    The Eclipse Foundation makes available all content in this plug-in
+    ("Content"). Unless otherwise indicated below, the Content is provided
+    to you under the terms and conditions of the Eclipse Public License
+    Version 1.0 ("EPL"). A copy of the EPL is available at http://
+    www.eclipse.org/legal/epl-v10.html. For purposes of the EPL, "Program"
+    will mean the Content.
+    
+    If you did not receive this Content directly from the Eclipse
+    Foundation, the Content is being redistributed by another party
+    ("Redistributor") and different terms and conditions may apply to your
+    use of any object code in the Content. Check the Redistributor's
+    license that was provided with the Content. If no such license exists,
+    contact the Redistributor. Unless otherwise indicated below, the terms
+    and conditions of the EPL still apply to any source code in the
+    Content and such source code may be obtained at http://www.eclipse.org.  
+
+  18. Some of the cuBLAS library routines uses code from
+    OpenAI, which is subject to the following license:
+
+    License URL 
+    https://github.com/openai/openai-gemm/blob/master/LICENSE
+    
+    License Text 
+    The MIT License
+    
+    Copyright (c) 2016 OpenAI (http://openai.com), 2016 Google Inc.
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.   
+
+  19. Licensee's use of the Visual Studio Setup Configuration
+    Samples is subject to the following license:
+
+    The MIT License (MIT) 
+    Copyright (C) Microsoft Corporation. All rights reserved.
+    
+    Permission is hereby granted, free of charge, to any person 
+    obtaining a copy of this software and associated documentation 
+    files (the "Software"), to deal in the Software without restriction, 
+    including without limitation the rights to use, copy, modify, merge, 
+    publish, distribute, sublicense, and/or sell copies of the Software, 
+    and to permit persons to whom the Software is furnished to do so, 
+    subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included 
+    in all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 
+    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.  
+
+  20. Licensee's use of linmath.h header for CPU functions for
+    GL vector/matrix operations from lunarG is subject to the
+    Apache License Version 2.0.
+
+  21. The DX12-CUDA sample uses the d3dx12.h header, which is
+    subject to the MIT license.
+
+  22. Components of the driver and compiler used for binary management, including 
+    nvFatBin, nvcc, and cuobjdump, use the Zstandard library which is subject to
+	the following license:
+
+    BSD License
+
+    For Zstandard software
+
+    Copyright (c) Meta Platforms, Inc. and affiliates. All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without modification,
+ 	are permitted provided that the following conditions are met:
+
+        * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+
+        * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+
+        * Neither the name Facebook, nor Meta, nor the names of its contributors may
+      be used to endorse or promote products derived from this software without
+      specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY
+    DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+    BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+    OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+    WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+    OF SUCH DAMAGE.
+
+-----------------
diff --git a/licenses/NVIDIA-CUDA-NOTICE.txt b/licenses/NVIDIA-CUDA-NOTICE.txt
new file mode 100644
index 00000000..2cab53eb
--- /dev/null
+++ b/licenses/NVIDIA-CUDA-NOTICE.txt
@@ -0,0 +1,19 @@
+NVIDIA CUDA Toolkit (runtime libraries)
+Copyright (C) NVIDIA Corporation. All rights reserved.
+https://developer.nvidia.com/cuda-toolkit
+
+When Jungfraujoch is built with CUDA support (JFJOCH_USE_CUDA=ON, the default), the binaries
+statically link and redistribute portions of the NVIDIA CUDA runtime and math libraries,
+including the CUDA runtime (cudart) and cuFFT.
+
+These NVIDIA components are not covered by the GPLv3 license of Jungfraujoch. They are
+redistributed under the NVIDIA CUDA Toolkit End User License Agreement (EULA), which permits
+redistribution of the runtime components listed in its attachments:
+
+  * EULA: see licenses/NVIDIA-CUDA-EULA.txt (verbatim CUDA Toolkit 12.8 EULA, as shipped in
+    $CUDA_HOME/EULA.txt), also at https://docs.nvidia.com/cuda/eula/index.html
+  * Redistributable component list: see "Attachment A" of that EULA for the runtime components
+    that may be redistributed.
+
+When building against a different CUDA Toolkit version, replace licenses/NVIDIA-CUDA-EULA.txt
+with the EULA.txt shipped by that toolkit.
diff --git a/licenses/Qt6-LGPL-3.0.txt b/licenses/Qt6-LGPL-3.0.txt
new file mode 100644
index 00000000..0a041280
--- /dev/null
+++ b/licenses/Qt6-LGPL-3.0.txt
@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
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+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
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+  2. Conveying Modified Versions.
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+  If you modify a copy of the Library, and, in your modifications, a
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+  The object code form of an Application may incorporate material from
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+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
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+
+   b) Accompany the object code with a copy of the GNU GPL and this license
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+
+  4. Combined Works.
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+  You may convey a Combined Work under terms of your choice that,
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+portions of the Library contained in the Combined Work and reverse
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+the following:
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+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
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+   GNU GPL, and only to the extent that such information is
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+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
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+   Information in the manner specified by section 6 of the GNU GPL
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+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
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+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
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+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
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+received it does not specify a version number of the GNU Lesser
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+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
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+Library.
diff --git a/licenses/Qt6-NOTICE.txt b/licenses/Qt6-NOTICE.txt
new file mode 100644
index 00000000..6a0b7bf0
--- /dev/null
+++ b/licenses/Qt6-NOTICE.txt
@@ -0,0 +1,24 @@
+Qt 6
+Copyright (C) The Qt Company Ltd. and other contributors.
+https://www.qt.io/
+
+The Jungfraujoch viewer (jfjoch_viewer) uses the Qt 6 framework under the terms of the
+GNU Lesser General Public License, version 3 (LGPL-3.0). The Qt modules used are:
+Core, Gui, Widgets, Charts, Concurrent, OpenGL, OpenGLWidgets, and (on Linux) DBus.
+
+LGPL-3.0 compliance for the distributed viewer:
+
+  * Qt is used as provided by The Qt Company under the LGPL-3.0 open-source terms; no Qt
+    source code has been modified.
+  * The viewer links Qt dynamically. On Windows and macOS the Qt shared libraries are
+    deployed next to the application by windeployqt / macdeployqt; the user may therefore
+    replace them with a compatible build of Qt, as the LGPL requires.
+  * The corresponding source code for the exact version of Qt used can be obtained from
+    https://download.qt.io/ (and from https://code.qt.io/). The Qt version is reported in
+    the viewer's Help > About dialog.
+
+Full license texts:
+  * LGPL-3.0: see licenses/Qt6-LGPL-3.0.txt (verbatim GNU Lesser General Public License v3),
+    also at https://www.gnu.org/licenses/lgpl-3.0.html
+  * GPL-3.0 (the base license that LGPL-3.0 extends) is included in the top-level LICENSE
+    file of this distribution and in licenses/slsDetectorPackage-GPL-3.0.txt.
diff --git a/licenses/base64-macaron.txt b/licenses/base64-macaron.txt
new file mode 100644
index 00000000..74ebc3c2
--- /dev/null
+++ b/licenses/base64-macaron.txt
@@ -0,0 +1,24 @@
+Base64 encoder/decoder (single-header "Macaron" implementation)
+Vendored at include/base64/Base64.h
+
+The MIT License (MIT)
+Copyright (c) 2016-2024 tomykaira
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/licenses/bitshuffle-hperf.txt b/licenses/bitshuffle-hperf.txt
new file mode 100644
index 00000000..ab55200b
--- /dev/null
+++ b/licenses/bitshuffle-hperf.txt
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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diff --git a/licenses/bitshuffle.txt b/licenses/bitshuffle.txt
new file mode 100644
index 00000000..1365ed69
--- /dev/null
+++ b/licenses/bitshuffle.txt
@@ -0,0 +1,21 @@
+Bitshuffle - Filter for improving compression of typed binary data.
+
+Copyright (c) 2014 Kiyoshi Masui (kiyo@physics.ubc.ca)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/licenses/catch2.txt b/licenses/catch2.txt
new file mode 100644
index 00000000..36b7cd93
--- /dev/null
+++ b/licenses/catch2.txt
@@ -0,0 +1,23 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
diff --git a/licenses/ceres-solver.txt b/licenses/ceres-solver.txt
new file mode 100644
index 00000000..b5d967ca
--- /dev/null
+++ b/licenses/ceres-solver.txt
@@ -0,0 +1,257 @@
+Ceres Solver - A fast non-linear least squares minimizer
+Copyright 2023 Google Inc. All rights reserved.
+http://ceres-solver.org/
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+* Neither the name of Google Inc. nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+----------------------------------------------------------------------------------------------------------------------------
+
+                              Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
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+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
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+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+-------------------------------------------------------------------------------------------------------------------------------
+
+Some of the code in the examples directory derives from libmv, which is
+distributed under the MIT license as described below
+
+
+Copyright (c) 2007-2011 libmv authors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to
+deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+IN THE SOFTWARE.
diff --git a/licenses/cpp-httplib.txt b/licenses/cpp-httplib.txt
new file mode 100644
index 00000000..3e5ed359
--- /dev/null
+++ b/licenses/cpp-httplib.txt
@@ -0,0 +1,22 @@
+The MIT License (MIT)
+
+Copyright (c) 2017 yhirose
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
diff --git a/licenses/eigen-README.txt b/licenses/eigen-README.txt
new file mode 100644
index 00000000..11af93ca
--- /dev/null
+++ b/licenses/eigen-README.txt
@@ -0,0 +1,6 @@
+Eigen is primarily MPL2 licensed. See COPYING.MPL2 and these links:
+  http://www.mozilla.org/MPL/2.0/
+  http://www.mozilla.org/MPL/2.0/FAQ.html
+
+Some files contain third-party code under BSD or other MPL2-compatible licenses,
+whence the other COPYING.* files here.
\ No newline at end of file
diff --git a/licenses/eigen.txt b/licenses/eigen.txt
new file mode 100644
index 00000000..ee6256cd
--- /dev/null
+++ b/licenses/eigen.txt
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.
diff --git a/licenses/fast-feedback-indexer.txt b/licenses/fast-feedback-indexer.txt
new file mode 100644
index 00000000..f9ab447d
--- /dev/null
+++ b/licenses/fast-feedback-indexer.txt
@@ -0,0 +1,22 @@
+The code in the **eigen** directory has it's own license
+* http://www.eigen.tuxfamily.org
+* https://www.mozilla.org/en-US/MPL/2.0
+
+Python has it's own license
+* https://docs.python.org/3/license.html#psf-license
+
+For the rest, the BSD-3-Clause applies.
+
+### BSD-3-Clause
+
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/fftw.txt b/licenses/fftw.txt
new file mode 100644
index 00000000..623b6258
--- /dev/null
+++ b/licenses/fftw.txt
@@ -0,0 +1,340 @@
+		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+		    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+			    NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	    How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year  name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/licenses/gemmi.txt b/licenses/gemmi.txt
new file mode 100644
index 00000000..14e2f777
--- /dev/null
+++ b/licenses/gemmi.txt
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.
diff --git a/licenses/hdf5.txt b/licenses/hdf5.txt
new file mode 100644
index 00000000..60abcc29
--- /dev/null
+++ b/licenses/hdf5.txt
@@ -0,0 +1,111 @@
+Copyright Notice and License Terms for
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by The Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+This software library and utilities is covered by the 3-clause BSD License.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted for any purpose (including commercial purposes)
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions, and the following disclaimer in the documentation
+   and/or materials provided with the distribution.
+
+3. Neither the name of The HDF Group, the name of the University, nor the
+   name of any Contributor may be used to endorse or promote products derived
+   from this software without specific prior written permission from
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER:
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+“AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+For further details, please refer to the full license text available
+at https://opensource.org/licenses/bsd-3-clause
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to The HDF Group, without imposing a
+separate written license agreement for such Enhancements, then you hereby
+grant the following license: a non-exclusive, royalty-free perpetual license
+to install, use, modify, prepare derivative works, incorporate into other
+computer software, distribute, and sublicense such enhancements or derivative
+works thereof, in binary and source code form.
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at
+the University of Illinois, Fortner Software, Unidata Program Center
+(netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler
+(gzip), and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley
+National Laboratory (LBNL) and the United States Department of Energy
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from Lawrence Livermore
+National Laboratory and the United States Department of Energy under
+Prime Contract No. DE-AC52-07NA27344.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of
+California, Lawrence Livermore National Laboratory (UC LLNL).
+The following statement applies to those portions of the product and must
+be retained in any redistribution of source code, binaries, documentation,
+and/or accompanying materials:
+
+   This work was partially produced at the University of California,
+   Lawrence Livermore National Laboratory (UC LLNL) under contract
+   no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
+   (DOE) and The Regents of the University of California (University)
+   for the operation of UC LLNL.
+
+   DISCLAIMER:
+   THIS WORK WAS PREPARED AS AN ACCOUNT OF WORK SPONSORED BY AN AGENCY OF
+   THE UNITED STATES GOVERNMENT. NEITHER THE UNITED STATES GOVERNMENT NOR
+   THE UNIVERSITY OF CALIFORNIA NOR ANY OF THEIR EMPLOYEES, MAKES ANY
+   WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY OR RESPONSIBILITY
+   FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION,
+   APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE
+   WOULD NOT INFRINGE PRIVATELY- OWNED RIGHTS. REFERENCE HEREIN TO ANY
+   SPECIFIC COMMERCIAL PRODUCTS, PROCESS, OR SERVICE BY TRADE NAME,
+   TRADEMARK, MANUFACTURER, OR OTHERWISE, DOES NOT NECESSARILY CONSTITUTE
+   OR IMPLY ITS ENDORSEMENT, RECOMMENDATION, OR FAVORING BY THE UNITED
+   STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA. THE VIEWS AND
+   OPINIONS OF AUTHORS EXPRESSED HEREIN DO NOT NECESSARILY STATE OR REFLECT
+   THOSE OF THE UNITED STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA,
+   AND SHALL NOT BE USED FOR ADVERTISING OR PRODUCT ENDORSEMENT PURPOSES.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the National Science
+Foundation under Federal Award No. 2534078.
+
+-----------------------------------------------------------------------------
\ No newline at end of file
diff --git a/licenses/libjpeg-turbo.txt b/licenses/libjpeg-turbo.txt
new file mode 100644
index 00000000..2204864f
--- /dev/null
+++ b/licenses/libjpeg-turbo.txt
@@ -0,0 +1,135 @@
+libjpeg-turbo Licenses
+======================
+
+libjpeg-turbo is covered by two compatible BSD-style open source licenses:
+
+- The IJG (Independent JPEG Group) License, which is listed in
+  [README.ijg](README.ijg)
+
+  This license applies to the libjpeg API library and associated programs,
+  including any code inherited from libjpeg and any modifications to that
+  code.  Note that the libjpeg-turbo SIMD source code bears the
+  [zlib License](https://opensource.org/licenses/Zlib), but in the context of
+  the overall libjpeg API library, the terms of the zlib License are subsumed
+  by the terms of the IJG License.
+
+- The Modified (3-clause) BSD License, which is listed below
+
+  This license applies to the TurboJPEG API library and associated programs, as
+  well as the build system.  Note that the TurboJPEG API library wraps the
+  libjpeg API library, so in the context of the overall TurboJPEG API library,
+  both the terms of the IJG License and the terms of the Modified (3-clause)
+  BSD License apply.
+
+
+Complying with the libjpeg-turbo Licenses
+=========================================
+
+This section provides a roll-up of the libjpeg-turbo licensing terms, to the
+best of our understanding.  This is not a license in and of itself.  It is
+intended solely for clarification.
+
+1.  If you are distributing a modified version of the libjpeg-turbo source,
+    then:
+
+    1.  You cannot alter or remove any existing copyright or license notices
+        from the source.
+
+        **Origin**
+        - Clause 1 of the IJG License
+        - Clause 1 of the Modified BSD License
+        - Clauses 1 and 3 of the zlib License
+
+    2.  You must add your own copyright notice to the header of each source
+        file you modified, so others can tell that you modified that file.  (If
+        there is not an existing copyright header in that file, then you can
+        simply add a notice stating that you modified the file.)
+
+        **Origin**
+        - Clause 1 of the IJG License
+        - Clause 2 of the zlib License
+
+    3.  You must include the IJG README file, and you must not alter any of the
+        copyright or license text in that file.
+
+        **Origin**
+        - Clause 1 of the IJG License
+
+2.  If you are distributing only libjpeg-turbo binaries without the source, or
+    if you are distributing an application that statically links with
+    libjpeg-turbo, then:
+
+    1.  Your product documentation must include a message stating:
+
+        This software is based in part on the work of the Independent JPEG
+        Group.
+
+        **Origin**
+        - Clause 2 of the IJG license
+
+    2.  If your binary distribution includes or uses the TurboJPEG API, then
+        your product documentation must include the text of the Modified BSD
+        License (see below.)
+
+        **Origin**
+        - Clause 2 of the Modified BSD License
+
+3.  You cannot use the name of the IJG or The libjpeg-turbo Project or the
+    contributors thereof in advertising, publicity, etc.
+
+    **Origin**
+    - IJG License
+    - Clause 3 of the Modified BSD License
+
+4.  The IJG and The libjpeg-turbo Project do not warrant libjpeg-turbo to be
+    free of defects, nor do we accept any liability for undesirable
+    consequences resulting from your use of the software.
+
+    **Origin**
+    - IJG License
+    - Modified BSD License
+    - zlib License
+
+
+The Modified (3-clause) BSD License
+===================================
+
+Copyright (C)2009-2023 D. R. Commander.  All Rights Reserved.<br>
+Copyright (C)2015 Viktor Szathmáry.  All Rights Reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+- Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+- Neither the name of the libjpeg-turbo Project nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS",
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+
+Why Two Licenses?
+=================
+
+The zlib License could have been used instead of the Modified (3-clause) BSD
+License, and since the IJG License effectively subsumes the distribution
+conditions of the zlib License, this would have effectively placed
+libjpeg-turbo binary distributions under the IJG License.  However, the IJG
+License specifically refers to the Independent JPEG Group and does not extend
+attribution and endorsement protections to other entities.  Thus, it was
+desirable to choose a license that granted us the same protections for new code
+that were granted to the IJG for code derived from their software.
diff --git a/licenses/libtiff.txt b/licenses/libtiff.txt
new file mode 100644
index 00000000..12d5ef23
--- /dev/null
+++ b/licenses/libtiff.txt
@@ -0,0 +1,49 @@
+# LibTIFF license
+
+Copyright © 1988-1997 Sam Leffler\
+Copyright © 1991-1997 Silicon Graphics, Inc.
+
+Permission to use, copy, modify, distribute, and sell this software and 
+its documentation for any purpose is hereby granted without fee, provided
+that (i) the above copyright notices and this permission notice appear in
+all copies of the software and related documentation, and (ii) the names of
+Sam Leffler and Silicon Graphics may not be used in any advertising or
+publicity relating to the software without the specific, prior written
+permission of Sam Leffler and Silicon Graphics.
+
+THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, 
+EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY 
+WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  
+
+IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR
+ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND,
+OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
+WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF 
+LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE 
+OF THIS SOFTWARE.
+
+# Lempel-Ziv & Welch Compression (tif_lzw.c) license
+The code of tif_lzw.c is derived from the compress program whose code is
+derived from software contributed to Berkeley by James A. Woods,
+derived from original work by Spencer Thomas and Joseph Orost.
+
+The original Berkeley copyright notice appears below in its entirety:
+
+Copyright (c) 1985, 1986 The Regents of the University of California.
+All rights reserved.
+
+This code is derived from software contributed to Berkeley by
+James A. Woods, derived from original work by Spencer Thomas
+and Joseph Orost.
+
+Redistribution and use in source and binary forms are permitted
+provided that the above copyright notice and this paragraph are
+duplicated in all such forms and that any documentation,
+advertising materials, and other materials related to such
+distribution and use acknowledge that the software was developed
+by the University of California, Berkeley.  The name of the
+University may not be used to endorse or promote products derived
+from this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
diff --git a/licenses/libzmq.txt b/licenses/libzmq.txt
new file mode 100644
index 00000000..a612ad98
--- /dev/null
+++ b/licenses/libzmq.txt
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.
diff --git a/licenses/lz4.txt b/licenses/lz4.txt
new file mode 100644
index 00000000..74c2cdd7
--- /dev/null
+++ b/licenses/lz4.txt
@@ -0,0 +1,24 @@
+LZ4 Library
+Copyright (c) 2011-2016, Yann Collet
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/licenses/nlohmann-json.txt b/licenses/nlohmann-json.txt
new file mode 100644
index 00000000..ffef714b
--- /dev/null
+++ b/licenses/nlohmann-json.txt
@@ -0,0 +1,21 @@
+MIT License 
+
+Copyright (c) 2013-2020 Niels Lohmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/licenses/slsDetectorPackage-GPL-3.0.txt b/licenses/slsDetectorPackage-GPL-3.0.txt
new file mode 100644
index 00000000..16d2eeb5
--- /dev/null
+++ b/licenses/slsDetectorPackage-GPL-3.0.txt
@@ -0,0 +1,688 @@
+Valid-License-Identifier: GPL-3.0
+Valid-License-Identifier: GPL-3.0+
+SPDX-URL: https://spdx.org/licenses/GPL-3.0-or-later.html
+Usage-Guide:
+  To use this license in source code, put one of the following SPDX
+  tag/value pairs into a comment according to the placement
+  guidelines in the licensing rules documentation.
+  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
+    SPDX-License-Identifier: GPL-3.0
+  For 'GNU Library General Public License (LGPL) version 3.0 or any later
+  version' use:
+    SPDX-License-Identifier: GPL-3.0-or-later
+License-Text:
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+  An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License.  If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+  1. Source Code.
+
+  The "source code" for a work means the preferred form of the work
+for making modifications to it.  "Object code" means any non-source
+form of a work.
+
+  A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+  The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form.  A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+  The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities.  However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work.  For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+  The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+  The Corresponding Source for a work in source code form is that
+same work.
+
+  2. Basic Permissions.
+
+  All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met.  This License explicitly affirms your unlimited
+permission to run the unmodified Program.  The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work.  This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+  You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force.  You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright.  Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+  Conveying under any other circumstances is permitted solely under
+the conditions stated below.  Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+  3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+  No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+  When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+  4. Conveying Verbatim Copies.
+
+  You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+  You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+  5. Conveying Modified Source Versions.
+
+  You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+    a) The work must carry prominent notices stating that you modified
+    it, and giving a relevant date.
+
+    b) The work must carry prominent notices stating that it is
+    released under this License and any conditions added under section
+    7.  This requirement modifies the requirement in section 4 to
+    "keep intact all notices".
+
+    c) You must license the entire work, as a whole, under this
+    License to anyone who comes into possession of a copy.  This
+    License will therefore apply, along with any applicable section 7
+    additional terms, to the whole of the work, and all its parts,
+    regardless of how they are packaged.  This License gives no
+    permission to license the work in any other way, but it does not
+    invalidate such permission if you have separately received it.
+
+    d) If the work has interactive user interfaces, each must display
+    Appropriate Legal Notices; however, if the Program has interactive
+    interfaces that do not display Appropriate Legal Notices, your
+    work need not make them do so.
+
+  A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit.  Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+
+  6. Conveying Non-Source Forms.
+
+  You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:
+
+    a) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by the
+    Corresponding Source fixed on a durable physical medium
+    customarily used for software interchange.
+
+    b) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by a
+    written offer, valid for at least three years and valid for as
+    long as you offer spare parts or customer support for that product
+    model, to give anyone who possesses the object code either (1) a
+    copy of the Corresponding Source for all the software in the
+    product that is covered by this License, on a durable physical
+    medium customarily used for software interchange, for a price no
+    more than your reasonable cost of physically performing this
+    conveying of source, or (2) access to copy the
+    Corresponding Source from a network server at no charge.
+
+    c) Convey individual copies of the object code with a copy of the
+    written offer to provide the Corresponding Source.  This
+    alternative is allowed only occasionally and noncommercially, and
+    only if you received the object code with such an offer, in accord
+    with subsection 6b.
+
+    d) Convey the object code by offering access from a designated
+    place (gratis or for a charge), and offer equivalent access to the
+    Corresponding Source in the same way through the same place at no
+    further charge.  You need not require recipients to copy the
+    Corresponding Source along with the object code.  If the place to
+    copy the object code is a network server, the Corresponding Source
+    may be on a different server (operated by you or a third party)
+    that supports equivalent copying facilities, provided you maintain
+    clear directions next to the object code saying where to find the
+    Corresponding Source.  Regardless of what server hosts the
+    Corresponding Source, you remain obligated to ensure that it is
+    available for as long as needed to satisfy these requirements.
+
+    e) Convey the object code using peer-to-peer transmission, provided
+    you inform other peers where the object code and Corresponding
+    Source of the work are being offered to the general public at no
+    charge under subsection 6d.
+
+  A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+  A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling.  In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage.  For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product.  A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+  "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source.  The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+
+  If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information.  But this requirement does not apply
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+
+  7. Additional Terms.
+
+  "Additional permissions" are terms that supplement the terms of this
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+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
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+apply only to part of the Program, that part may be used separately
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+  When you convey a copy of a covered work, you may at your option
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+  Additional terms, permissive or non-permissive, may be stated in the
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+  You may not propagate or modify a covered work except as expressly
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+this License (including any patent licenses granted under the third
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+  However, if you cease all violation of this License, then your
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+  Moreover, your license from a particular copyright holder is
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+
+  Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
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+
+  9. Acceptance Not Required for Having Copies.
+
+  You are not required to accept this License in order to receive or
+run a copy of the Program.  Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance.  However,
+nothing other than this License grants you permission to propagate or
+modify any covered work.  These actions infringe copyright if you do
+not accept this License.  Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+  10. Automatic Licensing of Downstream Recipients.
+
+  Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License.  You are not responsible
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+
+  An "entity transaction" is a transaction transferring control of an
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+the predecessor has it or can get it with reasonable efforts.
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+  You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License.  For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+  11. Patents.
+
+  A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based.  The
+work thus licensed is called the contributor's "contributor version".
+
+  A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version.  For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+  Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
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+
+  In the following three paragraphs, a "patent license" is any express
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+(such as an express permission to practice a patent or covenant not to
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+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+  If you convey a covered work, knowingly relying on a patent license,
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+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients.  "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+  If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
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+conveyed by you (or copies made from those copies), or (b) primarily
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+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/licenses/slsDetectorPackage-LGPL-3.0.txt b/licenses/slsDetectorPackage-LGPL-3.0.txt
new file mode 100644
index 00000000..4f5dc3f1
--- /dev/null
+++ b/licenses/slsDetectorPackage-LGPL-3.0.txt
@@ -0,0 +1,179 @@
+Valid-License-Identifier: LGPL-3.0
+Valid-License-Identifier: LGPL-3.0+
+SPDX-URL: https://spdx.org/licenses/LGPL-3.0-or-later.html
+Usage-Guide:
+  To use this license in source code, put one of the following SPDX
+  tag/value pairs into a comment according to the placement
+  guidelines in the licensing rules documentation.
+  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
+    SPDX-License-Identifier: LGPL-3.0
+  For 'GNU Library General Public License (LGPL) version 3.0 or any later
+  version' use:
+    SPDX-License-Identifier: LGPL-3.0-or-later
+License-Text:
+
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
diff --git a/licenses/spdlog.txt b/licenses/spdlog.txt
new file mode 100644
index 00000000..4b1b2335
--- /dev/null
+++ b/licenses/spdlog.txt
@@ -0,0 +1,25 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 - present, Gabi Melman and spdlog contributors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+-- NOTE: Third party dependency used by this software --
+This software depends on the fmt lib (MIT License),
+and users must comply to its license: https://raw.githubusercontent.com/fmtlib/fmt/master/LICENSE
diff --git a/licenses/tinycbor.txt b/licenses/tinycbor.txt
new file mode 100644
index 00000000..4aad977c
--- /dev/null
+++ b/licenses/tinycbor.txt
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Intel Corporation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/licenses/xbflash-qspi.txt b/licenses/xbflash-qspi.txt
new file mode 100644
index 00000000..2d57c902
--- /dev/null
+++ b/licenses/xbflash-qspi.txt
@@ -0,0 +1,517 @@
+All userspace code authored by Xilinx or Advanced Micro Devices is
+released under the following license:
+
+Copyright (C) 2016-2022 Xilinx, Inc
+Copyright (C) 2022-2023 Advanced Micro Devices, Inc
+
+Licensed under the Apache License, Version 2.0 (the "License"). You may
+not use this file except in compliance with the License. A copy of the
+License is located at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
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diff --git a/licenses/xilinx-hls-headers.txt b/licenses/xilinx-hls-headers.txt
new file mode 100644
index 00000000..59096f43
--- /dev/null
+++ b/licenses/xilinx-hls-headers.txt
@@ -0,0 +1,18 @@
+Source of the headers:
+https://github.com/Xilinx/HLS_arbitrary_Precision_Types
+xilinx_hls_lib_2022_1.tgz (in Vitis HLS 2022.1)
+
+Copyright 2011-2019 Xilinx, Inc.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
diff --git a/licenses/zlib.txt b/licenses/zlib.txt
new file mode 100644
index 00000000..e866d7ac
--- /dev/null
+++ b/licenses/zlib.txt
@@ -0,0 +1,19 @@
+(C) 1995-2024 Jean-loup Gailly and Mark Adler
+
+This software is provided 'as-is', without any express or implied
+warranty. In no event will the authors be held liable for any damages
+arising from the use of this software.
+
+Permission is granted to anyone to use this software for any purpose,
+including commercial applications, and to alter it and redistribute it
+freely, subject to the following restrictions:
+
+1. The origin of this software must not be misrepresented; you must not
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+
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+
+3. This notice may not be removed or altered from any source distribution.
diff --git a/licenses/zstd.txt b/licenses/zstd.txt
new file mode 100644
index 00000000..75800288
--- /dev/null
+++ b/licenses/zstd.txt
@@ -0,0 +1,30 @@
+BSD License
+
+For Zstandard software
+
+Copyright (c) Meta Platforms, Inc. and affiliates. All rights reserved.
+
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+are permitted provided that the following conditions are met:
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+
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+
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+
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+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index fcd99edc..09654a9f 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -72,6 +72,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJochCalibrationWindow.h
         windows/JFJochHelperWindow.cpp
         windows/JFJochHelperWindow.h
+        windows/JFJochLicenseWindow.cpp
+        windows/JFJochLicenseWindow.h
         image_viewer/JFJochImage.cpp
         image_viewer/JFJochImage.h
         windows/JFJochAzIntWindow.cpp
diff --git a/viewer/JFJochViewerMenu.cpp b/viewer/JFJochViewerMenu.cpp
index fa39e87a..aa96fcf0 100644
--- a/viewer/JFJochViewerMenu.cpp
+++ b/viewer/JFJochViewerMenu.cpp
@@ -14,6 +14,7 @@
 #include <QDialogButtonBox>
 
 #include "JFJochViewerWindow.h"
+#include "windows/JFJochLicenseWindow.h"
 #include "../common/GitInfo.h"
 #include "../common/CUDAWrapper.h"
 
@@ -67,6 +68,9 @@ JFJochViewerMenu::JFJochViewerMenu(QWidget *parent) : QMenuBar(parent) {
     // Add "About" action
     const QAction *aboutAction = helpMenu->addAction("About");
     connect(aboutAction, &QAction::triggered, this, &JFJochViewerMenu::aboutSelected);
+
+    const QAction *licensesAction = helpMenu->addAction("Third-party Licenses");
+    connect(licensesAction, &QAction::triggered, this, &JFJochViewerMenu::licensesSelected);
 }
 
 void JFJochViewerMenu::AddWindowEntry(JFJochHelperWindow *window, const QString &name) {
@@ -117,6 +121,15 @@ void JFJochViewerMenu::aboutSelected() {
     aboutBox.exec();
 }
 
+void JFJochViewerMenu::licensesSelected() {
+    // Lazily create the modeless window and keep it; raise it if already open.
+    if (licenseWindow == nullptr)
+        licenseWindow = new JFJochLicenseWindow(window());
+    licenseWindow->show();
+    licenseWindow->raise();
+    licenseWindow->activateWindow();
+}
+
 void JFJochViewerMenu::openSelected() {
     QString fileName = QFileDialog::getOpenFileName(
         this,
diff --git a/viewer/JFJochViewerMenu.h b/viewer/JFJochViewerMenu.h
index 6d64a674..f741d936 100644
--- a/viewer/JFJochViewerMenu.h
+++ b/viewer/JFJochViewerMenu.h
@@ -7,6 +7,8 @@
 
 #include "windows/JFJochHelperWindow.h"
 
+class JFJochLicenseWindow;
+
 class JFJochViewerMenu : public QMenuBar {
     Q_OBJECT
     QAction *toggleImageWindowAction = nullptr;
@@ -17,6 +19,7 @@ class JFJochViewerMenu : public QMenuBar {
     QAction *toggleCalibrationWindowAction = nullptr;
 
     QMenu *windowMenu = nullptr;
+    JFJochLicenseWindow *licenseWindow = nullptr;
 public:
     explicit JFJochViewerMenu(QWidget *parent = nullptr);
     ~JFJochViewerMenu() override = default;
@@ -35,6 +38,7 @@ signals:
 
 private slots:
     void aboutSelected();
+    void licensesSelected();
     void quitSelected();
     void openSelected();
     void openHttpSelected();
diff --git a/viewer/resources/generate_licenses_html.mjs b/viewer/resources/generate_licenses_html.mjs
new file mode 100644
index 00000000..95b2caa0
--- /dev/null
+++ b/viewer/resources/generate_licenses_html.mjs
@@ -0,0 +1,71 @@
+// Generate viewer/resources/third_party_licenses.html from the repo-level licenses/ texts.
+//
+// The viewer embeds this file as a Qt resource (:/third_party_licenses.html) and shows it in the
+// "Third-party Licenses" window (QTextBrowser). It is committed so the Windows/macOS viewer build
+// needs no generator at build time; re-run this on Linux when licenses/ changes:
+//
+//   node viewer/resources/generate_licenses_html.mjs
+//
+import { readFileSync, readdirSync, writeFileSync } from "node:fs";
+import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
+
+const here = dirname(fileURLToPath(import.meta.url));
+const licensesDir = join(here, "..", "..", "licenses");
+const outFile = join(here, "third_party_licenses.html");
+
+const esc = (s) =>
+  s.replace(/&/g, "&amp;").replace(/</g, "&lt;").replace(/>/g, "&gt;");
+
+// Friendlier titles for the few non-obvious file names; otherwise the file stem is used.
+const titles = {
+  "Qt6-NOTICE": "Qt 6",
+  "Qt6-LGPL-3.0": "Qt 6 — LGPL-3.0 (full text)",
+  "NVIDIA-CUDA-NOTICE": "NVIDIA CUDA Toolkit",
+  "NVIDIA-CUDA-EULA": "NVIDIA CUDA Toolkit — EULA (full text)",
+  "base64-macaron": "Base64 (Macaron)",
+  "cpp-httplib": "cpp-httplib",
+  "eigen-README": "Eigen (notes)",
+  "fast-feedback-indexer": "Fast feedback indexer",
+  "nlohmann-json": "nlohmann/json",
+  "xbflash-qspi": "xbflash.qspi",
+  "xilinx-hls-headers": "Xilinx HLS arbitrary-precision headers",
+  "slsDetectorPackage-GPL-3.0": "slsDetectorPackage (GPL-3.0)",
+  "slsDetectorPackage-LGPL-3.0": "slsDetectorPackage (LGPL-3.0)",
+};
+
+const files = readdirSync(licensesDir)
+  .filter((f) => f.endsWith(".txt"))
+  .sort((a, b) => a.localeCompare(b));
+
+const entries = files.map((f) => {
+  const stem = f.replace(/\.txt$/, "");
+  return { id: stem, title: titles[stem] || stem, text: readFileSync(join(licensesDir, f), "utf8").trimEnd() };
+});
+
+const toc = entries.map((e) => `<li><a href="#${e.id}">${esc(e.title)}</a></li>`).join("\n");
+const sections = entries
+  .map((e) => `<h2 id="${e.id}">${esc(e.title)}</h2>\n<pre>${esc(e.text)}</pre>`)
+  .join("\n<hr>\n");
+
+const html = `<!DOCTYPE html>
+<!-- Generated by viewer/resources/generate_licenses_html.mjs - do not edit by hand. -->
+<html>
+<head><meta charset="utf-8"><title>Third-party licenses</title></head>
+<body>
+<h1>Third-party software licenses</h1>
+<p>The Jungfraujoch viewer is licensed under the GNU General Public License v3 (GPL-3.0).
+It builds on the third-party components listed below, each under its own license. The complete
+manifest with copyright holders is in THIRD_PARTY_NOTICES.md in the source distribution.</p>
+<h2>Contents</h2>
+<ul>
+${toc}
+</ul>
+<hr>
+${sections}
+</body>
+</html>
+`;
+
+writeFileSync(outFile, html, "utf8");
+console.log(`Wrote ${outFile} (${entries.length} components).`);
diff --git a/viewer/resources/resources.qrc b/viewer/resources/resources.qrc
index 5c88d1d9..45f4c289 100644
--- a/viewer/resources/resources.qrc
+++ b/viewer/resources/resources.qrc
@@ -6,5 +6,6 @@
 <RCC>
     <qresource prefix="/">
         <file>jfjoch.png</file>
+        <file>third_party_licenses.html</file>
     </qresource>
 </RCC>
\ No newline at end of file
diff --git a/viewer/resources/third_party_licenses.html b/viewer/resources/third_party_licenses.html
new file mode 100644
index 00000000..f5cab524
--- /dev/null
+++ b/viewer/resources/third_party_licenses.html
@@ -0,0 +1,5812 @@
+<!DOCTYPE html>
+<!-- Generated by viewer/resources/generate_licenses_html.mjs - do not edit by hand. -->
+<html>
+<head><meta charset="utf-8"><title>Third-party licenses</title></head>
+<body>
+<h1>Third-party software licenses</h1>
+<p>The Jungfraujoch viewer is licensed under the GNU General Public License v3 (GPL-3.0).
+It builds on the third-party components listed below, each under its own license. The complete
+manifest with copyright holders is in THIRD_PARTY_NOTICES.md in the source distribution.</p>
+<h2>Contents</h2>
+<ul>
+<li><a href="#base64-macaron">Base64 (Macaron)</a></li>
+<li><a href="#bitshuffle-hperf">bitshuffle-hperf</a></li>
+<li><a href="#bitshuffle">bitshuffle</a></li>
+<li><a href="#catch2">catch2</a></li>
+<li><a href="#ceres-solver">ceres-solver</a></li>
+<li><a href="#cpp-httplib">cpp-httplib</a></li>
+<li><a href="#eigen-README">Eigen (notes)</a></li>
+<li><a href="#eigen">eigen</a></li>
+<li><a href="#fast-feedback-indexer">Fast feedback indexer</a></li>
+<li><a href="#fftw">fftw</a></li>
+<li><a href="#gemmi">gemmi</a></li>
+<li><a href="#hdf5">hdf5</a></li>
+<li><a href="#libjpeg-turbo">libjpeg-turbo</a></li>
+<li><a href="#libtiff">libtiff</a></li>
+<li><a href="#libzmq">libzmq</a></li>
+<li><a href="#lz4">lz4</a></li>
+<li><a href="#nlohmann-json">nlohmann/json</a></li>
+<li><a href="#NVIDIA-CUDA-EULA">NVIDIA CUDA Toolkit — EULA (full text)</a></li>
+<li><a href="#NVIDIA-CUDA-NOTICE">NVIDIA CUDA Toolkit</a></li>
+<li><a href="#Qt6-LGPL-3.0">Qt 6 — LGPL-3.0 (full text)</a></li>
+<li><a href="#Qt6-NOTICE">Qt 6</a></li>
+<li><a href="#slsDetectorPackage-GPL-3.0">slsDetectorPackage (GPL-3.0)</a></li>
+<li><a href="#slsDetectorPackage-LGPL-3.0">slsDetectorPackage (LGPL-3.0)</a></li>
+<li><a href="#spdlog">spdlog</a></li>
+<li><a href="#tinycbor">tinycbor</a></li>
+<li><a href="#xbflash-qspi">xbflash.qspi</a></li>
+<li><a href="#xilinx-hls-headers">Xilinx HLS arbitrary-precision headers</a></li>
+<li><a href="#zlib">zlib</a></li>
+<li><a href="#zstd">zstd</a></li>
+</ul>
+<hr>
+<h2 id="base64-macaron">Base64 (Macaron)</h2>
+<pre>Base64 encoder/decoder (single-header "Macaron" implementation)
+Vendored at include/base64/Base64.h
+
+The MIT License (MIT)
+Copyright (c) 2016-2024 tomykaira
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</pre>
+<hr>
+<h2 id="bitshuffle-hperf">bitshuffle-hperf</h2>
+<pre>
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
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+
+      "Legal Entity" shall mean the union of the acting entity and all
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+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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+
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+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
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+      of this License, Derivative Works shall not include works that remain
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+      "Contribution" shall mean any work of authorship, including
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+      to that Work or Derivative Works thereof, that is intentionally
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+      and issue tracking systems that are managed by, or on behalf of, the
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+      designated in writing by the copyright owner as "Not a Contribution."
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+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
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+      this License, without any additional terms or conditions.
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+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
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+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
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+      on Your own behalf and on Your sole responsibility, not on behalf
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+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+      file or class name and description of purpose be included on the
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+
+   Copyright 2023 Kal Conley
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.</pre>
+<hr>
+<h2 id="bitshuffle">bitshuffle</h2>
+<pre>Bitshuffle - Filter for improving compression of typed binary data.
+
+Copyright (c) 2014 Kiyoshi Masui (kiyo@physics.ubc.ca)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.</pre>
+<hr>
+<h2 id="catch2">catch2</h2>
+<pre>Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.</pre>
+<hr>
+<h2 id="ceres-solver">ceres-solver</h2>
+<pre>Ceres Solver - A fast non-linear least squares minimizer
+Copyright 2023 Google Inc. All rights reserved.
+http://ceres-solver.org/
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+* Neither the name of Google Inc. nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+----------------------------------------------------------------------------------------------------------------------------
+
+                              Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+-------------------------------------------------------------------------------------------------------------------------------
+
+Some of the code in the examples directory derives from libmv, which is
+distributed under the MIT license as described below
+
+
+Copyright (c) 2007-2011 libmv authors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to
+deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+IN THE SOFTWARE.</pre>
+<hr>
+<h2 id="cpp-httplib">cpp-httplib</h2>
+<pre>The MIT License (MIT)
+
+Copyright (c) 2017 yhirose
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.</pre>
+<hr>
+<h2 id="eigen-README">Eigen (notes)</h2>
+<pre>Eigen is primarily MPL2 licensed. See COPYING.MPL2 and these links:
+  http://www.mozilla.org/MPL/2.0/
+  http://www.mozilla.org/MPL/2.0/FAQ.html
+
+Some files contain third-party code under BSD or other MPL2-compatible licenses,
+whence the other COPYING.* files here.</pre>
+<hr>
+<h2 id="eigen">eigen</h2>
+<pre>Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.</pre>
+<hr>
+<h2 id="fast-feedback-indexer">Fast feedback indexer</h2>
+<pre>The code in the **eigen** directory has it's own license
+* http://www.eigen.tuxfamily.org
+* https://www.mozilla.org/en-US/MPL/2.0
+
+Python has it's own license
+* https://docs.python.org/3/license.html#psf-license
+
+For the rest, the BSD-3-Clause applies.
+
+### BSD-3-Clause
+
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</pre>
+<hr>
+<h2 id="fftw">fftw</h2>
+<pre>		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+		    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+			    NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	    How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    &lt;one line to give the program's name and a brief idea of what it does.&gt;
+    Copyright (C) &lt;year&gt;  &lt;name of author&gt;
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year  name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  &lt;signature of Ty Coon&gt;, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.</pre>
+<hr>
+<h2 id="gemmi">gemmi</h2>
+<pre>Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.</pre>
+<hr>
+<h2 id="hdf5">hdf5</h2>
+<pre>Copyright Notice and License Terms for
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by The Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+This software library and utilities is covered by the 3-clause BSD License.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted for any purpose (including commercial purposes)
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions, and the following disclaimer in the documentation
+   and/or materials provided with the distribution.
+
+3. Neither the name of The HDF Group, the name of the University, nor the
+   name of any Contributor may be used to endorse or promote products derived
+   from this software without specific prior written permission from
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER:
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+“AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+For further details, please refer to the full license text available
+at https://opensource.org/licenses/bsd-3-clause
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to The HDF Group, without imposing a
+separate written license agreement for such Enhancements, then you hereby
+grant the following license: a non-exclusive, royalty-free perpetual license
+to install, use, modify, prepare derivative works, incorporate into other
+computer software, distribute, and sublicense such enhancements or derivative
+works thereof, in binary and source code form.
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at
+the University of Illinois, Fortner Software, Unidata Program Center
+(netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler
+(gzip), and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley
+National Laboratory (LBNL) and the United States Department of Energy
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from Lawrence Livermore
+National Laboratory and the United States Department of Energy under
+Prime Contract No. DE-AC52-07NA27344.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of
+California, Lawrence Livermore National Laboratory (UC LLNL).
+The following statement applies to those portions of the product and must
+be retained in any redistribution of source code, binaries, documentation,
+and/or accompanying materials:
+
+   This work was partially produced at the University of California,
+   Lawrence Livermore National Laboratory (UC LLNL) under contract
+   no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
+   (DOE) and The Regents of the University of California (University)
+   for the operation of UC LLNL.
+
+   DISCLAIMER:
+   THIS WORK WAS PREPARED AS AN ACCOUNT OF WORK SPONSORED BY AN AGENCY OF
+   THE UNITED STATES GOVERNMENT. NEITHER THE UNITED STATES GOVERNMENT NOR
+   THE UNIVERSITY OF CALIFORNIA NOR ANY OF THEIR EMPLOYEES, MAKES ANY
+   WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY OR RESPONSIBILITY
+   FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION,
+   APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE
+   WOULD NOT INFRINGE PRIVATELY- OWNED RIGHTS. REFERENCE HEREIN TO ANY
+   SPECIFIC COMMERCIAL PRODUCTS, PROCESS, OR SERVICE BY TRADE NAME,
+   TRADEMARK, MANUFACTURER, OR OTHERWISE, DOES NOT NECESSARILY CONSTITUTE
+   OR IMPLY ITS ENDORSEMENT, RECOMMENDATION, OR FAVORING BY THE UNITED
+   STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA. THE VIEWS AND
+   OPINIONS OF AUTHORS EXPRESSED HEREIN DO NOT NECESSARILY STATE OR REFLECT
+   THOSE OF THE UNITED STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA,
+   AND SHALL NOT BE USED FOR ADVERTISING OR PRODUCT ENDORSEMENT PURPOSES.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the National Science
+Foundation under Federal Award No. 2534078.
+
+-----------------------------------------------------------------------------</pre>
+<hr>
+<h2 id="libjpeg-turbo">libjpeg-turbo</h2>
+<pre>libjpeg-turbo Licenses
+======================
+
+libjpeg-turbo is covered by two compatible BSD-style open source licenses:
+
+- The IJG (Independent JPEG Group) License, which is listed in
+  [README.ijg](README.ijg)
+
+  This license applies to the libjpeg API library and associated programs,
+  including any code inherited from libjpeg and any modifications to that
+  code.  Note that the libjpeg-turbo SIMD source code bears the
+  [zlib License](https://opensource.org/licenses/Zlib), but in the context of
+  the overall libjpeg API library, the terms of the zlib License are subsumed
+  by the terms of the IJG License.
+
+- The Modified (3-clause) BSD License, which is listed below
+
+  This license applies to the TurboJPEG API library and associated programs, as
+  well as the build system.  Note that the TurboJPEG API library wraps the
+  libjpeg API library, so in the context of the overall TurboJPEG API library,
+  both the terms of the IJG License and the terms of the Modified (3-clause)
+  BSD License apply.
+
+
+Complying with the libjpeg-turbo Licenses
+=========================================
+
+This section provides a roll-up of the libjpeg-turbo licensing terms, to the
+best of our understanding.  This is not a license in and of itself.  It is
+intended solely for clarification.
+
+1.  If you are distributing a modified version of the libjpeg-turbo source,
+    then:
+
+    1.  You cannot alter or remove any existing copyright or license notices
+        from the source.
+
+        **Origin**
+        - Clause 1 of the IJG License
+        - Clause 1 of the Modified BSD License
+        - Clauses 1 and 3 of the zlib License
+
+    2.  You must add your own copyright notice to the header of each source
+        file you modified, so others can tell that you modified that file.  (If
+        there is not an existing copyright header in that file, then you can
+        simply add a notice stating that you modified the file.)
+
+        **Origin**
+        - Clause 1 of the IJG License
+        - Clause 2 of the zlib License
+
+    3.  You must include the IJG README file, and you must not alter any of the
+        copyright or license text in that file.
+
+        **Origin**
+        - Clause 1 of the IJG License
+
+2.  If you are distributing only libjpeg-turbo binaries without the source, or
+    if you are distributing an application that statically links with
+    libjpeg-turbo, then:
+
+    1.  Your product documentation must include a message stating:
+
+        This software is based in part on the work of the Independent JPEG
+        Group.
+
+        **Origin**
+        - Clause 2 of the IJG license
+
+    2.  If your binary distribution includes or uses the TurboJPEG API, then
+        your product documentation must include the text of the Modified BSD
+        License (see below.)
+
+        **Origin**
+        - Clause 2 of the Modified BSD License
+
+3.  You cannot use the name of the IJG or The libjpeg-turbo Project or the
+    contributors thereof in advertising, publicity, etc.
+
+    **Origin**
+    - IJG License
+    - Clause 3 of the Modified BSD License
+
+4.  The IJG and The libjpeg-turbo Project do not warrant libjpeg-turbo to be
+    free of defects, nor do we accept any liability for undesirable
+    consequences resulting from your use of the software.
+
+    **Origin**
+    - IJG License
+    - Modified BSD License
+    - zlib License
+
+
+The Modified (3-clause) BSD License
+===================================
+
+Copyright (C)2009-2023 D. R. Commander.  All Rights Reserved.&lt;br&gt;
+Copyright (C)2015 Viktor Szathmáry.  All Rights Reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+- Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+- Neither the name of the libjpeg-turbo Project nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS",
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+
+Why Two Licenses?
+=================
+
+The zlib License could have been used instead of the Modified (3-clause) BSD
+License, and since the IJG License effectively subsumes the distribution
+conditions of the zlib License, this would have effectively placed
+libjpeg-turbo binary distributions under the IJG License.  However, the IJG
+License specifically refers to the Independent JPEG Group and does not extend
+attribution and endorsement protections to other entities.  Thus, it was
+desirable to choose a license that granted us the same protections for new code
+that were granted to the IJG for code derived from their software.</pre>
+<hr>
+<h2 id="libtiff">libtiff</h2>
+<pre># LibTIFF license
+
+Copyright © 1988-1997 Sam Leffler\
+Copyright © 1991-1997 Silicon Graphics, Inc.
+
+Permission to use, copy, modify, distribute, and sell this software and 
+its documentation for any purpose is hereby granted without fee, provided
+that (i) the above copyright notices and this permission notice appear in
+all copies of the software and related documentation, and (ii) the names of
+Sam Leffler and Silicon Graphics may not be used in any advertising or
+publicity relating to the software without the specific, prior written
+permission of Sam Leffler and Silicon Graphics.
+
+THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, 
+EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY 
+WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  
+
+IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR
+ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND,
+OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
+WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF 
+LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE 
+OF THIS SOFTWARE.
+
+# Lempel-Ziv &amp; Welch Compression (tif_lzw.c) license
+The code of tif_lzw.c is derived from the compress program whose code is
+derived from software contributed to Berkeley by James A. Woods,
+derived from original work by Spencer Thomas and Joseph Orost.
+
+The original Berkeley copyright notice appears below in its entirety:
+
+Copyright (c) 1985, 1986 The Regents of the University of California.
+All rights reserved.
+
+This code is derived from software contributed to Berkeley by
+James A. Woods, derived from original work by Spencer Thomas
+and Joseph Orost.
+
+Redistribution and use in source and binary forms are permitted
+provided that the above copyright notice and this paragraph are
+duplicated in all such forms and that any documentation,
+advertising materials, and other materials related to such
+distribution and use acknowledge that the software was developed
+by the University of California, Berkeley.  The name of the
+University may not be used to endorse or promote products derived
+from this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.</pre>
+<hr>
+<h2 id="libzmq">libzmq</h2>
+<pre>Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.</pre>
+<hr>
+<h2 id="lz4">lz4</h2>
+<pre>LZ4 Library
+Copyright (c) 2011-2016, Yann Collet
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</pre>
+<hr>
+<h2 id="nlohmann-json">nlohmann/json</h2>
+<pre>MIT License 
+
+Copyright (c) 2013-2020 Niels Lohmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.</pre>
+<hr>
+<h2 id="NVIDIA-CUDA-EULA">NVIDIA CUDA Toolkit — EULA (full text)</h2>
+<pre>End User License Agreement
+--------------------------
+
+NVIDIA Software License Agreement and CUDA Supplement to
+Software License Agreement.
+
+The CUDA Toolkit End User License Agreement applies to the
+NVIDIA CUDA Toolkit, the NVIDIA CUDA Samples, the NVIDIA
+Display Driver, NVIDIA Nsight tools (Visual Studio Edition),
+and the associated documentation on CUDA APIs, programming
+model and development tools. If you do not agree with the
+terms and conditions of the license agreement, then do not
+download or use the software.
+
+Last updated: January 12, 2024.
+
+
+Preface
+-------
+
+The Software License Agreement in Chapter 1 and the Supplement
+in Chapter 2 contain license terms and conditions that govern
+the use of NVIDIA toolkit. By accepting this agreement, you
+agree to comply with all the terms and conditions applicable
+to the product(s) included herein.
+
+
+NVIDIA Driver
+
+
+Description
+
+This package contains the operating system driver and
+fundamental system software components for NVIDIA GPUs.
+
+
+NVIDIA CUDA Toolkit
+
+
+Description
+
+The NVIDIA CUDA Toolkit provides command-line and graphical
+tools for building, debugging and optimizing the performance
+of applications accelerated by NVIDIA GPUs, runtime and math
+libraries, and documentation including programming guides,
+user manuals, and API references.
+
+
+Default Install Location of CUDA Toolkit
+
+Windows platform:
+
+%ProgramFiles%\NVIDIA GPU Computing Toolkit\CUDA\v#.#
+
+Linux platform:
+
+/usr/local/cuda-#.#
+
+Mac platform:
+
+/Developer/NVIDIA/CUDA-#.#
+
+
+NVIDIA CUDA Samples
+
+
+Description
+
+CUDA Samples are now located in
+https://github.com/nvidia/cuda-samples, which includes
+instructions for obtaining, building, and running the samples.
+They are no longer included in the CUDA toolkit.
+
+
+NVIDIA Nsight Visual Studio Edition (Windows only)
+
+
+Description
+
+NVIDIA Nsight Development Platform, Visual Studio Edition is a
+development environment integrated into Microsoft Visual
+Studio that provides tools for debugging, profiling, analyzing
+and optimizing your GPU computing and graphics applications.
+
+
+Default Install Location of Nsight Visual Studio Edition
+
+Windows platform:
+
+%ProgramFiles(x86)%\NVIDIA Corporation\Nsight Visual Studio Edition #.#
+
+
+1. License Agreement for NVIDIA Software Development Kits
+---------------------------------------------------------
+
+
+Important Notice—Read before downloading, installing,
+copying or using the licensed software:
+-------------------------------------------------------
+
+This license agreement, including exhibits attached
+("Agreement”) is a legal agreement between you and NVIDIA
+Corporation ("NVIDIA") and governs your use of a NVIDIA
+software development kit (“SDK”).
+
+Each SDK has its own set of software and materials, but here
+is a description of the types of items that may be included in
+a SDK: source code, header files, APIs, data sets and assets
+(examples include images, textures, models, scenes, videos,
+native API input/output files), binary software, sample code,
+libraries, utility programs, programming code and
+documentation.
+
+This Agreement can be accepted only by an adult of legal age
+of majority in the country in which the SDK is used.
+
+If you are entering into this Agreement on behalf of a company
+or other legal entity, you represent that you have the legal
+authority to bind the entity to this Agreement, in which case
+“you” will mean the entity you represent.
+
+If you don’t have the required age or authority to accept
+this Agreement, or if you don’t accept all the terms and
+conditions of this Agreement, do not download, install or use
+the SDK.
+
+You agree to use the SDK only for purposes that are permitted
+by (a) this Agreement, and (b) any applicable law, regulation
+or generally accepted practices or guidelines in the relevant
+jurisdictions.
+
+
+1.1. License
+
+
+1.1.1. License Grant
+
+Subject to the terms of this Agreement, NVIDIA hereby grants
+you a non-exclusive, non-transferable license, without the
+right to sublicense (except as expressly provided in this
+Agreement) to:
+
+  1. Install and use the SDK,
+
+  2. Modify and create derivative works of sample source code
+    delivered in the SDK, and
+
+  3. Distribute those portions of the SDK that are identified
+    in this Agreement as distributable, as incorporated in
+    object code format into a software application that meets
+    the distribution requirements indicated in this Agreement.
+
+
+1.1.2. Distribution Requirements
+
+These are the distribution requirements for you to exercise
+the distribution grant:
+
+  1. Your application must have material additional
+    functionality, beyond the included portions of the SDK.
+
+  2. The distributable portions of the SDK shall only be
+    accessed by your application.
+
+  3. The following notice shall be included in modifications
+    and derivative works of sample source code distributed:
+    “This software contains source code provided by NVIDIA
+    Corporation.”
+
+  4. Unless a developer tool is identified in this Agreement
+    as distributable, it is delivered for your internal use
+    only.
+
+  5. The terms under which you distribute your application
+    must be consistent with the terms of this Agreement,
+    including (without limitation) terms relating to the
+    license grant and license restrictions and protection of
+    NVIDIA’s intellectual property rights. Additionally, you
+    agree that you will protect the privacy, security and
+    legal rights of your application users.
+
+  6. You agree to notify NVIDIA in writing of any known or
+    suspected distribution or use of the SDK not in compliance
+    with the requirements of this Agreement, and to enforce
+    the terms of your agreements with respect to distributed
+    SDK.
+
+
+1.1.3. Authorized Users
+
+You may allow employees and contractors of your entity or of
+your subsidiary(ies) to access and use the SDK from your
+secure network to perform work on your behalf.
+
+If you are an academic institution you may allow users
+enrolled or employed by the academic institution to access and
+use the SDK from your secure network.
+
+You are responsible for the compliance with the terms of this
+Agreement by your authorized users. If you become aware that
+your authorized users didn’t follow the terms of this
+Agreement, you agree to take reasonable steps to resolve the
+non-compliance and prevent new occurrences.
+
+
+1.1.4. Pre-Release SDK
+
+The SDK versions identified as alpha, beta, preview or
+otherwise as pre-release, may not be fully functional, may
+contain errors or design flaws, and may have reduced or
+different security, privacy, accessibility, availability, and
+reliability standards relative to commercial versions of
+NVIDIA software and materials. Use of a pre-release SDK may
+result in unexpected results, loss of data, project delays or
+other unpredictable damage or loss.
+
+You may use a pre-release SDK at your own risk, understanding
+that pre-release SDKs are not intended for use in production
+or business-critical systems.
+
+NVIDIA may choose not to make available a commercial version
+of any pre-release SDK. NVIDIA may also choose to abandon
+development and terminate the availability of a pre-release
+SDK at any time without liability.
+
+
+1.1.5. Updates
+
+NVIDIA may, at its option, make available patches, workarounds
+or other updates to this SDK. Unless the updates are provided
+with their separate governing terms, they are deemed part of
+the SDK licensed to you as provided in this Agreement. You
+agree that the form and content of the SDK that NVIDIA
+provides may change without prior notice to you. While NVIDIA
+generally maintains compatibility between versions, NVIDIA may
+in some cases make changes that introduce incompatibilities in
+future versions of the SDK.
+
+
+1.1.6. Components Under Other Licenses
+
+The SDK may come bundled with, or otherwise include or be
+distributed with, NVIDIA or third-party components with
+separate legal notices or terms as may be described in
+proprietary notices accompanying the SDK. If and to the extent
+there is a conflict between the terms in this Agreement and
+the license terms associated with the component, the license
+terms associated with the components control only to the
+extent necessary to resolve the conflict.
+
+Subject to the other terms of this Agreement, you may use the
+SDK to develop and test applications released under Open
+Source Initiative (OSI) approved open source software
+licenses.
+
+
+1.1.7. Reservation of Rights
+
+NVIDIA reserves all rights, title, and interest in and to the
+SDK, not expressly granted to you under this Agreement.
+
+
+1.2. Limitations
+
+The following license limitations apply to your use of the
+SDK:
+
+  1. You may not reverse engineer, decompile or disassemble,
+    or remove copyright or other proprietary notices from any
+    portion of the SDK or copies of the SDK.
+
+  2. Except as expressly provided in this Agreement, you may
+    not copy, sell, rent, sublicense, transfer, distribute,
+    modify, or create derivative works of any portion of the
+    SDK. For clarity, you may not distribute or sublicense the
+    SDK as a stand-alone product.
+
+  3. Unless you have an agreement with NVIDIA for this
+    purpose, you may not indicate that an application created
+    with the SDK is sponsored or endorsed by NVIDIA.
+
+  4. You may not bypass, disable, or circumvent any
+    encryption, security, digital rights management or
+    authentication mechanism in the SDK.
+
+  5. You may not use the SDK in any manner that would cause it
+    to become subject to an open source software license. As
+    examples, licenses that require as a condition of use,
+    modification, and/or distribution that the SDK be:
+
+      a. Disclosed or distributed in source code form;
+
+      b. Licensed for the purpose of making derivative works;
+        or
+
+      c. Redistributable at no charge.
+
+  6.  You acknowledge that the SDK as delivered is not tested
+    or certified by NVIDIA for use in connection with the
+    design, construction, maintenance, and/or operation of any
+    system where the use or failure of such system could
+    result in a situation that threatens the safety of human
+    life or results in catastrophic damages (each, a "Critical
+    Application"). Examples of Critical Applications include
+    use in avionics, navigation, autonomous vehicle
+    applications, ai solutions for automotive products,
+    military, medical, life support or other life critical
+    applications. NVIDIA shall not be liable to you or any
+    third party, in whole or in part, for any claims or
+    damages arising from such uses. You are solely responsible
+    for ensuring that any product or service developed with
+    the SDK as a whole includes sufficient features to comply
+    with all applicable legal and regulatory standards and
+    requirements.
+
+  7.  You agree to defend, indemnify and hold harmless NVIDIA
+    and its affiliates, and their respective employees,
+    contractors, agents, officers and directors, from and
+    against any and all claims, damages, obligations, losses,
+    liabilities, costs or debt, fines, restitutions and
+    expenses (including but not limited to attorney’s fees
+    and costs incident to establishing the right of
+    indemnification) arising out of or related to products or
+    services that use the SDK in or for Critical Applications,
+    and for use of the SDK outside of the scope of this
+    Agreement or not in compliance with its terms.
+
+  8. You may not reverse engineer, decompile or disassemble
+    any portion of the output generated using SDK elements for
+    the purpose of translating such output artifacts to target
+    a non-NVIDIA platform.
+
+
+1.3. Ownership
+
+  1.  NVIDIA or its licensors hold all rights, title and
+    interest in and to the SDK and its modifications and
+    derivative works, including their respective intellectual
+    property rights, subject to your rights under Section
+    1.3.2. This SDK may include software and materials from
+    NVIDIA’s licensors, and these licensors are intended
+    third party beneficiaries that may enforce this Agreement
+    with respect to their intellectual property rights.
+
+  2.  You hold all rights, title and interest in and to your
+    applications and your derivative works of the sample
+    source code delivered in the SDK, including their
+    respective intellectual property rights, subject to
+    NVIDIA’s rights under Section 1.3.1.
+
+  3. You may, but don’t have to, provide to NVIDIA
+    suggestions, feature requests or other feedback regarding
+    the SDK, including possible enhancements or modifications
+    to the SDK. For any feedback that you voluntarily provide,
+    you hereby grant NVIDIA and its affiliates a perpetual,
+    non-exclusive, worldwide, irrevocable license to use,
+    reproduce, modify, license, sublicense (through multiple
+    tiers of sublicensees), and distribute (through multiple
+    tiers of distributors) it without the payment of any
+    royalties or fees to you. NVIDIA will use feedback at its
+    choice. NVIDIA is constantly looking for ways to improve
+    its products, so you may send feedback to NVIDIA through
+    the developer portal at https://developer.nvidia.com.
+
+
+1.4. No Warranties
+
+THE SDK IS PROVIDED BY NVIDIA “AS IS” AND “WITH ALL
+FAULTS.” TO THE MAXIMUM EXTENT PERMITTED BY LAW, NVIDIA AND
+ITS AFFILIATES EXPRESSLY DISCLAIM ALL WARRANTIES OF ANY KIND
+OR NATURE, WHETHER EXPRESS, IMPLIED OR STATUTORY, INCLUDING,
+BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE, TITLE, NON-INFRINGEMENT, OR THE
+ABSENCE OF ANY DEFECTS THEREIN, WHETHER LATENT OR PATENT. NO
+WARRANTY IS MADE ON THE BASIS OF TRADE USAGE, COURSE OF
+DEALING OR COURSE OF TRADE.
+
+
+1.5. Limitation of Liability
+
+TO THE MAXIMUM EXTENT PERMITTED BY LAW, NVIDIA AND ITS
+AFFILIATES SHALL NOT BE LIABLE FOR ANY (I) SPECIAL, INCIDENTAL,
+PUNITIVE OR CONSEQUENTIAL DAMAGES, OR (II) DAMAGES FOR (A) ANY 
+LOST PROFITS, LOSS OF USE, LOSS OF DATA OR LOSS OF GOODWILL, 
+OR THE COSTS OF PROCURING SUBSTITUTE PRODUCTS, ARISING OUT OF 
+OR IN CONNECTION WITH THIS AGREEMENT OR THE USE OR PERFORMANCE 
+OF THE SDK, WHETHER SUCH LIABILITY ARISES FROM ANY CLAIM BASED 
+UPON BREACH OF CONTRACT, BREACH OF WARRANTY, TORT (INCLUDING 
+NEGLIGENCE), PRODUCT LIABILITY OR ANY OTHER CAUSE OF ACTION OR 
+THEORY OF LIABILITY. IN NO EVENT WILL NVIDIA’S AND ITS AFFILIATES
+TOTAL CUMULATIVE LIABILITY UNDER OR ARISING OUT OF THIS
+AGREEMENT EXCEED US$10.00. THE NATURE OF THE LIABILITY OR THE
+NUMBER OF CLAIMS OR SUITS SHALL NOT ENLARGE OR EXTEND THIS
+LIMIT.
+
+These exclusions and limitations of liability shall apply
+regardless if NVIDIA or its affiliates have been advised of
+the possibility of such damages, and regardless of whether a
+remedy fails its essential purpose. These exclusions and
+limitations of liability form an essential basis of the
+bargain between the parties, and, absent any of these
+exclusions or limitations of liability, the provisions of this
+Agreement, including, without limitation, the economic terms,
+would be substantially different.
+
+
+1.6. Termination
+
+  1. This Agreement will continue to apply until terminated by
+    either you or NVIDIA as described below.
+
+  2. If you want to terminate this Agreement, you may do so by
+    stopping to use the SDK.
+
+  3. NVIDIA may, at any time, terminate this Agreement if:
+
+      a. (i) you fail to comply with any term of this
+        Agreement and the non-compliance is not fixed within
+        thirty (30) days following notice from NVIDIA (or
+        immediately if you violate NVIDIA’s intellectual
+        property rights);
+
+      b. (ii) you commence or participate in any legal
+        proceeding against NVIDIA with respect to the SDK; or
+
+      c. (iii) NVIDIA decides to no longer provide the SDK in
+        a country or, in NVIDIA’s sole discretion, the
+        continued use of it is no longer commercially viable.
+
+  4. Upon any termination of this Agreement, you agree to
+    promptly discontinue use of the SDK and destroy all copies
+    in your possession or control. Your prior distributions in
+    accordance with this Agreement are not affected by the
+    termination of this Agreement. Upon written request, you
+    will certify in writing that you have complied with your
+    commitments under this section. Upon any termination of
+    this Agreement all provisions survive except for the
+    license grant provisions.
+
+
+1.7. General
+
+If you wish to assign this Agreement or your rights and
+obligations, including by merger, consolidation, dissolution
+or operation of law, contact NVIDIA to ask for permission. Any
+attempted assignment not approved by NVIDIA in writing shall
+be void and of no effect. NVIDIA may assign, delegate or
+transfer this Agreement and its rights and obligations, and if
+to a non-affiliate you will be notified.
+
+You agree to cooperate with NVIDIA and provide reasonably
+requested information to verify your compliance with this
+Agreement.
+
+This Agreement will be governed in all respects by the laws of
+the United States and of the State of Delaware, without regard to the
+conflicts of laws principles. The United Nations Convention on
+Contracts for the International Sale of Goods is specifically
+disclaimed. You agree to all terms of this Agreement in the
+English language.
+
+The state or federal courts residing in Santa Clara County,
+California shall have exclusive jurisdiction over any dispute
+or claim arising out of this Agreement. Notwithstanding this,
+you agree that NVIDIA shall still be allowed to apply for
+injunctive remedies or an equivalent type of urgent legal
+relief in any jurisdiction.
+
+If any court of competent jurisdiction determines that any
+provision of this Agreement is illegal, invalid or
+unenforceable, such provision will be construed as limited to
+the extent necessary to be consistent with and fully
+enforceable under the law and the remaining provisions will
+remain in full force and effect. Unless otherwise specified,
+remedies are cumulative.
+
+Each party acknowledges and agrees that the other is an
+independent contractor in the performance of this Agreement.
+
+The SDK has been developed entirely at private expense and is
+“commercial items” consisting of “commercial computer
+software” and “commercial computer software
+documentation” provided with RESTRICTED RIGHTS. Use,
+duplication or disclosure by the U.S. Government or a U.S.
+Government subcontractor is subject to the restrictions in
+this Agreement pursuant to DFARS 227.7202-3(a) or as set forth
+in subparagraphs (c)(1) and (2) of the Commercial Computer
+Software - Restricted Rights clause at FAR 52.227-19, as
+applicable. Contractor/manufacturer is NVIDIA, 2788 San Tomas
+Expressway, Santa Clara, CA 95051.
+
+The SDK is subject to United States export laws and
+regulations. You agree that you will not ship, transfer or
+export the SDK into any country, or use the SDK in any manner,
+prohibited by the United States Bureau of Industry and
+Security or economic sanctions regulations administered by the
+U.S. Department of Treasury’s Office of Foreign Assets
+Control (OFAC), or any applicable export laws, restrictions or
+regulations. These laws include restrictions on destinations,
+end users and end use. By accepting this Agreement, you
+confirm that you are not located in a country currently 
+embargoed by the U.S. or otherwise prohibited from receiving 
+the SDK under U.S. law.
+
+Any notice delivered by NVIDIA to you under this Agreement
+will be delivered via mail, email or fax. You agree that any
+notices that NVIDIA sends you electronically will satisfy any
+legal communication requirements. Please direct your legal
+notices or other correspondence to NVIDIA Corporation, 2788
+San Tomas Expressway, Santa Clara, California 95051, United
+States of America, Attention: Legal Department.
+
+This Agreement and any exhibits incorporated into this
+Agreement constitute the entire agreement of the parties with
+respect to the subject matter of this Agreement and supersede
+all prior negotiations or documentation exchanged between the
+parties relating to this SDK license. Any additional and/or
+conflicting terms on documents issued by you are null, void,
+and invalid. Any amendment or waiver under this Agreement
+shall be in writing and signed by representatives of both
+parties.
+
+
+2. CUDA Toolkit Supplement to Software License Agreement for
+NVIDIA Software Development Kits
+------------------------------------------------------------
+
+The terms in this supplement govern your use of the NVIDIA
+CUDA Toolkit SDK under the terms of your license agreement
+(“Agreement”) as modified by this supplement. Capitalized
+terms used but not defined below have the meaning assigned to
+them in the Agreement.
+
+This supplement is an exhibit to the Agreement and is
+incorporated as an integral part of the Agreement. In the
+event of conflict between the terms in this supplement and the
+terms in the Agreement, the terms in this supplement govern.
+
+
+2.1. License Scope
+
+The SDK is licensed for you to develop applications only for
+use in systems with NVIDIA GPUs.
+
+
+2.2. Distribution
+
+The portions of the SDK that are distributable under the
+Agreement are listed in Attachment A.
+
+
+2.3. Operating Systems
+
+Those portions of the SDK designed exclusively for use on the
+Linux or FreeBSD operating systems, or other operating systems
+derived from the source code to these operating systems, may
+be copied and redistributed for use in accordance with this
+Agreement, provided that the object code files are not
+modified in any way (except for unzipping of compressed
+files).
+
+
+2.4. Audio and Video Encoders and Decoders
+
+You acknowledge and agree that it is your sole responsibility
+to obtain any additional third-party licenses required to
+make, have made, use, have used, sell, import, and offer for
+sale your products or services that include or incorporate any
+third-party software and content relating to audio and/or
+video encoders and decoders from, including but not limited
+to, Microsoft, Thomson, Fraunhofer IIS, Sisvel S.p.A.,
+MPEG-LA, and Coding Technologies. NVIDIA does not grant to you
+under this Agreement any necessary patent or other rights with
+respect to any audio and/or video encoders and decoders.
+
+
+2.5. Licensing
+
+If the distribution terms in this Agreement are not suitable
+for your organization, or for any questions regarding this
+Agreement, please contact NVIDIA at
+nvidia-compute-license-questions@nvidia.com.
+
+
+2.6. Attachment A
+
+The following CUDA Toolkit files may be distributed with
+applications developed by you, including certain
+variations of these files that have version number or
+architecture specific information embedded in the file name -
+as an example only, for release version 9.0 of the 64-bit
+Windows software, the file cudart64_90.dll is redistributable.
+
+Component
+
+CUDA Runtime
+
+Windows
+
+cudart.dll, cudart_static.lib, cudadevrt.lib
+
+Mac OSX
+
+libcudart.dylib, libcudart_static.a, libcudadevrt.a
+
+Linux
+
+libcudart.so, libcudart_static.a, libcudadevrt.a
+
+Android
+
+libcudart.so, libcudart_static.a, libcudadevrt.a
+
+Component
+
+CUDA FFT Library
+
+Windows
+
+cufft.dll, cufftw.dll, cufft.lib, cufftw.lib
+
+Mac OSX
+
+libcufft.dylib, libcufft_static.a, libcufftw.dylib,
+libcufftw_static.a
+
+Linux
+
+libcufft.so, libcufft_static.a, libcufftw.so,
+libcufftw_static.a
+
+Android
+
+libcufft.so, libcufft_static.a, libcufftw.so,
+libcufftw_static.a
+
+Component
+
+CUDA BLAS Library
+
+Windows
+
+cublas.dll, cublasLt.dll
+
+Mac OSX
+
+libcublas.dylib, libcublasLt.dylib, libcublas_static.a,
+libcublasLt_static.a
+
+Linux
+
+libcublas.so, libcublasLt.so, libcublas_static.a,
+libcublasLt_static.a
+
+Android
+
+libcublas.so, libcublasLt.so, libcublas_static.a,
+libcublasLt_static.a
+
+Component
+
+NVIDIA "Drop-in" BLAS Library
+
+Windows
+
+nvblas.dll
+
+Mac OSX
+
+libnvblas.dylib
+
+Linux
+
+libnvblas.so
+
+Component
+
+CUDA Sparse Matrix Library
+
+Windows
+
+cusparse.dll, cusparse.lib
+
+Mac OSX
+
+libcusparse.dylib, libcusparse_static.a
+
+Linux
+
+libcusparse.so, libcusparse_static.a
+
+Android
+
+libcusparse.so, libcusparse_static.a
+
+Component
+
+CUDA Linear Solver Library
+
+Windows
+
+cusolver.dll, cusolver.lib
+
+Mac OSX
+
+libcusolver.dylib, libcusolver_static.a
+
+Linux
+
+libcusolver.so, libcusolver_static.a
+
+Android
+
+libcusolver.so, libcusolver_static.a
+
+Component
+
+CUDA Random Number Generation Library
+
+Windows
+
+curand.dll, curand.lib
+
+Mac OSX
+
+libcurand.dylib, libcurand_static.a
+
+Linux
+
+libcurand.so, libcurand_static.a
+
+Android
+
+libcurand.so, libcurand_static.a
+
+Component
+
+NVIDIA Performance Primitives Library
+
+Windows
+
+nppc.dll, nppc.lib, nppial.dll, nppial.lib, nppicc.dll,
+nppicc.lib, nppicom.dll, nppicom.lib, nppidei.dll,
+nppidei.lib, nppif.dll, nppif.lib, nppig.dll, nppig.lib,
+nppim.dll, nppim.lib, nppist.dll, nppist.lib, nppisu.dll,
+nppisu.lib, nppitc.dll, nppitc.lib, npps.dll, npps.lib
+
+Mac OSX
+
+libnppc.dylib, libnppc_static.a, libnppial.dylib,
+libnppial_static.a, libnppicc.dylib, libnppicc_static.a,
+libnppicom.dylib, libnppicom_static.a, libnppidei.dylib,
+libnppidei_static.a, libnppif.dylib, libnppif_static.a,
+libnppig.dylib, libnppig_static.a, libnppim.dylib,
+libnppisu_static.a, libnppitc.dylib, libnppitc_static.a,
+libnpps.dylib, libnpps_static.a
+
+Linux
+
+libnppc.so, libnppc_static.a, libnppial.so,
+libnppial_static.a, libnppicc.so, libnppicc_static.a,
+libnppicom.so, libnppicom_static.a, libnppidei.so,
+libnppidei_static.a, libnppif.so, libnppif_static.a
+libnppig.so, libnppig_static.a, libnppim.so,
+libnppim_static.a, libnppist.so, libnppist_static.a,
+libnppisu.so, libnppisu_static.a, libnppitc.so
+libnppitc_static.a, libnpps.so, libnpps_static.a
+
+Android
+
+libnppc.so, libnppc_static.a, libnppial.so,
+libnppial_static.a, libnppicc.so, libnppicc_static.a,
+libnppicom.so, libnppicom_static.a, libnppidei.so,
+libnppidei_static.a, libnppif.so, libnppif_static.a
+libnppig.so, libnppig_static.a, libnppim.so,
+libnppim_static.a, libnppist.so, libnppist_static.a,
+libnppisu.so, libnppisu_static.a, libnppitc.so
+libnppitc_static.a, libnpps.so, libnpps_static.a
+
+Component
+
+NVIDIA JPEG Library
+
+Windows
+
+nvjpeg.lib, nvjpeg.dll
+
+Linux
+
+libnvjpeg.so, libnvjpeg_static.a
+
+Component
+
+Internal common library required for statically linking to
+cuBLAS, cuSPARSE, cuFFT, cuRAND, nvJPEG and NPP
+
+Mac OSX
+
+libculibos.a
+
+Linux
+
+libculibos.a
+
+Component
+
+NVIDIA Runtime Compilation Library and Header
+
+All
+
+nvrtc.h
+
+Windows
+
+nvrtc.dll, nvrtc-builtins.dll
+
+Mac OSX
+
+libnvrtc.dylib, libnvrtc-builtins.dylib
+
+Linux
+
+libnvrtc.so, libnvrtc-builtins.so, libnvrtc_static.a, libnvrtx-builtins_static.a
+
+Component
+
+NVIDIA Optimizing Compiler Library
+
+Windows
+
+nvvm.dll
+
+Mac OSX
+
+libnvvm.dylib
+
+Linux
+
+libnvvm.so
+
+Component
+
+NVIDIA JIT Linking Library
+
+Windows
+
+libnvJitLink.dll, libnvJitLink.lib
+
+Linux
+
+libnvJitLink.so, libnvJitLink_static.a
+
+Component
+
+NVIDIA Common Device Math Functions Library
+
+Windows
+
+libdevice.10.bc
+
+Mac OSX
+
+libdevice.10.bc
+
+Linux
+
+libdevice.10.bc
+
+Component
+
+CUDA Occupancy Calculation Header Library
+
+All
+
+cuda_occupancy.h
+
+Component
+
+CUDA Half Precision Headers
+
+All
+
+cuda_fp16.h, cuda_fp16.hpp
+
+Component
+
+CUDA Profiling Tools Interface (CUPTI) Library
+
+Windows
+
+cupti.dll
+
+Mac OSX
+
+libcupti.dylib
+
+Linux
+
+libcupti.so
+
+Component
+
+NVIDIA Tools Extension Library
+
+Windows
+
+nvToolsExt.dll, nvToolsExt.lib
+
+Mac OSX
+
+libnvToolsExt.dylib
+
+Linux
+
+libnvToolsExt.so
+
+Component
+
+NVIDIA CUDA Driver Libraries
+
+Linux
+
+libcuda.so, libnvidia-ptxjitcompiler.so, libnvptxcompiler_static.a
+
+Component
+
+NVIDIA CUDA File IO Libraries and Header
+
+All
+
+cufile.h
+
+Linux
+
+libcufile.so, libcufile_rdma.so, libcufile_static.a,
+libcufile_rdma_static.a
+
+In addition to the rights above, for parties that are
+developing software intended solely for use on Jetson
+development kits or Jetson modules, and running Linux for
+Tegra software, the following shall apply:
+
+  * The SDK may be distributed in its entirety, as provided by
+    NVIDIA, and without separation of its components, for you
+    and/or your licensees to create software development kits
+    for use only on the Jetson platform and running Linux for
+    Tegra software.
+
+
+2.7. Attachment B
+
+
+Additional Licensing Obligations
+
+The following third party components included in the SOFTWARE
+are licensed to Licensee pursuant to the following terms and
+conditions:
+
+  1. Licensee's use of the GDB third party component is
+    subject to the terms and conditions of GNU GPL v3:
+
+    This product includes copyrighted third-party software licensed
+    under the terms of the GNU General Public License v3 ("GPL v3").
+    All third-party software packages are copyright by their respective
+    authors. GPL v3 terms and conditions are hereby incorporated into
+    the Agreement by this reference:     http://www.gnu.org/licenses/gpl.txt
+
+    Consistent with these licensing requirements, the software
+    listed below is provided under the terms of the specified
+    open source software licenses. To obtain source code for
+    software provided under licenses that require
+    redistribution of source code, including the GNU General
+    Public License (GPL) and GNU Lesser General Public License
+    (LGPL), contact oss-requests@nvidia.com. This offer is
+    valid for a period of three (3) years from the date of the
+    distribution of this product by NVIDIA CORPORATION.
+
+    Component          License
+    CUDA-GDB           GPL v3  
+
+  2. Licensee represents and warrants that any and all third
+    party licensing and/or royalty payment obligations in
+    connection with Licensee's use of the H.264 video codecs
+    are solely the responsibility of Licensee.
+
+  3. Licensee's use of the Thrust library is subject to the
+    terms and conditions of the Apache License Version 2.0.
+    All third-party software packages are copyright by their
+    respective authors. Apache License Version 2.0 terms and
+    conditions are hereby incorporated into the Agreement by
+    this reference.
+    http://www.apache.org/licenses/LICENSE-2.0.html
+
+    In addition, Licensee acknowledges the following notice:
+    Thrust includes source code from the Boost Iterator,
+    Tuple, System, and Random Number libraries.
+
+    Boost Software License - Version 1.0 - August 17th, 2003
+    . . . .
+    
+    Permission is hereby granted, free of charge, to any person or 
+    organization obtaining a copy of the software and accompanying 
+    documentation covered by this license (the "Software") to use, 
+    reproduce, display, distribute, execute, and transmit the Software, 
+    and to prepare derivative works of the Software, and to permit 
+    third-parties to whom the Software is furnished to do so, all 
+    subject to the following:
+    
+    The copyright notices in the Software and this entire statement, 
+    including the above license grant, this restriction and the following 
+    disclaimer, must be included in all copies of the Software, in whole 
+    or in part, and all derivative works of the Software, unless such 
+    copies or derivative works are solely in the form of machine-executable 
+    object code generated by a source language processor.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND 
+    NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR 
+    ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+    OTHER DEALINGS IN THE SOFTWARE.  
+
+  4. Licensee's use of the LLVM third party component is
+    subject to the following terms and conditions:
+
+    ======================================================
+    LLVM Release License
+    ======================================================
+    University of Illinois/NCSA
+    Open Source License
+    
+    Copyright (c) 2003-2010 University of Illinois at Urbana-Champaign.
+    All rights reserved.
+    
+    Developed by:
+    
+        LLVM Team
+    
+        University of Illinois at Urbana-Champaign
+    
+        http://llvm.org
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to 
+    deal with the Software without restriction, including without limitation the
+    rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+    sell copies of the Software, and to permit persons to whom the Software is 
+    furnished to do so, subject to the following conditions:
+    
+    *  Redistributions of source code must retain the above copyright notice, 
+       this list of conditions and the following disclaimers.
+    
+    *  Redistributions in binary form must reproduce the above copyright 
+       notice, this list of conditions and the following disclaimers in the 
+       documentation and/or other materials provided with the distribution.
+    
+    *  Neither the names of the LLVM Team, University of Illinois at Urbana-
+       Champaign, nor the names of its contributors may be used to endorse or
+       promote products derived from this Software without specific prior 
+       written permission.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL 
+    THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+    ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS WITH THE SOFTWARE.  
+
+  5. Licensee's use of the PCRE third party component is
+    subject to the following terms and conditions:
+
+    ------------
+    PCRE LICENCE
+    ------------
+    PCRE is a library of functions to support regular expressions whose syntax
+    and semantics are as close as possible to those of the Perl 5 language.
+    Release 8 of PCRE is distributed under the terms of the "BSD" licence, as
+    specified below. The documentation for PCRE, supplied in the "doc" 
+    directory, is distributed under the same terms as the software itself. The
+    basic library functions are written in C and are freestanding. Also 
+    included in the distribution is a set of C++ wrapper functions, and a just-
+    in-time compiler that can be used to optimize pattern matching. These are 
+    both optional features that can be omitted when the library is built.
+    
+    THE BASIC LIBRARY FUNCTIONS
+    ---------------------------
+    Written by:       Philip Hazel
+    Email local part: ph10
+    Email domain:     cam.ac.uk
+    University of Cambridge Computing Service,
+    Cambridge, England.
+    Copyright (c) 1997-2012 University of Cambridge
+    All rights reserved.
+    
+    PCRE JUST-IN-TIME COMPILATION SUPPORT
+    -------------------------------------
+    Written by:       Zoltan Herczeg
+    Email local part: hzmester
+    Emain domain:     freemail.hu
+    Copyright(c) 2010-2012 Zoltan Herczeg
+    All rights reserved.
+    
+    STACK-LESS JUST-IN-TIME COMPILER
+    --------------------------------
+    Written by:       Zoltan Herczeg
+    Email local part: hzmester
+    Emain domain:     freemail.hu
+    Copyright(c) 2009-2012 Zoltan Herczeg
+    All rights reserved.
+    
+    THE C++ WRAPPER FUNCTIONS
+    -------------------------
+    Contributed by:   Google Inc.
+    Copyright (c) 2007-2012, Google Inc.
+    All rights reserved.
+
+    THE "BSD" LICENCE
+    -----------------
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+      * Redistributions of source code must retain the above copyright notice, 
+        this list of conditions and the following disclaimer.
+    
+      * Redistributions in binary form must reproduce the above copyright 
+        notice, this list of conditions and the following disclaimer in the 
+        documentation and/or other materials provided with the distribution.
+    
+      * Neither the name of the University of Cambridge nor the name of Google 
+        Inc. nor the names of their contributors may be used to endorse or 
+        promote products derived from this software without specific prior 
+        written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+    ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  6. Some of the cuBLAS library routines were written by or
+    derived from code written by Vasily Volkov and are subject
+    to the Modified Berkeley Software Distribution License as
+    follows:
+
+    Copyright (c) 2007-2009, Regents of the University of California
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the University of California, Berkeley nor
+          the names of its contributors may be used to endorse or promote
+          products derived from this software without specific prior
+          written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+    STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  7. Some of the cuBLAS library routines were written by or
+    derived from code written by Davide Barbieri and are
+    subject to the Modified Berkeley Software Distribution
+    License as follows:
+
+    Copyright (c) 2008-2009 Davide Barbieri @ University of Rome Tor Vergata.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * The name of the author may not be used to endorse or promote
+          products derived from this software without specific prior
+          written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+    INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+    STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.  
+
+  8. Some of the cuBLAS library routines were derived from
+    code developed by the University of Tennessee and are
+    subject to the Modified Berkeley Software Distribution
+    License as follows:
+
+    Copyright (c) 2010 The University of Tennessee.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer listed in this license in the documentation and/or
+          other materials provided with the distribution.
+        * Neither the name of the copyright holders nor the names of its
+          contributors may be used to endorse or promote products derived
+          from this software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  9. Some of the cuBLAS library routines were written by or
+    derived from code written by Jonathan Hogg and are subject
+    to the Modified Berkeley Software Distribution License as
+    follows:
+
+    Copyright (c) 2012, The Science and Technology Facilities Council (STFC).
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the STFC nor the names of its contributors
+          may be used to endorse or promote products derived from this
+          software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE STFC BE
+    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+    BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+    WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+    OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+    IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  10. Some of the cuBLAS library routines were written by or
+    derived from code written by Ahmad M. Abdelfattah, David
+    Keyes, and Hatem Ltaief, and are subject to the Apache
+    License, Version 2.0, as follows:
+
+     -- (C) Copyright 2013 King Abdullah University of Science and Technology
+      Authors:
+      Ahmad Abdelfattah (ahmad.ahmad@kaust.edu.sa)
+      David Keyes (david.keyes@kaust.edu.sa)
+      Hatem Ltaief (hatem.ltaief@kaust.edu.sa)
+    
+      Redistribution  and  use  in  source and binary forms, with or without
+      modification,  are  permitted  provided  that the following conditions
+      are met:
+    
+      * Redistributions  of  source  code  must  retain  the above copyright
+        notice,  this  list  of  conditions  and  the  following  disclaimer.
+      * Redistributions  in  binary  form must reproduce the above copyright
+        notice,  this list of conditions and the following disclaimer in the
+        documentation  and/or other materials provided with the distribution.
+      * Neither  the  name of the King Abdullah University of Science and
+        Technology nor the names of its contributors may be used to endorse 
+        or promote products derived from this software without specific prior 
+        written permission.
+    
+      THIS  SOFTWARE  IS  PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+      ``AS IS''  AND  ANY  EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+      LIMITED  TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+      A  PARTICULAR  PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+      HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+      SPECIAL,  EXEMPLARY,  OR  CONSEQUENTIAL  DAMAGES  (INCLUDING,  BUT NOT
+      LIMITED  TO,  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+      DATA,  OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+      THEORY  OF  LIABILITY,  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+      (INCLUDING  NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+      OF  THIS  SOFTWARE,  EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE  
+
+  11. Some of the cuSPARSE library routines were written by or
+    derived from code written by Li-Wen Chang and are subject
+    to the NCSA Open Source License as follows:
+
+    Copyright (c) 2012, University of Illinois.
+    
+    All rights reserved.
+    
+    Developed by: IMPACT Group, University of Illinois, http://impact.crhc.illinois.edu
+    
+    Permission is hereby granted, free of charge, to any person obtaining
+    a copy of this software and associated documentation files (the
+    "Software"), to deal with the Software without restriction, including
+    without limitation the rights to use, copy, modify, merge, publish,
+    distribute, sublicense, and/or sell copies of the Software, and to
+    permit persons to whom the Software is furnished to do so, subject to
+    the following conditions:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimers in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the names of IMPACT Group, University of Illinois, nor
+          the names of its contributors may be used to endorse or promote
+          products derived from this Software without specific prior
+          written permission.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+    NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT
+    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+    IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+    IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE
+    SOFTWARE.  
+
+  12. Some of the cuRAND library routines were written by or
+    derived from code written by Mutsuo Saito and Makoto
+    Matsumoto and are subject to the following license:
+
+    Copyright (c) 2009, 2010 Mutsuo Saito, Makoto Matsumoto and Hiroshima
+    University. All rights reserved.
+    
+    Copyright (c) 2011 Mutsuo Saito, Makoto Matsumoto, Hiroshima
+    University and University of Tokyo.  All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of the Hiroshima University nor the names of
+          its contributors may be used to endorse or promote products
+          derived from this software without specific prior written
+          permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  13. Some of the cuRAND library routines were derived from
+    code developed by D. E. Shaw Research and are subject to
+    the following license:
+
+    Copyright 2010-2011, D. E. Shaw Research.
+    
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions, and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+          copyright notice, this list of conditions, and the following
+          disclaimer in the documentation and/or other materials provided
+          with the distribution.
+        * Neither the name of D. E. Shaw Research nor the names of its
+          contributors may be used to endorse or promote products derived
+          from this software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  14. Some of the Math library routines were written by or
+    derived from code developed by Norbert Juffa and are
+    subject to the following license:
+
+    Copyright (c) 2015-2017, Norbert Juffa
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without 
+    modification, are permitted provided that the following conditions
+    are met:
+    
+    1. Redistributions of source code must retain the above copyright 
+       notice, this list of conditions and the following disclaimer.
+    
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  15. Licensee's use of the lz4 third party component is
+    subject to the following terms and conditions:
+
+    Copyright (C) 2011-2013, Yann Collet.
+    BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are
+    met:
+    
+        * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above
+    copyright notice, this list of conditions and the following disclaimer
+    in the documentation and/or other materials provided with the
+    distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
+
+  16. The NPP library uses code from the Boost Math Toolkit,
+    and is subject to the following license:
+
+    Boost Software License - Version 1.0 - August 17th, 2003
+    . . . .
+    
+    Permission is hereby granted, free of charge, to any person or 
+    organization obtaining a copy of the software and accompanying 
+    documentation covered by this license (the "Software") to use, 
+    reproduce, display, distribute, execute, and transmit the Software, 
+    and to prepare derivative works of the Software, and to permit 
+    third-parties to whom the Software is furnished to do so, all 
+    subject to the following:
+    
+    The copyright notices in the Software and this entire statement, 
+    including the above license grant, this restriction and the following 
+    disclaimer, must be included in all copies of the Software, in whole 
+    or in part, and all derivative works of the Software, unless such 
+    copies or derivative works are solely in the form of machine-executable 
+    object code generated by a source language processor.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND 
+    NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR 
+    ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR 
+    OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING 
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+    OTHER DEALINGS IN THE SOFTWARE.  
+
+  17. Portions of the Nsight Eclipse Edition is subject to the
+    following license:
+
+    The Eclipse Foundation makes available all content in this plug-in
+    ("Content"). Unless otherwise indicated below, the Content is provided
+    to you under the terms and conditions of the Eclipse Public License
+    Version 1.0 ("EPL"). A copy of the EPL is available at http://
+    www.eclipse.org/legal/epl-v10.html. For purposes of the EPL, "Program"
+    will mean the Content.
+    
+    If you did not receive this Content directly from the Eclipse
+    Foundation, the Content is being redistributed by another party
+    ("Redistributor") and different terms and conditions may apply to your
+    use of any object code in the Content. Check the Redistributor's
+    license that was provided with the Content. If no such license exists,
+    contact the Redistributor. Unless otherwise indicated below, the terms
+    and conditions of the EPL still apply to any source code in the
+    Content and such source code may be obtained at http://www.eclipse.org.  
+
+  18. Some of the cuBLAS library routines uses code from
+    OpenAI, which is subject to the following license:
+
+    License URL 
+    https://github.com/openai/openai-gemm/blob/master/LICENSE
+    
+    License Text 
+    The MIT License
+    
+    Copyright (c) 2016 OpenAI (http://openai.com), 2016 Google Inc.
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.   
+
+  19. Licensee's use of the Visual Studio Setup Configuration
+    Samples is subject to the following license:
+
+    The MIT License (MIT) 
+    Copyright (C) Microsoft Corporation. All rights reserved.
+    
+    Permission is hereby granted, free of charge, to any person 
+    obtaining a copy of this software and associated documentation 
+    files (the "Software"), to deal in the Software without restriction, 
+    including without limitation the rights to use, copy, modify, merge, 
+    publish, distribute, sublicense, and/or sell copies of the Software, 
+    and to permit persons to whom the Software is furnished to do so, 
+    subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included 
+    in all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS 
+    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.  
+
+  20. Licensee's use of linmath.h header for CPU functions for
+    GL vector/matrix operations from lunarG is subject to the
+    Apache License Version 2.0.
+
+  21. The DX12-CUDA sample uses the d3dx12.h header, which is
+    subject to the MIT license.
+
+  22. Components of the driver and compiler used for binary management, including 
+    nvFatBin, nvcc, and cuobjdump, use the Zstandard library which is subject to
+	the following license:
+
+    BSD License
+
+    For Zstandard software
+
+    Copyright (c) Meta Platforms, Inc. and affiliates. All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without modification,
+ 	are permitted provided that the following conditions are met:
+
+        * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+
+        * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+
+        * Neither the name Facebook, nor Meta, nor the names of its contributors may
+      be used to endorse or promote products derived from this software without
+      specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY
+    DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+    BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+    OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+    WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+    OF SUCH DAMAGE.
+
+-----------------</pre>
+<hr>
+<h2 id="NVIDIA-CUDA-NOTICE">NVIDIA CUDA Toolkit</h2>
+<pre>NVIDIA CUDA Toolkit (runtime libraries)
+Copyright (C) NVIDIA Corporation. All rights reserved.
+https://developer.nvidia.com/cuda-toolkit
+
+When Jungfraujoch is built with CUDA support (JFJOCH_USE_CUDA=ON, the default), the binaries
+statically link and redistribute portions of the NVIDIA CUDA runtime and math libraries,
+including the CUDA runtime (cudart) and cuFFT.
+
+These NVIDIA components are not covered by the GPLv3 license of Jungfraujoch. They are
+redistributed under the NVIDIA CUDA Toolkit End User License Agreement (EULA), which permits
+redistribution of the runtime components listed in its attachments:
+
+  * EULA: see licenses/NVIDIA-CUDA-EULA.txt (verbatim CUDA Toolkit 12.8 EULA, as shipped in
+    $CUDA_HOME/EULA.txt), also at https://docs.nvidia.com/cuda/eula/index.html
+  * Redistributable component list: see "Attachment A" of that EULA for the runtime components
+    that may be redistributed.
+
+When building against a different CUDA Toolkit version, replace licenses/NVIDIA-CUDA-EULA.txt
+with the EULA.txt shipped by that toolkit.</pre>
+<hr>
+<h2 id="Qt6-LGPL-3.0">Qt 6 — LGPL-3.0 (full text)</h2>
+<pre>                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. &lt;https://fsf.org/&gt;
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.</pre>
+<hr>
+<h2 id="Qt6-NOTICE">Qt 6</h2>
+<pre>Qt 6
+Copyright (C) The Qt Company Ltd. and other contributors.
+https://www.qt.io/
+
+The Jungfraujoch viewer (jfjoch_viewer) uses the Qt 6 framework under the terms of the
+GNU Lesser General Public License, version 3 (LGPL-3.0). The Qt modules used are:
+Core, Gui, Widgets, Charts, Concurrent, OpenGL, OpenGLWidgets, and (on Linux) DBus.
+
+LGPL-3.0 compliance for the distributed viewer:
+
+  * Qt is used as provided by The Qt Company under the LGPL-3.0 open-source terms; no Qt
+    source code has been modified.
+  * The viewer links Qt dynamically. On Windows and macOS the Qt shared libraries are
+    deployed next to the application by windeployqt / macdeployqt; the user may therefore
+    replace them with a compatible build of Qt, as the LGPL requires.
+  * The corresponding source code for the exact version of Qt used can be obtained from
+    https://download.qt.io/ (and from https://code.qt.io/). The Qt version is reported in
+    the viewer's Help &gt; About dialog.
+
+Full license texts:
+  * LGPL-3.0: see licenses/Qt6-LGPL-3.0.txt (verbatim GNU Lesser General Public License v3),
+    also at https://www.gnu.org/licenses/lgpl-3.0.html
+  * GPL-3.0 (the base license that LGPL-3.0 extends) is included in the top-level LICENSE
+    file of this distribution and in licenses/slsDetectorPackage-GPL-3.0.txt.</pre>
+<hr>
+<h2 id="slsDetectorPackage-GPL-3.0">slsDetectorPackage (GPL-3.0)</h2>
+<pre>Valid-License-Identifier: GPL-3.0
+Valid-License-Identifier: GPL-3.0+
+SPDX-URL: https://spdx.org/licenses/GPL-3.0-or-later.html
+Usage-Guide:
+  To use this license in source code, put one of the following SPDX
+  tag/value pairs into a comment according to the placement
+  guidelines in the licensing rules documentation.
+  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
+    SPDX-License-Identifier: GPL-3.0
+  For 'GNU Library General Public License (LGPL) version 3.0 or any later
+  version' use:
+    SPDX-License-Identifier: GPL-3.0-or-later
+License-Text:
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. &lt;https://fsf.org/&gt;
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
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+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    &lt;one line to give the program's name and a brief idea of what it does.&gt;
+    Copyright (C) &lt;year&gt;  &lt;name of author&gt;
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see &lt;https://www.gnu.org/licenses/&gt;.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
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+
+    &lt;program&gt;  Copyright (C) &lt;year&gt;  &lt;name of author&gt;
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+&lt;https://www.gnu.org/licenses/&gt;.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+&lt;https://www.gnu.org/licenses/why-not-lgpl.html&gt;.</pre>
+<hr>
+<h2 id="slsDetectorPackage-LGPL-3.0">slsDetectorPackage (LGPL-3.0)</h2>
+<pre>Valid-License-Identifier: LGPL-3.0
+Valid-License-Identifier: LGPL-3.0+
+SPDX-URL: https://spdx.org/licenses/LGPL-3.0-or-later.html
+Usage-Guide:
+  To use this license in source code, put one of the following SPDX
+  tag/value pairs into a comment according to the placement
+  guidelines in the licensing rules documentation.
+  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
+    SPDX-License-Identifier: LGPL-3.0
+  For 'GNU Library General Public License (LGPL) version 3.0 or any later
+  version' use:
+    SPDX-License-Identifier: LGPL-3.0-or-later
+License-Text:
+
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. &lt;https://fsf.org/&gt;
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
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+
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+
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+
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+
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+  3. Object Code Incorporating Material from Library Header Files.
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+  You may convey a Combined Work under terms of your choice that,
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+
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+   c) For a Combined Work that displays copyright notices during
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+
+   d) Do one of the following:
+
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+
+   e) Provide Installation Information, but only if you would otherwise
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+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
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+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
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+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
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+
+  If the Library as you received it specifies that a proxy can decide
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+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.</pre>
+<hr>
+<h2 id="spdlog">spdlog</h2>
+<pre>The MIT License (MIT)
+
+Copyright (c) 2016 - present, Gabi Melman and spdlog contributors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+-- NOTE: Third party dependency used by this software --
+This software depends on the fmt lib (MIT License),
+and users must comply to its license: https://raw.githubusercontent.com/fmtlib/fmt/master/LICENSE</pre>
+<hr>
+<h2 id="tinycbor">tinycbor</h2>
+<pre>MIT License
+
+Copyright (c) 2017 Intel Corporation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.</pre>
+<hr>
+<h2 id="xbflash-qspi">xbflash.qspi</h2>
+<pre>All userspace code authored by Xilinx or Advanced Micro Devices is
+released under the following license:
+
+Copyright (C) 2016-2022 Xilinx, Inc
+Copyright (C) 2022-2023 Advanced Micro Devices, Inc
+
+Licensed under the Apache License, Version 2.0 (the "License"). You may
+not use this file except in compliance with the License. A copy of the
+License is located at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+License for the specific language governing permissions and limitations
+under the License.
+
+All Linux kernel driver code included in "xocl" or "xclmgmt" authored by
+Xilinx is released under the terms of GNU General Public License version 2:
+
+Copyright (C) 2016-2022 Xilinx, Inc. All rights reserved.
+Copyright (C) 2022-2023 Advanced Micro Devices, Inc. All rights reserved.
+
+This software is licensed under the terms of the GNU General Public
+License version 2, as published by the Free Software Foundation, and
+may be copied, distributed, and modified under those terms.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+
+All Linux kernel driver code included in "zocl" authored by Xilinx is
+released under the terms of either Apache License, Version 2.0,
+or alternatively under the terms of the GNU General Public License
+version 2:
+
+Copyright (C) 2016-2020 Xilinx, Inc. All rights reserved.
+Copyright (C) 2022-2023 Advanced Micro Devices, Inc. All rights reserved.
+
+This software is licensed under the terms of the GNU General Public
+License version 2, as published by the Free Software Foundation, and
+may be copied, distributed, and modified under those terms.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You may use the Linux kernel driver code according to either of these
+licenses as is most appropriate for your project on a case-by-case basis.
+
+The full text for both licenses is included for reference below.
+
+
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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+---------------------------------------------------------------------------
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+  3. You may copy and distribute the Program (or a work based on it,
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+  4. You may not copy, modify, sublicense, or distribute the Program
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+  5. You are not required to accept this License, since you have not
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+  6. Each time you redistribute the Program (or any work based on the
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+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
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+
+If any portion of this section is held invalid or unenforceable under
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+circumstances.
+
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+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS</pre>
+<hr>
+<h2 id="xilinx-hls-headers">Xilinx HLS arbitrary-precision headers</h2>
+<pre>Source of the headers:
+https://github.com/Xilinx/HLS_arbitrary_Precision_Types
+xilinx_hls_lib_2022_1.tgz (in Vitis HLS 2022.1)
+
+Copyright 2011-2019 Xilinx, Inc.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.</pre>
+<hr>
+<h2 id="zlib">zlib</h2>
+<pre>(C) 1995-2024 Jean-loup Gailly and Mark Adler
+
+This software is provided 'as-is', without any express or implied
+warranty. In no event will the authors be held liable for any damages
+arising from the use of this software.
+
+Permission is granted to anyone to use this software for any purpose,
+including commercial applications, and to alter it and redistribute it
+freely, subject to the following restrictions:
+
+1. The origin of this software must not be misrepresented; you must not
+   claim that you wrote the original software. If you use this software
+   in a product, an acknowledgment in the product documentation would be
+   appreciated but is not required.
+
+2. Altered source versions must be plainly marked as such, and must not be
+   misrepresented as being the original software.
+
+3. This notice may not be removed or altered from any source distribution.</pre>
+<hr>
+<h2 id="zstd">zstd</h2>
+<pre>BSD License
+
+For Zstandard software
+
+Copyright (c) Meta Platforms, Inc. and affiliates. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+ * Neither the name Facebook, nor Meta, nor the names of its contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</pre>
+</body>
+</html>
diff --git a/viewer/windows/JFJochLicenseWindow.cpp b/viewer/windows/JFJochLicenseWindow.cpp
new file mode 100644
index 00000000..138cd038
--- /dev/null
+++ b/viewer/windows/JFJochLicenseWindow.cpp
@@ -0,0 +1,23 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochLicenseWindow.h"
+
+#include <QFile>
+#include <QTextBrowser>
+#include <QVBoxLayout>
+
+JFJochLicenseWindow::JFJochLicenseWindow(QWidget *parent) : QDialog(parent) {
+    setWindowTitle("Third-party Licenses");
+    resize(800, 600);
+
+    auto *browser = new QTextBrowser(this);
+    browser->setOpenExternalLinks(true);   // license URLs open in the system browser
+
+    QFile file(":/third_party_licenses.html");
+    if (file.open(QIODevice::ReadOnly | QIODevice::Text))
+        browser->setHtml(QString::fromUtf8(file.readAll()));
+
+    auto *layout = new QVBoxLayout(this);
+    layout->addWidget(browser);
+}
diff --git a/viewer/windows/JFJochLicenseWindow.h b/viewer/windows/JFJochLicenseWindow.h
new file mode 100644
index 00000000..20288bce
--- /dev/null
+++ b/viewer/windows/JFJochLicenseWindow.h
@@ -0,0 +1,13 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QDialog>
+
+// Modeless window showing the third-party license texts (from :/third_party_licenses.html).
+class JFJochLicenseWindow : public QDialog {
+    Q_OBJECT
+public:
+    explicit JFJochLicenseWindow(QWidget *parent = nullptr);
+};
-- 
2.52.0


From 1ea5897fcabbdb062524df883c275a2f517087bf Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 18:50:20 +0200
Subject: [PATCH 170/228] windows: vendor wingetopt and scope server-only
 targets out of viewer-only builds

MSVC/Windows build fixes:

- Force JFJOCH_VIEWER_ONLY ON for Windows and macOS; the broker/receiver/FPGA/
  writer server stack is Linux-only, so those platforms build the viewer subset.
- Vendor an OpenBSD/NetBSD getopt/getopt_long shim (tools/wingetopt/, BSD/ISC)
  as a WIN32-only static lib -- the MSVC CRT has no <getopt.h> -- and link it
  into the four portable CLI tools on Windows.
- jfjoch_extract_hkl.cpp: include <getopt.h> explicitly (it relied on glibc's
  transitive <unistd.h>).
- jfjoch_process.cpp: guard <unistd.h> with #ifndef _WIN32.
- Guard JFJochStreamWriter and jfjoch_writer with IF(NOT JFJOCH_VIEWER_ONLY):
  the former pulls in JFJochImagePuller, the latter uses a fork()/waitpid()
  multi-process design; neither belongs to the portable viewer subset.
- Record wingetopt in THIRD_PARTY_NOTICES.md and licenses/.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt                             |  19 +-
 THIRD_PARTY_NOTICES.md                     |   1 +
 licenses/COLLECT.sh                        |   1 +
 licenses/wingetopt.txt                     |  54 ++
 tools/CMakeLists.txt                       |   8 +
 tools/jfjoch_extract_hkl.cpp               |   1 +
 tools/jfjoch_process.cpp                   |   4 +-
 tools/wingetopt/LICENSE                    |  54 ++
 tools/wingetopt/getopt.c                   | 562 +++++++++++++++++++++
 tools/wingetopt/getopt.h                   | 105 ++++
 viewer/resources/third_party_licenses.html |  57 +++
 writer/CMakeLists.txt                      |  17 +-
 12 files changed, 876 insertions(+), 7 deletions(-)
 create mode 100644 licenses/wingetopt.txt
 create mode 100644 tools/wingetopt/LICENSE
 create mode 100644 tools/wingetopt/getopt.c
 create mode 100644 tools/wingetopt/getopt.h

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fd16f609..c8a8c622 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,7 +12,15 @@ SET(JFJOCH_WRITER_ONLY           OFF CACHE BOOL "Compile HDF5 writer only")
 SET(JFJOCH_INSTALL_DRIVER_SOURCE OFF CACHE BOOL "Install kernel driver source (ignored if building writer only; necessary for RPM building)")
 SET(JFJOCH_USE_CUDA              ON CACHE BOOL "Compile Jungfraujoch with CUDA")
 SET(JFJOCH_VIEWER_BUILD          OFF CACHE BOOL "Compile Jungfraujoch viewer")
-SET(JFJOCH_VIEWER_ONLY           OFF CACHE BOOL "Compile only jfjoch_viewer and its dependencies")
+
+# Only the viewer (and its portable dependency tree) is supported on Windows and macOS -- the
+# broker/receiver/FPGA/writer server stack is Linux-only. Force viewer-only on those platforms so a
+# plain configure builds the right subset; on Linux it remains a user-togglable option.
+IF (WIN32 OR APPLE)
+    SET(JFJOCH_VIEWER_ONLY ON CACHE BOOL "Compile only jfjoch_viewer and its dependencies" FORCE)
+ELSE()
+    SET(JFJOCH_VIEWER_ONLY OFF CACHE BOOL "Compile only jfjoch_viewer and its dependencies")
+ENDIF()
 
 SET (ZLIB_USE_STATIC_LIBS TRUE)
 
@@ -241,6 +249,15 @@ FetchContent_Declare(Eigen3
         EXCLUDE_FROM_ALL
         OVERRIDE_FIND_PACKAGE)
 
+# getopt/getopt_long shim for Windows: the MSVC CRT has no <getopt.h>. Vendored OpenBSD/NetBSD
+# implementation (BSD-licensed). Built only on Windows and defined here, before the subdirectories,
+# so the portable CLI tools in tools/ can link it. A no-op on Linux/macOS, where getopt lives in
+# libc (macOS uses the system getopt even though it is also a forced viewer-only platform).
+IF (WIN32)
+    ADD_LIBRARY(wingetopt STATIC tools/wingetopt/getopt.c tools/wingetopt/getopt.h)
+    TARGET_INCLUDE_DIRECTORIES(wingetopt PUBLIC tools/wingetopt)
+ENDIF()
+
 IF (JFJOCH_VIEWER_ONLY)
     # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
     # (broker here provides JFJochAPI only; its service targets are gated out.)
diff --git a/THIRD_PARTY_NOTICES.md b/THIRD_PARTY_NOTICES.md
index 06d156c8..664e9f8b 100644
--- a/THIRD_PARTY_NOTICES.md
+++ b/THIRD_PARTY_NOTICES.md
@@ -50,6 +50,7 @@ These are copied into the source tree (see the path) rather than fetched.
 | [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](licenses/xilinx-hls-headers.txt) |
 | [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](licenses/gemmi.txt) |
 | [xbflash.qspi](https://github.com/Xilinx/XRT) | `tools/xbflash.qspi/` | Xilinx / AMD | Apache-2.0 | [xbflash-qspi.txt](licenses/xbflash-qspi.txt) |
+| [wingetopt](https://github.com/alex85k/wingetopt) | `tools/wingetopt/` | Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | [wingetopt.txt](licenses/wingetopt.txt) |
 
 ## Runtime libraries and SDKs (shipped in binaries, not in the source tree)
 
diff --git a/licenses/COLLECT.sh b/licenses/COLLECT.sh
index b8dbb98f..466ae701 100644
--- a/licenses/COLLECT.sh
+++ b/licenses/COLLECT.sh
@@ -70,6 +70,7 @@ copy_license lz4.txt                 compression/lz4/LICENSE
 copy_license xilinx-hls-headers.txt  fpga/include/LICENSE.HLS_Headers
 copy_license gemmi.txt               gemmi_gph/LICENSE.txt
 copy_license xbflash-qspi.txt        tools/xbflash.qspi/LICENSE
+copy_license wingetopt.txt           tools/wingetopt/LICENSE
 
 # --- Runtime SDK license texts, copied from their system install (best effort) ---------------
 # These come from outside the build tree; the committed copies are authoritative if absent here.
diff --git a/licenses/wingetopt.txt b/licenses/wingetopt.txt
new file mode 100644
index 00000000..b1ded6d8
--- /dev/null
+++ b/licenses/wingetopt.txt
@@ -0,0 +1,54 @@
+#### AUTHORS:
+
+* Todd C. Miller <Todd.Miller@courtesan.com>
+* The NetBSD Foundation, Inc.
+* Alexei Kasatkin is the author of trivial CMakeLists.txt, build script itself is Public Domain
+
+#### LICENSE
+
+    Copyright (c) 2002 Todd C. Miller <Todd.Miller@courtesan.com>
+    
+    Permission to use, copy, modify, and distribute this software for any
+    purpose with or without fee is hereby granted, provided that the above
+    copyright notice and this permission notice appear in all copies.
+    
+    THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+    WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+    MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+    ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+    WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+    ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+    OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+    
+    Sponsored in part by the Defense Advanced Research Projects
+    Agency (DARPA) and Air Force Research Laboratory, Air Force
+    Materiel Command, USAF, under agreement number F39502-99-1-0512.
+
+***
+
+    Copyright (c) 2000 The NetBSD Foundation, Inc.
+    All rights reserved.
+    
+    This code is derived from software contributed to The NetBSD Foundation
+    by Dieter Baron and Thomas Klausner.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions
+    are met:
+    1. Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS
+    ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+    TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+    PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS
+    BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 499a4045..a887d94b 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -20,6 +20,14 @@ ADD_EXECUTABLE(jfjoch_azint jfjoch_azint.cpp)
 TARGET_LINK_LIBRARIES(jfjoch_azint JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_azint RUNTIME COMPONENT viewer)
 
+# On Windows these CLIs get getopt/getopt_long from the vendored wingetopt shim (libc has none).
+IF (WIN32)
+    TARGET_LINK_LIBRARIES(jfjoch_extract_hkl wingetopt)
+    TARGET_LINK_LIBRARIES(jfjoch_process wingetopt)
+    TARGET_LINK_LIBRARIES(jfjoch_scale wingetopt)
+    TARGET_LINK_LIBRARIES(jfjoch_azint wingetopt)
+ENDIF()
+
 # Online / hardware tools (broker, FPGA, receiver, detector). They link the non-portable
 # libraries and are Linux-only, so they are skipped in a viewer-only build.
 IF(NOT JFJOCH_VIEWER_ONLY)
diff --git a/tools/jfjoch_extract_hkl.cpp b/tools/jfjoch_extract_hkl.cpp
index 0fe7d22b..d6d1be76 100644
--- a/tools/jfjoch_extract_hkl.cpp
+++ b/tools/jfjoch_extract_hkl.cpp
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include <fstream>
+#include <getopt.h>
 
 #include "XdsIntegrateParser.h"
 #include "../reader/JFJochHDF5Reader.h"
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 9657294e..17174300 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -4,7 +4,9 @@
 #include <iostream>
 #include <vector>
 #include <string>
-#include <unistd.h>
+#ifndef _WIN32
+#include <unistd.h>   // not on MSVC; only pulled getopt transitively on Linux (<getopt.h> below)
+#endif
 #include <future>
 #include <mutex>
 #include <atomic>
diff --git a/tools/wingetopt/LICENSE b/tools/wingetopt/LICENSE
new file mode 100644
index 00000000..b1ded6d8
--- /dev/null
+++ b/tools/wingetopt/LICENSE
@@ -0,0 +1,54 @@
+#### AUTHORS:
+
+* Todd C. Miller <Todd.Miller@courtesan.com>
+* The NetBSD Foundation, Inc.
+* Alexei Kasatkin is the author of trivial CMakeLists.txt, build script itself is Public Domain
+
+#### LICENSE
+
+    Copyright (c) 2002 Todd C. Miller <Todd.Miller@courtesan.com>
+    
+    Permission to use, copy, modify, and distribute this software for any
+    purpose with or without fee is hereby granted, provided that the above
+    copyright notice and this permission notice appear in all copies.
+    
+    THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+    WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+    MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+    ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+    WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+    ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+    OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+    
+    Sponsored in part by the Defense Advanced Research Projects
+    Agency (DARPA) and Air Force Research Laboratory, Air Force
+    Materiel Command, USAF, under agreement number F39502-99-1-0512.
+
+***
+
+    Copyright (c) 2000 The NetBSD Foundation, Inc.
+    All rights reserved.
+    
+    This code is derived from software contributed to The NetBSD Foundation
+    by Dieter Baron and Thomas Klausner.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions
+    are met:
+    1. Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS
+    ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+    TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+    PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS
+    BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.
diff --git a/tools/wingetopt/getopt.c b/tools/wingetopt/getopt.c
new file mode 100644
index 00000000..6b477ef7
--- /dev/null
+++ b/tools/wingetopt/getopt.c
@@ -0,0 +1,562 @@
+/*	$OpenBSD: getopt_long.c,v 1.23 2007/10/31 12:34:57 chl Exp $	*/
+/*	$NetBSD: getopt_long.c,v 1.15 2002/01/31 22:43:40 tv Exp $	*/
+
+/*
+ * Copyright (c) 2002 Todd C. Miller <Todd.Miller@courtesan.com>
+ *
+ * Permission to use, copy, modify, and distribute this software for any
+ * purpose with or without fee is hereby granted, provided that the above
+ * copyright notice and this permission notice appear in all copies.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+ * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+ * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+ * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+ * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ *
+ * Sponsored in part by the Defense Advanced Research Projects
+ * Agency (DARPA) and Air Force Research Laboratory, Air Force
+ * Materiel Command, USAF, under agreement number F39502-99-1-0512.
+ */
+/*-
+ * Copyright (c) 2000 The NetBSD Foundation, Inc.
+ * All rights reserved.
+ *
+ * This code is derived from software contributed to The NetBSD Foundation
+ * by Dieter Baron and Thomas Klausner.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS
+ * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS
+ * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include <errno.h>
+#include <stdlib.h>
+#include <string.h>
+#include <getopt.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <windows.h>
+
+#define	REPLACE_GETOPT		/* use this getopt as the system getopt(3) */
+
+#ifdef REPLACE_GETOPT
+int	opterr = 1;		/* if error message should be printed */
+int	optind = 1;		/* index into parent argv vector */
+int	optopt = '?';		/* character checked for validity */
+#undef	optreset		/* see getopt.h */
+#define	optreset		__mingw_optreset
+int	optreset;		/* reset getopt */
+char    *optarg;		/* argument associated with option */
+#endif
+
+#define PRINT_ERROR	((opterr) && (*options != ':'))
+
+#define FLAG_PERMUTE	0x01	/* permute non-options to the end of argv */
+#define FLAG_ALLARGS	0x02	/* treat non-options as args to option "-1" */
+#define FLAG_LONGONLY	0x04	/* operate as getopt_long_only */
+
+/* return values */
+#define	BADCH		(int)'?'
+#define	BADARG		((*options == ':') ? (int)':' : (int)'?')
+#define	INORDER 	(int)1
+
+#ifndef __CYGWIN__
+#define __progname __argv[0]
+#else
+extern char __declspec(dllimport) *__progname;
+#endif
+
+#ifdef __CYGWIN__
+static char EMSG[] = "";
+#else
+#define	EMSG		""
+#endif
+
+static int getopt_internal(int, char * const *, const char *,
+			   const struct option *, int *, int);
+static int parse_long_options(char * const *, const char *,
+			      const struct option *, int *, int);
+static int gcd(int, int);
+static void permute_args(int, int, int, char * const *);
+
+static char *place = EMSG; /* option letter processing */
+
+/* XXX: set optreset to 1 rather than these two */
+static int nonopt_start = -1; /* first non option argument (for permute) */
+static int nonopt_end = -1;   /* first option after non options (for permute) */
+
+/* Error messages */
+static const char recargchar[] = "option requires an argument -- %c";
+static const char recargstring[] = "option requires an argument -- %s";
+static const char ambig[] = "ambiguous option -- %.*s";
+static const char noarg[] = "option doesn't take an argument -- %.*s";
+static const char illoptchar[] = "unknown option -- %c";
+static const char illoptstring[] = "unknown option -- %s";
+
+static void
+_vwarnx(const char *fmt,va_list ap)
+{
+  (void)fprintf(stderr,"%s: ",__progname);
+  if (fmt != NULL)
+    (void)vfprintf(stderr,fmt,ap);
+  (void)fprintf(stderr,"\n");
+}
+
+static void
+warnx(const char *fmt,...)
+{
+  va_list ap;
+  va_start(ap,fmt);
+  _vwarnx(fmt,ap);
+  va_end(ap);
+}
+
+/*
+ * Compute the greatest common divisor of a and b.
+ */
+static int
+gcd(int a, int b)
+{
+	int c;
+
+	c = a % b;
+	while (c != 0) {
+		a = b;
+		b = c;
+		c = a % b;
+	}
+
+	return (b);
+}
+
+/*
+ * Exchange the block from nonopt_start to nonopt_end with the block
+ * from nonopt_end to opt_end (keeping the same order of arguments
+ * in each block).
+ */
+static void
+permute_args(int panonopt_start, int panonopt_end, int opt_end,
+	char * const *nargv)
+{
+	int cstart, cyclelen, i, j, ncycle, nnonopts, nopts, pos;
+	char *swap;
+
+	/*
+	 * compute lengths of blocks and number and size of cycles
+	 */
+	nnonopts = panonopt_end - panonopt_start;
+	nopts = opt_end - panonopt_end;
+	ncycle = gcd(nnonopts, nopts);
+	cyclelen = (opt_end - panonopt_start) / ncycle;
+
+	for (i = 0; i < ncycle; i++) {
+		cstart = panonopt_end+i;
+		pos = cstart;
+		for (j = 0; j < cyclelen; j++) {
+			if (pos >= panonopt_end)
+				pos -= nnonopts;
+			else
+				pos += nopts;
+			swap = nargv[pos];
+			/* LINTED const cast */
+			((char **) nargv)[pos] = nargv[cstart];
+			/* LINTED const cast */
+			((char **)nargv)[cstart] = swap;
+		}
+	}
+}
+
+/*
+ * parse_long_options --
+ *	Parse long options in argc/argv argument vector.
+ * Returns -1 if short_too is set and the option does not match long_options.
+ */
+static int
+parse_long_options(char * const *nargv, const char *options,
+	const struct option *long_options, int *idx, int short_too)
+{
+	char *current_argv, *has_equal;
+	size_t current_argv_len;
+	int i, ambiguous, match;
+
+#define IDENTICAL_INTERPRETATION(_x, _y)                                \
+	(long_options[(_x)].has_arg == long_options[(_y)].has_arg &&    \
+	 long_options[(_x)].flag == long_options[(_y)].flag &&          \
+	 long_options[(_x)].val == long_options[(_y)].val)
+
+	current_argv = place;
+	match = -1;
+	ambiguous = 0;
+
+	optind++;
+
+	if ((has_equal = strchr(current_argv, '=')) != NULL) {
+		/* argument found (--option=arg) */
+		current_argv_len = has_equal - current_argv;
+		has_equal++;
+	} else
+		current_argv_len = strlen(current_argv);
+
+	for (i = 0; long_options[i].name; i++) {
+		/* find matching long option */
+		if (strncmp(current_argv, long_options[i].name,
+		    current_argv_len))
+			continue;
+
+		if (strlen(long_options[i].name) == current_argv_len) {
+			/* exact match */
+			match = i;
+			ambiguous = 0;
+			break;
+		}
+		/*
+		 * If this is a known short option, don't allow
+		 * a partial match of a single character.
+		 */
+		if (short_too && current_argv_len == 1)
+			continue;
+
+		if (match == -1)	/* partial match */
+			match = i;
+		else if (!IDENTICAL_INTERPRETATION(i, match))
+			ambiguous = 1;
+	}
+	if (ambiguous) {
+		/* ambiguous abbreviation */
+		if (PRINT_ERROR)
+			warnx(ambig, (int)current_argv_len,
+			     current_argv);
+		optopt = 0;
+		return (BADCH);
+	}
+	if (match != -1) {		/* option found */
+		if (long_options[match].has_arg == no_argument
+		    && has_equal) {
+			if (PRINT_ERROR)
+				warnx(noarg, (int)current_argv_len,
+				     current_argv);
+			/*
+			 * XXX: GNU sets optopt to val regardless of flag
+			 */
+			if (long_options[match].flag == NULL)
+				optopt = long_options[match].val;
+			else
+				optopt = 0;
+			return (BADARG);
+		}
+		if (long_options[match].has_arg == required_argument ||
+		    long_options[match].has_arg == optional_argument) {
+			if (has_equal)
+				optarg = has_equal;
+			else if (long_options[match].has_arg ==
+			    required_argument) {
+				/*
+				 * optional argument doesn't use next nargv
+				 */
+				optarg = nargv[optind++];
+			}
+		}
+		if ((long_options[match].has_arg == required_argument)
+		    && (optarg == NULL)) {
+			/*
+			 * Missing argument; leading ':' indicates no error
+			 * should be generated.
+			 */
+			if (PRINT_ERROR)
+				warnx(recargstring,
+				    current_argv);
+			/*
+			 * XXX: GNU sets optopt to val regardless of flag
+			 */
+			if (long_options[match].flag == NULL)
+				optopt = long_options[match].val;
+			else
+				optopt = 0;
+			--optind;
+			return (BADARG);
+		}
+	} else {			/* unknown option */
+		if (short_too) {
+			--optind;
+			return (-1);
+		}
+		if (PRINT_ERROR)
+			warnx(illoptstring, current_argv);
+		optopt = 0;
+		return (BADCH);
+	}
+	if (idx)
+		*idx = match;
+	if (long_options[match].flag) {
+		*long_options[match].flag = long_options[match].val;
+		return (0);
+	} else
+		return (long_options[match].val);
+#undef IDENTICAL_INTERPRETATION
+}
+
+/*
+ * getopt_internal --
+ *	Parse argc/argv argument vector.  Called by user level routines.
+ */
+static int
+getopt_internal(int nargc, char * const *nargv, const char *options,
+	const struct option *long_options, int *idx, int flags)
+{
+	const char *oli;				/* option letter list index */
+	int optchar, short_too;
+	static int posixly_correct = -1;
+
+	if (options == NULL)
+		return (-1);
+
+	/*
+	 * XXX Some GNU programs (like cvs) set optind to 0 instead of
+	 * XXX using optreset.  Work around this braindamage.
+	 */
+	if (optind == 0)
+		optind = optreset = 1;
+
+	/*
+	 * Disable GNU extensions if POSIXLY_CORRECT is set or options
+	 * string begins with a '+'.
+	 *
+	 * CV, 2009-12-14: Check POSIXLY_CORRECT anew if optind == 0 or
+	 *                 optreset != 0 for GNU compatibility.
+	 */
+	if (posixly_correct == -1 || optreset != 0)
+		posixly_correct = (getenv("POSIXLY_CORRECT") != NULL);
+	if (*options == '-')
+		flags |= FLAG_ALLARGS;
+	else if (posixly_correct || *options == '+')
+		flags &= ~FLAG_PERMUTE;
+	if (*options == '+' || *options == '-')
+		options++;
+
+	optarg = NULL;
+	if (optreset)
+		nonopt_start = nonopt_end = -1;
+start:
+	if (optreset || !*place) {		/* update scanning pointer */
+		optreset = 0;
+		if (optind >= nargc) {          /* end of argument vector */
+			place = EMSG;
+			if (nonopt_end != -1) {
+				/* do permutation, if we have to */
+				permute_args(nonopt_start, nonopt_end,
+				    optind, nargv);
+				optind -= nonopt_end - nonopt_start;
+			}
+			else if (nonopt_start != -1) {
+				/*
+				 * If we skipped non-options, set optind
+				 * to the first of them.
+				 */
+				optind = nonopt_start;
+			}
+			nonopt_start = nonopt_end = -1;
+			return (-1);
+		}
+		if (*(place = nargv[optind]) != '-' ||
+		    (place[1] == '\0' && strchr(options, '-') == NULL)) {
+			place = EMSG;		/* found non-option */
+			if (flags & FLAG_ALLARGS) {
+				/*
+				 * GNU extension:
+				 * return non-option as argument to option 1
+				 */
+				optarg = nargv[optind++];
+				return (INORDER);
+			}
+			if (!(flags & FLAG_PERMUTE)) {
+				/*
+				 * If no permutation wanted, stop parsing
+				 * at first non-option.
+				 */
+				return (-1);
+			}
+			/* do permutation */
+			if (nonopt_start == -1)
+				nonopt_start = optind;
+			else if (nonopt_end != -1) {
+				permute_args(nonopt_start, nonopt_end,
+				    optind, nargv);
+				nonopt_start = optind -
+				    (nonopt_end - nonopt_start);
+				nonopt_end = -1;
+			}
+			optind++;
+			/* process next argument */
+			goto start;
+		}
+		if (nonopt_start != -1 && nonopt_end == -1)
+			nonopt_end = optind;
+
+		/*
+		 * If we have "-" do nothing, if "--" we are done.
+		 */
+		if (place[1] != '\0' && *++place == '-' && place[1] == '\0') {
+			optind++;
+			place = EMSG;
+			/*
+			 * We found an option (--), so if we skipped
+			 * non-options, we have to permute.
+			 */
+			if (nonopt_end != -1) {
+				permute_args(nonopt_start, nonopt_end,
+				    optind, nargv);
+				optind -= nonopt_end - nonopt_start;
+			}
+			nonopt_start = nonopt_end = -1;
+			return (-1);
+		}
+	}
+
+	/*
+	 * Check long options if:
+	 *  1) we were passed some
+	 *  2) the arg is not just "-"
+	 *  3) either the arg starts with -- we are getopt_long_only()
+	 */
+	if (long_options != NULL && place != nargv[optind] &&
+	    (*place == '-' || (flags & FLAG_LONGONLY))) {
+		short_too = 0;
+		if (*place == '-')
+			place++;		/* --foo long option */
+		else if (*place != ':' && strchr(options, *place) != NULL)
+			short_too = 1;		/* could be short option too */
+
+		optchar = parse_long_options(nargv, options, long_options,
+		    idx, short_too);
+		if (optchar != -1) {
+			place = EMSG;
+			return (optchar);
+		}
+	}
+
+	if ((optchar = (int)*place++) == (int)':' ||
+	    (optchar == (int)'-' && *place != '\0') ||
+	    (oli = strchr(options, optchar)) == NULL) {
+		/*
+		 * If the user specified "-" and  '-' isn't listed in
+		 * options, return -1 (non-option) as per POSIX.
+		 * Otherwise, it is an unknown option character (or ':').
+		 */
+		if (optchar == (int)'-' && *place == '\0')
+			return (-1);
+		if (!*place)
+			++optind;
+		if (PRINT_ERROR)
+			warnx(illoptchar, optchar);
+		optopt = optchar;
+		return (BADCH);
+	}
+	if (long_options != NULL && optchar == 'W' && oli[1] == ';') {
+		/* -W long-option */
+		if (*place)			/* no space */
+			/* NOTHING */;
+		else if (++optind >= nargc) {	/* no arg */
+			place = EMSG;
+			if (PRINT_ERROR)
+				warnx(recargchar, optchar);
+			optopt = optchar;
+			return (BADARG);
+		} else				/* white space */
+			place = nargv[optind];
+		optchar = parse_long_options(nargv, options, long_options,
+		    idx, 0);
+		place = EMSG;
+		return (optchar);
+	}
+	if (*++oli != ':') {			/* doesn't take argument */
+		if (!*place)
+			++optind;
+	} else {				/* takes (optional) argument */
+		optarg = NULL;
+		if (*place)			/* no white space */
+			optarg = place;
+		else if (oli[1] != ':') {	/* arg not optional */
+			if (++optind >= nargc) {	/* no arg */
+				place = EMSG;
+				if (PRINT_ERROR)
+					warnx(recargchar, optchar);
+				optopt = optchar;
+				return (BADARG);
+			} else
+				optarg = nargv[optind];
+		}
+		place = EMSG;
+		++optind;
+	}
+	/* dump back option letter */
+	return (optchar);
+}
+
+#ifdef REPLACE_GETOPT
+/*
+ * getopt --
+ *	Parse argc/argv argument vector.
+ *
+ * [eventually this will replace the BSD getopt]
+ */
+WINGETOPT_API int
+getopt(int nargc, char * const *nargv, const char *options)
+{
+
+	/*
+	 * We don't pass FLAG_PERMUTE to getopt_internal() since
+	 * the BSD getopt(3) (unlike GNU) has never done this.
+	 *
+	 * Furthermore, since many privileged programs call getopt()
+	 * before dropping privileges it makes sense to keep things
+	 * as simple (and bug-free) as possible.
+	 */
+	return (getopt_internal(nargc, nargv, options, NULL, NULL, 0));
+}
+#endif /* REPLACE_GETOPT */
+
+/*
+ * getopt_long --
+ *	Parse argc/argv argument vector.
+ */
+WINGETOPT_API int
+getopt_long(int nargc, char * const *nargv, const char *options,
+    const struct option *long_options, int *idx)
+{
+
+	return (getopt_internal(nargc, nargv, options, long_options, idx,
+	    FLAG_PERMUTE));
+}
+
+/*
+ * getopt_long_only --
+ *	Parse argc/argv argument vector.
+ */
+WINGETOPT_API int
+getopt_long_only(int nargc, char * const *nargv, const char *options,
+    const struct option *long_options, int *idx)
+{
+
+	return (getopt_internal(nargc, nargv, options, long_options, idx,
+	    FLAG_PERMUTE|FLAG_LONGONLY));
+}
diff --git a/tools/wingetopt/getopt.h b/tools/wingetopt/getopt.h
new file mode 100644
index 00000000..c7ff5085
--- /dev/null
+++ b/tools/wingetopt/getopt.h
@@ -0,0 +1,105 @@
+#ifndef __GETOPT_H__
+/**
+ * DISCLAIMER
+ * This file has no copyright assigned and is placed in the Public Domain.
+ * This file is a part of the w64 mingw-runtime package.
+ *
+ * The w64 mingw-runtime package and its code is distributed in the hope that it 
+ * will be useful but WITHOUT ANY WARRANTY.  ALL WARRANTIES, EXPRESSED OR 
+ * IMPLIED ARE HEREBY DISCLAIMED.  This includes but is not limited to 
+ * warranties of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ */
+
+#define __GETOPT_H__
+
+/* All the headers include this file. */
+#include <crtdefs.h>
+
+#if defined( WINGETOPT_SHARED_LIB )
+# if defined( BUILDING_WINGETOPT_DLL )
+#  define WINGETOPT_API __declspec(dllexport)
+# else
+#  define WINGETOPT_API __declspec(dllimport)
+# endif
+#else
+# define WINGETOPT_API
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+WINGETOPT_API extern int optind;		/* index of first non-option in argv      */
+WINGETOPT_API extern int optopt;		/* single option character, as parsed     */
+WINGETOPT_API extern int opterr;		/* flag to enable built-in diagnostics... */
+				/* (user may set to zero, to suppress)    */
+
+WINGETOPT_API extern char *optarg;		/* pointer to argument of current option  */
+
+WINGETOPT_API extern int getopt(int nargc, char * const *nargv, const char *options);
+
+#ifdef _BSD_SOURCE
+/*
+ * BSD adds the non-standard `optreset' feature, for reinitialisation
+ * of `getopt' parsing.  We support this feature, for applications which
+ * proclaim their BSD heritage, before including this header; however,
+ * to maintain portability, developers are advised to avoid it.
+ */
+# define optreset  __mingw_optreset
+WINGETOPT_API extern int optreset;
+#endif
+#ifdef __cplusplus
+}
+#endif
+/*
+ * POSIX requires the `getopt' API to be specified in `unistd.h';
+ * thus, `unistd.h' includes this header.  However, we do not want
+ * to expose the `getopt_long' or `getopt_long_only' APIs, when
+ * included in this manner.  Thus, close the standard __GETOPT_H__
+ * declarations block, and open an additional __GETOPT_LONG_H__
+ * specific block, only when *not* __UNISTD_H_SOURCED__, in which
+ * to declare the extended API.
+ */
+#endif /* !defined(__GETOPT_H__) */
+
+#if !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__)
+#define __GETOPT_LONG_H__
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct option		/* specification for a long form option...	*/
+{
+  const char *name;		/* option name, without leading hyphens */
+  int         has_arg;		/* does it take an argument?		*/
+  int        *flag;		/* where to save its status, or NULL	*/
+  int         val;		/* its associated status value		*/
+};
+
+enum    		/* permitted values for its `has_arg' field...	*/
+{
+  no_argument = 0,      	/* option never takes an argument	*/
+  required_argument,		/* option always requires an argument	*/
+  optional_argument		/* option may take an argument		*/
+};
+
+WINGETOPT_API extern int getopt_long(int nargc, char * const *nargv, const char *options,
+    const struct option *long_options, int *idx);
+WINGETOPT_API extern int getopt_long_only(int nargc, char * const *nargv, const char *options,
+    const struct option *long_options, int *idx);
+/*
+ * Previous MinGW implementation had...
+ */
+#ifndef HAVE_DECL_GETOPT
+/*
+ * ...for the long form API only; keep this for compatibility.
+ */
+# define HAVE_DECL_GETOPT	1
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) */
diff --git a/viewer/resources/third_party_licenses.html b/viewer/resources/third_party_licenses.html
index f5cab524..1b2a4ec2 100644
--- a/viewer/resources/third_party_licenses.html
+++ b/viewer/resources/third_party_licenses.html
@@ -34,6 +34,7 @@ manifest with copyright holders is in THIRD_PARTY_NOTICES.md in the source distr
 <li><a href="#slsDetectorPackage-LGPL-3.0">slsDetectorPackage (LGPL-3.0)</a></li>
 <li><a href="#spdlog">spdlog</a></li>
 <li><a href="#tinycbor">tinycbor</a></li>
+<li><a href="#wingetopt">wingetopt</a></li>
 <li><a href="#xbflash-qspi">xbflash.qspi</a></li>
 <li><a href="#xilinx-hls-headers">Xilinx HLS arbitrary-precision headers</a></li>
 <li><a href="#zlib">zlib</a></li>
@@ -5218,6 +5219,62 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.</pre>
 <hr>
+<h2 id="wingetopt">wingetopt</h2>
+<pre>#### AUTHORS:
+
+* Todd C. Miller &lt;Todd.Miller@courtesan.com&gt;
+* The NetBSD Foundation, Inc.
+* Alexei Kasatkin is the author of trivial CMakeLists.txt, build script itself is Public Domain
+
+#### LICENSE
+
+    Copyright (c) 2002 Todd C. Miller &lt;Todd.Miller@courtesan.com&gt;
+    
+    Permission to use, copy, modify, and distribute this software for any
+    purpose with or without fee is hereby granted, provided that the above
+    copyright notice and this permission notice appear in all copies.
+    
+    THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+    WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+    MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+    ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+    WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+    ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+    OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+    
+    Sponsored in part by the Defense Advanced Research Projects
+    Agency (DARPA) and Air Force Research Laboratory, Air Force
+    Materiel Command, USAF, under agreement number F39502-99-1-0512.
+
+***
+
+    Copyright (c) 2000 The NetBSD Foundation, Inc.
+    All rights reserved.
+    
+    This code is derived from software contributed to The NetBSD Foundation
+    by Dieter Baron and Thomas Klausner.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions
+    are met:
+    1. Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS
+    ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+    TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+    PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS
+    BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+    POSSIBILITY OF SUCH DAMAGE.</pre>
+<hr>
 <h2 id="xbflash-qspi">xbflash.qspi</h2>
 <pre>All userspace code authored by Xilinx or Advanced Micro Devices is
 released under the following license:
diff --git a/writer/CMakeLists.txt b/writer/CMakeLists.txt
index 94eb4499..d9222b83 100644
--- a/writer/CMakeLists.txt
+++ b/writer/CMakeLists.txt
@@ -35,9 +35,16 @@ ADD_LIBRARY(JFJochWriter STATIC
 
 TARGET_LINK_LIBRARIES(JFJochWriter JFJochPreview JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
 
-ADD_LIBRARY(JFJochStreamWriter StreamWriter.cpp StreamWriter.h)
-TARGET_LINK_LIBRARIES(JFJochStreamWriter JFJochWriter JFJochImagePuller)
+# The streaming writer and the jfjoch_writer service belong to the Linux server stack, not the
+# portable viewer subset: JFJochStreamWriter pulls in JFJochImagePuller (not built in a viewer-only
+# tree) and jfjoch_writer uses a fork()/waitpid() multi-process design (<sys/wait.h>, no Windows
+# equivalent). The portable JFJochWriter library above is what the CLI tools and viewer need; these
+# two targets are not. (Windows/macOS force JFJOCH_VIEWER_ONLY, so this also excludes them there.)
+IF (NOT JFJOCH_VIEWER_ONLY)
+    ADD_LIBRARY(JFJochStreamWriter StreamWriter.cpp StreamWriter.h)
+    TARGET_LINK_LIBRARIES(JFJochStreamWriter JFJochWriter JFJochImagePuller)
 
-ADD_EXECUTABLE(jfjoch_writer jfjoch_writer.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_writer JFJochStreamWriter)
-INSTALL(TARGETS jfjoch_writer RUNTIME COMPONENT writer)
+    ADD_EXECUTABLE(jfjoch_writer jfjoch_writer.cpp)
+    TARGET_LINK_LIBRARIES(jfjoch_writer JFJochStreamWriter)
+    INSTALL(TARGETS jfjoch_writer RUNTIME COMPONENT writer)
+ENDIF()
-- 
2.52.0


From 0c1babd0ca47b8f298a51cde22ba8f04ade74c20 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Sat, 20 Jun 2026 22:33:12 +0200
Subject: [PATCH 171/228] CMake: provide Eigen externally again; fix cpack NSIS
 icon escape

Revert Eigen from the FetchContent OVERRIDE_FIND_PACKAGE vendoring (cd394c52,
d4d2d0d8) back to an external find_package(Eigen3) dependency, like zlib. The
OVERRIDE_FIND_PACKAGE mechanism makes the Visual-Studio-bundled CMake (4.x
"-msvc") intermittently segfault during configure -- ~1/3 of fresh configures,
and 100% with Ceres CUDA enabled. The fault is in CMake's own FetchContent
variable-stack cleanup, reached when Ceres' find_package(Eigen3) resolves the
override through a nested FetchContent_MakeAvailable. Stock Kitware CMake runs
the identical scripts fine, so it is a bug in the VS-bundled cmake binary;
providing Eigen externally avoids that path entirely and is stable with Ceres
CUDA both on and off (verified 0 crashes; full CUDA build + NSIS installer
succeed under the VS-bundled cmake).

Also fix CPACK_NSIS_INSTALLED_ICON_NAME: the backslash value was written
verbatim into CPackConfig.cmake, where "\j" is an invalid escape that cmake 4.x
(CMP0010 strict) rejects when cpack re-parses it, so cpack failed under the
VS-bundled cmake (older/Kitware cpack only warned). Use a forward slash.

- image_analysis: keep Ceres USE_CUDA OFF (Jungfraujoch does not use Ceres' GPU
  solvers) but drop the now-obsolete "required to avoid the Windows cmake crash"
  rationale from the comment.
- docs: Eigen is a required external dependency again (SOFTWARE.md); the Windows
  viewer build provides zlib + Eigen externally (JFJOCH_VIEWER.md).
- THIRD_PARTY_NOTICES: move Eigen from the fetched-and-linked table to the
  external runtime-libraries table.

Docker images still need Eigen re-added (5.0.1, source build) -- to follow.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 CMakeLists.txt                | 34 ++++++++-----------
 THIRD_PARTY_NOTICES.md        |  7 ++--
 docs/JFJOCH_VIEWER.md         | 61 +++++++++++++++++++++++++++++++++++
 docs/SOFTWARE.md              | 15 ++++++---
 image_analysis/CMakeLists.txt |  5 ++-
 5 files changed, 93 insertions(+), 29 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c8a8c622..b073efa0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -229,25 +229,16 @@ FetchContent_MakeAvailable(fftw)
 TARGET_INCLUDE_DIRECTORIES(fftw3f INTERFACE $<BUILD_INTERFACE:${fftw_SOURCE_DIR}/api>)
 ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 
-# Eigen (header-only): consumed by Ceres and by the analysis libs directly, and by ffbidx under
-# CUDA. Not auto-provided by FetchContent and absent on Windows, so vendor it here. OVERRIDE_FIND_PACKAGE
-# routes every find_package(Eigen3) -- ours, Ceres', ffbidx' -- to this copy and bypasses the version
-# request (they ask for 3.4; this is a newer major). ffbidx's own bundled eigen is disabled below
-# (GIT_SUBMODULES "" on fast-indexer) so it does not create a duplicate Eigen3::Eigen target.
-SET(EIGEN_BUILD_DOC OFF CACHE BOOL "" FORCE)
-SET(EIGEN_BUILD_TESTING OFF CACHE BOOL "" FORCE)
-SET(EIGEN_BUILD_PKGCONFIG OFF CACHE BOOL "" FORCE)
-# Ceres' install(EXPORT CeresExport) is unconditional and its ceres target transitively links the
-# eigen target, so eigen must live in an installed export set or generation fails ("eigen is not in
-# any export set"). As a subproject Eigen defaults EIGEN_BUILD_CMAKE_PACKAGE OFF, which skips its
-# install(EXPORT Eigen3Targets); force it ON so eigen is exported and Ceres' export resolves.
-SET(EIGEN_BUILD_CMAKE_PACKAGE ON CACHE BOOL "" FORCE)
-FetchContent_Declare(Eigen3
-        GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
-        GIT_TAG 5.0.1
-        GIT_SHALLOW TRUE
-        EXCLUDE_FROM_ALL
-        OVERRIDE_FIND_PACKAGE)
+# Eigen is an EXTERNAL dependency (like ZLIB), resolved by find_package(Eigen3) in the subdirectories
+# that need it (image_analysis, and transitively Ceres and ffbidx). It is deliberately NOT vendored
+# via FetchContent: declaring Eigen with OVERRIDE_FIND_PACKAGE makes the CMake bundled with Visual
+# Studio (cmake 4.x "-msvc") intermittently SEGFAULT during configure. The fault is in CMake's own
+# FetchContent variable-stack cleanup, reached when Ceres' find_package(Eigen3) resolves the override
+# through a nested FetchContent_MakeAvailable -- ~1 in 3 fresh configures, and 100% with Ceres CUDA on.
+# Stock Kitware CMake runs the identical scripts fine, so it is a bug in the VS-bundled cmake binary;
+# providing Eigen externally avoids that code path entirely and is stable (verified, both Ceres CUDA
+# on and off). Provide it via the system package on Linux (eigen3-devel / libeigen3-dev) or a build
+# prefix on Windows (point CMAKE_PREFIX_PATH / Eigen3_DIR at it), exactly as for ZLIB.
 
 # getopt/getopt_long shim for Windows: the MSVC CRT has no <getopt.h>. Vendored OpenBSD/NetBSD
 # implementation (BSD-licensed). Built only on Windows and defined here, before the subdirectories,
@@ -379,7 +370,10 @@ elseif (WIN32)
     # Start Menu shortcut for the viewer ("<exe basename>;<label>"). The shortcut and the
     # Add/Remove Programs entry both use the .exe's embedded icon.
     set(CPACK_PACKAGE_EXECUTABLES "jfjoch_viewer;Jungfraujoch Viewer")
-    set(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\jfjoch_viewer.exe")
+    # Forward slash on purpose: CPack writes this value verbatim into CPackConfig.cmake, and a
+    # backslash there ("bin\jfjoch...") is an invalid escape that cmake 4.x (CMP0010 strict, e.g. the
+    # VS-bundled cmake) rejects when cpack re-parses it. Windows accepts the forward slash at runtime.
+    set(CPACK_NSIS_INSTALLED_ICON_NAME "bin/jfjoch_viewer.exe")
 elseif (EXISTS "/etc/debian_version")
     set(CPACK_PACKAGE_LICENSE "GPL-3.0-only")
     set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
diff --git a/THIRD_PARTY_NOTICES.md b/THIRD_PARTY_NOTICES.md
index 664e9f8b..7b117a5d 100644
--- a/THIRD_PARTY_NOTICES.md
+++ b/THIRD_PARTY_NOTICES.md
@@ -26,7 +26,6 @@ linked into the Jungfraujoch executables.
 | [libzmq (ZeroMQ)](https://github.com/zeromq/libzmq) | 4.3.5 | iMatix and contributors | MPL-2.0 | [libzmq.txt](licenses/libzmq.txt) |
 | [libtiff](https://gitlab.com/libtiff/libtiff) | 4.7.1 | Sam Leffler; SGI | libtiff (BSD-like) | [libtiff.txt](licenses/libtiff.txt) |
 | [FFTW](https://www.fftw.org/) | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | [fftw.txt](licenses/fftw.txt) |
-| [Eigen](https://gitlab.com/libeigen/eigen) | 5.0.1 | Eigen contributors | MPL-2.0 (+ BSD parts) | [eigen.txt](licenses/eigen.txt), [README](licenses/eigen-README.txt) |
 | [Ceres Solver](https://github.com/ceres-solver/ceres-solver) | (pinned) | Google Inc. and contributors | BSD-3-Clause | [ceres-solver.txt](licenses/ceres-solver.txt) |
 | [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) | (pinned) | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](licenses/fast-feedback-indexer.txt) |
 | [libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) | (pinned) | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | [libjpeg-turbo.txt](licenses/libjpeg-turbo.txt) |
@@ -59,6 +58,7 @@ These are copied into the source tree (see the path) rather than fetched.
 | [Qt 6](https://www.qt.io/) | `jfjoch_viewer` | LGPL-3.0 | [notice](licenses/Qt6-NOTICE.txt), [LGPL-3.0](licenses/Qt6-LGPL-3.0.txt) |
 | [NVIDIA CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit) (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | [notice](licenses/NVIDIA-CUDA-NOTICE.txt), [EULA](licenses/NVIDIA-CUDA-EULA.txt) |
 | [zlib](https://zlib.net/) | everywhere (compression) | Zlib | [zlib.txt](licenses/zlib.txt) |
+| [Eigen](https://gitlab.com/libeigen/eigen) | analysis libs, Ceres, ffbidx (header-only) | MPL-2.0 (+ BSD parts) | [eigen.txt](licenses/eigen.txt), [README](licenses/eigen-README.txt) |
 
 ## Frontend (npm) dependencies
 
@@ -74,8 +74,9 @@ served frontend, so the shipped web UI carries its own attribution.
 
 ## Notes on weak-copyleft and attribution-sensitive components
 
-* **MPL-2.0** (Eigen, GEMMI, libzmq): file-level copyleft. The corresponding source is available as
-  part of this GPL-3.0 source distribution; GEMMI is vendored in `gemmi_gph/` in trimmed form.
+* **MPL-2.0** (Eigen, GEMMI, libzmq): file-level copyleft. GEMMI is vendored in `gemmi_gph/` in
+  trimmed form; libzmq is fetched at build time; Eigen is provided externally (header-only). The
+  corresponding source is available from each project upstream.
 * **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
 * **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the
   corresponding `licenses/` text.
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index 5a7ff0a8..99c63799 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -55,3 +55,64 @@ can drive it:
 - `LoadImage(image_number, summation=1)` — navigate to an image in the already-open dataset.
 
 `summation` sums that many consecutive images before display.
+
+## Building from source on Windows
+
+`jfjoch_viewer` is the one Jungfraujoch component that is cross-platform: it builds on Windows 11
+with MSVC and the full CUDA GPU path. (The rest of Jungfraujoch — broker, receiver, FPGA host — is
+Linux-only.) There is no pre-built Windows package yet, so build it from source. On Windows the
+build is automatically restricted to the viewer and the libraries it needs (`JFJOCH_VIEWER_ONLY` is
+forced on), and the remaining dependencies are fetched and built automatically (the first configure
+needs network access).
+
+Verified toolchain:
+
+- Windows 11
+- Visual Studio 2026 with the C++ (MSVC) toolset — required; CUDA on Windows builds through MSVC
+- CUDA Toolkit 13.3 (12.8 or newer is required) — for the GPU indexing/integration path
+- Qt 6.11 for MSVC (`msvc2022_64`), including the **Qt Charts** module — e.g. `C:\Qt\6.11.1\msvc2022_64`
+- CMake plus Ninja. The CMake that ships with Visual Studio is the simplest choice and works out of
+  the box — it comes with the C++ workload, so there is nothing extra to install. Any recent
+  standalone CMake (from cmake.org, or the one bundled with Qt in `C:\Qt\Tools\CMake_64`) works too.
+- zlib and Eigen — the two libraries not auto-fetched on Windows. Build/install both into one prefix
+  (here `C:\deps`) and point CMake at it:
+  ```
+  :: static zlib
+  git clone --branch v1.3.1 https://github.com/madler/zlib
+  cmake -G Ninja -S zlib -B zlib-build -DCMAKE_INSTALL_PREFIX=C:/deps
+  cmake --build zlib-build --target install
+  :: Eigen (header-only)
+  git clone --branch 5.0.1 https://gitlab.com/libeigen/eigen.git
+  cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=C:/deps
+  cmake --build eigen-build --target install
+  ```
+- Optional: [NSIS](https://nsis.sourceforge.io) to build the `.exe` installer.
+
+Configure and build from an **x64 Native Tools Command Prompt for VS 2026** (so `cl`, `nvcc` and
+`ninja` are on `PATH`):
+
+```
+cmake -G Ninja -B build-win -DCMAKE_BUILD_TYPE=Release ^
+  -DCMAKE_CUDA_COMPILER="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v13.3/bin/nvcc.exe" ^
+  -DZLIB_ROOT=C:/deps ^
+  -DCMAKE_PREFIX_PATH="C:/deps;C:/Qt/6.11.1/msvc2022_64"
+cmake --build build-win --target jfjoch_viewer
+```
+
+Notes:
+
+- Presetting `CMAKE_CUDA_COMPILER` is recommended on Windows so the CUDA toolchain is detected
+  reliably.
+- For a machine without an NVIDIA GPU, add `-DJFJOCH_USE_CUDA=OFF`: the viewer then runs the same
+  pipeline on the CPU (FFTW indexer) at lower throughput.
+
+To produce a self-contained installer (bundles the Qt runtime via `windeployqt` and the analysis
+CLIs), with NSIS installed:
+
+```
+cd build-win
+cpack
+```
+
+The NSIS generator is selected automatically on Windows (no `-G` needed); this writes
+`jfjoch-<version>-win64.exe`.
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index 6357695e..6f338c73 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -7,16 +7,21 @@ On experimental basis we also build repositories for Ubuntu 22.04 and 24.04.
 Running Jungfraujoch on Red Hat Enterprise Linux 7 is currently not tested and not recommended,
 but likely possible with providing some packages from external repositories.
 
+The desktop viewer `jfjoch_viewer` (only) can additionally be built on **Windows 11** with Visual
+Studio 2026 (MSVC), CUDA 13.3 and Qt 6.11 — see
+[jfjoch_viewer ▸ Building from source on Windows](JFJOCH_VIEWER.md#building-from-source-on-windows).
+The rest of Jungfraujoch is Linux-only.
+
 
 ## Software dependencies
 Required:
 * C++20 compiler and C++20 standard library; recommended GCC 11+ or clang 14+ (Intel OneAPI, AMD AOCC)
-* CMake version 3.21 or newer + GNU make tool
+* CMake version 3.26 or newer + a build tool (GNU make or Ninja)
 * zlib compression library
-* EIGEN library (only on a compilation system)
-* HDF5 library version 1.10 or newer - see [github.com/HDFGroup/hdf5](https://github.com/HDFGroup/hdf5)
-* TIFF library - see [gitlab.com/libtiff/libtiff](https://gitlab.com/libtiff/libtiff)
-* JPEG library (preferably jpeg-turbo) - see [github.com/libjpeg-turbo/libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo)
+* Eigen (header-only linear algebra library), version 3.4 or newer
+
+HDF5, libtiff and libjpeg-turbo used to be required system packages; they are now downloaded and
+built automatically by CMake (see the note below), so they no longer need to be installed.
 
 Optional:
 * CUDA compiler version 12.8 or newer - required for the MX fast feedback indexer and GPU analysis
diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 6b656767..57d3b884 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -1,5 +1,8 @@
 SET(PROVIDE_UNINSTALL_TARGET OFF)
-SET(USE_CUDA OFF CACHE BOOL "Force Ceres to build without CUDA" FORCE)
+# Force Ceres to build WITHOUT its own CUDA support: Jungfraujoch never uses Ceres' GPU solvers, so
+# this just drops unused code and build time (Ceres would otherwise enable CUDA whenever a toolkit is
+# found). See the Eigen note in the top-level CMakeLists for the related Windows/cmake history.
+SET(USE_CUDA OFF CACHE BOOL "Force Ceres to build without CUDA (Jungfraujoch does not use Ceres' GPU solvers)" FORCE)
 
 # Prevent MKL from being found (guarantees no MKL)
 SET(CMAKE_DISABLE_FIND_PACKAGE_MKL TRUE)
-- 
2.52.0


From ec8a45dc09bbd01e73d4a4472e7978ca5e4a8080 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 09:17:52 +0200
Subject: [PATCH 172/228] windows: bundle cuFFT in installer and tag the
 CUDA/CPU variant

cuFFT is the only CUDA component linked dynamically (cudart and the
fast-feedback indexer are static), so the prior Windows installer would
fail to launch the GPU path on a host without a CUDA toolkit. Ship
cufft64_*.dll next to the viewer (CUDA 13 keeps it in bin/x64, earlier
toolkits in bin); the DLL is self-contained, so the installed app needs
only an NVIDIA driver.

Tag the variant where it matters and nowhere else: the installer
filename (-cuda<major> / -cpu) and the Add/Remove Programs entry
("Jungfraujoch (CUDA)" / "(CPU)") advertise it, while the install folder
and Start Menu group stay plain "Jungfraujoch" -- the CUDA build is a
strict superset, so the two variants share a location and replace each
other.

Docs: SOFTWARE.md + JFJOCH_VIEWER.md.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 CMakeLists.txt        | 21 ++++++++++++++++++---
 docs/JFJOCH_VIEWER.md | 19 +++++++++++++++----
 docs/SOFTWARE.md      |  4 +++-
 viewer/CMakeLists.txt | 15 +++++++++++++++
 4 files changed, 51 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b073efa0..af868b1e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -361,11 +361,26 @@ elseif (WIN32)
     # GPLv3 text shown as the click-through license page of the installer.
     set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
 
-    # Name the install folder and Start Menu group "Jungfraujoch". CPack uses this single
-    # variable for both; without it they default to "jfjoch <version>".
+    # Branding is split across three CPack knobs so the CUDA/CPU variant surfaces exactly where we
+    # want it and nowhere else:
+    #   - Install folder + Start Menu group come from CPACK_PACKAGE_INSTALL_DIRECTORY and
+    #     CPACK_NSIS_PACKAGE_NAME (the latter feeds $(^Name), the Start Menu group's default folder).
+    #     Both stay plain "Jungfraujoch", so the Start Menu group carries no variant tag and the two
+    #     builds install to the same place (CUDA is a strict superset -- they replace, not coexist).
+    #   - CPACK_NSIS_DISPLAY_NAME is the Add/Remove Programs entry -- tagged "(CUDA)"/"(CPU)".
+    #   - CPACK_PACKAGE_FILE_NAME is the installer .exe filename -- tagged "-cuda<major>"/"-cpu", so
+    #     the (much larger) CUDA download is self-identifying, with the CUDA major version baked in.
+    # The tag follows JFJOCH_CUDA_AVAILABLE automatically; CUDAToolkit_VERSION_MAJOR is set whenever
+    # it is ON (find_package(CUDAToolkit) ran in the same guard above).
     set(CPACK_PACKAGE_INSTALL_DIRECTORY "Jungfraujoch")
-    set(CPACK_NSIS_DISPLAY_NAME "Jungfraujoch")
     set(CPACK_NSIS_PACKAGE_NAME "Jungfraujoch")
+    if (JFJOCH_CUDA_AVAILABLE)
+        set(CPACK_NSIS_DISPLAY_NAME "Jungfraujoch (CUDA)")
+        set(CPACK_PACKAGE_FILE_NAME "jfjoch-${JFJOCH_VERSION}-win64-cuda${CUDAToolkit_VERSION_MAJOR}")
+    else()
+        set(CPACK_NSIS_DISPLAY_NAME "Jungfraujoch (CPU)")
+        set(CPACK_PACKAGE_FILE_NAME "jfjoch-${JFJOCH_VERSION}-win64-cpu")
+    endif()
 
     # Start Menu shortcut for the viewer ("<exe basename>;<label>"). The shortcut and the
     # Add/Remove Programs entry both use the .exe's embedded icon.
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index 99c63799..ddce90ca 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -106,13 +106,24 @@ Notes:
 - For a machine without an NVIDIA GPU, add `-DJFJOCH_USE_CUDA=OFF`: the viewer then runs the same
   pipeline on the CPU (FFTW indexer) at lower throughput.
 
-To produce a self-contained installer (bundles the Qt runtime via `windeployqt` and the analysis
-CLIs), with NSIS installed:
+To produce a self-contained installer (bundles the Qt runtime via `windeployqt`, the analysis CLIs,
+and — on the CUDA build — the cuFFT runtime DLL, so the target host needs no Qt and no CUDA toolkit,
+only an NVIDIA GPU driver), with NSIS installed:
 
 ```
 cd build-win
 cpack
 ```
 
-The NSIS generator is selected automatically on Windows (no `-G` needed); this writes
-`jfjoch-<version>-win64.exe`.
+The NSIS generator is selected automatically on Windows (no `-G` needed). The installer filename and
+the Add/Remove Programs entry mark the CUDA/CPU variant, while the install folder and Start Menu
+group stay plain `Jungfraujoch` (the two variants share an install location and replace each other —
+CUDA is a strict superset):
+
+| Build | Installer file | Add/Remove Programs |
+| --- | --- | --- |
+| CUDA (default) | `jfjoch-<version>-win64-cuda<major>.exe` | `Jungfraujoch (CUDA)` |
+| `-DJFJOCH_USE_CUDA=OFF` | `jfjoch-<version>-win64-cpu.exe` | `Jungfraujoch (CPU)` |
+
+`<major>` is the CUDA toolkit major version (e.g. `cuda13`). The cuFFT DLL is ~256 MB, so the CUDA
+installer is correspondingly larger — hence the variant tag in the filename.
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index 6f338c73..b661fba2 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -10,7 +10,9 @@ but likely possible with providing some packages from external repositories.
 The desktop viewer `jfjoch_viewer` (only) can additionally be built on **Windows 11** with Visual
 Studio 2026 (MSVC), CUDA 13.3 and Qt 6.11 — see
 [jfjoch_viewer ▸ Building from source on Windows](JFJOCH_VIEWER.md#building-from-source-on-windows).
-The rest of Jungfraujoch is Linux-only.
+The Windows installer bundles the Qt runtime, and on the CUDA build the CUDA runtime (cuFFT) as
+well, so end users need neither Qt nor a CUDA toolkit installed — only an NVIDIA GPU driver for the
+GPU path. The rest of Jungfraujoch is Linux-only.
 
 
 ## Software dependencies
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 09654a9f..cab9d63c 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -168,3 +168,18 @@ IF(Qt6_VERSION VERSION_GREATER_EQUAL "6.5")
             NO_UNSUPPORTED_PLATFORM_ERROR)
     INSTALL(SCRIPT ${jfjoch_viewer_deploy_script} COMPONENT viewer)
 ENDIF()
+
+# Bundle the cuFFT runtime DLL next to the viewer so the installed app runs on Windows hosts that
+# have an NVIDIA driver but no CUDA toolkit. cuFFT is the ONLY CUDA component we link dynamically
+# (cudart and the fast-feedback indexer are static), so it is the one runtime file the toolkit would
+# otherwise have to provide; the DLL is self-contained (depends only on KERNEL32). CUDA 13 keeps
+# redistributable DLLs in bin/x64, earlier toolkits in bin -- glob both. Windows + GPU build only.
+IF(WIN32 AND JFJOCH_CUDA_AVAILABLE)
+    FILE(GLOB _cufft_dll
+            "${CUDAToolkit_BIN_DIR}/x64/cufft64_*.dll"
+            "${CUDAToolkit_BIN_DIR}/cufft64_*.dll")
+    IF(NOT _cufft_dll)
+        MESSAGE(FATAL_ERROR "cuFFT runtime DLL not found under ${CUDAToolkit_BIN_DIR}")
+    ENDIF()
+    INSTALL(FILES ${_cufft_dll} DESTINATION bin COMPONENT viewer)
+ENDIF()
-- 
2.52.0


From 23d27f30c4a439f3ed32ba1bc435a6d01354e4e5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 09:52:30 +0200
Subject: [PATCH 173/228] reader: split raw-image reading into HDF5ImageLocator
 + HDF5ImageSource

Decouple the raw-pixel side of JFJochHDF5Reader from the rest as the first
step toward swappable per-dataset metadata snapshots.

- HDF5ImageLocator: single owner of the legacy/VDS/contiguous layout resolution
  plus a persistent open-file cache, replacing the four duplicated resolvers
  (GetImageLocation, ReadSpots, ReadReflections) and their per-call file caches.
  Also hosts the source-mapping logic (former GetHDF5DataSource body).
- HDF5ImageSource: raw-pixel reading (locator + LoadImageDataset); the part whose
  links to files stay fixed while the metadata master may change.
- JFJochHDF5Reader keeps a thin GetImageLocation/GetRawImage/GetHDF5DataSource that
  delegate to image_source_; the six layout members are gone, parsed into a local
  Layout handed to the source at the end of ReadFile. Cache cleared on Close().

Verified: tests/jfjoch_test [HDF5] (79 cases / 1775 assertions), and
jfjoch_process/azint/extract_hkl/scale relink unchanged.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/CMakeLists.txt       |   4 +
 reader/HDF5ImageLocator.cpp | 160 +++++++++++++++++++
 reader/HDF5ImageLocator.h   |  60 +++++++
 reader/HDF5ImageSource.cpp  |  66 ++++++++
 reader/HDF5ImageSource.h    |  36 +++++
 reader/JFJochHDF5Reader.cpp | 307 ++++++------------------------------
 reader/JFJochHDF5Reader.h   |  19 +--
 7 files changed, 379 insertions(+), 273 deletions(-)
 create mode 100644 reader/HDF5ImageLocator.cpp
 create mode 100644 reader/HDF5ImageLocator.h
 create mode 100644 reader/HDF5ImageSource.cpp
 create mode 100644 reader/HDF5ImageSource.h

diff --git a/reader/CMakeLists.txt b/reader/CMakeLists.txt
index 75ee565e..8e8793ea 100644
--- a/reader/CMakeLists.txt
+++ b/reader/CMakeLists.txt
@@ -2,6 +2,10 @@ ADD_LIBRARY(JFJochReader STATIC
         JFJochReader.cpp JFJochReader.h
         JFJochHDF5Reader.cpp
         JFJochHDF5Reader.h
+        HDF5ImageLocator.cpp
+        HDF5ImageLocator.h
+        HDF5ImageSource.cpp
+        HDF5ImageSource.h
         JFJochReaderImage.cpp
         JFJochReaderImage.h
         JFJochReaderDataset.cpp
diff --git a/reader/HDF5ImageLocator.cpp b/reader/HDF5ImageLocator.cpp
new file mode 100644
index 00000000..5132a904
--- /dev/null
+++ b/reader/HDF5ImageLocator.cpp
@@ -0,0 +1,160 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "HDF5ImageLocator.h"
+#include "../common/JFJochException.h"
+
+namespace {
+    // Coalesce consecutive single-image mappings into one contiguous range when the source and
+    // virtual images stay contiguous in the same file/dataset.
+    void AppendOrExtendSourceMapping(std::vector<HDF5DataSourceMessage> &ret,
+                                     const std::string &filename,
+                                     const std::string &dataset,
+                                     uint64_t source_first_image,
+                                     uint64_t virtual_first_image,
+                                     uint64_t image_count) {
+        if (image_count == 0)
+            return;
+
+        if (!ret.empty()) {
+            auto &last = ret.back();
+            if (last.filename == filename
+                && last.dataset == dataset
+                && last.source_first_image + last.image_count == source_first_image
+                && last.virtual_first_image + last.image_count == virtual_first_image) {
+                last.image_count += image_count;
+                return;
+            }
+        }
+
+        ret.push_back(HDF5DataSourceMessage{
+            .filename = filename,
+            .dataset = dataset,
+            .source_first_image = source_first_image,
+            .virtual_first_image = virtual_first_image,
+            .image_count = image_count
+        });
+    }
+}
+
+void HDF5ImageLocator::Configure(Layout layout) {
+    file_cache_.clear();
+    layout_ = std::move(layout);
+}
+
+void HDF5ImageLocator::Clear() {
+    file_cache_.clear();
+    layout_ = Layout{};
+}
+
+std::shared_ptr<HDF5ReadOnlyFile> HDF5ImageLocator::OpenCached(const std::string &path) const {
+    auto it = file_cache_.find(path);
+    if (it != file_cache_.end())
+        return it->second;
+    auto file = std::make_shared<HDF5ReadOnlyFile>(path);
+    file_cache_[path] = file;
+    return file;
+}
+
+HDF5ImageLocator::Location HDF5ImageLocator::Resolve(int64_t global_image) const {
+    if (global_image < 0)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Image out of bounds");
+
+    if (layout_.format == FileWriterFormat::NXmxLegacy) {
+        const uint32_t file_id = global_image / layout_.images_per_file;
+        const uint32_t local_index = global_image % layout_.images_per_file;
+        return {OpenCached(layout_.legacy_files.at(file_id)), local_index};
+    }
+
+    if (layout_.format == FileWriterFormat::NXmxVDS
+        && layout_.data_layout == HDF5DataSetLayout::VIRTUAL) {
+        const auto image = static_cast<hsize_t>(global_image);
+        for (const auto &mapping: layout_.vds_mappings) {
+            if (!mapping.ContainsVirtualImage(image))
+                continue;
+            return {OpenCached(mapping.filename), static_cast<uint32_t>(mapping.SourceImage(image))};
+        }
+        throw JFJochException(JFJochExceptionCategory::HDF5,
+                              "Image not covered by /entry/data/data VDS mappings");
+    }
+
+    // Contiguous / integrated: pixels live in the master file at the global index.
+    if (!layout_.master_file)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Master file not loaded");
+    return {layout_.master_file, static_cast<uint32_t>(global_image)};
+}
+
+std::vector<HDF5DataSourceMessage> HDF5ImageLocator::GetSourceMapping(uint64_t first_image,
+                                                                      std::optional<uint64_t> image_count,
+                                                                      uint64_t total_images) const {
+    if (first_image > total_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "First image outside dataset range");
+
+    const uint64_t requested_count = image_count.value_or(total_images - first_image);
+    if (first_image + requested_count > total_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Requested image range outside dataset range");
+
+    std::vector<HDF5DataSourceMessage> ret;
+    if (requested_count == 0)
+        return ret;
+
+    // Integrated / contiguous source: link directly to the original master file.
+    if (layout_.format == FileWriterFormat::NXmxVDS && layout_.data_layout != HDF5DataSetLayout::VIRTUAL) {
+        AppendOrExtendSourceMapping(ret, layout_.master_filename, "/entry/data/data",
+                                    first_image, 0, requested_count);
+        return ret;
+    }
+
+    // VDS source: expand VDS mappings to original source files, not to the VDS master.
+    if (layout_.format == FileWriterFormat::NXmxVDS && layout_.data_layout == HDF5DataSetLayout::VIRTUAL) {
+        for (uint64_t local_image = 0; local_image < requested_count; ++local_image) {
+            const hsize_t virtual_image = first_image + local_image;
+
+            bool found = false;
+            for (const auto &mapping: layout_.vds_mappings) {
+                if (!mapping.ContainsVirtualImage(virtual_image))
+                    continue;
+
+                const uint64_t source_image = mapping.SourceImage(virtual_image);
+                const std::string dataset = mapping.dataset.empty() ? "/entry/data/data" : mapping.dataset;
+
+                AppendOrExtendSourceMapping(ret, mapping.filename, dataset, source_image, local_image, 1);
+                found = true;
+                break;
+            }
+
+            if (!found)
+                throw JFJochException(JFJochExceptionCategory::HDF5,
+                                      "Image not covered by /entry/data/data VDS mappings");
+        }
+
+        return ret;
+    }
+
+    // Legacy source: link directly to the linked data files.
+    if (layout_.format == FileWriterFormat::NXmxLegacy) {
+        if (layout_.images_per_file == 0)
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "Cannot generate HDF5 source mapping: images_per_file is zero");
+
+        for (uint64_t local_image = 0; local_image < requested_count; ++local_image) {
+            const uint64_t source_global_image = first_image + local_image;
+            const uint64_t file_id = source_global_image / layout_.images_per_file;
+            const uint64_t source_image = source_global_image % layout_.images_per_file;
+
+            if (file_id >= layout_.legacy_files.size())
+                throw JFJochException(JFJochExceptionCategory::HDF5,
+                                      "Legacy image source file missing");
+
+            AppendOrExtendSourceMapping(ret, layout_.legacy_files.at(file_id), "/entry/data/data",
+                                        source_image, local_image, 1);
+        }
+
+        return ret;
+    }
+
+    throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                          "Unsupported HDF5 file layout for source mapping");
+}
diff --git a/reader/HDF5ImageLocator.h b/reader/HDF5ImageLocator.h
new file mode 100644
index 00000000..de69ae2b
--- /dev/null
+++ b/reader/HDF5ImageLocator.h
@@ -0,0 +1,60 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <map>
+#include <memory>
+#include <optional>
+#include <string>
+#include <vector>
+
+#include "../writer/HDF5Objects.h"      // HDF5ReadOnlyFile, HDF5VirtualDatasetMapping, HDF5DataSetLayout
+#include "../common/JFJochMessages.h"   // FileWriterFormat, HDF5DataSourceMessage
+
+// Turns a global image number into the HDF5 file + local index that physically holds its pixels,
+// for all three on-disk layouts (legacy linked data files, VDS, contiguous/integrated). This is
+// the part of the reader whose "links to files stay" constant: it knows where the raw images
+// live, independent of which master file the per-image metadata is read from.
+//
+// Open data-file handles are cached, so scanning many images (e.g. reprocessing) does not reopen
+// the same file on every read. HDF5 is not thread-safe, so every call must be made with the
+// global hdf5_mutex held by the caller; the locator does no locking of its own.
+class HDF5ImageLocator {
+public:
+    struct Location {
+        std::shared_ptr<HDF5ReadOnlyFile> file;
+        uint32_t local_index = 0;
+    };
+
+    // Layout description, filled by the reader once the master file has been parsed. All paths
+    // are absolute: legacy data files and VDS mapping filenames are resolved relative to the
+    // master before being handed over, so the locator never deals with relative paths.
+    struct Layout {
+        FileWriterFormat format = FileWriterFormat::NoFile;
+        HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
+        std::shared_ptr<HDF5ReadOnlyFile> master_file;
+        std::string master_filename;
+        std::vector<std::string> legacy_files;
+        size_t images_per_file = 1;
+        std::vector<HDF5VirtualDatasetMapping> vds_mappings;
+    };
+
+    void Configure(Layout layout);
+    void Clear();
+
+    // Resolve a global image number to {file, local index}. Throws if the image is not covered
+    // by the layout. Does not bounds-check against the total image count - the caller does that.
+    Location Resolve(int64_t global_image) const;
+
+    // Source mapping for re-writing a derived file (e.g. _process.h5) so it links back to the
+    // original pixel sources rather than to a master. total_images is supplied by the caller.
+    std::vector<HDF5DataSourceMessage> GetSourceMapping(uint64_t first_image,
+                                                        std::optional<uint64_t> image_count,
+                                                        uint64_t total_images) const;
+
+private:
+    Layout layout_;
+    mutable std::map<std::string, std::shared_ptr<HDF5ReadOnlyFile> > file_cache_;
+    std::shared_ptr<HDF5ReadOnlyFile> OpenCached(const std::string &path) const;
+};
diff --git a/reader/HDF5ImageSource.cpp b/reader/HDF5ImageSource.cpp
new file mode 100644
index 00000000..42464817
--- /dev/null
+++ b/reader/HDF5ImageSource.cpp
@@ -0,0 +1,66 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "HDF5ImageSource.h"
+#include "../common/JFJochException.h"
+
+void HDF5ImageSource::Configure(HDF5ImageLocator::Layout layout) {
+    locator_.Configure(std::move(layout));
+}
+
+void HDF5ImageSource::Clear() {
+    locator_.Clear();
+}
+
+HDF5ImageLocator::Location HDF5ImageSource::Resolve(int64_t global) const {
+    return locator_.Resolve(global);
+}
+
+std::vector<HDF5DataSourceMessage> HDF5ImageSource::GetSourceMapping(uint64_t first_image,
+                                                                     std::optional<uint64_t> image_count,
+                                                                     uint64_t total_images) const {
+    return locator_.GetSourceMapping(first_image, image_count, total_images);
+}
+
+CompressedImage HDF5ImageSource::ReadImageAt(std::vector<uint8_t> &buffer,
+                                             const HDF5ImageLocator::Location &loc) const {
+    return LoadImageDataset(buffer, *loc.file, loc.local_index);
+}
+
+CompressedImage HDF5ImageSource::LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number) {
+    std::vector<hsize_t> start = {static_cast<hsize_t>(number), 0, 0};
+
+    const std::string dataset_name = "/entry/data/data";
+
+    HDF5DataSet dataset(file, dataset_name);
+    HDF5DataSpace dataspace(dataset);
+    HDF5DataType datatype(dataset);
+    HDF5Dcpl dcpl(dataset);
+
+    if (dataspace.GetNumOfDimensions() != 3)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "/entry/data/data dataset must be 3D");
+
+    auto dim = dataspace.GetDimensions();
+
+    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
+    auto chunk_size = dcpl.GetChunking();
+
+    if ((chunk_size.size() == 3) && (chunk_size[0] == 1) && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2])) {
+        dataset.ReadDirectChunk(tmp, start);
+        algorithm = dcpl.GetCompression();
+    } else {
+        dataset.ReadVectorToU8(tmp, start, {1, dim[1], dim[2]});
+        algorithm = CompressionAlgorithm::NO_COMPRESSION;
+    }
+
+    if (datatype.IsFloat())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Float datasets not supported at this time");
+
+    return {
+        tmp, dim[2], dim[1],
+        CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
+        algorithm
+    };
+}
diff --git a/reader/HDF5ImageSource.h b/reader/HDF5ImageSource.h
new file mode 100644
index 00000000..ac45020c
--- /dev/null
+++ b/reader/HDF5ImageSource.h
@@ -0,0 +1,36 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <cstdint>
+#include <optional>
+#include <vector>
+
+#include "HDF5ImageLocator.h"
+#include "../common/CompressedImage.h"
+
+// Raw-pixel side of the reader. Turns a global image number into a CompressedImage, using
+// HDF5ImageLocator to find the file (with its open-file cache). This is the part whose "links
+// to files stay" constant: switching which master the per-image metadata is read from never
+// touches it. Caller must hold the global hdf5_mutex (HDF5 is not thread-safe).
+class HDF5ImageSource {
+public:
+    void Configure(HDF5ImageLocator::Layout layout);
+    void Clear();
+
+    // Where image `global` physically lives. Also used by the metadata source to find the data
+    // file that holds a legacy/VDS image's per-image metadata.
+    HDF5ImageLocator::Location Resolve(int64_t global) const;
+
+    // Read the pixels at a resolved location into a CompressedImage backed by `buffer`.
+    CompressedImage ReadImageAt(std::vector<uint8_t> &buffer, const HDF5ImageLocator::Location &loc) const;
+
+    std::vector<HDF5DataSourceMessage> GetSourceMapping(uint64_t first_image,
+                                                        std::optional<uint64_t> image_count,
+                                                        uint64_t total_images) const;
+
+private:
+    HDF5ImageLocator locator_;
+    static CompressedImage LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number);
+};
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 590d2100..0bbbe8dc 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -288,15 +288,23 @@ void JFJochHDF5Reader::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDatas
 
 void JFJochHDF5Reader::ReadFile(const std::string &filename) {
     std::unique_lock ul(hdf5_mutex);
+    image_source_.Clear();
     try {
         auto dataset = std::make_shared<JFJochReaderDataset>();
         master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
         master_filename = filename;
         dataset->experiment = default_experiment;
 
+        // Image-layout state is accumulated locally while parsing, then handed to image_locator_
+        // at the end. format stays NoFile if the master carries no image data.
+        FileWriterFormat format = FileWriterFormat::NoFile;
+        HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
+        std::vector<std::string> legacy_format_files;
+        std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
+        size_t images_per_file = 1;
+
         std::filesystem::path master_path(filename);
-        master_file_directory = master_path.parent_path().string();
-        vds_data_mappings.clear();
+        std::string master_file_directory = master_path.parent_path().string();
 
         dataset->arm_date = master_file->GetString("/entry/start_time");
 
@@ -679,12 +687,27 @@ void JFJochHDF5Reader::ReadFile(const std::string &filename) {
 
         ReadROIMetadata(*master_file, *dataset);
 
+        // Hand the parsed image layout to the locator. VDS mapping filenames are resolved to
+        // absolute paths here so the locator only ever deals with real paths.
+        for (auto &m : vds_data_mappings)
+            m.filename = ResolveRelativeToMaster(master_file_directory, m.filename);
+        image_source_.Configure(HDF5ImageLocator::Layout{
+            .format = format,
+            .data_layout = data_layout,
+            .master_file = master_file,
+            .master_filename = master_filename,
+            .legacy_files = std::move(legacy_format_files),
+            .images_per_file = images_per_file,
+            .vds_mappings = std::move(vds_data_mappings)
+        });
+
         dataset->experiment.ImagesPerTrigger(number_of_images);
         cached_geom = dataset->experiment.GetDiffractionGeometry();
         SetStartMessage(dataset);
     } catch (const std::exception &e) {
         master_file = {};
         number_of_images = 0;
+        image_source_.Clear();
         SetStartMessage({});
         throw;
     }
@@ -695,77 +718,10 @@ uint64_t JFJochHDF5Reader::GetNumberOfImages() const {
     return number_of_images;
 }
 
-CompressedImage JFJochHDF5Reader::LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number) {
-    std::vector<hsize_t> start = {static_cast<hsize_t>(number), 0, 0};
-
-    const std::string dataset_name = "/entry/data/data";
-
-    HDF5DataSet dataset(file, dataset_name);
-    HDF5DataSpace dataspace(dataset);
-    HDF5DataType datatype(dataset);
-    HDF5Dcpl dcpl(dataset);
-
-    if (dataspace.GetNumOfDimensions() != 3)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "/entry/data/data dataset must be 3D");
-
-    auto dim = dataspace.GetDimensions();
-
-    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
-    auto chunk_size = dcpl.GetChunking();
-
-    if ((chunk_size.size() == 3) && (chunk_size[0] == 1) && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2])) {
-        dataset.ReadDirectChunk(tmp, start);
-        algorithm = dcpl.GetCompression();
-    } else {
-        dataset.ReadVectorToU8(tmp, start, {1, dim[1], dim[2]});
-        algorithm = CompressionAlgorithm::NO_COMPRESSION;
-    }
-
-    if (datatype.IsFloat())
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Float datasets not supported at this time");
-
-    return {
-        tmp, dim[2], dim[1],
-        CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
-        algorithm
-    };
-}
-
-std::pair<std::shared_ptr<HDF5ReadOnlyFile>, uint32_t> JFJochHDF5Reader::GetImageLocation(int64_t image_number) {
-    if (image_number >= number_of_images || image_number < 0)
+HDF5ImageLocator::Location JFJochHDF5Reader::GetImageLocation(int64_t image_number) const {
+    if (image_number >= static_cast<int64_t>(number_of_images) || image_number < 0)
         throw JFJochException(JFJochExceptionCategory::HDF5, "Image out of bounds");
-
-    uint32_t image_id;
-    std::shared_ptr<HDF5ReadOnlyFile> data_file;
-
-    if (format == FileWriterFormat::NXmxLegacy) {
-        uint32_t file_id = image_number / images_per_file;
-        image_id = image_number % images_per_file;
-        data_file = std::make_shared<HDF5ReadOnlyFile>(legacy_format_files.at(file_id));
-    } else if (format == FileWriterFormat::NXmxVDS && data_layout == HDF5DataSetLayout::VIRTUAL) {
-        const auto image = static_cast<hsize_t>(image_number);
-
-        for (const auto &mapping: vds_data_mappings) {
-            if (!mapping.ContainsVirtualImage(image))
-                continue;
-
-            image_id = static_cast<uint32_t>(mapping.SourceImage(image));
-            data_file = std::make_shared<HDF5ReadOnlyFile>(
-                ResolveRelativeToMaster(master_file_directory, mapping.filename)
-            );
-            return {std::move(data_file), image_id};
-        }
-
-        throw JFJochException(JFJochExceptionCategory::HDF5,
-                              "Image not covered by /entry/data/data VDS mappings");
-    } else {
-        image_id = image_number;
-        data_file = master_file;
-    }
-
-    return {std::move(data_file), image_id};
+    return image_source_.Resolve(image_number);
 }
 
 std::shared_ptr<JFJochReaderRawImage> JFJochHDF5Reader::GetRawImage(int64_t image_number) {
@@ -775,9 +731,9 @@ std::shared_ptr<JFJochReaderRawImage> JFJochHDF5Reader::GetRawImage(int64_t imag
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot load image if file not loaded");
 
-    auto [source_file, image_id] = GetImageLocation(image_number);
+    auto loc = GetImageLocation(image_number);
     auto ret = std::make_shared<JFJochReaderRawImage>();
-    ret->image = LoadImageDataset(ret->image_buffer, *source_file, image_id);
+    ret->image = image_source_.ReadImageAt(ret->image_buffer, loc);
     return ret;
 }
 
@@ -921,9 +877,11 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot load image if file not loaded");
 
-    auto [source_file, image_id] = GetImageLocation(image_number);
+    auto loc = GetImageLocation(image_number);
+    auto &source_file = loc.file;
+    const uint32_t image_id = loc.local_index;
 
-    message.image = LoadImageDataset(buffer, *source_file, image_id);
+    message.image = image_source_.ReadImageAt(buffer, loc);
     message.number = image_number;
 
     const auto master_image = static_cast<hsize_t>(image_number);
@@ -1037,11 +995,9 @@ void JFJochHDF5Reader::Close() {
     std::unique_lock ul(hdf5_mutex);
     master_file = {};
     number_of_images = 0;
-    legacy_format_files.clear();
-    vds_data_mappings.clear();
-    master_file_directory.clear();
     master_filename.clear();
     cached_geom = DiffractionGeometry{};
+    image_source_.Clear();
     SetStartMessage({});
 }
 
@@ -1109,35 +1065,6 @@ CompressedImage JFJochHDF5Reader::ReadCalibration(std::vector<uint8_t> &tmp, con
     };
 }
 
-void AppendOrExtendSourceMapping(std::vector<HDF5DataSourceMessage> &ret,
-                                 const std::string &filename,
-                                 const std::string &dataset,
-                                 uint64_t source_first_image,
-                                 uint64_t virtual_first_image,
-                                 uint64_t image_count) {
-    if (image_count == 0)
-        return;
-
-    if (!ret.empty()) {
-        auto &last = ret.back();
-        if (last.filename == filename
-            && last.dataset == dataset
-            && last.source_first_image + last.image_count == source_first_image
-            && last.virtual_first_image + last.image_count == virtual_first_image) {
-            last.image_count += image_count;
-            return;
-        }
-    }
-
-    ret.push_back(HDF5DataSourceMessage{
-        .filename = filename,
-        .dataset = dataset,
-        .source_first_image = source_first_image,
-        .virtual_first_image = virtual_first_image,
-        .image_count = image_count
-    });
-};
-
 std::vector<HDF5DataSourceMessage> JFJochHDF5Reader::GetHDF5DataSource(uint64_t first_image,
                                                                        std::optional<uint64_t> image_count) const {
     std::unique_lock ul(hdf5_mutex);
@@ -1146,90 +1073,7 @@ std::vector<HDF5DataSourceMessage> JFJochHDF5Reader::GetHDF5DataSource(uint64_t
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot generate HDF5 source mapping if file not loaded");
 
-    if (first_image > number_of_images)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "First image outside dataset range");
-
-    const uint64_t requested_count = image_count.value_or(number_of_images - first_image);
-    if (first_image + requested_count > number_of_images)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Requested image range outside dataset range");
-
-    std::vector<HDF5DataSourceMessage> ret;
-    if (requested_count == 0)
-        return ret;
-
-    // Integrated / contiguous source: link directly to original master file.
-    if (format == FileWriterFormat::NXmxVDS && data_layout != HDF5DataSetLayout::VIRTUAL) {
-        AppendOrExtendSourceMapping(ret,
-                                    master_filename,
-                                    "/entry/data/data",
-                                    first_image,
-                                    0,
-                                    requested_count);
-        return ret;
-    }
-
-    // VDS source: expand VDS mappings to original source files, not to the VDS master.
-    if (format == FileWriterFormat::NXmxVDS && data_layout == HDF5DataSetLayout::VIRTUAL) {
-        for (uint64_t local_image = 0; local_image < requested_count; ++local_image) {
-            const hsize_t virtual_image = first_image + local_image;
-
-            bool found = false;
-            for (const auto &mapping: vds_data_mappings) {
-                if (!mapping.ContainsVirtualImage(virtual_image))
-                    continue;
-
-                const uint64_t source_image = mapping.SourceImage(virtual_image);
-                const std::string filename = ResolveRelativeToMaster(master_file_directory, mapping.filename);
-                const std::string dataset = mapping.dataset.empty() ? "/entry/data/data" : mapping.dataset;
-
-                AppendOrExtendSourceMapping(ret,
-                                            filename,
-                                            dataset,
-                                            source_image,
-                                            local_image,
-                                            1);
-                found = true;
-                break;
-            }
-
-            if (!found)
-                throw JFJochException(JFJochExceptionCategory::HDF5,
-                                      "Image not covered by /entry/data/data VDS mappings");
-        }
-
-        return ret;
-    }
-
-    // Legacy source: link directly to linked data files.
-    if (format == FileWriterFormat::NXmxLegacy) {
-        if (images_per_file == 0)
-            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                                  "Cannot generate HDF5 source mapping: images_per_file is zero");
-
-        for (uint64_t local_image = 0; local_image < requested_count; ++local_image) {
-            const uint64_t source_global_image = first_image + local_image;
-            const uint64_t file_id = source_global_image / images_per_file;
-            const uint64_t source_image = source_global_image % images_per_file;
-
-            if (file_id >= legacy_format_files.size())
-                throw JFJochException(JFJochExceptionCategory::HDF5,
-                                      "Legacy image source file missing");
-
-            AppendOrExtendSourceMapping(ret,
-                                        legacy_format_files.at(file_id),
-                                        "/entry/data/data",
-                                        source_image,
-                                        local_image,
-                                        1);
-        }
-
-        return ret;
-    }
-
-    throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                          "Unsupported HDF5 file layout for source mapping");
+    return image_source_.GetSourceMapping(first_image, image_count, number_of_images);
 }
 
 
@@ -1255,19 +1099,6 @@ std::vector<IntegrationOutcome> JFJochHDF5Reader::ReadReflections(size_t start_i
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot read reflections if file not loaded");
 
-    // Cache of data files opened during this call (keyed by path) to avoid
-    // re-opening the same file for every image in a multi-image batch.
-    std::map<std::string, std::shared_ptr<HDF5ReadOnlyFile> > open_files;
-
-    auto get_data_file = [&](const std::string &path) -> std::shared_ptr<HDF5ReadOnlyFile> {
-        auto it = open_files.find(path);
-        if (it != open_files.end())
-            return it->second;
-        auto f = std::make_shared<HDF5ReadOnlyFile>(path);
-        open_files[path] = f;
-        return f;
-    };
-
     std::vector<IntegrationOutcome> ret;
     ret.reserve(end_image_val - start_image + 1);
 
@@ -1277,23 +1108,11 @@ std::vector<IntegrationOutcome> JFJochHDF5Reader::ReadReflections(size_t start_i
         // Generic (non-image-specific) detector geometry from experiment setup.
         outcome.geom = cached_geom;
 
-        // Determine which HDF5 file holds the reflections and MX metadata for
-        // this image, and what local image index to use within that file.
-        HDF5Object *meta_file = master_file.get();
-        size_t meta_image_id = img;
-
-        std::shared_ptr<HDF5ReadOnlyFile> owned_source; // keeps the file alive
-
-        if (format == FileWriterFormat::NXmxLegacy) {
-            // Reflections and per-image MX data are in the individual data files,
-            // addressed by the source-local image index.
-            const size_t file_id = img / images_per_file;
-            meta_image_id = img % images_per_file;
-            owned_source = get_data_file(legacy_format_files.at(file_id));
-            meta_file = owned_source.get();
-        }
-        // NXmxVDS with contiguous layout (integrated): everything is in master_file
-        // with global indices — the defaults set above are correct.
+        // Per-image reflections and MX metadata live in the same file as the image pixels,
+        // at the source-local index (the locator keeps the data-file handle cached).
+        const auto loc = GetImageLocation(static_cast<int64_t>(img));
+        HDF5Object *meta_file = loc.file.get();
+        const size_t meta_image_id = loc.local_index;
 
         // ── reflections ──────────────────────────────────────────────────────
         const std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
@@ -1339,46 +1158,12 @@ std::vector<SpotToSave> JFJochHDF5Reader::ReadSpots(int64_t image) const {
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot read spots if file not loaded");
 
-    // Cache of data files opened during this call (keyed by path) to avoid
-    // re-opening the same file for every image in a multi-image batch.
-    std::map<std::string, std::shared_ptr<HDF5ReadOnlyFile> > open_files;
+    // Spot/MX data lives in the same file as the image pixels, at the source-local index
+    // (the locator keeps the data-file handle cached across calls).
+    const auto loc = GetImageLocation(image);
+    HDF5Object *meta_file = loc.file.get();
+    const size_t meta_image_id = loc.local_index;
 
-    auto get_data_file = [&](const std::string &path) -> std::shared_ptr<HDF5ReadOnlyFile> {
-        auto it = open_files.find(path);
-        if (it != open_files.end())
-            return it->second;
-        auto f = std::make_shared<HDF5ReadOnlyFile>(path);
-        open_files[path] = f;
-        return f;
-    };
-
-    std::vector<SpotToSave> ret;
-
-    // Resolve which HDF5 file and local image index hold the MX spot data.
-    // Uses the same logic as LoadImage_i / ReadReflections so all three
-    // code paths stay in sync.
-    HDF5Object *meta_file = master_file.get();
-    size_t meta_image_id = image;
-
-    std::shared_ptr<HDF5ReadOnlyFile> owned_source;
-
-    if (format == FileWriterFormat::NXmxLegacy) {
-        const size_t file_id = image / images_per_file;
-        meta_image_id = image % images_per_file;
-        owned_source = get_data_file(legacy_format_files.at(file_id));
-        meta_file = owned_source.get();
-    } else if (format == FileWriterFormat::NXmxVDS && data_layout == HDF5DataSetLayout::VIRTUAL) {
-        for (const auto &mapping: vds_data_mappings) {
-            if (!mapping.ContainsVirtualImage(image))
-                continue;
-            meta_image_id = mapping.SourceImage(image);
-            owned_source = get_data_file(ResolveRelativeToMaster(master_file_directory, mapping.filename));
-            meta_file = owned_source.get();
-            break;
-        }
-    }
-    // NXmxVDS contiguous / NXmxIntegrated: master_file with global index —
-    // the defaults set above are already correct.
     DataMessage tmp_message;
     tmp_message.number = static_cast<int64_t>(image);
 
diff --git a/reader/JFJochHDF5Reader.h b/reader/JFJochHDF5Reader.h
index 137f2ad6..4271ec6d 100644
--- a/reader/JFJochHDF5Reader.h
+++ b/reader/JFJochHDF5Reader.h
@@ -5,23 +5,20 @@
 
 #include "JFJochReader.h"
 #include "JFJochReaderSpots.h"
+#include "HDF5ImageSource.h"
 #include "../writer/HDF5Objects.h"
 #include "../image_analysis/IntegrationOutcome.h"
 
 class JFJochHDF5Reader : public JFJochReader {
-    FileWriterFormat format = FileWriterFormat::NoFile;
-    HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
+    // Raw-pixel side: where each image physically lives + the open-file cache. Stays fixed while
+    // the metadata read from master_file may change.
+    HDF5ImageSource image_source_;
 
+    // Metadata side: the master file the per-image and dataset-level metadata is read from.
     std::shared_ptr<HDF5ReadOnlyFile> master_file;
-
-    DiffractionGeometry cached_geom;
-
-    std::vector<std::string> legacy_format_files;
-    std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
-    std::string master_file_directory;
     std::string master_filename;
 
-    size_t images_per_file = 1;
+    DiffractionGeometry cached_geom;
     size_t number_of_images = 0;
 
     bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
@@ -30,8 +27,6 @@ class JFJochHDF5Reader : public JFJochReader {
                      int64_t image_number,
                      bool update_dataset) override;
 
-    CompressedImage LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number);
-
     template <class T>
     void ReadVector(std::vector<T> &v,
                     HDF5Object &file,
@@ -39,7 +34,7 @@ class JFJochHDF5Reader : public JFJochReader {
                     size_t image0,
                     size_t nimages);
 
-    std::pair<std::shared_ptr<HDF5ReadOnlyFile>, uint32_t> GetImageLocation(int64_t image_number);
+    HDF5ImageLocator::Location GetImageLocation(int64_t image_number) const;
     std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
 
     // Read the master-file ROI definitions: logical definitions into experiment.ROI()
-- 
2.52.0


From 9434878c92fe6e4c7457ba49bd092e304787710c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 10:12:53 +0200
Subject: [PATCH 174/228] reader: split metadata reading into
 HDF5MetadataSource + snapshot map

Complete the image/metadata decoupling. JFJochHDF5Reader is now a thin JFJochReader
facade composing one shared HDF5ImageSource (raw pixels) with a name->HDF5MetadataSource
map and an active selection ("snapshots").

- HDF5MetadataSource owns one master file: dataset-level parse (Open, ex-ReadFile),
  per-image metadata (FillPerImage, ex-LoadImage_i), ReadSpots/ReadReflections/
  ReadCalibration, and the master-first helpers. It locates per-image metadata either via
  the shared image source (original file: metadata co-located with pixels) or in its own
  master at the global index (integrated _process.h5 snapshot) - so switching snapshots
  never reloads pixels.
- Facade adds RegisterSnapshot/SetActiveSnapshot/SnapshotNames/ActiveSnapshot; ReadFile
  registers the original as "Original". All existing JFJochReader callers are unchanged.
- The global hdf5_mutex is taken once in the facade; the sources assume it is held.

Adds JFJochReader_Snapshots test (original _master.h5 + a reprocessing _process.h5 over
the same images: pixels stay from the original, metadata follows the active snapshot).

Verified: tests/jfjoch_test [HDF5] (80 cases / 1810 assertions), plus jfjoch_process/
azint/extract_hkl/scale and jfjoch_viewer all build against the refactored reader.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/CMakeLists.txt         |    2 +
 reader/HDF5MetadataSource.cpp | 1125 +++++++++++++++++++++++++++++++
 reader/HDF5MetadataSource.h   |   68 ++
 reader/JFJochHDF5Reader.cpp   | 1195 +++------------------------------
 reader/JFJochHDF5Reader.h     |   48 +-
 tests/JFJochReaderTest.cpp    |  118 ++++
 6 files changed, 1437 insertions(+), 1119 deletions(-)
 create mode 100644 reader/HDF5MetadataSource.cpp
 create mode 100644 reader/HDF5MetadataSource.h

diff --git a/reader/CMakeLists.txt b/reader/CMakeLists.txt
index 8e8793ea..c3377b70 100644
--- a/reader/CMakeLists.txt
+++ b/reader/CMakeLists.txt
@@ -6,6 +6,8 @@ ADD_LIBRARY(JFJochReader STATIC
         HDF5ImageLocator.h
         HDF5ImageSource.cpp
         HDF5ImageSource.h
+        HDF5MetadataSource.cpp
+        HDF5MetadataSource.h
         JFJochReaderImage.cpp
         JFJochReaderImage.h
         JFJochReaderDataset.cpp
diff --git a/reader/HDF5MetadataSource.cpp b/reader/HDF5MetadataSource.cpp
new file mode 100644
index 00000000..8a784b05
--- /dev/null
+++ b/reader/HDF5MetadataSource.cpp
@@ -0,0 +1,1125 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <cmath>
+#include <set>
+
+#include "HDF5MetadataSource.h"
+#include "spdlog/fmt/fmt.h"
+#include "../image_analysis/bragg_integration/CalcISigma.h"
+#include "../image_analysis/spot_finding/SpotUtils.h"
+#include "../common/GridScanSettings.h"
+#include "../common/JFJochMath.h"
+#include "../common/ROIDefinition.h"
+
+inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
+    if (val.empty())
+        return {gemmi::CrystalSystem::Triclinic, 'P'};
+
+    if (val.size() != 2)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong Bravais lattice encoding");
+
+    gemmi::CrystalSystem cs;
+    char centering = val[1];
+    std::set<char> allowed_centering;
+
+    switch (val[0]) {
+        case 'a':
+            cs = gemmi::CrystalSystem::Triclinic;
+            allowed_centering = {'P'};
+            break;
+        case 'm':
+            cs = gemmi::CrystalSystem::Monoclinic;
+            allowed_centering = {'P', 'A', 'B', 'C'};
+            break;
+        case 'o':
+            cs = gemmi::CrystalSystem::Orthorhombic;
+            allowed_centering = {'P', 'A', 'B', 'C', 'I', 'F'};
+            break;
+        case 't':
+            cs = gemmi::CrystalSystem::Tetragonal;
+            allowed_centering = {'P', 'I'};
+            break;
+        case 'h':
+            if (centering == 'P')
+                cs = gemmi::CrystalSystem::Hexagonal;
+            else if (centering == 'R')
+                cs = gemmi::CrystalSystem::Trigonal;
+            allowed_centering = {'P', 'R'};
+            break;
+        case 'c':
+            cs = gemmi::CrystalSystem::Cubic;
+            allowed_centering = {'P', 'F', 'I'};
+            break;
+        default:
+            // allowed_centering is empty and exception will be always thrown
+            break;
+    }
+
+    if (!allowed_centering.contains(centering))
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid lattice encoding " + val);
+
+    return {cs, centering};
+}
+
+std::vector<hsize_t> GetDimension(HDF5Object &object, const std::string &path) {
+    const auto dim = object.GetDimension(path);
+    if (dim.size() != 3)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/data/data");
+    return dim;
+}
+
+std::vector<HDF5VirtualDatasetMapping> ReadVDSImageMappings(HDF5Object &file,
+                                                            const std::string &dataset_name) {
+    HDF5DataSet dataset(file, dataset_name);
+    HDF5Dcpl dcpl(dataset);
+    auto mappings = dcpl.GetVirtualMappings();
+
+    if (mappings.empty())
+        throw JFJochException(JFJochExceptionCategory::HDF5,
+                              dataset_name + " is not a virtual dataset");
+
+    for (const auto &mapping: mappings) {
+        if (mapping.dataset.empty())
+            throw JFJochException(JFJochExceptionCategory::HDF5,
+                                  "VDS mapping has empty source dataset name");
+        if (mapping.virtual_start.size() != 3)
+            throw JFJochException(JFJochExceptionCategory::HDF5,
+                                  "Only 3D image VDS mappings are supported");
+    }
+
+    return mappings;
+}
+
+std::string ResolveRelativeToMaster(const std::string &directory,
+                                    const std::string &filename) {
+    std::filesystem::path path(filename);
+    if (path.is_absolute() || directory.empty())
+        return filename;
+
+    return (std::filesystem::path(directory) / path).string();
+}
+
+template<class T>
+void ReadVector(std::vector<T> &v,
+                HDF5Object &file,
+                const std::string &dataset_name,
+                size_t image0,
+                size_t nimages) {
+    try {
+        auto tmp = file.ReadOptVector<T>(dataset_name);
+        if (tmp.size() <= nimages) {
+            v.resize(image0 + nimages);
+            for (int i = 0; i < tmp.size(); i++)
+                v[image0 + i] = tmp[i];
+        }
+    } catch (JFJochException &e) {
+    }
+}
+
+std::string removeSuffix(const std::string &s, const std::string &suffix) {
+    if (s.ends_with(suffix))
+        return s.substr(0, s.size() - suffix.size());
+
+    return s;
+}
+
+std::string dataset_name(const std::string &path) {
+    std::string file = std::filesystem::path(path).filename().string();
+    file = removeSuffix(file, "_master.h5");
+    // If previous suffix was not found, try removing this one
+    file = removeSuffix(file, ".h5");
+    return file;
+}
+
+bool ReadReflectionsFromGroup(HDF5Object &file,
+                              const std::string &image_group_name,
+                              std::vector<Reflection> &reflections) {
+    if (!file.Exists("/entry/reflections") || !file.Exists(image_group_name))
+        return false;
+
+    auto h = file.ReadOptVector<int32_t>(image_group_name + "/h");
+    auto k = file.ReadOptVector<int32_t>(image_group_name + "/k");
+    auto l = file.ReadOptVector<int32_t>(image_group_name + "/l");
+    auto predicted_x = file.ReadOptVector<float>(image_group_name + "/predicted_x");
+    auto predicted_y = file.ReadOptVector<float>(image_group_name + "/predicted_y");
+    auto obs_x = file.ReadOptVector<float>(image_group_name + "/observed_x");
+    auto obs_y = file.ReadOptVector<float>(image_group_name + "/observed_y");
+    auto d = file.ReadOptVector<float>(image_group_name + "/d");
+    auto int_sum = file.ReadOptVector<float>(image_group_name + "/int_sum");
+    auto int_err = file.ReadOptVector<float>(image_group_name + "/int_err");
+    auto bkg = file.ReadOptVector<float>(image_group_name + "/background_mean");
+    auto lp = file.ReadOptVector<float>(image_group_name + "/lp");
+    auto partiality = file.ReadOptVector<float>(image_group_name + "/partiality");
+    auto phi = file.ReadOptVector<float>(image_group_name + "/delta_phi");
+    auto zeta = file.ReadOptVector<float>(image_group_name + "/zeta");
+    auto image_scale_corr = file.ReadOptVector<float>(image_group_name + "/image_scale_corr");
+
+    if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
+        || h.size() != predicted_x.size() || h.size() != predicted_y.size()
+        || h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size())
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of reflections dataset");
+
+    for (size_t i = 0; i < h.size(); i++) {
+        float lp_val = 0.0;
+        if (lp.size() > i && lp[i] != 0.0f)
+            lp_val = 1.0f / lp[i];
+
+        float partiality_val = -1.0f;
+        if (partiality.size() > i && partiality[i] >= 0.0f)
+            partiality_val = partiality[i];
+        float delta_phi_val = NAN;
+        if (phi.size() > i)
+            delta_phi_val = phi[i];
+        float zeta_val = NAN;
+        if (zeta.size() > i)
+            zeta_val = zeta[i];
+
+        float image_scale_corr_val = 1.0f; // Default is 1.0, if we don't know any better
+        if (image_scale_corr.size() > i)
+            image_scale_corr_val = image_scale_corr[i];
+
+        float obs_x_val = NAN;
+        float obs_y_val = NAN;
+
+        if (obs_x.size() > i && obs_y.size() > i) {
+            obs_x_val = obs_x[i];
+            obs_y_val = obs_y[i];
+        }
+
+        Reflection r{
+            .h = h.at(i),
+            .k = k.at(i),
+            .l = l.at(i),
+            .delta_phi_deg = delta_phi_val,
+            .predicted_x = predicted_x.at(i),
+            .predicted_y = predicted_y.at(i),
+            .observed_x = obs_x_val,
+            .observed_y = obs_y_val,
+            .d = d.at(i),
+            .I = int_sum.at(i),
+            .bkg = bkg.at(i),
+            .sigma = int_err.at(i),
+            .rlp = lp_val,
+            .partiality = partiality_val,
+            .zeta = zeta_val,
+            .image_scale_corr = image_scale_corr_val
+        };
+        reflections.emplace_back(r);
+    }
+
+    return true;
+}
+
+template<class T>
+std::optional<T> ReadElementMasterFirst(HDF5Object &master_file,
+                                        HDF5Object &source_file,
+                                        const std::string &path,
+                                        hsize_t master_image,
+                                        hsize_t source_image) {
+    if (master_file.Exists(path))
+        return master_file.ReadElement<T>(path, master_image);
+    if (source_file.Exists(path))
+        return source_file.ReadElement<T>(path, source_image);
+    return {};
+}
+
+template<class T>
+std::vector<T> ReadVectorMasterFirst(HDF5Object &master_file,
+                                     HDF5Object &source_file,
+                                     const std::string &path,
+                                     const std::vector<hsize_t> &master_start,
+                                     const std::vector<hsize_t> &source_start,
+                                     const std::vector<hsize_t> &size) {
+    if (master_file.Exists(path))
+        return master_file.ReadOptVector<T>(path, master_start, size);
+    if (source_file.Exists(path))
+        return source_file.ReadOptVector<T>(path, source_start, size);
+    return {};
+}
+
+void HDF5MetadataSource::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const {
+    // ROI definitions live in /entry/roi_defs (kept separate from the per-image ROI
+    // results in /entry/roi so that older readers, which iterate /entry/roi, are not
+    // disturbed by the bitmap and definition subgroups).
+    if (!file.Exists("/entry/roi_defs"))
+        return;
+
+    if (file.Exists("/entry/roi_defs/roi_map")) {
+        auto dim = file.GetDimension("/entry/roi_defs/roi_map");   // [y, x]
+        if (dim.size() == 2)
+            dataset.roi_map = file.ReadOptVector<uint16_t>("/entry/roi_defs/roi_map",
+                                                           {0, 0}, {dim[0], dim[1]});
+    }
+
+    ROIDefinition defs;
+    for (const auto &name: file.FindLeafs("/entry/roi_defs")) {
+        const std::string base = "/entry/roi_defs/" + name;
+        // Skip the roi_map bitmask; only named ROI subgroups carry a definition.
+        if (name == "roi_map" || !file.Exists(base + "/type"))
+            continue;
+
+        dataset.roi_bit_index[name] = static_cast<uint16_t>(file.GetInt(base + "/bit_index"));
+
+        const std::string type = file.GetString(base + "/type");
+        if (type == "box")
+            defs.boxes.emplace_back(name, file.GetInt(base + "/min_x_pxl"), file.GetInt(base + "/max_x_pxl"),
+                                          file.GetInt(base + "/min_y_pxl"), file.GetInt(base + "/max_y_pxl"));
+        else if (type == "circle")
+            defs.circles.emplace_back(name, file.GetFloat(base + "/center_x_pxl"), file.GetFloat(base + "/center_y_pxl"),
+                                            file.GetFloat(base + "/radius_pxl"));
+        else if (type == "azim") {
+            const float qmin = file.GetFloat(base + "/q_min_recipA");
+            const float qmax = file.GetFloat(base + "/q_max_recipA");
+            float phi_min = 0, phi_max = 0;
+            if (file.Exists(base + "/phi_min_deg") && file.Exists(base + "/phi_max_deg")) {
+                phi_min = file.GetFloat(base + "/phi_min_deg");
+                phi_max = file.GetFloat(base + "/phi_max_deg");
+            }
+            const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
+            const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
+            defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
+        }
+    }
+
+    if (!defs.boxes.empty() || !defs.circles.empty() || !defs.azimuthal.empty())
+        dataset.experiment.ROI().SetROI(defs);
+}
+
+HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filename,
+                                                       const DiffractionExperiment &default_experiment) {
+    try {
+        auto dataset = std::make_shared<JFJochReaderDataset>();
+        master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
+        master_filename = filename;
+        dataset->experiment = default_experiment;
+
+        // Image-layout state is accumulated locally while parsing, then handed to image_locator_
+        // at the end. format stays NoFile if the master carries no image data.
+        FileWriterFormat format = FileWriterFormat::NoFile;
+        HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
+        std::vector<std::string> legacy_format_files;
+        std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
+        size_t images_per_file = 1;
+
+        std::filesystem::path master_path(filename);
+        std::string master_file_directory = master_path.parent_path().string();
+
+        dataset->arm_date = master_file->GetString("/entry/start_time");
+
+        dataset->experiment.FilePrefix(dataset_name(filename));
+
+        // JFJochReader is always using int32_t
+        dataset->experiment.BitDepthImage(32);
+        dataset->experiment.PixelSigned(true);
+
+        size_t image_size_x = 0;
+        size_t image_size_y = 0;
+
+        if (master_file->Exists("/entry/data/data")) {
+            HDF5DataSet data_dataset(*master_file, "/entry/data/data");
+            HDF5Dcpl dcpl(data_dataset);
+            data_layout = dcpl.GetLayout();
+
+            auto dim = GetDimension(*master_file, "/entry/data/data");
+            number_of_images = dim[0];
+            image_size_y = dim[1];
+            image_size_x = dim[2];
+
+            images_per_file = number_of_images;
+            if (data_layout == HDF5DataSetLayout::VIRTUAL)
+                vds_data_mappings = ReadVDSImageMappings(*master_file, "/entry/data/data");
+
+            if (master_file->Exists("/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image"))
+                dataset->efficiency = master_file->ReadVector<float>(
+                    "/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");
+            else
+                dataset->efficiency = std::vector<float>(number_of_images, 1.0);
+
+            if (master_file->Exists("/entry/roi"))
+                dataset->roi = master_file->FindLeafs("/entry/roi");
+
+            for (const auto &s: dataset->roi) {
+                dataset->roi_max.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/max"));
+                dataset->roi_sum.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum"));
+                dataset->roi_sum_sq.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum_sq"));
+                dataset->roi_npixel.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/npixel"));
+                dataset->roi_x.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/x"));
+                dataset->roi_y.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/y"));
+            }
+
+            if (master_file->Exists("/entry/MX")) {
+                if (master_file->Exists("/entry/MX/peakCountUnfiltered"))
+                    dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/peakCountUnfiltered");
+                else
+                    dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
+
+                dataset->spot_count_low_res = master_file->ReadOptVector<float>("/entry/MX/peakCountLowRes");
+                dataset->spot_count_indexed = master_file->ReadOptVector<float>("/entry/MX/peakCountIndexed");
+                dataset->spot_count_ice_rings = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRingRes");
+
+                dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
+                dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
+                dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
+                dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
+                // Master files write indexedLatticeCount; data files / the per-file MX
+                // plugin use indexingLatticeCount. Accept either for backward compatibility.
+                dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexedLatticeCount");
+                if (dataset->indexing_lattice_count.empty())
+                    dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
+                dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
+                dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
+                dataset->image_scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
+                dataset->image_scale_cc = master_file->ReadOptVector<float>("/entry/MX/imageScaleCC");
+                dataset->image_scale_b = master_file->ReadOptVector<float>("/entry/MX/imageScaleBFactor");
+                dataset->integrated_reflections = master_file->ReadOptVector<float>("/entry/MX/integratedReflections");
+            }
+            if (master_file->Exists("/entry/image"))
+                dataset->max_value = master_file->ReadOptVector<int64_t>("/entry/image/max_value");
+
+            format = FileWriterFormat::NXmxVDS;
+        } else if (master_file->Exists("/entry/data/data_000001")) {
+            format = FileWriterFormat::NXmxLegacy;
+            data_layout = HDF5DataSetLayout::CONTIGUOUS;
+
+            legacy_format_files.clear();
+
+            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
+            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
+
+            //size_t expected_images = master_file->GetInt("/entry/instrument/detector/detectorSpecific/nimages");
+
+            images_per_file = 0;
+            number_of_images = 0;
+            uint32_t nfiles = 0;
+
+            std::filesystem::path file_path(filename);
+            std::filesystem::path directory = file_path.parent_path();
+
+            while (true) {
+                std::string dname = fmt::format("/entry/data/data_{:06d}", nfiles + 1);
+                if (!master_file->Exists(dname))
+                    break;
+
+                size_t fimages = 0;
+
+                try {
+                    auto fname = ResolveRelativeToMaster(directory.string(),
+                                                         master_file->GetLinkedFileName(dname));
+
+                    HDF5ReadOnlyFile data_file(fname);
+
+                    fimages = GetDimension(data_file, "/entry/data/data")[0];
+
+                    legacy_format_files.push_back(fname);
+
+                    if (nfiles == 0 && data_file.Exists("/entry/roi"))
+                        dataset->roi = data_file.FindLeafs("/entry/roi");
+
+                    dataset->roi_max.resize(dataset->roi.size());
+                    dataset->roi_npixel.resize(dataset->roi.size());
+                    dataset->roi_sum.resize(dataset->roi.size());
+                    dataset->roi_sum_sq.resize(dataset->roi.size());
+                    dataset->roi_x.resize(dataset->roi.size());
+                    dataset->roi_y.resize(dataset->roi.size());
+
+                    for (int i = 0; i < dataset->roi.size(); i++) {
+                        auto roi_name = dataset->roi[i];
+                        ReadVector(dataset->roi_max.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/max",
+                                   number_of_images, fimages);
+                        ReadVector(dataset->roi_npixel.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/npixel",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->roi_sum.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/sum",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->roi_sum_sq.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/sum_sq",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->roi_x.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/x",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->roi_y.at(i),
+                                   data_file, "/entry/roi/" + roi_name + "/y",
+                                   number_of_images, fimages);
+                    }
+
+                    if (data_file.Exists("/entry/detector")) {
+                        ReadVector(dataset->efficiency,
+                                   data_file, "/entry/detector/data_collection_efficiency_image",
+                                   number_of_images, fimages);
+                    }
+
+                    if (data_file.Exists("/entry/MX")) {
+                        if (data_file.Exists("/entry/MX/peakCountUnfiltered"))
+                            ReadVector(dataset->spot_count,
+                                       data_file, "/entry/MX/peakCountUnfiltered",
+                                       number_of_images, fimages);
+                        else
+                            ReadVector(dataset->spot_count,
+                                       data_file, "/entry/MX/nPeaks",
+                                       number_of_images, fimages);
+
+                        ReadVector(dataset->spot_count_ice_rings,
+                                   data_file, "/entry/MX/peakCountIceRingRes",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->spot_count_low_res,
+                                   data_file, "/entry/MX/peakCountLowRes",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->spot_count_indexed,
+                                   data_file, "/entry/MX/peakCountIndexed",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->indexing_result,
+                                   data_file, "/entry/MX/imageIndexed",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->bkg_estimate,
+                                   data_file, "/entry/MX/bkgEstimate",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->profile_radius,
+                                   data_file, "/entry/MX/profileRadius",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->indexing_lattice_count,
+                                   data_file, "/entry/MX/indexingLatticeCount",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->mosaicity_deg,
+                                   data_file, "/entry/MX/mosaicity",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->b_factor,
+                                   data_file, "/entry/MX/bFactor",
+                                   number_of_images, fimages);
+
+                        ReadVector(dataset->resolution_estimate,
+                                   data_file, "/entry/MX/resolutionEstimate",
+                                   number_of_images, fimages);
+                    }
+
+                    if (data_file.Exists("/entry/image")) {
+                        ReadVector(dataset->max_value,
+                                   data_file, "/entry/image/max_value",
+                                   number_of_images, fimages);
+                    }
+                } catch (JFJochException &e) {
+                }
+
+                if (nfiles == 0)
+                    images_per_file = fimages;
+                number_of_images += fimages;
+                nfiles++;
+            }
+        } else {
+            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
+            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
+            number_of_images = 0;
+        }
+
+        if (master_file->Exists("/entry/MX")) {
+            auto indexing = master_file->GetString("/entry/MX/indexing_algorithm", "none");
+            if (indexing == "fft" || indexing == "FFT (CUDA)" || indexing == "FFT (FFTW)")
+                dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
+            else if (indexing == "ffbidx" || indexing == "FFBIDX")
+                dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
+        }
+
+        auto ring_current_A = master_file->GetOptFloat("/entry/source/current");
+        if (ring_current_A) dataset->experiment.RingCurrent_mA(ring_current_A.value() * 1000.0);
+
+        dataset->experiment.DetectIceRings(
+            master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/detect_ice_rings").value_or(false));
+        dataset->experiment.PoniRot1_rad(
+            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot1").value_or(0.0));
+        dataset->experiment.PoniRot2_rad(
+            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
+        dataset->experiment.PoniRot3_rad(
+            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
+        dataset->experiment.SampleTemperature_K(master_file->GetOptFloat("/entry/sample/temperature"));
+
+        dataset->experiment.BeamX_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_x"));
+        dataset->experiment.BeamY_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_y"));
+
+        float det_distance = master_file->GetFloat("/entry/instrument/detector/distance");
+        if (det_distance < 0.001)
+            det_distance = 0.1; // Set to 100 mm, if det distance is less than 1 mm
+        dataset->experiment.DetectorDistance_mm(det_distance * 1000.0);
+
+        const float incident_wavelength_A = master_file->GetFloat("/entry/instrument/beam/incident_wavelength");
+        dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / incident_wavelength_A);
+
+        // NXmx incident_wavelength_spread is the absolute FWHM (Angstrom); store it
+        // as the relative bandwidth FWHM (dlambda/lambda) used internally.
+        if (const auto spread = master_file->GetOptFloat("/entry/instrument/beam/incident_wavelength_spread"))
+            if (incident_wavelength_A > 0.0f)
+                dataset->experiment.BandwidthFWHM(spread.value() / incident_wavelength_A);
+
+        dataset->error_value = master_file->GetOptInt("/entry/instrument/detector/error_value");
+
+        dataset->jfjoch_release = master_file->GetString("/entry/instrument/detector/detectorSpecific/jfjoch_release");
+
+        InstrumentMetadata metadata;
+        metadata.InstrumentName(master_file->GetString("/entry/instrument/name"));
+        metadata.SourceName(master_file->GetString("/entry/source/name"));
+        dataset->experiment.ImportInstrumentMetadata(metadata);
+
+        if (master_file->Exists("/entry/sample/transformations")) {
+            if (master_file->Exists("/entry/sample/transformations/omega")) {
+                auto omega = ReadAxis(master_file.get(), "omega");
+                dataset->experiment.Goniometer(omega);
+            } else if (master_file->Exists("/entry/sample/grid_scan")) {
+                GridScanSettings grid(
+                    master_file->GetInt("/entry/sample/grid_scan/n_fast"),
+                    master_file->GetFloat("/entry/sample/grid_scan/step_x") * 1e6f,
+                    master_file->GetFloat("/entry/sample/grid_scan/step_y") * 1e6f,
+                    master_file->GetOptBool("/entry/sample/grid_scan/snake_scan").value_or(false),
+                    master_file->GetOptBool("/entry/sample/grid_scan/vertical_scan").value_or(false)
+                );
+                grid.ImageNum(number_of_images);
+                dataset->experiment.GridScan(grid);
+            }
+        }
+
+        auto tmp = master_file->ReadOptVector<float>("/entry/sample/unit_cell");
+        if (tmp.size() == 6)
+            dataset->experiment.SetUnitCell(UnitCell{
+                .a = tmp[0],
+                .b = tmp[1],
+                .c = tmp[2],
+                .alpha = tmp[3],
+                .beta = tmp[4],
+                .gamma = tmp[5]
+            });
+        dataset->experiment.SpaceGroupNumber(master_file->GetOptInt("/entry/sample/space_group_number"));
+        dataset->experiment.SampleName(master_file->GetString("/entry/sample/name"));
+
+
+        if (master_file->Exists("/entry/instrument/attenuator"))
+            dataset->experiment.AttenuatorTransmission(
+                master_file->GetOptFloat("/entry/instrument/attenuator/attenuator_transmission"));
+        dataset->experiment.TotalFlux(master_file->GetOptFloat("/entry/instrument/beam/total_flux"));
+
+        if (master_file->Exists("/entry/azint") && master_file->Exists("/entry/azint/bin_to_q")) {
+            HDF5DataSet bin_to_q_dataset(*master_file, "/entry/azint/bin_to_q");
+            HDF5DataSpace bin_to_q_dataspace(bin_to_q_dataset);
+            auto dim = bin_to_q_dataspace.GetDimensions();
+
+            if (dim.size() == 1) {
+                dataset->azimuthal_bins = 0;
+                dataset->q_bins = dim[0];
+                bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q);
+            } else if (dim.size() == 2) {
+                dataset->azimuthal_bins = dim[0];
+                dataset->q_bins = dim[1];
+                dataset->az_int_bin_to_q.resize(dim[0] * dim[1]);
+                bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q, {0, 0}, dim);
+            } else
+                throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/azint/image dataset");
+            if (master_file->Exists("/entry/azint/bin_to_phi")) {
+                HDF5DataSet bin_to_phi_dataset(*master_file, "/entry/azint/bin_to_phi");
+                if (dataset->q_bins > 0) {
+                    dataset->az_int_bin_to_phi.resize(dim[0] * dim[1]);
+                    bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi, {0, 0}, dim);
+                } else {
+                    bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi);
+                }
+            }
+        }
+
+        // Read fluorescence spectrum if present
+        if (master_file->Exists("/entry/instrument/fluorescence")) {
+            auto energy = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/energy");
+            auto data = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/data");
+            if (!energy.empty() && energy.size() == data.size())
+                dataset->experiment.FluorescenceSpectrum(XrayFluorescenceSpectrum(energy, data));
+        }
+
+        auto detector_name = master_file->GetString("/entry/instrument/detector/description");
+
+        DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
+        detector.PixelSize_um(master_file->GetFloat("/entry/instrument/detector/x_pixel_size") * 1e6);
+        detector.SaturationLimit(master_file->GetInt("/entry/instrument/detector/saturation_value"));
+        detector.MinFrameTime(std::chrono::microseconds(0));
+        detector.MinCountTime(std::chrono::microseconds(0));
+        detector.ReadOutTime(std::chrono::nanoseconds(0));
+        dataset->experiment.Detector(detector);
+
+        dataset->experiment.FrameTime(
+            std::chrono::duration_cast<std::chrono::nanoseconds>(
+                std::chrono::duration<float>(
+                    master_file->GetFloat("/entry/instrument/detector/frame_time"))),
+            std::chrono::duration_cast<std::chrono::nanoseconds>(
+                std::chrono::duration<float>(
+                    master_file->GetFloat("/entry/instrument/detector/count_time")))
+        );
+
+        if (master_file->Exists("/entry/instrument/detector/calibration")) {
+            dataset->calibration_data = master_file->FindLeafs("/entry/instrument/detector/calibration");
+            std::sort(dataset->calibration_data.begin(), dataset->calibration_data.end());
+        }
+
+        if (image_size_x * image_size_y > 0) {
+            auto mask_tmp = master_file->ReadOptVector<uint32_t>(
+                "/entry/instrument/detector/pixel_mask",
+                {0, 0},
+                {image_size_y, image_size_x}
+            );
+            if (mask_tmp.empty())
+                mask_tmp = master_file->ReadOptVector<uint32_t>(
+                    "/entry/instrument/detector/detectorSpecific/pixel_mask",
+                    {0, 0},
+                    {image_size_y, image_size_x}
+                );
+            if (mask_tmp.empty())
+                mask_tmp = std::vector<uint32_t>(image_size_x * image_size_y);
+            dataset->pixel_mask = PixelMask(mask_tmp);
+        }
+
+        ReadROIMetadata(*master_file, *dataset);
+
+        // Resolve VDS mapping filenames to absolute paths so the image source's locator only ever
+        // deals with real paths, then report the layout to the caller.
+        for (auto &m : vds_data_mappings)
+            m.filename = ResolveRelativeToMaster(master_file_directory, m.filename);
+
+        dataset->experiment.ImagesPerTrigger(number_of_images);
+        cached_geom = dataset->experiment.GetDiffractionGeometry();
+        dataset_ = dataset;
+
+        return OpenResult{
+            .image_layout = HDF5ImageLocator::Layout{
+                .format = format,
+                .data_layout = data_layout,
+                .master_file = master_file,
+                .master_filename = master_filename,
+                .legacy_files = std::move(legacy_format_files),
+                .images_per_file = images_per_file,
+                .vds_mappings = std::move(vds_data_mappings)
+            },
+            .number_of_images = number_of_images
+        };
+    } catch (const std::exception &e) {
+        master_file = {};
+        master_filename.clear();
+        number_of_images = 0;
+        dataset_.reset();
+        cached_geom = DiffractionGeometry{};
+        throw;
+    }
+}
+
+HDF5ImageLocator::Location HDF5MetadataSource::ResolveMeta(int64_t global) const {
+    // Per-image metadata is co-located with the pixels for the original file (resolve via the
+    // shared image source); for an integrated _process.h5 snapshot it lives in this master at the
+    // global index.
+    if (image_source_)
+        return image_source_->Resolve(global);
+    return {master_file, static_cast<uint32_t>(global)};
+}
+
+// Reads spot data for a single image from the appropriate HDF5 source.
+// master_image / source_image are the logical indices within master_file and
+// source_file respectively (identical for NXmxVDS contiguous / integrated;
+// differ for NXmxLegacy and NXmxVDS virtual layouts).
+// Appends assembled SpotToSave entries to message.spots and fills the
+// spot_count* fields; does NOT touch the image pixel data.
+static void ReadSpotsFromFiles(HDF5Object &master_file,
+                               HDF5Object &source_file,
+                               hsize_t master_image,
+                               hsize_t source_image,
+                               int64_t image_number,
+                               const DiffractionGeometry &geom,
+                               DataMessage &message) {
+    auto spot_count_opt = ReadElementMasterFirst<uint32_t>(master_file,
+                                                           source_file,
+                                                           "/entry/MX/nPeaks",
+                                                           master_image,
+                                                           source_image);
+    if (!spot_count_opt.has_value() || spot_count_opt.value() == 0)
+        return;
+
+    const size_t spot_count = spot_count_opt.value();
+
+    auto spot_x = ReadVectorMasterFirst<float>(
+        master_file, source_file,
+        "/entry/MX/peakXPosRaw",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_y = ReadVectorMasterFirst<float>(
+        master_file, source_file,
+        "/entry/MX/peakYPosRaw",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_intensity = ReadVectorMasterFirst<float>(
+        master_file, source_file,
+        "/entry/MX/peakTotalIntensity",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+
+    if (spot_x.size() < spot_count || spot_y.size() < spot_count || spot_intensity.size() < spot_count)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of spot dataset");
+
+    auto spot_indexed = ReadVectorMasterFirst<uint8_t>(
+        master_file, source_file,
+        "/entry/MX/peakIndexed",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_ice = ReadVectorMasterFirst<uint8_t>(
+        master_file, source_file,
+        "/entry/MX/peakIceRingRes",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_h = ReadVectorMasterFirst<int32_t>(
+        master_file, source_file,
+        "/entry/MX/peakH",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_k = ReadVectorMasterFirst<int32_t>(
+        master_file, source_file,
+        "/entry/MX/peakK",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+    auto spot_l = ReadVectorMasterFirst<int32_t>(
+        master_file, source_file,
+        "/entry/MX/peakL",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+
+    auto spot_lattice = ReadVectorMasterFirst<int8_t>(
+        master_file, source_file,
+        "/entry/MX/peakLattice",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+        );
+
+    auto spot_dist_ewald_sphere = ReadVectorMasterFirst<float>(
+        master_file, source_file,
+        "/entry/MX/peakDistEwaldSphere",
+        {master_image, 0}, {source_image, 0}, {1, spot_count}
+    );
+
+    message.spots.reserve(message.spots.size() + spot_count);
+    for (size_t i = 0; i < spot_count; i++) {
+        const auto x = spot_x.at(i);
+        const auto y = spot_y.at(i);
+
+        SpotToSave s{
+            .x = x,
+            .y = y,
+            .intensity = spot_intensity.at(i),
+            .image = image_number,
+            .d_A = geom.PxlToRes(x, y)
+        };
+        if (spot_indexed.size() > i)
+            s.indexed = (spot_indexed.at(i) != 0);
+        if (spot_h.size() > i)
+            s.h = spot_h.at(i);
+        if (spot_k.size() > i)
+            s.k = spot_k.at(i);
+        if (spot_l.size() > i)
+            s.l = spot_l.at(i);
+        if (spot_dist_ewald_sphere.size() > i)
+            s.dist_ewald_sphere = spot_dist_ewald_sphere.at(i);
+        if (spot_ice.size() > i)
+            s.ice_ring = (spot_ice.at(i) != 0);
+        if (spot_lattice.size() > i)
+            s.lattice = spot_lattice.at(i);
+        message.spots.emplace_back(s);
+    }
+
+    if (auto v = ReadElementMasterFirst<uint32_t>(master_file, source_file,
+                                                  "/entry/MX/peakCountUnfiltered",
+                                                  master_image, source_image); v)
+        message.spot_count = v;
+    else
+        message.spot_count = spot_count_opt;
+
+    message.spot_count_ice_rings = ReadElementMasterFirst<uint32_t>(
+        master_file, source_file, "/entry/MX/peakCountIceRingRes", master_image, source_image);
+    message.spot_count_low_res = ReadElementMasterFirst<uint32_t>(
+        master_file, source_file, "/entry/MX/peakCountLowRes", master_image, source_image);
+    message.spot_count_indexed = ReadElementMasterFirst<uint32_t>(
+        master_file, source_file, "/entry/MX/peakCountIndexed", master_image, source_image);
+
+    GenerateSpotPlot(message, 1.5);
+}
+
+void HDF5MetadataSource::FillPerImage(DataMessage &message, int64_t image_number,
+                                      const std::shared_ptr<const JFJochReaderDataset> &dataset) const {
+    auto loc = ResolveMeta(image_number);
+    auto &source_file = loc.file;
+    const uint32_t image_id = loc.local_index;
+
+    const auto master_image = static_cast<hsize_t>(image_number);
+    const auto source_image = static_cast<hsize_t>(image_id);
+
+    ReadSpotsFromFiles(*master_file, *source_file, master_image, source_image,
+                       image_number, dataset->experiment.GetDiffractionGeometry(), message);
+
+    if (!dataset->az_int_bin_to_q.empty()) {
+        if (dataset->azimuthal_bins == 0) {
+            message.az_int_profile = ReadVectorMasterFirst<float>(
+                *master_file,
+                *source_file,
+                "/entry/azint/image",
+                {master_image, 0},
+                {source_image, 0},
+                {1, dataset->az_int_bin_to_q.size()}
+            );
+        } else {
+            message.az_int_profile = ReadVectorMasterFirst<float>(
+                *master_file,
+                *source_file,
+                "/entry/azint/image",
+                {master_image, 0, 0},
+                {source_image, 0, 0},
+                {1, dataset->azimuthal_bins, dataset->q_bins}
+            );
+        }
+    }
+    if (dataset->integrated_reflections.size() > image_number)
+        message.integrated_reflections = static_cast<int64_t>(std::lround(
+            dataset->integrated_reflections.at(image_number)));
+    if (dataset->resolution_estimate.size() > image_number)
+        message.resolution_estimate = dataset->resolution_estimate[image_number];
+    if (dataset->indexing_result.size() > image_number)
+        message.indexing_result = dataset->indexing_result[image_number];
+    if (dataset->indexing_lattice_count.size() > image_number)
+        message.indexing_lattice_count = dataset->indexing_lattice_count[image_number];
+    if (dataset->bkg_estimate.size() > image_number)
+        message.bkg_estimate = dataset->bkg_estimate[image_number];
+    if (dataset->efficiency.size() > image_number)
+        message.image_collection_efficiency = dataset->efficiency[image_number];
+    if (dataset->profile_radius.size() > image_number)
+        message.profile_radius = dataset->profile_radius[image_number];
+    if (dataset->mosaicity_deg.size() > image_number)
+        message.mosaicity_deg = dataset->mosaicity_deg[image_number];
+    if (dataset->b_factor.size() > image_number)
+        message.b_factor = dataset->b_factor[image_number];
+    if (dataset->image_scale_b.size() > image_number)
+        message.image_scale_b_factor = dataset->image_scale_b[image_number];
+    if (dataset->image_scale_factor.size() > image_number)
+        message.image_scale_factor = dataset->image_scale_factor[image_number];
+    if (dataset->image_scale_cc.size() > image_number)
+        message.image_scale_cc = dataset->image_scale_cc[image_number];
+    if (dataset->indexing_result.size() > image_number
+        && dataset->indexing_result[image_number] != 0
+        && (master_file->Exists("/entry/MX/latticeIndexed") ||
+            source_file->Exists("/entry/MX/latticeIndexed"))) {
+        std::vector<float> tmp = ReadVectorMasterFirst<float>(
+            *master_file,
+            *source_file,
+            "/entry/MX/latticeIndexed",
+            {master_image, 0},
+            {source_image, 0},
+            {1, 9}
+        );
+
+        if (tmp.size() == 9)
+            message.indexing_lattice = CrystalLattice(tmp);
+
+        std::optional<std::string> lattice;
+        if (master_file->Exists("/entry/MX/bravaisLattice"))
+            lattice = master_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_number);
+        else
+            lattice = source_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_id);
+
+        std::optional<uint32_t> niggli_opt;
+        if (master_file->Exists("/entry/MX/niggli_class"))
+            niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_number);
+        else if (master_file->Exists("/entry/MX/niggliClass"))
+            niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_number);
+        else if (source_file->Exists("/entry/MX/niggli_class"))
+            niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_id);
+        else if (source_file->Exists("/entry/MX/niggliClass"))
+            niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_id);
+
+        if (lattice && !lattice->empty()) {
+            auto symm_info = parse_bravais_lattice(lattice.value());
+
+            message.lattice_type = LatticeMessage{
+                .centering = symm_info.second,
+                .niggli_class = static_cast<int64_t>(niggli_opt.value_or(0)),
+                .crystal_system = symm_info.first,
+            };
+        }
+    }
+
+    const std::string master_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_number);
+    const std::string source_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_id);
+
+    if (!ReadReflectionsFromGroup(*master_file, master_reflection_group_name, message.reflections))
+        ReadReflectionsFromGroup(*source_file, source_reflection_group_name, message.reflections);
+    if (!message.reflections.empty()) {
+        CalcISigma(message);
+        CalcWilsonBFactor(message, !message.b_factor.has_value());
+    }
+}
+
+std::optional<GoniometerAxis> HDF5MetadataSource::ReadAxis(HDF5Object *file, const std::string &name) {
+    std::string dname = "/entry/sample/transformations/" + name;
+
+    if (!file->Exists(dname))
+        return {};
+
+
+    HDF5DataSet dataset(*file, dname);
+    std::vector<double> angle;
+    dataset.ReadVector(angle);
+
+    if (angle.size() < 2)
+        return {};
+
+    std::vector<double> end = file->ReadOptVector<double>(dname + "_end");
+
+    double start = angle[0];
+    double incr = angle[1] - angle[0];
+
+    if (dataset.ReadAttrStr("transformation_type") != "rotation")
+        return {};
+
+    std::vector<double> axis_vec = dataset.ReadAttrVec("vector");
+    if (axis_vec.size() != 3)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              dname + " Vector must have 3 elements");
+
+    Coord axis(axis_vec[0], axis_vec[1], axis_vec[2]);
+    GoniometerAxis g_axis(name, start, incr, axis, {});
+    if (!end.empty())
+        g_axis.ScreeningWedge(end[0] - angle[0]);
+
+    return g_axis;
+}
+
+CompressedImage HDF5MetadataSource::ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const {
+    std::vector<hsize_t> start = {0, 0};
+    if (!master_file)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Master file not loaded");
+    if (!master_file->Exists("/entry/instrument/detector/calibration/" + name))
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Calibration dataset not found");
+
+    HDF5DataSet dataset(*master_file, "/entry/instrument/detector/calibration/" + name);
+    HDF5DataSpace dataspace(dataset);
+    HDF5DataType datatype(dataset);
+    HDF5Dcpl dcpl(dataset);
+
+    if (dataspace.GetNumOfDimensions() != 2)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Calibration dataset must be 2D");
+
+    auto dim = dataspace.GetDimensions();
+
+    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
+    dataset.ReadVectorToU8(tmp, start, {dim[0], dim[1]});
+    algorithm = CompressionAlgorithm::NO_COMPRESSION;
+
+    return {
+        tmp, dim[1], dim[0],
+        CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
+        algorithm
+    };
+}
+
+
+std::vector<IntegrationOutcome> HDF5MetadataSource::ReadReflections(size_t start_image,
+                                                                   std::optional<size_t> end_image) const {
+    if (start_image >= number_of_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "start_image must be less than number_of_images");
+
+    const size_t end_image_val = end_image.value_or(number_of_images - 1);
+
+    if (end_image_val < start_image)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "end_image must be greater or equal to start_image if provided");
+
+    if (end_image_val >= number_of_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "end_image must be less than number_of_images");
+
+    if (!master_file)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Cannot read reflections if file not loaded");
+
+    std::vector<IntegrationOutcome> ret;
+    ret.reserve(end_image_val - start_image + 1);
+
+    for (size_t img = start_image; img <= end_image_val; img++) {
+        IntegrationOutcome outcome;
+
+        // Generic (non-image-specific) detector geometry from experiment setup.
+        outcome.geom = cached_geom;
+
+        // Per-image reflections and MX metadata live in the same file as the image pixels,
+        // at the source-local index (the locator keeps the data-file handle cached).
+        const auto loc = ResolveMeta(static_cast<int64_t>(img));
+        HDF5Object *meta_file = loc.file.get();
+        const size_t meta_image_id = loc.local_index;
+
+        // ── reflections ──────────────────────────────────────────────────────
+        const std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
+        ReadReflectionsFromGroup(*meta_file, refl_group, outcome.reflections);
+
+        // ── per-image mosaicity ───────────────────────────────────────────────
+        if (meta_file->Exists("/entry/MX/mosaicity")) {
+            try {
+                outcome.mosaicity_deg =
+                        meta_file->ReadElement<float>("/entry/MX/mosaicity", meta_image_id);
+            } catch (...) {
+            }
+        }
+
+        // ── indexed lattice (stored as 9-element row-major matrix) ────────────
+        if (meta_file->Exists("/entry/MX/latticeIndexed")) {
+            try {
+                auto lattice_vec = meta_file->ReadOptVector<float>(
+                    "/entry/MX/latticeIndexed", {meta_image_id, 0}, {1, 9});
+                if (lattice_vec.size() == 9)
+                    outcome.latt = CrystalLattice(lattice_vec);
+            } catch (...) {
+            }
+        }
+
+        ret.push_back(std::move(outcome));
+    }
+
+    return ret;
+}
+
+std::vector<SpotToSave> HDF5MetadataSource::ReadSpots(int64_t image) const {
+    if (image < 0)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+            "image number must be non-negative");
+    if (image >= number_of_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "image must be less than number_of_images");
+
+    if (!master_file)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Cannot read spots if file not loaded");
+
+    // Per-image spot/MX data, resolved the same way as the pixels (or in our own master at the
+    // global index for an integrated _process.h5 snapshot).
+    const auto loc = ResolveMeta(image);
+    HDF5Object *meta_file = loc.file.get();
+    const size_t meta_image_id = loc.local_index;
+
+    DataMessage tmp_message;
+    tmp_message.number = static_cast<int64_t>(image);
+
+    ReadSpotsFromFiles(*master_file, *meta_file,
+                       image, meta_image_id,
+                       static_cast<int64_t>(image),
+                       cached_geom,
+                       tmp_message);
+
+    return tmp_message.spots;
+}
diff --git a/reader/HDF5MetadataSource.h b/reader/HDF5MetadataSource.h
new file mode 100644
index 00000000..1196b721
--- /dev/null
+++ b/reader/HDF5MetadataSource.h
@@ -0,0 +1,68 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <memory>
+#include <optional>
+#include <string>
+#include <vector>
+
+#include "JFJochReaderDataset.h"
+#include "HDF5ImageSource.h"
+#include "../common/JFJochMessages.h"
+#include "../common/SpotToSave.h"
+#include "../common/GoniometerAxis.h"
+#include "../common/DiffractionExperiment.h"
+#include "../common/DiffractionGeometry.h"
+#include "../image_analysis/IntegrationOutcome.h"
+
+// Metadata side of the reader: everything read from one master file that is NOT raw pixels -
+// dataset-level metadata (geometry, mask, ROI definitions, azimuthal mapping, the per-image plot
+// arrays) and per-image metadata (spots, reflections, MX scalars, azimuthal profile, lattice).
+//
+// This is the swappable part: a dataset can have several metadata sources over the same images
+// (the original _master.h5 plus reprocessing _process.h5 snapshots). Per-image metadata is
+// located either through the shared image source (original file: metadata sits in the same files
+// as the pixels) or in this master at the global index (integrated _process.h5 snapshot).
+//
+// HDF5 is not thread-safe; all calls must be made with the global hdf5_mutex held by the caller.
+class HDF5MetadataSource {
+public:
+    struct OpenResult {
+        HDF5ImageLocator::Layout image_layout;   // layout implied by this master (for the image source)
+        uint64_t number_of_images = 0;
+    };
+
+    // Parse a master file's dataset-level metadata into a JFJochReaderDataset. default_experiment
+    // seeds the dataset's experiment. Returns the image layout it implies; the caller decides
+    // whether to use it to configure the shared image source.
+    OpenResult Open(const std::string &filename, const DiffractionExperiment &default_experiment);
+
+    // How per-image metadata is located: with image_source set, metadata is co-located with the
+    // pixels (original file); when null it lives in this master at the global index.
+    void UseImageSourceForMetadata(const HDF5ImageSource *image_source) { image_source_ = image_source; }
+
+    std::shared_ptr<JFJochReaderDataset> Dataset() const { return dataset_; }
+    uint64_t NumberOfImages() const { return number_of_images; }
+
+    // Per-image metadata (spots, azimuthal profile, MX scalars, lattice, reflections) into msg.
+    void FillPerImage(DataMessage &message, int64_t image_number,
+                      const std::shared_ptr<const JFJochReaderDataset> &dataset) const;
+
+    std::vector<SpotToSave> ReadSpots(int64_t image) const;
+    std::vector<IntegrationOutcome> ReadReflections(size_t start_image, std::optional<size_t> end_image) const;
+    CompressedImage ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const;
+
+private:
+    std::shared_ptr<HDF5ReadOnlyFile> master_file;
+    std::string master_filename;
+    std::shared_ptr<JFJochReaderDataset> dataset_;
+    DiffractionGeometry cached_geom;
+    uint64_t number_of_images = 0;
+    const HDF5ImageSource *image_source_ = nullptr;
+
+    HDF5ImageLocator::Location ResolveMeta(int64_t global) const;
+    std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
+    void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
+};
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 0bbbe8dc..de90417d 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -1,713 +1,35 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#include <cmath>
-#include <set>
-
 #include "JFJochHDF5Reader.h"
-#include "spdlog/fmt/fmt.h"
-#include "../image_analysis/bragg_integration/CalcISigma.h"
-#include "../image_analysis/spot_finding/SpotUtils.h"
-#include "../common/GridScanSettings.h"
-#include "../common/JFJochMath.h"
-#include "../common/ROIDefinition.h"
-
-inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
-    if (val.empty())
-        return {gemmi::CrystalSystem::Triclinic, 'P'};
-
-    if (val.size() != 2)
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong Bravais lattice encoding");
-
-    gemmi::CrystalSystem cs;
-    char centering = val[1];
-    std::set<char> allowed_centering;
-
-    switch (val[0]) {
-        case 'a':
-            cs = gemmi::CrystalSystem::Triclinic;
-            allowed_centering = {'P'};
-            break;
-        case 'm':
-            cs = gemmi::CrystalSystem::Monoclinic;
-            allowed_centering = {'P', 'A', 'B', 'C'};
-            break;
-        case 'o':
-            cs = gemmi::CrystalSystem::Orthorhombic;
-            allowed_centering = {'P', 'A', 'B', 'C', 'I', 'F'};
-            break;
-        case 't':
-            cs = gemmi::CrystalSystem::Tetragonal;
-            allowed_centering = {'P', 'I'};
-            break;
-        case 'h':
-            if (centering == 'P')
-                cs = gemmi::CrystalSystem::Hexagonal;
-            else if (centering == 'R')
-                cs = gemmi::CrystalSystem::Trigonal;
-            allowed_centering = {'P', 'R'};
-            break;
-        case 'c':
-            cs = gemmi::CrystalSystem::Cubic;
-            allowed_centering = {'P', 'F', 'I'};
-            break;
-        default:
-            // allowed_centering is empty and exception will be always thrown
-            break;
-    }
-
-    if (!allowed_centering.contains(centering))
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid lattice encoding " + val);
-
-    return {cs, centering};
-}
-
-std::vector<hsize_t> GetDimension(HDF5Object &object, const std::string &path) {
-    const auto dim = object.GetDimension(path);
-    if (dim.size() != 3)
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/data/data");
-    return dim;
-}
-
-std::vector<HDF5VirtualDatasetMapping> ReadVDSImageMappings(HDF5Object &file,
-                                                            const std::string &dataset_name) {
-    HDF5DataSet dataset(file, dataset_name);
-    HDF5Dcpl dcpl(dataset);
-    auto mappings = dcpl.GetVirtualMappings();
-
-    if (mappings.empty())
-        throw JFJochException(JFJochExceptionCategory::HDF5,
-                              dataset_name + " is not a virtual dataset");
-
-    for (const auto &mapping: mappings) {
-        if (mapping.dataset.empty())
-            throw JFJochException(JFJochExceptionCategory::HDF5,
-                                  "VDS mapping has empty source dataset name");
-        if (mapping.virtual_start.size() != 3)
-            throw JFJochException(JFJochExceptionCategory::HDF5,
-                                  "Only 3D image VDS mappings are supported");
-    }
-
-    return mappings;
-}
-
-std::string ResolveRelativeToMaster(const std::string &directory,
-                                    const std::string &filename) {
-    std::filesystem::path path(filename);
-    if (path.is_absolute() || directory.empty())
-        return filename;
-
-    return (std::filesystem::path(directory) / path).string();
-}
-
-template<class T>
-void JFJochHDF5Reader::ReadVector(std::vector<T> &v,
-                                  HDF5Object &file,
-                                  const std::string &dataset_name,
-                                  size_t image0,
-                                  size_t nimages) {
-    try {
-        auto tmp = file.ReadOptVector<T>(dataset_name);
-        if (tmp.size() <= nimages) {
-            v.resize(image0 + nimages);
-            for (int i = 0; i < tmp.size(); i++)
-                v[image0 + i] = tmp[i];
-        }
-    } catch (JFJochException &e) {
-    }
-}
-
-std::string removeSuffix(const std::string &s, const std::string &suffix) {
-    if (s.ends_with(suffix))
-        return s.substr(0, s.size() - suffix.size());
-
-    return s;
-}
-
-std::string dataset_name(const std::string &path) {
-    std::string file = std::filesystem::path(path).filename().string();
-    file = removeSuffix(file, "_master.h5");
-    // If previous suffix was not found, try removing this one
-    file = removeSuffix(file, ".h5");
-    return file;
-}
-
-bool ReadReflectionsFromGroup(HDF5Object &file,
-                              const std::string &image_group_name,
-                              std::vector<Reflection> &reflections) {
-    if (!file.Exists("/entry/reflections") || !file.Exists(image_group_name))
-        return false;
-
-    auto h = file.ReadOptVector<int32_t>(image_group_name + "/h");
-    auto k = file.ReadOptVector<int32_t>(image_group_name + "/k");
-    auto l = file.ReadOptVector<int32_t>(image_group_name + "/l");
-    auto predicted_x = file.ReadOptVector<float>(image_group_name + "/predicted_x");
-    auto predicted_y = file.ReadOptVector<float>(image_group_name + "/predicted_y");
-    auto obs_x = file.ReadOptVector<float>(image_group_name + "/observed_x");
-    auto obs_y = file.ReadOptVector<float>(image_group_name + "/observed_y");
-    auto d = file.ReadOptVector<float>(image_group_name + "/d");
-    auto int_sum = file.ReadOptVector<float>(image_group_name + "/int_sum");
-    auto int_err = file.ReadOptVector<float>(image_group_name + "/int_err");
-    auto bkg = file.ReadOptVector<float>(image_group_name + "/background_mean");
-    auto lp = file.ReadOptVector<float>(image_group_name + "/lp");
-    auto partiality = file.ReadOptVector<float>(image_group_name + "/partiality");
-    auto phi = file.ReadOptVector<float>(image_group_name + "/delta_phi");
-    auto zeta = file.ReadOptVector<float>(image_group_name + "/zeta");
-    auto image_scale_corr = file.ReadOptVector<float>(image_group_name + "/image_scale_corr");
-
-    if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
-        || h.size() != predicted_x.size() || h.size() != predicted_y.size()
-        || h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size())
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of reflections dataset");
-
-    for (size_t i = 0; i < h.size(); i++) {
-        float lp_val = 0.0;
-        if (lp.size() > i && lp[i] != 0.0f)
-            lp_val = 1.0f / lp[i];
-
-        float partiality_val = -1.0f;
-        if (partiality.size() > i && partiality[i] >= 0.0f)
-            partiality_val = partiality[i];
-        float delta_phi_val = NAN;
-        if (phi.size() > i)
-            delta_phi_val = phi[i];
-        float zeta_val = NAN;
-        if (zeta.size() > i)
-            zeta_val = zeta[i];
-
-        float image_scale_corr_val = 1.0f; // Default is 1.0, if we don't know any better
-        if (image_scale_corr.size() > i)
-            image_scale_corr_val = image_scale_corr[i];
-
-        float obs_x_val = NAN;
-        float obs_y_val = NAN;
-
-        if (obs_x.size() > i && obs_y.size() > i) {
-            obs_x_val = obs_x[i];
-            obs_y_val = obs_y[i];
-        }
-
-        Reflection r{
-            .h = h.at(i),
-            .k = k.at(i),
-            .l = l.at(i),
-            .delta_phi_deg = delta_phi_val,
-            .predicted_x = predicted_x.at(i),
-            .predicted_y = predicted_y.at(i),
-            .observed_x = obs_x_val,
-            .observed_y = obs_y_val,
-            .d = d.at(i),
-            .I = int_sum.at(i),
-            .bkg = bkg.at(i),
-            .sigma = int_err.at(i),
-            .rlp = lp_val,
-            .partiality = partiality_val,
-            .zeta = zeta_val,
-            .image_scale_corr = image_scale_corr_val
-        };
-        reflections.emplace_back(r);
-    }
-
-    return true;
-}
-
-template<class T>
-std::optional<T> ReadElementMasterFirst(HDF5Object &master_file,
-                                        HDF5Object &source_file,
-                                        const std::string &path,
-                                        hsize_t master_image,
-                                        hsize_t source_image) {
-    if (master_file.Exists(path))
-        return master_file.ReadElement<T>(path, master_image);
-    if (source_file.Exists(path))
-        return source_file.ReadElement<T>(path, source_image);
-    return {};
-}
-
-template<class T>
-std::vector<T> ReadVectorMasterFirst(HDF5Object &master_file,
-                                     HDF5Object &source_file,
-                                     const std::string &path,
-                                     const std::vector<hsize_t> &master_start,
-                                     const std::vector<hsize_t> &source_start,
-                                     const std::vector<hsize_t> &size) {
-    if (master_file.Exists(path))
-        return master_file.ReadOptVector<T>(path, master_start, size);
-    if (source_file.Exists(path))
-        return source_file.ReadOptVector<T>(path, source_start, size);
-    return {};
-}
-
-void JFJochHDF5Reader::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const {
-    // ROI definitions live in /entry/roi_defs (kept separate from the per-image ROI
-    // results in /entry/roi so that older readers, which iterate /entry/roi, are not
-    // disturbed by the bitmap and definition subgroups).
-    if (!file.Exists("/entry/roi_defs"))
-        return;
-
-    if (file.Exists("/entry/roi_defs/roi_map")) {
-        auto dim = file.GetDimension("/entry/roi_defs/roi_map");   // [y, x]
-        if (dim.size() == 2)
-            dataset.roi_map = file.ReadOptVector<uint16_t>("/entry/roi_defs/roi_map",
-                                                           {0, 0}, {dim[0], dim[1]});
-    }
-
-    ROIDefinition defs;
-    for (const auto &name: file.FindLeafs("/entry/roi_defs")) {
-        const std::string base = "/entry/roi_defs/" + name;
-        // Skip the roi_map bitmask; only named ROI subgroups carry a definition.
-        if (name == "roi_map" || !file.Exists(base + "/type"))
-            continue;
-
-        dataset.roi_bit_index[name] = static_cast<uint16_t>(file.GetInt(base + "/bit_index"));
-
-        const std::string type = file.GetString(base + "/type");
-        if (type == "box")
-            defs.boxes.emplace_back(name, file.GetInt(base + "/min_x_pxl"), file.GetInt(base + "/max_x_pxl"),
-                                          file.GetInt(base + "/min_y_pxl"), file.GetInt(base + "/max_y_pxl"));
-        else if (type == "circle")
-            defs.circles.emplace_back(name, file.GetFloat(base + "/center_x_pxl"), file.GetFloat(base + "/center_y_pxl"),
-                                            file.GetFloat(base + "/radius_pxl"));
-        else if (type == "azim") {
-            const float qmin = file.GetFloat(base + "/q_min_recipA");
-            const float qmax = file.GetFloat(base + "/q_max_recipA");
-            float phi_min = 0, phi_max = 0;
-            if (file.Exists(base + "/phi_min_deg") && file.Exists(base + "/phi_max_deg")) {
-                phi_min = file.GetFloat(base + "/phi_min_deg");
-                phi_max = file.GetFloat(base + "/phi_max_deg");
-            }
-            const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
-            const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
-            defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
-        }
-    }
-
-    if (!defs.boxes.empty() || !defs.circles.empty() || !defs.azimuthal.empty())
-        dataset.experiment.ROI().SetROI(defs);
-}
+#include "../common/JFJochException.h"
 
 void JFJochHDF5Reader::ReadFile(const std::string &filename) {
     std::unique_lock ul(hdf5_mutex);
     image_source_.Clear();
+    snapshots_.clear();
+    active_metadata_.reset();
+    active_snapshot_.clear();
+    number_of_images = 0;
     try {
-        auto dataset = std::make_shared<JFJochReaderDataset>();
-        master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
-        master_filename = filename;
-        dataset->experiment = default_experiment;
-
-        // Image-layout state is accumulated locally while parsing, then handed to image_locator_
-        // at the end. format stays NoFile if the master carries no image data.
-        FileWriterFormat format = FileWriterFormat::NoFile;
-        HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
-        std::vector<std::string> legacy_format_files;
-        std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
-        size_t images_per_file = 1;
-
-        std::filesystem::path master_path(filename);
-        std::string master_file_directory = master_path.parent_path().string();
-
-        dataset->arm_date = master_file->GetString("/entry/start_time");
-
-        dataset->experiment.FilePrefix(dataset_name(filename));
-
-        // JFJochReader is always using int32_t
-        dataset->experiment.BitDepthImage(32);
-        dataset->experiment.PixelSigned(true);
-
-        size_t image_size_x = 0;
-        size_t image_size_y = 0;
-
-        if (master_file->Exists("/entry/data/data")) {
-            HDF5DataSet data_dataset(*master_file, "/entry/data/data");
-            HDF5Dcpl dcpl(data_dataset);
-            data_layout = dcpl.GetLayout();
-
-            auto dim = GetDimension(*master_file, "/entry/data/data");
-            number_of_images = dim[0];
-            image_size_y = dim[1];
-            image_size_x = dim[2];
-
-            images_per_file = number_of_images;
-            if (data_layout == HDF5DataSetLayout::VIRTUAL)
-                vds_data_mappings = ReadVDSImageMappings(*master_file, "/entry/data/data");
-
-            if (master_file->Exists("/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image"))
-                dataset->efficiency = master_file->ReadVector<float>(
-                    "/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");
-            else
-                dataset->efficiency = std::vector<float>(number_of_images, 1.0);
-
-            if (master_file->Exists("/entry/roi"))
-                dataset->roi = master_file->FindLeafs("/entry/roi");
-
-            for (const auto &s: dataset->roi) {
-                dataset->roi_max.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/max"));
-                dataset->roi_sum.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum"));
-                dataset->roi_sum_sq.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum_sq"));
-                dataset->roi_npixel.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/npixel"));
-                dataset->roi_x.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/x"));
-                dataset->roi_y.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/y"));
-            }
-
-            if (master_file->Exists("/entry/MX")) {
-                if (master_file->Exists("/entry/MX/peakCountUnfiltered"))
-                    dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/peakCountUnfiltered");
-                else
-                    dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
-
-                dataset->spot_count_low_res = master_file->ReadOptVector<float>("/entry/MX/peakCountLowRes");
-                dataset->spot_count_indexed = master_file->ReadOptVector<float>("/entry/MX/peakCountIndexed");
-                dataset->spot_count_ice_rings = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRingRes");
-
-                dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
-                dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
-                dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
-                dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
-                // Master files write indexedLatticeCount; data files / the per-file MX
-                // plugin use indexingLatticeCount. Accept either for backward compatibility.
-                dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexedLatticeCount");
-                if (dataset->indexing_lattice_count.empty())
-                    dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
-                dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
-                dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
-                dataset->image_scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
-                dataset->image_scale_cc = master_file->ReadOptVector<float>("/entry/MX/imageScaleCC");
-                dataset->image_scale_b = master_file->ReadOptVector<float>("/entry/MX/imageScaleBFactor");
-                dataset->integrated_reflections = master_file->ReadOptVector<float>("/entry/MX/integratedReflections");
-            }
-            if (master_file->Exists("/entry/image"))
-                dataset->max_value = master_file->ReadOptVector<int64_t>("/entry/image/max_value");
-
-            format = FileWriterFormat::NXmxVDS;
-        } else if (master_file->Exists("/entry/data/data_000001")) {
-            format = FileWriterFormat::NXmxLegacy;
-            data_layout = HDF5DataSetLayout::CONTIGUOUS;
-
-            legacy_format_files.clear();
-
-            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
-            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
-
-            //size_t expected_images = master_file->GetInt("/entry/instrument/detector/detectorSpecific/nimages");
-
-            images_per_file = 0;
-            number_of_images = 0;
-            uint32_t nfiles = 0;
-
-            std::filesystem::path file_path(filename);
-            std::filesystem::path directory = file_path.parent_path();
-
-            while (true) {
-                std::string dname = fmt::format("/entry/data/data_{:06d}", nfiles + 1);
-                if (!master_file->Exists(dname))
-                    break;
-
-                size_t fimages = 0;
-
-                try {
-                    auto fname = ResolveRelativeToMaster(directory.string(),
-                                                         master_file->GetLinkedFileName(dname));
-
-                    HDF5ReadOnlyFile data_file(fname);
-
-                    fimages = GetDimension(data_file, "/entry/data/data")[0];
-
-                    legacy_format_files.push_back(fname);
-
-                    if (nfiles == 0 && data_file.Exists("/entry/roi"))
-                        dataset->roi = data_file.FindLeafs("/entry/roi");
-
-                    dataset->roi_max.resize(dataset->roi.size());
-                    dataset->roi_npixel.resize(dataset->roi.size());
-                    dataset->roi_sum.resize(dataset->roi.size());
-                    dataset->roi_sum_sq.resize(dataset->roi.size());
-                    dataset->roi_x.resize(dataset->roi.size());
-                    dataset->roi_y.resize(dataset->roi.size());
-
-                    for (int i = 0; i < dataset->roi.size(); i++) {
-                        auto roi_name = dataset->roi[i];
-                        ReadVector(dataset->roi_max.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/max",
-                                   number_of_images, fimages);
-                        ReadVector(dataset->roi_npixel.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/npixel",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->roi_sum.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/sum",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->roi_sum_sq.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/sum_sq",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->roi_x.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/x",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->roi_y.at(i),
-                                   data_file, "/entry/roi/" + roi_name + "/y",
-                                   number_of_images, fimages);
-                    }
-
-                    if (data_file.Exists("/entry/detector")) {
-                        ReadVector(dataset->efficiency,
-                                   data_file, "/entry/detector/data_collection_efficiency_image",
-                                   number_of_images, fimages);
-                    }
-
-                    if (data_file.Exists("/entry/MX")) {
-                        if (data_file.Exists("/entry/MX/peakCountUnfiltered"))
-                            ReadVector(dataset->spot_count,
-                                       data_file, "/entry/MX/peakCountUnfiltered",
-                                       number_of_images, fimages);
-                        else
-                            ReadVector(dataset->spot_count,
-                                       data_file, "/entry/MX/nPeaks",
-                                       number_of_images, fimages);
-
-                        ReadVector(dataset->spot_count_ice_rings,
-                                   data_file, "/entry/MX/peakCountIceRingRes",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->spot_count_low_res,
-                                   data_file, "/entry/MX/peakCountLowRes",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->spot_count_indexed,
-                                   data_file, "/entry/MX/peakCountIndexed",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->indexing_result,
-                                   data_file, "/entry/MX/imageIndexed",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->bkg_estimate,
-                                   data_file, "/entry/MX/bkgEstimate",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->profile_radius,
-                                   data_file, "/entry/MX/profileRadius",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->indexing_lattice_count,
-                                   data_file, "/entry/MX/indexingLatticeCount",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->mosaicity_deg,
-                                   data_file, "/entry/MX/mosaicity",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->b_factor,
-                                   data_file, "/entry/MX/bFactor",
-                                   number_of_images, fimages);
-
-                        ReadVector(dataset->resolution_estimate,
-                                   data_file, "/entry/MX/resolutionEstimate",
-                                   number_of_images, fimages);
-                    }
-
-                    if (data_file.Exists("/entry/image")) {
-                        ReadVector(dataset->max_value,
-                                   data_file, "/entry/image/max_value",
-                                   number_of_images, fimages);
-                    }
-                } catch (JFJochException &e) {
-                }
-
-                if (nfiles == 0)
-                    images_per_file = fimages;
-                number_of_images += fimages;
-                nfiles++;
-            }
-        } else {
-            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
-            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
-            number_of_images = 0;
-        }
-
-        if (master_file->Exists("/entry/MX")) {
-            auto indexing = master_file->GetString("/entry/MX/indexing_algorithm", "none");
-            if (indexing == "fft" || indexing == "FFT (CUDA)" || indexing == "FFT (FFTW)")
-                dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
-            else if (indexing == "ffbidx" || indexing == "FFBIDX")
-                dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
-        }
-
-        auto ring_current_A = master_file->GetOptFloat("/entry/source/current");
-        if (ring_current_A) dataset->experiment.RingCurrent_mA(ring_current_A.value() * 1000.0);
-
-        dataset->experiment.DetectIceRings(
-            master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/detect_ice_rings").value_or(false));
-        dataset->experiment.PoniRot1_rad(
-            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot1").value_or(0.0));
-        dataset->experiment.PoniRot2_rad(
-            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
-        dataset->experiment.PoniRot3_rad(
-            master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
-        dataset->experiment.SampleTemperature_K(master_file->GetOptFloat("/entry/sample/temperature"));
-
-        dataset->experiment.BeamX_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_x"));
-        dataset->experiment.BeamY_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_y"));
-
-        float det_distance = master_file->GetFloat("/entry/instrument/detector/distance");
-        if (det_distance < 0.001)
-            det_distance = 0.1; // Set to 100 mm, if det distance is less than 1 mm
-        dataset->experiment.DetectorDistance_mm(det_distance * 1000.0);
-
-        const float incident_wavelength_A = master_file->GetFloat("/entry/instrument/beam/incident_wavelength");
-        dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / incident_wavelength_A);
-
-        // NXmx incident_wavelength_spread is the absolute FWHM (Angstrom); store it
-        // as the relative bandwidth FWHM (dlambda/lambda) used internally.
-        if (const auto spread = master_file->GetOptFloat("/entry/instrument/beam/incident_wavelength_spread"))
-            if (incident_wavelength_A > 0.0f)
-                dataset->experiment.BandwidthFWHM(spread.value() / incident_wavelength_A);
-
-        dataset->error_value = master_file->GetOptInt("/entry/instrument/detector/error_value");
-
-        dataset->jfjoch_release = master_file->GetString("/entry/instrument/detector/detectorSpecific/jfjoch_release");
-
-        InstrumentMetadata metadata;
-        metadata.InstrumentName(master_file->GetString("/entry/instrument/name"));
-        metadata.SourceName(master_file->GetString("/entry/source/name"));
-        dataset->experiment.ImportInstrumentMetadata(metadata);
-
-        if (master_file->Exists("/entry/sample/transformations")) {
-            if (master_file->Exists("/entry/sample/transformations/omega")) {
-                auto omega = ReadAxis(master_file.get(), "omega");
-                dataset->experiment.Goniometer(omega);
-            } else if (master_file->Exists("/entry/sample/grid_scan")) {
-                GridScanSettings grid(
-                    master_file->GetInt("/entry/sample/grid_scan/n_fast"),
-                    master_file->GetFloat("/entry/sample/grid_scan/step_x") * 1e6f,
-                    master_file->GetFloat("/entry/sample/grid_scan/step_y") * 1e6f,
-                    master_file->GetOptBool("/entry/sample/grid_scan/snake_scan").value_or(false),
-                    master_file->GetOptBool("/entry/sample/grid_scan/vertical_scan").value_or(false)
-                );
-                grid.ImageNum(number_of_images);
-                dataset->experiment.GridScan(grid);
-            }
-        }
-
-        auto tmp = master_file->ReadOptVector<float>("/entry/sample/unit_cell");
-        if (tmp.size() == 6)
-            dataset->experiment.SetUnitCell(UnitCell{
-                .a = tmp[0],
-                .b = tmp[1],
-                .c = tmp[2],
-                .alpha = tmp[3],
-                .beta = tmp[4],
-                .gamma = tmp[5]
-            });
-        dataset->experiment.SpaceGroupNumber(master_file->GetOptInt("/entry/sample/space_group_number"));
-        dataset->experiment.SampleName(master_file->GetString("/entry/sample/name"));
-
-
-        if (master_file->Exists("/entry/instrument/attenuator"))
-            dataset->experiment.AttenuatorTransmission(
-                master_file->GetOptFloat("/entry/instrument/attenuator/attenuator_transmission"));
-        dataset->experiment.TotalFlux(master_file->GetOptFloat("/entry/instrument/beam/total_flux"));
-
-        if (master_file->Exists("/entry/azint") && master_file->Exists("/entry/azint/bin_to_q")) {
-            HDF5DataSet bin_to_q_dataset(*master_file, "/entry/azint/bin_to_q");
-            HDF5DataSpace bin_to_q_dataspace(bin_to_q_dataset);
-            auto dim = bin_to_q_dataspace.GetDimensions();
-
-            if (dim.size() == 1) {
-                dataset->azimuthal_bins = 0;
-                dataset->q_bins = dim[0];
-                bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q);
-            } else if (dim.size() == 2) {
-                dataset->azimuthal_bins = dim[0];
-                dataset->q_bins = dim[1];
-                dataset->az_int_bin_to_q.resize(dim[0] * dim[1]);
-                bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q, {0, 0}, dim);
-            } else
-                throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/azint/image dataset");
-            if (master_file->Exists("/entry/azint/bin_to_phi")) {
-                HDF5DataSet bin_to_phi_dataset(*master_file, "/entry/azint/bin_to_phi");
-                if (dataset->q_bins > 0) {
-                    dataset->az_int_bin_to_phi.resize(dim[0] * dim[1]);
-                    bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi, {0, 0}, dim);
-                } else {
-                    bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi);
-                }
-            }
-        }
-
-        // Read fluorescence spectrum if present
-        if (master_file->Exists("/entry/instrument/fluorescence")) {
-            auto energy = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/energy");
-            auto data = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/data");
-            if (!energy.empty() && energy.size() == data.size())
-                dataset->experiment.FluorescenceSpectrum(XrayFluorescenceSpectrum(energy, data));
-        }
-
-        auto detector_name = master_file->GetString("/entry/instrument/detector/description");
-
-        DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
-        detector.PixelSize_um(master_file->GetFloat("/entry/instrument/detector/x_pixel_size") * 1e6);
-        detector.SaturationLimit(master_file->GetInt("/entry/instrument/detector/saturation_value"));
-        detector.MinFrameTime(std::chrono::microseconds(0));
-        detector.MinCountTime(std::chrono::microseconds(0));
-        detector.ReadOutTime(std::chrono::nanoseconds(0));
-        dataset->experiment.Detector(detector);
-
-        dataset->experiment.FrameTime(
-            std::chrono::duration_cast<std::chrono::nanoseconds>(
-                std::chrono::duration<float>(
-                    master_file->GetFloat("/entry/instrument/detector/frame_time"))),
-            std::chrono::duration_cast<std::chrono::nanoseconds>(
-                std::chrono::duration<float>(
-                    master_file->GetFloat("/entry/instrument/detector/count_time")))
-        );
-
-        if (master_file->Exists("/entry/instrument/detector/calibration")) {
-            dataset->calibration_data = master_file->FindLeafs("/entry/instrument/detector/calibration");
-            std::sort(dataset->calibration_data.begin(), dataset->calibration_data.end());
-        }
-
-        if (image_size_x * image_size_y > 0) {
-            auto mask_tmp = master_file->ReadOptVector<uint32_t>(
-                "/entry/instrument/detector/pixel_mask",
-                {0, 0},
-                {image_size_y, image_size_x}
-            );
-            if (mask_tmp.empty())
-                mask_tmp = master_file->ReadOptVector<uint32_t>(
-                    "/entry/instrument/detector/detectorSpecific/pixel_mask",
-                    {0, 0},
-                    {image_size_y, image_size_x}
-                );
-            if (mask_tmp.empty())
-                mask_tmp = std::vector<uint32_t>(image_size_x * image_size_y);
-            dataset->pixel_mask = PixelMask(mask_tmp);
-        }
-
-        ReadROIMetadata(*master_file, *dataset);
-
-        // Hand the parsed image layout to the locator. VDS mapping filenames are resolved to
-        // absolute paths here so the locator only ever deals with real paths.
-        for (auto &m : vds_data_mappings)
-            m.filename = ResolveRelativeToMaster(master_file_directory, m.filename);
-        image_source_.Configure(HDF5ImageLocator::Layout{
-            .format = format,
-            .data_layout = data_layout,
-            .master_file = master_file,
-            .master_filename = master_filename,
-            .legacy_files = std::move(legacy_format_files),
-            .images_per_file = images_per_file,
-            .vds_mappings = std::move(vds_data_mappings)
-        });
-
-        dataset->experiment.ImagesPerTrigger(number_of_images);
-        cached_geom = dataset->experiment.GetDiffractionGeometry();
-        SetStartMessage(dataset);
+        auto metadata = std::make_shared<HDF5MetadataSource>();
+        auto open_result = metadata->Open(filename, default_experiment);
+
+        image_source_.Configure(std::move(open_result.image_layout));
+        // Original file: per-image metadata is co-located with the pixels.
+        metadata->UseImageSourceForMetadata(&image_source_);
+        number_of_images = open_result.number_of_images;
+
+        snapshots_["Original"] = metadata;
+        active_metadata_ = metadata;
+        active_snapshot_ = "Original";
+        SetStartMessage(metadata->Dataset());
     } catch (const std::exception &e) {
-        master_file = {};
-        number_of_images = 0;
         image_source_.Clear();
+        snapshots_.clear();
+        active_metadata_.reset();
+        active_snapshot_.clear();
+        number_of_images = 0;
         SetStartMessage({});
         throw;
     }
@@ -718,6 +40,16 @@ uint64_t JFJochHDF5Reader::GetNumberOfImages() const {
     return number_of_images;
 }
 
+void JFJochHDF5Reader::Close() {
+    std::unique_lock ul(hdf5_mutex);
+    image_source_.Clear();
+    snapshots_.clear();
+    active_metadata_.reset();
+    active_snapshot_.clear();
+    number_of_images = 0;
+    SetStartMessage({});
+}
+
 HDF5ImageLocator::Location JFJochHDF5Reader::GetImageLocation(int64_t image_number) const {
     if (image_number >= static_cast<int64_t>(number_of_images) || image_number < 0)
         throw JFJochException(JFJochExceptionCategory::HDF5, "Image out of bounds");
@@ -727,7 +59,7 @@ HDF5ImageLocator::Location JFJochHDF5Reader::GetImageLocation(int64_t image_numb
 std::shared_ptr<JFJochReaderRawImage> JFJochHDF5Reader::GetRawImage(int64_t image_number) {
     std::unique_lock ul(hdf5_mutex);
 
-    if (!master_file)
+    if (!active_metadata_)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot load image if file not loaded");
 
@@ -737,441 +69,112 @@ std::shared_ptr<JFJochReaderRawImage> JFJochHDF5Reader::GetRawImage(int64_t imag
     return ret;
 }
 
-// Reads spot data for a single image from the appropriate HDF5 source.
-// master_image / source_image are the logical indices within master_file and
-// source_file respectively (identical for NXmxVDS contiguous / integrated;
-// differ for NXmxLegacy and NXmxVDS virtual layouts).
-// Appends assembled SpotToSave entries to message.spots and fills the
-// spot_count* fields; does NOT touch the image pixel data.
-static void ReadSpotsFromFiles(HDF5Object &master_file,
-                               HDF5Object &source_file,
-                               hsize_t master_image,
-                               hsize_t source_image,
-                               int64_t image_number,
-                               const DiffractionGeometry &geom,
-                               DataMessage &message) {
-    auto spot_count_opt = ReadElementMasterFirst<uint32_t>(master_file,
-                                                           source_file,
-                                                           "/entry/MX/nPeaks",
-                                                           master_image,
-                                                           source_image);
-    if (!spot_count_opt.has_value() || spot_count_opt.value() == 0)
-        return;
-
-    const size_t spot_count = spot_count_opt.value();
-
-    auto spot_x = ReadVectorMasterFirst<float>(
-        master_file, source_file,
-        "/entry/MX/peakXPosRaw",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_y = ReadVectorMasterFirst<float>(
-        master_file, source_file,
-        "/entry/MX/peakYPosRaw",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_intensity = ReadVectorMasterFirst<float>(
-        master_file, source_file,
-        "/entry/MX/peakTotalIntensity",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-
-    if (spot_x.size() < spot_count || spot_y.size() < spot_count || spot_intensity.size() < spot_count)
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of spot dataset");
-
-    auto spot_indexed = ReadVectorMasterFirst<uint8_t>(
-        master_file, source_file,
-        "/entry/MX/peakIndexed",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_ice = ReadVectorMasterFirst<uint8_t>(
-        master_file, source_file,
-        "/entry/MX/peakIceRingRes",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_h = ReadVectorMasterFirst<int32_t>(
-        master_file, source_file,
-        "/entry/MX/peakH",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_k = ReadVectorMasterFirst<int32_t>(
-        master_file, source_file,
-        "/entry/MX/peakK",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-    auto spot_l = ReadVectorMasterFirst<int32_t>(
-        master_file, source_file,
-        "/entry/MX/peakL",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-
-    auto spot_lattice = ReadVectorMasterFirst<int8_t>(
-        master_file, source_file,
-        "/entry/MX/peakLattice",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-        );
-
-    auto spot_dist_ewald_sphere = ReadVectorMasterFirst<float>(
-        master_file, source_file,
-        "/entry/MX/peakDistEwaldSphere",
-        {master_image, 0}, {source_image, 0}, {1, spot_count}
-    );
-
-    message.spots.reserve(message.spots.size() + spot_count);
-    for (size_t i = 0; i < spot_count; i++) {
-        const auto x = spot_x.at(i);
-        const auto y = spot_y.at(i);
-
-        SpotToSave s{
-            .x = x,
-            .y = y,
-            .intensity = spot_intensity.at(i),
-            .image = image_number,
-            .d_A = geom.PxlToRes(x, y)
-        };
-        if (spot_indexed.size() > i)
-            s.indexed = (spot_indexed.at(i) != 0);
-        if (spot_h.size() > i)
-            s.h = spot_h.at(i);
-        if (spot_k.size() > i)
-            s.k = spot_k.at(i);
-        if (spot_l.size() > i)
-            s.l = spot_l.at(i);
-        if (spot_dist_ewald_sphere.size() > i)
-            s.dist_ewald_sphere = spot_dist_ewald_sphere.at(i);
-        if (spot_ice.size() > i)
-            s.ice_ring = (spot_ice.at(i) != 0);
-        if (spot_lattice.size() > i)
-            s.lattice = spot_lattice.at(i);
-        message.spots.emplace_back(s);
-    }
-
-    if (auto v = ReadElementMasterFirst<uint32_t>(master_file, source_file,
-                                                  "/entry/MX/peakCountUnfiltered",
-                                                  master_image, source_image); v)
-        message.spot_count = v;
-    else
-        message.spot_count = spot_count_opt;
-
-    message.spot_count_ice_rings = ReadElementMasterFirst<uint32_t>(
-        master_file, source_file, "/entry/MX/peakCountIceRingRes", master_image, source_image);
-    message.spot_count_low_res = ReadElementMasterFirst<uint32_t>(
-        master_file, source_file, "/entry/MX/peakCountLowRes", master_image, source_image);
-    message.spot_count_indexed = ReadElementMasterFirst<uint32_t>(
-        master_file, source_file, "/entry/MX/peakCountIndexed", master_image, source_image);
-
-    GenerateSpotPlot(message, 1.5);
-}
-
 bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
                                    DataMessage &message,
                                    std::vector<uint8_t> &buffer,
                                    int64_t image_number,
                                    bool update_dataset) {
     std::unique_lock ul(hdf5_mutex);
+    (void) update_dataset;
 
     if (!dataset)
-        return {};
-
-    if (!master_file)
+        return false;
+    if (!active_metadata_)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot load image if file not loaded");
 
+    // Pixels from the shared image source, per-image metadata from the active snapshot.
     auto loc = GetImageLocation(image_number);
-    auto &source_file = loc.file;
-    const uint32_t image_id = loc.local_index;
-
     message.image = image_source_.ReadImageAt(buffer, loc);
     message.number = image_number;
-
-    const auto master_image = static_cast<hsize_t>(image_number);
-    const auto source_image = static_cast<hsize_t>(image_id);
-
-    ReadSpotsFromFiles(*master_file, *source_file, master_image, source_image,
-                       image_number, dataset->experiment.GetDiffractionGeometry(), message);
-
-    if (!dataset->az_int_bin_to_q.empty()) {
-        if (dataset->azimuthal_bins == 0) {
-            message.az_int_profile = ReadVectorMasterFirst<float>(
-                *master_file,
-                *source_file,
-                "/entry/azint/image",
-                {master_image, 0},
-                {source_image, 0},
-                {1, dataset->az_int_bin_to_q.size()}
-            );
-        } else {
-            message.az_int_profile = ReadVectorMasterFirst<float>(
-                *master_file,
-                *source_file,
-                "/entry/azint/image",
-                {master_image, 0, 0},
-                {source_image, 0, 0},
-                {1, dataset->azimuthal_bins, dataset->q_bins}
-            );
-        }
-    }
-    if (dataset->integrated_reflections.size() > image_number)
-        message.integrated_reflections = static_cast<int64_t>(std::lround(
-            dataset->integrated_reflections.at(image_number)));
-    if (dataset->resolution_estimate.size() > image_number)
-        message.resolution_estimate = dataset->resolution_estimate[image_number];
-    if (dataset->indexing_result.size() > image_number)
-        message.indexing_result = dataset->indexing_result[image_number];
-    if (dataset->indexing_lattice_count.size() > image_number)
-        message.indexing_lattice_count = dataset->indexing_lattice_count[image_number];
-    if (dataset->bkg_estimate.size() > image_number)
-        message.bkg_estimate = dataset->bkg_estimate[image_number];
-    if (dataset->efficiency.size() > image_number)
-        message.image_collection_efficiency = dataset->efficiency[image_number];
-    if (dataset->profile_radius.size() > image_number)
-        message.profile_radius = dataset->profile_radius[image_number];
-    if (dataset->mosaicity_deg.size() > image_number)
-        message.mosaicity_deg = dataset->mosaicity_deg[image_number];
-    if (dataset->b_factor.size() > image_number)
-        message.b_factor = dataset->b_factor[image_number];
-    if (dataset->image_scale_b.size() > image_number)
-        message.image_scale_b_factor = dataset->image_scale_b[image_number];
-    if (dataset->image_scale_factor.size() > image_number)
-        message.image_scale_factor = dataset->image_scale_factor[image_number];
-    if (dataset->image_scale_cc.size() > image_number)
-        message.image_scale_cc = dataset->image_scale_cc[image_number];
-    if (dataset->indexing_result.size() > image_number
-        && dataset->indexing_result[image_number] != 0
-        && (master_file->Exists("/entry/MX/latticeIndexed") ||
-            source_file->Exists("/entry/MX/latticeIndexed"))) {
-        std::vector<float> tmp = ReadVectorMasterFirst<float>(
-            *master_file,
-            *source_file,
-            "/entry/MX/latticeIndexed",
-            {master_image, 0},
-            {source_image, 0},
-            {1, 9}
-        );
-
-        if (tmp.size() == 9)
-            message.indexing_lattice = CrystalLattice(tmp);
-
-        std::optional<std::string> lattice;
-        if (master_file->Exists("/entry/MX/bravaisLattice"))
-            lattice = master_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_number);
-        else
-            lattice = source_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_id);
-
-        std::optional<uint32_t> niggli_opt;
-        if (master_file->Exists("/entry/MX/niggli_class"))
-            niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_number);
-        else if (master_file->Exists("/entry/MX/niggliClass"))
-            niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_number);
-        else if (source_file->Exists("/entry/MX/niggli_class"))
-            niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_id);
-        else if (source_file->Exists("/entry/MX/niggliClass"))
-            niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_id);
-
-        if (lattice && !lattice->empty()) {
-            auto symm_info = parse_bravais_lattice(lattice.value());
-
-            message.lattice_type = LatticeMessage{
-                .centering = symm_info.second,
-                .niggli_class = static_cast<int64_t>(niggli_opt.value_or(0)),
-                .crystal_system = symm_info.first,
-            };
-        }
-    }
-
-    const std::string master_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_number);
-    const std::string source_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_id);
-
-    if (!ReadReflectionsFromGroup(*master_file, master_reflection_group_name, message.reflections))
-        ReadReflectionsFromGroup(*source_file, source_reflection_group_name, message.reflections);
-    if (!message.reflections.empty()) {
-        CalcISigma(message);
-        CalcWilsonBFactor(message, !message.b_factor.has_value());
-    }
+    active_metadata_->FillPerImage(message, image_number, dataset);
     return true;
 }
 
-void JFJochHDF5Reader::Close() {
-    std::unique_lock ul(hdf5_mutex);
-    master_file = {};
-    number_of_images = 0;
-    master_filename.clear();
-    cached_geom = DiffractionGeometry{};
-    image_source_.Clear();
-    SetStartMessage({});
-}
-
-std::optional<GoniometerAxis> JFJochHDF5Reader::ReadAxis(HDF5Object *file, const std::string &name) {
-    std::string dname = "/entry/sample/transformations/" + name;
-
-    if (!file->Exists(dname))
-        return {};
-
-
-    HDF5DataSet dataset(*file, dname);
-    std::vector<double> angle;
-    dataset.ReadVector(angle);
-
-    if (angle.size() < 2)
-        return {};
-
-    std::vector<double> end = file->ReadOptVector<double>(dname + "_end");
-
-    double start = angle[0];
-    double incr = angle[1] - angle[0];
-
-    if (dataset.ReadAttrStr("transformation_type") != "rotation")
-        return {};
-
-    std::vector<double> axis_vec = dataset.ReadAttrVec("vector");
-    if (axis_vec.size() != 3)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              dname + " Vector must have 3 elements");
-
-    Coord axis(axis_vec[0], axis_vec[1], axis_vec[2]);
-    GoniometerAxis g_axis(name, start, incr, axis, {});
-    if (!end.empty())
-        g_axis.ScreeningWedge(end[0] - angle[0]);
-
-    return g_axis;
-}
-
-CompressedImage JFJochHDF5Reader::ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const {
-    std::vector<hsize_t> start = {0, 0};
-    if (!master_file)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Master file not loaded");
-    if (!master_file->Exists("/entry/instrument/detector/calibration/" + name))
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Calibration dataset not found");
-
-    HDF5DataSet dataset(*master_file, "/entry/instrument/detector/calibration/" + name);
-    HDF5DataSpace dataspace(dataset);
-    HDF5DataType datatype(dataset);
-    HDF5Dcpl dcpl(dataset);
-
-    if (dataspace.GetNumOfDimensions() != 2)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Calibration dataset must be 2D");
-
-    auto dim = dataspace.GetDimensions();
-
-    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
-    dataset.ReadVectorToU8(tmp, start, {dim[0], dim[1]});
-    algorithm = CompressionAlgorithm::NO_COMPRESSION;
-
-    return {
-        tmp, dim[1], dim[0],
-        CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
-        algorithm
-    };
-}
-
 std::vector<HDF5DataSourceMessage> JFJochHDF5Reader::GetHDF5DataSource(uint64_t first_image,
                                                                        std::optional<uint64_t> image_count) const {
     std::unique_lock ul(hdf5_mutex);
 
-    if (!master_file)
+    if (!active_metadata_)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot generate HDF5 source mapping if file not loaded");
 
     return image_source_.GetSourceMapping(first_image, image_count, number_of_images);
 }
 
-
 std::vector<IntegrationOutcome> JFJochHDF5Reader::ReadReflections(size_t start_image,
                                                                   std::optional<size_t> end_image) const {
     std::unique_lock ul(hdf5_mutex);
 
-    if (start_image >= number_of_images)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "start_image must be less than number_of_images");
-
-    const size_t end_image_val = end_image.value_or(number_of_images - 1);
-
-    if (end_image_val < start_image)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "end_image must be greater or equal to start_image if provided");
-
-    if (end_image_val >= number_of_images)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "end_image must be less than number_of_images");
-
-    if (!master_file)
+    if (!active_metadata_)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot read reflections if file not loaded");
 
-    std::vector<IntegrationOutcome> ret;
-    ret.reserve(end_image_val - start_image + 1);
-
-    for (size_t img = start_image; img <= end_image_val; img++) {
-        IntegrationOutcome outcome;
-
-        // Generic (non-image-specific) detector geometry from experiment setup.
-        outcome.geom = cached_geom;
-
-        // Per-image reflections and MX metadata live in the same file as the image pixels,
-        // at the source-local index (the locator keeps the data-file handle cached).
-        const auto loc = GetImageLocation(static_cast<int64_t>(img));
-        HDF5Object *meta_file = loc.file.get();
-        const size_t meta_image_id = loc.local_index;
-
-        // ── reflections ──────────────────────────────────────────────────────
-        const std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
-        ReadReflectionsFromGroup(*meta_file, refl_group, outcome.reflections);
-
-        // ── per-image mosaicity ───────────────────────────────────────────────
-        if (meta_file->Exists("/entry/MX/mosaicity")) {
-            try {
-                outcome.mosaicity_deg =
-                        meta_file->ReadElement<float>("/entry/MX/mosaicity", meta_image_id);
-            } catch (...) {
-            }
-        }
-
-        // ── indexed lattice (stored as 9-element row-major matrix) ────────────
-        if (meta_file->Exists("/entry/MX/latticeIndexed")) {
-            try {
-                auto lattice_vec = meta_file->ReadOptVector<float>(
-                    "/entry/MX/latticeIndexed", {meta_image_id, 0}, {1, 9});
-                if (lattice_vec.size() == 9)
-                    outcome.latt = CrystalLattice(lattice_vec);
-            } catch (...) {
-            }
-        }
-
-        ret.push_back(std::move(outcome));
-    }
-
-    return ret;
+    return active_metadata_->ReadReflections(start_image, end_image);
 }
 
 std::vector<SpotToSave> JFJochHDF5Reader::ReadSpots(int64_t image) const {
     std::unique_lock ul(hdf5_mutex);
 
-    if (image < 0)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-            "image number must be non-negative");
-    if (image >= number_of_images)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "image must be less than number_of_images");
-
-    if (!master_file)
+    if (!active_metadata_)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Cannot read spots if file not loaded");
 
-    // Spot/MX data lives in the same file as the image pixels, at the source-local index
-    // (the locator keeps the data-file handle cached across calls).
-    const auto loc = GetImageLocation(image);
-    HDF5Object *meta_file = loc.file.get();
-    const size_t meta_image_id = loc.local_index;
-
-    DataMessage tmp_message;
-    tmp_message.number = static_cast<int64_t>(image);
-
-    ReadSpotsFromFiles(*master_file, *meta_file,
-                       image, meta_image_id,
-                       static_cast<int64_t>(image),
-                       cached_geom,
-                       tmp_message);
-
-    return tmp_message.spots;
+    return active_metadata_->ReadSpots(image);
+}
+
+CompressedImage JFJochHDF5Reader::ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const {
+    std::unique_lock ul(hdf5_mutex);
+
+    if (!active_metadata_)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Master file not loaded");
+
+    return active_metadata_->ReadCalibration(tmp, name);
+}
+
+void JFJochHDF5Reader::RegisterSnapshot(const std::string &name, const std::string &master_path) {
+    std::unique_lock ul(hdf5_mutex);
+
+    if (!active_metadata_)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Open a dataset before registering a snapshot");
+
+    auto metadata = std::make_shared<HDF5MetadataSource>();
+    auto open_result = metadata->Open(master_path, default_experiment);
+
+    if (open_result.number_of_images != number_of_images)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Snapshot image count does not match the open dataset");
+
+    // Snapshot pixels come from the existing image source; its own (integrated) master holds the
+    // per-image metadata at the global index.
+    metadata->UseImageSourceForMetadata(nullptr);
+    snapshots_[name] = metadata;
+}
+
+void JFJochHDF5Reader::SetActiveSnapshot(const std::string &name) {
+    std::unique_lock ul(hdf5_mutex);
+
+    auto it = snapshots_.find(name);
+    if (it == snapshots_.end())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown snapshot: " + name);
+
+    active_metadata_ = it->second;
+    active_snapshot_ = name;
+    SetStartMessage(active_metadata_->Dataset());
+}
+
+std::vector<std::string> JFJochHDF5Reader::SnapshotNames() const {
+    std::unique_lock ul(hdf5_mutex);
+
+    std::vector<std::string> names;
+    names.reserve(snapshots_.size());
+    for (const auto &[name, _]: snapshots_)
+        names.push_back(name);
+    return names;
+}
+
+std::string JFJochHDF5Reader::ActiveSnapshot() const {
+    std::unique_lock ul(hdf5_mutex);
+    return active_snapshot_;
 }
diff --git a/reader/JFJochHDF5Reader.h b/reader/JFJochHDF5Reader.h
index 4271ec6d..3c69cc0e 100644
--- a/reader/JFJochHDF5Reader.h
+++ b/reader/JFJochHDF5Reader.h
@@ -1,49 +1,44 @@
-// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
 #pragma once
 
+#include <map>
+#include <memory>
+#include <optional>
+#include <string>
+#include <vector>
+
 #include "JFJochReader.h"
 #include "JFJochReaderSpots.h"
 #include "HDF5ImageSource.h"
+#include "HDF5MetadataSource.h"
 #include "../writer/HDF5Objects.h"
 #include "../image_analysis/IntegrationOutcome.h"
 
+// Composes one shared raw-image source with one or more metadata sources ("snapshots") over the
+// same images: the original _master.h5 plus optional reprocessing _process.h5 results. The active
+// snapshot supplies the dataset and per-image metadata; the image source always supplies pixels,
+// so switching snapshots never reloads image data.
 class JFJochHDF5Reader : public JFJochReader {
-    // Raw-pixel side: where each image physically lives + the open-file cache. Stays fixed while
-    // the metadata read from master_file may change.
     HDF5ImageSource image_source_;
-
-    // Metadata side: the master file the per-image and dataset-level metadata is read from.
-    std::shared_ptr<HDF5ReadOnlyFile> master_file;
-    std::string master_filename;
-
-    DiffractionGeometry cached_geom;
+    std::map<std::string, std::shared_ptr<HDF5MetadataSource> > snapshots_;
+    std::shared_ptr<HDF5MetadataSource> active_metadata_;
+    std::string active_snapshot_;
     size_t number_of_images = 0;
 
     bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
-                     DataMessage& message,
+                     DataMessage &message,
                      std::vector<uint8_t> &buffer,
                      int64_t image_number,
                      bool update_dataset) override;
 
-    template <class T>
-    void ReadVector(std::vector<T> &v,
-                    HDF5Object &file,
-                    const std::string &dataset_name,
-                    size_t image0,
-                    size_t nimages);
-
     HDF5ImageLocator::Location GetImageLocation(int64_t image_number) const;
-    std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
 
-    // Read the master-file ROI definitions: logical definitions into experiment.ROI()
-    // and the roi_map bitmask (+ bit index) into the dataset. Present for all formats.
-    void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
 public:
     ~JFJochHDF5Reader() override = default;
 
-    void ReadFile(const std::string& filename);
+    void ReadFile(const std::string &filename);
 
     uint64_t GetNumberOfImages() const override;
 
@@ -61,4 +56,11 @@ public:
     CompressedImage ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const;
 
     std::shared_ptr<JFJochReaderRawImage> GetRawImage(int64_t image_number) override;
-};
\ No newline at end of file
+
+    // Metadata snapshots over the same images. The original file is registered as "Original" on
+    // ReadFile and is the initial active snapshot; reprocessing results can be added later.
+    void RegisterSnapshot(const std::string &name, const std::string &master_path);
+    void SetActiveSnapshot(const std::string &name);
+    std::vector<std::string> SnapshotNames() const;
+    std::string ActiveSnapshot() const;
+};
diff --git a/tests/JFJochReaderTest.cpp b/tests/JFJochReaderTest.cpp
index 91dc0bf3..1d63a9e1 100644
--- a/tests/JFJochReaderTest.cpp
+++ b/tests/JFJochReaderTest.cpp
@@ -2609,5 +2609,123 @@ TEST_CASE("JFJochReader_ReadSpots_Integrated", "[HDF5][Full]") {
 
     remove("read_spots_integrated_master.h5");
 
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+TEST_CASE("JFJochReader_Snapshots", "[HDF5][Full]") {
+    RegisterHDF5Filter();
+
+    DiffractionExperiment x(DetJF(1));
+    x.FilePrefix("test_snap").ImagesPerTrigger(4).OverwriteExistingFiles(true);
+    x.BitDepthImage(16).ImagesPerFile(1).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
+    x.Compression(CompressionAlgorithm::NO_COMPRESSION);
+
+    // 1. Original dataset: distinct pixels + "original" MX metadata (not indexed, bkg = 10 + i).
+    std::vector<int16_t> image(x.GetPixelsNum());
+    {
+        StartMessage start_message;
+        x.FillMessage(start_message);
+        FileWriter file_set(start_message);
+        ScanResultGenerator generator(x);
+        for (int i = 0; i < 4; i++) {
+            image[5678] = 100 + i;
+            DataMessage message{};
+            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = i;
+            message.indexing_result = false;
+            message.bkg_estimate = 10.0 + i;
+            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+            generator.Add(message);
+        }
+        EndMessage end_message;
+        end_message.max_image_number = 4;
+        generator.FillEndMessage(end_message);
+        file_set.WriteHDF5(end_message);
+        file_set.Finalize();
+    }
+
+    // 2. A reprocessing result over the same 4 images: integrated master, "reprocessed" MX
+    //    metadata (all indexed, bkg = 99 + i) and deliberately wrong pixels that must NOT surface
+    //    (snapshot pixels still come from the original image source).
+    {
+        DiffractionExperiment px(x);
+        px.FilePrefix("test_snap_proc").SetFileWriterFormat(FileWriterFormat::NXmxIntegrated);
+        StartMessage start_message;
+        px.FillMessage(start_message);
+        FileWriter file_set(start_message);
+        ScanResultGenerator generator(px);
+        std::vector<int16_t> proc_image(x.GetPixelsNum(), 7);
+        for (int i = 0; i < 4; i++) {
+            DataMessage message{};
+            message.image = CompressedImage(proc_image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = i;
+            message.indexing_result = true;
+            message.bkg_estimate = 99.0 + i;
+            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+            generator.Add(message);
+        }
+        EndMessage end_message;
+        end_message.max_image_number = 4;
+        generator.FillEndMessage(end_message);
+        file_set.WriteHDF5(end_message);
+        file_set.Finalize();
+    }
+
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("test_snap_master.h5"));
+        REQUIRE(reader.GetNumberOfImages() == 4);
+        CHECK(reader.ActiveSnapshot() == "Original");
+        CHECK(reader.SnapshotNames() == std::vector<std::string>{"Original"});
+
+        // Dataset-level plot arrays come from the active (original) metadata source.
+        REQUIRE(reader.GetDataset()->bkg_estimate.size() == 4);
+        CHECK(reader.GetDataset()->bkg_estimate[2] == Catch::Approx(12.0));
+
+        auto orig0 = reader.LoadImage(0);
+        REQUIRE(orig0);
+        CHECK(orig0->Image()[5678] == 100);
+        REQUIRE(orig0->ImageData().indexing_result.has_value());
+        CHECK(orig0->ImageData().indexing_result.value() == false);
+        CHECK(orig0->ImageData().bkg_estimate.value() == Catch::Approx(10.0));
+
+        // Register the reprocessing result as a second metadata source over the same images.
+        REQUIRE_NOTHROW(reader.RegisterSnapshot("Reprocess", "test_snap_proc_master.h5"));
+        {
+            auto names = reader.SnapshotNames();
+            CHECK(std::find(names.begin(), names.end(), "Original") != names.end());
+            CHECK(std::find(names.begin(), names.end(), "Reprocess") != names.end());
+        }
+
+        REQUIRE_NOTHROW(reader.SetActiveSnapshot("Reprocess"));
+        CHECK(reader.ActiveSnapshot() == "Reprocess");
+        // Plots now come from the reprocessing master.
+        CHECK(reader.GetDataset()->bkg_estimate[2] == Catch::Approx(101.0));
+
+        auto repro0 = reader.LoadImage(0);
+        REQUIRE(repro0);
+        // Pixels still from the original image source, not the 7's stored in the process file.
+        CHECK(repro0->Image()[5678] == 100);
+        // Metadata from the reprocessing snapshot.
+        CHECK(repro0->ImageData().indexing_result.value() == true);
+        CHECK(repro0->ImageData().bkg_estimate.value() == Catch::Approx(99.0));
+
+        // Switch back to the original metadata.
+        REQUIRE_NOTHROW(reader.SetActiveSnapshot("Original"));
+        auto orig0b = reader.LoadImage(0);
+        REQUIRE(orig0b);
+        CHECK(orig0b->Image()[5678] == 100);
+        CHECK(orig0b->ImageData().indexing_result.value() == false);
+
+        REQUIRE_THROWS(reader.SetActiveSnapshot("Nonexistent"));
+    }
+
+    remove("test_snap_master.h5");
+    remove("test_snap_data_000001.h5");
+    remove("test_snap_data_000002.h5");
+    remove("test_snap_data_000003.h5");
+    remove("test_snap_data_000004.h5");
+    remove("test_snap_proc_master.h5");
+
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
\ No newline at end of file
-- 
2.52.0


From 4697f1055556ae289f896a3e2e284fe562101849 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 10:36:18 +0200
Subject: [PATCH 175/228] process: extract reprocessing workflow into shared
 JFJochProcess library

The full processing workflow no longer lives in the CLIs. New process/JFJochProcess
encapsulates it for jfjoch_process, jfjoch_azint and (later) the viewer:

- ProcessMode {AzimuthalIntegration, FullAnalysis}; ProcessConfig carries run control
  (range, threads, output prefix, spot finding, rotation + scaling options, reference
  data) while the DiffractionExperiment carries all algorithm settings.
- Run() executes setup -> optional two-pass rotation pre-pass -> parallel per-image loop
  (std::thread) -> optional scaling/merging post-pass -> NXmxIntegrated _process.h5 that
  links back to the original images. ProcessResult returns stats + merge text.
- Cancel() / std::atomic<bool> (receiver style), checked between images; the CLIs install
  a SIGINT handler that calls it (fixes the previous Ctrl+C gap), the viewer will use the
  same hook. JFJochProcessObserver streams progress / per-image results for a live GUI.

jfjoch_process.cpp and jfjoch_azint.cpp are now thin: argument parsing + experiment
configuration, then JFJochProcess::Run + stats printing. Behaviour and usage messages
are unchanged.

Adds JFJochProcessTest (azimuthal integration round-trip, no-output run, pre-cancel) over
a small generated dataset.

Verified: tests/jfjoch_test [HDF5] (83 cases / 1854 assertions); jfjoch_azint and
jfjoch_process run end-to-end on lyso_test (azint 20 images; full analysis recovers the
lysozyme cell at 25% indexing).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CMakeLists.txt              |   2 +
 process/CMakeLists.txt      |   9 +
 process/JFJochProcess.cpp   | 418 +++++++++++++++++++++++++++++++
 process/JFJochProcess.h     | 100 ++++++++
 tests/CMakeLists.txt        |   3 +-
 tests/JFJochProcessTest.cpp | 133 ++++++++++
 tools/CMakeLists.txt        |   4 +-
 tools/jfjoch_azint.cpp      | 207 +++------------
 tools/jfjoch_process.cpp    | 486 ++++--------------------------------
 9 files changed, 760 insertions(+), 602 deletions(-)
 create mode 100644 process/CMakeLists.txt
 create mode 100644 process/JFJochProcess.cpp
 create mode 100644 process/JFJochProcess.h
 create mode 100644 tests/JFJochProcessTest.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index af868b1e..0148f365 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -262,6 +262,7 @@ IF (JFJOCH_VIEWER_ONLY)
     ADD_SUBDIRECTORY(image_analysis)
     ADD_SUBDIRECTORY(broker)
     ADD_SUBDIRECTORY(reader)
+    ADD_SUBDIRECTORY(process)
     ADD_SUBDIRECTORY(viewer)
     ADD_SUBDIRECTORY(tools)   # builds only the portable analysis tools (process/scale/azint/extract_hkl)
 ELSE()
@@ -286,6 +287,7 @@ ELSE()
         ADD_SUBDIRECTORY(acquisition_device)
         ADD_SUBDIRECTORY(receiver)
         ADD_SUBDIRECTORY(image_analysis)
+        ADD_SUBDIRECTORY(process)
         ADD_SUBDIRECTORY(tests)
         ADD_SUBDIRECTORY(tools)
     ENDIF()
diff --git a/process/CMakeLists.txt b/process/CMakeLists.txt
new file mode 100644
index 00000000..4ebcbac7
--- /dev/null
+++ b/process/CMakeLists.txt
@@ -0,0 +1,9 @@
+# SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+# SPDX-License-Identifier: GPL-3.0-only
+
+ADD_LIBRARY(JFJochProcess STATIC
+        JFJochProcess.cpp
+        JFJochProcess.h
+)
+
+TARGET_LINK_LIBRARIES(JFJochProcess JFJochReader JFJochImageAnalysis JFJochWriter)
diff --git a/process/JFJochProcess.cpp b/process/JFJochProcess.cpp
new file mode 100644
index 00000000..6167a449
--- /dev/null
+++ b/process/JFJochProcess.cpp
@@ -0,0 +1,418 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochProcess.h"
+
+#include <algorithm>
+#include <atomic>
+#include <chrono>
+#include <cmath>
+#include <functional>
+#include <future>
+#include <numeric>
+#include <set>
+#include <sstream>
+
+#include "../reader/JFJochHDF5Reader.h"
+#include "../common/Logger.h"
+#include "../common/AzimuthalIntegrationMapping.h"
+#include "../common/AzimuthalIntegrationProfile.h"
+#include "../common/CUDAWrapper.h"
+#include "../common/time_utc.h"
+#include "../writer/FileWriter.h"
+#include "../image_analysis/MXAnalysisWithoutFPGA.h"
+#include "../image_analysis/IndexAndRefine.h"
+#include "../image_analysis/indexing/IndexerThreadPool.h"
+#include "../image_analysis/azint/AzIntEngineCPU.h"
+#include "../image_analysis/image_preprocessing/ImagePreprocessorCPU.h"
+#include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
+#include "../image_analysis/scale_merge/Merge.h"
+#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
+#include "../image_analysis/WriteReflections.h"
+
+namespace {
+    // Pick up to requested_images ordinals spread evenly across [0, images_to_process) for the
+    // first pass of two-pass rotation indexing.
+    std::vector<int> select_equally_spaced_image_ordinals(int images_to_process, int requested_images) {
+        std::vector<int> ret;
+        if (images_to_process <= 0 || requested_images <= 0)
+            return ret;
+
+        const int n = std::min(images_to_process, requested_images);
+        if (n == 1) {
+            ret.push_back(0);
+            return ret;
+        }
+
+        std::set<int> unique_ordinals;
+        for (int i = 0; i < n; i++)
+            unique_ordinals.insert(static_cast<int>(
+                std::llround(static_cast<double>(i) * static_cast<double>(images_to_process - 1) /
+                             static_cast<double>(n - 1))));
+
+        ret.assign(unique_ordinals.begin(), unique_ordinals.end());
+        return ret;
+    }
+}
+
+JFJochProcess::JFJochProcess(JFJochHDF5Reader &reader, DiffractionExperiment experiment,
+                             PixelMask pixel_mask, ProcessConfig config)
+    : reader_(reader), experiment_(std::move(experiment)),
+      pixel_mask_(std::move(pixel_mask)), config_(std::move(config)) {}
+
+ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
+    Logger logger("JFJochProcess");
+    ProcessResult result;
+
+    const auto dataset = reader_.GetDataset();
+    if (!dataset)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "No experiment dataset found in the input file");
+
+    if (config_.stride <= 0)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image stride must be positive");
+
+    const auto total_images_in_file = static_cast<int>(reader_.GetNumberOfImages());
+    int end_image = config_.end_image;
+    if (end_image < 0 || end_image > total_images_in_file)
+        end_image = total_images_in_file;
+    const int start_image = config_.start_image;
+    const int images_to_process = (end_image - start_image) / config_.stride;
+    if (images_to_process <= 0) {
+        logger.Warning("No images to process (start {}, end {}, stride {}, total {})",
+                       start_image, end_image, config_.stride, total_images_in_file);
+        return result;
+    }
+
+    const bool full = (config_.mode == ProcessMode::FullAnalysis);
+    const bool write_files = !config_.output_prefix.empty();
+
+    // Output/runtime invariants. Algorithm settings (indexing, scaling, integration, polarization,
+    // space group, unit cell, ...) are configured on experiment_ by the caller.
+    experiment_.BitDepthImage(32).PixelSigned(true);
+    experiment_.Mode(DetectorMode::Standard);
+    experiment_.OverwriteExistingFiles(true);
+    experiment_.FilePrefix(config_.output_prefix.empty() ? "output" : config_.output_prefix);
+    experiment_.SetFileWriterFormat(FileWriterFormat::NXmxLegacy);
+    experiment_.ImagesPerTrigger(images_to_process);
+    experiment_.NumTriggers(1);
+    if (full)
+        experiment_.Compression(CompressionAlgorithm::BSHUF_LZ4);
+
+    AzimuthalIntegrationMapping mapping(experiment_, pixel_mask_);
+
+    JFJochReceiverPlots plots;
+    plots.Setup(experiment_, mapping);
+
+    // Output file (NXmxIntegrated master that links back to the original images).
+    StartMessage start_message;
+    experiment_.FillMessage(start_message);
+    start_message.arm_date = dataset->arm_date;
+    start_message.az_int_bin_to_q = mapping.GetBinToQ();
+    start_message.az_int_bin_to_two_theta = mapping.GetBinToTwoTheta();
+    start_message.az_int_q_bin_count = mapping.GetQBinCount();
+    start_message.az_int_phi_bin_count = mapping.GetAzimuthalBinCount();
+    if (mapping.GetAzimuthalBinCount() > 1)
+        start_message.az_int_bin_to_phi = mapping.GetBinToPhi();
+    start_message.pixel_mask["default"] = pixel_mask_.GetMask(experiment_);
+    if (full) {
+        start_message.rois = experiment_.ROI().ExportMetadata();
+        if (!experiment_.ROI().empty())
+            start_message.roi_map = experiment_.ExportROIMap();
+        start_message.max_spot_count = experiment_.GetMaxSpotCount();
+    }
+    start_message.master_suffix = "process";
+    start_message.file_format = FileWriterFormat::NXmxIntegrated;
+    start_message.write_master_file = true;
+    start_message.write_images = false;
+    start_message.hdf5_source_data = reader_.GetHDF5DataSource(start_image, images_to_process);
+
+    std::unique_ptr<FileWriter> writer;
+    if (write_files)
+        writer = std::make_unique<FileWriter>(start_message);
+
+    logger.Info("Processing {} images (range {}-{}, stride {}) using {} threads [{}]",
+                images_to_process, start_image, end_image, config_.stride, config_.nthreads,
+                full ? "full analysis" : "azimuthal integration");
+    if (observer)
+        observer->OnPhase(full ? "Full analysis" : "Azimuthal integration");
+
+    // Full-analysis shared engines.
+    std::unique_ptr<IndexerThreadPool> indexer_pool;
+    std::unique_ptr<IndexAndRefine> indexer;
+    if (full) {
+        indexer_pool = std::make_unique<IndexerThreadPool>(experiment_.GetIndexingSettings());
+        indexer = std::make_unique<IndexAndRefine>(experiment_, indexer_pool.get());
+        if (!config_.reference_data.empty())
+            indexer->ReferenceIntensities(config_.reference_data);
+    }
+
+    const auto start_time = std::chrono::steady_clock::now();
+
+    // First pass of two-pass rotation indexing (full analysis only).
+    if (full && config_.forced_rotation_lattice.has_value()) {
+        indexer->ForceRotationIndexerLattice(*config_.forced_rotation_lattice);
+        logger.Info("Rotation indexer lattice forced externally - skipping first pass");
+    } else if (full && config_.rotation_indexing && config_.two_pass_rotation) {
+        if (observer)
+            observer->OnPhase("Rotation indexing (first pass)");
+        const auto selected = select_equally_spaced_image_ordinals(images_to_process,
+                                                                   config_.rotation_indexing_image_count);
+        logger.Info("First-pass rotation indexing using {} images{}", selected.size(),
+                    config_.reuse_rotation_spots ? " and stored spots" : "");
+
+        for (const int ordinal: selected) {
+            if (cancelled_) break;
+            const int image_idx = start_image + ordinal * config_.stride;
+            DataMessage msg{};
+            msg.number = image_idx;
+            msg.original_number = image_idx;
+            try {
+                if (config_.reuse_rotation_spots) {
+                    msg.spots = reader_.ReadSpots(image_idx);
+                } else {
+                    auto img = reader_.GetRawImage(image_idx);
+                    if (!img) continue;
+                    MXAnalysisWithoutFPGA analysis(experiment_, mapping, pixel_mask_, *indexer);
+                    AzimuthalIntegrationProfile profile(mapping);
+                    auto first_pass = config_.spot_finding;
+                    first_pass.indexing = false;
+                    first_pass.quick_integration = false;
+                    msg.image = img->image;
+                    if (dataset->efficiency.size() > image_idx)
+                        msg.image_collection_efficiency = dataset->efficiency[image_idx];
+                    analysis.Analyze(msg, profile, first_pass);
+                }
+                indexer->AddImageToRotationIndexer(msg);
+            } catch (const std::exception &e) {
+                logger.Warning("First-pass rotation indexing failed for image {}: {}", image_idx, e.what());
+            }
+        }
+
+        if (!cancelled_ && !indexer->FinalizeRotationIndexing().has_value())
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "Two-pass rotation indexing failed");
+        if (!cancelled_)
+            logger.Info("Two-pass rotation indexing found lattice");
+    }
+
+    // Main per-image loop, spread over N worker threads pulling from a shared counter. HDF5 reads
+    // are serialized by the global hdf5_mutex; the analysis runs in parallel.
+    std::atomic<int> next_ordinal = 0;
+    std::atomic<int> finished_count = 0;
+    std::atomic<uint64_t> total_uncompressed_bytes = 0;
+
+    auto azint_worker = [&]() {
+        std::vector<uint8_t> decompression_buffer;
+        ImagePreprocessorCPU preprocessor(experiment_, pixel_mask_);
+        ImagePreprocessorBuffer buffer(experiment_.GetPixelsNum());
+        AzIntEngineCPU azint(mapping);
+        AzimuthalIntegrationProfile profile(mapping);
+
+        while (!cancelled_) {
+            const int ordinal = next_ordinal.fetch_add(1);
+            const int image_idx = start_image + ordinal * config_.stride;
+            if (image_idx >= end_image) break;
+
+            std::shared_ptr<JFJochReaderRawImage> img;
+            try {
+                img = reader_.GetRawImage(image_idx);
+            } catch (const std::exception &e) {
+                logger.Error("Failed to load image {}: {}", image_idx, e.what());
+                continue;
+            }
+            if (!img) continue;
+
+            DataMessage msg{};
+            msg.image = img->image;
+            msg.number = ordinal;
+            msg.original_number = image_idx;
+            if (dataset->efficiency.size() > image_idx)
+                msg.image_collection_efficiency = dataset->efficiency[image_idx];
+            total_uncompressed_bytes += msg.image.GetUncompressedSize();
+
+            const auto t0 = std::chrono::steady_clock::now();
+            try {
+                const uint8_t *image_ptr = msg.image.GetUncompressedPtr(decompression_buffer);
+                preprocessor.Analyze(buffer, image_ptr, msg.image.GetMode());
+                azint.Run(buffer, profile);
+            } catch (const std::exception &e) {
+                logger.Error("Error integrating image {}: {}", image_idx, e.what());
+                continue;
+            }
+            msg.azint_time_s = std::chrono::duration<float>(std::chrono::steady_clock::now() - t0).count();
+            msg.processing_time_s = msg.azint_time_s;
+            msg.az_int_profile = profile.GetResult();
+            msg.az_int_profile_count = profile.GetPixelCount();
+            msg.az_int_profile_std = profile.GetStd();
+            msg.bkg_estimate = profile.GetBkgEstimate(mapping.Settings());
+            msg.run_number = experiment_.GetRunNumber();
+            msg.run_name = experiment_.GetRunName();
+
+            plots.Add(msg, profile);
+            if (writer) writer->Write(msg);
+            if (observer) observer->OnImageProcessed(msg);
+            const int done = finished_count.fetch_add(1) + 1;
+            if (observer) observer->OnProgress(done, images_to_process);
+        }
+    };
+
+    auto full_worker = [&]() {
+        pin_gpu();   // round-robin per worker thread; must precede engine construction
+        MXAnalysisWithoutFPGA analysis(experiment_, mapping, pixel_mask_, *indexer);
+        AzimuthalIntegrationProfile profile(mapping);
+
+        while (!cancelled_) {
+            const int ordinal = next_ordinal.fetch_add(1);
+            const int image_idx = start_image + ordinal * config_.stride;
+            if (image_idx >= end_image) break;
+
+            std::shared_ptr<JFJochReaderRawImage> img;
+            try {
+                img = reader_.GetRawImage(image_idx);
+            } catch (const std::exception &e) {
+                logger.Error("Failed to load image {}: {}", image_idx, e.what());
+                continue;
+            }
+            if (!img) continue;
+
+            DataMessage msg{};
+            msg.image = img->image;
+            msg.number = ordinal;
+            msg.original_number = image_idx;
+            if (dataset->efficiency.size() > image_idx)
+                msg.image_collection_efficiency = dataset->efficiency[image_idx];
+            total_uncompressed_bytes += msg.image.GetUncompressedSize();
+
+            const auto t0 = std::chrono::steady_clock::now();
+            try {
+                analysis.Analyze(msg, profile, config_.spot_finding);
+            } catch (const std::exception &e) {
+                logger.Error("Error analyzing image {}: {}", image_idx, e.what());
+                continue;
+            }
+            msg.processing_time_s = std::chrono::duration<float>(std::chrono::steady_clock::now() - t0).count();
+            msg.run_number = experiment_.GetRunNumber();
+            msg.run_name = experiment_.GetRunName();
+
+            plots.Add(msg, profile);
+            if (writer) writer->Write(msg);
+            if (observer) observer->OnImageProcessed(msg);
+            const int done = finished_count.fetch_add(1) + 1;
+            if (observer) observer->OnProgress(done, images_to_process);
+        }
+    };
+
+    if (observer)
+        observer->OnPhase("Processing images");
+
+    std::function<void()> worker = full ? std::function<void()>(full_worker)
+                                        : std::function<void()>(azint_worker);
+    std::vector<std::future<void> > futures;
+    futures.reserve(config_.nthreads);
+    for (int i = 0; i < config_.nthreads; ++i)
+        futures.push_back(std::async(std::launch::async, worker));
+    for (auto &f: futures)
+        f.get();
+
+    const auto end_time = std::chrono::steady_clock::now();
+    result.cancelled = cancelled_;
+    result.images_processed = finished_count.load();
+    result.processing_time_s = std::chrono::duration<double>(end_time - start_time).count();
+    if (result.processing_time_s > 0.0) {
+        result.frame_rate_hz = static_cast<double>(result.images_processed) / result.processing_time_s;
+        result.throughput_MBs = static_cast<double>(total_uncompressed_bytes) / (result.processing_time_s * 1e6);
+    }
+    result.mean_processing_time = plots.GetMeanProcessingTime();
+    result.indexing_rate = plots.GetIndexingRate();
+
+    // End message (also written to the file).
+    EndMessage end_msg;
+    end_msg.max_image_number = result.images_processed;
+    end_msg.images_collected_count = result.images_processed;
+    end_msg.images_sent_to_write_count = result.images_processed;
+    end_msg.end_date = time_UTC(std::chrono::system_clock::now());
+    end_msg.run_number = experiment_.GetRunNumber();
+    end_msg.run_name = experiment_.GetRunName();
+    end_msg.bkg_estimate = plots.GetBkgEstimate();
+    end_msg.az_int_result["dataset"] = plots.GetAzIntProfile();
+    end_msg.indexing_rate = result.indexing_rate;
+
+    if (full && !cancelled_) {
+        if (const auto rot = indexer->FinalizeRotationIndexing(); rot.has_value()) {
+            end_msg.rotation_lattice = rot->lattice;
+            end_msg.rotation_lattice_type = LatticeMessage{
+                .centering = rot->search_result.centering,
+                .niggli_class = rot->search_result.niggli_class,
+                .crystal_system = rot->search_result.system
+            };
+            result.rotation_lattice_found = true;
+        }
+        result.consensus_cell = indexer->GetConsensusUnitCell();
+        end_msg.unit_cell = result.consensus_cell;
+    }
+
+    // Scaling and merging (full analysis only).
+    if (full && !cancelled_ && result.indexing_rate.has_value() && result.indexing_rate > 0
+        && (config_.run_scaling || !config_.reference_data.empty())) {
+        if (observer)
+            observer->OnPhase("Scaling and merging");
+
+        const bool pixel_refine_path =
+            experiment_.GetIndexingSettings().GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::PixelRefine;
+
+        // ScaleOnTheFly is only for the classical, no-reference path; with a reference (or
+        // PixelRefine) each image is already scaled, so we merge directly.
+        if (config_.reference_data.empty() && !pixel_refine_path) {
+            logger.Info("Running scaling ...");
+            ScalingResult scale_result(0);
+            for (int i = 0; i < config_.scaling_iter; i++) {
+                auto merge_result = MergeAll(experiment_, indexer->GetIntegrationOutcome(), false);
+                scale_result = indexer->ScaleAllImages(merge_result);
+            }
+        }
+
+        MergeOnTheFly merge_engine(experiment_);
+        if (result.consensus_cell.has_value())
+            merge_engine.ReferenceCell(*result.consensus_cell);
+        merge_engine.RefineErrorModel(indexer->GetIntegrationOutcome());
+        for (const auto &outcome: indexer->GetIntegrationOutcome())
+            merge_engine.AddImage(outcome);
+
+        auto merged_reflections = merge_engine.ExportReflections();
+        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer->GetIntegrationOutcome(),
+                                                         config_.reference_data);
+        logger.Info("Merge complete ({} unique reflections)", merged_reflections.size());
+
+        std::ostringstream stats_text;
+        if (!experiment_.GetGemmiSpaceGroup().has_value()) {
+            SearchSpaceGroupOptions sg_opts;
+            sg_opts.crystal_system.reset();
+            sg_opts.centering = '\0';
+            sg_opts.merge_friedel = experiment_.GetScalingSettings().GetMergeFriedel();
+            sg_opts.d_min_limit_A = experiment_.GetScalingSettings().GetHighResolutionLimit_A().value_or(0.0);
+            sg_opts.min_operator_cc = 0.80;
+            sg_opts.min_pairs_per_operator = 20;
+            sg_opts.min_total_compared = 100;
+            sg_opts.test_systematic_absences = true;
+            stats_text << SearchSpaceGroupResultToText(SearchSpaceGroup(merged_reflections, sg_opts)) << "\n\n";
+        }
+        stats_text << merged_statistics;
+        result.merge_statistics_text = stats_text.str();
+
+        if (result.consensus_cell && write_files)
+            WriteReflections(merged_reflections, *result.consensus_cell, experiment_, config_.output_prefix);
+    }
+
+    if (writer) {
+        writer->WriteHDF5(end_msg);
+        writer->Finalize();
+        result.written_master_path = config_.output_prefix + "_process.h5";
+    }
+
+    if (observer)
+        observer->OnPhase(cancelled_ ? "Cancelled" : "Done");
+    logger.Info("{} {} images in {:.2f} s ({:.2f} Hz)", cancelled_ ? "Cancelled after" : "Processed",
+                result.images_processed, result.processing_time_s, result.frame_rate_hz);
+    return result;
+}
diff --git a/process/JFJochProcess.h b/process/JFJochProcess.h
new file mode 100644
index 00000000..ecaf3c58
--- /dev/null
+++ b/process/JFJochProcess.h
@@ -0,0 +1,100 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <atomic>
+#include <optional>
+#include <string>
+#include <vector>
+
+#include "../common/DiffractionExperiment.h"
+#include "../common/PixelMask.h"
+#include "../common/CrystalLattice.h"
+#include "../common/Reflection.h"            // MergedReflection
+#include "../common/JFJochMessages.h"        // DataMessage
+#include "../common/JFJochReceiverPlots.h"   // MeanProcessingTime
+#include "../image_analysis/spot_finding/SpotFindingSettings.h"
+
+class JFJochHDF5Reader;
+
+// Offline reprocessing of a stored Jungfraujoch HDF5 dataset, shared by jfjoch_process,
+// jfjoch_azint and (later) the viewer. The full processing workflow lives here, not in the CLIs:
+// setup, an optional two-pass rotation-indexing pre-pass, a parallel per-image loop (std::thread),
+// an optional scaling/merging post-pass, and the _process.h5 output. The detector geometry and all
+// algorithm settings are configured on the DiffractionExperiment by the caller; ProcessConfig only
+// carries run control. Cancellable from any thread (e.g. SIGINT or a GUI button) via Cancel().
+enum class ProcessMode {
+    AzimuthalIntegration,   // preprocess + azimuthal integration only (jfjoch_azint)
+    FullAnalysis            // spot finding + indexing + refinement + integration (jfjoch_process)
+};
+
+struct ProcessConfig {
+    ProcessMode mode = ProcessMode::FullAnalysis;
+
+    int start_image = 0;
+    int end_image = -1;     // -1 => to the end of the dataset
+    int stride = 1;
+    int nthreads = 1;
+
+    // Output prefix for the _process.h5 (and scaled reflections). Empty => process without writing.
+    std::string output_prefix;
+
+    SpotFindingSettings spot_finding;   // FullAnalysis spot finding
+
+    // Rotation indexing (FullAnalysis)
+    bool rotation_indexing = false;
+    bool two_pass_rotation = true;
+    bool reuse_rotation_spots = true;
+    int rotation_indexing_image_count = 30;
+    std::optional<CrystalLattice> forced_rotation_lattice;
+
+    // Scaling / merging (FullAnalysis). reference_data (from a reference MTZ) also drives the
+    // per-image live scaling path when present.
+    bool run_scaling = false;
+    int64_t scaling_iter = 3;
+    std::vector<MergedReflection> reference_data;
+};
+
+struct ProcessResult {
+    bool cancelled = false;
+    uint64_t images_processed = 0;
+    double processing_time_s = 0.0;
+    double frame_rate_hz = 0.0;
+    double throughput_MBs = 0.0;
+    std::optional<float> indexing_rate;
+    std::optional<UnitCell> consensus_cell;
+    bool rotation_lattice_found = false;
+    MeanProcessingTime mean_processing_time{};
+    std::optional<std::string> written_master_path;
+    std::string merge_statistics_text;   // populated when scaling/merging ran
+};
+
+// Callbacks for progress and live results. Methods may be called from worker threads, so an
+// implementation must be thread-safe. The default no-ops suit the CLIs.
+class JFJochProcessObserver {
+public:
+    virtual ~JFJochProcessObserver() = default;
+    virtual void OnPhase(const std::string &phase) {}
+    virtual void OnProgress(uint64_t done, uint64_t total) {}
+    virtual void OnImageProcessed(const DataMessage &msg) {}
+};
+
+class JFJochProcess {
+    JFJochHDF5Reader &reader_;
+    DiffractionExperiment experiment_;
+    PixelMask pixel_mask_;
+    ProcessConfig config_;
+    std::atomic<bool> cancelled_{false};
+
+public:
+    JFJochProcess(JFJochHDF5Reader &reader, DiffractionExperiment experiment,
+                  PixelMask pixel_mask, ProcessConfig config);
+
+    // Runs the configured workflow to completion or until Cancel(). Throws on setup failure.
+    ProcessResult Run(JFJochProcessObserver *observer = nullptr);
+
+    // Request cancellation; safe to call from any thread (the worker loop checks between images).
+    void Cancel() { cancelled_ = true; }
+    bool IsCancelled() const { return cancelled_; }
+};
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index eb32e313..7707b3c8 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -45,6 +45,7 @@ ADD_EXECUTABLE(jfjoch_test
         ModuleSummationTest.cpp
         ZMQMetadataSocketTest.cpp
         JFJochReaderTest.cpp
+        JFJochProcessTest.cpp
         MovingAverageTest.cpp
         ImageMetadataTest.cpp
         JFJochReceiverLiteTest.cpp
@@ -77,7 +78,7 @@ ADD_EXECUTABLE(jfjoch_test
 )
 
 target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochStreamWriter
-                      JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
+                      JFJochProcess JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
                       jfjoch_xds_plugin)
 target_include_directories(jfjoch_test PRIVATE .)
 
diff --git a/tests/JFJochProcessTest.cpp b/tests/JFJochProcessTest.cpp
new file mode 100644
index 00000000..5e744016
--- /dev/null
+++ b/tests/JFJochProcessTest.cpp
@@ -0,0 +1,133 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+#include <filesystem>
+
+#include "../common/DiffractionExperiment.h"
+#include "../common/ScanResultGenerator.h"
+#include "../writer/FileWriter.h"
+#include "../reader/JFJochHDF5Reader.h"
+#include "../process/JFJochProcess.h"
+
+namespace {
+    // Write a small VDS dataset of `n` flat images and return nothing (prefix_master.h5 +
+    // prefix_data_000001.h5 land in the test working directory).
+    void WriteTestDataset(const std::string &prefix, int n) {
+        RegisterHDF5Filter();
+
+        DiffractionExperiment x(DetJF(1));
+        x.FilePrefix(prefix).ImagesPerTrigger(n).OverwriteExistingFiles(true);
+        x.BitDepthImage(16).ImagesPerFile(n).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
+        x.Compression(CompressionAlgorithm::NO_COMPRESSION);
+        x.BeamX_pxl(512).BeamY_pxl(256).DetectorDistance_mm(150).IncidentEnergy_keV(WVL_1A_IN_KEV)
+                .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
+
+        std::vector<int16_t> image(x.GetPixelsNum(), 5);
+        StartMessage start_message;
+        x.FillMessage(start_message);
+        FileWriter file_set(start_message);
+        ScanResultGenerator generator(x);
+        for (int i = 0; i < n; i++) {
+            DataMessage message{};
+            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = i;
+            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+            generator.Add(message);
+        }
+        EndMessage end_message;
+        end_message.max_image_number = n;
+        generator.FillEndMessage(end_message);
+        file_set.WriteHDF5(end_message);
+        file_set.Finalize();
+    }
+}
+
+TEST_CASE("JFJochProcess_AzInt", "[HDF5][Full]") {
+    WriteTestDataset("process_azint_in", 8);
+
+    JFJochHDF5Reader reader;
+    REQUIRE_NOTHROW(reader.ReadFile("process_azint_in_master.h5"));
+    auto dataset = reader.GetDataset();
+    REQUIRE(dataset);
+
+    ProcessConfig config;
+    config.mode = ProcessMode::AzimuthalIntegration;
+    config.nthreads = 2;
+    config.output_prefix = "process_azint_out";
+
+    JFJochProcess process(reader, dataset->experiment, dataset->pixel_mask, config);
+    ProcessResult result;
+    REQUIRE_NOTHROW(result = process.Run());
+
+    CHECK_FALSE(result.cancelled);
+    CHECK(result.images_processed == 8);
+    REQUIRE(result.written_master_path.has_value());
+
+    {
+        // The _process.h5 links back to the source images and carries an azimuthal profile per image.
+        JFJochHDF5Reader out;
+        REQUIRE_NOTHROW(out.ReadFile("process_azint_out_process.h5"));
+        CHECK(out.GetNumberOfImages() == 8);
+        std::shared_ptr<JFJochReaderImage> img;
+        REQUIRE_NOTHROW(img = out.LoadImage(0));
+        REQUIRE(img);
+        CHECK_FALSE(img->ImageData().az_int_profile.empty());
+    }
+
+    reader.Close();
+    remove("process_azint_in_master.h5");
+    remove("process_azint_in_data_000001.h5");
+    remove("process_azint_out_process.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+TEST_CASE("JFJochProcess_NoOutput", "[HDF5][Full]") {
+    WriteTestDataset("process_noout_in", 6);
+
+    JFJochHDF5Reader reader;
+    REQUIRE_NOTHROW(reader.ReadFile("process_noout_in_master.h5"));
+    auto dataset = reader.GetDataset();
+
+    // Empty output prefix => process without writing any file.
+    ProcessConfig config;
+    config.mode = ProcessMode::AzimuthalIntegration;
+    config.nthreads = 3;
+
+    JFJochProcess process(reader, dataset->experiment, dataset->pixel_mask, config);
+    auto result = process.Run();
+
+    CHECK_FALSE(result.cancelled);
+    CHECK(result.images_processed == 6);
+    CHECK_FALSE(result.written_master_path.has_value());
+
+    reader.Close();
+    remove("process_noout_in_master.h5");
+    remove("process_noout_in_data_000001.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+TEST_CASE("JFJochProcess_Cancel", "[HDF5][Full]") {
+    WriteTestDataset("process_cancel_in", 8);
+
+    JFJochHDF5Reader reader;
+    REQUIRE_NOTHROW(reader.ReadFile("process_cancel_in_master.h5"));
+    auto dataset = reader.GetDataset();
+
+    ProcessConfig config;
+    config.mode = ProcessMode::AzimuthalIntegration;
+    config.nthreads = 2;
+
+    JFJochProcess process(reader, dataset->experiment, dataset->pixel_mask, config);
+    process.Cancel();   // cancel before running: the worker loop stops immediately
+    auto result = process.Run();
+
+    CHECK(result.cancelled);
+    CHECK(result.images_processed == 0);
+    CHECK_FALSE(result.written_master_path.has_value());
+
+    reader.Close();
+    remove("process_cancel_in_master.h5");
+    remove("process_cancel_in_data_000001.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index a887d94b..d3e88ed8 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -9,7 +9,7 @@ TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
 INSTALL(TARGETS jfjoch_extract_hkl RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_process jfjoch_process.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_process JFJochReader JFJochImageAnalysis JFJochWriter)
+TARGET_LINK_LIBRARIES(jfjoch_process JFJochProcess JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_process RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_scale jfjoch_scale.cpp)
@@ -17,7 +17,7 @@ TARGET_LINK_LIBRARIES(jfjoch_scale JFJochReader JFJochImageAnalysis JFJochWriter
 INSTALL(TARGETS jfjoch_scale RUNTIME COMPONENT viewer)
 
 ADD_EXECUTABLE(jfjoch_azint jfjoch_azint.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_azint JFJochReader JFJochImageAnalysis JFJochWriter)
+TARGET_LINK_LIBRARIES(jfjoch_azint JFJochProcess JFJochReader JFJochImageAnalysis JFJochWriter)
 INSTALL(TARGETS jfjoch_azint RUNTIME COMPONENT viewer)
 
 # On Windows these CLIs get getopt/getopt_long from the vendored wingetopt shim (libc has none).
diff --git a/tools/jfjoch_azint.cpp b/tools/jfjoch_azint.cpp
index cdc1d7bd..87cdf564 100644
--- a/tools/jfjoch_azint.cpp
+++ b/tools/jfjoch_azint.cpp
@@ -1,12 +1,10 @@
 // SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
+#include <atomic>
+#include <csignal>
 #include <iostream>
 #include <string>
-#include <vector>
-#include <future>
-#include <atomic>
-#include <chrono>
 #include <optional>
 #include <algorithm>
 #include <getopt.h>
@@ -16,15 +14,8 @@
 #include "../common/Definitions.h"
 #include "../common/DiffractionExperiment.h"
 #include "../common/PixelMask.h"
-#include "../common/AzimuthalIntegrationMapping.h"
-#include "../common/AzimuthalIntegrationProfile.h"
-#include "../common/time_utc.h"
 #include "../common/print_license.h"
-#include "../image_analysis/azint/AzIntEngineCPU.h"
-#include "../image_analysis/image_preprocessing/ImagePreprocessorCPU.h"
-#include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
-#include "../common/JFJochReceiverPlots.h"
-#include "../writer/FileWriter.h"
+#include "../process/JFJochProcess.h"
 
 void print_usage() {
     std::cout << "Usage ./jfjoch_azint {<options>} <input.h5>" << std::endl;
@@ -113,6 +104,14 @@ bool parse_on_off(const char *arg, bool &out) {
     return false;
 }
 
+namespace {
+    std::atomic<JFJochProcess *> g_active_process{nullptr};
+    void handle_sigint(int) {
+        if (auto *p = g_active_process.load())
+            p->Cancel();
+    }
+}
+
 int main(int argc, char **argv) {
     for (int i = 0; i < argc; i++)
         std::cout << argv[i] << " ";
@@ -211,6 +210,11 @@ int main(int argc, char **argv) {
     const std::string input_file = argv[optind];
     logger.Verbose(verbose);
 
+    if (image_stride <= 0) {
+        logger.Error("Image stride must be positive");
+        exit(EXIT_FAILURE);
+    }
+
     // 1. Read input file
     JFJochHDF5Reader reader;
     try {
@@ -227,32 +231,10 @@ int main(int argc, char **argv) {
     }
     logger.Info("Loaded dataset from {}", input_file);
 
-    if (image_stride <= 0) {
-        logger.Error("Image stride must be positive");
-        exit(EXIT_FAILURE);
-    }
-
-    const uint64_t total_images_in_file = reader.GetNumberOfImages();
-    if (end_image < 0 || end_image > total_images_in_file)
-        end_image = total_images_in_file;
-
-    const int images_to_process = (end_image - start_image) / image_stride;
-    if (images_to_process <= 0) {
-        logger.Warning("No images to process (Start: {}, End: {}, Stride: {}, Total: {})",
-                       start_image, end_image, image_stride, total_images_in_file);
-        return 0;
-    }
-
-    // 2. Set up experiment - defaults come from the input file, overridden by command line
+    // 2. Build experiment: defaults from the input file, overridden by command line. Output and
+    //    runtime invariants are set inside JFJochProcess; here we only configure the geometry and
+    //    azimuthal-integration settings.
     DiffractionExperiment experiment(dataset->experiment);
-    experiment.BitDepthImage(32).PixelSigned(true);
-    experiment.Mode(DetectorMode::Standard);
-    experiment.FilePrefix(output_prefix);
-    experiment.OverwriteExistingFiles(true);
-    experiment.SetFileWriterFormat(FileWriterFormat::NXmxLegacy);
-    experiment.ImagesPerTrigger(images_to_process);
-    experiment.NumTriggers(1);
-
     if (beam_x.has_value()) experiment.BeamX_pxl(beam_x.value());
     if (beam_y.has_value()) experiment.BeamY_pxl(beam_y.value());
     if (detector_distance_mm.has_value()) experiment.DetectorDistance_mm(detector_distance_mm.value());
@@ -282,142 +264,33 @@ int main(int argc, char **argv) {
                 azint_settings.IsPolarizationCorrection() ? "on" : "off",
                 azint_settings.IsSolidAngleCorrection() ? "on" : "off");
 
-    PixelMask pixel_mask = dataset->pixel_mask;
-    AzimuthalIntegrationMapping mapping(experiment, pixel_mask);
+    // 3. Run the shared azimuthal-integration workflow.
+    ProcessConfig config;
+    config.mode = ProcessMode::AzimuthalIntegration;
+    config.start_image = start_image;
+    config.end_image = end_image;
+    config.stride = image_stride;
+    config.nthreads = nthreads;
+    config.output_prefix = output_prefix;
 
-    JFJochReceiverPlots plots;
-    plots.Setup(experiment, mapping);
+    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
 
-    // 3. Set up the output file
-    StartMessage start_message;
-    experiment.FillMessage(start_message);
-    start_message.arm_date = dataset->arm_date;
-    start_message.az_int_bin_to_q = mapping.GetBinToQ();
-    start_message.az_int_bin_to_two_theta = mapping.GetBinToTwoTheta();
-    start_message.az_int_q_bin_count = mapping.GetQBinCount();
-    start_message.az_int_phi_bin_count = mapping.GetAzimuthalBinCount();
-    if (mapping.GetAzimuthalBinCount() > 1)
-        start_message.az_int_bin_to_phi = mapping.GetBinToPhi();
-    start_message.pixel_mask["default"] = pixel_mask.GetMask(experiment);
-    start_message.master_suffix = "process";
-    start_message.file_format = FileWriterFormat::NXmxIntegrated;
-    start_message.write_master_file = true;
-    start_message.write_images = false;
-    start_message.hdf5_source_data = reader.GetHDF5DataSource(start_image, images_to_process);
+    g_active_process = &process;
+    std::signal(SIGINT, handle_sigint);
 
-    std::unique_ptr<FileWriter> writer;
+    ProcessResult result;
     try {
-        if (!output_prefix.empty())
-            writer = std::make_unique<FileWriter>(start_message);
+        result = process.Run();
     } catch (const std::exception &e) {
-        logger.Error("Failed to initialize file writer: {}", e.what());
+        logger.Error("Processing failed: {}", e.what());
         exit(EXIT_FAILURE);
     }
+    g_active_process = nullptr;
 
-    logger.Info("Starting azimuthal integration of {} images (range {}-{}) using {} threads",
-                images_to_process, start_image, end_image, nthreads);
-
-    // 4. Process images on N CPU threads
-    std::atomic<int> next_image = 0;
-    std::atomic<int> finished_count = 0;
-    std::atomic<uint64_t> total_uncompressed_bytes = 0;
-
-    const auto start_time = std::chrono::steady_clock::now();
-
-    auto worker = [&]() {
-        std::vector<uint8_t> decompression_buffer;
-        ImagePreprocessorCPU preprocessor(experiment, pixel_mask);
-        ImagePreprocessorBuffer buffer(experiment.GetPixelsNum());
-        AzIntEngineCPU azint(mapping);
-        AzimuthalIntegrationProfile profile(mapping);
-
-        while (true) {
-            const int image_ordinal = next_image.fetch_add(1);
-            const int image_idx = start_image + image_ordinal * image_stride;
-            if (image_idx >= end_image) break;
-
-            std::shared_ptr<JFJochReaderRawImage> img;
-            try {
-                img = reader.GetRawImage(image_idx);
-            } catch (const std::exception &e) {
-                logger.Error("Failed to load image {}: {}", image_idx, e.what());
-                continue;
-            }
-            if (!img) continue;
-
-            DataMessage msg{};
-            msg.image = img->image;
-            msg.number = image_ordinal;
-            msg.original_number = image_idx;
-            if (dataset->efficiency.size() > image_idx)
-                msg.image_collection_efficiency = dataset->efficiency[image_idx];
-            total_uncompressed_bytes += msg.image.GetUncompressedSize();
-
-            const auto azint_start = std::chrono::steady_clock::now();
-            try {
-                const uint8_t *image_ptr = msg.image.GetUncompressedPtr(decompression_buffer);
-                preprocessor.Analyze(buffer, image_ptr, msg.image.GetMode());
-                azint.Run(buffer, profile);
-            } catch (const std::exception &e) {
-                logger.Error("Error integrating image {}: {}", image_idx, e.what());
-                continue;
-            }
-            const auto azint_end = std::chrono::steady_clock::now();
-
-            msg.azint_time_s = std::chrono::duration<float>(azint_end - azint_start).count();
-            msg.processing_time_s = msg.azint_time_s;
-            msg.az_int_profile = profile.GetResult();
-            msg.az_int_profile_count = profile.GetPixelCount();
-            msg.az_int_profile_std = profile.GetStd();
-            msg.bkg_estimate = profile.GetBkgEstimate(mapping.Settings());
-            msg.run_number = experiment.GetRunNumber();
-            msg.run_name = experiment.GetRunName();
-
-            plots.Add(msg, profile);
-            if (writer)
-                writer->Write(msg);
-
-            const int done = finished_count.fetch_add(1) + 1;
-            if (done % 1000 == 0) {
-                const double elapsed_s = std::chrono::duration<double>(
-                    std::chrono::steady_clock::now() - start_time).count();
-                const double frame_rate_hz = (elapsed_s > 0.0) ? (done / elapsed_s) : 0.0;
-                logger.Info("Integrated {} / {} images ({:.1f} Hz)", done, images_to_process, frame_rate_hz);
-            }
-        }
-    };
-
-    std::vector<std::future<void> > futures;
-    futures.reserve(nthreads);
-    for (int i = 0; i < nthreads; ++i)
-        futures.push_back(std::async(std::launch::async, worker));
-    for (auto &f: futures)
-        f.get();
-
-    const auto end_time = std::chrono::steady_clock::now();
-
-    // 5. Finalize output file
-    EndMessage end_msg;
-    end_msg.max_image_number = images_to_process;
-    end_msg.images_collected_count = images_to_process;
-    end_msg.images_sent_to_write_count = images_to_process;
-    end_msg.end_date = time_UTC(std::chrono::system_clock::now());
-    end_msg.run_number = experiment.GetRunNumber();
-    end_msg.run_name = experiment.GetRunName();
-    end_msg.bkg_estimate = plots.GetBkgEstimate();
-    end_msg.az_int_result["dataset"] = plots.GetAzIntProfile();
-
-    if (writer) {
-        writer->WriteHDF5(end_msg);
-        writer->Finalize();
-    }
-
-    // 6. Report statistics
-    const double processing_time = std::chrono::duration<double>(end_time - start_time).count();
-    const double throughput_MBs = static_cast<double>(total_uncompressed_bytes) / (processing_time * 1e6);
-    const double frame_rate = static_cast<double>(finished_count.load()) / processing_time;
-
-    std::cout << fmt::format("Processing time:  {:.2f} s", processing_time) << std::endl;
-    std::cout << fmt::format("Frame rate:       {:.2f} Hz", frame_rate) << std::endl;
-    std::cout << fmt::format("Total throughput: {:.2f} MB/s", throughput_MBs) << std::endl;
+    // 4. Report statistics
+    std::cout << fmt::format("Processing time:  {:.2f} s", result.processing_time_s) << std::endl;
+    std::cout << fmt::format("Frame rate:       {:.2f} Hz", result.frame_rate_hz) << std::endl;
+    std::cout << fmt::format("Total throughput: {:.2f} MB/s", result.throughput_MBs) << std::endl;
+    if (result.cancelled)
+        logger.Warning("Processing was cancelled after {} images", result.images_processed);
 }
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 17174300..e9474cae 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -38,6 +38,8 @@
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
 #include "../image_analysis/WriteReflections.h"
 #include "../image_analysis/UpdateReflectionResolution.h"
+#include "../process/JFJochProcess.h"
+#include <csignal>
 
 void print_usage() {
     std::cout << "Usage jfjoch_process {<options>} <input.h5>" << std::endl;
@@ -249,31 +251,12 @@ std::optional<CrystalLattice> parse_lattice_arg(const char *arg) {
     return CrystalLattice(vals);
 }
 
-std::vector<int> select_equally_spaced_image_ordinals(int images_to_process, int requested_images) {
-    std::vector<int> ret;
-
-    if (images_to_process <= 0 || requested_images <= 0)
-        return ret;
-
-    const int n = std::min(images_to_process, requested_images);
-    ret.reserve(n);
-
-    if (n == 1) {
-        ret.push_back(0);
-        return ret;
+namespace {
+    std::atomic<JFJochProcess *> g_active_process{nullptr};
+    void handle_sigint(int) {
+        if (auto *p = g_active_process.load())
+            p->Cancel();
     }
-
-    std::set<int> unique_ordinals;
-    for (int i = 0; i < n; i++) {
-        const auto ordinal = static_cast<int>(
-            std::llround(static_cast<double>(i) * static_cast<double>(images_to_process - 1) /
-                         static_cast<double>(n - 1))
-        );
-        unique_ordinals.insert(ordinal);
-    }
-
-    ret.assign(unique_ordinals.begin(), unique_ordinals.end());
-    return ret;
 }
 
 int main(int argc, char **argv) {
@@ -741,424 +724,63 @@ int main(int argc, char **argv) {
     if (d_min_spot_finding > 0.0f)
         spot_settings.high_resolution_limit = d_min_spot_finding;
 
-    // Initialize Analysis Components
-    PixelMask pixel_mask = dataset->pixel_mask;
+    // Run the shared full-analysis workflow (rotation indexing + scaling/merging live in
+    // JFJochProcess; the experiment above carries all algorithm settings).
+    ProcessConfig config;
+    config.mode = ProcessMode::FullAnalysis;
+    config.start_image = start_image;
+    config.end_image = end_image;
+    config.stride = image_stride;
+    config.nthreads = nthreads;
+    config.output_prefix = output_prefix;
+    config.spot_finding = spot_settings;
+    config.rotation_indexing = rotation_indexing;
+    config.two_pass_rotation = two_pass_rotation;
+    config.reuse_rotation_spots = reuse_rotation_spots;
+    config.rotation_indexing_image_count = rotation_indexing_image_count;
+    config.forced_rotation_lattice = forced_rotation_lattice;
+    config.run_scaling = run_scaling;
+    config.scaling_iter = scaling_iter;
+    config.reference_data = reference_data;
 
-    // If dataset has a mask you wish to use, you might need to load it into pixel_mask here
-    // e.g. pixel_mask.LoadUserMask(dataset->pixel_mask, ...);
+    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
 
-    AzimuthalIntegrationMapping mapping(experiment, pixel_mask);
-    IndexerThreadPool indexer_pool(experiment.GetIndexingSettings());
+    g_active_process = &process;
+    std::signal(SIGINT, handle_sigint);
 
-    // Statistics collector
-    JFJochReceiverPlots plots;
-    plots.Setup(experiment, mapping);
-
-    StartMessage start_message;
-    experiment.FillMessage(start_message);
-    start_message.arm_date = dataset->arm_date; // Use original arm date
-    start_message.az_int_bin_to_q = mapping.GetBinToQ();
-    start_message.az_int_q_bin_count = mapping.GetQBinCount();
-    if (mapping.GetAzimuthalBinCount() > 1)
-        start_message.az_int_bin_to_phi = mapping.GetBinToPhi();
-
-    start_message.pixel_mask["default"] = pixel_mask.GetMask(experiment);
-    start_message.rois = experiment.ROI().ExportMetadata();
-    if (!experiment.ROI().empty())
-        start_message.roi_map = experiment.ExportROIMap();
-    start_message.max_spot_count = experiment.GetMaxSpotCount();
-    start_message.master_suffix = "process";
-
-    start_message.file_format = FileWriterFormat::NXmxIntegrated;
-    start_message.write_master_file = true;
-    start_message.write_images = false;
-    start_message.hdf5_source_data = reader.GetHDF5DataSource(start_image, images_to_process);
-
-    std::unique_ptr<FileWriter> writer;
+    ProcessResult result;
     try {
-        if (!output_prefix.empty())
-            writer = std::make_unique<FileWriter>(start_message);
+        result = process.Run();
     } catch (const std::exception &e) {
-        logger.Error("Failed to initialize file writer: {}", e.what());
+        logger.Error("Processing failed: {}", e.what());
         exit(EXIT_FAILURE);
     }
+    g_active_process = nullptr;
 
-    std::atomic<int> processed_count = 0;
-    std::atomic<uint64_t> total_uncompressed_bytes = 0;
+    if (!result.merge_statistics_text.empty())
+        std::cout << std::endl << result.merge_statistics_text << std::endl;
 
-    // Mimic JFJochReceiver lattice handling (IndexAndRefine handles the logic per thread,
-    // but we need a central accumulator or use the pool's functionality if IndexAndRefine wraps it)
-    // Here we will use per-thread IndexAndRefine which uses the shared thread pool.
-
-    auto start_time = std::chrono::steady_clock::now();
-
-    IndexAndRefine indexer(experiment, &indexer_pool);
-    if (!reference_data.empty())
-        indexer.ReferenceIntensities(reference_data);
-
-    if (forced_rotation_lattice.has_value()) {
-        indexer.ForceRotationIndexerLattice(*forced_rotation_lattice);
-        logger.Info("Rotation indexer lattice forced externally - skipping first pass indexing");
-    } else if (rotation_indexing && two_pass_rotation) {
-        const auto selected_ordinals = select_equally_spaced_image_ordinals(
-            images_to_process, rotation_indexing_image_count);
-
-        logger.Info("Running first pass rotation indexing using {} equally-spaced images{}",
-                    selected_ordinals.size(),
-                    reuse_rotation_spots ? " and stored spots" : "");
-
-        for (const auto image_ordinal: selected_ordinals) {
-            const int image_idx = start_image + image_ordinal * image_stride;
-
-            DataMessage msg{};
-            msg.number = image_idx;
-            msg.original_number = image_idx;
-
-            try {
-                if (reuse_rotation_spots) {
-                    msg.spots = reader.ReadSpots(image_idx);
-                } else {
-                    auto img = reader.GetRawImage(image_idx);
-                    if (!img)
-                        continue;
-
-                    MXAnalysisWithoutFPGA analysis(experiment, mapping, pixel_mask, indexer);
-                    AzimuthalIntegrationProfile profile(mapping);
-
-                    auto first_pass_spot_settings = spot_settings;
-                    first_pass_spot_settings.indexing = false;
-                    first_pass_spot_settings.quick_integration = false;
-
-                    msg.image = img->image;
-                    if (dataset->efficiency.size() > image_idx)
-                        msg.image_collection_efficiency = dataset->efficiency[image_idx];
-
-                    analysis.Analyze(msg, profile, first_pass_spot_settings);
-                }
-               indexer.AddImageToRotationIndexer(msg);
-            } catch (const std::exception &e) {
-                logger.Warning("Failed to add image {} to first-pass rotation indexing: {}", image_idx, e.what());
-            }
-        }
-
-        const auto rotation_indexing_result = indexer.FinalizeRotationIndexing();
-
-        if (!rotation_indexing_result.has_value()) {
-            logger.Error("Two-pass rotation indexing failed - stopping without processing images");
-            return EXIT_FAILURE;
-        }
-
-        logger.Info("Two-pass rotation indexing found lattice");
+    // Report statistics
+    std::cout << fmt::format("Processing time: {:.2f} s", result.processing_time_s) << std::endl;
+    std::cout << fmt::format("Frame rate:      {:.2f} Hz", result.frame_rate_hz) << std::endl;
+    std::cout << fmt::format("Total throughput:{:.2f} MB/s", result.throughput_MBs) << std::endl;
+    if (result.indexing_rate.has_value())
+        std::cout << fmt::format("Indexing rate:   {:.2f}%", result.indexing_rate.value() * 100.0) << std::endl;
+    if (result.consensus_cell.has_value()) {
+        const auto &c = result.consensus_cell.value();
+        std::cout << fmt::format("Unit cell:       a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
+                                 c.a, c.b, c.c, c.alpha, c.beta, c.gamma) << std::endl;
     }
 
-    std::atomic<int> finished_count = 0;
-
-    auto worker = [&](int thread_id) {
-        // Spread the per-image GPU pipeline across all visible GPUs (round-robin).
-        // Must run before building the analysis resources so their CUDA streams/engines are
-        // created on this thread's device.
-        pin_gpu();
-
-        // Thread-local analysis resources
-        MXAnalysisWithoutFPGA analysis(experiment, mapping, pixel_mask, indexer);
-
-        AzimuthalIntegrationProfile profile(mapping);
-
-        while (true) {
-            int image_ordinal = processed_count.fetch_add(1);
-            int image_idx = start_image + image_ordinal * image_stride;
-
-            if (image_idx >= end_image) break;
-
-            // Load Image
-            std::shared_ptr<JFJochReaderRawImage> img;
-            try {
-                img = reader.GetRawImage(image_idx);
-            } catch (const std::exception &e) {
-                logger.Error("Failed to load image {}: {}", image_idx, e.what());
-                continue;
-            }
-
-            if (!img) continue;
-
-            DataMessage msg{};
-
-            msg.image = img->image;
-            msg.number = image_ordinal;
-            msg.original_number = image_idx;
-            if (dataset->efficiency.size() > image_idx) msg.image_collection_efficiency = dataset->efficiency[image_idx];
-
-            total_uncompressed_bytes += msg.image.GetUncompressedSize();
-
-            auto image_start_time = std::chrono::high_resolution_clock::now();
-
-            // Analyze
-            try {
-                analysis.Analyze(msg, profile, spot_settings);
-            } catch (const std::exception &e) {
-                logger.Error("Error analyzing image {}: {}", image_idx, e.what());
-                continue;
-            }
-
-            auto image_end_time = std::chrono::high_resolution_clock::now();
-            std::chrono::duration<float> image_duration = image_end_time - image_start_time;
-
-            msg.processing_time_s = image_duration.count();
-            msg.run_number = experiment.GetRunNumber();
-            msg.run_name = experiment.GetRunName();
-
-            plots.Add(msg, profile);
-            // Write Result
-            if (writer)
-                writer->Write(msg);
-
-            finished_count.fetch_add(1);
-
-            // Progress log
-            if (image_ordinal > 0 && image_ordinal % 100 == 0) {
-                std::optional<float> indexing_rate = plots.GetIndexingRate();
-
-                const auto now = std::chrono::steady_clock::now();
-                const double elapsed_s = std::chrono::duration<double>(now - start_time).count();
-                const int processed_images = finished_count.load();
-                const double frame_rate_hz = (elapsed_s > 0.0) ? (processed_images / elapsed_s) : 0.0;
-
-                if (indexing_rate.has_value()) {
-                    logger.Info("Processed {} / {} images ({:.2f} Hz, indexing rate {:.1f}%)",
-                                image_ordinal, images_to_process,
-                                frame_rate_hz,
-                                indexing_rate.value() * 100.0f);
-                } else {
-                    logger.Info("Processed {} / {} images ({:.2f} Hz, indexing rate N/A)",
-                                image_ordinal, images_to_process,
-                                frame_rate_hz);
-                }
-            }
-        }
-
-        // Finalize per-thread indexing (if any per-thread aggregation is needed, though pool handles most)
-        // IndexAndRefine doesn't have a per-thread finalize that returns a lattice,
-        // the main lattice determination is usually done on the aggregated results in the pool or main thread
-    };
-
-    // Launch threads
-    std::vector<std::future<void> > futures;
-    futures.reserve(nthreads);
-    for (int i = 0; i < nthreads; ++i) {
-        futures.push_back(std::async(std::launch::async, worker, i));
-    }
-
-    // Wait for completion
-    for (auto &f: futures) {
-        f.get();
-    }
-
-    auto end_time = std::chrono::steady_clock::now();
-
-    // 5. Finalize Statistics and Write EndMessage
-    EndMessage end_msg;
-    end_msg.max_image_number = images_to_process;
-    end_msg.images_collected_count = images_to_process;
-    end_msg.images_sent_to_write_count = images_to_process;
-    end_msg.end_date = time_UTC(std::chrono::system_clock::now());
-    end_msg.run_number = experiment.GetRunNumber();
-    end_msg.run_name = experiment.GetRunName();
-
-    // Gather statistics from plots
-    end_msg.bkg_estimate = plots.GetBkgEstimate();
-    end_msg.indexing_rate = plots.GetIndexingRate();
-    end_msg.az_int_result["dataset"] = plots.GetAzIntProfile();
-
-    // Finalize Indexing (Global) to get rotation lattice
-    // We create a temporary IndexAndRefine to call Finalize() which aggregates pool results
-    const auto rotation_indexer_ret = indexer.FinalizeRotationIndexing();
-
-    if (rotation_indexer_ret.has_value()) {
-        end_msg.rotation_lattice = rotation_indexer_ret->lattice;
-        end_msg.rotation_lattice_type = LatticeMessage{
-            .centering = rotation_indexer_ret->search_result.centering,
-            .niggli_class = rotation_indexer_ret->search_result.niggli_class,
-            .crystal_system = rotation_indexer_ret->search_result.system
-        };
-        logger.Info("Rotation Indexing found lattice");
-    }
-
-    std::vector<uint8_t> merging_mask_uc(images_to_process, 1);
-
-    auto consensus_start_time = std::chrono::steady_clock::now();
-    const auto consensus_cell = indexer.GetConsensusUnitCell();
-    auto consensus_end_time = std::chrono::steady_clock::now();
-    auto consensus_duration = std::chrono::duration<double>(consensus_end_time - consensus_start_time).count();
-
-    if (consensus_cell) {
-        logger.Info("Consensus unit cell found in {:.2f} ms", consensus_duration * 1e3);
-        logger.Info("UC:         a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
-                        consensus_cell->a, consensus_cell->b, consensus_cell->c,
-                        consensus_cell->alpha, consensus_cell->beta, consensus_cell->gamma);
-    } else
-        logger.Info("Consensus unit cell not found - calculation tool {:.2f} ms", consensus_duration * 1e3);
-    end_msg.unit_cell = consensus_cell;
-
-    if (end_msg.indexing_rate.has_value()
-        && end_msg.indexing_rate > 0
-        && (run_scaling || !reference_data.empty())) {
-
-        const bool pixel_refine_path =
-            (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine);
-
-        // Scaling is only the classical, no-reference ScaleOnTheFly post-pass.
-        // - With a reference (classical path): per-image live scaling already ran.
-        // - With PixelRefine: each image was scaled by PixelRefine itself.
-        // In both of those cases we must NOT run ScaleOnTheFly again - we go
-        // straight to merging on the per-image image_scale_corr.
-        if (reference_data.empty() && !pixel_refine_path) {
-            logger.Info("Running scaling ...");
-            ScalingResult scale_result(0);
-
-            auto scale_start = std::chrono::steady_clock::now();
-            for (int i = 0; i < scaling_iter; i++) {
-                auto iter_start = std::chrono::steady_clock::now();
-                auto merge_result = MergeAll(experiment, indexer.GetIntegrationOutcome(), false);
-                scale_result = indexer.ScaleAllImages(merge_result);
-                scale_result.SaveToFile(output_prefix + "_iter" + std::to_string(i) + "_scale.dat");
-                auto iter_end = std::chrono::steady_clock::now();
-                double iter_time = std::chrono::duration<double>(iter_end - iter_start).count();
-                logger.Info("Scaling iteration {} took {:.3f} seconds", i, iter_time);
-            }
-
-            end_msg.image_scale_factor = scale_result.image_scale_g;
-            end_msg.image_scale_cc = scale_result.image_cc;
-            end_msg.image_scale_mosaicity = scale_result.mosaicity_deg;
-            end_msg.image_scale_b_factor = scale_result.image_bfactor_Ang2;
-
-            auto scale_end = std::chrono::steady_clock::now();
-            double scale_time = std::chrono::duration<double>(scale_end - scale_start).count();
-            logger.Info("Scaling completed in {:.2f} s", scale_time);
-        } else if (pixel_refine_path) {
-            logger.Info("PixelRefine scaled each image during processing; merging directly (no ScaleOnTheFly)");
-        } else {
-            logger.Info("Reference provided: per-image live scaling already applied; merging directly");
-        }
-
-        // --- Phase 1 diagnostic: distribution of the per-image scale CC vs the
-        // reference. High per-image CC with low merged CC1/2 => each image is fine
-        // and the cross-image merge is the problem; low per-image CC => the
-        // per-image extraction itself is noise. Logged for any reference run.
-        {
-            std::vector<float> ccs;
-            for (const auto &i : indexer.GetIntegrationOutcome())
-                if (i.image_scale_cc && std::isfinite(*i.image_scale_cc))
-                    ccs.push_back(*i.image_scale_cc);
-            if (!ccs.empty()) {
-                std::sort(ccs.begin(), ccs.end());
-                const double mean = std::accumulate(ccs.begin(), ccs.end(), 0.0) / ccs.size();
-                auto q = [&](double f) { return ccs[std::min(ccs.size() - 1, static_cast<size_t>(f * ccs.size()))]; };
-                logger.Info("Per-image scale CC vs reference: n={} mean={:.3f} median={:.3f} "
-                            "p10={:.3f} p90={:.3f} min={:.3f} max={:.3f}",
-                            ccs.size(), mean, q(0.5), q(0.1), q(0.9), ccs.front(), ccs.back());
-            } else {
-                logger.Info("Per-image scale CC vs reference: none available");
-            }
-        }
-
-        auto merge_start = std::chrono::steady_clock::now();
-
-        MergeOnTheFly merge_engine(experiment);
-        if (consensus_cell.has_value())
-            merge_engine.ReferenceCell(*consensus_cell);
-        // Fit the global error model (sigma'^2 = a*sigma^2 + (b*I)^2, XDS form) from the
-        // spread of symmetry equivalents before merging, so the merged sigmas reflect the
-        // real scatter rather than counting statistics alone.
-        merge_engine.RefineErrorModel(indexer.GetIntegrationOutcome());
-        if (merge_engine.ErrorModelActive()) {
-            const double a = merge_engine.ErrorModelA();
-            const double b = merge_engine.ErrorModelB();
-            const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
-            logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
-        }
-        const auto &merge_outcomes = indexer.GetIntegrationOutcome();
-        std::vector<char> dcch_reject;
-        if (delta_cchalf_nsigma) {
-            dcch_reject = merge_engine.DeltaCChalfReject(merge_outcomes, *delta_cchalf_nsigma);
-            const size_t nrej = std::count(dcch_reject.begin(), dcch_reject.end(), static_cast<char>(1));
-            logger.Info("CC1/2-delta rejection (deltaCChalf < mean - {:.1f} stddev) removed {} / {} images",
-                        *delta_cchalf_nsigma, nrej, dcch_reject.size());
-        }
-        for (size_t i = 0; i < merge_outcomes.size(); ++i) {
-            if (!dcch_reject.empty() && dcch_reject[i])
-                continue;
-            merge_engine.AddImage(merge_outcomes[i]);
-        }
-        if (merge_engine.RejectedCount() > 0)
-            logger.Info("Outlier rejection (>{:.1f} sigma from the per-reflection median) removed {} observations",
-                        experiment.GetScalingSettings().GetOutlierRejectNsigma(), merge_engine.RejectedCount());
-
-        auto merged_reflections = merge_engine.ExportReflections();
-        auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);
-
-        auto merge_end = std::chrono::steady_clock::now();
-        double merge_time = std::chrono::duration<double>(merge_end - merge_start).count();
-
-        logger.Info("Merge completed in {:.2f} s ({} unique reflections)", merge_time, merged_reflections.size());
-
-        if (!experiment.GetGemmiSpaceGroup().has_value()) {
-            logger.Info("Searching for space group from P1-merged reflections ...");
-
-            SearchSpaceGroupOptions sg_opts;
-            sg_opts.crystal_system.reset();
-            sg_opts.centering = '\0';
-            sg_opts.merge_friedel = experiment.GetScalingSettings().GetMergeFriedel();
-            sg_opts.d_min_limit_A = experiment.GetScalingSettings().GetHighResolutionLimit_A().value_or(0.0);
-            sg_opts.min_i_over_sigma = 0.0;
-            sg_opts.min_operator_cc = 0.80;
-            sg_opts.min_pairs_per_operator = 20;
-            sg_opts.min_total_compared = 100;
-            sg_opts.test_systematic_absences = true;
-
-            const auto sg_search = SearchSpaceGroup(merged_reflections, sg_opts);
-
-            std::cout << std::endl << SearchSpaceGroupResultToText(sg_search) << std::endl << std::endl;
-        }
-
-        std::cout << merged_statistics;
-
-        if (consensus_cell && !output_prefix.empty())
-            WriteReflections(merged_reflections, *consensus_cell, experiment, output_prefix);
-    }
-
-    // Write End Message
-    if (writer) {
-        writer->WriteHDF5(end_msg);
-        auto stats = writer->Finalize();
-    }
-
-    // 6. Report Statistics to Console
-    double processing_time = std::chrono::duration<double>(end_time - start_time).count();
-    double throughput_MBs = static_cast<double>(total_uncompressed_bytes) / (processing_time * 1e6);
-    double frame_rate = static_cast<double>(images_to_process) / processing_time;
-
-    std::cout << fmt::format("Processing time: {:.2f} s", processing_time) << std::endl;
-    std::cout << fmt::format("Frame rate:      {:.2f} Hz", frame_rate) << std::endl;
-    std::cout << fmt::format("Total throughput:{:.2f} MB/s", throughput_MBs) << std::endl;
-
-    // Print extended stats similar to Receiver
-    if (end_msg.indexing_rate.has_value()) {
-        std::cout << fmt::format("Indexing rate:   {:.2f}%", end_msg.indexing_rate.value() * 100.0) << std::endl;
-    }
-
-    auto image_mean_time = plots.GetMeanProcessingTime();
+    const auto &t = result.mean_processing_time;
     std::cout << fmt::format(
-        "Per-image time: (mean; milliseconds): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} scaling {:.2f} total {:.2f}",
-        image_mean_time.compression * 1e3,
-        image_mean_time.preprocessing * 1e3,
-        image_mean_time.azint * 1e3,
-        image_mean_time.spot_finding * 1e3,
-        image_mean_time.indexing * 1e3,
-        image_mean_time.refinement * 1e3,
-        image_mean_time.indexing_analysis * 1e3,
-        image_mean_time.bragg_prediction * 1e3,
-        image_mean_time.integration * 1e3,
-        image_mean_time.image_scale * 1e3,
-        image_mean_time.processing * 1e3)
-    << std::endl;
+        "Per-image time (mean; ms): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} "
+        "indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} "
+        "scaling {:.2f} total {:.2f}",
+        t.compression * 1e3, t.preprocessing * 1e3, t.azint * 1e3, t.spot_finding * 1e3,
+        t.indexing * 1e3, t.refinement * 1e3, t.indexing_analysis * 1e3, t.bragg_prediction * 1e3,
+        t.integration * 1e3, t.image_scale * 1e3, t.processing * 1e3) << std::endl;
+
+    if (result.cancelled)
+        logger.Warning("Processing was cancelled after {} images", result.images_processed);
 }
-- 
2.52.0


From 39599bc090b531f797acdb7c18920a15ecbf09e5 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 14:16:34 +0200
Subject: [PATCH 176/228] tests: git-LFS large-dataset harness + jfjoch_process
 include cleanup

- .gitattributes tracks tests/data/*.h5 via git-LFS for big reference datasets.
- tests/TestData.h resolves tests/data files and reports absent / unfetched-LFS-pointer
  so tests can SKIP() instead of failing; tests/data/README.md documents fetching + the
  expected lyso_rotation/lyso_serial datasets.
- JFJochProcessLargeTest: a Catch start-up listener that prints dataset availability, plus
  [large] full-analysis runs (rotation indexing + serial) that SKIP when data is absent.
  Verified against the real 1800-image lyso rotation set (100% indexing, cell 78.2/78.2/37.8)
  and skips cleanly without it.
- jfjoch_process.cpp: drop the ~15 now-unused workflow includes left after the JFJochProcess
  extraction.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .gitattributes                   |   3 +
 tests/CMakeLists.txt             |   2 +
 tests/JFJochProcessLargeTest.cpp | 120 +++++++++++++++++++++++++++++++
 tests/TestData.h                 |  28 ++++++++
 tests/data/README.md             |  35 +++++++++
 tools/jfjoch_process.cpp         |  37 ++--------
 6 files changed, 195 insertions(+), 30 deletions(-)
 create mode 100644 tests/JFJochProcessLargeTest.cpp
 create mode 100644 tests/TestData.h
 create mode 100644 tests/data/README.md

diff --git a/.gitattributes b/.gitattributes
index 717b707e..b81e799d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,2 +1,5 @@
 *.mcs filter=lfs diff=lfs merge=lfs -text
 *.mcs.gz filter=lfs diff=lfs merge=lfs -text
+
+# Large reference datasets for the [large] Catch tests (git-LFS; may not be pulled in CI).
+tests/data/*.h5 filter=lfs diff=lfs merge=lfs -text
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 7707b3c8..11c98990 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -46,6 +46,8 @@ ADD_EXECUTABLE(jfjoch_test
         ZMQMetadataSocketTest.cpp
         JFJochReaderTest.cpp
         JFJochProcessTest.cpp
+        JFJochProcessLargeTest.cpp
+        TestData.h
         MovingAverageTest.cpp
         ImageMetadataTest.cpp
         JFJochReceiverLiteTest.cpp
diff --git a/tests/JFJochProcessLargeTest.cpp b/tests/JFJochProcessLargeTest.cpp
new file mode 100644
index 00000000..e20fe7de
--- /dev/null
+++ b/tests/JFJochProcessLargeTest.cpp
@@ -0,0 +1,120 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+// End-to-end JFJochProcess runs over real JUNGFRAU datasets that are kept in git-LFS under
+// tests/data. They are tagged [large] and SKIP() when the data is not present (e.g. LFS not
+// pulled), so the default test run stays fast and CI without the data still passes.
+
+#include <catch2/catch_all.hpp>
+#include <catch2/reporters/catch_reporter_event_listener.hpp>
+#include <catch2/reporters/catch_reporter_registrars.hpp>
+
+#include <iostream>
+#include <thread>
+
+#include "TestData.h"
+#include "../common/DiffractionExperiment.h"
+#include "../common/IndexingSettings.h"
+#include "../reader/JFJochHDF5Reader.h"
+#include "../process/JFJochProcess.h"
+
+namespace {
+    // Start-up hook: report once whether the large datasets are available, so it is obvious why
+    // the [large] tests skip when they do.
+    class LargeDataListener : public Catch::EventListenerBase {
+    public:
+        using Catch::EventListenerBase::EventListenerBase;
+        void testRunStarting(Catch::TestRunInfo const &) override {
+            const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
+            const bool ser = jfjoch_test::LargeDataFile("lyso_serial_master.h5").has_value();
+            std::cout << "[jfjoch_test] large datasets in " << jfjoch_test::LargeDataDir()
+                      << ": rotation=" << (rot ? "yes" : "no")
+                      << " serial=" << (ser ? "yes" : "no")
+                      << " ([large] tests skip when absent)" << std::endl;
+        }
+    };
+
+    int default_threads() {
+        const unsigned hc = std::thread::hardware_concurrency();
+        return hc == 0 ? 4 : static_cast<int>(hc);
+    }
+}
+
+CATCH_REGISTER_LISTENER(LargeDataListener)
+
+TEST_CASE("JFJochProcess_LysoRotation", "[large]") {
+    const auto master = jfjoch_test::LargeDataFile("lyso_rotation_master.h5");
+    if (!master)
+        SKIP("lyso_rotation_master.h5 not available (git-lfs data not pulled)");
+
+    RegisterHDF5Filter();
+    JFJochHDF5Reader reader;
+    REQUIRE_NOTHROW(reader.ReadFile(*master));
+    auto dataset = reader.GetDataset();
+    REQUIRE(dataset);
+
+    DiffractionExperiment experiment(dataset->experiment);
+    IndexingSettings indexing;
+    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
+    indexing.RotationIndexing(true);
+    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
+    experiment.ImportIndexingSettings(indexing);
+
+    ProcessConfig config;
+    config.mode = ProcessMode::FullAnalysis;
+    config.nthreads = default_threads();
+    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
+    config.spot_finding.indexing = true;
+    config.rotation_indexing = true;
+    config.two_pass_rotation = true;
+    config.reuse_rotation_spots = false;   // redo spot finding (raw dataset may carry no spots)
+
+    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
+    ProcessResult result;
+    REQUIRE_NOTHROW(result = process.Run());
+
+    CHECK_FALSE(result.cancelled);
+    CHECK(result.images_processed == reader.GetNumberOfImages());
+    REQUIRE(result.indexing_rate.has_value());
+    CHECK(result.indexing_rate.value() > 0.1f);          // a real rotation series indexes well
+    CHECK(result.consensus_cell.has_value());
+
+    reader.Close();
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+TEST_CASE("JFJochProcess_LysoSerial", "[large]") {
+    const auto master = jfjoch_test::LargeDataFile("lyso_serial_master.h5");
+    if (!master)
+        SKIP("lyso_serial_master.h5 not available (git-lfs data not pulled)");
+
+    RegisterHDF5Filter();
+    JFJochHDF5Reader reader;
+    REQUIRE_NOTHROW(reader.ReadFile(*master));
+    auto dataset = reader.GetDataset();
+    REQUIRE(dataset);
+
+    DiffractionExperiment experiment(dataset->experiment);
+    IndexingSettings indexing;
+    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
+    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
+    experiment.ImportIndexingSettings(indexing);
+
+    ProcessConfig config;
+    config.mode = ProcessMode::FullAnalysis;
+    config.nthreads = default_threads();
+    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
+    config.spot_finding.indexing = true;
+
+    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
+    ProcessResult result;
+    REQUIRE_NOTHROW(result = process.Run());
+
+    CHECK_FALSE(result.cancelled);
+    CHECK(result.images_processed == reader.GetNumberOfImages());
+    REQUIRE(result.indexing_rate.has_value());
+    CHECK(result.indexing_rate.value() > 0.0f);          // serial stills: at least some hits index
+
+    reader.Close();
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
diff --git a/tests/TestData.h b/tests/TestData.h
new file mode 100644
index 00000000..9dd9ea71
--- /dev/null
+++ b/tests/TestData.h
@@ -0,0 +1,28 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <filesystem>
+#include <optional>
+#include <string>
+
+// Helpers for the large reference datasets used by the [large] Catch tests. The datasets live
+// under <repo>/tests/data and are tracked with git-LFS, so they are often NOT present (LFS not
+// pulled, e.g. in CI). Tests run from <build>/tests, so the directory is reached via ../../.
+namespace jfjoch_test {
+    inline std::string LargeDataDir() { return "../../tests/data"; }
+
+    // Path to a large dataset file if it is present and looks like real data rather than an
+    // unfetched git-LFS pointer (those are tiny text stubs); std::nullopt otherwise. Tests should
+    // SKIP() when this returns nullopt.
+    inline std::optional<std::string> LargeDataFile(const std::string &name) {
+        const std::string path = LargeDataDir() + "/" + name;
+        std::error_code ec;
+        if (!std::filesystem::is_regular_file(path, ec))
+            return std::nullopt;
+        if (ec || std::filesystem::file_size(path, ec) < 4096 || ec)
+            return std::nullopt;   // an LFS pointer file is well under 4 kB; an HDF5 master is not
+        return path;
+    }
+}
diff --git a/tests/data/README.md b/tests/data/README.md
new file mode 100644
index 00000000..9a711c5d
--- /dev/null
+++ b/tests/data/README.md
@@ -0,0 +1,35 @@
+# Large reference test datasets (git-LFS)
+
+The `[large]` Catch tests in `tests/` run the full analysis/processing pipeline over real
+JUNGFRAU datasets that are too big to keep as ordinary git blobs. They are tracked with
+**git-LFS** (see the `tests/data/*.h5` rule in the top-level `.gitattributes`).
+
+These files are **not required** to build or to run the normal test suite: every test that
+needs them resolves the path through `jfjoch_test::LargeDataFile()` (`tests/TestData.h`) and
+`SKIP()`s when the file is absent or is still an unfetched LFS pointer. `jfjoch_test` also
+prints, at start-up, whether this directory is populated.
+
+## Fetching
+
+```
+git lfs install
+git lfs pull            # or: git lfs pull --include "tests/data/*.h5"
+```
+
+## Expected files
+
+Place each dataset's master **and its `_data_NNNNNN.h5` files** in this directory:
+
+| File                          | Dataset                                  |
+|-------------------------------|------------------------------------------|
+| `lyso_rotation_master.h5`     | lysozyme rotation series (~1800 images)  |
+| `lyso_serial_master.h5`       | lysozyme serial / jet stills (~5000 images) |
+
+To point the tests at an existing local dataset without copying, symlink it:
+
+```
+ln -s /path/to/your_master.h5            tests/data/lyso_rotation_master.h5
+ln -s /path/to/your_data_000001.h5       tests/data/...
+```
+
+(The master references its data files by relative name, so keep them side by side.)
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index e9474cae..519fc328 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -1,45 +1,22 @@
 // SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
 // SPDX-License-Identifier: GPL-3.0-only
 
-#include <iostream>
-#include <vector>
-#include <string>
-#ifndef _WIN32
-#include <unistd.h>   // not on MSVC; only pulled getopt transitively on Linux (<getopt.h> below)
-#endif
-#include <future>
-#include <mutex>
-#include <atomic>
-#include <chrono>
-#include <fstream>
-#include <sstream>
-#include <getopt.h>
 #include <algorithm>
-#include <numeric>
-#include <cmath>
-#include <set>
+#include <atomic>
+#include <csignal>
+#include <getopt.h>
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <vector>
 
 #include "../reader/JFJochHDF5Reader.h"
 #include "../common/Logger.h"
 #include "../common/DiffractionExperiment.h"
 #include "../common/PixelMask.h"
-#include "../common/AzimuthalIntegrationMapping.h"
-#include "../common/time_utc.h"
 #include "../common/print_license.h"
-#include "../image_analysis/MXAnalysisWithoutFPGA.h"
-#include "../image_analysis/indexing/IndexerFactory.h"
-#include "../common/CUDAWrapper.h"
-#include "../writer/FileWriter.h"
-#include "../image_analysis/IndexAndRefine.h"
-#include "../common/JFJochReceiverPlots.h"
-#include "../compression/JFJochCompressor.h"
 #include "../image_analysis/LoadFCalcFromMtz.h"
-#include "../image_analysis/scale_merge/Merge.h"
-#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
-#include "../image_analysis/WriteReflections.h"
-#include "../image_analysis/UpdateReflectionResolution.h"
 #include "../process/JFJochProcess.h"
-#include <csignal>
 
 void print_usage() {
     std::cout << "Usage jfjoch_process {<options>} <input.h5>" << std::endl;
-- 
2.52.0


From 800ffecd20dfed2e3f0614e11cdcc8f77310e136 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 14:26:48 +0200
Subject: [PATCH 177/228] process/viewer: command-line generator +
 JFJochProcessController (GUI engine)

Foundation for making processing a first-class GUI activity:

- process/JFJochProcessCommandLine: reconstruct the equivalent jfjoch_process / jfjoch_azint
  command line from a ProcessConfig + DiffractionExperiment + input path, for handing a job
  off to a cluster. Unit-tested (full + azint).
- viewer/JFJochProcessController: runs one JFJochProcess job off the GUI thread (its own private
  reader; HDF5 access is globally serialized so it is safe next to the interactive reader) and
  reports back via queued Qt signals (started/phaseChanged/progress/finished/failed). Cancel()
  forwards to JFJochProcess::Cancel(). Progress is throttled to ~200 updates per run.

The visible processing UI (jobs window + snapshot switcher + converged settings) builds on this.

Verified: tests/jfjoch_test [process]; jfjoch_viewer links and builds against JFJochProcess.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 process/CMakeLists.txt               |   2 +
 process/JFJochProcessCommandLine.cpp | 138 +++++++++++++++++++++++++++
 process/JFJochProcessCommandLine.h   |  18 ++++
 tests/JFJochProcessTest.cpp          |  48 ++++++++++
 viewer/CMakeLists.txt                |   4 +-
 viewer/JFJochProcessController.cpp   |  73 ++++++++++++++
 viewer/JFJochProcessController.h     |  57 +++++++++++
 7 files changed, 339 insertions(+), 1 deletion(-)
 create mode 100644 process/JFJochProcessCommandLine.cpp
 create mode 100644 process/JFJochProcessCommandLine.h
 create mode 100644 viewer/JFJochProcessController.cpp
 create mode 100644 viewer/JFJochProcessController.h

diff --git a/process/CMakeLists.txt b/process/CMakeLists.txt
index 4ebcbac7..17c11c0c 100644
--- a/process/CMakeLists.txt
+++ b/process/CMakeLists.txt
@@ -4,6 +4,8 @@
 ADD_LIBRARY(JFJochProcess STATIC
         JFJochProcess.cpp
         JFJochProcess.h
+        JFJochProcessCommandLine.cpp
+        JFJochProcessCommandLine.h
 )
 
 TARGET_LINK_LIBRARIES(JFJochProcess JFJochReader JFJochImageAnalysis JFJochWriter)
diff --git a/process/JFJochProcessCommandLine.cpp b/process/JFJochProcessCommandLine.cpp
new file mode 100644
index 00000000..50586ae3
--- /dev/null
+++ b/process/JFJochProcessCommandLine.cpp
@@ -0,0 +1,138 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochProcessCommandLine.h"
+#include "../common/DiffractionExperiment.h"
+
+#include <sstream>
+#include <vector>
+
+namespace {
+    std::string quote_if_needed(const std::string &s) {
+        if (s.find_first_of(" \t\"'") == std::string::npos)
+            return s;
+        std::string out = "\"";
+        for (char c: s) {
+            if (c == '"' || c == '\\')
+                out += '\\';
+            out += c;
+        }
+        out += '"';
+        return out;
+    }
+
+    const char *indexing_alg_flag(IndexingAlgorithmEnum a) {
+        switch (a) {
+            case IndexingAlgorithmEnum::FFBIDX: return "ffbidx";
+            case IndexingAlgorithmEnum::FFT:    return "fft";
+            case IndexingAlgorithmEnum::FFTW:   return "fftw";
+            case IndexingAlgorithmEnum::None:   return "none";
+            case IndexingAlgorithmEnum::Auto:
+            default:                            return "auto";
+        }
+    }
+
+    const char *refine_flag(GeomRefinementAlgorithmEnum r) {
+        switch (r) {
+            case GeomRefinementAlgorithmEnum::None:            return "none";
+            case GeomRefinementAlgorithmEnum::OrientationOnly: return "orientation";
+            case GeomRefinementAlgorithmEnum::PixelRefine:     return "pixelrefine";
+            case GeomRefinementAlgorithmEnum::BeamCenter:
+            default:                                           return "beam_and_lattice";
+        }
+    }
+
+    std::string num(double v) {
+        std::ostringstream o;
+        o << v;
+        return o.str();
+    }
+}
+
+std::string JFJochProcessCommandLine(const ProcessConfig &config,
+                                     const DiffractionExperiment &experiment,
+                                     const std::string &input_file) {
+    std::vector<std::string> args;
+    const bool azint = (config.mode == ProcessMode::AzimuthalIntegration);
+    args.emplace_back(azint ? "jfjoch_azint" : "jfjoch_process");
+
+    auto add = [&](const std::string &flag, const std::string &val) {
+        args.push_back(flag);
+        args.push_back(val);
+    };
+
+    if (!config.output_prefix.empty())
+        add("-o", config.output_prefix);
+    add("-N", std::to_string(config.nthreads));
+    if (config.start_image != 0)
+        add("-s", std::to_string(config.start_image));
+    if (config.end_image >= 0)
+        add("-e", std::to_string(config.end_image));
+    if (config.stride != 1)
+        add("-t", std::to_string(config.stride));
+
+    if (azint) {
+        const auto a = experiment.GetAzimuthalIntegrationSettings();
+        add("--min-q", num(a.GetLowQ_recipA()));
+        add("--max-q", num(a.GetHighQ_recipA()));
+        add("--q-spacing", num(a.GetQSpacing_recipA()));
+        add("--azimuthal-bins", std::to_string(a.GetAzimuthalBinCount()));
+        add("--polarization-correction", a.IsPolarizationCorrection() ? "on" : "off");
+        add("--solid-angle-correction", a.IsSolidAngleCorrection() ? "on" : "off");
+    } else {
+        const auto &sf = config.spot_finding;
+        add("--spot-sigma", num(sf.signal_to_noise_threshold));
+        add("--spot-threshold", std::to_string(sf.photon_count_threshold));
+        add("--spot-high-resolution", num(sf.high_resolution_limit));
+        add("--max-spots", std::to_string(experiment.GetMaxSpotCount()));
+
+        const auto idx = experiment.GetIndexingSettings();
+        add("-X", indexing_alg_flag(idx.GetAlgorithm()));
+        add("-r", refine_flag(idx.GetGeomRefinementAlgorithm()));
+
+        if (const auto sg = experiment.GetSpaceGroupNumber())
+            add("-S", std::to_string(*sg));
+        if (const auto uc = experiment.GetUnitCell()) {
+            std::ostringstream o;
+            o << uc->a << "," << uc->b << "," << uc->c << "," << uc->alpha << "," << uc->beta << "," << uc->gamma;
+            add("-C", o.str());
+        }
+        if (const auto bw = experiment.GetBandwidthFWHM())
+            add("--bandwidth", num(*bw));
+
+        const auto bragg = experiment.GetBraggIntegrationSettings();
+        std::ostringstream radii;
+        radii << bragg.GetR1() << "," << bragg.GetR2() << "," << bragg.GetR3();
+        add("--integration-radius", radii.str());
+
+        if (config.rotation_indexing) {
+            if (config.two_pass_rotation)
+                add("-R", std::to_string(config.rotation_indexing_image_count));
+            else
+                args.emplace_back("--single-pass-rotation");
+            if (!config.reuse_rotation_spots)
+                args.emplace_back("--redo-rotation-spots");
+        }
+
+        if (config.run_scaling) {
+            args.emplace_back("-M");
+            const auto sc = experiment.GetScalingSettings();
+            if (const auto pm = sc.GetPartialityModel())
+                add("-P", *pm == PartialityModel::Unity ? "unity" : *pm == PartialityModel::Rotation ? "rot" : "fixed");
+            if (!sc.GetMergeFriedel())
+                args.emplace_back("-A");
+            if (sc.GetRefineB())
+                args.emplace_back("-B");
+        }
+    }
+
+    args.push_back(input_file);
+
+    std::ostringstream cmd;
+    for (size_t i = 0; i < args.size(); i++) {
+        if (i)
+            cmd << ' ';
+        cmd << quote_if_needed(args[i]);
+    }
+    return cmd.str();
+}
diff --git a/process/JFJochProcessCommandLine.h b/process/JFJochProcessCommandLine.h
new file mode 100644
index 00000000..da0ad3e8
--- /dev/null
+++ b/process/JFJochProcessCommandLine.h
@@ -0,0 +1,18 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <string>
+
+#include "JFJochProcess.h"   // ProcessConfig, ProcessMode
+
+class DiffractionExperiment;
+
+// Reconstruct an equivalent jfjoch_process / jfjoch_azint command line for a configured run, so a
+// job set up in the GUI can be handed off to a cluster. Covers the settings that matter for the
+// run, not every obscure flag; geometry is taken from the input file, so geometry overrides are
+// not emitted.
+std::string JFJochProcessCommandLine(const ProcessConfig &config,
+                                     const DiffractionExperiment &experiment,
+                                     const std::string &input_file);
diff --git a/tests/JFJochProcessTest.cpp b/tests/JFJochProcessTest.cpp
index 5e744016..bf25799d 100644
--- a/tests/JFJochProcessTest.cpp
+++ b/tests/JFJochProcessTest.cpp
@@ -9,6 +9,7 @@
 #include "../writer/FileWriter.h"
 #include "../reader/JFJochHDF5Reader.h"
 #include "../process/JFJochProcess.h"
+#include "../process/JFJochProcessCommandLine.h"
 
 namespace {
     // Write a small VDS dataset of `n` flat images and return nothing (prefix_master.h5 +
@@ -131,3 +132,50 @@ TEST_CASE("JFJochProcess_Cancel", "[HDF5][Full]") {
     remove("process_cancel_in_data_000001.h5");
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
+
+TEST_CASE("JFJochProcessCommandLine_Full", "[process]") {
+    DiffractionExperiment x(DetJF(1));
+    IndexingSettings idx;
+    idx.Algorithm(IndexingAlgorithmEnum::FFT);
+    idx.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
+    x.ImportIndexingSettings(idx);
+    x.SpaceGroupNumber(96);
+
+    ProcessConfig config;
+    config.mode = ProcessMode::FullAnalysis;
+    config.nthreads = 8;
+    config.output_prefix = "run1";
+    config.end_image = 500;
+    config.rotation_indexing = true;
+    config.two_pass_rotation = true;
+    config.rotation_indexing_image_count = 30;
+    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
+
+    const std::string cmd = JFJochProcessCommandLine(config, x, "/data/lyso_master.h5");
+    CHECK(cmd.rfind("jfjoch_process", 0) == 0);
+    CHECK(cmd.find("-N 8") != std::string::npos);
+    CHECK(cmd.find("-e 500") != std::string::npos);
+    CHECK(cmd.find("-o run1") != std::string::npos);
+    CHECK(cmd.find("-X fft") != std::string::npos);
+    CHECK(cmd.find("-S 96") != std::string::npos);
+    CHECK(cmd.find("-R 30") != std::string::npos);
+    CHECK(cmd.find("/data/lyso_master.h5") != std::string::npos);
+}
+
+TEST_CASE("JFJochProcessCommandLine_AzInt", "[process]") {
+    DiffractionExperiment x(DetJF(1));
+    AzimuthalIntegrationSettings a;
+    a.AzimuthalBinCount(4);
+    x.ImportAzimuthalIntegrationSettings(a);
+
+    ProcessConfig config;
+    config.mode = ProcessMode::AzimuthalIntegration;
+    config.nthreads = 2;
+    config.output_prefix = "az";
+
+    const std::string cmd = JFJochProcessCommandLine(config, x, "in.h5");
+    CHECK(cmd.rfind("jfjoch_azint", 0) == 0);
+    CHECK(cmd.find("--azimuthal-bins 4") != std::string::npos);
+    CHECK(cmd.find("--min-q") != std::string::npos);
+    CHECK(cmd.find("in.h5") != std::string::npos);
+}
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index cab9d63c..0ecc75d1 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -29,6 +29,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         image_viewer/JFJochSimpleImage.h
         JFJochImageReadingWorker.cpp
         JFJochImageReadingWorker.h
+        JFJochProcessController.cpp
+        JFJochProcessController.h
         JFJochViewerDatasetInfo.cpp
         JFJochViewerDatasetInfo.h
         JFJochViewerSidePanel.cpp
@@ -99,7 +101,7 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::Concurrent
         Qt6::OpenGL Qt6::OpenGLWidgets
-        JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis
+        JFJochReader JFJochLogger JFJochCommon JFJochWriter JFJochImageAnalysis JFJochProcess
         fftw3f)
 
 # Native GUI app per platform: a .app bundle on macOS, GUI subsystem (no console window) on
diff --git a/viewer/JFJochProcessController.cpp b/viewer/JFJochProcessController.cpp
new file mode 100644
index 00000000..ee3e1bc1
--- /dev/null
+++ b/viewer/JFJochProcessController.cpp
@@ -0,0 +1,73 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochProcessController.h"
+#include "../reader/JFJochHDF5Reader.h"
+
+#include <QMetaType>
+
+JFJochProcessController::JFJochProcessController(QObject *parent) : QObject(parent) {
+    qRegisterMetaType<ProcessResult>("ProcessResult");
+}
+
+JFJochProcessController::~JFJochProcessController() {
+    cancel();
+    joinWorker_();
+}
+
+void JFJochProcessController::joinWorker_() {
+    if (worker_.joinable())
+        worker_.join();
+}
+
+void JFJochProcessController::start(const QString &file_path, DiffractionExperiment experiment,
+                                    PixelMask pixel_mask, ProcessConfig config) {
+    if (running_.exchange(true))
+        return;   // a job is already running
+
+    cancel_pending_ = false;
+    joinWorker_();   // reap the previous (finished) worker, if any
+    worker_ = std::thread(&JFJochProcessController::run_, this,
+                          file_path, std::move(experiment), std::move(pixel_mask), std::move(config));
+    emit started();
+}
+
+void JFJochProcessController::cancel() {
+    cancel_pending_ = true;
+    if (auto *p = active_.load())
+        p->Cancel();
+}
+
+void JFJochProcessController::run_(QString file_path, DiffractionExperiment experiment,
+                                   PixelMask pixel_mask, ProcessConfig config) {
+    try {
+        JFJochHDF5Reader reader;
+        reader.ReadFile(file_path.toStdString());
+
+        JFJochProcess process(reader, std::move(experiment), std::move(pixel_mask), std::move(config));
+        active_ = &process;
+        if (cancel_pending_)
+            process.Cancel();
+
+        ProcessResult result = process.Run(this);
+
+        active_ = nullptr;
+        running_ = false;
+        emit finished(result);
+    } catch (const std::exception &e) {
+        active_ = nullptr;
+        running_ = false;
+        emit failed(QString::fromStdString(e.what()));
+    }
+}
+
+void JFJochProcessController::OnPhase(const std::string &phase) {
+    emit phaseChanged(QString::fromStdString(phase));
+}
+
+void JFJochProcessController::OnProgress(uint64_t done, uint64_t total) {
+    // Throttle to ~200 updates so a long run does not flood the GUI event queue.
+    const uint64_t step = total > 200 ? total / 200 : 1;
+    if (done == total || done % step == 0)
+        emit progress(done, total);
+}
diff --git a/viewer/JFJochProcessController.h b/viewer/JFJochProcessController.h
new file mode 100644
index 00000000..50e0f16e
--- /dev/null
+++ b/viewer/JFJochProcessController.h
@@ -0,0 +1,57 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QObject>
+#include <QString>
+
+#include <atomic>
+#include <thread>
+
+#include "../process/JFJochProcess.h"
+#include "../common/DiffractionExperiment.h"
+#include "../common/PixelMask.h"
+
+Q_DECLARE_METATYPE(ProcessResult)
+
+// Runs one JFJochProcess job off the GUI thread and reports back via queued Qt signals. The job
+// opens its own private JFJochHDF5Reader on the file (HDF5 access is globally serialized, so this
+// is safe alongside the interactive reader), so the viewer becomes a processing frontend without
+// blocking the UI. Cancel() is forwarded to JFJochProcess::Cancel() (atomic) and works from any
+// thread / at any point of the run.
+class JFJochProcessController : public QObject, private JFJochProcessObserver {
+    Q_OBJECT
+public:
+    explicit JFJochProcessController(QObject *parent = nullptr);
+    ~JFJochProcessController() override;
+
+    bool running() const { return running_; }
+
+public slots:
+    // Start a job over `file_path` with the given (fully configured) experiment + mask + config.
+    // Ignored if a job is already running.
+    void start(const QString &file_path, DiffractionExperiment experiment,
+               PixelMask pixel_mask, ProcessConfig config);
+    void cancel();
+
+signals:
+    void started();
+    void phaseChanged(QString phase);
+    void progress(quint64 done, quint64 total);
+    void finished(ProcessResult result);
+    void failed(QString error);
+
+private:
+    // JFJochProcessObserver - called from worker threads, forwarded as queued signals.
+    void OnPhase(const std::string &phase) override;
+    void OnProgress(uint64_t done, uint64_t total) override;
+
+    void run_(QString file_path, DiffractionExperiment experiment, PixelMask pixel_mask, ProcessConfig config);
+    void joinWorker_();
+
+    std::thread worker_;
+    std::atomic<JFJochProcess *> active_{nullptr};
+    std::atomic<bool> running_{false};
+    std::atomic<bool> cancel_pending_{false};
+};
-- 
2.52.0


From 5bfa70c4a6a62fc50895255e1f92de73c2505e3e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 14:38:17 +0200
Subject: [PATCH 178/228] viewer: Processing jobs window - run jfjoch_process
 in-GUI + result snapshots

Makes the viewer a processing frontend, not just an image viewer:

- JFJochProcessingJobsWindow (menu "Processing"): a table of processing jobs on the open
  dataset. "New job" configures mode (full/azint), image count, threads, output, and (full)
  rotation indexing + scale/merge, using the viewer's current processing settings. A job can
  be Run locally (off the GUI thread via JFJochProcessController, with live status/progress and
  Cancel) or its jfjoch_process command line copied for a cluster.
- A finished local run is registered as a reader metadata snapshot and becomes the active
  dataset (bottom plots + per-image overlays follow it); "View results" / "Show original" switch
  between runs - so several settings attempts on one dataset can be compared.
- JFJochImageReadingWorker gains GetReprocessingInputs() (one locked read of file + experiment +
  mask + spot-finding settings, so jobs share the interactive settings) and
  RegisterProcessingSnapshot/SetActiveSnapshot slots + snapshotsChanged signal over the reader's
  snapshot API. Files only (not live HTTP).

First-cut / open ends: one job at a time; output lands in the working dir (FileWriter rejects
absolute prefixes); Bragg/scaling settings still use defaults until the converged settings
window lands. Viewer builds and runs (offscreen) cleanly.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         |   2 +
 viewer/JFJochImageReadingWorker.cpp           |  61 ++++
 viewer/JFJochImageReadingWorker.h             |  20 ++
 viewer/JFJochViewerWindow.cpp                 |  13 +
 viewer/windows/JFJochProcessingJobsWindow.cpp | 270 ++++++++++++++++++
 viewer/windows/JFJochProcessingJobsWindow.h   |  66 +++++
 6 files changed, 432 insertions(+)
 create mode 100644 viewer/windows/JFJochProcessingJobsWindow.cpp
 create mode 100644 viewer/windows/JFJochProcessingJobsWindow.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 0ecc75d1..728c498a 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -97,6 +97,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJochViewerReciprocalSpaceWindow.h
         windows/JFJochMagnifierWindow.cpp
         windows/JFJochMagnifierWindow.h
+        windows/JFJochProcessingJobsWindow.cpp
+        windows/JFJochProcessingJobsWindow.h
 )
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::Concurrent
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index d9cca04b..d5af4b4b 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -894,3 +894,64 @@ void JFJochImageReadingWorker::LoadSpots(int64_t start_image, int64_t end_image,
     emit spotsLoaded(result);
 }
 
+ReprocessingInputs JFJochImageReadingWorker::GetReprocessingInputs() const {
+    QMutexLocker ul(&m);
+    ReprocessingInputs in;
+    if (http_mode || current_file.isEmpty() || !current_image_ptr)
+        return in;
+    in.file = current_file;
+    in.experiment = curr_experiment;
+    in.pixel_mask = current_image_ptr->Dataset().pixel_mask;
+    in.spot_finding = spot_finding_settings;
+    in.valid = true;
+    return in;
+}
+
+void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
+    // Assumes m locked! Switch the reader's active metadata snapshot and refresh the view.
+    file_reader.SetActiveSnapshot(name.toStdString());
+    auto dataset = file_reader.GetDataset();
+    if (!dataset)
+        return;
+
+    curr_experiment = dataset->experiment;
+    curr_experiment.ImportIndexingSettings(indexing_settings);
+    curr_experiment.ImportAzimuthalIntegrationSettings(azint_settings);
+    UpdateAzint_i(dataset.get());
+    emit datasetLoaded(dataset);
+
+    QStringList names;
+    for (const auto &n: file_reader.SnapshotNames())
+        names << QString::fromStdString(n);
+    emit snapshotsChanged(names, QString::fromStdString(file_reader.ActiveSnapshot()));
+
+    if (current_image.has_value())
+        LoadImage_i(current_image.value(), current_summation);
+}
+
+void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString name, QString master_path) {
+    QMutexLocker ul(&m);
+    if (http_mode) {
+        logger.Error("Processing snapshots are only available for files");
+        return;
+    }
+    try {
+        file_reader.RegisterSnapshot(name.toStdString(), master_path.toStdString());
+        ActivateSnapshot_i(name);
+    } catch (const std::exception &e) {
+        logger.Error("Failed to register snapshot {}: {}", name.toStdString(), e.what());
+        emit fileLoadError("Snapshot error", QString::fromStdString(e.what()));
+    }
+}
+
+void JFJochImageReadingWorker::SetActiveSnapshot(QString name) {
+    QMutexLocker ul(&m);
+    if (http_mode)
+        return;
+    try {
+        ActivateSnapshot_i(name);
+    } catch (const std::exception &e) {
+        logger.Error("Failed to activate snapshot {}: {}", name.toStdString(), e.what());
+    }
+}
+
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 6ab4e7e4..dbe49f93 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -33,6 +33,15 @@ Q_DECLARE_METATYPE(std::shared_ptr<const SimpleImage>)
 Q_DECLARE_METATYPE(BrokerStatus)
 Q_DECLARE_METATYPE(ROIDefinition)
 
+// Everything a reprocessing job needs, captured from the worker's current state in one locked read.
+struct ReprocessingInputs {
+    bool valid = false;
+    QString file;
+    DiffractionExperiment experiment;
+    PixelMask pixel_mask;
+    SpotFindingSettings spot_finding;
+};
+
 class JFJochImageReadingWorker : public QObject {
     Q_OBJECT
 
@@ -122,6 +131,7 @@ private:
     void SetROIDefinition_i(const ROIDefinition &rois);
     void ApplyROIOverrideToImage_i();   // rewrite current_image_ptr's dataset with roi_override_
     void setAutoLoadMode_i(AutoloadMode mode);
+    void ActivateSnapshot_i(const QString &name);
 
 signals:
     void datasetLoaded(std::shared_ptr<const JFJochReaderDataset>);
@@ -137,11 +147,16 @@ signals:
     void brokerStatusUpdated(BrokerStatus status);
     void httpConnectionChanged(bool connected, QString addr);
     void liveRateChanged(double hz);
+    void snapshotsChanged(QStringList names, QString active);
 
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
     ~JFJochImageReadingWorker() override = default;
 
+    // Captures the current file + experiment + mask + spot-finding settings so a processing job
+    // uses exactly the same settings as interactive analysis. Thread-safe (locks the worker mutex).
+    ReprocessingInputs GetReprocessingInputs() const;
+
 private slots:
     void AutoLoadTimerExpired();
     void StatusTimerExpired();
@@ -176,4 +191,9 @@ public slots:
     void LoadCalibration(QString dataset);
     void setAutoLoadMode(AutoloadMode mode);
     void setAutoLoadJump(int64_t val);
+
+    // Register a reprocessing result (_process.h5) as a metadata snapshot over the same images and
+    // make it the active dataset; SetActiveSnapshot switches between registered snapshots.
+    void RegisterProcessingSnapshot(QString name, QString master_path);
+    void SetActiveSnapshot(QString name);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 7ec2f070..36139c4c 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -19,6 +19,7 @@
 #include "dbus/JFJochViewerAdaptor.h"
 #endif
 #include "windows/JFJochViewerProcessingWindow.h"
+#include "windows/JFJochProcessingJobsWindow.h"
 #include "windows/JFJochViewerSpotListWindow.h"
 #include "windows/JFJochViewerReflectionListWindow.h"
 #include "windows/JFJochCalibrationWindow.h"
@@ -110,6 +111,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
     auto magnifierWindow = new JFJochMagnifierWindow(this);
 
+    auto processingJobsWindow = new JFJochProcessingJobsWindow(reading_worker, this);
+
     menuBar->AddWindowEntry(tableWindow, "Image list");
     menuBar->AddWindowEntry(spotWindow, "Spot list");
     menuBar->AddWindowEntry(reflectionWindow, "Reflection list");
@@ -120,6 +123,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(azintWindow, "Azimuthal integration settings");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
+    menuBar->AddWindowEntry(processingJobsWindow, "Processing");
 
 #ifdef JFJOCH_VIEWER_DBUS
     if (dbus) {
@@ -377,6 +381,15 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(this, &JFJochViewerWindow::setAutoForeground,
             viewer, &JFJochDiffractionImage::setAutoForeground);
 
+    // Processing jobs: run jfjoch_process locally / copy a cluster command line, and surface
+    // finished runs as switchable dataset snapshots.
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::registerSnapshot,
+            reading_worker, &JFJochImageReadingWorker::RegisterProcessingSnapshot);
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::activateSnapshot,
+            reading_worker, &JFJochImageReadingWorker::SetActiveSnapshot);
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::writeStatusBar,
+            statusbar, &JFJochViewerStatusBar::display);
+
     if (!file.isEmpty())
         LoadFile(file, 0, 1, false);
 }
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
new file mode 100644
index 00000000..800553fe
--- /dev/null
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -0,0 +1,270 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochProcessingJobsWindow.h"
+#include "../../process/JFJochProcessCommandLine.h"
+
+#include <QApplication>
+#include <QCheckBox>
+#include <QClipboard>
+#include <QComboBox>
+#include <QDialog>
+#include <QDialogButtonBox>
+#include <QFileInfo>
+#include <QFormLayout>
+#include <QHeaderView>
+#include <QLineEdit>
+#include <QMessageBox>
+#include <QPushButton>
+#include <QSpinBox>
+#include <QTableWidget>
+#include <QToolBar>
+#include <QVBoxLayout>
+
+#include <thread>
+
+namespace {
+    enum Column { COL_NAME = 0, COL_MODE, COL_IMAGES, COL_STATUS, COL_INDEX, COL_CELL, COL_COUNT };
+
+    int default_threads() {
+        const unsigned hc = std::thread::hardware_concurrency();
+        return hc == 0 ? 4 : static_cast<int>(hc);
+    }
+}
+
+JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent)
+    : JFJochHelperWindow(parent), worker_(worker) {
+    setWindowTitle("Processing");
+    resize(720, 280);
+
+    controller_ = new JFJochProcessController(this);
+    connect(controller_, &JFJochProcessController::phaseChanged, this, &JFJochProcessingJobsWindow::onPhase);
+    connect(controller_, &JFJochProcessController::progress, this, &JFJochProcessingJobsWindow::onProgress);
+    connect(controller_, &JFJochProcessController::finished, this, &JFJochProcessingJobsWindow::onFinished);
+    connect(controller_, &JFJochProcessController::failed, this, &JFJochProcessingJobsWindow::onFailed);
+
+    auto *toolbar = addToolBar("Jobs");
+    toolbar->setMovable(false);
+    toolbar->addAction("New job…", this, &JFJochProcessingJobsWindow::newJob);
+    toolbar->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
+    toolbar->addSeparator();
+    toolbar->addAction("View results", this, &JFJochProcessingJobsWindow::viewResults);
+    toolbar->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
+
+    table_ = new QTableWidget(0, COL_COUNT, this);
+    table_->setHorizontalHeaderLabels({"Name", "Mode", "Images", "Status", "Index %", "Unit cell"});
+    table_->horizontalHeader()->setStretchLastSection(true);
+    table_->setSelectionBehavior(QAbstractItemView::SelectRows);
+    table_->setSelectionMode(QAbstractItemView::SingleSelection);
+    table_->setEditTriggers(QAbstractItemView::NoEditTriggers);
+    setCentralWidget(table_);
+}
+
+int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec &spec) {
+    QDialog dlg(this);
+    dlg.setWindowTitle("New processing job");
+
+    auto *mode = new QComboBox(&dlg);
+    mode->addItem("Full analysis", static_cast<int>(ProcessMode::FullAnalysis));
+    mode->addItem("Azimuthal integration", static_cast<int>(ProcessMode::AzimuthalIntegration));
+
+    auto *images = new QSpinBox(&dlg);
+    images->setRange(0, 1'000'000'000);
+    images->setValue(0);
+    images->setSpecialValueText("all");
+
+    auto *threads = new QSpinBox(&dlg);
+    threads->setRange(1, 256);
+    threads->setValue(default_threads());
+
+    auto *save = new QCheckBox("Save _process.h5", &dlg);
+    save->setChecked(true);
+
+    const QString stem = QFileInfo(inputs.file).completeBaseName().remove(QStringLiteral("_master"));
+    auto *prefix = new QLineEdit(QStringLiteral("%1_run%2").arg(stem).arg(job_counter_ + 1), &dlg);
+
+    auto *rotation = new QCheckBox("Rotation indexing (two-pass)", &dlg);
+    rotation->setChecked(inputs.experiment.GetGoniometer().has_value());
+    auto *scaling = new QCheckBox("Scale && merge", &dlg);
+
+    auto sync_full = [&] {
+        const bool full = mode->currentData().toInt() == static_cast<int>(ProcessMode::FullAnalysis);
+        rotation->setEnabled(full);
+        scaling->setEnabled(full);
+    };
+    connect(mode, &QComboBox::currentIndexChanged, &dlg, sync_full);
+    sync_full();
+
+    auto *form = new QFormLayout;
+    form->addRow("Mode", mode);
+    form->addRow("Images", images);
+    form->addRow("Threads", threads);
+    form->addRow(save);
+    form->addRow("Output prefix", prefix);
+    form->addRow(rotation);
+    form->addRow(scaling);
+
+    int result = 0;
+    auto *run = new QPushButton("Run locally", &dlg);
+    auto *copy = new QPushButton("Copy command", &dlg);
+    auto *cancel = new QPushButton("Cancel", &dlg);
+    run->setDefault(true);
+    connect(run, &QPushButton::clicked, &dlg, [&] { result = 1; dlg.accept(); });
+    connect(copy, &QPushButton::clicked, &dlg, [&] { result = 2; dlg.accept(); });
+    connect(cancel, &QPushButton::clicked, &dlg, [&] { result = 0; dlg.reject(); });
+
+    auto *buttons = new QHBoxLayout;
+    buttons->addStretch();
+    buttons->addWidget(run);
+    buttons->addWidget(copy);
+    buttons->addWidget(cancel);
+
+    auto *layout = new QVBoxLayout(&dlg);
+    layout->addLayout(form);
+    layout->addLayout(buttons);
+
+    dlg.exec();
+    if (result != 0) {
+        spec.mode = static_cast<ProcessMode>(mode->currentData().toInt());
+        spec.images = images->value();
+        spec.threads = threads->value();
+        spec.save = save->isChecked();
+        spec.prefix = prefix->text();
+        spec.rotation = rotation->isEnabled() && rotation->isChecked();
+        spec.scaling = scaling->isEnabled() && scaling->isChecked();
+    }
+    return result;
+}
+
+ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const ReprocessingInputs &inputs) const {
+    ProcessConfig config;
+    config.mode = spec.mode;
+    config.nthreads = spec.threads;
+    config.end_image = spec.images > 0 ? spec.images : -1;
+    config.output_prefix = spec.save ? spec.prefix.toStdString() : std::string();
+    config.spot_finding = inputs.spot_finding;
+    if (spec.mode == ProcessMode::FullAnalysis) {
+        config.rotation_indexing = spec.rotation;
+        config.two_pass_rotation = true;
+        config.run_scaling = spec.scaling;
+    }
+    return config;
+}
+
+void JFJochProcessingJobsWindow::newJob() {
+    const ReprocessingInputs inputs = worker_->GetReprocessingInputs();
+    if (!inputs.valid) {
+        QMessageBox::information(this, "Processing", "Open a file first (processing is not available for live HTTP data).");
+        return;
+    }
+
+    JobSpec spec;
+    const int action = askJob(inputs, spec);
+    if (action == 0)
+        return;
+
+    const ProcessConfig config = buildConfig(spec, inputs);
+
+    if (action == 2) {   // copy command line
+        const QString cmd = QString::fromStdString(
+            JFJochProcessCommandLine(config, inputs.experiment, inputs.file.toStdString()));
+        QApplication::clipboard()->setText(cmd);
+        QMessageBox::information(this, "Command line", cmd + "\n\n(copied to clipboard)");
+        return;
+    }
+
+    if (controller_->running()) {
+        QMessageBox::information(this, "Processing", "A job is already running; wait for it to finish or cancel it.");
+        return;
+    }
+
+    const bool full = spec.mode == ProcessMode::FullAnalysis;
+    const QString name = QStringLiteral("%1 %2").arg(full ? "Full" : "AzInt").arg(++job_counter_);
+
+    const int row = table_->rowCount();
+    table_->insertRow(row);
+    table_->setItem(row, COL_NAME, new QTableWidgetItem(name));
+    table_->setItem(row, COL_MODE, new QTableWidgetItem(full ? "Full" : "AzInt"));
+    table_->setItem(row, COL_IMAGES, new QTableWidgetItem(spec.images > 0 ? QString::number(spec.images) : "all"));
+    table_->setItem(row, COL_STATUS, new QTableWidgetItem("queued"));
+    table_->setItem(row, COL_INDEX, new QTableWidgetItem("-"));
+    table_->setItem(row, COL_CELL, new QTableWidgetItem("-"));
+
+    JobInfo info;
+    info.name = name;
+    if (spec.save)
+        info.snapshot_path = QString::fromStdString(config.output_prefix) + "_process.h5";
+    jobs_.push_back(info);
+    running_row_ = row;
+
+    controller_->start(inputs.file, inputs.experiment, inputs.pixel_mask, config);
+    emit writeStatusBar("Started processing job " + name);
+}
+
+void JFJochProcessingJobsWindow::cancelJob() {
+    if (controller_->running()) {
+        controller_->cancel();
+        emit writeStatusBar("Cancelling processing job…");
+    }
+}
+
+void JFJochProcessingJobsWindow::viewResults() {
+    const int row = table_->currentRow();
+    if (row < 0 || row >= static_cast<int>(jobs_.size()))
+        return;
+    if (!jobs_[row].has_result) {
+        QMessageBox::information(this, "Processing", "This job has no saved results to view.");
+        return;
+    }
+    emit activateSnapshot(jobs_[row].name);
+}
+
+void JFJochProcessingJobsWindow::showOriginal() {
+    emit activateSnapshot("Original");
+}
+
+void JFJochProcessingJobsWindow::setStatus(int row, const QString &text) {
+    if (row >= 0 && row < table_->rowCount())
+        table_->item(row, COL_STATUS)->setText(text);
+}
+
+void JFJochProcessingJobsWindow::onPhase(QString phase) {
+    if (running_row_ >= 0 && phase != "Processing images")
+        setStatus(running_row_, phase);
+}
+
+void JFJochProcessingJobsWindow::onProgress(quint64 done, quint64 total) {
+    if (running_row_ >= 0)
+        setStatus(running_row_, QStringLiteral("running %1%").arg(total ? done * 100 / total : 0));
+}
+
+void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
+    const int row = running_row_;
+    running_row_ = -1;
+    if (row < 0 || row >= static_cast<int>(jobs_.size()))
+        return;
+
+    setStatus(row, result.cancelled ? "cancelled" : "done");
+    if (result.indexing_rate.has_value())
+        table_->item(row, COL_INDEX)->setText(QStringLiteral("%1%").arg(result.indexing_rate.value() * 100.0, 0, 'f', 0));
+    if (result.consensus_cell.has_value()) {
+        const auto &c = result.consensus_cell.value();
+        table_->item(row, COL_CELL)->setText(
+            QStringLiteral("%1 %2 %3  %4 %5 %6")
+                .arg(c.a, 0, 'f', 1).arg(c.b, 0, 'f', 1).arg(c.c, 0, 'f', 1)
+                .arg(c.alpha, 0, 'f', 1).arg(c.beta, 0, 'f', 1).arg(c.gamma, 0, 'f', 1));
+    }
+
+    if (!result.cancelled && result.written_master_path.has_value() && !jobs_[row].snapshot_path.isEmpty()) {
+        jobs_[row].has_result = true;
+        emit registerSnapshot(jobs_[row].name, jobs_[row].snapshot_path);   // also activates it
+    }
+    emit writeStatusBar(result.cancelled ? "Processing cancelled" : "Processing finished");
+}
+
+void JFJochProcessingJobsWindow::onFailed(QString error) {
+    const int row = running_row_;
+    running_row_ = -1;
+    setStatus(row, "failed");
+    QMessageBox::warning(this, "Processing failed", error);
+}
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
new file mode 100644
index 00000000..a679c850
--- /dev/null
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -0,0 +1,66 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QString>
+#include <vector>
+
+#include "JFJochHelperWindow.h"
+#include "../JFJochProcessController.h"
+#include "../JFJochImageReadingWorker.h"   // ReprocessingInputs
+
+class QTableWidget;
+
+// Makes processing a first-class GUI activity: a table of processing jobs run on the current
+// dataset. A job can be run locally (off the GUI thread, via JFJochProcessController) or its
+// jfjoch_process command line copied for a cluster. A finished local run is registered as a
+// reader snapshot so its results become a selectable view of the dataset.
+class JFJochProcessingJobsWindow : public JFJochHelperWindow {
+    Q_OBJECT
+public:
+    explicit JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent = nullptr);
+
+signals:
+    void registerSnapshot(QString name, QString master_path);
+    void activateSnapshot(QString name);
+    void writeStatusBar(QString message, int timeout_ms = 0);
+
+private slots:
+    void newJob();
+    void cancelJob();
+    void viewResults();
+    void showOriginal();
+    void onPhase(QString phase);
+    void onProgress(quint64 done, quint64 total);
+    void onFinished(ProcessResult result);
+    void onFailed(QString error);
+
+private:
+    struct JobInfo {
+        QString name;
+        QString snapshot_path;   // empty unless saved
+        bool has_result = false;
+    };
+    struct JobSpec {
+        ProcessMode mode = ProcessMode::FullAnalysis;
+        int images = 0;          // 0 == all
+        int threads = 4;
+        bool save = true;
+        QString prefix;
+        bool rotation = false;
+        bool scaling = false;
+    };
+
+    // Returns 0 = cancel, 1 = run locally, 2 = copy command line; fills spec from the dialog.
+    int askJob(const ReprocessingInputs &inputs, JobSpec &spec);
+    ProcessConfig buildConfig(const JobSpec &spec, const ReprocessingInputs &inputs) const;
+    void setStatus(int row, const QString &text);
+
+    JFJochImageReadingWorker *worker_;
+    JFJochProcessController *controller_;
+    QTableWidget *table_;
+    int running_row_ = -1;
+    int job_counter_ = 0;
+    std::vector<JobInfo> jobs_;
+};
-- 
2.52.0


From ed8fb5d37cab669aa72777e13a93638ad9f64eb1 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 16:05:25 +0200
Subject: [PATCH 179/228] tests: add lyso rotation dataset (1800 images) via
 git-LFS

Real reference dataset for the [large] JFJochProcess_LysoRotation test, stored with git-LFS
(tests/data/*.h5). lyso_rotation_master.h5 is the 1800-image lysozyme rotation series
(its data files keep the names the master links to). The test indexes it at 100% with cell
~78.2/78.2/37.8; it SKIPs when the data is not pulled.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/data/fixed_data_000001.h5    | 3 +++
 tests/data/fixed_data_000002.h5    | 3 +++
 tests/data/lyso_rotation_master.h5 | 3 +++
 3 files changed, 9 insertions(+)
 create mode 100644 tests/data/fixed_data_000001.h5
 create mode 100644 tests/data/fixed_data_000002.h5
 create mode 100644 tests/data/lyso_rotation_master.h5

diff --git a/tests/data/fixed_data_000001.h5 b/tests/data/fixed_data_000001.h5
new file mode 100644
index 00000000..1d7774f7
--- /dev/null
+++ b/tests/data/fixed_data_000001.h5
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8a7bed7ebfafd8257f0cbbf9a8cdf0a05a37c83bf16a86c8e8ca9aee6bc9e872
+size 1119814999
diff --git a/tests/data/fixed_data_000002.h5 b/tests/data/fixed_data_000002.h5
new file mode 100644
index 00000000..03109107
--- /dev/null
+++ b/tests/data/fixed_data_000002.h5
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d21528332bab94bcfd4c551b54340aa9b73bba0a3d9d8b09d6579491595daacf
+size 894266381
diff --git a/tests/data/lyso_rotation_master.h5 b/tests/data/lyso_rotation_master.h5
new file mode 100644
index 00000000..7cd924a1
--- /dev/null
+++ b/tests/data/lyso_rotation_master.h5
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:53194c3b2f57fdd27a2dd183a475cb614c7f00fab7d4df7c270adb2ff9005c58
+size 10205832
-- 
2.52.0


From c916cf8b2d7fb546a17a5d747bec0e99c157f0cb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 16:46:56 +0200
Subject: [PATCH 180/228] tests: drop the serial [large] test (serial dataset
 not shipped)

Only the ~1800-image rotation dataset is kept in LFS; a separate ~5000-image serial set is too
large to ship, and the serial path can be exercised by running the rotation series in serial
mode if needed. Removes JFJochProcess_LysoSerial and the serial entry from the start-up listener
and README. The rotation [large] test now runs against the committed data and passes.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/JFJochProcessLargeTest.cpp | 40 +-------------------------------
 tests/data/README.md             | 25 ++++++++------------
 2 files changed, 11 insertions(+), 54 deletions(-)

diff --git a/tests/JFJochProcessLargeTest.cpp b/tests/JFJochProcessLargeTest.cpp
index e20fe7de..064d06ef 100644
--- a/tests/JFJochProcessLargeTest.cpp
+++ b/tests/JFJochProcessLargeTest.cpp
@@ -26,10 +26,8 @@ namespace {
         using Catch::EventListenerBase::EventListenerBase;
         void testRunStarting(Catch::TestRunInfo const &) override {
             const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
-            const bool ser = jfjoch_test::LargeDataFile("lyso_serial_master.h5").has_value();
-            std::cout << "[jfjoch_test] large datasets in " << jfjoch_test::LargeDataDir()
+            std::cout << "[jfjoch_test] large dataset in " << jfjoch_test::LargeDataDir()
                       << ": rotation=" << (rot ? "yes" : "no")
-                      << " serial=" << (ser ? "yes" : "no")
                       << " ([large] tests skip when absent)" << std::endl;
         }
     };
@@ -82,39 +80,3 @@ TEST_CASE("JFJochProcess_LysoRotation", "[large]") {
     reader.Close();
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
-
-TEST_CASE("JFJochProcess_LysoSerial", "[large]") {
-    const auto master = jfjoch_test::LargeDataFile("lyso_serial_master.h5");
-    if (!master)
-        SKIP("lyso_serial_master.h5 not available (git-lfs data not pulled)");
-
-    RegisterHDF5Filter();
-    JFJochHDF5Reader reader;
-    REQUIRE_NOTHROW(reader.ReadFile(*master));
-    auto dataset = reader.GetDataset();
-    REQUIRE(dataset);
-
-    DiffractionExperiment experiment(dataset->experiment);
-    IndexingSettings indexing;
-    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
-    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
-    experiment.ImportIndexingSettings(indexing);
-
-    ProcessConfig config;
-    config.mode = ProcessMode::FullAnalysis;
-    config.nthreads = default_threads();
-    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
-    config.spot_finding.indexing = true;
-
-    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
-    ProcessResult result;
-    REQUIRE_NOTHROW(result = process.Run());
-
-    CHECK_FALSE(result.cancelled);
-    CHECK(result.images_processed == reader.GetNumberOfImages());
-    REQUIRE(result.indexing_rate.has_value());
-    CHECK(result.indexing_rate.value() > 0.0f);          // serial stills: at least some hits index
-
-    reader.Close();
-    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
-}
diff --git a/tests/data/README.md b/tests/data/README.md
index 9a711c5d..ccf842d5 100644
--- a/tests/data/README.md
+++ b/tests/data/README.md
@@ -16,20 +16,15 @@ git lfs install
 git lfs pull            # or: git lfs pull --include "tests/data/*.h5"
 ```
 
-## Expected files
+## Datasets
 
-Place each dataset's master **and its `_data_NNNNNN.h5` files** in this directory:
+| File                       | Dataset                                 | Shipped   |
+|----------------------------|-----------------------------------------|-----------|
+| `lyso_rotation_master.h5`  | lysozyme rotation series (~1800 images) | yes (LFS) |
 
-| File                          | Dataset                                  |
-|-------------------------------|------------------------------------------|
-| `lyso_rotation_master.h5`     | lysozyme rotation series (~1800 images)  |
-| `lyso_serial_master.h5`       | lysozyme serial / jet stills (~5000 images) |
-
-To point the tests at an existing local dataset without copying, symlink it:
-
-```
-ln -s /path/to/your_master.h5            tests/data/lyso_rotation_master.h5
-ln -s /path/to/your_data_000001.h5       tests/data/...
-```
-
-(The master references its data files by relative name, so keep them side by side.)
+`lyso_rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
+drives `JFJochProcess_LysoRotation`. A separate serial dataset is intentionally **not** shipped
+to keep the repository small — the rotation series can be run in serial mode (full analysis
+without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
+data files here as real files (not symlinks, if you intend to commit them via LFS); the master
+references its data files by relative name, so keep them side by side.
-- 
2.52.0


From 74f36710e48bb8bc26b1f20a4b0db019e0f561e9 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 17:09:20 +0200
Subject: [PATCH 181/228] viewer: converge processing settings into one tabbed
 window + Bragg/scaling

One "Processing settings" window with tabs: Spot finding & indexing | Azimuthal | Bragg
integration | Scaling, replacing the two separate settings windows. The spot/index and azimuthal
tabs reuse the existing windows' widgets unchanged (their content is lifted into tabs via
takeCentralWidget), so all their logic/signals keep working; Bragg integration and scaling are new
editable panels (previously not adjustable in the GUI).

JFJochImageReadingWorker gains UpdateBraggIntegrationSettings / UpdateScalingSettings; both persist
as worker state and are re-imported into curr_experiment on file load / dataset update (like the
indexing/azint settings), so they apply to interactive analysis (Bragg) and flow into processing
jobs via GetReprocessingInputs (Bragg + scaling). Scaling only affects the job post-pass, so it is
just stored, not reanalyzed.

Verified: jfjoch_viewer builds and runs (offscreen) with the converged window.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         |  6 ++
 viewer/JFJochImageReadingWorker.cpp           | 24 +++++-
 viewer/JFJochImageReadingWorker.h             |  8 ++
 viewer/JFJochViewerWindow.cpp                 | 18 +++--
 .../windows/JFJochBraggIntegrationPanel.cpp   | 51 ++++++++++++
 viewer/windows/JFJochBraggIntegrationPanel.h  | 29 +++++++
 viewer/windows/JFJochScalingPanel.cpp         | 77 +++++++++++++++++++
 viewer/windows/JFJochScalingPanel.h           | 33 ++++++++
 viewer/windows/JFJochSettingsWindow.cpp       | 40 ++++++++++
 viewer/windows/JFJochSettingsWindow.h         | 33 ++++++++
 10 files changed, 312 insertions(+), 7 deletions(-)
 create mode 100644 viewer/windows/JFJochBraggIntegrationPanel.cpp
 create mode 100644 viewer/windows/JFJochBraggIntegrationPanel.h
 create mode 100644 viewer/windows/JFJochScalingPanel.cpp
 create mode 100644 viewer/windows/JFJochScalingPanel.h
 create mode 100644 viewer/windows/JFJochSettingsWindow.cpp
 create mode 100644 viewer/windows/JFJochSettingsWindow.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 728c498a..8bddcb3f 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -99,6 +99,12 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         windows/JFJochMagnifierWindow.h
         windows/JFJochProcessingJobsWindow.cpp
         windows/JFJochProcessingJobsWindow.h
+        windows/JFJochSettingsWindow.cpp
+        windows/JFJochSettingsWindow.h
+        windows/JFJochBraggIntegrationPanel.cpp
+        windows/JFJochBraggIntegrationPanel.h
+        windows/JFJochScalingPanel.cpp
+        windows/JFJochScalingPanel.h
 )
 
 TARGET_LINK_LIBRARIES(jfjoch_viewer Qt6::Core Qt6::Gui Qt6::Widgets Qt6::Charts Qt6::Concurrent
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index d5af4b4b..509fe1c9 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -89,10 +89,14 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
                                                    const DiffractionExperiment &experiment, QObject *parent)
     : QObject(parent),
       indexing_settings(experiment.GetIndexingSettings()),
-      azint_settings(experiment.GetAzimuthalIntegrationSettings()) {
+      azint_settings(experiment.GetAzimuthalIntegrationSettings()),
+      bragg_settings(experiment.GetBraggIntegrationSettings()),
+      scaling_settings(experiment.GetScalingSettings()) {
     qRegisterMetaType<QVector<QRect>>("QVector<QRect>");
     qRegisterMetaType<BrokerStatus>("BrokerStatus");
     qRegisterMetaType<ROIDefinition>("ROIDefinition");
+    qRegisterMetaType<BraggIntegrationSettings>("BraggIntegrationSettings");
+    qRegisterMetaType<ScalingSettings>("ScalingSettings");
     spot_finding_settings = settings;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
@@ -276,6 +280,8 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
             roi_override_.reset();   // new file: use its ROIs, forget any earlier edits
             curr_experiment.ImportIndexingSettings(indexing_settings);
             curr_experiment.ImportAzimuthalIntegrationSettings(azint_settings);
+            curr_experiment.ImportBraggIntegrationSettings(bragg_settings);
+            curr_experiment.ImportScalingSettings(scaling_settings);
             UpdateAzint_i(dataset.get());
         }
 
@@ -457,6 +463,8 @@ void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionEx
         curr_experiment.ROI().SetROI(*roi_override_);   // keep edited ROIs across settings changes
     curr_experiment.ImportIndexingSettings(indexing_settings);
     curr_experiment.ImportAzimuthalIntegrationSettings(azint_settings);
+    curr_experiment.ImportBraggIntegrationSettings(bragg_settings);
+    curr_experiment.ImportScalingSettings(scaling_settings);
     UpdateAzint_i(dataset.get());
 
     emit datasetLoaded(dataset);
@@ -579,6 +587,20 @@ void JFJochImageReadingWorker::UpdateAzintSettings(const AzimuthalIntegrationSet
     UpdateDataset_i(std::nullopt);
 }
 
+void JFJochImageReadingWorker::UpdateBraggIntegrationSettings(BraggIntegrationSettings settings) {
+    QMutexLocker locker(&m);
+    bragg_settings = settings;
+    UpdateDataset_i(std::nullopt);
+}
+
+void JFJochImageReadingWorker::UpdateScalingSettings(ScalingSettings settings) {
+    QMutexLocker locker(&m);
+    scaling_settings = settings;
+    // Scaling only affects the processing-job post-pass (jobs read curr_experiment via
+    // GetReprocessingInputs), not interactive single-image analysis - just store + import it.
+    curr_experiment.ImportScalingSettings(scaling_settings);
+}
+
 void JFJochImageReadingWorker::SetROIDefinition(const ROIDefinition &rois) {
     QMutexLocker locker(&m);
     SetROIDefinition_i(rois);
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index dbe49f93..beadf56c 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -15,6 +15,8 @@
 #include "../common/Logger.h"
 #include "../reader/JFJochHttpReader.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
+#include "../common/BraggIntegrationSettings.h"
+#include "../common/ScalingSettings.h"
 #include "../image_analysis/bragg_prediction/BraggPrediction.h"
 #include "SimpleImage.h"
 #include "../common/MovingAverage.h"
@@ -27,6 +29,8 @@ Q_DECLARE_METATYPE(DiffractionExperiment)
 Q_DECLARE_METATYPE(SpotFindingSettings)
 Q_DECLARE_METATYPE(IndexingSettings)
 Q_DECLARE_METATYPE(AzimuthalIntegrationSettings)
+Q_DECLARE_METATYPE(BraggIntegrationSettings)
+Q_DECLARE_METATYPE(ScalingSettings)
 
 Q_DECLARE_METATYPE(UnitCell)
 Q_DECLARE_METATYPE(std::shared_ptr<const SimpleImage>)
@@ -67,6 +71,8 @@ private:
     std::optional<ROIDefinition> roi_override_;
     IndexingSettings indexing_settings;
     AzimuthalIntegrationSettings azint_settings;
+    BraggIntegrationSettings bragg_settings;
+    ScalingSettings scaling_settings;
     std::unique_ptr<IndexerThreadPool> indexing;
 
     std::shared_ptr<JFJochReaderImage> current_image_ptr;
@@ -177,6 +183,8 @@ public slots:
     void UpdateSpotFindingSettings(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
     void ReanalyzeImages(bool input);
     void UpdateAzintSettings(const AzimuthalIntegrationSettings& settings);
+    void UpdateBraggIntegrationSettings(BraggIntegrationSettings settings);
+    void UpdateScalingSettings(ScalingSettings settings);
 
     void SetROIDefinition(const ROIDefinition &rois);
     void DownloadROIsFromServer();
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 36139c4c..c2948e21 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -20,6 +20,7 @@
 #endif
 #include "windows/JFJochViewerProcessingWindow.h"
 #include "windows/JFJochProcessingJobsWindow.h"
+#include "windows/JFJochSettingsWindow.h"
 #include "windows/JFJochViewerSpotListWindow.h"
 #include "windows/JFJochViewerReflectionListWindow.h"
 #include "windows/JFJochCalibrationWindow.h"
@@ -103,11 +104,13 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     auto metadataWindow = new JFJochViewerMetadataWindow(this);
     auto spotWindow = new JFJochViewerSpotListWindow(this);
     auto reflectionWindow = new JFJochViewerReflectionListWindow(this);
-    auto processingWindow = new JFJochViewerProcessingWindow(spot_finding_settings, indexing_settings, this);
+    auto settingsWindow = new JFJochSettingsWindow(spot_finding_settings, indexing_settings,
+                                                  experiment.GetAzimuthalIntegrationSettings(),
+                                                  experiment.GetBraggIntegrationSettings(),
+                                                  experiment.GetScalingSettings(), this);
     auto calibrationWindow = new JFJochCalibrationWindow(this);
     auto reciprocalWindow = new JFJochViewerReciprocalSpaceWindow(this);
 
-    auto azintWindow = new JFJochAzIntWindow(experiment.GetAzimuthalIntegrationSettings(), this);
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
     auto magnifierWindow = new JFJochMagnifierWindow(this);
 
@@ -117,10 +120,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(spotWindow, "Spot list");
     menuBar->AddWindowEntry(reflectionWindow, "Reflection list");
     menuBar->AddWindowEntry(metadataWindow, "Image metadata");
-    menuBar->AddWindowEntry(processingWindow, "Image processing settings");
+    menuBar->AddWindowEntry(settingsWindow, "Processing settings");
     menuBar->AddWindowEntry(calibrationWindow, "Calibration image viewer");
     menuBar->AddWindowEntry(reciprocalWindow, "Reciprocal space viewer");
-    menuBar->AddWindowEntry(azintWindow, "Azimuthal integration settings");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
     menuBar->AddWindowEntry(processingJobsWindow, "Processing");
@@ -260,8 +262,12 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
             reflectionWindow, &JFJochViewerReflectionListWindow::imageLoaded);
 
-    connect(processingWindow, &JFJochViewerProcessingWindow::settingsChanged,
+    connect(settingsWindow, &JFJochSettingsWindow::spotFindingChanged,
             reading_worker, &JFJochImageReadingWorker::UpdateSpotFindingSettings);
+    connect(settingsWindow, &JFJochSettingsWindow::braggChanged,
+            reading_worker, &JFJochImageReadingWorker::UpdateBraggIntegrationSettings);
+    connect(settingsWindow, &JFJochSettingsWindow::scalingChanged,
+            reading_worker, &JFJochImageReadingWorker::UpdateScalingSettings);
 
     connect(reflectionWindow, &JFJochHelperWindow::zoom, viewer, &JFJochDiffractionImage::centerOnSpot);
     connect(spotWindow, &JFJochHelperWindow::zoom, viewer, &JFJochDiffractionImage::centerOnSpot);
@@ -343,7 +349,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
             reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::setFeatureColor);
 
-    connect(azintWindow, &JFJochAzIntWindow::settingsChanged,
+    connect(settingsWindow, &JFJochSettingsWindow::azintChanged,
             reading_worker, &JFJochImageReadingWorker::UpdateAzintSettings);
 
     connect(azintImageWindow, &JFJoch2DAzintImageWindow::zoomOnBin,
diff --git a/viewer/windows/JFJochBraggIntegrationPanel.cpp b/viewer/windows/JFJochBraggIntegrationPanel.cpp
new file mode 100644
index 00000000..10fa7e64
--- /dev/null
+++ b/viewer/windows/JFJochBraggIntegrationPanel.cpp
@@ -0,0 +1,51 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochBraggIntegrationPanel.h"
+
+#include <QFormLayout>
+#include <QGroupBox>
+#include <QVBoxLayout>
+
+JFJochBraggIntegrationPanel::JFJochBraggIntegrationPanel(const BraggIntegrationSettings &settings, QWidget *parent)
+    : QWidget(parent) {
+    auto *layout = new QVBoxLayout(this);
+    auto *group = new QGroupBox("Bragg integration", this);
+    auto *form = new QFormLayout(group);
+
+    m_r1 = new SliderPlusBox(1.0, 20.0, 0.5, 1, this);
+    m_r1->setValue(settings.GetR1());
+    form->addRow("Signal box radius r1 [px]", m_r1);
+
+    m_r2 = new SliderPlusBox(1.0, 25.0, 0.5, 1, this);
+    m_r2->setValue(settings.GetR2());
+    form->addRow("Background inner radius r2 [px]", m_r2);
+
+    m_r3 = new SliderPlusBox(1.0, 30.0, 0.5, 1, this);
+    m_r3->setValue(settings.GetR3());
+    form->addRow("Background outer radius r3 [px]", m_r3);
+
+    m_profileMultiplier = new SliderPlusBox(1.0, 15.0, 0.5, 1, this);
+    m_profileMultiplier->setValue(settings.GetProfileMultiplier());
+    form->addRow("Profile multiplier (PixelRefine)", m_profileMultiplier);
+
+    m_dMin = new SliderPlusBox(0.3, 5.0, 0.1, 1, this);
+    m_dMin->setValue(settings.GetDMinLimit_A());
+    form->addRow("High-resolution limit [Å]", m_dMin);
+
+    layout->addWidget(group);
+    layout->addStretch();
+
+    for (auto *slider: {m_r1, m_r2, m_r3, m_profileMultiplier, m_dMin})
+        connect(slider, &SliderPlusBox::valueChanged, this, [this](double) { emitChanged(); });
+}
+
+void JFJochBraggIntegrationPanel::emitChanged() {
+    BraggIntegrationSettings s;
+    s.R1(static_cast<float>(m_r1->value()))
+     .R2(static_cast<float>(m_r2->value()))
+     .R3(static_cast<float>(m_r3->value()))
+     .ProfileMultiplier(static_cast<float>(m_profileMultiplier->value()))
+     .DMinLimit_A(static_cast<float>(m_dMin->value()));
+    emit settingsChanged(s);
+}
diff --git a/viewer/windows/JFJochBraggIntegrationPanel.h b/viewer/windows/JFJochBraggIntegrationPanel.h
new file mode 100644
index 00000000..daddeba6
--- /dev/null
+++ b/viewer/windows/JFJochBraggIntegrationPanel.h
@@ -0,0 +1,29 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QWidget>
+
+#include "../widgets/SliderPlusBox.h"
+#include "../../common/BraggIntegrationSettings.h"
+
+// Bragg integration settings as a tab panel for the converged settings window. Emits a fresh
+// BraggIntegrationSettings whenever a control changes (only the exposed fields are controlled;
+// the rest keep their defaults).
+class JFJochBraggIntegrationPanel : public QWidget {
+    Q_OBJECT
+    SliderPlusBox *m_r1;
+    SliderPlusBox *m_r2;
+    SliderPlusBox *m_r3;
+    SliderPlusBox *m_profileMultiplier;
+    SliderPlusBox *m_dMin;
+
+    void emitChanged();
+
+public:
+    explicit JFJochBraggIntegrationPanel(const BraggIntegrationSettings &settings, QWidget *parent = nullptr);
+
+signals:
+    void settingsChanged(BraggIntegrationSettings settings);
+};
diff --git a/viewer/windows/JFJochScalingPanel.cpp b/viewer/windows/JFJochScalingPanel.cpp
new file mode 100644
index 00000000..31378da3
--- /dev/null
+++ b/viewer/windows/JFJochScalingPanel.cpp
@@ -0,0 +1,77 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochScalingPanel.h"
+
+#include <QCheckBox>
+#include <QComboBox>
+#include <QFormLayout>
+#include <QGroupBox>
+#include <QVBoxLayout>
+
+JFJochScalingPanel::JFJochScalingPanel(const ScalingSettings &settings, QWidget *parent)
+    : QWidget(parent) {
+    auto *layout = new QVBoxLayout(this);
+    auto *group = new QGroupBox("Scaling && merging", this);
+    auto *form = new QFormLayout(group);
+
+    m_partiality = new QComboBox(this);
+    m_partiality->addItem("Fixed", static_cast<int>(PartialityModel::Fixed));
+    m_partiality->addItem("Rotation", static_cast<int>(PartialityModel::Rotation));
+    m_partiality->addItem("Unity", static_cast<int>(PartialityModel::Unity));
+    const auto pm = settings.GetPartialityModel().value_or(PartialityModel::Fixed);
+    if (const int idx = m_partiality->findData(static_cast<int>(pm)); idx >= 0)
+        m_partiality->setCurrentIndex(idx);
+    form->addRow("Partiality model", m_partiality);
+
+    m_mergeFriedel = new QCheckBox("Merge Friedel pairs", this);
+    m_mergeFriedel->setChecked(settings.GetMergeFriedel());
+    form->addRow("", m_mergeFriedel);
+
+    m_refineB = new QCheckBox("Refine per-image B-factor", this);
+    m_refineB->setChecked(settings.GetRefineB());
+    form->addRow("", m_refineB);
+
+    m_minPartiality = new SliderPlusBox(0.0, 1.0, 0.01, 2, this);
+    m_minPartiality->setValue(settings.GetMinPartiality());
+    form->addRow("Minimum partiality", m_minPartiality);
+
+    m_outlierNsigma = new SliderPlusBox(0.0, 10.0, 0.5, 1, this);
+    m_outlierNsigma->setValue(settings.GetOutlierRejectNsigma());
+    form->addRow("Outlier rejection [σ, 0 = off]", m_outlierNsigma);
+
+    m_limitResolution = new QCheckBox("Limit resolution", this);
+    m_limitResolution->setChecked(settings.GetHighResolutionLimit_A().has_value());
+    form->addRow("", m_limitResolution);
+
+    m_highRes = new SliderPlusBox(0.5, 5.0, 0.1, 1, this);
+    m_highRes->setValue(settings.GetHighResolutionLimit_A().value_or(2.0));
+    m_highRes->setEnabled(m_limitResolution->isChecked());
+    form->addRow("High-resolution limit [Å]", m_highRes);
+
+    layout->addWidget(group);
+    layout->addStretch();
+
+    connect(m_partiality, &QComboBox::currentIndexChanged, this, [this](int) { emitChanged(); });
+    connect(m_mergeFriedel, &QCheckBox::toggled, this, [this](bool) { emitChanged(); });
+    connect(m_refineB, &QCheckBox::toggled, this, [this](bool) { emitChanged(); });
+    connect(m_minPartiality, &SliderPlusBox::valueChanged, this, [this](double) { emitChanged(); });
+    connect(m_outlierNsigma, &SliderPlusBox::valueChanged, this, [this](double) { emitChanged(); });
+    connect(m_limitResolution, &QCheckBox::toggled, this, [this](bool checked) {
+        m_highRes->setEnabled(checked);
+        emitChanged();
+    });
+    connect(m_highRes, &SliderPlusBox::valueChanged, this, [this](double) { emitChanged(); });
+}
+
+void JFJochScalingPanel::emitChanged() {
+    ScalingSettings s;
+    s.SetPartialityModel(static_cast<PartialityModel>(m_partiality->currentData().toInt()));
+    s.MergeFriedel(m_mergeFriedel->isChecked());
+    s.RefineB(m_refineB->isChecked());
+    s.MinPartiality(m_minPartiality->value());
+    s.OutlierRejectNsigma(m_outlierNsigma->value());
+    if (m_limitResolution->isChecked())
+        s.HighResolutionLimit_A(m_highRes->value());
+    emit settingsChanged(s);
+}
diff --git a/viewer/windows/JFJochScalingPanel.h b/viewer/windows/JFJochScalingPanel.h
new file mode 100644
index 00000000..4cc87ca2
--- /dev/null
+++ b/viewer/windows/JFJochScalingPanel.h
@@ -0,0 +1,33 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QWidget>
+
+#include "../widgets/SliderPlusBox.h"
+#include "../../common/ScalingSettings.h"
+
+class QComboBox;
+class QCheckBox;
+
+// Scaling / merging settings as a tab panel for the converged settings window. These feed
+// processing jobs (the scale/merge post-pass); the viewer's single-image analysis ignores them.
+class JFJochScalingPanel : public QWidget {
+    Q_OBJECT
+    QComboBox *m_partiality;
+    QCheckBox *m_mergeFriedel;
+    QCheckBox *m_refineB;
+    QCheckBox *m_limitResolution;
+    SliderPlusBox *m_highRes;
+    SliderPlusBox *m_minPartiality;
+    SliderPlusBox *m_outlierNsigma;
+
+    void emitChanged();
+
+public:
+    explicit JFJochScalingPanel(const ScalingSettings &settings, QWidget *parent = nullptr);
+
+signals:
+    void settingsChanged(ScalingSettings settings);
+};
diff --git a/viewer/windows/JFJochSettingsWindow.cpp b/viewer/windows/JFJochSettingsWindow.cpp
new file mode 100644
index 00000000..51b6ee2d
--- /dev/null
+++ b/viewer/windows/JFJochSettingsWindow.cpp
@@ -0,0 +1,40 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochSettingsWindow.h"
+
+#include <QTabWidget>
+
+JFJochSettingsWindow::JFJochSettingsWindow(const SpotFindingSettings &spot, const IndexingSettings &indexing,
+                                           const AzimuthalIntegrationSettings &azint,
+                                           const BraggIntegrationSettings &bragg,
+                                           const ScalingSettings &scaling, QWidget *parent)
+    : JFJochHelperWindow(parent) {
+    setWindowTitle("Processing settings");
+
+    // Reuse the existing spot/index + azimuthal windows: build them (kept hidden) and lift their
+    // content into tabs, so all their existing widgets, logic and signals keep working.
+    m_processing = new JFJochViewerProcessingWindow(spot, indexing, this);
+    m_azint = new JFJochAzIntWindow(azint, this);
+    m_bragg = new JFJochBraggIntegrationPanel(bragg, this);
+    m_scaling = new JFJochScalingPanel(scaling, this);
+
+    auto *tabs = new QTabWidget(this);
+    tabs->addTab(m_processing->takeCentralWidget(), "Spot finding && indexing");
+    tabs->addTab(m_azint->takeCentralWidget(), "Azimuthal");
+    tabs->addTab(m_bragg, "Bragg integration");
+    tabs->addTab(m_scaling, "Scaling");
+    setCentralWidget(tabs);
+
+    m_processing->hide();   // the emptied shells stay alive only to drive their signals
+    m_azint->hide();
+
+    connect(m_processing, &JFJochViewerProcessingWindow::settingsChanged,
+            this, &JFJochSettingsWindow::spotFindingChanged);
+    connect(m_azint, &JFJochAzIntWindow::settingsChanged,
+            this, &JFJochSettingsWindow::azintChanged);
+    connect(m_bragg, &JFJochBraggIntegrationPanel::settingsChanged,
+            this, &JFJochSettingsWindow::braggChanged);
+    connect(m_scaling, &JFJochScalingPanel::settingsChanged,
+            this, &JFJochSettingsWindow::scalingChanged);
+}
diff --git a/viewer/windows/JFJochSettingsWindow.h b/viewer/windows/JFJochSettingsWindow.h
new file mode 100644
index 00000000..ccb2dc27
--- /dev/null
+++ b/viewer/windows/JFJochSettingsWindow.h
@@ -0,0 +1,33 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include "JFJochHelperWindow.h"
+#include "JFJochViewerProcessingWindow.h"
+#include "JFJochAzIntWindow.h"
+#include "JFJochBraggIntegrationPanel.h"
+#include "JFJochScalingPanel.h"
+
+// One tabbed window converging all processing settings: Spot finding & indexing | Azimuthal |
+// Bragg integration | Scaling. The first two tabs reuse the existing settings widgets (their
+// content is lifted into tabs, keeping all their logic), Bragg + scaling are new. Single source of
+// truth for both interactive single-image analysis and processing jobs.
+class JFJochSettingsWindow : public JFJochHelperWindow {
+    Q_OBJECT
+    JFJochViewerProcessingWindow *m_processing;
+    JFJochAzIntWindow *m_azint;
+    JFJochBraggIntegrationPanel *m_bragg;
+    JFJochScalingPanel *m_scaling;
+
+public:
+    JFJochSettingsWindow(const SpotFindingSettings &spot, const IndexingSettings &indexing,
+                         const AzimuthalIntegrationSettings &azint, const BraggIntegrationSettings &bragg,
+                         const ScalingSettings &scaling, QWidget *parent = nullptr);
+
+signals:
+    void spotFindingChanged(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
+    void azintChanged(const AzimuthalIntegrationSettings &settings);
+    void braggChanged(BraggIntegrationSettings settings);
+    void scalingChanged(ScalingSettings settings);
+};
-- 
2.52.0


From 95223fc281ef9cd025a1513923233751aa85d877 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 07:17:31 +0200
Subject: [PATCH 182/228] CI: Tests needs LFS to get rotation dataset

---
 .gitea/workflows/build_and_test.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index ac19d87e..960b671c 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -31,6 +31,16 @@ jobs:
       CTEST_OUTPUT_ON_FAILURE: '1'
     steps:
       - uses: actions/checkout@v4
+      - name: Configure auth and fetch LFS
+        shell: bash
+        env:
+          GITEA_TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
+        run: |
+          git lfs install --local
+          AUTH=$(git config --local http.${{ github.server_url }}/.extraheader)
+          git config --local --unset http.${{ github.server_url }}/.extraheader
+          git config --local http.${{ github.server_url }}/${{ github.repository }}.git/info/lfs/objects/batch.extraheader "$AUTH"
+          git lfs pull
       - name: Build tests
         shell: bash
         run: |
-- 
2.52.0


From 940b7e34d482b3a5d258d5bd202462427b4ba527 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 08:30:49 +0200
Subject: [PATCH 183/228] viewer: indexing algorithm/refinement radio groups,
 rotation fix, live job plots

Processing settings:
- Split the spot/index settings widget into two tabs (Spot finding | Indexing)
  via TakeSpotFindingPage()/TakeIndexingPage().
- Indexing tab now exposes the indexing algorithm (Auto/FFBIDX/FFT/FFTW/None) and
  geometry refinement (None/Orientation/Beam center/Pixel refine) as radio groups
  with short explanations.
- Fix: UpdateSpotFindingSettings dropped algorithm + geometry-refinement when
  copying into indexing_settings (the geom checkbox was a no-op); both now flow
  into jobs via curr_experiment.

Processing jobs window:
- Rotation indexing from the job dialog now also sets RotationIndexing(true) on
  the experiment's IndexingSettings; otherwise IndexAndRefine builds no rotation
  indexer and the two-pass pre-pass throws.
- Status cell shows a QProgressBar with "<done> / <expected>".
- Live results: JFJochProcessController::OnImageProcessed accumulates per-image
  results into a JFJochReaderDataset and emits it throttled (~4 Hz) as liveDataset,
  forwarded to the dataset-info plots so they update while a job runs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp           |   2 +
 viewer/JFJochProcessController.cpp            |  55 +++++++++
 viewer/JFJochProcessController.h              |  13 ++
 viewer/JFJochViewerWindow.cpp                 |   5 +-
 viewer/JFJochViewerWindow.h                   |   3 +
 viewer/windows/JFJochProcessingJobsWindow.cpp |  46 ++++++-
 viewer/windows/JFJochProcessingJobsWindow.h   |   4 +
 viewer/windows/JFJochSettingsWindow.cpp       |   3 +-
 .../windows/JFJochViewerProcessingWindow.cpp  | 113 +++++++++++++-----
 viewer/windows/JFJochViewerProcessingWindow.h |  17 ++-
 10 files changed, 216 insertions(+), 45 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 509fe1c9..7614cfd6 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -557,6 +557,8 @@ void JFJochImageReadingWorker::UpdateSpotFindingSettings(const SpotFindingSettin
     QMutexLocker locker(&m);
     spot_finding_settings = settings;
 
+    indexing_settings.Algorithm(indexing.GetAlgorithm());
+    indexing_settings.GeomRefinementAlgorithm(indexing.GetGeomRefinementAlgorithm());
     indexing_settings.Tolerance(indexing.GetTolerance());
     indexing_settings.ViableCellMinSpots(indexing.GetViableCellMinSpots());
     indexing_settings.IndexIceRings(indexing.GetIndexIceRings());
diff --git a/viewer/JFJochProcessController.cpp b/viewer/JFJochProcessController.cpp
index ee3e1bc1..7adc058c 100644
--- a/viewer/JFJochProcessController.cpp
+++ b/viewer/JFJochProcessController.cpp
@@ -6,8 +6,11 @@
 
 #include <QMetaType>
 
+#include <cmath>
+
 JFJochProcessController::JFJochProcessController(QObject *parent) : QObject(parent) {
     qRegisterMetaType<ProcessResult>("ProcessResult");
+    qRegisterMetaType<std::shared_ptr<const JFJochReaderDataset>>("std::shared_ptr<const JFJochReaderDataset>");
 }
 
 JFJochProcessController::~JFJochProcessController() {
@@ -44,6 +47,16 @@ void JFJochProcessController::run_(QString file_path, DiffractionExperiment expe
         JFJochHDF5Reader reader;
         reader.ReadFile(file_path.toStdString());
 
+        // Seed the live dataset with the experiment so the chart has geometry context; per-image
+        // results are filled in by OnImageProcessed as the run progresses.
+        {
+            auto base = std::make_shared<JFJochReaderDataset>();
+            base->experiment = experiment;
+            std::lock_guard lock(live_mutex_);
+            live_dataset_ = std::move(base);
+            last_live_emit_ = {};
+        }
+
         JFJochProcess process(reader, std::move(experiment), std::move(pixel_mask), std::move(config));
         active_ = &process;
         if (cancel_pending_)
@@ -71,3 +84,45 @@ void JFJochProcessController::OnProgress(uint64_t done, uint64_t total) {
     if (done == total || done % step == 0)
         emit progress(done, total);
 }
+
+void JFJochProcessController::OnImageProcessed(const DataMessage &msg) {
+    std::shared_ptr<JFJochReaderDataset> snapshot;
+    {
+        std::lock_guard lock(live_mutex_);
+        if (!live_dataset_)
+            return;
+
+        // Place each available per-image result at its ordinal; gaps (images still being processed
+        // by other threads) read back as NaN.
+        const int64_t i = msg.number;
+        auto put = [i](std::vector<float> &v, float val) {
+            if (static_cast<int64_t>(v.size()) <= i)
+                v.resize(i + 1, NAN);
+            v[i] = val;
+        };
+        auto &d = *live_dataset_;
+        if (msg.spot_count)            put(d.spot_count, *msg.spot_count);
+        if (msg.spot_count_indexed)    put(d.spot_count_indexed, *msg.spot_count_indexed);
+        if (msg.spot_count_low_res)    put(d.spot_count_low_res, *msg.spot_count_low_res);
+        if (msg.spot_count_ice_rings)  put(d.spot_count_ice_rings, *msg.spot_count_ice_rings);
+        if (msg.indexing_result)       put(d.indexing_result, *msg.indexing_result ? 1.0f : 0.0f);
+        if (msg.indexing_lattice_count) put(d.indexing_lattice_count, *msg.indexing_lattice_count);
+        if (msg.bkg_estimate)          put(d.bkg_estimate, *msg.bkg_estimate);
+        if (msg.resolution_estimate)   put(d.resolution_estimate, *msg.resolution_estimate);
+        if (msg.profile_radius)        put(d.profile_radius, *msg.profile_radius);
+        if (msg.mosaicity_deg)         put(d.mosaicity_deg, *msg.mosaicity_deg);
+        if (msg.b_factor)              put(d.b_factor, *msg.b_factor);
+        if (msg.integrated_reflections) put(d.integrated_reflections, *msg.integrated_reflections);
+        if (msg.image_scale_factor)    put(d.image_scale_factor, *msg.image_scale_factor);
+        if (msg.image_scale_cc)        put(d.image_scale_cc, *msg.image_scale_cc);
+        if (msg.image_scale_b_factor)  put(d.image_scale_b, *msg.image_scale_b_factor);
+
+        // Throttle to ~4 Hz so the GUI plots refresh smoothly without flooding the event queue.
+        const auto now = std::chrono::steady_clock::now();
+        if (now - last_live_emit_ < std::chrono::milliseconds(250))
+            return;
+        last_live_emit_ = now;
+        snapshot = std::make_shared<JFJochReaderDataset>(d);   // immutable copy for the GUI thread
+    }
+    emit liveDataset(snapshot);
+}
diff --git a/viewer/JFJochProcessController.h b/viewer/JFJochProcessController.h
index 50e0f16e..ff64ede0 100644
--- a/viewer/JFJochProcessController.h
+++ b/viewer/JFJochProcessController.h
@@ -7,11 +7,15 @@
 #include <QString>
 
 #include <atomic>
+#include <chrono>
+#include <memory>
+#include <mutex>
 #include <thread>
 
 #include "../process/JFJochProcess.h"
 #include "../common/DiffractionExperiment.h"
 #include "../common/PixelMask.h"
+#include "../reader/JFJochReaderDataset.h"
 
 Q_DECLARE_METATYPE(ProcessResult)
 
@@ -41,11 +45,14 @@ signals:
     void progress(quint64 done, quint64 total);
     void finished(ProcessResult result);
     void failed(QString error);
+    // Per-image results accumulated so far, for live dataset-info plots while a job runs (throttled).
+    void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
 
 private:
     // JFJochProcessObserver - called from worker threads, forwarded as queued signals.
     void OnPhase(const std::string &phase) override;
     void OnProgress(uint64_t done, uint64_t total) override;
+    void OnImageProcessed(const DataMessage &msg) override;
 
     void run_(QString file_path, DiffractionExperiment experiment, PixelMask pixel_mask, ProcessConfig config);
     void joinWorker_();
@@ -54,4 +61,10 @@ private:
     std::atomic<JFJochProcess *> active_{nullptr};
     std::atomic<bool> running_{false};
     std::atomic<bool> cancel_pending_{false};
+
+    // Live per-image results, accumulated by OnImageProcessed (worker threads) and emitted as
+    // immutable copies. live_mutex_ guards both the dataset and the throttle timestamp.
+    std::mutex live_mutex_;
+    std::shared_ptr<JFJochReaderDataset> live_dataset_;
+    std::chrono::steady_clock::time_point last_live_emit_;
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index c2948e21..bec373d1 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -114,7 +114,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
     auto magnifierWindow = new JFJochMagnifierWindow(this);
 
-    auto processingJobsWindow = new JFJochProcessingJobsWindow(reading_worker, this);
+    processingJobsWindow = new JFJochProcessingJobsWindow(reading_worker, this);
 
     menuBar->AddWindowEntry(tableWindow, "Image list");
     menuBar->AddWindowEntry(spotWindow, "Spot list");
@@ -434,6 +434,9 @@ void JFJochViewerWindow::NewDatasetInfo() {
             info, &JFJochViewerDatasetInfo::datasetLoaded);
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
             info, &JFJochViewerDatasetInfo::imageLoaded);
+    // Live processing results: refresh the plots while a job runs.
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::liveDataset,
+            info, &JFJochViewerDatasetInfo::datasetLoaded);
     connect(info, &JFJochViewerDatasetInfo::imageSelected,
             reading_worker, &JFJochImageReadingWorker::LoadImage);
     connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 56011e19..549bc15d 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -13,6 +13,8 @@
 #include "JFJochViewerStatusBar.h"
 #include "toolbar/JFJochViewerToolbarDisplay.h"
 
+class JFJochProcessingJobsWindow;
+
 class JFJochViewerWindow : public QMainWindow {
 Q_OBJECT
     const QString stylesheet = "background-color: rgb(255, 235, 230);";
@@ -25,6 +27,7 @@ private:
     JFJochImageReadingWorker *reading_worker;
     JFJochViewerToolbarDisplay *toolBarDisplay;
     JFJochViewerStatusBar *statusbar;
+    JFJochProcessingJobsWindow *processingJobsWindow;
 
     std::shared_ptr<const JFJochReaderDataset> lastDataset;  // added
     std::shared_ptr<const JFJochReaderImage> lastImage;      // added
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 800553fe..627a1be1 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -15,6 +15,7 @@
 #include <QHeaderView>
 #include <QLineEdit>
 #include <QMessageBox>
+#include <QProgressBar>
 #include <QPushButton>
 #include <QSpinBox>
 #include <QTableWidget>
@@ -42,6 +43,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     connect(controller_, &JFJochProcessController::progress, this, &JFJochProcessingJobsWindow::onProgress);
     connect(controller_, &JFJochProcessController::finished, this, &JFJochProcessingJobsWindow::onFinished);
     connect(controller_, &JFJochProcessController::failed, this, &JFJochProcessingJobsWindow::onFailed);
+    connect(controller_, &JFJochProcessController::liveDataset, this, &JFJochProcessingJobsWindow::liveDataset);
 
     auto *toolbar = addToolBar("Jobs");
     toolbar->setMovable(false);
@@ -165,9 +167,18 @@ void JFJochProcessingJobsWindow::newJob() {
 
     const ProcessConfig config = buildConfig(spec, inputs);
 
+    // Rotation indexing must be enabled on the indexing settings too (config.rotation_indexing only
+    // drives the two-pass pre-pass); otherwise IndexAndRefine never builds a rotation indexer.
+    DiffractionExperiment experiment = inputs.experiment;
+    if (spec.mode == ProcessMode::FullAnalysis) {
+        auto idx = experiment.GetIndexingSettings();
+        idx.RotationIndexing(spec.rotation);
+        experiment.ImportIndexingSettings(idx);
+    }
+
     if (action == 2) {   // copy command line
         const QString cmd = QString::fromStdString(
-            JFJochProcessCommandLine(config, inputs.experiment, inputs.file.toStdString()));
+            JFJochProcessCommandLine(config, experiment, inputs.file.toStdString()));
         QApplication::clipboard()->setText(cmd);
         QMessageBox::information(this, "Command line", cmd + "\n\n(copied to clipboard)");
         return;
@@ -190,6 +201,15 @@ void JFJochProcessingJobsWindow::newJob() {
     table_->setItem(row, COL_INDEX, new QTableWidgetItem("-"));
     table_->setItem(row, COL_CELL, new QTableWidgetItem("-"));
 
+    // A progress bar lives in the Status cell while the job runs; it shows the phase as text until
+    // image processing starts, then "<done> / <expected>" with the bar filling in the background.
+    running_bar_ = new QProgressBar(table_);
+    running_bar_->setAlignment(Qt::AlignCenter);
+    running_bar_->setRange(0, spec.images > 0 ? spec.images : 1);
+    running_bar_->setValue(0);
+    running_bar_->setFormat("queued");
+    table_->setCellWidget(row, COL_STATUS, running_bar_);
+
     JobInfo info;
     info.name = name;
     if (spec.save)
@@ -197,7 +217,7 @@ void JFJochProcessingJobsWindow::newJob() {
     jobs_.push_back(info);
     running_row_ = row;
 
-    controller_->start(inputs.file, inputs.experiment, inputs.pixel_mask, config);
+    controller_->start(inputs.file, experiment, inputs.pixel_mask, config);
     emit writeStatusBar("Started processing job " + name);
 }
 
@@ -229,18 +249,29 @@ void JFJochProcessingJobsWindow::setStatus(int row, const QString &text) {
 }
 
 void JFJochProcessingJobsWindow::onPhase(QString phase) {
-    if (running_row_ >= 0 && phase != "Processing images")
-        setStatus(running_row_, phase);
+    // The "Processing images" phase is shown by onProgress; other phases (first pass, scaling, ...)
+    // show their name as text over an empty bar.
+    if (!running_bar_ || phase == "Processing images")
+        return;
+    running_bar_->setRange(0, 1);
+    running_bar_->setValue(0);
+    running_bar_->setFormat(phase);
 }
 
 void JFJochProcessingJobsWindow::onProgress(quint64 done, quint64 total) {
-    if (running_row_ >= 0)
-        setStatus(running_row_, QStringLiteral("running %1%").arg(total ? done * 100 / total : 0));
+    if (!running_bar_)
+        return;
+    running_bar_->setRange(0, static_cast<int>(total));
+    running_bar_->setValue(static_cast<int>(done));
+    running_bar_->setFormat("%v / %m");
 }
 
 void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
     const int row = running_row_;
     running_row_ = -1;
+    if (row >= 0)
+        table_->removeCellWidget(row, COL_STATUS);   // deletes running_bar_
+    running_bar_ = nullptr;
     if (row < 0 || row >= static_cast<int>(jobs_.size()))
         return;
 
@@ -265,6 +296,9 @@ void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
 void JFJochProcessingJobsWindow::onFailed(QString error) {
     const int row = running_row_;
     running_row_ = -1;
+    if (row >= 0)
+        table_->removeCellWidget(row, COL_STATUS);   // deletes running_bar_
+    running_bar_ = nullptr;
     setStatus(row, "failed");
     QMessageBox::warning(this, "Processing failed", error);
 }
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index a679c850..8302a743 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -11,6 +11,7 @@
 #include "../JFJochImageReadingWorker.h"   // ReprocessingInputs
 
 class QTableWidget;
+class QProgressBar;
 
 // Makes processing a first-class GUI activity: a table of processing jobs run on the current
 // dataset. A job can be run locally (off the GUI thread, via JFJochProcessController) or its
@@ -25,6 +26,8 @@ signals:
     void registerSnapshot(QString name, QString master_path);
     void activateSnapshot(QString name);
     void writeStatusBar(QString message, int timeout_ms = 0);
+    // Live per-image results while a job runs, for the dataset-info plots.
+    void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
 
 private slots:
     void newJob();
@@ -60,6 +63,7 @@ private:
     JFJochImageReadingWorker *worker_;
     JFJochProcessController *controller_;
     QTableWidget *table_;
+    QProgressBar *running_bar_ = nullptr;   // lives in the running row's Status cell
     int running_row_ = -1;
     int job_counter_ = 0;
     std::vector<JobInfo> jobs_;
diff --git a/viewer/windows/JFJochSettingsWindow.cpp b/viewer/windows/JFJochSettingsWindow.cpp
index 51b6ee2d..2f5f2ca0 100644
--- a/viewer/windows/JFJochSettingsWindow.cpp
+++ b/viewer/windows/JFJochSettingsWindow.cpp
@@ -20,7 +20,8 @@ JFJochSettingsWindow::JFJochSettingsWindow(const SpotFindingSettings &spot, cons
     m_scaling = new JFJochScalingPanel(scaling, this);
 
     auto *tabs = new QTabWidget(this);
-    tabs->addTab(m_processing->takeCentralWidget(), "Spot finding && indexing");
+    tabs->addTab(m_processing->TakeSpotFindingPage(), "Spot finding");
+    tabs->addTab(m_processing->TakeIndexingPage(), "Indexing");
     tabs->addTab(m_azint->takeCentralWidget(), "Azimuthal");
     tabs->addTab(m_bragg, "Bragg integration");
     tabs->addTab(m_scaling, "Scaling");
diff --git a/viewer/windows/JFJochViewerProcessingWindow.cpp b/viewer/windows/JFJochViewerProcessingWindow.cpp
index adcc8f2e..6df8821c 100644
--- a/viewer/windows/JFJochViewerProcessingWindow.cpp
+++ b/viewer/windows/JFJochViewerProcessingWindow.cpp
@@ -6,19 +6,44 @@
 #include <QHBoxLayout>
 #include <QGroupBox>
 #include <QFormLayout>
-#include <QCloseEvent>
+#include <QButtonGroup>
+#include <QRadioButton>
+#include <vector>
+
+namespace {
+    struct RadioChoice { const char *label; int value; };
+
+    // A titled group of mutually-exclusive radio buttons, with an optional explanatory line.
+    QGroupBox *MakeRadioGroup(const QString &title, const QString &help,
+                              const std::vector<RadioChoice> &choices, int current,
+                              QButtonGroup *group, QWidget *parent) {
+        auto *box = new QGroupBox(title, parent);
+        auto *layout = new QVBoxLayout(box);
+        if (!help.isEmpty()) {
+            auto *label = new QLabel(help, box);
+            label->setWordWrap(true);
+            layout->addWidget(label);
+        }
+        for (const auto &c: choices) {
+            auto *button = new QRadioButton(c.label, box);
+            button->setChecked(c.value == current);
+            group->addButton(button, c.value);
+            layout->addWidget(button);
+        }
+        return box;
+    }
+}
 
 JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSettings &settings, const IndexingSettings& indexing,QWidget *parent)
         : JFJochHelperWindow(parent), m_settings(settings), m_indexing(indexing) {
 
     setWindowTitle("Image processing settings");
 
-    QWidget *centralWidget = new QWidget(this);
-    setCentralWidget(centralWidget);
+    // --- Spot finding page ---
+    m_spotFindingPage = new QWidget(this);
+    auto spotLayout = new QVBoxLayout(m_spotFindingPage);
 
-    auto mainLayout = new QVBoxLayout(centralWidget);
-
-    auto generalGroup = new QGroupBox("Spot finding", this);
+    auto generalGroup = new QGroupBox("Spot finding", m_spotFindingPage);
     auto generalLayout = new QFormLayout(generalGroup);
 
     m_enableCheckBox = new QCheckBox("Enable", this);
@@ -68,34 +93,58 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
     m_highResSpuriousGapOneOverD->setEnabled(gapFilterEnabled);
     generalLayout->addRow("Gap threshold in Q-space [A^-1]:", m_highResSpuriousGapOneOverD);
 
-     auto processingGroup = new QGroupBox("Other steps", this);
-     auto processingLayout = new QFormLayout(processingGroup);
-
     m_iceRingWidthQRecipA = new SliderPlusBox(0.0, 0.3, 0.001, 3, this);
     m_iceRingWidthQRecipA->setValue(m_settings.ice_ring_width_Q_recipA);
     generalLayout->addRow("Ice ring width in Q-space [A^-1]:", m_iceRingWidthQRecipA);
 
+    auto processingGroup = new QGroupBox("Other steps", m_spotFindingPage);
+    auto processingLayout = new QFormLayout(processingGroup);
+
     m_quickIntegrationCheckBox = new QCheckBox("Enable Bragg Integration", this);
     m_quickIntegrationCheckBox->setChecked(m_settings.quick_integration);
     processingLayout->addRow("", m_quickIntegrationCheckBox);
 
-    // Indexing group
-    auto indexingGroup = new QGroupBox("Indexing", this);
-    auto indexingLayout = new QFormLayout(indexingGroup);
+    spotLayout->addWidget(generalGroup);
+    spotLayout->addWidget(processingGroup);
+    spotLayout->addStretch();
+
+    // --- Indexing page ---
+    m_indexingPage = new QWidget(this);
+    auto indexLayout = new QVBoxLayout(m_indexingPage);
 
     m_indexingCheckBox = new QCheckBox("Enable Indexing", this);
     m_indexingCheckBox->setChecked(m_settings.indexing);
-    indexingLayout->addRow("", m_indexingCheckBox);
+    indexLayout->addWidget(m_indexingCheckBox);
+
+    m_indexAlgGroup = new QButtonGroup(this);
+    indexLayout->addWidget(MakeRadioGroup(
+        "Indexing algorithm",
+        "FFBIDX is fast but needs a known cell; FFT/FFTW index de-novo (FFT on GPU, FFTW on CPU). "
+        "Auto picks the best available.",
+        {{"Auto", static_cast<int>(IndexingAlgorithmEnum::Auto)},
+         {"FFBIDX — GPU, needs known cell", static_cast<int>(IndexingAlgorithmEnum::FFBIDX)},
+         {"FFT — GPU, de-novo", static_cast<int>(IndexingAlgorithmEnum::FFT)},
+         {"FFTW — CPU, de-novo", static_cast<int>(IndexingAlgorithmEnum::FFTW)},
+         {"None — skip indexing", static_cast<int>(IndexingAlgorithmEnum::None)}},
+        static_cast<int>(m_indexing.GetAlgorithm()), m_indexAlgGroup, m_indexingPage));
+
+    m_geomRefGroup = new QButtonGroup(this);
+    indexLayout->addWidget(MakeRadioGroup(
+        "Geometry refinement",
+        "How the geometry is refined once a lattice is found.",
+        {{"None", static_cast<int>(GeomRefinementAlgorithmEnum::None)},
+         {"Orientation only", static_cast<int>(GeomRefinementAlgorithmEnum::OrientationOnly)},
+         {"Beam center + lattice", static_cast<int>(GeomRefinementAlgorithmEnum::BeamCenter)},
+         {"Pixel refinement (experimental)", static_cast<int>(GeomRefinementAlgorithmEnum::PixelRefine)}},
+        static_cast<int>(m_indexing.GetGeomRefinementAlgorithm()), m_geomRefGroup, m_indexingPage));
+
+    auto indexingGroup = new QGroupBox("Indexing parameters", m_indexingPage);
+    auto indexingLayout = new QFormLayout(indexingGroup);
 
     m_idxIndexIceRings = new QCheckBox("Index ice rings", this);
     m_idxIndexIceRings->setChecked(m_indexing.GetIndexIceRings());
     indexingLayout->addRow("", m_idxIndexIceRings);
 
-    m_geomRefinementCheckBox = new QCheckBox("Refine beam center", this);
-    m_geomRefinementCheckBox->setChecked(m_indexing.GetGeomRefinementAlgorithm() == GeomRefinementAlgorithmEnum::BeamCenter);
-    indexingLayout->addRow("", m_geomRefinementCheckBox);
-
-    // Indexing settings UI
     m_idxTolerance = new SliderPlusBox(0.0, 0.5, 0.001, 3, this);
     m_idxTolerance->setValue(m_indexing.GetTolerance());
     indexingLayout->addRow("Indexing tolerance", m_idxTolerance);
@@ -108,14 +157,10 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
     m_idxViableCellMinSpots->setValue(static_cast<double>(m_indexing.GetViableCellMinSpots()));
     indexingLayout->addRow("Viable cell min spots", m_idxViableCellMinSpots);
 
-    auto buttonsLayout = new QHBoxLayout();
-    buttonsLayout->addStretch();
-
-    mainLayout->addWidget(generalGroup);
-    mainLayout->addWidget(indexingGroup);
-    mainLayout->addWidget(processingGroup);
-    mainLayout->addLayout(buttonsLayout);
+    indexLayout->addWidget(indexingGroup);
+    indexLayout->addStretch();
 
+    // --- Connections ---
     connect(m_enableCheckBox, &QCheckBox::toggled, [this](bool checked) {
         m_settings.enable = checked;
         Update();
@@ -191,6 +236,16 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
         Update();
     });
 
+    connect(m_indexAlgGroup, &QButtonGroup::idClicked, [this](int id) {
+        m_indexing.Algorithm(static_cast<IndexingAlgorithmEnum>(id));
+        Update();
+    });
+
+    connect(m_geomRefGroup, &QButtonGroup::idClicked, [this](int id) {
+        m_indexing.GeomRefinementAlgorithm(static_cast<GeomRefinementAlgorithmEnum>(id));
+        Update();
+    });
+
     // Indexing settings signals
     connect(m_idxTolerance, &SliderPlusBox::valueChanged, [this](double val) {
         m_indexing.Tolerance(static_cast<float>(val));
@@ -207,14 +262,6 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
         Update();
     });
 
-    connect(m_geomRefinementCheckBox, &QCheckBox::toggled, [this](bool checked) {
-        if (checked)
-            m_indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
-        else
-            m_indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::None);
-        Update();
-    });
-
     connect(m_idxViableCellMinSpots, &SliderPlusBox::valueChanged, [this](double val) {
         m_indexing.ViableCellMinSpots(static_cast<int64_t>(std::lround(val)));
         Update();
diff --git a/viewer/windows/JFJochViewerProcessingWindow.h b/viewer/windows/JFJochViewerProcessingWindow.h
index df6488de..0049f9fe 100644
--- a/viewer/windows/JFJochViewerProcessingWindow.h
+++ b/viewer/windows/JFJochViewerProcessingWindow.h
@@ -13,6 +13,10 @@
 #include "../widgets/SliderPlusBox.h"
 #include "../../image_analysis/spot_finding/SpotFindingSettings.h"
 
+class QButtonGroup;
+
+// Holds the spot finding and indexing controls. The two are exposed as separate pages
+// (TakeSpotFindingPage / TakeIndexingPage) so the settings window can show them as two tabs.
 class JFJochViewerProcessingWindow : public JFJochHelperWindow {
     Q_OBJECT
 
@@ -31,7 +35,8 @@ class JFJochViewerProcessingWindow : public JFJochHelperWindow {
     QCheckBox *m_indexingCheckBox;
     QCheckBox *m_quickIntegrationCheckBox;
 
-    QCheckBox *m_geomRefinementCheckBox;
+    QButtonGroup *m_indexAlgGroup;                 // indexing algorithm (FFBIDX/FFT/FFTW/Auto/None)
+    QButtonGroup *m_geomRefGroup;                  // geometry refinement (None/Orientation/Beam/Pixel)
 
     SliderPlusBox *m_idxTolerance;                 // [0.0 .. 0.5], step 0.001
     SliderPlusBox *m_idxUnitCellDistTolerance;     // [0.0001 .. 0.2001], step 0.0001
@@ -40,6 +45,9 @@ class JFJochViewerProcessingWindow : public JFJochHelperWindow {
 
     SliderPlusBox *m_iceRingWidthQRecipA;
 
+    QWidget *m_spotFindingPage;
+    QWidget *m_indexingPage;
+
     SpotFindingSettings m_settings;
     IndexingSettings m_indexing;
 
@@ -48,9 +56,10 @@ public:
     explicit JFJochViewerProcessingWindow(const SpotFindingSettings &settings, const IndexingSettings& indexing,
         QWidget *parent = nullptr);
 
+    // The two pages, for lifting into tabs. Ownership passes to the caller (e.g. a QTabWidget).
+    QWidget *TakeSpotFindingPage() { return m_spotFindingPage; }
+    QWidget *TakeIndexingPage() { return m_indexingPage; }
+
 signals:
     void settingsChanged(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
 };
-
-
-
-- 
2.52.0


From 9c417d322f3f10d68b461372770961b7c6d38e8f Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 08:35:56 +0200
Subject: [PATCH 184/228] viewer: dock the processing panel next to the plots;
 HTTP-mode notice

- Convert JFJochProcessingJobsWindow from a standalone helper window into a
  dockable QWidget panel (toolbar + stacked table/message), placed in the bottom
  dock area and split horizontally to sit in the bottom-right corner next to the
  dataset-info plots. Its show/hide toggle moves to the Window menu via the new
  JFJochViewerMenu::AddDockEntry.
- When connected to a live HTTP stream the panel shows "Dataset re-processing is
  currently available only in File mode" and disables the toolbar, driven by the
  worker's httpConnectionChanged signal.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerMenu.cpp                   |  7 ++++
 viewer/JFJochViewerMenu.h                     |  3 ++
 viewer/JFJochViewerWindow.cpp                 | 18 ++++++++-
 viewer/JFJochViewerWindow.h                   |  3 ++
 viewer/windows/JFJochProcessingJobsWindow.cpp | 40 ++++++++++++++-----
 viewer/windows/JFJochProcessingJobsWindow.h   | 20 +++++++---
 6 files changed, 74 insertions(+), 17 deletions(-)

diff --git a/viewer/JFJochViewerMenu.cpp b/viewer/JFJochViewerMenu.cpp
index aa96fcf0..4f766c06 100644
--- a/viewer/JFJochViewerMenu.cpp
+++ b/viewer/JFJochViewerMenu.cpp
@@ -12,6 +12,7 @@
 #include <QLineEdit>
 #include <QSpinBox>
 #include <QDialogButtonBox>
+#include <QDockWidget>
 
 #include "JFJochViewerWindow.h"
 #include "windows/JFJochLicenseWindow.h"
@@ -81,6 +82,12 @@ void JFJochViewerMenu::AddWindowEntry(JFJochHelperWindow *window, const QString
     connect(window, &JFJochHelperWindow::closing, [action] {action->setChecked(false);});
 }
 
+void JFJochViewerMenu::AddDockEntry(QDockWidget *dock, const QString &name) {
+    auto *action = dock->toggleViewAction();   // checkable, stays in sync with the dock visibility
+    action->setText(name);
+    windowMenu->addAction(action);
+}
+
 
 void JFJochViewerMenu::aboutSelected() {
     QPixmap pixmap(":/jfjoch.png");
diff --git a/viewer/JFJochViewerMenu.h b/viewer/JFJochViewerMenu.h
index f741d936..04d87754 100644
--- a/viewer/JFJochViewerMenu.h
+++ b/viewer/JFJochViewerMenu.h
@@ -8,6 +8,7 @@
 #include "windows/JFJochHelperWindow.h"
 
 class JFJochLicenseWindow;
+class QDockWidget;
 
 class JFJochViewerMenu : public QMenuBar {
     Q_OBJECT
@@ -25,6 +26,8 @@ public:
     ~JFJochViewerMenu() override = default;
 
     void AddWindowEntry(JFJochHelperWindow *window, const QString &name);
+    // Adds a dock's show/hide toggle to the Window menu (for docked panels).
+    void AddDockEntry(QDockWidget *dock, const QString &name);
 
 signals:
     void fileOpenSelected(const QString &filename, qint64 image_number, qint64 summation, bool retry);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index bec373d1..d86e4907 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -125,7 +125,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar->AddWindowEntry(reciprocalWindow, "Reciprocal space viewer");
     menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
     menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
-    menuBar->AddWindowEntry(processingJobsWindow, "Processing");
+    // processingJobsWindow is docked (bottom, next to the plots), not a standalone window - see below.
 
 #ifdef JFJOCH_VIEWER_DBUS
     if (dbus) {
@@ -395,6 +395,21 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::SetActiveSnapshot);
     connect(processingJobsWindow, &JFJochProcessingJobsWindow::writeStatusBar,
             statusbar, &JFJochViewerStatusBar::display);
+    connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
+            processingJobsWindow, &JFJochProcessingJobsWindow::onHttpConnectionChanged);
+
+    // Dock the processing panel in the bottom-right corner, next to the dataset-info plots.
+    auto processingDock = new QDockWidget("Processing", this);
+    processingDock->setAllowedAreas(Qt::BottomDockWidgetArea);
+    processingDock->setFeatures(
+        QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetFloatable | QDockWidget::DockWidgetClosable);
+    processingDock->setWidget(processingJobsWindow);
+    addDockWidget(Qt::BottomDockWidgetArea, processingDock);
+    if (lastDatasetInfoDock) {
+        splitDockWidget(lastDatasetInfoDock, processingDock, Qt::Horizontal);
+        resizeDocks({lastDatasetInfoDock, processingDock}, {650, 350}, Qt::Horizontal);
+    }
+    menuBar->AddDockEntry(processingDock, "Processing");
 
     if (!file.isEmpty())
         LoadFile(file, 0, 1, false);
@@ -428,6 +443,7 @@ void JFJochViewerWindow::NewDatasetInfo() {
     dock->setAttribute(Qt::WA_DeleteOnClose);
     dock->setWidget(info);
     addDockWidget(Qt::BottomDockWidgetArea, dock);
+    lastDatasetInfoDock = dock;
 
     // Wire signals like the initial dataset_info
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 549bc15d..38d5153a 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -14,6 +14,7 @@
 #include "toolbar/JFJochViewerToolbarDisplay.h"
 
 class JFJochProcessingJobsWindow;
+class QDockWidget;
 
 class JFJochViewerWindow : public QMainWindow {
 Q_OBJECT
@@ -34,6 +35,8 @@ private:
 
     QProgressDialog *retryDialog = nullptr;
 
+    QDockWidget *lastDatasetInfoDock = nullptr;   // most recent dataset-info dock, for docking layout
+
     QThread *reading_thread;
 
     void keyPressEvent(QKeyEvent *event) override;
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 627a1be1..4ed1805f 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -13,11 +13,13 @@
 #include <QFileInfo>
 #include <QFormLayout>
 #include <QHeaderView>
+#include <QLabel>
 #include <QLineEdit>
 #include <QMessageBox>
 #include <QProgressBar>
 #include <QPushButton>
 #include <QSpinBox>
+#include <QStackedWidget>
 #include <QTableWidget>
 #include <QToolBar>
 #include <QVBoxLayout>
@@ -34,9 +36,8 @@ namespace {
 }
 
 JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent)
-    : JFJochHelperWindow(parent), worker_(worker) {
+    : QWidget(parent), worker_(worker) {
     setWindowTitle("Processing");
-    resize(720, 280);
 
     controller_ = new JFJochProcessController(this);
     connect(controller_, &JFJochProcessController::phaseChanged, this, &JFJochProcessingJobsWindow::onPhase);
@@ -45,13 +46,13 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     connect(controller_, &JFJochProcessController::failed, this, &JFJochProcessingJobsWindow::onFailed);
     connect(controller_, &JFJochProcessController::liveDataset, this, &JFJochProcessingJobsWindow::liveDataset);
 
-    auto *toolbar = addToolBar("Jobs");
-    toolbar->setMovable(false);
-    toolbar->addAction("New job…", this, &JFJochProcessingJobsWindow::newJob);
-    toolbar->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
-    toolbar->addSeparator();
-    toolbar->addAction("View results", this, &JFJochProcessingJobsWindow::viewResults);
-    toolbar->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
+    toolbar_ = new QToolBar("Jobs", this);
+    toolbar_->setMovable(false);
+    toolbar_->addAction("New job…", this, &JFJochProcessingJobsWindow::newJob);
+    toolbar_->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
+    toolbar_->addSeparator();
+    toolbar_->addAction("View results", this, &JFJochProcessingJobsWindow::viewResults);
+    toolbar_->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
 
     table_ = new QTableWidget(0, COL_COUNT, this);
     table_->setHorizontalHeaderLabels({"Name", "Mode", "Images", "Status", "Index %", "Unit cell"});
@@ -59,7 +60,26 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     table_->setSelectionBehavior(QAbstractItemView::SelectRows);
     table_->setSelectionMode(QAbstractItemView::SingleSelection);
     table_->setEditTriggers(QAbstractItemView::NoEditTriggers);
-    setCentralWidget(table_);
+
+    auto *message = new QLabel("Dataset re-processing is currently available only in File mode.\n\n"
+                               "Open a stored HDF5 file to run processing jobs.", this);
+    message->setAlignment(Qt::AlignCenter);
+    message->setWordWrap(true);
+
+    stack_ = new QStackedWidget(this);
+    stack_->addWidget(table_);     // page 0
+    stack_->addWidget(message);    // page 1
+
+    auto *layout = new QVBoxLayout(this);
+    layout->setContentsMargins(0, 0, 0, 0);
+    layout->addWidget(toolbar_);
+    layout->addWidget(stack_);
+}
+
+void JFJochProcessingJobsWindow::onHttpConnectionChanged(bool connected, QString addr) {
+    // Re-processing reads a stored HDF5 file; it is not available for the live HTTP stream.
+    stack_->setCurrentIndex(connected ? 1 : 0);
+    toolbar_->setEnabled(!connected);
 }
 
 int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec &spec) {
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index 8302a743..4394cbcf 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -4,20 +4,23 @@
 #pragma once
 
 #include <QString>
+#include <QWidget>
 #include <vector>
 
-#include "JFJochHelperWindow.h"
 #include "../JFJochProcessController.h"
 #include "../JFJochImageReadingWorker.h"   // ReprocessingInputs
 
 class QTableWidget;
 class QProgressBar;
+class QStackedWidget;
+class QToolBar;
 
-// Makes processing a first-class GUI activity: a table of processing jobs run on the current
-// dataset. A job can be run locally (off the GUI thread, via JFJochProcessController) or its
-// jfjoch_process command line copied for a cluster. A finished local run is registered as a
-// reader snapshot so its results become a selectable view of the dataset.
-class JFJochProcessingJobsWindow : public JFJochHelperWindow {
+// Makes processing a first-class GUI activity: a dockable panel with a table of processing jobs run
+// on the current dataset. A job can be run locally (off the GUI thread, via JFJochProcessController)
+// or its jfjoch_process command line copied for a cluster. A finished local run is registered as a
+// reader snapshot so its results become a selectable view of the dataset. Re-processing reads a
+// stored HDF5 file, so the panel shows an explanatory message while connected to a live HTTP stream.
+class JFJochProcessingJobsWindow : public QWidget {
     Q_OBJECT
 public:
     explicit JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent = nullptr);
@@ -29,6 +32,9 @@ signals:
     // Live per-image results while a job runs, for the dataset-info plots.
     void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
 
+public slots:
+    void onHttpConnectionChanged(bool connected, QString addr);
+
 private slots:
     void newJob();
     void cancelJob();
@@ -62,6 +68,8 @@ private:
 
     JFJochImageReadingWorker *worker_;
     JFJochProcessController *controller_;
+    QToolBar *toolbar_;
+    QStackedWidget *stack_;                 // page 0: jobs table, page 1: HTTP-mode message
     QTableWidget *table_;
     QProgressBar *running_bar_ = nullptr;   // lives in the running row's Status cell
     int running_row_ = -1;
-- 
2.52.0


From 42219d8c5b36ed34dede82d801704360ec490460 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 09:58:51 +0200
Subject: [PATCH 185/228] viewer: fix bottom-dock height, window size, and
 snapshot-switch lag

Regressions from docking the processing panel + live plots:
- Default window size is now screen-aware (fits a laptop) instead of a fixed
  1200x1200.
- Give the bottom dock area a guaranteed height (resizeDocks vertical) and a
  minimum height on the dataset-info chart, so the plot and its axis labels stay
  visible next to the processing panel.
- Activating a metadata snapshot (Show original / View results) no longer re-runs
  full analysis: it re-reads the image against the snapshot's stored results with
  reanalysis suppressed, instead of re-indexing on every switch.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp | 8 +++++++-
 viewer/JFJochViewerDatasetInfo.cpp  | 1 +
 viewer/JFJochViewerWindow.cpp       | 8 +++++++-
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 7614cfd6..7ed4f76f 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -949,8 +949,14 @@ void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
         names << QString::fromStdString(n);
     emit snapshotsChanged(names, QString::fromStdString(file_reader.ActiveSnapshot()));
 
-    if (current_image.has_value())
+    if (current_image.has_value()) {
+        // A snapshot carries its own per-image results; just re-read the image against the new
+        // metadata source, never re-run analysis (that would re-index on every snapshot switch).
+        const bool prev_reanalyze = auto_reanalyze;
+        auto_reanalyze = false;
         LoadImage_i(current_image.value(), current_summation);
+        auto_reanalyze = prev_reanalyze;
+    }
 }
 
 void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString name, QString master_path) {
diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 8301746e..9dfd709a 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -27,6 +27,7 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
 
     stack = new QStackedWidget(this);
     chart_view = new JFJochDatasetInfoChartView(this);
+    chart_view->setMinimumHeight(200);   // keep the plot readable even when the dock is small
     grid_scan_image = new JFJochGridScanImage(this);
 
     stack->addWidget(chart_view);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index d86e4907..30919876 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -7,6 +7,8 @@
 #include <QThread>
 #include <QDockWidget>
 #include <QKeyEvent>
+#include <QGuiApplication>
+#include <QScreen>
 
 #include "JFJochImageReadingWorker.h"
 #include "image_viewer/JFJochDiffractionImage.h"
@@ -54,7 +56,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     setStyleSheet(stylesheet);
     setWindowTitle("Jungfraujoch image viewer");
-    resize(1200, 1200);
+    // Start large on a big display but fit within a laptop screen.
+    const QRect avail = QGuiApplication::primaryScreen()->availableGeometry();
+    resize(qMin(1200, avail.width() - 100), qMin(1100, avail.height() - 100));
 
     SpotFindingSettings spot_finding_settings = DiffractionExperiment::DefaultDataProcessingSettings();
 
@@ -408,6 +412,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     if (lastDatasetInfoDock) {
         splitDockWidget(lastDatasetInfoDock, processingDock, Qt::Horizontal);
         resizeDocks({lastDatasetInfoDock, processingDock}, {650, 350}, Qt::Horizontal);
+        // Give the bottom area enough height so the plots and their labels are fully visible.
+        resizeDocks({lastDatasetInfoDock, processingDock}, {340, 340}, Qt::Vertical);
     }
     menuBar->AddDockEntry(processingDock, "Processing");
 
-- 
2.52.0


From b735aec1c4cb7dc3b1acd317e1c887f8cf7dd6e9 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 11:09:21 +0200
Subject: [PATCH 186/228] viewer: show effective indexing algorithm; disable
 GPU options without CUDA

- The Indexing tab now shows what the selected algorithm resolves to on this
  machine/dataset ("Effective on this system: ..."), mirroring
  DiffractionExperiment::GetIndexingAlgorithm() so Auto is no longer ambiguous
  (GPU present? unit cell known?). Cell-known state is forwarded from the loaded
  dataset via JFJochSettingsWindow::datasetLoaded.
- FFBIDX and FFT (GPU) radio options are disabled on builds without CUDA, where
  only the FFTW CPU indexer exists.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp                 |  2 +
 viewer/windows/JFJochSettingsWindow.cpp       |  4 ++
 viewer/windows/JFJochSettingsWindow.h         |  3 ++
 .../windows/JFJochViewerProcessingWindow.cpp  | 54 +++++++++++++++++++
 viewer/windows/JFJochViewerProcessingWindow.h |  7 +++
 5 files changed, 70 insertions(+)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 30919876..9c5491cc 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -266,6 +266,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
             reflectionWindow, &JFJochViewerReflectionListWindow::imageLoaded);
 
+    connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
+            settingsWindow, &JFJochSettingsWindow::datasetLoaded);
     connect(settingsWindow, &JFJochSettingsWindow::spotFindingChanged,
             reading_worker, &JFJochImageReadingWorker::UpdateSpotFindingSettings);
     connect(settingsWindow, &JFJochSettingsWindow::braggChanged,
diff --git a/viewer/windows/JFJochSettingsWindow.cpp b/viewer/windows/JFJochSettingsWindow.cpp
index 2f5f2ca0..1988d5a1 100644
--- a/viewer/windows/JFJochSettingsWindow.cpp
+++ b/viewer/windows/JFJochSettingsWindow.cpp
@@ -39,3 +39,7 @@ JFJochSettingsWindow::JFJochSettingsWindow(const SpotFindingSettings &spot, cons
     connect(m_scaling, &JFJochScalingPanel::settingsChanged,
             this, &JFJochSettingsWindow::scalingChanged);
 }
+
+void JFJochSettingsWindow::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> in_dataset) {
+    m_processing->setUnitCellKnown(in_dataset && in_dataset->experiment.GetUnitCell().has_value());
+}
diff --git a/viewer/windows/JFJochSettingsWindow.h b/viewer/windows/JFJochSettingsWindow.h
index ccb2dc27..387810f5 100644
--- a/viewer/windows/JFJochSettingsWindow.h
+++ b/viewer/windows/JFJochSettingsWindow.h
@@ -25,6 +25,9 @@ public:
                          const AzimuthalIntegrationSettings &azint, const BraggIntegrationSettings &bragg,
                          const ScalingSettings &scaling, QWidget *parent = nullptr);
 
+    // Forwards the dataset's unit-cell state to the indexing tab (to resolve the Auto algorithm).
+    void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> in_dataset) override;
+
 signals:
     void spotFindingChanged(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
     void azintChanged(const AzimuthalIntegrationSettings &settings);
diff --git a/viewer/windows/JFJochViewerProcessingWindow.cpp b/viewer/windows/JFJochViewerProcessingWindow.cpp
index 6df8821c..a5cdc3a1 100644
--- a/viewer/windows/JFJochViewerProcessingWindow.cpp
+++ b/viewer/windows/JFJochViewerProcessingWindow.cpp
@@ -10,9 +10,21 @@
 #include <QRadioButton>
 #include <vector>
 
+#include "../../common/CUDAWrapper.h"   // get_gpu_count()
+
 namespace {
     struct RadioChoice { const char *label; int value; };
 
+    QString algorithm_name(IndexingAlgorithmEnum a) {
+        switch (a) {
+            case IndexingAlgorithmEnum::FFBIDX: return "FFBIDX (GPU)";
+            case IndexingAlgorithmEnum::FFT:    return "FFT (GPU)";
+            case IndexingAlgorithmEnum::FFTW:   return "FFTW (CPU)";
+            case IndexingAlgorithmEnum::Auto:   return "Auto";
+            default:                            return "None";
+        }
+    }
+
     // A titled group of mutually-exclusive radio buttons, with an optional explanatory line.
     QGroupBox *MakeRadioGroup(const QString &title, const QString &help,
                               const std::vector<RadioChoice> &choices, int current,
@@ -128,6 +140,19 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
          {"None — skip indexing", static_cast<int>(IndexingAlgorithmEnum::None)}},
         static_cast<int>(m_indexing.GetAlgorithm()), m_indexAlgGroup, m_indexingPage));
 
+#ifndef JFJOCH_USE_CUDA
+    // The GPU indexers are not built without CUDA - only FFTW (CPU) is available.
+    for (int id: {static_cast<int>(IndexingAlgorithmEnum::FFBIDX), static_cast<int>(IndexingAlgorithmEnum::FFT)}) {
+        if (auto *button = m_indexAlgGroup->button(id)) {
+            button->setEnabled(false);
+            button->setToolTip("Requires a CUDA build");
+        }
+    }
+#endif
+
+    m_resolvedAlgLabel = new QLabel(m_indexingPage);
+    indexLayout->addWidget(m_resolvedAlgLabel);
+
     m_geomRefGroup = new QButtonGroup(this);
     indexLayout->addWidget(MakeRadioGroup(
         "Geometry refinement",
@@ -238,6 +263,7 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
 
     connect(m_indexAlgGroup, &QButtonGroup::idClicked, [this](int id) {
         m_indexing.Algorithm(static_cast<IndexingAlgorithmEnum>(id));
+        UpdateResolvedAlgorithmLabel();
         Update();
     });
 
@@ -271,9 +297,37 @@ JFJochViewerProcessingWindow::JFJochViewerProcessingWindow(const SpotFindingSett
         m_settings.ice_ring_width_Q_recipA = static_cast<float>(val);
         Update();
     });
+
+    UpdateResolvedAlgorithmLabel();
 }
 
 void JFJochViewerProcessingWindow::Update() {
     const auto max_spots = std::lround(m_maxSpotCount->value());
     emit settingsChanged(m_settings, m_indexing, max_spots);
 }
+
+void JFJochViewerProcessingWindow::setUnitCellKnown(bool known) {
+    m_unitCellKnown = known;
+    UpdateResolvedAlgorithmLabel();
+}
+
+void JFJochViewerProcessingWindow::UpdateResolvedAlgorithmLabel() {
+    // Mirror DiffractionExperiment::GetIndexingAlgorithm() so the user sees what Auto/FFBIDX
+    // actually resolve to on this machine (GPU present?) and dataset (unit cell known?).
+    const bool gpu = get_gpu_count() > 0;
+    IndexingAlgorithmEnum resolved;
+    switch (m_indexing.GetAlgorithm()) {
+        case IndexingAlgorithmEnum::FFBIDX:
+            resolved = m_unitCellKnown ? IndexingAlgorithmEnum::FFBIDX : IndexingAlgorithmEnum::None;
+            break;
+        case IndexingAlgorithmEnum::Auto:
+            resolved = !gpu ? IndexingAlgorithmEnum::FFTW
+                            : (m_unitCellKnown ? IndexingAlgorithmEnum::FFBIDX : IndexingAlgorithmEnum::FFT);
+            break;
+        case IndexingAlgorithmEnum::FFT:  resolved = IndexingAlgorithmEnum::FFT;  break;
+        case IndexingAlgorithmEnum::FFTW: resolved = IndexingAlgorithmEnum::FFTW; break;
+        default:                          resolved = IndexingAlgorithmEnum::None; break;
+    }
+    m_resolvedAlgLabel->setText("Effective on this system: " + algorithm_name(resolved)
+                                + (gpu ? "" : "  (no GPU detected)"));
+}
diff --git a/viewer/windows/JFJochViewerProcessingWindow.h b/viewer/windows/JFJochViewerProcessingWindow.h
index 0049f9fe..ee37c1d7 100644
--- a/viewer/windows/JFJochViewerProcessingWindow.h
+++ b/viewer/windows/JFJochViewerProcessingWindow.h
@@ -37,6 +37,8 @@ class JFJochViewerProcessingWindow : public JFJochHelperWindow {
 
     QButtonGroup *m_indexAlgGroup;                 // indexing algorithm (FFBIDX/FFT/FFTW/Auto/None)
     QButtonGroup *m_geomRefGroup;                  // geometry refinement (None/Orientation/Beam/Pixel)
+    QLabel *m_resolvedAlgLabel;                    // what Auto/FFBIDX resolves to on this system
+    bool m_unitCellKnown = false;                  // drives FFBIDX vs FFT resolution of Auto
 
     SliderPlusBox *m_idxTolerance;                 // [0.0 .. 0.5], step 0.001
     SliderPlusBox *m_idxUnitCellDistTolerance;     // [0.0001 .. 0.2001], step 0.0001
@@ -52,6 +54,7 @@ class JFJochViewerProcessingWindow : public JFJochHelperWindow {
     IndexingSettings m_indexing;
 
     void Update();
+    void UpdateResolvedAlgorithmLabel();   // refresh the "effective on this system" hint
 public:
     explicit JFJochViewerProcessingWindow(const SpotFindingSettings &settings, const IndexingSettings& indexing,
         QWidget *parent = nullptr);
@@ -60,6 +63,10 @@ public:
     QWidget *TakeSpotFindingPage() { return m_spotFindingPage; }
     QWidget *TakeIndexingPage() { return m_indexingPage; }
 
+public slots:
+    // Whether the current dataset has a known unit cell (affects how Auto/FFBIDX resolve).
+    void setUnitCellKnown(bool known);
+
 signals:
     void settingsChanged(const SpotFindingSettings &settings, const IndexingSettings &indexing, int64_t max_spots);
 };
-- 
2.52.0


From aceff23ce20eb4656bac3bf1c7ffb8971a481be1 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 11:28:47 +0200
Subject: [PATCH 187/228] viewer: overlay one plot line per processing run
 (with editable names)

The dataset-info plot now overlays every run as a separate named line instead of
replacing the plot when a snapshot is activated:

- Reader gains AllSnapshotDatasets() (every snapshot's dataset, Original first).
- The worker owns the run collection: a stable snapshot id plus an editable
  display label (RunData), emitted as runsChanged(runs, active_id) on file open,
  snapshot register, activate and rename. RenameRun(id, label) updates the legend
  label without touching the reader key (decoupled id vs label).
- The chart view draws the active run as the primary series (markers, hover,
  binning, axes) and the other runs as overlay lines sharing its axes, with a
  legend shown when overlaying (appendSeries factored out for both).
- The dataset-info widget holds the run list + the live run, extracts the selected
  metric from each (ExtractMetric), and unions the available metrics across runs.
- The live run is its own "Live" overlay (lightweight per-tick refresh, no combo
  rebuild); it is cleared on finish so the persisted snapshot takes over.
- The processing jobs table gets a "Started" column and an editable Name column;
  editing a name renames that run's legend label.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHDF5Reader.cpp                   |  14 ++
 reader/JFJochHDF5Reader.h                     |   3 +
 viewer/CMakeLists.txt                         |   1 +
 viewer/JFJochImageReadingWorker.cpp           |  37 +++-
 viewer/JFJochImageReadingWorker.h             |   8 +-
 viewer/JFJochViewerDatasetInfo.cpp            | 172 ++++++++++--------
 viewer/JFJochViewerDatasetInfo.h              |  13 +-
 viewer/JFJochViewerWindow.cpp                 |  15 +-
 viewer/JFJochViewerWindow.h                   |   2 +
 viewer/RunData.h                              |  22 +++
 viewer/charts/JFJochDatasetInfoChartView.cpp  | 120 ++++++++----
 viewer/charts/JFJochDatasetInfoChartView.h    |  43 ++---
 viewer/windows/JFJochProcessingJobsWindow.cpp |  61 +++++--
 viewer/windows/JFJochProcessingJobsWindow.h   |  10 +-
 14 files changed, 358 insertions(+), 163 deletions(-)
 create mode 100644 viewer/RunData.h

diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index de90417d..e5b60f71 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -178,3 +178,17 @@ std::string JFJochHDF5Reader::ActiveSnapshot() const {
     std::unique_lock ul(hdf5_mutex);
     return active_snapshot_;
 }
+
+std::vector<std::pair<std::string, std::shared_ptr<const JFJochReaderDataset>>>
+JFJochHDF5Reader::AllSnapshotDatasets() const {
+    std::unique_lock ul(hdf5_mutex);
+    std::vector<std::pair<std::string, std::shared_ptr<const JFJochReaderDataset>>> out;
+    out.reserve(snapshots_.size());
+    // "Original" first, then the rest, so overlay colours stay stable across updates.
+    if (auto it = snapshots_.find("Original"); it != snapshots_.end())
+        out.emplace_back(it->first, it->second->Dataset());
+    for (const auto &[name, source]: snapshots_)
+        if (name != "Original")
+            out.emplace_back(name, source->Dataset());
+    return out;
+}
diff --git a/reader/JFJochHDF5Reader.h b/reader/JFJochHDF5Reader.h
index 3c69cc0e..1af4a689 100644
--- a/reader/JFJochHDF5Reader.h
+++ b/reader/JFJochHDF5Reader.h
@@ -63,4 +63,7 @@ public:
     void SetActiveSnapshot(const std::string &name);
     std::vector<std::string> SnapshotNames() const;
     std::string ActiveSnapshot() const;
+
+    // All snapshot datasets (name -> dataset), for overlaying every run's plots at once.
+    std::vector<std::pair<std::string, std::shared_ptr<const JFJochReaderDataset>>> AllSnapshotDatasets() const;
 };
diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 8bddcb3f..2d41295f 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -29,6 +29,7 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         image_viewer/JFJochSimpleImage.h
         JFJochImageReadingWorker.cpp
         JFJochImageReadingWorker.h
+        RunData.h
         JFJochProcessController.cpp
         JFJochProcessController.h
         JFJochViewerDatasetInfo.cpp
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 7ed4f76f..f7a1d18b 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -97,6 +97,8 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
     qRegisterMetaType<ROIDefinition>("ROIDefinition");
     qRegisterMetaType<BraggIntegrationSettings>("BraggIntegrationSettings");
     qRegisterMetaType<ScalingSettings>("ScalingSettings");
+    qRegisterMetaType<RunData>("RunData");
+    qRegisterMetaType<QVector<RunData>>("QVector<RunData>");
     spot_finding_settings = settings;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
@@ -287,6 +289,12 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
 
         emit datasetLoaded(dataset);
 
+        // Reset the run collection for the freshly opened file (file mode only has snapshots).
+        run_labels_.clear();
+        if (!http_mode)
+            run_labels_["Original"] = "Original";
+        EmitRuns_i();
+
         auto end = std::chrono::high_resolution_clock::now();
         auto duration = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
         logger.Info(fmt::format("Loaded file {} in {} ms", filename.toStdString(), duration));
@@ -948,6 +956,7 @@ void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
     for (const auto &n: file_reader.SnapshotNames())
         names << QString::fromStdString(n);
     emit snapshotsChanged(names, QString::fromStdString(file_reader.ActiveSnapshot()));
+    EmitRuns_i();
 
     if (current_image.has_value()) {
         // A snapshot carries its own per-image results; just re-read the image against the new
@@ -959,17 +968,37 @@ void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
     }
 }
 
-void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString name, QString master_path) {
+void JFJochImageReadingWorker::EmitRuns_i() {
+    // Assumes m locked! Build the run list (every snapshot dataset + its display label).
+    QVector<RunData> runs;
+    if (!http_mode) {
+        for (const auto &[id, dataset]: file_reader.AllSnapshotDatasets()) {
+            const auto it = run_labels_.find(id);
+            const QString label = (it != run_labels_.end()) ? it->second : QString::fromStdString(id);
+            runs.push_back(RunData{QString::fromStdString(id), label, dataset});
+        }
+    }
+    emit runsChanged(runs, http_mode ? QString() : QString::fromStdString(file_reader.ActiveSnapshot()));
+}
+
+void JFJochImageReadingWorker::RenameRun(QString id, QString label) {
+    QMutexLocker ul(&m);
+    run_labels_[id.toStdString()] = label;
+    EmitRuns_i();
+}
+
+void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString id, QString label, QString master_path) {
     QMutexLocker ul(&m);
     if (http_mode) {
         logger.Error("Processing snapshots are only available for files");
         return;
     }
     try {
-        file_reader.RegisterSnapshot(name.toStdString(), master_path.toStdString());
-        ActivateSnapshot_i(name);
+        file_reader.RegisterSnapshot(id.toStdString(), master_path.toStdString());
+        run_labels_[id.toStdString()] = label;
+        ActivateSnapshot_i(id);   // activates + emits datasetLoaded / snapshotsChanged / runsChanged
     } catch (const std::exception &e) {
-        logger.Error("Failed to register snapshot {}: {}", name.toStdString(), e.what());
+        logger.Error("Failed to register snapshot {}: {}", id.toStdString(), e.what());
         emit fileLoadError("Snapshot error", QString::fromStdString(e.what()));
     }
 }
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index beadf56c..9a3092ab 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -46,6 +46,8 @@ struct ReprocessingInputs {
     SpotFindingSettings spot_finding;
 };
 
+#include "RunData.h"
+
 class JFJochImageReadingWorker : public QObject {
     Q_OBJECT
 
@@ -69,6 +71,7 @@ private:
     // Once the user edits ROIs they override whatever the file carried, for this and
     // every subsequently loaded image, until a new file is opened.
     std::optional<ROIDefinition> roi_override_;
+    std::map<std::string, QString> run_labels_;   // snapshot id -> editable display label
     IndexingSettings indexing_settings;
     AzimuthalIntegrationSettings azint_settings;
     BraggIntegrationSettings bragg_settings;
@@ -138,6 +141,7 @@ private:
     void ApplyROIOverrideToImage_i();   // rewrite current_image_ptr's dataset with roi_override_
     void setAutoLoadMode_i(AutoloadMode mode);
     void ActivateSnapshot_i(const QString &name);
+    void EmitRuns_i();   // emit runsChanged with every snapshot dataset + its label
 
 signals:
     void datasetLoaded(std::shared_ptr<const JFJochReaderDataset>);
@@ -154,6 +158,7 @@ signals:
     void httpConnectionChanged(bool connected, QString addr);
     void liveRateChanged(double hz);
     void snapshotsChanged(QStringList names, QString active);
+    void runsChanged(QVector<RunData> runs, QString active_id);
 
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
@@ -202,6 +207,7 @@ public slots:
 
     // Register a reprocessing result (_process.h5) as a metadata snapshot over the same images and
     // make it the active dataset; SetActiveSnapshot switches between registered snapshots.
-    void RegisterProcessingSnapshot(QString name, QString master_path);
+    void RegisterProcessingSnapshot(QString id, QString label, QString master_path);
     void SetActiveSnapshot(QString name);
+    void RenameRun(QString id, QString label);   // change a run's display label (legend)
 };
diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 9dfd709a..e4bb366d 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -83,7 +83,20 @@ void JFJochViewerDatasetInfo::UpdateLabels() {
         combo_box->addItem("Spot count (ice rings)", 3);
         combo_box->addItem("Spot count (low res.)", 4);
 
-        if (!dataset->indexing_result.empty()) {
+        // Offer indexing/scaling metrics if the active run, any overlay run, or the live run has them.
+        bool has_indexing = !dataset->indexing_result.empty();
+        bool has_scale = !dataset->image_scale_factor.empty();
+        for (const auto &r: runs_)
+            if (r.dataset) {
+                has_indexing = has_indexing || !r.dataset->indexing_result.empty();
+                has_scale = has_scale || !r.dataset->image_scale_factor.empty();
+            }
+        if (live_run_) {
+            has_indexing = has_indexing || !live_run_->indexing_result.empty();
+            has_scale = has_scale || !live_run_->image_scale_factor.empty();
+        }
+
+        if (has_indexing) {
             combo_box->insertSeparator(1000);
             combo_box->addItem("Indexing result", 5);
             combo_box->addItem("Profile radius", 6);
@@ -93,7 +106,7 @@ void JFJochViewerDatasetInfo::UpdateLabels() {
             combo_box->addItem("Indexing lattice count", 13);
         }
 
-        if (!dataset->image_scale_factor.empty()) {
+        if (has_scale) {
             combo_box->insertSeparator(1000);
             combo_box->addItem("Scale factor", 10);
             combo_box->addItem("CC", 11);
@@ -122,7 +135,7 @@ void JFJochViewerDatasetInfo::datasetLoaded(std::shared_ptr<const JFJochReaderDa
             combo_box->setCurrentIndex(0);
         UpdatePlot();
     } else {
-        chart_view->loadValues<float>({}, 0, false);
+        chart_view->loadValues({}, 0, false);
         grid_scan_image->clear();
         UpdateLabels();
     }
@@ -140,6 +153,46 @@ void JFJochViewerDatasetInfo::imageSelectedInChart(int64_t number) {
     emit imageSelected(number, 1);
 }
 
+std::vector<float> JFJochViewerDatasetInfo::ExtractMetric(const JFJochReaderDataset &ds, int val,
+                                                          bool &one_over_d2) const {
+    one_over_d2 = false;
+    std::vector<float> data;
+    if (val == 0) data = ds.bkg_estimate;
+    else if (val == 1) data = ds.spot_count;
+    else if (val == 2) data = ds.spot_count_indexed;
+    else if (val == 3) data = ds.spot_count_ice_rings;
+    else if (val == 4) data = ds.spot_count_low_res;
+    else if (val == 5) data = ds.indexing_result;
+    else if (val == 6) data = ds.profile_radius;
+    else if (val == 7) { data = ds.resolution_estimate; one_over_d2 = true; }
+    else if (val == 8) data = ds.b_factor;
+    else if (val == 9) data = ds.mosaicity_deg;
+    else if (val == 10) data = ds.image_scale_factor;
+    else if (val == 11) data = ds.image_scale_cc;
+    else if (val == 12) data = ds.integrated_reflections;
+    else if (val == 13) data = ds.indexing_lattice_count;
+    else if (val >= 100) {
+        const int roi_index = (val - 100) / 4;
+        if (val % 4 == 0) {
+            if (roi_index < ds.roi_sum.size() && ds.roi_sum.size() == ds.roi_npixel.size())
+                for (int i = 0; i < ds.roi_sum[roi_index].size(); i++)
+                    data.push_back(static_cast<float>(ds.roi_sum[roi_index][i])
+                                   / static_cast<float>(ds.roi_npixel[roi_index][i]));
+        } else if (val % 4 == 1) {
+            if (roi_index < ds.roi_sum.size()) {
+                data.reserve(ds.roi_sum[roi_index].size());
+                for (auto &v: ds.roi_sum[roi_index])
+                    data.push_back(v);
+            }
+        } else if (val % 4 == 2) {
+            if (roi_index < ds.roi_x.size()) data = ds.roi_x[roi_index];
+        } else if (val % 4 == 3) {
+            if (roi_index < ds.roi_y.size()) data = ds.roi_y[roi_index];
+        }
+    }
+    return data;
+}
+
 void JFJochViewerDatasetInfo::UpdatePlot() {
     int index = combo_box->currentIndex();
     if (combo_box->count() == 0 || index < 0)
@@ -147,83 +200,58 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
 
     int val = combo_box->itemData(index).toInt();
 
-    if (dataset) {
-        int64_t image_number = 0;
-        if (image)
-            image_number = image->ImageData().number;
+    if (!dataset) {
+        grid_button->setEnabled(false);
+        return;
+    }
 
-        bool one_over_d2 = false;
-        std::vector<float> data;
-        if (val == 0)
-            data = dataset->bkg_estimate;
-        else if (val == 1)
-            data = dataset->spot_count;
-        else if (val == 2)
-            data = dataset->spot_count_indexed;
-        else if (val == 3)
-            data = dataset->spot_count_ice_rings;
-        else if (val == 4)
-            data = dataset->spot_count_low_res;
-        else if (val == 5)
-            data = dataset->indexing_result;
-        else if (val == 6)
-            data = dataset->profile_radius;
-        else if (val == 7) {
-            data = dataset->resolution_estimate;
-            one_over_d2 = true;
-        } else if (val == 8) {
-            data = dataset->b_factor;
-        } else if (val == 9) {
-            data = dataset->mosaicity_deg;
-        } else if (val == 10) {
-            data = dataset->image_scale_factor;
-        } else if (val == 11) {
-            data = dataset->image_scale_cc;
-        } else if (val == 12) {
-            data = dataset->integrated_reflections;
-        } else if (val == 13) {
-            data = dataset->indexing_lattice_count;
-        } else if (val >= 100) {
-            int roi_index = (val - 100) / 4;
+    const int64_t image_number = image ? image->ImageData().number : 0;
 
-            if (val % 4 == 0) {
-                if (roi_index < dataset->roi_sum.size() && dataset->roi_sum.size() == dataset->roi_npixel.size()) {
-                    for(int i = 0; i < dataset->roi_sum[roi_index].size(); i++) {
-                        data.push_back(static_cast<float>(dataset->roi_sum[roi_index][i])
-                            / static_cast<float>(dataset->roi_npixel[roi_index][i]));
-                    }
-                }
-            } else if (val % 4 == 1) {
-                if (roi_index < dataset->roi_sum.size()) {
-                    data.reserve(dataset->roi_sum[roi_index].size());
-                    for (auto &v: dataset->roi_sum[roi_index])
-                        data.push_back(v);
-                }
-            } else if (val % 4 == 2) {
-                if (roi_index < dataset->roi_x.size())
-                    data = dataset->roi_x[roi_index];
-            } else if (val % 4 == 3) {
-                if (roi_index < dataset->roi_y.size())
-                    data = dataset->roi_y[roi_index];
-            }
-        }
+    bool one_over_d2 = false;
+    std::vector<float> data = ExtractMetric(*dataset, val, one_over_d2);
 
-        chart_view->loadValues(data, image_number, one_over_d2, dataset.get());
-        if (dataset->experiment.GetGridScan()) {
-            stack->setCurrentWidget(grid_scan_image);
-            grid_scan_image->loadData(data, dataset->experiment.GetGridScan().value(), one_over_d2);
-            grid_button->setEnabled(true);
-            grid_button->setChecked(true);
-        } else {
-            grid_scan_image->clear();
-            stack->setCurrentWidget(chart_view);
-            grid_button->setEnabled(false);
-        }
+    // One overlay line per other run, plus the in-progress live run.
+    std::vector<JFJochDatasetInfoChartView::NamedSeries> overlays;
+    QString primary_name;
+    for (const auto &run: runs_) {
+        if (run.id == active_id_) { primary_name = run.label; continue; }
+        if (!run.dataset || run.dataset == dataset) continue;   // never draw the active run twice
+        bool ignore = false;
+        overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore)});
+    }
+    if (live_run_ && live_run_ != dataset) {
+        bool ignore = false;
+        overlays.push_back({QStringLiteral("Live"), ExtractMetric(*live_run_, val, ignore)});
+    }
+
+    chart_view->loadValues(data, image_number, one_over_d2, dataset.get(), primary_name, std::move(overlays));
+
+    if (dataset->experiment.GetGridScan()) {
+        stack->setCurrentWidget(grid_scan_image);
+        grid_scan_image->loadData(data, dataset->experiment.GetGridScan().value(), one_over_d2);
+        grid_button->setEnabled(true);
+        grid_button->setChecked(true);
     } else {
+        grid_scan_image->clear();
+        stack->setCurrentWidget(chart_view);
         grid_button->setEnabled(false);
     }
 }
 
+void JFJochViewerDatasetInfo::runsChanged(QVector<RunData> runs, QString active_id) {
+    runs_ = std::move(runs);
+    active_id_ = std::move(active_id);
+    UpdateLabels();
+    if (last_selection < combo_box->count())
+        combo_box->setCurrentIndex(last_selection);
+    UpdatePlot();
+}
+
+void JFJochViewerDatasetInfo::liveRunUpdated(std::shared_ptr<const JFJochReaderDataset> in_dataset) {
+    live_run_ = std::move(in_dataset);
+    UpdatePlot();   // lightweight refresh; no combo rebuild on every live tick
+}
+
 void JFJochViewerDatasetInfo::comboBoxSelected(int index) {
     UpdatePlot();
 }
diff --git a/viewer/JFJochViewerDatasetInfo.h b/viewer/JFJochViewerDatasetInfo.h
index f6eb8be5..1e84f557 100644
--- a/viewer/JFJochViewerDatasetInfo.h
+++ b/viewer/JFJochViewerDatasetInfo.h
@@ -10,21 +10,28 @@
 #include "charts/JFJochDatasetInfoChartView.h"
 #include "../reader/JFJochReader.h"
 #include "image_viewer/JFJochGridScanImage.h"
+#include "RunData.h"
 
 class JFJochViewerDatasetInfo : public QWidget {
     Q_OBJECT
     QComboBox *combo_box;
     JFJochDatasetInfoChartView *chart_view;
     const std::vector<float> *GetDataset();
-    std::shared_ptr<const JFJochReaderDataset> dataset;
+    std::shared_ptr<const JFJochReaderDataset> dataset;     // the active (primary) run
     std::shared_ptr<const JFJochReaderImage> image;
     JFJochGridScanImage *grid_scan_image = nullptr;
 
+    QVector<RunData> runs_;                                 // all runs, for overlay lines
+    QString active_id_;                                     // which run is primary
+    std::shared_ptr<const JFJochReaderDataset> live_run_;   // in-progress reprocessing, if any
+
     QStackedWidget *stack = nullptr;
     QPushButton *grid_button = nullptr;
 
     int last_selection;
     void UpdatePlot();
+    // Pull the metric selected by combo value `val` out of one run's dataset.
+    std::vector<float> ExtractMetric(const JFJochReaderDataset &ds, int val, bool &one_over_d2) const;
 
     void UpdateLabels();
 signals:
@@ -41,6 +48,10 @@ public slots:
     void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
     void imageLoaded(std::shared_ptr<const JFJochReaderImage> image);
     void setColorMap(int color_map);
+    // All runs (original + reprocessing snapshots) and which one is active/primary.
+    void runsChanged(QVector<RunData> runs, QString active_id);
+    // Live results of the in-progress reprocessing run (updated as it goes), or nullptr to clear.
+    void liveRunUpdated(std::shared_ptr<const JFJochReaderDataset> dataset);
 };
 
 
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 9c5491cc..56a4ad1f 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -401,8 +401,15 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::SetActiveSnapshot);
     connect(processingJobsWindow, &JFJochProcessingJobsWindow::writeStatusBar,
             statusbar, &JFJochViewerStatusBar::display);
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::renameRun,
+            reading_worker, &JFJochImageReadingWorker::RenameRun);
     connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
             processingJobsWindow, &JFJochProcessingJobsWindow::onHttpConnectionChanged);
+    connect(reading_worker, &JFJochImageReadingWorker::runsChanged, this,
+            [this](QVector<RunData> runs, QString active) {
+                lastRuns = std::move(runs);
+                lastActiveRunId = std::move(active);
+            });
 
     // Dock the processing panel in the bottom-right corner, next to the dataset-info plots.
     auto processingDock = new QDockWidget("Processing", this);
@@ -442,6 +449,7 @@ void JFJochViewerWindow::NewDatasetInfo() {
     auto info = new JFJochViewerDatasetInfo(this);
     info->datasetLoaded(lastDataset);
     info->imageLoaded(lastImage);
+    info->runsChanged(lastRuns, lastActiveRunId);
 
     auto dock = new QDockWidget(QString("Dataset info"), this);
     dock->setAllowedAreas(Qt::BottomDockWidgetArea);
@@ -458,9 +466,12 @@ void JFJochViewerWindow::NewDatasetInfo() {
             info, &JFJochViewerDatasetInfo::datasetLoaded);
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
             info, &JFJochViewerDatasetInfo::imageLoaded);
-    // Live processing results: refresh the plots while a job runs.
+    // All runs (original + reprocessing snapshots) overlay as separate lines.
+    connect(reading_worker, &JFJochImageReadingWorker::runsChanged,
+            info, &JFJochViewerDatasetInfo::runsChanged);
+    // Live processing results: the in-progress run as its own overlay line.
     connect(processingJobsWindow, &JFJochProcessingJobsWindow::liveDataset,
-            info, &JFJochViewerDatasetInfo::datasetLoaded);
+            info, &JFJochViewerDatasetInfo::liveRunUpdated);
     connect(info, &JFJochViewerDatasetInfo::imageSelected,
             reading_worker, &JFJochImageReadingWorker::LoadImage);
     connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 38d5153a..c1ce10e5 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -32,6 +32,8 @@ private:
 
     std::shared_ptr<const JFJochReaderDataset> lastDataset;  // added
     std::shared_ptr<const JFJochReaderImage> lastImage;      // added
+    QVector<RunData> lastRuns;                               // for dataset-info docks opened later
+    QString lastActiveRunId;
 
     QProgressDialog *retryDialog = nullptr;
 
diff --git a/viewer/RunData.h b/viewer/RunData.h
new file mode 100644
index 00000000..1731832e
--- /dev/null
+++ b/viewer/RunData.h
@@ -0,0 +1,22 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QString>
+#include <QVector>
+#include <QMetaType>
+#include <memory>
+
+#include "../reader/JFJochReaderDataset.h"
+
+// One processing run (the original file or a reprocessing snapshot), for overlaying its plots.
+// id is the stable reader-snapshot key; label is the editable display name shown in the legend.
+struct RunData {
+    QString id;
+    QString label;
+    std::shared_ptr<const JFJochReaderDataset> dataset;
+};
+
+Q_DECLARE_METATYPE(RunData)
+Q_DECLARE_METATYPE(QVector<RunData>)
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index c1f33399..bd73362a 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -128,6 +128,71 @@ void JFJochDatasetInfoChartView::resetZoom() {
     chart()->zoomReset();
 }
 
+void JFJochDatasetInfoChartView::loadValues(const std::vector<float> &input, int64_t image, bool one_over_d2,
+                                            const JFJochReaderDataset *dataset, const QString &primaryName,
+                                            std::vector<NamedSeries> overlays) {
+    m_yOneOverD = one_over_d2;
+    primaryName_ = primaryName;
+
+    // d -> 1/d^2 for resolution plots; identity otherwise. Applied to every series alike.
+    auto transform = [one_over_d2](const std::vector<float> &in, std::vector<float> &out) {
+        out.resize(in.size());
+        for (size_t i = 0; i < in.size(); i++) {
+            if (one_over_d2) {
+                const float d = in[i];
+                out[i] = std::isfinite(d) ? 1.0f / (d * d) : 0.0f;
+            } else
+                out[i] = in[i];
+        }
+    };
+
+    transform(input, values);
+    overlays_ = std::move(overlays);
+    for (auto &ov: overlays_)
+        transform(ov.values, ov.values);   // in-place
+
+    if (dataset != nullptr) {
+        goniometer_axis = dataset->experiment.GetGoniometer();
+        image_time_us = dataset->experiment.GetImageTime().count();
+    } else {
+        goniometer_axis = {};
+        image_time_us = {};
+    }
+
+    curr_image = image;
+    updateChart();
+}
+
+void JFJochDatasetInfoChartView::appendSeries(QLineSeries *s, const std::vector<float> &vals,
+                                              double &mn, double &mx) const {
+    if (binning == 1) {
+        for (int i = 0; i < static_cast<int>(vals.size()); i++) {
+            const double v = vals[static_cast<size_t>(i)];
+            if (!std::isfinite(v)) continue;
+            s->append(i, v);
+            mn = std::min(mn, v);
+            mx = std::max(mx, v);
+        }
+    } else {
+        for (int i = 0; i < static_cast<int>(vals.size() / static_cast<size_t>(binning)); i++) {
+            double tmp = 0.0;
+            int64_t count = 0;
+            for (int b = 0; b < binning; b++) {
+                const int64_t idx = static_cast<int64_t>(i) * binning + b;
+                if (idx >= static_cast<int64_t>(vals.size())) break;
+                const double v = vals[static_cast<size_t>(idx)];
+                if (std::isfinite(v)) { tmp += v; count++; }
+            }
+            if (count > 0) {
+                const double mean = tmp / static_cast<double>(count);
+                s->append((i + 0.5) * binning, mean);
+                mn = std::min(mn, mean);
+                mx = std::max(mx, mean);
+            }
+        }
+    }
+}
+
 void JFJochDatasetInfoChartView::updateChart() {
     // Important: drop any stale QObject pointers BEFORE rebuilding the chart.
     series = nullptr;
@@ -156,44 +221,23 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         // At least one full point
 
         series = new QLineSeries(this);
+        if (!primaryName_.isEmpty())
+            series->setName(primaryName_);
         currentSeries = new QScatterSeries(this);
 
         double dispMin = std::numeric_limits<double>::infinity();
         double dispMax = -std::numeric_limits<double>::infinity();
 
-        if (binning == 1) {
-            for (int i = 0; i < static_cast<int>(values.size()); i++) {
-                if (!std::isfinite(values[static_cast<size_t>(i)])) continue;
-                const double disp = values[static_cast<size_t>(i)];
-                if (!std::isfinite(disp)) continue;
-                series->append(i, disp);
-                if (disp < dispMin) dispMin = disp;
-                if (disp > dispMax) dispMax = disp;
-            }
-        } else {
-            for (int i = 0; i < static_cast<int>(values.size() / static_cast<size_t>(binning)); i++) {
-                double tmp = 0.0;
-                int64_t count = 0;
-                for (int b = 0; b < binning; b++) {
-                    const int64_t idx = static_cast<int64_t>(i) * binning + b;
-                    if (idx >= static_cast<int64_t>(values.size()))
-                        break;
-                    const double v = values[static_cast<size_t>(idx)];
-                    if (std::isfinite(v)) {
-                        tmp += v;
-                        count++;
-                    }
-                }
-                if (count > 0) {
-                    const double mean = tmp / static_cast<double>(count);
-                    const double disp = mean;
-                    if (std::isfinite(disp)) {
-                        series->append((i + 0.5) * binning, disp);
-                        if (disp < dispMin) dispMin = disp;
-                        if (disp > dispMax) dispMax = disp;
-                    }
-                }
-            }
+        appendSeries(series, values, dispMin, dispMax);
+
+        // Overlay runs share the primary's axes and range; build them now so the Y range fits all.
+        std::vector<QLineSeries *> overlayLines;
+        overlayLines.reserve(overlays_.size());
+        for (const auto &ov: overlays_) {
+            auto *line = new QLineSeries(this);
+            line->setName(ov.name);
+            appendSeries(line, ov.values, dispMin, dispMax);
+            overlayLines.push_back(line);
         }
 
         // ---- current point marker as binned value when binning > 1 ----
@@ -366,6 +410,16 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
                 axisY->setLabelsVisible(true);
             }
         }
+
+        // Attach overlay lines to the primary series' final axes; show the legend when overlaying.
+        const auto finalAxes = series->attachedAxes();
+        for (auto *line: overlayLines) {
+            chart()->addSeries(line);
+            for (auto *ax: finalAxes)
+                line->attachAxis(ax);
+        }
+        chart()->legend()->setVisible(!overlays_.empty());
+        chart()->legend()->setAlignment(Qt::AlignBottom);
     }
 }
 
diff --git a/viewer/charts/JFJochDatasetInfoChartView.h b/viewer/charts/JFJochDatasetInfoChartView.h
index f26e5bea..62fa0ca6 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.h
+++ b/viewer/charts/JFJochDatasetInfoChartView.h
@@ -29,6 +29,7 @@ class JFJochDatasetInfoChartView : public QChartView {
     int64_t m_hoverPendingIdx = -1;
 
     std::vector<float> values;
+    QString primaryName_;                 // legend name of the active (primary) run
     int64_t binning = 1;
     int64_t curr_image = 0;
 
@@ -44,6 +45,14 @@ class JFJochDatasetInfoChartView : public QChartView {
     // Build regular (index or goniometer) chart
     void buildTimeDomainChart();
 
+public:
+    // One overlay line (a non-active run), drawn alongside the primary series with a legend entry.
+    struct NamedSeries { QString name; std::vector<float> values; };
+private:
+    std::vector<NamedSeries> overlays_;
+    // Append (binned) finite points of vals to s, extending the [mn, mx] data range.
+    void appendSeries(QLineSeries *s, const std::vector<float> &vals, double &mn, double &mx) const;
+
     // FFT view toggle
     bool m_showFFT = false;
 
@@ -76,36 +85,14 @@ public slots:
     void resetZoom();
 
 public:
-    template<class T>
-    void loadValues(const std::vector<T> &input,
+    // Load the primary (active) run's values plus any overlay runs. one_over_d2 applies the same
+    // d -> 1/d^2 transform to every series; primaryName/overlay names drive the legend.
+    void loadValues(const std::vector<float> &input,
         int64_t image,
         bool one_over_d2,
-        const JFJochReaderDataset *dataset = nullptr) {
-        m_yOneOverD = one_over_d2;
-
-        values.resize(input.size());
-
-        if (dataset != nullptr) {
-            goniometer_axis = dataset->experiment.GetGoniometer();
-            image_time_us = dataset->experiment.GetImageTime().count();
-        } else {
-            goniometer_axis = {};
-            image_time_us = {};
-        }
-
-        for (int i = 0; i < input.size(); i++) {
-            if (one_over_d2) {
-                float d = static_cast<float>(input[i]);
-                if (!std::isfinite(d))
-                    values[i] = 0.0f;
-                else
-                    values[i] = 1.0f / (d * d);
-            } else
-                values[i] = static_cast<float>(input[i]);
-        }
-        curr_image = image;
-        updateChart();
-    }
+        const JFJochReaderDataset *dataset = nullptr,
+        const QString &primaryName = QString(),
+        std::vector<NamedSeries> overlays = {});
 };
 
 
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 4ed1805f..0546bb09 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -8,6 +8,7 @@
 #include <QCheckBox>
 #include <QClipboard>
 #include <QComboBox>
+#include <QDateTime>
 #include <QDialog>
 #include <QDialogButtonBox>
 #include <QFileInfo>
@@ -27,7 +28,7 @@
 #include <thread>
 
 namespace {
-    enum Column { COL_NAME = 0, COL_MODE, COL_IMAGES, COL_STATUS, COL_INDEX, COL_CELL, COL_COUNT };
+    enum Column { COL_NAME = 0, COL_STARTED, COL_MODE, COL_IMAGES, COL_STATUS, COL_INDEX, COL_CELL, COL_COUNT };
 
     int default_threads() {
         const unsigned hc = std::thread::hardware_concurrency();
@@ -55,11 +56,21 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     toolbar_->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
 
     table_ = new QTableWidget(0, COL_COUNT, this);
-    table_->setHorizontalHeaderLabels({"Name", "Mode", "Images", "Status", "Index %", "Unit cell"});
+    table_->setHorizontalHeaderLabels({"Name", "Started", "Mode", "Images", "Status", "Index %", "Unit cell"});
     table_->horizontalHeader()->setStretchLastSection(true);
     table_->setSelectionBehavior(QAbstractItemView::SelectRows);
     table_->setSelectionMode(QAbstractItemView::SingleSelection);
-    table_->setEditTriggers(QAbstractItemView::NoEditTriggers);
+    // Only the Name column is editable (per-item flags); editing it renames the run's legend label.
+    table_->setEditTriggers(QAbstractItemView::DoubleClicked | QAbstractItemView::EditKeyPressed);
+    connect(table_, &QTableWidget::itemChanged, this, [this](QTableWidgetItem *item) {
+        if (item->column() != COL_NAME)
+            return;
+        const int row = item->row();
+        if (row < 0 || row >= static_cast<int>(jobs_.size()) || item->text() == jobs_[row].label)
+            return;
+        jobs_[row].label = item->text();
+        emit renameRun(jobs_[row].id, jobs_[row].label);
+    });
 
     auto *message = new QLabel("Dataset re-processing is currently available only in File mode.\n\n"
                                "Open a stored HDF5 file to run processing jobs.", this);
@@ -210,16 +221,33 @@ void JFJochProcessingJobsWindow::newJob() {
     }
 
     const bool full = spec.mode == ProcessMode::FullAnalysis;
-    const QString name = QStringLiteral("%1 %2").arg(full ? "Full" : "AzInt").arg(++job_counter_);
+    const int run_number = ++job_counter_;
+    const QString label = QStringLiteral("%1 %2").arg(full ? "Full" : "AzInt").arg(run_number);
+    const QString id = QStringLiteral("run-%1").arg(run_number);
+
+    JobInfo info;
+    info.id = id;
+    info.label = label;
+    if (spec.save)
+        info.snapshot_path = QString::fromStdString(config.output_prefix) + "_process.h5";
 
     const int row = table_->rowCount();
     table_->insertRow(row);
-    table_->setItem(row, COL_NAME, new QTableWidgetItem(name));
-    table_->setItem(row, COL_MODE, new QTableWidgetItem(full ? "Full" : "AzInt"));
-    table_->setItem(row, COL_IMAGES, new QTableWidgetItem(spec.images > 0 ? QString::number(spec.images) : "all"));
-    table_->setItem(row, COL_STATUS, new QTableWidgetItem("queued"));
-    table_->setItem(row, COL_INDEX, new QTableWidgetItem("-"));
-    table_->setItem(row, COL_CELL, new QTableWidgetItem("-"));
+    jobs_.push_back(info);   // jobs_[row] must exist before setItem(COL_NAME) fires itemChanged
+
+    auto fixed = [](const QString &text) {   // a non-editable cell
+        auto *cell = new QTableWidgetItem(text);
+        cell->setFlags(cell->flags() & ~Qt::ItemIsEditable);
+        return cell;
+    };
+
+    table_->setItem(row, COL_NAME, new QTableWidgetItem(label));   // editable (default flags)
+    table_->setItem(row, COL_STARTED, fixed(QDateTime::currentDateTime().toString("HH:mm:ss")));
+    table_->setItem(row, COL_MODE, fixed(full ? "Full" : "AzInt"));
+    table_->setItem(row, COL_IMAGES, fixed(spec.images > 0 ? QString::number(spec.images) : "all"));
+    table_->setItem(row, COL_STATUS, fixed("queued"));
+    table_->setItem(row, COL_INDEX, fixed("-"));
+    table_->setItem(row, COL_CELL, fixed("-"));
 
     // A progress bar lives in the Status cell while the job runs; it shows the phase as text until
     // image processing starts, then "<done> / <expected>" with the bar filling in the background.
@@ -230,15 +258,10 @@ void JFJochProcessingJobsWindow::newJob() {
     running_bar_->setFormat("queued");
     table_->setCellWidget(row, COL_STATUS, running_bar_);
 
-    JobInfo info;
-    info.name = name;
-    if (spec.save)
-        info.snapshot_path = QString::fromStdString(config.output_prefix) + "_process.h5";
-    jobs_.push_back(info);
     running_row_ = row;
 
     controller_->start(inputs.file, experiment, inputs.pixel_mask, config);
-    emit writeStatusBar("Started processing job " + name);
+    emit writeStatusBar("Started processing job " + label);
 }
 
 void JFJochProcessingJobsWindow::cancelJob() {
@@ -256,7 +279,7 @@ void JFJochProcessingJobsWindow::viewResults() {
         QMessageBox::information(this, "Processing", "This job has no saved results to view.");
         return;
     }
-    emit activateSnapshot(jobs_[row].name);
+    emit activateSnapshot(jobs_[row].id);
 }
 
 void JFJochProcessingJobsWindow::showOriginal() {
@@ -287,6 +310,7 @@ void JFJochProcessingJobsWindow::onProgress(quint64 done, quint64 total) {
 }
 
 void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
+    emit liveDataset(nullptr);   // the finished run takes over from the live overlay
     const int row = running_row_;
     running_row_ = -1;
     if (row >= 0)
@@ -308,12 +332,13 @@ void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
 
     if (!result.cancelled && result.written_master_path.has_value() && !jobs_[row].snapshot_path.isEmpty()) {
         jobs_[row].has_result = true;
-        emit registerSnapshot(jobs_[row].name, jobs_[row].snapshot_path);   // also activates it
+        emit registerSnapshot(jobs_[row].id, jobs_[row].label, jobs_[row].snapshot_path);   // also activates it
     }
     emit writeStatusBar(result.cancelled ? "Processing cancelled" : "Processing finished");
 }
 
 void JFJochProcessingJobsWindow::onFailed(QString error) {
+    emit liveDataset(nullptr);   // clear the live overlay
     const int row = running_row_;
     running_row_ = -1;
     if (row >= 0)
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index 4394cbcf..c8f0eaa7 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -26,10 +26,11 @@ public:
     explicit JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent = nullptr);
 
 signals:
-    void registerSnapshot(QString name, QString master_path);
-    void activateSnapshot(QString name);
+    void registerSnapshot(QString id, QString label, QString master_path);
+    void activateSnapshot(QString id);
+    void renameRun(QString id, QString label);
     void writeStatusBar(QString message, int timeout_ms = 0);
-    // Live per-image results while a job runs, for the dataset-info plots.
+    // Live per-image results while a job runs, for the dataset-info plots (nullptr clears it).
     void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
 
 public slots:
@@ -47,7 +48,8 @@ private slots:
 
 private:
     struct JobInfo {
-        QString name;
+        QString id;              // stable reader-snapshot key
+        QString label;           // editable display name (legend / table)
         QString snapshot_path;   // empty unless saved
         bool has_result = false;
     };
-- 
2.52.0


From 2af822436eddc20ecd994db86815a2aabe25bad3 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 12:00:15 +0200
Subject: [PATCH 188/228] viewer: remove/clear runs, stable per-run colours,
 processing rate + ETA

- "Remove result" toolbar action drops a reprocessing run: reader RemoveSnapshot
  (Original is protected; if the removed run was active the view falls back to
  Original), worker RemoveRun, and the table row is removed.
- Opening a new file clears the jobs table (worker fileOpened -> clearJobs) to
  match the reader, which already resets snapshots on ReadFile.
- Plot fixes: each run keeps a stable colour by its position (Original = blue),
  so colours no longer swap when the active run changes; the current-image marker
  is hidden from the legend (was the stray "[Image #N]" entry).
- The status bar shows processing rate (Hz) and estimated remaining time while a
  job runs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/JFJochHDF5Reader.cpp                   | 12 ++++++
 reader/JFJochHDF5Reader.h                     |  1 +
 viewer/JFJochImageReadingWorker.cpp           | 11 +++++
 viewer/JFJochImageReadingWorker.h             |  2 +
 viewer/JFJochViewerDatasetInfo.cpp            | 31 ++++++++++---
 viewer/JFJochViewerWindow.cpp                 |  4 ++
 viewer/charts/JFJochDatasetInfoChartView.cpp  | 11 ++++-
 viewer/charts/JFJochDatasetInfoChartView.h    |  7 ++-
 viewer/windows/JFJochProcessingJobsWindow.cpp | 43 +++++++++++++++++++
 viewer/windows/JFJochProcessingJobsWindow.h   |  5 +++
 10 files changed, 119 insertions(+), 8 deletions(-)

diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index e5b60f71..3dfcd9cd 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -152,6 +152,18 @@ void JFJochHDF5Reader::RegisterSnapshot(const std::string &name, const std::stri
     snapshots_[name] = metadata;
 }
 
+void JFJochHDF5Reader::RemoveSnapshot(const std::string &name) {
+    std::unique_lock ul(hdf5_mutex);
+    if (name == "Original")
+        return;   // the original file metadata is always kept
+    snapshots_.erase(name);
+    if (active_snapshot_ == name) {
+        active_metadata_ = snapshots_.at("Original");
+        active_snapshot_ = "Original";
+        SetStartMessage(active_metadata_->Dataset());
+    }
+}
+
 void JFJochHDF5Reader::SetActiveSnapshot(const std::string &name) {
     std::unique_lock ul(hdf5_mutex);
 
diff --git a/reader/JFJochHDF5Reader.h b/reader/JFJochHDF5Reader.h
index 1af4a689..985ace03 100644
--- a/reader/JFJochHDF5Reader.h
+++ b/reader/JFJochHDF5Reader.h
@@ -60,6 +60,7 @@ public:
     // Metadata snapshots over the same images. The original file is registered as "Original" on
     // ReadFile and is the initial active snapshot; reprocessing results can be added later.
     void RegisterSnapshot(const std::string &name, const std::string &master_path);
+    void RemoveSnapshot(const std::string &name);   // "Original" cannot be removed
     void SetActiveSnapshot(const std::string &name);
     std::vector<std::string> SnapshotNames() const;
     std::string ActiveSnapshot() const;
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index f7a1d18b..b9d6725a 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -294,6 +294,7 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
         if (!http_mode)
             run_labels_["Original"] = "Original";
         EmitRuns_i();
+        emit fileOpened();   // listeners (e.g. the jobs table) reset their per-file state
 
         auto end = std::chrono::high_resolution_clock::now();
         auto duration = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
@@ -987,6 +988,16 @@ void JFJochImageReadingWorker::RenameRun(QString id, QString label) {
     EmitRuns_i();
 }
 
+void JFJochImageReadingWorker::RemoveRun(QString id) {
+    QMutexLocker ul(&m);
+    if (http_mode || id == "Original")
+        return;
+    file_reader.RemoveSnapshot(id.toStdString());
+    run_labels_.erase(id.toStdString());
+    // Refresh the (possibly now-Original) active view; ActivateSnapshot_i also re-emits runsChanged.
+    ActivateSnapshot_i(QString::fromStdString(file_reader.ActiveSnapshot()));
+}
+
 void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString id, QString label, QString master_path) {
     QMutexLocker ul(&m);
     if (http_mode) {
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 9a3092ab..6cc50558 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -159,6 +159,7 @@ signals:
     void liveRateChanged(double hz);
     void snapshotsChanged(QStringList names, QString active);
     void runsChanged(QVector<RunData> runs, QString active_id);
+    void fileOpened();   // a new file/stream was loaded - listeners should reset per-file state
 
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
@@ -210,4 +211,5 @@ public slots:
     void RegisterProcessingSnapshot(QString id, QString label, QString master_path);
     void SetActiveSnapshot(QString name);
     void RenameRun(QString id, QString label);   // change a run's display label (legend)
+    void RemoveRun(QString id);                  // drop a reprocessing snapshot (not "Original")
 };
diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index e4bb366d..cfb960d2 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -3,9 +3,24 @@
 
 #include <QGridLayout>
 #include <QPushButton>
+#include <QColor>
 
 #include "JFJochViewerDatasetInfo.h"
 
+namespace {
+    // Stable colour per run by its position in the run list (Original is index 0 -> blue), so a
+    // run keeps its colour whether it is the active (primary) line or an overlay.
+    QColor RunColor(int index) {
+        static const QColor palette[] = {
+            QColor(0x1f, 0x77, 0xb4), QColor(0xff, 0x7f, 0x0e), QColor(0x2c, 0xa0, 0x2c),
+            QColor(0xd6, 0x27, 0x28), QColor(0x94, 0x67, 0xbd), QColor(0x8c, 0x56, 0x4b),
+            QColor(0xe3, 0x77, 0xc2), QColor(0x7f, 0x7f, 0x7f),
+        };
+        constexpr int n = static_cast<int>(sizeof(palette) / sizeof(palette[0]));
+        return palette[((index % n) + n) % n];
+    }
+}
+
 JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(parent) {
     auto layout = new QGridLayout(this);
     combo_box = new QComboBox(this);
@@ -210,21 +225,27 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
     bool one_over_d2 = false;
     std::vector<float> data = ExtractMetric(*dataset, val, one_over_d2);
 
-    // One overlay line per other run, plus the in-progress live run.
+    // One overlay line per other run, plus the in-progress live run. Each run keeps a stable colour
+    // tied to its position in the list, so colours don't swap when the active run changes.
     std::vector<JFJochDatasetInfoChartView::NamedSeries> overlays;
     QString primary_name;
+    QColor primary_color;
+    int run_index = 0;
     for (const auto &run: runs_) {
-        if (run.id == active_id_) { primary_name = run.label; continue; }
+        const QColor color = RunColor(run_index++);
+        if (run.id == active_id_) { primary_name = run.label; primary_color = color; continue; }
         if (!run.dataset || run.dataset == dataset) continue;   // never draw the active run twice
         bool ignore = false;
-        overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore)});
+        overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore), color});
     }
     if (live_run_ && live_run_ != dataset) {
         bool ignore = false;
-        overlays.push_back({QStringLiteral("Live"), ExtractMetric(*live_run_, val, ignore)});
+        overlays.push_back({QStringLiteral("Live"), ExtractMetric(*live_run_, val, ignore),
+                            RunColor(static_cast<int>(runs_.size()))});
     }
 
-    chart_view->loadValues(data, image_number, one_over_d2, dataset.get(), primary_name, std::move(overlays));
+    chart_view->loadValues(data, image_number, one_over_d2, dataset.get(), primary_name,
+                           std::move(overlays), primary_color);
 
     if (dataset->experiment.GetGridScan()) {
         stack->setCurrentWidget(grid_scan_image);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 56a4ad1f..e9667d93 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -403,8 +403,12 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             statusbar, &JFJochViewerStatusBar::display);
     connect(processingJobsWindow, &JFJochProcessingJobsWindow::renameRun,
             reading_worker, &JFJochImageReadingWorker::RenameRun);
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::removeRun,
+            reading_worker, &JFJochImageReadingWorker::RemoveRun);
     connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
             processingJobsWindow, &JFJochProcessingJobsWindow::onHttpConnectionChanged);
+    connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
+            processingJobsWindow, &JFJochProcessingJobsWindow::clearJobs);
     connect(reading_worker, &JFJochImageReadingWorker::runsChanged, this,
             [this](QVector<RunData> runs, QString active) {
                 lastRuns = std::move(runs);
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index bd73362a..9dc5e79a 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -5,6 +5,7 @@
 #include <QApplication>
 #include <QClipboard>
 #include <QCategoryAxis>
+#include <QtCharts/QLegendMarker>
 
 #include "JFJochDatasetInfoChartView.h"
 
@@ -130,9 +131,10 @@ void JFJochDatasetInfoChartView::resetZoom() {
 
 void JFJochDatasetInfoChartView::loadValues(const std::vector<float> &input, int64_t image, bool one_over_d2,
                                             const JFJochReaderDataset *dataset, const QString &primaryName,
-                                            std::vector<NamedSeries> overlays) {
+                                            std::vector<NamedSeries> overlays, const QColor &primaryColor) {
     m_yOneOverD = one_over_d2;
     primaryName_ = primaryName;
+    primary_color_ = primaryColor;
 
     // d -> 1/d^2 for resolution plots; identity otherwise. Applied to every series alike.
     auto transform = [one_over_d2](const std::vector<float> &in, std::vector<float> &out) {
@@ -223,6 +225,8 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         series = new QLineSeries(this);
         if (!primaryName_.isEmpty())
             series->setName(primaryName_);
+        if (primary_color_.isValid())
+            series->setColor(primary_color_);
         currentSeries = new QScatterSeries(this);
 
         double dispMin = std::numeric_limits<double>::infinity();
@@ -236,6 +240,8 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         for (const auto &ov: overlays_) {
             auto *line = new QLineSeries(this);
             line->setName(ov.name);
+            if (ov.color.isValid())
+                line->setColor(ov.color);
             appendSeries(line, ov.values, dispMin, dispMax);
             overlayLines.push_back(line);
         }
@@ -418,6 +424,9 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
             for (auto *ax: finalAxes)
                 line->attachAxis(ax);
         }
+        // The current-image marker is not a run - keep it out of the legend.
+        for (auto *marker: chart()->legend()->markers(currentSeries))
+            marker->setVisible(false);
         chart()->legend()->setVisible(!overlays_.empty());
         chart()->legend()->setAlignment(Qt::AlignBottom);
     }
diff --git a/viewer/charts/JFJochDatasetInfoChartView.h b/viewer/charts/JFJochDatasetInfoChartView.h
index 62fa0ca6..7a1daf91 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.h
+++ b/viewer/charts/JFJochDatasetInfoChartView.h
@@ -11,6 +11,7 @@
 #include <QGraphicsLineItem>
 #include <QTimer>
 #include <QPointer>
+#include <QColor>
 
 #ifdef JFJOCH_USE_FFTW
 #include <fftw3.h>
@@ -47,9 +48,10 @@ class JFJochDatasetInfoChartView : public QChartView {
 
 public:
     // One overlay line (a non-active run), drawn alongside the primary series with a legend entry.
-    struct NamedSeries { QString name; std::vector<float> values; };
+    struct NamedSeries { QString name; std::vector<float> values; QColor color; };
 private:
     std::vector<NamedSeries> overlays_;
+    QColor primary_color_;                // colour of the active (primary) run, if assigned
     // Append (binned) finite points of vals to s, extending the [mn, mx] data range.
     void appendSeries(QLineSeries *s, const std::vector<float> &vals, double &mn, double &mx) const;
 
@@ -92,7 +94,8 @@ public:
         bool one_over_d2,
         const JFJochReaderDataset *dataset = nullptr,
         const QString &primaryName = QString(),
-        std::vector<NamedSeries> overlays = {});
+        std::vector<NamedSeries> overlays = {},
+        const QColor &primaryColor = QColor());
 };
 
 
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 0546bb09..b38e1a80 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -51,6 +51,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     toolbar_->setMovable(false);
     toolbar_->addAction("New job…", this, &JFJochProcessingJobsWindow::newJob);
     toolbar_->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
+    toolbar_->addAction("Remove result", this, &JFJochProcessingJobsWindow::removeResult);
     toolbar_->addSeparator();
     toolbar_->addAction("View results", this, &JFJochProcessingJobsWindow::viewResults);
     toolbar_->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
@@ -260,6 +261,7 @@ void JFJochProcessingJobsWindow::newJob() {
 
     running_row_ = row;
 
+    job_timer_.start();
     controller_->start(inputs.file, experiment, inputs.pixel_mask, config);
     emit writeStatusBar("Started processing job " + label);
 }
@@ -271,6 +273,36 @@ void JFJochProcessingJobsWindow::cancelJob() {
     }
 }
 
+void JFJochProcessingJobsWindow::removeResult() {
+    const int row = table_->currentRow();
+    if (row < 0 || row >= static_cast<int>(jobs_.size()))
+        return;
+    if (row == running_row_) {
+        QMessageBox::information(this, "Processing", "Cancel the running job before removing it.");
+        return;
+    }
+    emit removeRun(jobs_[row].id);   // drops the snapshot from the reader (no-op for Original)
+
+    QSignalBlocker block(table_);    // row removal must not look like a rename
+    table_->removeRow(row);
+    jobs_.erase(jobs_.begin() + row);
+    if (running_row_ > row)
+        --running_row_;
+}
+
+void JFJochProcessingJobsWindow::clearJobs() {
+    if (controller_->running())
+        controller_->cancel();
+    emit liveDataset(nullptr);
+
+    QSignalBlocker block(table_);
+    table_->setRowCount(0);
+    jobs_.clear();
+    job_counter_ = 0;
+    running_row_ = -1;
+    running_bar_ = nullptr;
+}
+
 void JFJochProcessingJobsWindow::viewResults() {
     const int row = table_->currentRow();
     if (row < 0 || row >= static_cast<int>(jobs_.size()))
@@ -307,6 +339,17 @@ void JFJochProcessingJobsWindow::onProgress(quint64 done, quint64 total) {
     running_bar_->setRange(0, static_cast<int>(total));
     running_bar_->setValue(static_cast<int>(done));
     running_bar_->setFormat("%v / %m");
+
+    // Processing rate and ETA in the status bar.
+    if (job_timer_.isValid() && done > 0) {
+        const double secs = job_timer_.elapsed() / 1000.0;
+        if (secs > 0.0) {
+            const double hz = done / secs;
+            const double remaining = hz > 0.0 ? (total - done) / hz : 0.0;
+            emit writeStatusBar(QStringLiteral("Processing %1 Hz — ~%2 s remaining")
+                                    .arg(hz, 0, 'f', 1).arg(qRound(remaining)));
+        }
+    }
 }
 
 void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index c8f0eaa7..55d5b56b 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -3,6 +3,7 @@
 
 #pragma once
 
+#include <QElapsedTimer>
 #include <QString>
 #include <QWidget>
 #include <vector>
@@ -29,16 +30,19 @@ signals:
     void registerSnapshot(QString id, QString label, QString master_path);
     void activateSnapshot(QString id);
     void renameRun(QString id, QString label);
+    void removeRun(QString id);
     void writeStatusBar(QString message, int timeout_ms = 0);
     // Live per-image results while a job runs, for the dataset-info plots (nullptr clears it).
     void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
 
 public slots:
     void onHttpConnectionChanged(bool connected, QString addr);
+    void clearJobs();   // reset the table on a new file
 
 private slots:
     void newJob();
     void cancelJob();
+    void removeResult();
     void viewResults();
     void showOriginal();
     void onPhase(QString phase);
@@ -74,6 +78,7 @@ private:
     QStackedWidget *stack_;                 // page 0: jobs table, page 1: HTTP-mode message
     QTableWidget *table_;
     QProgressBar *running_bar_ = nullptr;   // lives in the running row's Status cell
+    QElapsedTimer job_timer_;               // running job wall-clock, for rate + ETA
     int running_row_ = -1;
     int job_counter_ = 0;
     std::vector<JobInfo> jobs_;
-- 
2.52.0


From a412f96f3a0e0e32813abb4e535b86ee16c282fb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 12:13:39 +0200
Subject: [PATCH 189/228] viewer: give the current-image plot marker a fixed
 colour

The current-image marker (a scatter series) was picking an arbitrary theme colour
(green), which read as a stray series. Pin it to black so it's an unambiguous
"current image" dot, distinct from the run line colours. Its legend entry is
already hidden.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/charts/JFJochDatasetInfoChartView.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index 9dc5e79a..c2f7cda0 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -228,6 +228,8 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         if (primary_color_.isValid())
             series->setColor(primary_color_);
         currentSeries = new QScatterSeries(this);
+        currentSeries->setColor(Qt::black);     // "current image" marker: fixed, not a run colour
+        currentSeries->setMarkerSize(9.0);
 
         double dispMin = std::numeric_limits<double>::infinity();
         double dispMax = -std::numeric_limits<double>::infinity();
-- 
2.52.0


From 7ba097df1c2067a3898d5289dd350ee2d45336df Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 12:24:47 +0200
Subject: [PATCH 190/228] viewer: looser minimum heights so the bottom docks
 resize freely

Lower the dataset-info chart and jobs-table minimum heights (200 -> 80, table 60)
so the bottom dock area can be dragged smaller; the comfortable default size is
still set via resizeDocks.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp            | 2 +-
 viewer/windows/JFJochProcessingJobsWindow.cpp | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index cfb960d2..4adbda9a 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -42,7 +42,7 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
 
     stack = new QStackedWidget(this);
     chart_view = new JFJochDatasetInfoChartView(this);
-    chart_view->setMinimumHeight(200);   // keep the plot readable even when the dock is small
+    chart_view->setMinimumHeight(80);   // low floor so the bottom dock resizes freely (default is set via resizeDocks)
     grid_scan_image = new JFJochGridScanImage(this);
 
     stack->addWidget(chart_view);
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index b38e1a80..ca6dcb72 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -57,6 +57,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     toolbar_->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
 
     table_ = new QTableWidget(0, COL_COUNT, this);
+    table_->setMinimumHeight(60);   // let the bottom dock shrink freely
     table_->setHorizontalHeaderLabels({"Name", "Started", "Mode", "Images", "Status", "Index %", "Unit cell"});
     table_->horizontalHeader()->setStretchLastSection(true);
     table_->setSelectionBehavior(QAbstractItemView::SelectRows);
-- 
2.52.0


From b9f8c2b67580984d8205d36018e62465c727aa76 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 14:59:23 +0200
Subject: [PATCH 191/228] reader/viewer: snapshot image->original map; subset
 runs register and overlay

Foundation for a dataset (snapshot or, later, the main file) being a subset of the
truly collected images:
- JFJochReaderDataset gains source_image_number (image index -> original image
  number; empty = identity).
- HDF5MetadataSource reads /entry/detector/number into that map and an inverse
  (original -> local) map; FillPerImage / ReadSpots translate the requested global
  image to this source's local index via ToLocalIndex (return nothing if the image
  is not covered), so partial snapshots are correct and never read out of bounds.
- RegisterSnapshot now accepts a snapshot with fewer images than the dataset
  (only rejects more), so sub-range / strided reprocessing runs register.
- The dataset-info plot draws each run at its original image numbers (x map from
  source_image_number), so a subset run lands at the right place on the shared
  axis. The live run's map is filled from msg.original_number.

This makes the foundation ready for strided / filtered selections (e.g. reprocess
only images with >N spots) without restricting to a min-max sub-range.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 reader/HDF5MetadataSource.cpp                | 51 +++++++++++++++++---
 reader/HDF5MetadataSource.h                  |  9 ++++
 reader/JFJochHDF5Reader.cpp                  |  7 ++-
 reader/JFJochReaderDataset.h                 |  6 +++
 viewer/JFJochProcessController.cpp           |  4 ++
 viewer/JFJochViewerDatasetInfo.cpp           | 11 +++--
 viewer/charts/JFJochDatasetInfoChartView.cpp | 18 ++++---
 viewer/charts/JFJochDatasetInfoChartView.h   | 12 +++--
 8 files changed, 96 insertions(+), 22 deletions(-)

diff --git a/reader/HDF5MetadataSource.cpp b/reader/HDF5MetadataSource.cpp
index 8a784b05..bde7cd52 100644
--- a/reader/HDF5MetadataSource.cpp
+++ b/reader/HDF5MetadataSource.cpp
@@ -693,6 +693,23 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
 
         dataset->experiment.ImagesPerTrigger(number_of_images);
         cached_geom = dataset->experiment.GetDiffractionGeometry();
+
+        // Image-index -> original-image-number map (written as /entry/detector/number). When it is a
+        // genuine subset/strided selection, keep it so plots and per-image lookups use the original
+        // numbering; a plain 0..N-1 sequence is identity and left empty.
+        image_to_local_.clear();
+        auto numbers = master_file->ReadOptVector<uint64_t>("/entry/detector/number");
+        if (numbers.size() == number_of_images) {
+            bool identity = true;
+            for (size_t i = 0; i < numbers.size(); i++)
+                if (numbers[i] != i) { identity = false; break; }
+            if (!identity) {
+                dataset->source_image_number.assign(numbers.begin(), numbers.end());
+                for (size_t i = 0; i < numbers.size(); i++)
+                    image_to_local_[static_cast<int64_t>(numbers[i])] = static_cast<int64_t>(i);
+            }
+        }
+
         dataset_ = dataset;
 
         return OpenResult{
@@ -726,6 +743,15 @@ HDF5ImageLocator::Location HDF5MetadataSource::ResolveMeta(int64_t global) const
     return {master_file, static_cast<uint32_t>(global)};
 }
 
+std::optional<int64_t> HDF5MetadataSource::ToLocalIndex(int64_t image_number) const {
+    if (image_to_local_.empty())
+        return image_number;   // 1:1 source (identity)
+    const auto it = image_to_local_.find(image_number);
+    if (it == image_to_local_.end())
+        return std::nullopt;   // this source does not cover that image
+    return it->second;
+}
+
 // Reads spot data for a single image from the appropriate HDF5 source.
 // master_image / source_image are the logical indices within master_file and
 // source_file respectively (identical for NXmxVDS contiguous / integrated;
@@ -852,8 +878,13 @@ static void ReadSpotsFromFiles(HDF5Object &master_file,
     GenerateSpotPlot(message, 1.5);
 }
 
-void HDF5MetadataSource::FillPerImage(DataMessage &message, int64_t image_number,
+void HDF5MetadataSource::FillPerImage(DataMessage &message, int64_t requested_image,
                                       const std::shared_ptr<const JFJochReaderDataset> &dataset) const {
+    const auto local_opt = ToLocalIndex(requested_image);
+    if (!local_opt)
+        return;   // this metadata source does not cover the requested image
+    const int64_t image_number = *local_opt;   // local index into this source (identity for 1:1)
+
     auto loc = ResolveMeta(image_number);
     auto &source_file = loc.file;
     const uint32_t image_id = loc.local_index;
@@ -862,7 +893,7 @@ void HDF5MetadataSource::FillPerImage(DataMessage &message, int64_t image_number
     const auto source_image = static_cast<hsize_t>(image_id);
 
     ReadSpotsFromFiles(*master_file, *source_file, master_image, source_image,
-                       image_number, dataset->experiment.GetDiffractionGeometry(), message);
+                       requested_image, dataset->experiment.GetDiffractionGeometry(), message);
 
     if (!dataset->az_int_bin_to_q.empty()) {
         if (dataset->azimuthal_bins == 0) {
@@ -1094,10 +1125,16 @@ std::vector<IntegrationOutcome> HDF5MetadataSource::ReadReflections(size_t start
     return ret;
 }
 
-std::vector<SpotToSave> HDF5MetadataSource::ReadSpots(int64_t image) const {
-    if (image < 0)
+std::vector<SpotToSave> HDF5MetadataSource::ReadSpots(int64_t requested_image) const {
+    if (requested_image < 0)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
             "image number must be non-negative");
+
+    const auto local_opt = ToLocalIndex(requested_image);
+    if (!local_opt)
+        return {};   // this (subset) source does not cover the requested image
+    const int64_t image = *local_opt;
+
     if (image >= number_of_images)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "image must be less than number_of_images");
@@ -1107,17 +1144,17 @@ std::vector<SpotToSave> HDF5MetadataSource::ReadSpots(int64_t image) const {
                               "Cannot read spots if file not loaded");
 
     // Per-image spot/MX data, resolved the same way as the pixels (or in our own master at the
-    // global index for an integrated _process.h5 snapshot).
+    // local index for an integrated _process.h5 snapshot).
     const auto loc = ResolveMeta(image);
     HDF5Object *meta_file = loc.file.get();
     const size_t meta_image_id = loc.local_index;
 
     DataMessage tmp_message;
-    tmp_message.number = static_cast<int64_t>(image);
+    tmp_message.number = requested_image;
 
     ReadSpotsFromFiles(*master_file, *meta_file,
                        image, meta_image_id,
-                       static_cast<int64_t>(image),
+                       requested_image,
                        cached_geom,
                        tmp_message);
 
diff --git a/reader/HDF5MetadataSource.h b/reader/HDF5MetadataSource.h
index 1196b721..7731e4e5 100644
--- a/reader/HDF5MetadataSource.h
+++ b/reader/HDF5MetadataSource.h
@@ -6,6 +6,7 @@
 #include <memory>
 #include <optional>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
 #include "JFJochReaderDataset.h"
@@ -62,6 +63,14 @@ private:
     uint64_t number_of_images = 0;
     const HDF5ImageSource *image_source_ = nullptr;
 
+    // Inverse of dataset_->source_image_number (original image number -> local index in this
+    // master). Empty for a 1:1 source; populated when this metadata covers a subset of images.
+    std::unordered_map<int64_t, int64_t> image_to_local_;
+
+    // Translate a global/original image number to the local index in this metadata source, or
+    // nullopt if this source does not cover that image. Identity for a 1:1 source.
+    std::optional<int64_t> ToLocalIndex(int64_t image_number) const;
+
     HDF5ImageLocator::Location ResolveMeta(int64_t global) const;
     std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
     void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 3dfcd9cd..511f9f87 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -142,9 +142,12 @@ void JFJochHDF5Reader::RegisterSnapshot(const std::string &name, const std::stri
     auto metadata = std::make_shared<HDF5MetadataSource>();
     auto open_result = metadata->Open(master_path, default_experiment);
 
-    if (open_result.number_of_images != number_of_images)
+    // A snapshot may cover a subset of the images (a sub-range or filtered reprocessing); its
+    // /entry/detector/number map (read in Open) ties each snapshot image back to an original one.
+    // It just must not claim more images than the dataset has.
+    if (open_result.number_of_images > number_of_images)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "Snapshot image count does not match the open dataset");
+                              "Snapshot has more images than the open dataset");
 
     // Snapshot pixels come from the existing image source; its own (integrated) master holds the
     // per-image metadata at the global index.
diff --git a/reader/JFJochReaderDataset.h b/reader/JFJochReaderDataset.h
index d4dc7d44..6fe956f0 100644
--- a/reader/JFJochReaderDataset.h
+++ b/reader/JFJochReaderDataset.h
@@ -47,6 +47,12 @@ struct JFJochReaderDataset {
     std::vector<float> image_scale_b;
     std::vector<int64_t> max_value;
 
+    // Maps this dataset's image index -> the original/collected image number it came from.
+    // Empty means identity (image i == original image i). Lets a dataset be a subset (or strided
+    // selection) of the truly collected images: reprocessing snapshots over a sub-range, and (in
+    // future) a main dataset that was filtered on-the-fly during collection.
+    std::vector<int> source_image_number;
+
     std::vector<std::string> roi;
     std::vector<std::vector<int64_t>> roi_sum;
     std::vector<std::vector<int64_t>> roi_sum_sq;
diff --git a/viewer/JFJochProcessController.cpp b/viewer/JFJochProcessController.cpp
index 7adc058c..ff705c2a 100644
--- a/viewer/JFJochProcessController.cpp
+++ b/viewer/JFJochProcessController.cpp
@@ -101,6 +101,10 @@ void JFJochProcessController::OnImageProcessed(const DataMessage &msg) {
             v[i] = val;
         };
         auto &d = *live_dataset_;
+        // Map this ordinal back to its original image number (for the x-axis of subset/strided runs).
+        if (static_cast<int64_t>(d.source_image_number.size()) <= i)
+            d.source_image_number.resize(i + 1, 0);
+        d.source_image_number[i] = static_cast<int>(msg.original_number.value_or(msg.number));
         if (msg.spot_count)            put(d.spot_count, *msg.spot_count);
         if (msg.spot_count_indexed)    put(d.spot_count_indexed, *msg.spot_count_indexed);
         if (msg.spot_count_low_res)    put(d.spot_count_low_res, *msg.spot_count_low_res);
diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 4adbda9a..54657890 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -19,6 +19,11 @@ namespace {
         constexpr int n = static_cast<int>(sizeof(palette) / sizeof(palette[0]));
         return palette[((index % n) + n) % n];
     }
+
+    // A run's image->original-number map as floats for the chart x-axis (empty => identity).
+    std::vector<float> XForRun(const JFJochReaderDataset &ds) {
+        return {ds.source_image_number.begin(), ds.source_image_number.end()};
+    }
 }
 
 JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(parent) {
@@ -236,16 +241,16 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
         if (run.id == active_id_) { primary_name = run.label; primary_color = color; continue; }
         if (!run.dataset || run.dataset == dataset) continue;   // never draw the active run twice
         bool ignore = false;
-        overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore), color});
+        overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore), color, XForRun(*run.dataset)});
     }
     if (live_run_ && live_run_ != dataset) {
         bool ignore = false;
         overlays.push_back({QStringLiteral("Live"), ExtractMetric(*live_run_, val, ignore),
-                            RunColor(static_cast<int>(runs_.size()))});
+                            RunColor(static_cast<int>(runs_.size())), XForRun(*live_run_)});
     }
 
     chart_view->loadValues(data, image_number, one_over_d2, dataset.get(), primary_name,
-                           std::move(overlays), primary_color);
+                           std::move(overlays), primary_color, XForRun(*dataset));
 
     if (dataset->experiment.GetGridScan()) {
         stack->setCurrentWidget(grid_scan_image);
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index c2f7cda0..25e65dde 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -131,10 +131,12 @@ void JFJochDatasetInfoChartView::resetZoom() {
 
 void JFJochDatasetInfoChartView::loadValues(const std::vector<float> &input, int64_t image, bool one_over_d2,
                                             const JFJochReaderDataset *dataset, const QString &primaryName,
-                                            std::vector<NamedSeries> overlays, const QColor &primaryColor) {
+                                            std::vector<NamedSeries> overlays, const QColor &primaryColor,
+                                            std::vector<float> primaryX) {
     m_yOneOverD = one_over_d2;
     primaryName_ = primaryName;
     primary_color_ = primaryColor;
+    primary_x_ = std::move(primaryX);
 
     // d -> 1/d^2 for resolution plots; identity otherwise. Applied to every series alike.
     auto transform = [one_over_d2](const std::vector<float> &in, std::vector<float> &out) {
@@ -166,12 +168,16 @@ void JFJochDatasetInfoChartView::loadValues(const std::vector<float> &input, int
 }
 
 void JFJochDatasetInfoChartView::appendSeries(QLineSeries *s, const std::vector<float> &vals,
-                                              double &mn, double &mx) const {
+                                              const std::vector<float> &xs, double &mn, double &mx) const {
+    // x position for value index i: the mapped image number if available, else the index itself.
+    auto xpos = [&xs](int64_t i) -> double {
+        return i < static_cast<int64_t>(xs.size()) ? static_cast<double>(xs[i]) : static_cast<double>(i);
+    };
     if (binning == 1) {
         for (int i = 0; i < static_cast<int>(vals.size()); i++) {
             const double v = vals[static_cast<size_t>(i)];
             if (!std::isfinite(v)) continue;
-            s->append(i, v);
+            s->append(xpos(i), v);
             mn = std::min(mn, v);
             mx = std::max(mx, v);
         }
@@ -187,7 +193,7 @@ void JFJochDatasetInfoChartView::appendSeries(QLineSeries *s, const std::vector<
             }
             if (count > 0) {
                 const double mean = tmp / static_cast<double>(count);
-                s->append((i + 0.5) * binning, mean);
+                s->append(xpos(static_cast<int64_t>(i) * binning + binning / 2), mean);
                 mn = std::min(mn, mean);
                 mx = std::max(mx, mean);
             }
@@ -234,7 +240,7 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         double dispMin = std::numeric_limits<double>::infinity();
         double dispMax = -std::numeric_limits<double>::infinity();
 
-        appendSeries(series, values, dispMin, dispMax);
+        appendSeries(series, values, primary_x_, dispMin, dispMax);
 
         // Overlay runs share the primary's axes and range; build them now so the Y range fits all.
         std::vector<QLineSeries *> overlayLines;
@@ -244,7 +250,7 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
             line->setName(ov.name);
             if (ov.color.isValid())
                 line->setColor(ov.color);
-            appendSeries(line, ov.values, dispMin, dispMax);
+            appendSeries(line, ov.values, ov.x, dispMin, dispMax);
             overlayLines.push_back(line);
         }
 
diff --git a/viewer/charts/JFJochDatasetInfoChartView.h b/viewer/charts/JFJochDatasetInfoChartView.h
index 7a1daf91..ce3f6bca 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.h
+++ b/viewer/charts/JFJochDatasetInfoChartView.h
@@ -48,12 +48,15 @@ class JFJochDatasetInfoChartView : public QChartView {
 
 public:
     // One overlay line (a non-active run), drawn alongside the primary series with a legend entry.
-    struct NamedSeries { QString name; std::vector<float> values; QColor color; };
+    // x maps each value to an image number on the shared x-axis (empty => 0,1,2,... by index).
+    struct NamedSeries { QString name; std::vector<float> values; QColor color; std::vector<float> x; };
 private:
     std::vector<NamedSeries> overlays_;
     QColor primary_color_;                // colour of the active (primary) run, if assigned
-    // Append (binned) finite points of vals to s, extending the [mn, mx] data range.
-    void appendSeries(QLineSeries *s, const std::vector<float> &vals, double &mn, double &mx) const;
+    std::vector<float> primary_x_;        // x (image numbers) for the primary series; empty => index
+    // Append (binned) finite points of vals to s at x positions (xs empty => index), extending [mn,mx].
+    void appendSeries(QLineSeries *s, const std::vector<float> &vals, const std::vector<float> &xs,
+                      double &mn, double &mx) const;
 
     // FFT view toggle
     bool m_showFFT = false;
@@ -95,7 +98,8 @@ public:
         const JFJochReaderDataset *dataset = nullptr,
         const QString &primaryName = QString(),
         std::vector<NamedSeries> overlays = {},
-        const QColor &primaryColor = QColor());
+        const QColor &primaryColor = QColor(),
+        std::vector<float> primaryX = {});
 };
 
 
-- 
2.52.0


From 0f3009069f1428c345622a9ed4fd27288087c3a2 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 15:01:25 +0200
Subject: [PATCH 192/228] viewer: processing dialog takes start + end image,
 not a count

Replace the ambiguous "Images" count with explicit "Start image" and "End image"
spinboxes (end 0 = to the last image). buildConfig sets config.start_image /
end_image; the table shows the range ("start-end" / "all") and the progress bar
expects end-start images.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/windows/JFJochProcessingJobsWindow.cpp | 31 +++++++++++++------
 viewer/windows/JFJochProcessingJobsWindow.h   |  3 +-
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index ca6dcb72..9fc985ff 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -103,10 +103,14 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
     mode->addItem("Full analysis", static_cast<int>(ProcessMode::FullAnalysis));
     mode->addItem("Azimuthal integration", static_cast<int>(ProcessMode::AzimuthalIntegration));
 
-    auto *images = new QSpinBox(&dlg);
-    images->setRange(0, 1'000'000'000);
-    images->setValue(0);
-    images->setSpecialValueText("all");
+    auto *start_image = new QSpinBox(&dlg);
+    start_image->setRange(0, 1'000'000'000);
+    start_image->setValue(0);
+
+    auto *end_image = new QSpinBox(&dlg);
+    end_image->setRange(0, 1'000'000'000);
+    end_image->setValue(0);
+    end_image->setSpecialValueText("end");   // 0 => to the last image
 
     auto *threads = new QSpinBox(&dlg);
     threads->setRange(1, 256);
@@ -132,7 +136,8 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
 
     auto *form = new QFormLayout;
     form->addRow("Mode", mode);
-    form->addRow("Images", images);
+    form->addRow("Start image", start_image);
+    form->addRow("End image", end_image);
     form->addRow("Threads", threads);
     form->addRow(save);
     form->addRow("Output prefix", prefix);
@@ -161,7 +166,8 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
     dlg.exec();
     if (result != 0) {
         spec.mode = static_cast<ProcessMode>(mode->currentData().toInt());
-        spec.images = images->value();
+        spec.start_image = start_image->value();
+        spec.end_image = end_image->value();
         spec.threads = threads->value();
         spec.save = save->isChecked();
         spec.prefix = prefix->text();
@@ -175,7 +181,8 @@ ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const
     ProcessConfig config;
     config.mode = spec.mode;
     config.nthreads = spec.threads;
-    config.end_image = spec.images > 0 ? spec.images : -1;
+    config.start_image = spec.start_image;
+    config.end_image = spec.end_image > 0 ? spec.end_image : -1;   // 0 => to the end
     config.output_prefix = spec.save ? spec.prefix.toStdString() : std::string();
     config.spot_finding = inputs.spot_finding;
     if (spec.mode == ProcessMode::FullAnalysis) {
@@ -243,10 +250,16 @@ void JFJochProcessingJobsWindow::newJob() {
         return cell;
     };
 
+    const QString range_text = (spec.start_image == 0 && spec.end_image == 0)
+        ? QStringLiteral("all")
+        : QStringLiteral("%1–%2").arg(spec.start_image)
+              .arg(spec.end_image > 0 ? QString::number(spec.end_image) : QStringLiteral("end"));
+    const int expected = spec.end_image > spec.start_image ? spec.end_image - spec.start_image : 0;
+
     table_->setItem(row, COL_NAME, new QTableWidgetItem(label));   // editable (default flags)
     table_->setItem(row, COL_STARTED, fixed(QDateTime::currentDateTime().toString("HH:mm:ss")));
     table_->setItem(row, COL_MODE, fixed(full ? "Full" : "AzInt"));
-    table_->setItem(row, COL_IMAGES, fixed(spec.images > 0 ? QString::number(spec.images) : "all"));
+    table_->setItem(row, COL_IMAGES, fixed(range_text));
     table_->setItem(row, COL_STATUS, fixed("queued"));
     table_->setItem(row, COL_INDEX, fixed("-"));
     table_->setItem(row, COL_CELL, fixed("-"));
@@ -255,7 +268,7 @@ void JFJochProcessingJobsWindow::newJob() {
     // image processing starts, then "<done> / <expected>" with the bar filling in the background.
     running_bar_ = new QProgressBar(table_);
     running_bar_->setAlignment(Qt::AlignCenter);
-    running_bar_->setRange(0, spec.images > 0 ? spec.images : 1);
+    running_bar_->setRange(0, expected > 0 ? expected : 1);
     running_bar_->setValue(0);
     running_bar_->setFormat("queued");
     table_->setCellWidget(row, COL_STATUS, running_bar_);
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index 55d5b56b..d47815e7 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -59,7 +59,8 @@ private:
     };
     struct JobSpec {
         ProcessMode mode = ProcessMode::FullAnalysis;
-        int images = 0;          // 0 == all
+        int start_image = 0;
+        int end_image = 0;       // 0 == to the end
         int threads = 4;
         bool save = true;
         QString prefix;
-- 
2.52.0


From 03a09c43bc70d9808bd4a1b3bd8416cfdaf2a0ba Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 15:10:36 +0200
Subject: [PATCH 193/228] viewer: white-when-active inputs, teal accent, Status
 column visible

Styling:
- Entry widgets (line edits, spin boxes, combos, item views) are salmon (the GUI
  default) when inactive and turn white while focused/active.
- A teal accent (#2a9d8f) for selections and the QProgressBar chunk, against the
  salmon background.
- Move the jobs-table Status column (the progress bar) to column 2 so it stays
  visible in the narrow dock instead of scrolling off the right edge.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.h                   | 26 ++++++++++++++++++-
 viewer/windows/JFJochProcessingJobsWindow.cpp |  5 ++--
 2 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index c1ce10e5..56537bca 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -18,7 +18,31 @@ class QDockWidget;
 
 class JFJochViewerWindow : public QMainWindow {
 Q_OBJECT
-    const QString stylesheet = "background-color: rgb(255, 235, 230);";
+    // Salmon (GUI default) everywhere; entry widgets (line edits, spin boxes, combos, tables) turn
+    // white while focused/active. A teal accent (selection + progress chunks) adds some colour.
+    const QString stylesheet = R"(
+        background-color: rgb(255, 235, 230);
+
+        QLineEdit, QPlainTextEdit, QTextEdit, QAbstractSpinBox, QComboBox, QAbstractItemView {
+            background-color: rgb(255, 235, 230);
+            selection-background-color: #2a9d8f;
+            selection-color: white;
+        }
+        QLineEdit:focus, QPlainTextEdit:focus, QTextEdit:focus, QAbstractSpinBox:focus,
+        QComboBox:focus, QAbstractItemView:focus {
+            background-color: white;
+        }
+        QProgressBar {
+            border: 1px solid #d9b3aa;
+            border-radius: 3px;
+            background-color: rgb(255, 235, 230);
+            text-align: center;
+        }
+        QProgressBar::chunk {
+            background-color: #2a9d8f;
+            border-radius: 2px;
+        }
+    )";
 public:
     explicit JFJochViewerWindow(QWidget *parent = nullptr, bool dbus = true, const QString &file = "");
     ~JFJochViewerWindow() override;
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 9fc985ff..d955f837 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -28,7 +28,8 @@
 #include <thread>
 
 namespace {
-    enum Column { COL_NAME = 0, COL_STARTED, COL_MODE, COL_IMAGES, COL_STATUS, COL_INDEX, COL_CELL, COL_COUNT };
+    // Status (the progress bar) is column 2 so it stays visible in the narrow dock.
+    enum Column { COL_NAME = 0, COL_STATUS, COL_STARTED, COL_MODE, COL_IMAGES, COL_INDEX, COL_CELL, COL_COUNT };
 
     int default_threads() {
         const unsigned hc = std::thread::hardware_concurrency();
@@ -58,7 +59,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
 
     table_ = new QTableWidget(0, COL_COUNT, this);
     table_->setMinimumHeight(60);   // let the bottom dock shrink freely
-    table_->setHorizontalHeaderLabels({"Name", "Started", "Mode", "Images", "Status", "Index %", "Unit cell"});
+    table_->setHorizontalHeaderLabels({"Name", "Status", "Started", "Mode", "Images", "Index %", "Unit cell"});
     table_->horizontalHeader()->setStretchLastSection(true);
     table_->setSelectionBehavior(QAbstractItemView::SelectRows);
     table_->setSelectionMode(QAbstractItemView::SingleSelection);
-- 
2.52.0


From 95fe2ce781e09768fc71086d146e59f001d0ca7a Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 15:22:21 +0200
Subject: [PATCH 194/228] CI: Sign RPMs on upload

---
 .gitea/workflows/build_and_test.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index 960b671c..fa13a3ce 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -150,9 +150,13 @@ jobs:
             echo "No package files found for pattern: ${{ matrix.pkg_glob }}"
             exit 1
           fi
+          url="${{ matrix.upload_url }}"
+          if [[ "$url" == *"/rpm/"* ]]; then
+            url="${url}?sign=true"
+          fi
           for file in "${files[@]}"; do
-            echo "Uploading $file -> ${{ matrix.upload_url }}"
-            curl --fail --user __token__:"$TOKEN" --upload-file "$file" "${{ matrix.upload_url }}"                      
+            echo "Uploading $file -> $url"
+            curl --fail --user __token__:"$TOKEN" --upload-file "$file" "$url"                      
           done
           
           cd ..
-- 
2.52.0


From 67ad43a2b28eaba3185707fdbb6480f72141200d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 15:34:06 +0200
Subject: [PATCH 195/228] viewer: palette theming, Original as a run row,
 stable plot colours

Styling (now via the application palette in main(), not a stylesheet, so it
applies to every widget incl. dialogs):
- Entry fields and item views (line edits, spin boxes, combos, tables) are white
  when enabled and salmon (the GUI default) when disabled - so it's clear where
  you can type. Panels stay salmon (Window role).
- Teal (#2a9d8f) accent via the Highlight role: selections and progress-bar chunks.

Runs list / plots:
- The original file is listed as a first "Original" run (Mode "HDF5"); double-click
  any run row to show it (replaces the "Show original" button). The currently shown
  run is bold (driven by snapshotsChanged).
- Fix the colour "swap" when switching runs: the primary line is matched by the
  active-dataset pointer (not active_id_), so a run keeps its colour even while a
  datasetLoaded/runsChanged pair is mid-flight.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp            | 14 ++--
 viewer/JFJochViewerWindow.cpp                 |  3 +-
 viewer/JFJochViewerWindow.h                   | 27 +------
 viewer/jfjoch_viewer.cpp                      | 14 ++++
 viewer/windows/JFJochProcessingJobsWindow.cpp | 77 ++++++++++++++-----
 viewer/windows/JFJochProcessingJobsWindow.h   |  5 +-
 6 files changed, 87 insertions(+), 53 deletions(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 54657890..985c3f6f 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -231,15 +231,17 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
     std::vector<float> data = ExtractMetric(*dataset, val, one_over_d2);
 
     // One overlay line per other run, plus the in-progress live run. Each run keeps a stable colour
-    // tied to its position in the list, so colours don't swap when the active run changes.
+    // tied to its position in the list, so colours don't swap when the active run changes. The
+    // primary is matched by dataset pointer (not active_id_) so colour/name stay consistent even
+    // while a datasetLoaded/runsChanged pair is still arriving.
     std::vector<JFJochDatasetInfoChartView::NamedSeries> overlays;
     QString primary_name;
     QColor primary_color;
-    int run_index = 0;
-    for (const auto &run: runs_) {
-        const QColor color = RunColor(run_index++);
-        if (run.id == active_id_) { primary_name = run.label; primary_color = color; continue; }
-        if (!run.dataset || run.dataset == dataset) continue;   // never draw the active run twice
+    for (int i = 0; i < runs_.size(); i++) {
+        const auto &run = runs_[i];
+        if (!run.dataset) continue;
+        const QColor color = RunColor(i);
+        if (run.dataset == dataset) { primary_name = run.label; primary_color = color; continue; }
         bool ignore = false;
         overlays.push_back({run.label, ExtractMetric(*run.dataset, val, ignore), color, XForRun(*run.dataset)});
     }
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index e9667d93..d16a629e 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -54,7 +54,6 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     setDockOptions(dockOptions() & ~QMainWindow::DockOption::AllowTabbedDocks);
 
-    setStyleSheet(stylesheet);
     setWindowTitle("Jungfraujoch image viewer");
     // Start large on a big display but fit within a laptop screen.
     const QRect avail = QGuiApplication::primaryScreen()->availableGeometry();
@@ -409,6 +408,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             processingJobsWindow, &JFJochProcessingJobsWindow::onHttpConnectionChanged);
     connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
             processingJobsWindow, &JFJochProcessingJobsWindow::clearJobs);
+    connect(reading_worker, &JFJochImageReadingWorker::snapshotsChanged, processingJobsWindow,
+            [pw = processingJobsWindow](QStringList, QString active) { pw->setActiveRun(active); });
     connect(reading_worker, &JFJochImageReadingWorker::runsChanged, this,
             [this](QVector<RunData> runs, QString active) {
                 lastRuns = std::move(runs);
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 56537bca..e42b61cb 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -18,31 +18,8 @@ class QDockWidget;
 
 class JFJochViewerWindow : public QMainWindow {
 Q_OBJECT
-    // Salmon (GUI default) everywhere; entry widgets (line edits, spin boxes, combos, tables) turn
-    // white while focused/active. A teal accent (selection + progress chunks) adds some colour.
-    const QString stylesheet = R"(
-        background-color: rgb(255, 235, 230);
-
-        QLineEdit, QPlainTextEdit, QTextEdit, QAbstractSpinBox, QComboBox, QAbstractItemView {
-            background-color: rgb(255, 235, 230);
-            selection-background-color: #2a9d8f;
-            selection-color: white;
-        }
-        QLineEdit:focus, QPlainTextEdit:focus, QTextEdit:focus, QAbstractSpinBox:focus,
-        QComboBox:focus, QAbstractItemView:focus {
-            background-color: white;
-        }
-        QProgressBar {
-            border: 1px solid #d9b3aa;
-            border-radius: 3px;
-            background-color: rgb(255, 235, 230);
-            text-align: center;
-        }
-        QProgressBar::chunk {
-            background-color: #2a9d8f;
-            border-radius: 2px;
-        }
-    )";
+    // Theming is done via the application palette in main() (salmon panels, white entry fields,
+    // teal accent) so it applies consistently to every widget, including dialogs.
 public:
     explicit JFJochViewerWindow(QWidget *parent = nullptr, bool dbus = true, const QString &file = "");
     ~JFJochViewerWindow() override;
diff --git a/viewer/jfjoch_viewer.cpp b/viewer/jfjoch_viewer.cpp
index f325822b..863a3e48 100644
--- a/viewer/jfjoch_viewer.cpp
+++ b/viewer/jfjoch_viewer.cpp
@@ -3,6 +3,7 @@
 #include <QCommandLineOption>
 #include <QSplashScreen>
 #include <QTimer>
+#include <QPalette>
 
 #include "JFJochViewerWindow.h"
 #include "../writer/HDF5Objects.h"
@@ -16,6 +17,19 @@ int main(int argc, char *argv[]) {
     RegisterHDF5Filter();
     QApplication app(argc, argv);
 
+    // Theme via the palette (robust across widgets): salmon panels, white entry fields that fall back
+    // to salmon when disabled, and a teal accent for selections and progress-bar chunks.
+    app.setStyle("Fusion");
+    QPalette pal = app.palette();
+    pal.setColor(QPalette::Window, QColor(255, 235, 230));
+    pal.setColor(QPalette::Base, Qt::white);
+    pal.setColor(QPalette::AlternateBase, QColor(255, 245, 242));
+    pal.setColor(QPalette::Button, QColor(255, 235, 230));
+    pal.setColor(QPalette::Disabled, QPalette::Base, QColor(255, 235, 230));
+    pal.setColor(QPalette::Highlight, QColor(0x2a, 0x9d, 0x8f));
+    pal.setColor(QPalette::HighlightedText, Qt::white);
+    app.setPalette(pal);
+
     QIcon appIcon(":/jfjoch.png");
     app.setWindowIcon(appIcon);
 
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index d955f837..9e3ad20f 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -10,6 +10,7 @@
 #include <QComboBox>
 #include <QDateTime>
 #include <QDialog>
+#include <QFont>
 #include <QDialogButtonBox>
 #include <QFileInfo>
 #include <QFormLayout>
@@ -35,6 +36,12 @@ namespace {
         const unsigned hc = std::thread::hardware_concurrency();
         return hc == 0 ? 4 : static_cast<int>(hc);
     }
+
+    QTableWidgetItem *fixedItem(const QString &text) {   // a non-editable cell
+        auto *cell = new QTableWidgetItem(text);
+        cell->setFlags(cell->flags() & ~Qt::ItemIsEditable);
+        return cell;
+    }
 }
 
 JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent)
@@ -54,8 +61,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
     toolbar_->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
     toolbar_->addAction("Remove result", this, &JFJochProcessingJobsWindow::removeResult);
     toolbar_->addSeparator();
-    toolbar_->addAction("View results", this, &JFJochProcessingJobsWindow::viewResults);
-    toolbar_->addAction("Show original", this, &JFJochProcessingJobsWindow::showOriginal);
+    toolbar_->addAction("Show selected", this, &JFJochProcessingJobsWindow::viewResults);
 
     table_ = new QTableWidget(0, COL_COUNT, this);
     table_->setMinimumHeight(60);   // let the bottom dock shrink freely
@@ -74,6 +80,13 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
         jobs_[row].label = item->text();
         emit renameRun(jobs_[row].id, jobs_[row].label);
     });
+    // Double-click a row (other than its editable Name) to show that run in the plots/image.
+    connect(table_, &QTableWidget::cellDoubleClicked, this, [this](int row, int col) {
+        if (col == COL_NAME)
+            return;   // double-clicking Name edits the label
+        if (row >= 0 && row < static_cast<int>(jobs_.size()) && jobs_[row].has_result)
+            emit activateSnapshot(jobs_[row].id);
+    });
 
     auto *message = new QLabel("Dataset re-processing is currently available only in File mode.\n\n"
                                "Open a stored HDF5 file to run processing jobs.", this);
@@ -245,12 +258,6 @@ void JFJochProcessingJobsWindow::newJob() {
     table_->insertRow(row);
     jobs_.push_back(info);   // jobs_[row] must exist before setItem(COL_NAME) fires itemChanged
 
-    auto fixed = [](const QString &text) {   // a non-editable cell
-        auto *cell = new QTableWidgetItem(text);
-        cell->setFlags(cell->flags() & ~Qt::ItemIsEditable);
-        return cell;
-    };
-
     const QString range_text = (spec.start_image == 0 && spec.end_image == 0)
         ? QStringLiteral("all")
         : QStringLiteral("%1–%2").arg(spec.start_image)
@@ -258,12 +265,12 @@ void JFJochProcessingJobsWindow::newJob() {
     const int expected = spec.end_image > spec.start_image ? spec.end_image - spec.start_image : 0;
 
     table_->setItem(row, COL_NAME, new QTableWidgetItem(label));   // editable (default flags)
-    table_->setItem(row, COL_STARTED, fixed(QDateTime::currentDateTime().toString("HH:mm:ss")));
-    table_->setItem(row, COL_MODE, fixed(full ? "Full" : "AzInt"));
-    table_->setItem(row, COL_IMAGES, fixed(range_text));
-    table_->setItem(row, COL_STATUS, fixed("queued"));
-    table_->setItem(row, COL_INDEX, fixed("-"));
-    table_->setItem(row, COL_CELL, fixed("-"));
+    table_->setItem(row, COL_STARTED, fixedItem(QDateTime::currentDateTime().toString("HH:mm:ss")));
+    table_->setItem(row, COL_MODE, fixedItem(full ? "Full" : "AzInt"));
+    table_->setItem(row, COL_IMAGES, fixedItem(range_text));
+    table_->setItem(row, COL_STATUS, fixedItem("queued"));
+    table_->setItem(row, COL_INDEX, fixedItem("-"));
+    table_->setItem(row, COL_CELL, fixedItem("-"));
 
     // A progress bar lives in the Status cell while the job runs; it shows the phase as text until
     // image processing starts, then "<done> / <expected>" with the bar filling in the background.
@@ -292,11 +299,13 @@ void JFJochProcessingJobsWindow::removeResult() {
     const int row = table_->currentRow();
     if (row < 0 || row >= static_cast<int>(jobs_.size()))
         return;
+    if (jobs_[row].id == "Original")
+        return;   // the original file is always kept
     if (row == running_row_) {
         QMessageBox::information(this, "Processing", "Cancel the running job before removing it.");
         return;
     }
-    emit removeRun(jobs_[row].id);   // drops the snapshot from the reader (no-op for Original)
+    emit removeRun(jobs_[row].id);   // drops the snapshot from the reader
 
     QSignalBlocker block(table_);    // row removal must not look like a rename
     table_->removeRow(row);
@@ -316,6 +325,40 @@ void JFJochProcessingJobsWindow::clearJobs() {
     job_counter_ = 0;
     running_row_ = -1;
     running_bar_ = nullptr;
+    addOriginalRow();
+}
+
+void JFJochProcessingJobsWindow::addOriginalRow() {
+    // The file's own data, listed as the first run so it can be shown like any reprocessing run.
+    JobInfo info;
+    info.id = "Original";
+    info.label = "Original";
+    info.has_result = true;
+
+    const int row = table_->rowCount();
+    table_->insertRow(row);
+    jobs_.push_back(info);
+
+    QSignalBlocker block(table_);
+    table_->setItem(row, COL_NAME, fixedItem("Original"));   // reserved name, not editable
+    table_->setItem(row, COL_STATUS, fixedItem(""));
+    table_->setItem(row, COL_STARTED, fixedItem("—"));
+    table_->setItem(row, COL_MODE, fixedItem("HDF5"));
+    table_->setItem(row, COL_IMAGES, fixedItem("all"));
+    table_->setItem(row, COL_INDEX, fixedItem("-"));
+    table_->setItem(row, COL_CELL, fixedItem("-"));
+}
+
+void JFJochProcessingJobsWindow::setActiveRun(QString active_id) {
+    QSignalBlocker block(table_);
+    for (int row = 0; row < static_cast<int>(jobs_.size()); row++) {
+        auto *item = table_->item(row, COL_NAME);
+        if (!item)
+            continue;
+        QFont f = item->font();
+        f.setBold(jobs_[row].id == active_id);
+        item->setFont(f);
+    }
 }
 
 void JFJochProcessingJobsWindow::viewResults() {
@@ -329,10 +372,6 @@ void JFJochProcessingJobsWindow::viewResults() {
     emit activateSnapshot(jobs_[row].id);
 }
 
-void JFJochProcessingJobsWindow::showOriginal() {
-    emit activateSnapshot("Original");
-}
-
 void JFJochProcessingJobsWindow::setStatus(int row, const QString &text) {
     if (row >= 0 && row < table_->rowCount())
         table_->item(row, COL_STATUS)->setText(text);
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index d47815e7..27aad0f7 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -37,14 +37,14 @@ signals:
 
 public slots:
     void onHttpConnectionChanged(bool connected, QString addr);
-    void clearJobs();   // reset the table on a new file
+    void clearJobs();                    // reset the table on a new file (re-adds the Original row)
+    void setActiveRun(QString active_id);   // bold the row of the run currently shown in the plots
 
 private slots:
     void newJob();
     void cancelJob();
     void removeResult();
     void viewResults();
-    void showOriginal();
     void onPhase(QString phase);
     void onProgress(quint64 done, quint64 total);
     void onFinished(ProcessResult result);
@@ -72,6 +72,7 @@ private:
     int askJob(const ReprocessingInputs &inputs, JobSpec &spec);
     ProcessConfig buildConfig(const JobSpec &spec, const ReprocessingInputs &inputs) const;
     void setStatus(int row, const QString &text);
+    void addOriginalRow();   // the file's own data as the first, always-present run
 
     JFJochImageReadingWorker *worker_;
     JFJochProcessController *controller_;
-- 
2.52.0


From c86beeb393376bbf75fc7578dc59b15e062b791b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 15:59:21 +0200
Subject: [PATCH 196/228] rotation indexer: fix sub-range crash, explicit
 angle, settings + guards

Running rotation indexing on a sub-range (e.g. images 60-120) segfaulted: the
first pass passed the *global* image number to RotationIndexer::ProcessImage,
which indexes v_ (sized to the run's image count) -> out-of-bounds write.

- ProcessImage now takes an explicit mid-exposure angle (optional; falls back to
  the goniometer at the image index), so the indexer no longer assumes its slot
  index equals the goniometer image index. IndexAndRefine supplies it via
  RotationAngle(), matching the angle used for prediction. Added a bounds guard in
  ProcessImage so a bad index can never corrupt memory.
- JFJochProcess feeds the rotation indexer the local ordinal (not the global
  index), and shifts the goniometer (start += start_image*incr, incr *= stride,
  per-image wedge preserved) so local index i maps to the angle of original image
  start+i*stride - fixing rotation angles for the whole sub-range pipeline
  (prediction, refinement, output), not just the indexer.
- Expose "Rotation images" (number used for the first pass) in the job dialog,
  enabled when rotation indexing is on. (Count > available is already clamped by
  select_equally_spaced_image_ordinals.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_analysis/IndexAndRefine.cpp               | 11 +++++++++--
 image_analysis/IndexAndRefine.h                 |  1 +
 .../rotation_indexer/RotationIndexer.cpp        | 12 ++++++++++--
 .../rotation_indexer/RotationIndexer.h          |  8 +++++++-
 process/JFJochProcess.cpp                       | 17 ++++++++++++++++-
 viewer/windows/JFJochProcessingJobsWindow.cpp   | 10 ++++++++++
 viewer/windows/JFJochProcessingJobsWindow.h     |  1 +
 7 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 61b30861..10ba4991 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -28,9 +28,16 @@ IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool
     unit_cells.resize(x.GetImageNum());
 }
 
+std::optional<float> IndexAndRefine::RotationAngle(int64_t image) const {
+    // Mid-exposure rotation angle for image index `image`, matching the angle used for prediction.
+    if (const auto g = experiment.GetGoniometer())
+        return g->GetAngle_deg(static_cast<float>(image)) + g->GetWedge_deg() / 2.0f;
+    return std::nullopt;
+}
+
 void IndexAndRefine::AddImageToRotationIndexer(DataMessage &msg) {
     if (rotation_indexer)
-        rotation_indexer->ProcessImage(msg.number, msg.spots);
+        rotation_indexer->ProcessImage(msg.number, msg.spots, RotationAngle(msg.number));
 }
 
 IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetryRotation(DataMessage &msg) {
@@ -44,7 +51,7 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetryRotat
     if (!result.has_value()) {
         auto rot_cnt = rotation_indexer_counter.Process(msg.number);
         if (rot_cnt.first)
-            rotation_indexer->ProcessImage(msg.number, msg.spots);
+            rotation_indexer->ProcessImage(msg.number, msg.spots, RotationAngle(msg.number));
         if (rot_cnt.second)
             rotation_indexer->RunIndexing();
         result = rotation_indexer->GetLattice();
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index b8b3e9f2..5f42194d 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -82,6 +82,7 @@ class IndexAndRefine {
                               BraggPrediction &prediction,
                               const IndexingOutcome &outcome,
                               IntegrationOutcome &i_outcome);
+    std::optional<float> RotationAngle(int64_t image) const;   // mid-exposure angle for the indexer
 public:
     IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer);
 
diff --git a/image_analysis/rotation_indexer/RotationIndexer.cpp b/image_analysis/rotation_indexer/RotationIndexer.cpp
index 66f0dc98..f7a6de3b 100644
--- a/image_analysis/rotation_indexer/RotationIndexer.cpp
+++ b/image_analysis/rotation_indexer/RotationIndexer.cpp
@@ -13,6 +13,7 @@ RotationIndexer::RotationIndexer(const DiffractionExperiment &x, IndexerThreadPo
     : experiment(x),
       index_ice_rings(x.GetIndexingSettings().GetIndexIceRings()),
       v_(experiment.GetImageNum()),
+      angle_deg_(experiment.GetImageNum()),
       axis_(x.GetGoniometer()),
       geom_(x.GetDiffractionGeometry()),
       updated_geom_(geom_),
@@ -28,7 +29,7 @@ void RotationIndexer::RunIndexing() {
     coords.reserve(max_spots_per_image * v_.size());
 
     for (int i = 0; i < v_.size(); i++) {
-        const float angle_deg = axis_->GetAngle_deg(i) + axis_->GetWedge_deg() / 2.0f;
+        const float angle_deg = angle_deg_[i].value_or(axis_->GetAngle_deg(i) + axis_->GetWedge_deg() / 2.0f);
         const auto rot = axis_->GetTransformationAngle(angle_deg);
 
         for (const auto &s: v_[i])
@@ -115,19 +116,26 @@ void RotationIndexer::RunIndexing() {
     }
 }
 
-void RotationIndexer::ProcessImage(int64_t image, const std::vector<SpotToSave> &spots) {
+void RotationIndexer::ProcessImage(int64_t image, const std::vector<SpotToSave> &spots,
+                                   std::optional<float> angle_deg) {
     std::unique_lock ul(m);
 
     // For non-rotation just ignore the whole procedure
     if (!axis_)
         return;
 
+    // Guard: `image` is a slot in [0, image count); a bad index (e.g. a global number for a subset
+    // run) must not corrupt memory.
+    if (image < 0 || image >= static_cast<int64_t>(v_.size()))
+        return;
+
     if (accumulated_spots >= max_spots)
         return;
 
     if (indexed_lattice)
         return;
 
+    angle_deg_[image] = angle_deg;
     v_[image].reserve(spots.size());
 
     for (const auto &s: spots) {
diff --git a/image_analysis/rotation_indexer/RotationIndexer.h b/image_analysis/rotation_indexer/RotationIndexer.h
index ca6f4023..2878972b 100644
--- a/image_analysis/rotation_indexer/RotationIndexer.h
+++ b/image_analysis/rotation_indexer/RotationIndexer.h
@@ -29,6 +29,9 @@ class RotationIndexer {
     const bool index_ice_rings;
 
     std::vector<std::vector<SpotToSave>> v_;
+    // Per-image rotation angle (mid-exposure, deg) supplied by the caller; falls back to the
+    // goniometer evaluated at the image index when not given.
+    std::vector<std::optional<float>> angle_deg_;
 
     std::optional<GoniometerAxis> axis_;
     const DiffractionGeometry geom_;
@@ -43,7 +46,10 @@ class RotationIndexer {
     std::optional<CrystalLattice> indexed_lattice;
 public:
     RotationIndexer(const DiffractionExperiment& x, IndexerThreadPool& indexer);
-    void ProcessImage(int64_t image, const std::vector<SpotToSave>& spots);
+    // angle_deg is the image's mid-exposure rotation angle; if omitted, the goniometer angle at
+    // `image` is used (only valid when `image` is the goniometer's own image index).
+    void ProcessImage(int64_t image, const std::vector<SpotToSave>& spots,
+                      std::optional<float> angle_deg = std::nullopt);
     void RunIndexing();
     std::optional<RotationIndexerResult> GetLattice() const;
     void ForceLattice(const CrystalLattice& lattice);
diff --git a/process/JFJochProcess.cpp b/process/JFJochProcess.cpp
index 6167a449..1cd76517 100644
--- a/process/JFJochProcess.cpp
+++ b/process/JFJochProcess.cpp
@@ -99,6 +99,21 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
     if (full)
         experiment_.Compression(CompressionAlgorithm::BSHUF_LZ4);
 
+    // The pipeline indexes images 0..N-1 within this run; if we process a sub-range/strided
+    // selection, shift the goniometer so local index i maps to the angle of original image
+    // start+i*stride (keeping the per-image rotation wedge), otherwise rotation angles would be
+    // wrong for any start_image != 0.
+    if (const auto g = experiment_.GetGoniometer();
+        g.has_value() && (start_image != 0 || config_.stride != 1)) {
+        const float incr = g->GetIncrement_deg();
+        GoniometerAxis shifted(g->GetName(),
+                               g->GetStart_deg() + incr * static_cast<float>(start_image),
+                               incr * static_cast<float>(config_.stride),
+                               g->GetAxis(), g->GetHelicalStep());
+        shifted.ScreeningWedge(g->GetScreeningWedge().value_or(incr));
+        experiment_.Goniometer(shifted);
+    }
+
     AzimuthalIntegrationMapping mapping(experiment_, pixel_mask_);
 
     JFJochReceiverPlots plots;
@@ -165,7 +180,7 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
             if (cancelled_) break;
             const int image_idx = start_image + ordinal * config_.stride;
             DataMessage msg{};
-            msg.number = image_idx;
+            msg.number = ordinal;   // index into the rotation indexer (0..images_to_process-1)
             msg.original_number = image_idx;
             try {
                 if (config_.reuse_rotation_spots) {
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 9e3ad20f..ad41f9fa 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -138,14 +138,21 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
 
     auto *rotation = new QCheckBox("Rotation indexing (two-pass)", &dlg);
     rotation->setChecked(inputs.experiment.GetGoniometer().has_value());
+
+    auto *rotation_images = new QSpinBox(&dlg);   // images used to find the rotation lattice
+    rotation_images->setRange(2, 1'000'000);
+    rotation_images->setValue(spec.rotation_images);   // carries the default (30)
+
     auto *scaling = new QCheckBox("Scale && merge", &dlg);
 
     auto sync_full = [&] {
         const bool full = mode->currentData().toInt() == static_cast<int>(ProcessMode::FullAnalysis);
         rotation->setEnabled(full);
         scaling->setEnabled(full);
+        rotation_images->setEnabled(full && rotation->isChecked());
     };
     connect(mode, &QComboBox::currentIndexChanged, &dlg, sync_full);
+    connect(rotation, &QCheckBox::toggled, &dlg, sync_full);
     sync_full();
 
     auto *form = new QFormLayout;
@@ -156,6 +163,7 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
     form->addRow(save);
     form->addRow("Output prefix", prefix);
     form->addRow(rotation);
+    form->addRow("Rotation images", rotation_images);
     form->addRow(scaling);
 
     int result = 0;
@@ -186,6 +194,7 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
         spec.save = save->isChecked();
         spec.prefix = prefix->text();
         spec.rotation = rotation->isEnabled() && rotation->isChecked();
+        spec.rotation_images = rotation_images->value();
         spec.scaling = scaling->isEnabled() && scaling->isChecked();
     }
     return result;
@@ -202,6 +211,7 @@ ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const
     if (spec.mode == ProcessMode::FullAnalysis) {
         config.rotation_indexing = spec.rotation;
         config.two_pass_rotation = true;
+        config.rotation_indexing_image_count = spec.rotation_images;
         config.run_scaling = spec.scaling;
     }
     return config;
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index 27aad0f7..b185f2f1 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -65,6 +65,7 @@ private:
         bool save = true;
         QString prefix;
         bool rotation = false;
+        int rotation_images = 30;   // images used to find the rotation lattice (first pass)
         bool scaling = false;
     };
 
-- 
2.52.0


From 94125bd6cb7ada17bb56a4f0b1f73c039855e7cf Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 16:08:48 +0200
Subject: [PATCH 197/228] CI: reuse jfjoch_hdf5_test via artifact in dials-test

Build jfjoch_hdf5_test once in a new build-hdf5-test job and hand the binary
to dials-test as an artifact, instead of recompiling it from scratch in every
rocky9 processing job. Uses the christopherhx gitea-{upload,download}-artifact
fork (mirrored under gitea.psi.ch/actions) to avoid the stock v4 action's
GHESNotSupportedError. Probe scope: dials-test only; xds-* still self-build
until the round-trip is confirmed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .gitea/workflows/build_and_test.yml | 33 ++++++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index fa13a3ce..668c12d6 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -174,18 +174,45 @@ jobs:
                  python3 gitea_upload_file.py "$file"
             done
           fi
-  dials-test:
-    name: DIALS test
+  # Artifact-reuse probe: build jfjoch_hdf5_test once here and hand it to dials-test below, instead
+  # of every rocky9 processing job recompiling it from scratch (~12 min each). Once this round-trip
+  # is confirmed working on the PSI Gitea, the xds-* jobs can consume the same artifact the same way.
+  build-hdf5-test:
+    name: Build jfjoch_hdf5_test
     runs-on: jfjoch_rocky9
     steps:
       - uses: actions/checkout@v4
-      - name: Build processing test
+      - name: Build jfjoch_hdf5_test
         shell: bash
         run: |
           mkdir -p build
           cd build
           cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
           ninja -j16 jfjoch_hdf5_test
+      # Gitea 1.27 speaks the v4 artifact protocol, but stock actions/upload-artifact@v4 treats any
+      # non-github.com server as GHES and aborts with GHESNotSupportedError. The christopherhx fork
+      # (mirrored under gitea.psi.ch/actions) drops that check; pinning upstream @v3 also works.
+      - name: Upload jfjoch_hdf5_test
+        uses: https://gitea.psi.ch/actions/gitea-upload-artifact@v4
+        with:
+          name: jfjoch_hdf5_test-rocky9
+          path: build/tools/jfjoch_hdf5_test
+          retention-days: 1
+  dials-test:
+    name: DIALS test
+    runs-on: jfjoch_rocky9
+    needs: build-hdf5-test
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download jfjoch_hdf5_test
+        uses: https://gitea.psi.ch/actions/gitea-download-artifact@v4
+        with:
+          name: jfjoch_hdf5_test-rocky9
+          path: build/tools
+      # Artifacts are zipped, which discards the executable bit -- restore it before running.
+      - name: Restore executable bit
+        shell: bash
+        run: chmod +x build/tools/jfjoch_hdf5_test
       - name: Run DIALS processing on legacy format
         shell: bash
         run: |
-- 
2.52.0


From 961836837fc217647c2d32cbb734ed430b57ecc8 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 16:56:18 +0200
Subject: [PATCH 198/228] viewer: salmon group boxes; dataset-info x-axis spans
 the whole dataset

- Fusion fills QGroupBox interiors with a flat light colour, so the settings window
  lost its salmon look. A tiny app stylesheet (QGroupBox { background: transparent })
  makes them show the salmon window background again; entry widgets stay white via
  the palette.
- The dataset-info chart now fixes the x-axis to the whole dataset [0, n) (the
  largest run = the original file), so a subset run is drawn at its real image
  positions instead of being stretched to fill the plot. Subsets with binning bin
  by ordinal and place each point at its mapped image number (correct for the
  common contiguous sub-range).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp           | 9 ++++++++-
 viewer/charts/JFJochDatasetInfoChartView.cpp | 6 +++++-
 viewer/charts/JFJochDatasetInfoChartView.h   | 4 +++-
 viewer/jfjoch_viewer.cpp                     | 3 +++
 4 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 985c3f6f..aa0a535c 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -251,8 +251,15 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
                             RunColor(static_cast<int>(runs_.size())), XForRun(*live_run_)});
     }
 
+    // The whole dataset spans this many images (the largest run, i.e. the original file), so the
+    // x-axis is fixed to it and subset runs appear at their real position.
+    int64_t full_range = dataset->experiment.GetImageNum();
+    for (const auto &run: runs_)
+        if (run.dataset)
+            full_range = std::max<int64_t>(full_range, run.dataset->experiment.GetImageNum());
+
     chart_view->loadValues(data, image_number, one_over_d2, dataset.get(), primary_name,
-                           std::move(overlays), primary_color, XForRun(*dataset));
+                           std::move(overlays), primary_color, XForRun(*dataset), full_range);
 
     if (dataset->experiment.GetGridScan()) {
         stack->setCurrentWidget(grid_scan_image);
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index 25e65dde..77806db2 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -132,11 +132,12 @@ void JFJochDatasetInfoChartView::resetZoom() {
 void JFJochDatasetInfoChartView::loadValues(const std::vector<float> &input, int64_t image, bool one_over_d2,
                                             const JFJochReaderDataset *dataset, const QString &primaryName,
                                             std::vector<NamedSeries> overlays, const QColor &primaryColor,
-                                            std::vector<float> primaryX) {
+                                            std::vector<float> primaryX, int64_t fullRange) {
     m_yOneOverD = one_over_d2;
     primaryName_ = primaryName;
     primary_color_ = primaryColor;
     primary_x_ = std::move(primaryX);
+    full_range_ = fullRange;
 
     // d -> 1/d^2 for resolution plots; identity otherwise. Applied to every series alike.
     auto transform = [one_over_d2](const std::vector<float> &in, std::vector<float> &out) {
@@ -301,6 +302,9 @@ void JFJochDatasetInfoChartView::buildTimeDomainChart() {
         // ----- X axis handling -----
         QValueAxis *axisX = qobject_cast<QValueAxis *>(chart()->axisX(series));
         if (axisX) {
+            // Always span the whole dataset so a subset run shows at its real position, not stretched.
+            if (full_range_ > 1)
+                axisX->setRange(0, static_cast<double>(full_range_ - 1));
             if (goniometer_axis.has_value() && m_xUseGoniometerAxis) {
                 // Hide labels on numeric axis and move it to the top
 
diff --git a/viewer/charts/JFJochDatasetInfoChartView.h b/viewer/charts/JFJochDatasetInfoChartView.h
index ce3f6bca..98352e66 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.h
+++ b/viewer/charts/JFJochDatasetInfoChartView.h
@@ -54,6 +54,7 @@ private:
     std::vector<NamedSeries> overlays_;
     QColor primary_color_;                // colour of the active (primary) run, if assigned
     std::vector<float> primary_x_;        // x (image numbers) for the primary series; empty => index
+    int64_t full_range_ = 0;              // total images in the dataset; fixes the x-axis to [0, n)
     // Append (binned) finite points of vals to s at x positions (xs empty => index), extending [mn,mx].
     void appendSeries(QLineSeries *s, const std::vector<float> &vals, const std::vector<float> &xs,
                       double &mn, double &mx) const;
@@ -99,7 +100,8 @@ public:
         const QString &primaryName = QString(),
         std::vector<NamedSeries> overlays = {},
         const QColor &primaryColor = QColor(),
-        std::vector<float> primaryX = {});
+        std::vector<float> primaryX = {},
+        int64_t fullRange = 0);
 };
 
 
diff --git a/viewer/jfjoch_viewer.cpp b/viewer/jfjoch_viewer.cpp
index 863a3e48..6b2cb111 100644
--- a/viewer/jfjoch_viewer.cpp
+++ b/viewer/jfjoch_viewer.cpp
@@ -29,6 +29,9 @@ int main(int argc, char *argv[]) {
     pal.setColor(QPalette::Highlight, QColor(0x2a, 0x9d, 0x8f));
     pal.setColor(QPalette::HighlightedText, Qt::white);
     app.setPalette(pal);
+    // Fusion fills QGroupBox interiors with a flat light colour; make them transparent so they show
+    // the salmon window background like the rest of the UI (entry widgets stay white via the palette).
+    app.setStyleSheet("QGroupBox { background-color: transparent; }");
 
     QIcon appIcon(":/jfjoch.png");
     app.setWindowIcon(appIcon);
-- 
2.52.0


From 9defbffa67bcbbe58322a7bbd43040d6fcdd206e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 17:49:38 +0200
Subject: [PATCH 199/228] Revert "CI: reuse jfjoch_hdf5_test via artifact in
 dials-test"

This reverts commit 94125bd6cb7ada17bb56a4f0b1f73c039855e7cf.
---
 .gitea/workflows/build_and_test.yml | 33 +++--------------------------
 1 file changed, 3 insertions(+), 30 deletions(-)

diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index 668c12d6..fa13a3ce 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -174,45 +174,18 @@ jobs:
                  python3 gitea_upload_file.py "$file"
             done
           fi
-  # Artifact-reuse probe: build jfjoch_hdf5_test once here and hand it to dials-test below, instead
-  # of every rocky9 processing job recompiling it from scratch (~12 min each). Once this round-trip
-  # is confirmed working on the PSI Gitea, the xds-* jobs can consume the same artifact the same way.
-  build-hdf5-test:
-    name: Build jfjoch_hdf5_test
+  dials-test:
+    name: DIALS test
     runs-on: jfjoch_rocky9
     steps:
       - uses: actions/checkout@v4
-      - name: Build jfjoch_hdf5_test
+      - name: Build processing test
         shell: bash
         run: |
           mkdir -p build
           cd build
           cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
           ninja -j16 jfjoch_hdf5_test
-      # Gitea 1.27 speaks the v4 artifact protocol, but stock actions/upload-artifact@v4 treats any
-      # non-github.com server as GHES and aborts with GHESNotSupportedError. The christopherhx fork
-      # (mirrored under gitea.psi.ch/actions) drops that check; pinning upstream @v3 also works.
-      - name: Upload jfjoch_hdf5_test
-        uses: https://gitea.psi.ch/actions/gitea-upload-artifact@v4
-        with:
-          name: jfjoch_hdf5_test-rocky9
-          path: build/tools/jfjoch_hdf5_test
-          retention-days: 1
-  dials-test:
-    name: DIALS test
-    runs-on: jfjoch_rocky9
-    needs: build-hdf5-test
-    steps:
-      - uses: actions/checkout@v4
-      - name: Download jfjoch_hdf5_test
-        uses: https://gitea.psi.ch/actions/gitea-download-artifact@v4
-        with:
-          name: jfjoch_hdf5_test-rocky9
-          path: build/tools
-      # Artifacts are zipped, which discards the executable bit -- restore it before running.
-      - name: Restore executable bit
-        shell: bash
-        run: chmod +x build/tools/jfjoch_hdf5_test
       - name: Run DIALS processing on legacy format
         shell: bash
         run: |
-- 
2.52.0


From 5f3126e19ea04c09232204dd3315a768575f2968 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 17:51:57 +0200
Subject: [PATCH 200/228] CMake: Update FFBIDX to support MSVC

---
 image_analysis/indexing/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/image_analysis/indexing/CMakeLists.txt b/image_analysis/indexing/CMakeLists.txt
index 6b8dc312..c639d36a 100644
--- a/image_analysis/indexing/CMakeLists.txt
+++ b/image_analysis/indexing/CMakeLists.txt
@@ -25,7 +25,7 @@ IF (JFJOCH_CUDA_AVAILABLE)
     FetchContent_Declare(
             fast-indexer
             GIT_REPOSITORY https://github.com/paulscherrerinstitute/fast-feedback-indexer/
-            GIT_TAG ca9e17486a1eb96319a738acef33cc24c9cd8845
+            GIT_TAG a94fd4f5c55289e70860feea358182d2072e02b5
             GIT_SUBMODULES ""
     )
 
-- 
2.52.0


From ad5662732d14fecfbee801a4c54a503dc341f361 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 19:47:01 +0200
Subject: [PATCH 201/228] windows: auto-detect nvcc and drop manual CUDA/zlib
 flags

Locate nvcc via find_program (HINTS CUDA_PATH / /usr/local/cuda) before
CHECK_LANGUAGE(CUDA), so CMAKE_CUDA_COMPILER no longer has to be passed by
hand. CHECK_LANGUAGE only searches PATH, which is missed routinely on Windows
and intermittently on Linux; the CUDA installer always sets CUDA_PATH. An
explicit -DCMAKE_CUDA_COMPILER / $CUDACXX still wins.

Docs: zlib and Eigen are external find_package deps (not auto-fetched);
simplify the Windows configure to just CMAKE_PREFIX_PATH (no CMAKE_CUDA_COMPILER,
no ZLIB_ROOT); fix the Eigen 5.0.1 install recipe to disable BLAS/LAPACK
(they fail MSVC with C1128 /bigobj) and use cmake --install.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 CMakeLists.txt        | 15 +++++++++++++++
 docs/JFJOCH_VIEWER.md | 17 ++++++++++-------
 docs/SOFTWARE.md      |  5 ++++-
 3 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0148f365..7a5c6fcc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -45,6 +45,21 @@ SET(BUILD_FAST_INDEXER_STATIC ON)
 
 INCLUDE(CheckLanguage)
 INCLUDE(CheckIncludeFile)
+
+# Locate nvcc ourselves when it isn't already pinned (-DCMAKE_CUDA_COMPILER / $CUDACXX). CHECK_LANGUAGE
+# below only searches PATH, which is missed routinely on Windows and intermittently on Linux; the
+# standard CUDA install locations (CUDA_PATH on Windows, /usr/local/cuda on Linux) cover both, so the
+# compiler need not be passed by hand. Only set it when actually found, leaving CHECK_LANGUAGE to run
+# its normal detection otherwise.
+IF (JFJOCH_USE_CUDA AND NOT CMAKE_CUDA_COMPILER AND NOT DEFINED ENV{CUDACXX})
+    FIND_PROGRAM(_jfjoch_nvcc nvcc
+            HINTS ENV CUDA_PATH ENV CUDA_HOME ENV CUDA_ROOT /usr/local/cuda /opt/cuda
+            PATH_SUFFIXES bin)
+    IF (_jfjoch_nvcc)
+        SET(CMAKE_CUDA_COMPILER "${_jfjoch_nvcc}")
+    ENDIF()
+ENDIF()
+
 CHECK_LANGUAGE(CUDA)
 
 SET(CMAKE_CUDA_ARCHITECTURES 75 80 86 89 90 100 120) # T4, A100, RTX A4000, L4
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index ddce90ca..65e407ba 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -81,10 +81,12 @@ Verified toolchain:
   git clone --branch v1.3.1 https://github.com/madler/zlib
   cmake -G Ninja -S zlib -B zlib-build -DCMAKE_INSTALL_PREFIX=C:/deps
   cmake --build zlib-build --target install
-  :: Eigen (header-only)
+  :: Eigen (header-only) -- disable the BLAS/LAPACK/test targets (they fail to compile under MSVC),
+  :: then install the headers directly with `cmake --install` (no build step needed)
   git clone --branch 5.0.1 https://gitlab.com/libeigen/eigen.git
-  cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=C:/deps
-  cmake --build eigen-build --target install
+  cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=C:/deps ^
+    -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF
+  cmake --install eigen-build
   ```
 - Optional: [NSIS](https://nsis.sourceforge.io) to build the `.exe` installer.
 
@@ -93,16 +95,17 @@ Configure and build from an **x64 Native Tools Command Prompt for VS 2026** (so
 
 ```
 cmake -G Ninja -B build-win -DCMAKE_BUILD_TYPE=Release ^
-  -DCMAKE_CUDA_COMPILER="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v13.3/bin/nvcc.exe" ^
-  -DZLIB_ROOT=C:/deps ^
   -DCMAKE_PREFIX_PATH="C:/deps;C:/Qt/6.11.1/msvc2022_64"
 cmake --build build-win --target jfjoch_viewer
 ```
 
 Notes:
 
-- Presetting `CMAKE_CUDA_COMPILER` is recommended on Windows so the CUDA toolchain is detected
-  reliably.
+- `CMAKE_PREFIX_PATH` (the `C:/deps` prefix plus Qt) is the only required flag — CMake finds zlib and
+  Eigen from the prefix, so no separate `-DZLIB_ROOT` is needed.
+- The CUDA toolchain is located automatically from the `CUDA_PATH` environment variable that the
+  CUDA installer sets (or from `nvcc` on `PATH`). Pass `-DCMAKE_CUDA_COMPILER=".../bin/nvcc.exe"`
+  only if `nvcc` is installed in a nonstandard location and is not found.
 - For a machine without an NVIDIA GPU, add `-DJFJOCH_USE_CUDA=OFF`: the viewer then runs the same
   pipeline on the CPU (FFTW indexer) at lower throughput.
 
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index b661fba2..fa4b04c7 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -32,8 +32,11 @@ Optional:
 * Qt version 6 (for jfjoch_viewer)
 
 Many further dependencies (spdlog, Zstandard, HDF5, slsDetectorPackage, libzmq, libtiff,
-libjpeg-turbo, Eigen, Ceres, the fast feedback indexer, Catch2, ...) are downloaded automatically
+libjpeg-turbo, Ceres, the fast feedback indexer, Catch2, ...) are downloaded automatically
 by CMake and statically linked; building therefore requires network access on the first configure.
+zlib and Eigen are the exception — they must be preinstalled (found via `find_package`); on Windows,
+where they are not present system-wide, install them into a prefix and point `CMAKE_PREFIX_PATH` at
+it (see [Building from source on Windows](JFJOCH_VIEWER.md#building-from-source-on-windows)).
 Others are vendored directly in the source tree. The complete list of third-party components, with
 copyright holders, licenses and verbatim license texts, is in
 [THIRD_PARTY_NOTICES.md](../THIRD_PARTY_NOTICES.md) and the `licenses/` directory.
-- 
2.52.0


From 68f3394f4844a41948f455e685ff9a29227cd26b Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Mon, 22 Jun 2026 20:53:42 +0200
Subject: [PATCH 202/228] deps: pin external Eigen to 3.4.x across docs and
 Docker images

Eigen is an external find_package(Eigen3 3.4) dependency. Eigen's
same-major-version rule means a bare 3.4 request only accepts 3.x, so 5.x
cannot be used without changing every requester (jfjoch, Ceres, and the
upstream ffbidx). Standardise on Eigen 3.4.x:

- docs: correct the Windows Eigen install recipe to 3.4.0 and note the
  same-major constraint; SOFTWARE.md now says 3.4.x (not "3.4 or newer").
- docker/{rocky8,rocky9,ubuntu2204,ubuntu2404}: actually install Eigen 3.4.0
  from source to /opt/eigen-3.4 (header-only) and add it to CMAKE_PREFIX_PATH.
  The images previously installed no Eigen at all, relying on the obsolete
  "CMake fetches it" assumption; a rebuild would have failed at configure.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 docker/rocky8/Dockerfile     | 18 +++++++++++++++---
 docker/rocky9/Dockerfile     | 19 +++++++++++++++----
 docker/ubuntu2204/Dockerfile | 19 +++++++++++++++----
 docker/ubuntu2404/Dockerfile | 19 +++++++++++++++----
 docs/JFJOCH_VIEWER.md        |  7 ++++---
 docs/SOFTWARE.md             |  3 ++-
 6 files changed, 66 insertions(+), 19 deletions(-)

diff --git a/docker/rocky8/Dockerfile b/docker/rocky8/Dockerfile
index 53561969..88089eaa 100644
--- a/docker/rocky8/Dockerfile
+++ b/docker/rocky8/Dockerfile
@@ -4,8 +4,10 @@ LABEL authors="leonarski_f"
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-# HDF5, libtiff, libjpeg-turbo and Eigen are now built by the jungfraujoch CMake itself
-# (FetchContent / ExternalProject), so they are no longer pre-built here.
+ARG EIGEN_VERSION=3.4.0
+# HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
+# ExternalProject). Eigen is an external find_package(Eigen3 3.4) dependency, installed from source
+# below (3.4.x is required; Eigen's same-major-version rule rejects 5.x).
 
 # Update base and install common utilities
 RUN dnf -y update && \
@@ -127,7 +129,17 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
+# Eigen 3.4 (header-only) -- external find_package(Eigen3 3.4) dependency, installed to /opt/eigen-3.4.
+RUN set -eux; \
+    cd /tmp; \
+    git clone --depth 1 --branch ${EIGEN_VERSION} https://gitlab.com/libeigen/eigen.git; \
+    cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=/opt/eigen-3.4 \
+      -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF; \
+    cmake --install eigen-build; \
+    cd /; rm -rf /tmp/eigen /tmp/eigen-build
+
+# Make Qt and Eigen discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace
diff --git a/docker/rocky9/Dockerfile b/docker/rocky9/Dockerfile
index dbc1a9b4..6aa1d5d0 100644
--- a/docker/rocky9/Dockerfile
+++ b/docker/rocky9/Dockerfile
@@ -4,8 +4,10 @@ LABEL authors="leonarski_f"
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
-# (FetchContent / ExternalProject), so they are not provided here.
+ARG EIGEN_VERSION=3.4.0
+# HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
+# ExternalProject). Eigen is an external find_package(Eigen3 3.4) dependency, installed from source
+# below (3.4.x is required; Eigen's same-major-version rule rejects 5.x).
 ARG DIALS_VERSION=3.27.0
 ARG DIALS_TARBALL_URL=https://github.com/dials/dials/releases/download/v3.27.0/dials-v3-27-0-linux-x86_64.tar.xz
 ARG DIALS_PREFIX=/opt
@@ -163,8 +165,17 @@ RUN set -eux; \
           -O /opt/xds/durin-plugin.so \
           https://gitea.psi.ch/mx/durin/releases/download/1.0.0/libdurin-plugin.so.1.0.0
 
-# Make Qt discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
+# Eigen 3.4 (header-only) -- external find_package(Eigen3 3.4) dependency, installed to /opt/eigen-3.4.
+RUN set -eux; \
+    cd /tmp; \
+    git clone --depth 1 --branch ${EIGEN_VERSION} https://gitlab.com/libeigen/eigen.git; \
+    cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=/opt/eigen-3.4 \
+      -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF; \
+    cmake --install eigen-build; \
+    cd /; rm -rf /tmp/eigen /tmp/eigen-build
+
+# Make Qt and Eigen discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
 
 ENV LANG=en_US.UTF-8
 ENV LANGUAGE=en_US:en
diff --git a/docker/ubuntu2204/Dockerfile b/docker/ubuntu2204/Dockerfile
index c139ed8b..9e34c8e3 100644
--- a/docker/ubuntu2204/Dockerfile
+++ b/docker/ubuntu2204/Dockerfile
@@ -7,8 +7,10 @@ ENV DEBIAN_FRONTEND=noninteractive
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
-# (FetchContent / ExternalProject), so they are not pre-built here.
+ARG EIGEN_VERSION=3.4.0
+# HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
+# ExternalProject). Eigen is an external find_package(Eigen3 3.4) dependency, installed from source
+# below (3.4.x is required; Eigen's same-major-version rule rejects 5.x).
 
 # Update base and install toolchain + Qt dependencies
 # Notes:
@@ -152,8 +154,17 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-# Make Qt discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
+# Eigen 3.4 (header-only) -- external find_package(Eigen3 3.4) dependency, installed to /opt/eigen-3.4.
+RUN set -eux; \
+    cd /tmp; \
+    git clone --depth 1 --branch ${EIGEN_VERSION} https://gitlab.com/libeigen/eigen.git; \
+    cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=/opt/eigen-3.4 \
+      -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF; \
+    cmake --install eigen-build; \
+    cd /; rm -rf /tmp/eigen /tmp/eigen-build
+
+# Make Qt and Eigen discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace
diff --git a/docker/ubuntu2404/Dockerfile b/docker/ubuntu2404/Dockerfile
index 7449e9b1..8fb63a26 100644
--- a/docker/ubuntu2404/Dockerfile
+++ b/docker/ubuntu2404/Dockerfile
@@ -7,8 +7,10 @@ ENV DEBIAN_FRONTEND=noninteractive
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
 ARG NODE_MAJOR=22
-# HDF5, libtiff, libjpeg-turbo and Eigen are built by the jungfraujoch CMake itself now
-# (FetchContent / ExternalProject), so they are not provided here. nasm is required by the
+ARG EIGEN_VERSION=3.4.0
+# HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
+# ExternalProject). Eigen is an external find_package(Eigen3 3.4) dependency, installed from source
+# below (3.4.x is required; Eigen's same-major-version rule rejects 5.x). nasm is required by the
 # project's libjpeg-turbo ExternalProject for SIMD-accelerated JPEG.
 
 # Update base and install toolchain + static-Qt build dependencies
@@ -139,8 +141,17 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
-# Make Qt discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static
+# Eigen 3.4 (header-only) -- external find_package(Eigen3 3.4) dependency, installed to /opt/eigen-3.4.
+RUN set -eux; \
+    cd /tmp; \
+    git clone --depth 1 --branch ${EIGEN_VERSION} https://gitlab.com/libeigen/eigen.git; \
+    cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=/opt/eigen-3.4 \
+      -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF; \
+    cmake --install eigen-build; \
+    cd /; rm -rf /tmp/eigen /tmp/eigen-build
+
+# Make Qt and Eigen discoverable by CMake
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index 65e407ba..fe74af36 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -81,9 +81,10 @@ Verified toolchain:
   git clone --branch v1.3.1 https://github.com/madler/zlib
   cmake -G Ninja -S zlib -B zlib-build -DCMAKE_INSTALL_PREFIX=C:/deps
   cmake --build zlib-build --target install
-  :: Eigen (header-only) -- disable the BLAS/LAPACK/test targets (they fail to compile under MSVC),
-  :: then install the headers directly with `cmake --install` (no build step needed)
-  git clone --branch 5.0.1 https://gitlab.com/libeigen/eigen.git
+  :: Eigen 3.4 (header-only) -- install just the headers with `cmake --install`; the BLAS/LAPACK/test
+  :: targets are disabled since they are not needed (and fail to build under MSVC). Use the 3.4 series:
+  :: the project requests find_package(Eigen3 3.4), which Eigen's same-major rule rejects for 5.x.
+  git clone --branch 3.4.0 https://gitlab.com/libeigen/eigen.git
   cmake -G Ninja -S eigen -B eigen-build -DCMAKE_INSTALL_PREFIX=C:/deps ^
     -DEIGEN_BUILD_BLAS=OFF -DEIGEN_BUILD_LAPACK=OFF -DEIGEN_BUILD_DOC=OFF -DBUILD_TESTING=OFF
   cmake --install eigen-build
diff --git a/docs/SOFTWARE.md b/docs/SOFTWARE.md
index fa4b04c7..c3d252ba 100644
--- a/docs/SOFTWARE.md
+++ b/docs/SOFTWARE.md
@@ -20,7 +20,8 @@ Required:
 * C++20 compiler and C++20 standard library; recommended GCC 11+ or clang 14+ (Intel OneAPI, AMD AOCC)
 * CMake version 3.26 or newer + a build tool (GNU make or Ninja)
 * zlib compression library
-* Eigen (header-only linear algebra library), version 3.4 or newer
+* Eigen (header-only linear algebra library), version 3.4.x (the build requests `Eigen3 3.4`, which
+  Eigen's same-major-version rule does not satisfy with 5.x)
 
 HDF5, libtiff and libjpeg-turbo used to be required system packages; they are now downloaded and
 built automatically by CMake (see the note below), so they no longer need to be installed.
-- 
2.52.0


From ecc06d9abd89943126b47738d735985e21d9db3e Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 08:19:47 +0200
Subject: [PATCH 203/228] =?UTF-8?q?viewer:=20Phase=200=20redesign=20?=
 =?UTF-8?q?=E2=80=94=20slim=20headers,=20navy=20accent,=20icon=20nav?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

First pass of the viewer redesign (see docs/review/VIEWER_REDESIGN.md), no
structural change:

- TitleLabel: replace the 50px solid #FA7268 section bars with a slim 26px
  navy-bold header + coral accent rule, removing the "venetian blind" stack
  while keeping the salmon identity.
- Palette: switch the accent (QPalette::Highlight) from teal to navy #1F3A5F.
- Image toolbar: replace the unicode arrow glyphs (|<= <= => =>|) with flat
  media icons (first/prev/next/last) + tooltips, and a play icon on Movie.
- Bottom dock: give the per-dataset plot more default height (340 -> 420).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp               |  5 +++--
 viewer/JFJochViewerWindow.h                 |  2 +-
 viewer/jfjoch_viewer.cpp                    |  4 ++--
 viewer/toolbar/JFJochViewerToolbarImage.cpp | 18 ++++++++++++++----
 viewer/widgets/TitleLabel.cpp               | 18 ++++++++++++++----
 5 files changed, 34 insertions(+), 13 deletions(-)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index d16a629e..acfc4633 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -426,8 +426,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     if (lastDatasetInfoDock) {
         splitDockWidget(lastDatasetInfoDock, processingDock, Qt::Horizontal);
         resizeDocks({lastDatasetInfoDock, processingDock}, {650, 350}, Qt::Horizontal);
-        // Give the bottom area enough height so the plots and their labels are fully visible.
-        resizeDocks({lastDatasetInfoDock, processingDock}, {340, 340}, Qt::Vertical);
+        // Give the bottom area generous height: the per-dataset plot is a headline feature, so it
+        // gets real room rather than a thin strip.
+        resizeDocks({lastDatasetInfoDock, processingDock}, {420, 420}, Qt::Vertical);
     }
     menuBar->AddDockEntry(processingDock, "Processing");
 
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index e42b61cb..cc655dcd 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -19,7 +19,7 @@ class QDockWidget;
 class JFJochViewerWindow : public QMainWindow {
 Q_OBJECT
     // Theming is done via the application palette in main() (salmon panels, white entry fields,
-    // teal accent) so it applies consistently to every widget, including dialogs.
+    // navy accent) so it applies consistently to every widget, including dialogs.
 public:
     explicit JFJochViewerWindow(QWidget *parent = nullptr, bool dbus = true, const QString &file = "");
     ~JFJochViewerWindow() override;
diff --git a/viewer/jfjoch_viewer.cpp b/viewer/jfjoch_viewer.cpp
index 6b2cb111..bdaae45b 100644
--- a/viewer/jfjoch_viewer.cpp
+++ b/viewer/jfjoch_viewer.cpp
@@ -18,7 +18,7 @@ int main(int argc, char *argv[]) {
     QApplication app(argc, argv);
 
     // Theme via the palette (robust across widgets): salmon panels, white entry fields that fall back
-    // to salmon when disabled, and a teal accent for selections and progress-bar chunks.
+    // to salmon when disabled, and a navy accent for selections and progress-bar chunks.
     app.setStyle("Fusion");
     QPalette pal = app.palette();
     pal.setColor(QPalette::Window, QColor(255, 235, 230));
@@ -26,7 +26,7 @@ int main(int argc, char *argv[]) {
     pal.setColor(QPalette::AlternateBase, QColor(255, 245, 242));
     pal.setColor(QPalette::Button, QColor(255, 235, 230));
     pal.setColor(QPalette::Disabled, QPalette::Base, QColor(255, 235, 230));
-    pal.setColor(QPalette::Highlight, QColor(0x2a, 0x9d, 0x8f));
+    pal.setColor(QPalette::Highlight, QColor(0x1f, 0x3a, 0x5f));
     pal.setColor(QPalette::HighlightedText, Qt::white);
     app.setPalette(pal);
     // Fusion fills QGroupBox interiors with a flat light colour; make them transparent so they show
diff --git a/viewer/toolbar/JFJochViewerToolbarImage.cpp b/viewer/toolbar/JFJochViewerToolbarImage.cpp
index b570194e..74244ad6 100644
--- a/viewer/toolbar/JFJochViewerToolbarImage.cpp
+++ b/viewer/toolbar/JFJochViewerToolbarImage.cpp
@@ -3,6 +3,7 @@
 
 #include "JFJochViewerToolbarImage.h"
 #include <QTimer>
+#include <QStyle>
 
 JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(parent) {
     image_count_in_dataset = 0;
@@ -10,11 +11,15 @@ JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(p
     auto title = new QLabel("<b>Image number</b>   ", this);
     addWidget(title);
 
-    leftmost_button = new QPushButton("|⇐", this);
+    leftmost_button = new QPushButton(this);
+    leftmost_button->setIcon(style()->standardIcon(QStyle::SP_MediaSkipBackward));
+    leftmost_button->setToolTip("First image");
     leftmost_button->setFixedWidth(32);
     addWidget(leftmost_button);
 
-    left_button = new QPushButton("⇐", this);
+    left_button = new QPushButton(this);
+    left_button->setIcon(style()->standardIcon(QStyle::SP_MediaSeekBackward));
+    left_button->setToolTip("Previous (by jump)");
     left_button->setFixedWidth(32);
     addWidget(left_button);
 
@@ -30,11 +35,15 @@ JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(p
     total_number_label = new QLabel("/0", this);
     addWidget(total_number_label);
 
-    right_button = new QPushButton("⇒", this);
+    right_button = new QPushButton(this);
+    right_button->setIcon(style()->standardIcon(QStyle::SP_MediaSeekForward));
+    right_button->setToolTip("Next (by jump)");
     right_button->setFixedWidth(32);
     addWidget(right_button);
 
-    rightmost_button = new QPushButton("⇒|", this);
+    rightmost_button = new QPushButton(this);
+    rightmost_button->setIcon(style()->standardIcon(QStyle::SP_MediaSkipForward));
+    rightmost_button->setToolTip("Last image");
     rightmost_button->setFixedWidth(32);
     addWidget(rightmost_button);
 
@@ -57,6 +66,7 @@ JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(p
 
 
     movie_button = new QPushButton("&Movie");
+    movie_button->setIcon(style()->standardIcon(QStyle::SP_MediaPlay));
     movie_button->setCheckable(true);
     movie_button->setChecked(false);
     movie_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_M));
diff --git a/viewer/widgets/TitleLabel.cpp b/viewer/widgets/TitleLabel.cpp
index 5cd8dc3d..2f4ded10 100644
--- a/viewer/widgets/TitleLabel.cpp
+++ b/viewer/widgets/TitleLabel.cpp
@@ -4,8 +4,18 @@
 #include "TitleLabel.h"
 
 TitleLabel::TitleLabel(QString text, QWidget *parent) : QLabel(parent) {
-    setText(QString("<h3>%1</h3>").arg(text));
-    setStyleSheet("background-color: #FA7268; color: #ffffff;");
-    setAlignment(Qt::AlignmentFlag::AlignCenter);
-    setFixedHeight(50);
+    // Slim section header: navy bold text with a coral accent rule, in place of a heavy 50px
+    // full-width salmon bar. Keeps the salmon identity (the rule) while letting panels breathe.
+    setText(text);
+    QFont f = font();
+    f.setBold(true);
+    setFont(f);
+    setStyleSheet("QLabel {"
+                  " color: #1F3A5F;"
+                  " background-color: transparent;"
+                  " border-left: 3px solid #FA7268;"
+                  " border-bottom: 1px solid #FA7268;"
+                  " padding: 3px 6px 3px 8px; }");
+    setAlignment(Qt::AlignLeft | Qt::AlignVCenter);
+    setFixedHeight(26);
 }
-- 
2.52.0


From f5a146d21240b21fab1aefb02e490eefbb377ea9 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 08:28:50 +0200
Subject: [PATCH 204/228] =?UTF-8?q?viewer:=20Phase=201a=20=E2=80=94=20dock?=
 =?UTF-8?q?able=20shell=20with=20saved=20perspectives?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Make the layout reconfigurable, the foundation for the redesign:

- The diffraction image becomes the central widget; the right-hand side panel
  is now a dockable "Inspector" (QDockWidget, right area).
- Every dock and toolbar gets a stable objectName so QMainWindow saveState /
  restoreState round-trips. Dataset-info docks are numbered uniquely.
- Persist geometry + dock state to QSettings on close and restore on launch,
  so the user's arrangement resumes.
- New "View" menu with Image / Processing perspectives (show/hide the bottom
  plots + jobs panel) and "Reset layout" (back to the as-built arrangement,
  captured at startup).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerMenu.cpp   |  9 ++++++
 viewer/JFJochViewerMenu.h     |  4 +++
 viewer/JFJochViewerWindow.cpp | 61 ++++++++++++++++++++++++++++-------
 viewer/JFJochViewerWindow.h   |  9 ++++++
 4 files changed, 72 insertions(+), 11 deletions(-)

diff --git a/viewer/JFJochViewerMenu.cpp b/viewer/JFJochViewerMenu.cpp
index 4f766c06..ef60b2b4 100644
--- a/viewer/JFJochViewerMenu.cpp
+++ b/viewer/JFJochViewerMenu.cpp
@@ -65,6 +65,15 @@ JFJochViewerMenu::JFJochViewerMenu(QWidget *parent) : QMenuBar(parent) {
     const QAction *dockCalibration = dockMenu->addAction("New dataset info plot");
     connect(dockCalibration, &QAction::triggered, [this] { emit openDatasetInfo();});
 
+    QMenu *viewMenu = addMenu("View");
+    const QAction *imageLayout = viewMenu->addAction("Image layout");
+    connect(imageLayout, &QAction::triggered, this, &JFJochViewerMenu::imageLayoutSelected);
+    const QAction *processingLayout = viewMenu->addAction("Processing layout");
+    connect(processingLayout, &QAction::triggered, this, &JFJochViewerMenu::processingLayoutSelected);
+    viewMenu->addSeparator();
+    const QAction *resetLayout = viewMenu->addAction("Reset layout");
+    connect(resetLayout, &QAction::triggered, this, &JFJochViewerMenu::resetLayoutSelected);
+
     QMenu *helpMenu = addMenu("Help");
     // Add "About" action
     const QAction *aboutAction = helpMenu->addAction("About");
diff --git a/viewer/JFJochViewerMenu.h b/viewer/JFJochViewerMenu.h
index 04d87754..2a07ef2c 100644
--- a/viewer/JFJochViewerMenu.h
+++ b/viewer/JFJochViewerMenu.h
@@ -39,6 +39,10 @@ signals:
     void clearUserMaskSelected();
     void openDatasetInfo();
 
+    void imageLayoutSelected();
+    void processingLayoutSelected();
+    void resetLayoutSelected();
+
 private slots:
     void aboutSelected();
     void licensesSelected();
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index acfc4633..3befd9a9 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -3,12 +3,14 @@
 
 #include "JFJochViewerWindow.h"
 
-#include <QSplitter>
 #include <QThread>
 #include <QDockWidget>
 #include <QKeyEvent>
 #include <QGuiApplication>
 #include <QScreen>
+#include <QScrollArea>
+#include <QSettings>
+#include <QCloseEvent>
 
 #include "JFJochImageReadingWorker.h"
 #include "image_viewer/JFJochDiffractionImage.h"
@@ -43,10 +45,12 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     setFocusPolicy(Qt::StrongFocus);
 
     auto toolBarImage = new JFJochViewerToolbarImage(this);
+    toolBarImage->setObjectName("toolBarImage");   // objectName required for saveState/restoreState
     addToolBar(Qt::TopToolBarArea, toolBarImage);
     addToolBarBreak(Qt::TopToolBarArea);
 
     toolBarDisplay = new JFJochViewerToolbarDisplay(this);
+    toolBarDisplay->setObjectName("toolBarDisplay");
     addToolBar(Qt::TopToolBarArea, toolBarDisplay);
 
     statusbar = new JFJochViewerStatusBar(this);
@@ -77,14 +81,11 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     experiment.ImportIndexingSettings(indexing_settings);
     experiment.DetectIceRings(true);
 
-    // Central area: only the main horizontal splitter (image + side panel)
-    auto h_splitter = new QSplitter(this);
-    h_splitter->setOrientation(Qt::Horizontal);
-    setCentralWidget(h_splitter);
-
+    // Central area: the diffraction image. Everything else (inspector, plots, processing) is a
+    // dock, so the layout can be rearranged, saved, and switched between perspectives.
     auto viewer = new JFJochDiffractionImage(this);
-    viewer->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Expanding);
-    h_splitter->addWidget(viewer);
+    viewer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
+    setCentralWidget(viewer);
 
     auto side_panel = new JFJochViewerSidePanel(this);
     auto side_panel_scroll = new QScrollArea(this);
@@ -94,9 +95,13 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     side_panel_scroll->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded);
     side_panel_scroll->setMinimumWidth(450);
     side_panel_scroll->setMaximumWidth(600);
-    side_panel_scroll->setSizePolicy(QSizePolicy::Minimum, QSizePolicy::Minimum);
 
-    h_splitter->addWidget(side_panel_scroll);
+    inspectorDock = new QDockWidget("Inspector", this);
+    inspectorDock->setObjectName("inspectorDock");
+    inspectorDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
+    inspectorDock->setWidget(side_panel_scroll);
+    addDockWidget(Qt::RightDockWidgetArea, inspectorDock);
+    menuBar->AddDockEntry(inspectorDock, "Inspector");
 
     reading_worker = new JFJochImageReadingWorker(spot_finding_settings, experiment);
     reading_thread = new QThread(this);
@@ -417,7 +422,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             });
 
     // Dock the processing panel in the bottom-right corner, next to the dataset-info plots.
-    auto processingDock = new QDockWidget("Processing", this);
+    processingDock = new QDockWidget("Processing", this);
+    processingDock->setObjectName("processingDock");
     processingDock->setAllowedAreas(Qt::BottomDockWidgetArea);
     processingDock->setFeatures(
         QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetFloatable | QDockWidget::DockWidgetClosable);
@@ -432,6 +438,20 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     }
     menuBar->AddDockEntry(processingDock, "Processing");
 
+    connect(menuBar, &JFJochViewerMenu::imageLayoutSelected, this,
+            [this] { ApplyPerspective(Perspective::Image); });
+    connect(menuBar, &JFJochViewerMenu::processingLayoutSelected, this,
+            [this] { ApplyPerspective(Perspective::Processing); });
+    connect(menuBar, &JFJochViewerMenu::resetLayoutSelected, this,
+            [this] { if (!defaultLayoutState.isEmpty()) restoreState(defaultLayoutState); });
+
+    // Remember the freshly-built layout so "Reset layout" can return to it, then restore the
+    // user's last-used arrangement if they have one.
+    defaultLayoutState = saveState();
+    QSettings settings("PSI", "jfjoch_viewer");
+    restoreGeometry(settings.value("geometry").toByteArray());
+    restoreState(settings.value("windowState").toByteArray());
+
     if (!file.isEmpty())
         LoadFile(file, 0, 1, false);
 }
@@ -443,6 +463,24 @@ JFJochViewerWindow::~JFJochViewerWindow() {
     }
 }
 
+void JFJochViewerWindow::ApplyPerspective(Perspective p) {
+    // Image: just the image + inspector. Processing: also the dataset-info plots and jobs panel.
+    const bool processing = (p == Perspective::Processing);
+    if (inspectorDock) inspectorDock->setVisible(true);
+    if (processingDock) processingDock->setVisible(processing);
+    for (auto *d : findChildren<QDockWidget *>())
+        if (d->objectName().startsWith("datasetInfoDock"))
+            d->setVisible(processing);
+}
+
+void JFJochViewerWindow::closeEvent(QCloseEvent *event) {
+    // Persist the dock/toolbar arrangement and window geometry so the next launch resumes it.
+    QSettings settings("PSI", "jfjoch_viewer");
+    settings.setValue("geometry", saveGeometry());
+    settings.setValue("windowState", saveState());
+    QMainWindow::closeEvent(event);
+}
+
 void JFJochViewerWindow::LoadFile(const QString &filename, qint64 image_number, qint64 summation, bool retry) {
     emit LoadFileRequest(filename, image_number, summation, true);
 }
@@ -458,6 +496,7 @@ void JFJochViewerWindow::NewDatasetInfo() {
     info->runsChanged(lastRuns, lastActiveRunId);
 
     auto dock = new QDockWidget(QString("Dataset info"), this);
+    dock->setObjectName(QStringLiteral("datasetInfoDock%1").arg(datasetInfoCounter++));
     dock->setAllowedAreas(Qt::BottomDockWidgetArea);
     dock->setFeatures(
         QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetFloatable | QDockWidget::DockWidgetClosable |
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index cc655dcd..ea19a1d3 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -39,11 +39,20 @@ private:
     QProgressDialog *retryDialog = nullptr;
 
     QDockWidget *lastDatasetInfoDock = nullptr;   // most recent dataset-info dock, for docking layout
+    QDockWidget *inspectorDock = nullptr;         // image inspector (former right-hand side panel)
+    QDockWidget *processingDock = nullptr;        // processing jobs panel
+    QByteArray defaultLayoutState;                // captured after construction, for "Reset layout"
+    int datasetInfoCounter = 0;                   // gives each dataset-info dock a unique objectName
 
     QThread *reading_thread;
 
+    // Named layouts. Image = just the image + inspector; Processing = also the plots + jobs panel.
+    enum class Perspective { Image, Processing };
+    void ApplyPerspective(Perspective p);
+
     void keyPressEvent(QKeyEvent *event) override;
     void keyReleaseEvent(QKeyEvent *event) override;
+    void closeEvent(QCloseEvent *event) override;
 public slots:
     void LoadFile(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void LoadImage(qint64 image_number, qint64 summation);
-- 
2.52.0


From 58c60e03fe2d342b5995dc0f6941df04577e57e0 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 09:01:21 +0200
Subject: [PATCH 205/228] =?UTF-8?q?viewer:=20Phase=201b=20=E2=80=94=20inli?=
 =?UTF-8?q?ne=20MX/AzInt=20settings=20dock?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Surface a surgical subset of processing settings in an always-visible dock
instead of hidden windows:

- New JFJochViewerSettingsDock with an MX / AzInt segmented toggle.
  MX page: geometry (energy, distance, beam X/Y), a new unit-cell +
  space-group editor (no such input existed before; enables known-cell
  ffbidx), spot finding (S/N, photon count, min pixels/spot), indexing
  algorithm and geometry refinement. AzInt page: q range / spacing /
  azimuthal bins plus the existing powder-calibration widget.
- Edits feed straight into the worker (UpdateSpotFindingSettings,
  UpdateAzintSettings, UpdateDataset, FindCenter); fields populate from the
  loaded dataset.
- Add CeO2 and Silicon calibrant presets.
- Dock it left, objectName "settingsDock", show it in the Processing
  perspective (hidden in Image).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                       |   2 +
 viewer/JFJochViewerWindow.cpp               |  30 ++-
 viewer/JFJochViewerWindow.h                 |   1 +
 viewer/widgets/JFJochViewerSettingsDock.cpp | 268 ++++++++++++++++++++
 viewer/widgets/JFJochViewerSettingsDock.h   |  68 +++++
 viewer/widgets/PowderCalibrationWidget.cpp  |  10 +
 6 files changed, 378 insertions(+), 1 deletion(-)
 create mode 100644 viewer/widgets/JFJochViewerSettingsDock.cpp
 create mode 100644 viewer/widgets/JFJochViewerSettingsDock.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 2d41295f..105671d3 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -60,6 +60,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         widgets/SliderPlusBox.h
         widgets/JFJochViewerSidePanelChart.cpp
         widgets/JFJochViewerSidePanelChart.h
+        widgets/JFJochViewerSettingsDock.cpp
+        widgets/JFJochViewerSettingsDock.h
         windows/JFJochViewerSpotListWindow.cpp
         windows/JFJochViewerSpotListWindow.h
         image_viewer/JFJochAzIntImage.cpp
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 3befd9a9..ac1378fa 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -15,6 +15,7 @@
 #include "JFJochImageReadingWorker.h"
 #include "image_viewer/JFJochDiffractionImage.h"
 #include "JFJochViewerSidePanel.h"
+#include "widgets/JFJochViewerSettingsDock.h"
 #include "JFJochViewerStatusBar.h"
 #include "../common/CUDAWrapper.h"
 #include "windows/JFJochViewerImageListWindow.h"
@@ -421,6 +422,32 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
                 lastActiveRunId = std::move(active);
             });
 
+    // Inline settings dock: the surgical MX/AzInt subset, always visible (left), wired straight
+    // into the running analysis so edits re-run on the current image / dataset.
+    auto *settingsPanel = new JFJochViewerSettingsDock(spot_finding_settings, indexing_settings,
+                                                       experiment.GetAzimuthalIntegrationSettings(), this);
+    settingsDock = new QDockWidget("Settings", this);
+    settingsDock->setObjectName("settingsDock");
+    settingsDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
+    settingsDock->setWidget(settingsPanel);
+    addDockWidget(Qt::LeftDockWidgetArea, settingsDock);
+    menuBar->AddDockEntry(settingsDock, "Settings");
+
+    connect(settingsPanel, &JFJochViewerSettingsDock::spotFindingChanged,
+            reading_worker, &JFJochImageReadingWorker::UpdateSpotFindingSettings);
+    connect(settingsPanel, &JFJochViewerSettingsDock::azintChanged,
+            reading_worker, &JFJochImageReadingWorker::UpdateAzintSettings);
+    connect(settingsPanel, &JFJochViewerSettingsDock::experimentChanged,
+            reading_worker, &JFJochImageReadingWorker::UpdateDataset);
+    connect(settingsPanel, &JFJochViewerSettingsDock::findBeamCenter,
+            reading_worker, &JFJochImageReadingWorker::FindCenter);
+    connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
+            settingsPanel, &JFJochViewerSettingsDock::datasetLoaded);
+    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+            settingsPanel, &JFJochViewerSettingsDock::loadImage);
+    connect(settingsPanel, &JFJochViewerSettingsDock::ringsFromCalibration,
+            side_panel, &JFJochViewerSidePanel::SetRings);
+
     // Dock the processing panel in the bottom-right corner, next to the dataset-info plots.
     processingDock = new QDockWidget("Processing", this);
     processingDock->setObjectName("processingDock");
@@ -464,9 +491,10 @@ JFJochViewerWindow::~JFJochViewerWindow() {
 }
 
 void JFJochViewerWindow::ApplyPerspective(Perspective p) {
-    // Image: just the image + inspector. Processing: also the dataset-info plots and jobs panel.
+    // Image: just the image + inspector. Processing: also settings, dataset-info plots, jobs panel.
     const bool processing = (p == Perspective::Processing);
     if (inspectorDock) inspectorDock->setVisible(true);
+    if (settingsDock) settingsDock->setVisible(processing);
     if (processingDock) processingDock->setVisible(processing);
     for (auto *d : findChildren<QDockWidget *>())
         if (d->objectName().startsWith("datasetInfoDock"))
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index ea19a1d3..3c5960fb 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -40,6 +40,7 @@ private:
 
     QDockWidget *lastDatasetInfoDock = nullptr;   // most recent dataset-info dock, for docking layout
     QDockWidget *inspectorDock = nullptr;         // image inspector (former right-hand side panel)
+    QDockWidget *settingsDock = nullptr;          // inline MX/AzInt settings panel
     QDockWidget *processingDock = nullptr;        // processing jobs panel
     QByteArray defaultLayoutState;                // captured after construction, for "Reset layout"
     int datasetInfoCounter = 0;                   // gives each dataset-info dock a unique objectName
diff --git a/viewer/widgets/JFJochViewerSettingsDock.cpp b/viewer/widgets/JFJochViewerSettingsDock.cpp
new file mode 100644
index 00000000..2584a676
--- /dev/null
+++ b/viewer/widgets/JFJochViewerSettingsDock.cpp
@@ -0,0 +1,268 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochViewerSettingsDock.h"
+
+#include <QVBoxLayout>
+#include <QHBoxLayout>
+#include <QFormLayout>
+#include <QGroupBox>
+#include <QPushButton>
+#include <QButtonGroup>
+#include <QStackedWidget>
+#include <QCheckBox>
+#include <QComboBox>
+#include <QLabel>
+
+#include <cmath>
+
+#include "SliderPlusBox.h"
+#include "NumberLineEdit.h"
+#include "PowderCalibrationWidget.h"
+#include "TitleLabel.h"
+
+JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &spot,
+                                                   const IndexingSettings &indexing,
+                                                   const AzimuthalIntegrationSettings &azint,
+                                                   QWidget *parent)
+    : QWidget(parent), spot_(spot), indexing_(indexing), azint_(azint) {
+
+    // Segmented MX / AzInt toggle: the two communities pick their page; pages never share a screen.
+    auto *mxButton = new QPushButton("MX", this);
+    auto *azButton = new QPushButton("AzInt", this);
+    for (auto *b : {mxButton, azButton}) {
+        b->setCheckable(true);
+        b->setStyleSheet("QPushButton:checked { background-color: #1F3A5F; color: white; }");
+    }
+    mxButton->setChecked(true);
+    auto *group = new QButtonGroup(this);
+    group->setExclusive(true);
+    group->addButton(mxButton, 0);
+    group->addButton(azButton, 1);
+
+    auto *toggleRow = new QHBoxLayout();
+    toggleRow->setSpacing(0);
+    toggleRow->addWidget(mxButton);
+    toggleRow->addWidget(azButton);
+
+    auto *stack = new QStackedWidget(this);
+    stack->addWidget(BuildMXPage());
+    stack->addWidget(BuildAzIntPage());
+    connect(group, &QButtonGroup::idClicked, stack, &QStackedWidget::setCurrentIndex);
+
+    auto *layout = new QVBoxLayout(this);
+    layout->addLayout(toggleRow);
+    layout->addWidget(stack);
+    layout->addStretch();
+}
+
+QWidget *JFJochViewerSettingsDock::BuildMXPage() {
+    auto *page = new QWidget(this);
+    auto *layout = new QVBoxLayout(page);
+    layout->setContentsMargins(0, 0, 0, 0);
+
+    // --- Geometry ---
+    layout->addWidget(new TitleLabel("Geometry", page));
+    auto *geomGroup = new QGroupBox(page);
+    auto *geom = new QFormLayout(geomGroup);
+    energy_ = new NumberLineEdit(1.0, 200.0, 12.4, 4, "keV", page);
+    distance_ = new NumberLineEdit(10.0, 5000.0, 100.0, 2, "mm", page);
+    beamX_ = new NumberLineEdit(0.0, 20000.0, 0.0, 1, "px", page);
+    beamY_ = new NumberLineEdit(0.0, 20000.0, 0.0, 1, "px", page);
+    geom->addRow("Photon energy", energy_);
+    geom->addRow("Detector distance", distance_);
+    geom->addRow("Beam center X", beamX_);
+    geom->addRow("Beam center Y", beamY_);
+    layout->addWidget(geomGroup);
+    for (auto *f : {energy_, distance_, beamX_, beamY_})
+        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
+
+    // --- Unit cell + space group (new: no input existed before) ---
+    layout->addWidget(new TitleLabel("Unit cell", page));
+    auto *cellGroup = new QGroupBox(page);
+    auto *cell = new QFormLayout(cellGroup);
+    cellKnown_ = new QCheckBox("Known unit cell", page);
+    cell->addRow("", cellKnown_);
+    cellA_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
+    cellB_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
+    cellC_ = new NumberLineEdit(1.0, 2000.0, 38.0, 3, "Å", page);
+    cellAlpha_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
+    cellBeta_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
+    cellGamma_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
+    spaceGroup_ = new NumberLineEdit(0.0, 230.0, 0.0, 0, "", page);
+    auto *abc = new QHBoxLayout();
+    abc->addWidget(cellA_); abc->addWidget(cellB_); abc->addWidget(cellC_);
+    auto *angles = new QHBoxLayout();
+    angles->addWidget(cellAlpha_); angles->addWidget(cellBeta_); angles->addWidget(cellGamma_);
+    cell->addRow("a, b, c", abc);
+    cell->addRow("α, β, γ", angles);
+    cell->addRow("Space group", spaceGroup_);
+    layout->addWidget(cellGroup);
+
+    auto enableCellFields = [this](bool on) {
+        for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
+            f->setEnabled(on);
+    };
+    enableCellFields(false);
+    connect(cellKnown_, &QCheckBox::toggled, this, [this, enableCellFields](bool on) {
+        enableCellFields(on);
+        EmitExperiment();
+    });
+    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
+        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
+
+    // --- Spot finding ---
+    layout->addWidget(new TitleLabel("Spot finding", page));
+    auto *spotGroup = new QGroupBox(page);
+    auto *spot = new QFormLayout(spotGroup);
+    auto *snr = new SliderPlusBox(1.0, 10.0, 0.1, 1, page);
+    snr->setValue(spot_.signal_to_noise_threshold);
+    auto *count = new SliderPlusBox(0.0, 100.0, 1.0, 0, page);
+    count->setValue(std::lround(spot_.photon_count_threshold));
+    auto *minPix = new SliderPlusBox(1.0, 20.0, 1.0, 0, page);
+    minPix->setValue(std::lround(spot_.min_pix_per_spot));
+    spot->addRow("Signal/noise", snr);
+    spot->addRow("Photon count", count);
+    spot->addRow("Min pixels/spot", minPix);
+    layout->addWidget(spotGroup);
+    connect(snr, &SliderPlusBox::valueChanged, this, [this](double v) {
+        spot_.signal_to_noise_threshold = static_cast<float>(v); EmitSpotFinding(); });
+    connect(count, &SliderPlusBox::valueChanged, this, [this](double v) {
+        spot_.photon_count_threshold = static_cast<float>(v); EmitSpotFinding(); });
+    connect(minPix, &SliderPlusBox::valueChanged, this, [this](double v) {
+        spot_.min_pix_per_spot = std::lround(v); EmitSpotFinding(); });
+
+    // --- Indexing ---
+    layout->addWidget(new TitleLabel("Indexing", page));
+    auto *idxGroup = new QGroupBox(page);
+    auto *idx = new QFormLayout(idxGroup);
+    auto *algo = new QComboBox(page);
+    algo->addItem("Auto", static_cast<int>(IndexingAlgorithmEnum::Auto));
+    algo->addItem("FFBIDX (GPU, known cell)", static_cast<int>(IndexingAlgorithmEnum::FFBIDX));
+    algo->addItem("FFT (GPU, de-novo)", static_cast<int>(IndexingAlgorithmEnum::FFT));
+    algo->addItem("FFTW (CPU, de-novo)", static_cast<int>(IndexingAlgorithmEnum::FFTW));
+    algo->addItem("None", static_cast<int>(IndexingAlgorithmEnum::None));
+    algo->setCurrentIndex(algo->findData(static_cast<int>(indexing_.GetAlgorithm())));
+    auto *refine = new QComboBox(page);
+    refine->addItem("None", static_cast<int>(GeomRefinementAlgorithmEnum::None));
+    refine->addItem("Orientation only", static_cast<int>(GeomRefinementAlgorithmEnum::OrientationOnly));
+    refine->addItem("Beam center + lattice", static_cast<int>(GeomRefinementAlgorithmEnum::BeamCenter));
+    refine->addItem("Pixel refinement", static_cast<int>(GeomRefinementAlgorithmEnum::PixelRefine));
+    refine->setCurrentIndex(refine->findData(static_cast<int>(indexing_.GetGeomRefinementAlgorithm())));
+    idx->addRow("Algorithm", algo);
+    idx->addRow("Refinement", refine);
+    layout->addWidget(idxGroup);
+    connect(algo, &QComboBox::currentIndexChanged, this, [this, algo] {
+        indexing_.Algorithm(static_cast<IndexingAlgorithmEnum>(algo->currentData().toInt()));
+        EmitSpotFinding();
+    });
+    connect(refine, &QComboBox::currentIndexChanged, this, [this, refine] {
+        indexing_.GeomRefinementAlgorithm(static_cast<GeomRefinementAlgorithmEnum>(refine->currentData().toInt()));
+        EmitSpotFinding();
+    });
+
+    return page;
+}
+
+QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
+    auto *page = new QWidget(this);
+    auto *layout = new QVBoxLayout(page);
+    layout->setContentsMargins(0, 0, 0, 0);
+
+    layout->addWidget(new TitleLabel("Azimuthal integration", page));
+    auto *azGroup = new QGroupBox(page);
+    auto *az = new QFormLayout(azGroup);
+    auto *lowQ = new SliderPlusBox(1e-5, 10.0, 0.001, 4, page);
+    lowQ->setValue(azint_.GetLowQ_recipA());
+    auto *highQ = new SliderPlusBox(2e-5, 10.0, 0.001, 4, page);
+    highQ->setValue(azint_.GetHighQ_recipA());
+    auto *spacing = new SliderPlusBox(1e-5, 1.0, 0.001, 5, page, SliderPlusBox::ScaleType::Logarithmic);
+    spacing->setValue(azint_.GetQSpacing_recipA());
+    auto *azimBins = new QComboBox(page);
+    for (int b : {1, 2, 4, 8, 16, 32, 64, 128})
+        azimBins->addItem(QString::number(b), b);
+    azimBins->setCurrentIndex(azimBins->findData(azint_.GetAzimuthalBinCount()));
+    az->addRow("Low Q [Å⁻¹]", lowQ);
+    az->addRow("High Q [Å⁻¹]", highQ);
+    az->addRow("Q spacing [Å⁻¹]", spacing);
+    az->addRow("Azimuthal bins", azimBins);
+    layout->addWidget(azGroup);
+
+    auto emitAz = [=, this] {
+        azint_.QRange_recipA(static_cast<float>(lowQ->value()), static_cast<float>(highQ->value()));
+        azint_.QSpacing_recipA(static_cast<float>(spacing->value()));
+        azint_.AzimuthalBinCount(azimBins->currentData().toInt());
+        emit azintChanged(azint_);
+    };
+    connect(lowQ, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
+    connect(highQ, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
+    connect(spacing, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
+    connect(azimBins, &QComboBox::currentIndexChanged, this, [emitAz] { emitAz(); });
+
+    // Powder calibration (calibrant rings + geometry refinement) - reuse the existing widget.
+    layout->addWidget(new TitleLabel("Powder calibration", page));
+    powder_ = new PowderCalibrationWidget(page);
+    connect(powder_, &PowderCalibrationWidget::findBeamCenter, this, &JFJochViewerSettingsDock::findBeamCenter);
+    connect(powder_, &PowderCalibrationWidget::ringsFromCalibration, this, &JFJochViewerSettingsDock::ringsFromCalibration);
+    layout->addWidget(powder_);
+
+    return page;
+}
+
+void JFJochViewerSettingsDock::EmitSpotFinding() {
+    emit spotFindingChanged(spot_, indexing_, max_spots_);
+}
+
+void JFJochViewerSettingsDock::EmitExperiment() {
+    if (!have_experiment_)
+        return;
+    experiment_.IncidentEnergy_keV(static_cast<float>(energy_->value()));
+    experiment_.DetectorDistance_mm(static_cast<float>(distance_->value()));
+    experiment_.BeamX_pxl(static_cast<float>(beamX_->value()));
+    experiment_.BeamY_pxl(static_cast<float>(beamY_->value()));
+    if (cellKnown_->isChecked()) {
+        experiment_.SetUnitCell(UnitCell{
+            static_cast<float>(cellA_->value()), static_cast<float>(cellB_->value()),
+            static_cast<float>(cellC_->value()), static_cast<float>(cellAlpha_->value()),
+            static_cast<float>(cellBeta_->value()), static_cast<float>(cellGamma_->value())});
+        const int sg = static_cast<int>(std::lround(spaceGroup_->value()));
+        experiment_.SpaceGroupNumber(sg > 0 ? std::optional<int64_t>(sg) : std::nullopt);
+    } else {
+        experiment_.SetUnitCell(std::nullopt);
+        experiment_.SpaceGroupNumber(std::nullopt);
+    }
+    emit experimentChanged(experiment_);
+}
+
+void JFJochViewerSettingsDock::RefreshGeometryFields() {
+    // Populate fields from the loaded experiment. NumberLineEdit::setValue does not emit newValue
+    // (that fires only on user editing), so this cannot feed back into EmitExperiment.
+    energy_->setValue(experiment_.GetIncidentEnergy_keV());
+    distance_->setValue(experiment_.GetDetectorDistance_mm());
+    beamX_->setValue(experiment_.GetBeamX_pxl());
+    beamY_->setValue(experiment_.GetBeamY_pxl());
+
+    const auto cell = experiment_.GetUnitCell();
+    QSignalBlocker blockKnown(cellKnown_);
+    cellKnown_->setChecked(cell.has_value());
+    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
+        f->setEnabled(cell.has_value());
+    if (cell) {
+        cellA_->setValue(cell->a);   cellB_->setValue(cell->b);   cellC_->setValue(cell->c);
+        cellAlpha_->setValue(cell->alpha); cellBeta_->setValue(cell->beta); cellGamma_->setValue(cell->gamma);
+        spaceGroup_->setValue(experiment_.GetSpaceGroupNumber().value_or(0));
+    }
+}
+
+void JFJochViewerSettingsDock::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
+    if (!dataset)
+        return;
+    experiment_ = dataset->experiment;
+    have_experiment_ = true;
+    RefreshGeometryFields();
+}
+
+void JFJochViewerSettingsDock::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
+    if (powder_)
+        powder_->loadImage(image);
+}
diff --git a/viewer/widgets/JFJochViewerSettingsDock.h b/viewer/widgets/JFJochViewerSettingsDock.h
new file mode 100644
index 00000000..4794df21
--- /dev/null
+++ b/viewer/widgets/JFJochViewerSettingsDock.h
@@ -0,0 +1,68 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QWidget>
+#include <memory>
+
+#include "../../common/DiffractionExperiment.h"
+#include "../../common/IndexingSettings.h"
+#include "../../common/AzimuthalIntegrationSettings.h"
+#include "../../image_analysis/spot_finding/SpotFindingSettings.h"
+#include "../../reader/JFJochReaderDataset.h"
+#include "../../reader/JFJochReaderImage.h"
+
+class QStackedWidget;
+class QCheckBox;
+class QComboBox;
+class SliderPlusBox;
+class NumberLineEdit;
+class PowderCalibrationWidget;
+
+// Compact, always-visible settings panel with an MX / AzInt toggle: the surgical subset of
+// processing settings that the two communities reach for most, kept in a dock instead of a
+// hidden window. Edits feed straight back into the running analysis via the worker.
+class JFJochViewerSettingsDock : public QWidget {
+    Q_OBJECT
+public:
+    JFJochViewerSettingsDock(const SpotFindingSettings &spot, const IndexingSettings &indexing,
+                             const AzimuthalIntegrationSettings &azint, QWidget *parent = nullptr);
+
+public slots:
+    void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
+    void loadImage(std::shared_ptr<const JFJochReaderImage> image);
+
+signals:
+    void spotFindingChanged(const SpotFindingSettings &spot, const IndexingSettings &indexing, int64_t max_spots);
+    void azintChanged(const AzimuthalIntegrationSettings &settings);
+    void experimentChanged(const DiffractionExperiment &experiment);
+    void findBeamCenter(const UnitCell &calibrant, bool guess);
+    void ringsFromCalibration(QVector<float> rings);
+
+private:
+    SpotFindingSettings spot_;
+    IndexingSettings indexing_;
+    AzimuthalIntegrationSettings azint_;
+    DiffractionExperiment experiment_;
+    bool have_experiment_ = false;     // geometry edits only take effect once a dataset is loaded
+    int64_t max_spots_ = 1000;
+
+    // MX geometry + crystal fields
+    NumberLineEdit *energy_ = nullptr;
+    NumberLineEdit *distance_ = nullptr;
+    NumberLineEdit *beamX_ = nullptr;
+    NumberLineEdit *beamY_ = nullptr;
+    QCheckBox *cellKnown_ = nullptr;
+    NumberLineEdit *cellA_ = nullptr, *cellB_ = nullptr, *cellC_ = nullptr;
+    NumberLineEdit *cellAlpha_ = nullptr, *cellBeta_ = nullptr, *cellGamma_ = nullptr;
+    NumberLineEdit *spaceGroup_ = nullptr;
+
+    PowderCalibrationWidget *powder_ = nullptr;
+
+    QWidget *BuildMXPage();
+    QWidget *BuildAzIntPage();
+    void EmitSpotFinding();
+    void EmitExperiment();
+    void RefreshGeometryFields();
+};
diff --git a/viewer/widgets/PowderCalibrationWidget.cpp b/viewer/widgets/PowderCalibrationWidget.cpp
index 286f3c8a..8e24bf94 100644
--- a/viewer/widgets/PowderCalibrationWidget.cpp
+++ b/viewer/widgets/PowderCalibrationWidget.cpp
@@ -52,6 +52,14 @@ UnitCell PowderCalibrationWidget::GetCalibrant() const {
             uc = UnitCell(5.1769, 4.7218, 58.380, 89.440, 89.634, 75.854);
             break;
         case 2:
+            // CeO2, cubic fluorite (a = 5.4115 Å), NIST SRM 674b.
+            uc = UnitCell(5.4115, 5.4115, 5.4115, 90, 90, 90);
+            break;
+        case 3:
+            // Silicon, cubic (a = 5.43102 Å), NIST SRM 640.
+            uc = UnitCell(5.43102, 5.43102, 5.43102, 90, 90, 90);
+            break;
+        case 4:
             if (sample_cell)
                 uc = sample_cell.value();
             break;
@@ -66,6 +74,8 @@ void PowderCalibrationWidget::updateCalibrantList() {
 
     calibrantCombo->addItem("LaB6");
     calibrantCombo->addItem("Silver Behenate");
+    calibrantCombo->addItem("CeO2");
+    calibrantCombo->addItem("Silicon");
     if (sample_cell)
         calibrantCombo->addItem(QString("Current sample (%1 %2 %3 %4 %5 %6)")
             .arg(QString::number(sample_cell->a, 'f', 1))
-- 
2.52.0


From 9f9e13a4e40fd86534b70d7dc925f7821a9a9902 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 09:20:49 +0200
Subject: [PATCH 206/228] viewer: PSI logo + tidy beam-center row

- Show the PSI logo in the menu-bar corner, picking one of four interchangeable
  dot designs at random each launch. Embedded as PNGs (rasterised from the SVG
  sources, kept alongside) so no Qt SVG module dependency is needed.
- Settings dock: put beam center X and Y on a single "Beam center" row to save
  vertical space on laptop screens.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp               |  13 +
 viewer/resources/psi_01.png                 | Bin 0 -> 5818 bytes
 viewer/resources/psi_01_sp.svg              | 635 ++++++++++++++
 viewer/resources/psi_02.png                 | Bin 0 -> 7457 bytes
 viewer/resources/psi_02_sp.svg              | 851 +++++++++++++++++++
 viewer/resources/psi_03.png                 | Bin 0 -> 7142 bytes
 viewer/resources/psi_03_sp.svg              | 870 ++++++++++++++++++++
 viewer/resources/psi_04.png                 | Bin 0 -> 6204 bytes
 viewer/resources/psi_04_sp.svg              | 738 +++++++++++++++++
 viewer/resources/resources.qrc              |   4 +
 viewer/widgets/JFJochViewerSettingsDock.cpp |   6 +-
 11 files changed, 3115 insertions(+), 2 deletions(-)
 create mode 100644 viewer/resources/psi_01.png
 create mode 100644 viewer/resources/psi_01_sp.svg
 create mode 100644 viewer/resources/psi_02.png
 create mode 100644 viewer/resources/psi_02_sp.svg
 create mode 100644 viewer/resources/psi_03.png
 create mode 100644 viewer/resources/psi_03_sp.svg
 create mode 100644 viewer/resources/psi_04.png
 create mode 100644 viewer/resources/psi_04_sp.svg

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index ac1378fa..7d37b42f 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -11,6 +11,8 @@
 #include <QScrollArea>
 #include <QSettings>
 #include <QCloseEvent>
+#include <QRandomGenerator>
+#include <QLabel>
 
 #include "JFJochImageReadingWorker.h"
 #include "image_viewer/JFJochDiffractionImage.h"
@@ -43,6 +45,17 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     menuBar = new JFJochViewerMenu(this);
     setMenuBar(menuBar);
 
+    // PSI logo in the menu-bar corner. There are four interchangeable dot designs; pick one at
+    // random each launch, for fun.
+    {
+        const int n = QRandomGenerator::global()->bounded(1, 5);   // 1..4
+        QPixmap logoPixmap(QStringLiteral(":/psi_%1.png").arg(n, 2, 10, QLatin1Char('0')));
+        auto *logo = new QLabel(this);
+        logo->setPixmap(logoPixmap.scaledToHeight(22, Qt::SmoothTransformation));
+        logo->setContentsMargins(6, 0, 8, 0);
+        menuBar->setCornerWidget(logo, Qt::TopRightCorner);
+    }
+
     setFocusPolicy(Qt::StrongFocus);
 
     auto toolBarImage = new JFJochViewerToolbarImage(this);
diff --git a/viewer/resources/psi_01.png b/viewer/resources/psi_01.png
new file mode 100644
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diff --git a/viewer/resources/psi_01_sp.svg b/viewer/resources/psi_01_sp.svg
new file mode 100644
index 00000000..e6b0f8bc
--- /dev/null
+++ b/viewer/resources/psi_01_sp.svg
@@ -0,0 +1,635 @@
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diff --git a/viewer/resources/psi_02_sp.svg b/viewer/resources/psi_02_sp.svg
new file mode 100644
index 00000000..86334c66
--- /dev/null
+++ b/viewer/resources/psi_02_sp.svg
@@ -0,0 +1,851 @@
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diff --git a/viewer/resources/psi_03_sp.svg b/viewer/resources/psi_03_sp.svg
new file mode 100644
index 00000000..7d94b871
--- /dev/null
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new file mode 100644
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+    <circle class="cls-1" cx="24.5" cy="46.44" r=".57"/>
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+    <circle class="cls-1" cx="36.37" cy="43.79" r=".57"/>
+    <path class="cls-1" d="M27.41,44.12c.31,0,.57-.25.57-.57s-.25-.57-.57-.57-.57.25-.57.57.25.57.57.57Z"/>
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+    <circle class="cls-1" cx="34.49" cy="50.38" r=".57"/>
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+    <path class="cls-1" d="M40.02,47.94c.31,0,.57-.25.57-.57s-.25-.57-.57-.57-.57.25-.57.57.25.57.57.57Z"/>
+    <path class="cls-1" d="M37.25,48.52c0-.31-.25-.57-.57-.57s-.57.25-.57.57.25.57.57.57.57-.25.57-.57Z"/>
+    <path class="cls-1" d="M76.68,18.19c-.31,0-.57.25-.57.57s.25.57.57.57.57-.25.57-.57-.25-.57-.57-.57Z"/>
+    <path class="cls-1" d="M56.89,15.55c.31,0,.57-.25.57-.57s-.25-.57-.57-.57-.57.25-.57.57.25.57.57.57Z"/>
+    <path class="cls-1" d="M58.48,17.31c.31,0,.57-.25.57-.57s-.25-.57-.57-.57-.57.25-.57.57.25.57.57.57Z"/>
+    <path class="cls-1" d="M78.5,22.52c0-.31-.25-.57-.57-.57s-.57.25-.57.57.25.57.57.57.57-.25.57-.57Z"/>
+    <path class="cls-1" d="M67.16,16.57c.31,0,.57-.25.57-.57s-.25-.57-.57-.57-.57.25-.57.57.25.57.57.57Z"/>
+  </g>
+</svg>
\ No newline at end of file
diff --git a/viewer/resources/resources.qrc b/viewer/resources/resources.qrc
index 45f4c289..6ec0fb4b 100644
--- a/viewer/resources/resources.qrc
+++ b/viewer/resources/resources.qrc
@@ -7,5 +7,9 @@
     <qresource prefix="/">
         <file>jfjoch.png</file>
         <file>third_party_licenses.html</file>
+        <file>psi_01.png</file>
+        <file>psi_02.png</file>
+        <file>psi_03.png</file>
+        <file>psi_04.png</file>
     </qresource>
 </RCC>
\ No newline at end of file
diff --git a/viewer/widgets/JFJochViewerSettingsDock.cpp b/viewer/widgets/JFJochViewerSettingsDock.cpp
index 2584a676..f824bb00 100644
--- a/viewer/widgets/JFJochViewerSettingsDock.cpp
+++ b/viewer/widgets/JFJochViewerSettingsDock.cpp
@@ -71,8 +71,10 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     beamY_ = new NumberLineEdit(0.0, 20000.0, 0.0, 1, "px", page);
     geom->addRow("Photon energy", energy_);
     geom->addRow("Detector distance", distance_);
-    geom->addRow("Beam center X", beamX_);
-    geom->addRow("Beam center Y", beamY_);
+    auto *beam = new QHBoxLayout();
+    beam->addWidget(beamX_);
+    beam->addWidget(beamY_);
+    geom->addRow("Beam center", beam);
     layout->addWidget(geomGroup);
     for (auto *f : {energy_, distance_, beamX_, beamY_})
         connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
-- 
2.52.0


From 54526300a97b64a9f9926132653372536544f0cb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 09:40:41 +0200
Subject: [PATCH 207/228] viewer: promote Reanalyze image / Reanalyze dataset
 hero buttons

The two capabilities that set Jungfraujoch apart get prominent, paired navy
buttons at the right of the display toolbar, with purpose-drawn icons (a single
diffraction frame vs a stack of frames):

- "Reanalyze image" re-runs the analysis pipeline on the current image
  (worker Analyze).
- "Reanalyze dataset" opens a new whole-dataset processing job
  (JFJochProcessingJobsWindow::newJob, now public).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp               | 45 +++++++++++++++++++++
 viewer/windows/JFJochProcessingJobsWindow.h |  2 +-
 2 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 7d37b42f..fda87567 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -13,6 +13,8 @@
 #include <QCloseEvent>
 #include <QRandomGenerator>
 #include <QLabel>
+#include <QPainter>
+#include <QPushButton>
 
 #include "JFJochImageReadingWorker.h"
 #include "image_viewer/JFJochDiffractionImage.h"
@@ -41,6 +43,27 @@
 #include "image_viewer/JFJochSimpleImage.h"
 #include <QMessageBox>
 
+namespace {
+    // Paired "reanalyze" glyphs: a single diffraction frame (image) vs a stack of frames (dataset),
+    // drawn white so they read on the navy hero buttons.
+    QIcon FramesIcon(int frames) {
+        const int S = 28;
+        QPixmap pm(S, S);
+        pm.fill(Qt::transparent);
+        QPainter p(&pm);
+        p.setRenderHint(QPainter::Antialiasing);
+        p.setPen(QPen(Qt::white, 2.0));
+        p.setBrush(Qt::NoBrush);
+        const double side = 13.0, step = 4.0;
+        for (int i = frames - 1; i >= 0; --i)
+            p.drawRoundedRect(QRectF(4 + i * step, 4 + i * step, side, side), 2.5, 2.5);
+        p.setBrush(Qt::white);   // a diffraction "spot" in the front frame
+        p.drawEllipse(QPointF(4 + side / 2.0, 4 + side / 2.0), 2.0, 2.0);
+        p.end();
+        return QIcon(pm);
+    }
+}
+
 JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString &file) : QMainWindow(parent) {
     menuBar = new JFJochViewerMenu(this);
     setMenuBar(menuBar);
@@ -138,6 +161,28 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     processingJobsWindow = new JFJochProcessingJobsWindow(reading_worker, this);
 
+    // Two hero actions — the capabilities that set Jungfraujoch apart — promoted as prominent navy
+    // buttons at the right of the display toolbar: re-analyse the current image, or the whole dataset.
+    {
+        const QString heroStyle =
+            "QPushButton { background-color:#1F3A5F; color:white; font-weight:bold;"
+            " padding:3px 10px; border:none; border-radius:3px; }"
+            " QPushButton:hover { background-color:#16314f; }"
+            " QPushButton:disabled { background-color:#9aa6b3; }";
+        auto *reanalyzeImageBtn = new QPushButton(FramesIcon(1), " Reanalyze image", this);
+        reanalyzeImageBtn->setStyleSheet(heroStyle);
+        reanalyzeImageBtn->setToolTip("Re-run the analysis pipeline on the current image");
+        auto *reanalyzeDatasetBtn = new QPushButton(FramesIcon(3), " Reanalyze dataset", this);
+        reanalyzeDatasetBtn->setStyleSheet(heroStyle);
+        reanalyzeDatasetBtn->setToolTip("Re-process the whole dataset (opens a new processing job)");
+        toolBarDisplay->addWidget(reanalyzeImageBtn);
+        toolBarDisplay->addWidget(reanalyzeDatasetBtn);
+        connect(reanalyzeImageBtn, &QPushButton::clicked,
+                reading_worker, &JFJochImageReadingWorker::Analyze);
+        connect(reanalyzeDatasetBtn, &QPushButton::clicked,
+                processingJobsWindow, &JFJochProcessingJobsWindow::newJob);
+    }
+
     menuBar->AddWindowEntry(tableWindow, "Image list");
     menuBar->AddWindowEntry(spotWindow, "Spot list");
     menuBar->AddWindowEntry(reflectionWindow, "Reflection list");
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index b185f2f1..653dd3a8 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -39,9 +39,9 @@ public slots:
     void onHttpConnectionChanged(bool connected, QString addr);
     void clearJobs();                    // reset the table on a new file (re-adds the Original row)
     void setActiveRun(QString active_id);   // bold the row of the run currently shown in the plots
+    void newJob();                       // also the toolbar "Reanalyze dataset" hero action
 
 private slots:
-    void newJob();
     void cancelJob();
     void removeResult();
     void viewResults();
-- 
2.52.0


From e7edee6b2ed5bc6a384eea421ced4dc28e911087 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 09:49:36 +0200
Subject: [PATCH 208/228] =?UTF-8?q?viewer:=20Phase=201c=20=E2=80=94=20fold?=
 =?UTF-8?q?=20per-image=20plot=20into=20the=20dataset-info=20dock?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Remove the duplicated per-image plot from the side panel and host it in the
dataset-info dock instead:

- JFJochViewerDatasetInfo gains a "Per-image" toggle (next to Grid) that swaps
  the stacked view to the existing JFJochViewerSidePanelChart (azimuthal 1D,
  Wilson, I/sigma, spot and fluorescence profiles of the current image). The
  per-dataset metric combo is disabled while in per-image mode.
- The per-image profile follows the displayed image (imageLoaded forwarded).
- Drop the "Image statistics plot" section from JFJochViewerSidePanel.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp | 43 ++++++++++++++++++++++++------
 viewer/JFJochViewerDatasetInfo.h   |  4 +++
 viewer/JFJochViewerSidePanel.cpp   | 12 ++-------
 viewer/JFJochViewerSidePanel.h     |  2 --
 4 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index aa0a535c..bc0cb932 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -42,18 +42,25 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
     grid_button->setCheckable(true);
     grid_button->setEnabled(false);
 
+    image_button = new QPushButton("Per-image", this);
+    image_button->setFixedWidth(100);
+    image_button->setCheckable(true);
+
     layout->addWidget(reset_button, 0, 2);
     layout->addWidget(grid_button, 0, 3);
+    layout->addWidget(image_button, 0, 4);
 
     stack = new QStackedWidget(this);
     chart_view = new JFJochDatasetInfoChartView(this);
     chart_view->setMinimumHeight(80);   // low floor so the bottom dock resizes freely (default is set via resizeDocks)
     grid_scan_image = new JFJochGridScanImage(this);
+    image_chart = new JFJochViewerSidePanelChart(this);   // per-image profiles, folded in from the side panel
 
     stack->addWidget(chart_view);
     stack->addWidget(grid_scan_image);
+    stack->addWidget(image_chart);
 
-    layout->addWidget(stack, 1, 0, 1, 4);
+    layout->addWidget(stack, 1, 0, 1, 5);
 
     connect(chart_view, &JFJochDatasetInfoChartView::imageSelected,
             this, &JFJochViewerDatasetInfo::imageSelectedInChart);
@@ -79,11 +86,21 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
 
     connect(grid_button, &QPushButton::clicked,
             [this]() {
-                if (grid_button->isChecked() && dataset && dataset->experiment.GetGridScan())
-                    stack->setCurrentWidget(grid_scan_image);
-                else
-                    stack->setCurrentWidget(chart_view);
+                if (grid_button->isChecked()) {
+                    image_button->setChecked(false);
+                    combo_box->setEnabled(true);
+                }
+                UpdateView();
             });
+    connect(image_button, &QPushButton::clicked,
+            [this]() {
+                if (image_button->isChecked())
+                    grid_button->setChecked(false);
+                combo_box->setEnabled(!image_button->isChecked());   // the metric combo is for the dataset plot
+                UpdateView();
+            });
+    connect(image_chart, &JFJochViewerSidePanelChart::writeStatusBar,
+            [this](QString s, int t) { emit writeStatusBar(s, t); });
     setLayout(layout);
 }
 
@@ -167,6 +184,7 @@ void JFJochViewerDatasetInfo::imageLoaded(std::shared_ptr<const JFJochReaderImag
         chart_view->setImage(image->ImageData().number);
         grid_scan_image->setImage(image->ImageData().number);
     }
+    image_chart->loadImage(image);   // per-image profile follows the displayed image
 }
 
 void JFJochViewerDatasetInfo::imageSelectedInChart(int64_t number) {
@@ -262,15 +280,24 @@ void JFJochViewerDatasetInfo::UpdatePlot() {
                            std::move(overlays), primary_color, XForRun(*dataset), full_range);
 
     if (dataset->experiment.GetGridScan()) {
-        stack->setCurrentWidget(grid_scan_image);
         grid_scan_image->loadData(data, dataset->experiment.GetGridScan().value(), one_over_d2);
         grid_button->setEnabled(true);
-        grid_button->setChecked(true);
+        if (!image_button->isChecked())
+            grid_button->setChecked(true);
     } else {
         grid_scan_image->clear();
-        stack->setCurrentWidget(chart_view);
         grid_button->setEnabled(false);
     }
+    UpdateView();
+}
+
+void JFJochViewerDatasetInfo::UpdateView() {
+    if (image_button->isChecked())
+        stack->setCurrentWidget(image_chart);
+    else if (grid_button->isChecked() && dataset && dataset->experiment.GetGridScan())
+        stack->setCurrentWidget(grid_scan_image);
+    else
+        stack->setCurrentWidget(chart_view);
 }
 
 void JFJochViewerDatasetInfo::runsChanged(QVector<RunData> runs, QString active_id) {
diff --git a/viewer/JFJochViewerDatasetInfo.h b/viewer/JFJochViewerDatasetInfo.h
index 1e84f557..e3d21d1d 100644
--- a/viewer/JFJochViewerDatasetInfo.h
+++ b/viewer/JFJochViewerDatasetInfo.h
@@ -10,6 +10,7 @@
 #include "charts/JFJochDatasetInfoChartView.h"
 #include "../reader/JFJochReader.h"
 #include "image_viewer/JFJochGridScanImage.h"
+#include "widgets/JFJochViewerSidePanelChart.h"
 #include "RunData.h"
 
 class JFJochViewerDatasetInfo : public QWidget {
@@ -20,6 +21,7 @@ class JFJochViewerDatasetInfo : public QWidget {
     std::shared_ptr<const JFJochReaderDataset> dataset;     // the active (primary) run
     std::shared_ptr<const JFJochReaderImage> image;
     JFJochGridScanImage *grid_scan_image = nullptr;
+    JFJochViewerSidePanelChart *image_chart = nullptr;     // per-image profiles (azimuthal, Wilson, ...)
 
     QVector<RunData> runs_;                                 // all runs, for overlay lines
     QString active_id_;                                     // which run is primary
@@ -27,9 +29,11 @@ class JFJochViewerDatasetInfo : public QWidget {
 
     QStackedWidget *stack = nullptr;
     QPushButton *grid_button = nullptr;
+    QPushButton *image_button = nullptr;   // toggle: show per-image profiles instead of the metric
 
     int last_selection;
     void UpdatePlot();
+    void UpdateView();   // pick the stack page from the grid / per-image toggles
     // Pull the metric selected by combo value `val` out of one run's dataset.
     std::vector<float> ExtractMetric(const JFJochReaderDataset &ds, int val, bool &one_over_d2) const;
 
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index 85220768..30ce9694 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -99,16 +99,8 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
 
     layout->addWidget(res_rings);
 
-    layout->addWidget(new TitleLabel("Image statistics plot", this));
-    chart = new JFJochViewerSidePanelChart(this);
-    layout->addWidget(chart);
-
-    connect(this, &JFJochViewerSidePanel::imageLoaded,
-            chart, &JFJochViewerSidePanelChart::loadImage);
-    connect(chart, &JFJochViewerSidePanelChart::writeStatusBar,
-    [&] (QString string, int timeout_ms) {
-        emit writeStatusBar(string, timeout_ms);
-    });
+    // The per-image statistics plot now lives in the dataset-info dock (its "Per-image" toggle),
+    // so it is no longer duplicated here.
 
     layout->addWidget(new TitleLabel("ROI", this));
 
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 4aec0662..69c98279 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -11,13 +11,11 @@
 #include "widgets/JFJochViewerROIList.h"
 #include "../reader/JFJochReader.h"
 #include "charts/JFJochSimpleChartView.h"
-#include "widgets/JFJochViewerSidePanelChart.h"
 #include "widgets/ResolutionRingWidget.h"
 
 class JFJochViewerSidePanel : public QWidget {
     Q_OBJECT
 
-    JFJochViewerSidePanelChart *chart = nullptr;
     JFJochViewerROIList *roi_list = nullptr;
     ResolutionRingWidget *res_rings = nullptr;
 
-- 
2.52.0


From 03ac43da69cf6df0a53a6df77d89ca9fbf735617 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 10:19:56 +0200
Subject: [PATCH 209/228] =?UTF-8?q?viewer:=20panel=20polish=20=E2=80=94=20?=
 =?UTF-8?q?accordions,=20shared=20geometry,=20detector=20tilt,=20SG=20name?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Declutter the side and settings panels (review items a–f):

- New CollapsibleSection widget (slim navy header + coral rule + chevron).
- Inspector: Image features / Resolution rings / ROI are now collapsible and
  start folded (ROI auto-expands when ROIs change); drop the Data-analysis and
  Powder-calibration sections (they live in the hero buttons and settings dock).
- Settings dock: move Geometry to a shared section above the MX/AzInt toggle
  (both communities need it); add Detector tilt (PONI rot1/rot2, deg) and
  rename "Beam center" -> "Beam origin" with PONI/XDS tooltips; show the
  space-group number and resolved Hermann–Mauguin symbol on one line; wrap
  sections in accordions, anchored top with a bottom stretch so expanding one
  does not shift the others.
- Toolbar: drop the redundant "Image number" label.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                       |   2 +
 viewer/JFJochViewerSidePanel.cpp            |  51 +++----
 viewer/JFJochViewerSidePanel.h              |   3 +
 viewer/toolbar/JFJochViewerToolbarImage.cpp |   3 -
 viewer/widgets/CollapsibleSection.cpp       |  44 ++++++
 viewer/widgets/CollapsibleSection.h         |  23 +++
 viewer/widgets/JFJochViewerSettingsDock.cpp | 146 ++++++++++++++------
 viewer/widgets/JFJochViewerSettingsDock.h   |   9 +-
 8 files changed, 209 insertions(+), 72 deletions(-)
 create mode 100644 viewer/widgets/CollapsibleSection.cpp
 create mode 100644 viewer/widgets/CollapsibleSection.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 105671d3..85ed9d89 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -62,6 +62,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         widgets/JFJochViewerSidePanelChart.h
         widgets/JFJochViewerSettingsDock.cpp
         widgets/JFJochViewerSettingsDock.h
+        widgets/CollapsibleSection.cpp
+        widgets/CollapsibleSection.h
         windows/JFJochViewerSpotListWindow.cpp
         windows/JFJochViewerSpotListWindow.h
         image_viewer/JFJochAzIntImage.cpp
diff --git a/viewer/JFJochViewerSidePanel.cpp b/viewer/JFJochViewerSidePanel.cpp
index 30ce9694..8e36d32f 100644
--- a/viewer/JFJochViewerSidePanel.cpp
+++ b/viewer/JFJochViewerSidePanel.cpp
@@ -8,8 +8,8 @@
 #include "JFJochViewerSidePanel.h"
 
 #include "widgets/TitleLabel.h"
+#include "widgets/CollapsibleSection.h"
 #include "widgets/JFJochViewerImageStatistics.h"
-#include "widgets/PowderCalibrationWidget.h"
 
 JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent) {
 
@@ -21,7 +21,7 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     layout->addWidget(stats);
     connect(this, &JFJochViewerSidePanel::imageLoaded, stats, &JFJochViewerImageStatistics::loadImage);
 
-    layout->addWidget(new TitleLabel("Image features", this));
+    auto *featuresSection = new CollapsibleSection("Image features", this);
 
     auto spotToggleCheckBox = new QCheckBox("Show spots", this);
     spotToggleCheckBox->setCheckState(Qt::CheckState::Unchecked);
@@ -84,9 +84,13 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     image_feature_grid->addWidget(colorSelectButton, 3, 0);
     image_feature_grid->addWidget(spotColorSelectButton, 3, 1);
 
-    layout->addLayout(image_feature_grid);
+    featuresSection->setContentLayout(image_feature_grid);
+    featuresSection->setExpanded(false);
+    layout->addWidget(featuresSection);
 
-    layout->addWidget(new TitleLabel("Resolution rings", this));
+    auto *ringsSection = new CollapsibleSection("Resolution rings", this);
+    auto *ringsLayout = new QVBoxLayout();
+    ringsLayout->setContentsMargins(0, 0, 0, 0);
     res_rings = new ResolutionRingWidget(this);
 
     connect(res_rings, &ResolutionRingWidget::resRingsSet, [this] (const QVector<float> &v) {
@@ -97,12 +101,18 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
         emit ringModeSet(mode);
     });
 
-    layout->addWidget(res_rings);
+    ringsLayout->addWidget(res_rings);
+    ringsSection->setContentLayout(ringsLayout);
+    ringsSection->setExpanded(false);
+    layout->addWidget(ringsSection);
 
     // The per-image statistics plot now lives in the dataset-info dock (its "Per-image" toggle),
-    // so it is no longer duplicated here.
+    // and powder calibration / full analysis live in the settings dock and the hero buttons,
+    // so they are no longer duplicated here.
 
-    layout->addWidget(new TitleLabel("ROI", this));
+    roiSection = new CollapsibleSection("ROI", this);
+    auto *roiLayout = new QVBoxLayout();
+    roiLayout->setContentsMargins(0, 0, 0, 0);
 
     auto roiLabelsCheckBox = new QCheckBox("Show labels", this);
     roiLabelsCheckBox->setCheckState(Qt::CheckState::Unchecked);
@@ -115,35 +125,20 @@ JFJochViewerSidePanel::JFJochViewerSidePanel(QWidget *parent) : QWidget(parent)
     auto roiToggleRow = new QHBoxLayout();
     roiToggleRow->addWidget(roiLabelsCheckBox);
     roiToggleRow->addWidget(roiFillCheckBox);
-    layout->addLayout(roiToggleRow);
+    roiLayout->addLayout(roiToggleRow);
 
     roi_list = new JFJochViewerROIList(this);
-    layout->addWidget(roi_list);
+    roiLayout->addWidget(roi_list);
     connect(this, &JFJochViewerSidePanel::imageLoaded, roi_list, &JFJochViewerROIList::loadImage);
     connect(roi_list, &JFJochViewerROIList::roisChanged, this, &JFJochViewerSidePanel::roisChanged);
     connect(roi_list, &JFJochViewerROIList::selectedROIChanged, this, &JFJochViewerSidePanel::selectedROIChanged);
     connect(roi_list, &JFJochViewerROIList::downloadROIs, this, &JFJochViewerSidePanel::downloadROIs);
     connect(roi_list, &JFJochViewerROIList::uploadROIs, this, &JFJochViewerSidePanel::uploadROIs);
     connect(roi_list, &JFJochViewerROIList::maskFromROI, this, &JFJochViewerSidePanel::maskFromROI);
-
-    layout->addWidget(new TitleLabel("Data analysis", this));
-
-    auto analyzeButton = new QPushButton("Full analysis", this);
-    connect(analyzeButton, &QPushButton::clicked,[this] {emit analyze();});
-    layout->addWidget(analyzeButton);
-
-    // Calibrant selection combo box
-    layout->addWidget(new TitleLabel("Powder geometry calibration", this));
-
-    auto power_calibration = new PowderCalibrationWidget(this);
-    layout->addWidget(power_calibration);
-
-    connect(this, &JFJochViewerSidePanel::imageLoaded, power_calibration, &PowderCalibrationWidget::loadImage);
-    connect(power_calibration, &PowderCalibrationWidget::ringsFromCalibration, res_rings, &ResolutionRingWidget::setRings);
-    connect(power_calibration, &PowderCalibrationWidget::findBeamCenter,
-        [this] (const UnitCell& input, bool guess) {
-            emit findBeamCenter(input, guess);
-        });
+    connect(roi_list, &JFJochViewerROIList::roisChanged, this, [this] { roiSection->setExpanded(true); });
+    roiSection->setContentLayout(roiLayout);
+    roiSection->setExpanded(false);
+    layout->addWidget(roiSection);
 
     layout->addStretch();
     setLayout(layout); // Set the layout to the widget
diff --git a/viewer/JFJochViewerSidePanel.h b/viewer/JFJochViewerSidePanel.h
index 69c98279..4db1e4e7 100644
--- a/viewer/JFJochViewerSidePanel.h
+++ b/viewer/JFJochViewerSidePanel.h
@@ -13,11 +13,14 @@
 #include "charts/JFJochSimpleChartView.h"
 #include "widgets/ResolutionRingWidget.h"
 
+class CollapsibleSection;
+
 class JFJochViewerSidePanel : public QWidget {
     Q_OBJECT
 
     JFJochViewerROIList *roi_list = nullptr;
     ResolutionRingWidget *res_rings = nullptr;
+    CollapsibleSection *roiSection = nullptr;   // auto-expands when ROIs change
 
 signals:
     void showSpots(bool input);
diff --git a/viewer/toolbar/JFJochViewerToolbarImage.cpp b/viewer/toolbar/JFJochViewerToolbarImage.cpp
index 74244ad6..497550d9 100644
--- a/viewer/toolbar/JFJochViewerToolbarImage.cpp
+++ b/viewer/toolbar/JFJochViewerToolbarImage.cpp
@@ -8,9 +8,6 @@
 JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(parent) {
     image_count_in_dataset = 0;
 
-    auto title = new QLabel("<b>Image number</b>   ", this);
-    addWidget(title);
-
     leftmost_button = new QPushButton(this);
     leftmost_button->setIcon(style()->standardIcon(QStyle::SP_MediaSkipBackward));
     leftmost_button->setToolTip("First image");
diff --git a/viewer/widgets/CollapsibleSection.cpp b/viewer/widgets/CollapsibleSection.cpp
new file mode 100644
index 00000000..86748d00
--- /dev/null
+++ b/viewer/widgets/CollapsibleSection.cpp
@@ -0,0 +1,44 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "CollapsibleSection.h"
+
+#include <QToolButton>
+#include <QVBoxLayout>
+
+CollapsibleSection::CollapsibleSection(const QString &title, QWidget *parent) : QWidget(parent) {
+    auto *v = new QVBoxLayout(this);
+    v->setContentsMargins(0, 0, 0, 0);
+    v->setSpacing(0);
+
+    header_ = new QToolButton(this);
+    header_->setText(title);
+    header_->setCheckable(true);
+    header_->setChecked(true);
+    header_->setToolButtonStyle(Qt::ToolButtonTextBesideIcon);
+    header_->setArrowType(Qt::DownArrow);
+    header_->setCursor(Qt::PointingHandCursor);
+    header_->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
+    header_->setStyleSheet(
+        "QToolButton { color:#1F3A5F; font-weight:bold; text-align:left;"
+        " padding:3px 6px 3px 6px; border:none;"
+        " border-left:3px solid #FA7268; border-bottom:1px solid #FA7268; background:transparent; }");
+
+    content_ = new QWidget(this);
+
+    v->addWidget(header_);
+    v->addWidget(content_);
+
+    connect(header_, &QToolButton::toggled, this, [this](bool on) {
+        content_->setVisible(on);
+        header_->setArrowType(on ? Qt::DownArrow : Qt::RightArrow);
+    });
+}
+
+void CollapsibleSection::setContentLayout(QLayout *layout) {
+    content_->setLayout(layout);
+}
+
+void CollapsibleSection::setExpanded(bool on) {
+    header_->setChecked(on);
+}
diff --git a/viewer/widgets/CollapsibleSection.h b/viewer/widgets/CollapsibleSection.h
new file mode 100644
index 00000000..5bbf746a
--- /dev/null
+++ b/viewer/widgets/CollapsibleSection.h
@@ -0,0 +1,23 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QWidget>
+
+class QToolButton;
+class QLayout;
+
+// A slim collapsible section: a clickable navy header with a coral accent rule and a chevron,
+// over a content area that folds away. Used to keep the side and settings panels compact.
+class CollapsibleSection : public QWidget {
+    Q_OBJECT
+public:
+    explicit CollapsibleSection(const QString &title, QWidget *parent = nullptr);
+    void setContentLayout(QLayout *layout);
+    void setExpanded(bool on);
+
+private:
+    QToolButton *header_;
+    QWidget *content_;
+};
diff --git a/viewer/widgets/JFJochViewerSettingsDock.cpp b/viewer/widgets/JFJochViewerSettingsDock.cpp
index f824bb00..f130c717 100644
--- a/viewer/widgets/JFJochViewerSettingsDock.cpp
+++ b/viewer/widgets/JFJochViewerSettingsDock.cpp
@@ -6,7 +6,6 @@
 #include <QVBoxLayout>
 #include <QHBoxLayout>
 #include <QFormLayout>
-#include <QGroupBox>
 #include <QPushButton>
 #include <QButtonGroup>
 #include <QStackedWidget>
@@ -19,7 +18,9 @@
 #include "SliderPlusBox.h"
 #include "NumberLineEdit.h"
 #include "PowderCalibrationWidget.h"
-#include "TitleLabel.h"
+#include "CollapsibleSection.h"
+#include "../../common/JFJochMath.h"
+#include "../../gemmi_gph/gemmi/symmetry.hpp"
 
 JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &spot,
                                                    const IndexingSettings &indexing,
@@ -50,39 +51,63 @@ JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &sp
     stack->addWidget(BuildAzIntPage());
     connect(group, &QButtonGroup::idClicked, stack, &QStackedWidget::setCurrentIndex);
 
+    // Geometry is common to both communities, so it lives above the toggle rather than per page.
     auto *layout = new QVBoxLayout(this);
     layout->addLayout(toggleRow);
+    layout->addWidget(BuildGeometrySection());
     layout->addWidget(stack);
     layout->addStretch();
 }
 
+QWidget *JFJochViewerSettingsDock::BuildGeometrySection() {
+    auto *section = new CollapsibleSection("Geometry", this);
+    auto *geom = new QFormLayout();
+
+    energy_ = new NumberLineEdit(1.0, 200.0, 12.4, 4, "keV", this);
+    distance_ = new NumberLineEdit(10.0, 5000.0, 100.0, 2, "mm", this);
+    beamX_ = new NumberLineEdit(-20000.0, 20000.0, 0.0, 1, "px", this);
+    beamY_ = new NumberLineEdit(-20000.0, 20000.0, 0.0, 1, "px", this);
+    rot1_ = new NumberLineEdit(-180.0, 180.0, 0.0, 3, "°", this);
+    rot2_ = new NumberLineEdit(-180.0, 180.0, 0.0, 3, "°", this);
+
+    // The detector origin is the PONI (PyFAI) point; in MX (XDS-style) terms it is the beam origin,
+    // which coincides with the beam center only when the detector is untilted.
+    const QString beamTip =
+        "Beam origin (XDS convention): the PONI point where the un-tilted beam meets the detector. "
+        "Equals the beam center only when the detector tilt is zero.";
+    beamX_->setToolTip(beamTip);
+    beamY_->setToolTip(beamTip);
+    const QString tiltTip = "Detector tilt about the two in-plane axes (PyFAI PONI rot1 / rot2), in degrees.";
+    rot1_->setToolTip(tiltTip);
+    rot2_->setToolTip(tiltTip);
+
+    auto *beam = new QHBoxLayout();
+    beam->addWidget(beamX_);
+    beam->addWidget(beamY_);
+    auto *tilt = new QHBoxLayout();
+    tilt->addWidget(rot1_);
+    tilt->addWidget(rot2_);
+
+    geom->addRow("Photon energy", energy_);
+    geom->addRow("Detector distance", distance_);
+    geom->addRow("Beam origin", beam);
+    geom->addRow("Detector tilt", tilt);
+
+    for (auto *f : {energy_, distance_, beamX_, beamY_, rot1_, rot2_})
+        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
+
+    section->setContentLayout(geom);
+    return section;
+}
+
 QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     auto *page = new QWidget(this);
     auto *layout = new QVBoxLayout(page);
     layout->setContentsMargins(0, 0, 0, 0);
 
-    // --- Geometry ---
-    layout->addWidget(new TitleLabel("Geometry", page));
-    auto *geomGroup = new QGroupBox(page);
-    auto *geom = new QFormLayout(geomGroup);
-    energy_ = new NumberLineEdit(1.0, 200.0, 12.4, 4, "keV", page);
-    distance_ = new NumberLineEdit(10.0, 5000.0, 100.0, 2, "mm", page);
-    beamX_ = new NumberLineEdit(0.0, 20000.0, 0.0, 1, "px", page);
-    beamY_ = new NumberLineEdit(0.0, 20000.0, 0.0, 1, "px", page);
-    geom->addRow("Photon energy", energy_);
-    geom->addRow("Detector distance", distance_);
-    auto *beam = new QHBoxLayout();
-    beam->addWidget(beamX_);
-    beam->addWidget(beamY_);
-    geom->addRow("Beam center", beam);
-    layout->addWidget(geomGroup);
-    for (auto *f : {energy_, distance_, beamX_, beamY_})
-        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
-
     // --- Unit cell + space group (new: no input existed before) ---
-    layout->addWidget(new TitleLabel("Unit cell", page));
-    auto *cellGroup = new QGroupBox(page);
-    auto *cell = new QFormLayout(cellGroup);
+    auto *cellSection = new CollapsibleSection("Unit cell", page);
+    auto *cell = new QFormLayout();
     cellKnown_ = new QCheckBox("Known unit cell", page);
     cell->addRow("", cellKnown_);
     cellA_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
@@ -92,14 +117,21 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     cellBeta_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
     cellGamma_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
     spaceGroup_ = new NumberLineEdit(0.0, 230.0, 0.0, 0, "", page);
+    spaceGroup_->setToolTip("Space group number (1–230); 0 = unset.");
+    spaceGroupName_ = new QLabel("—", page);
     auto *abc = new QHBoxLayout();
     abc->addWidget(cellA_); abc->addWidget(cellB_); abc->addWidget(cellC_);
     auto *angles = new QHBoxLayout();
     angles->addWidget(cellAlpha_); angles->addWidget(cellBeta_); angles->addWidget(cellGamma_);
+    // Number and symbol split the line evenly, like the beam-origin row.
+    auto *sgRow = new QHBoxLayout();
+    sgRow->addWidget(spaceGroup_, 1);
+    sgRow->addWidget(spaceGroupName_, 1);
     cell->addRow("a, b, c", abc);
     cell->addRow("α, β, γ", angles);
-    cell->addRow("Space group", spaceGroup_);
-    layout->addWidget(cellGroup);
+    cell->addRow("Space group", sgRow);
+    cellSection->setContentLayout(cell);
+    layout->addWidget(cellSection);
 
     auto enableCellFields = [this](bool on) {
         for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
@@ -108,15 +140,19 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     enableCellFields(false);
     connect(cellKnown_, &QCheckBox::toggled, this, [this, enableCellFields](bool on) {
         enableCellFields(on);
+        UpdateSpaceGroupName();
         EmitExperiment();
     });
-    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
+    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_})
         connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
+    connect(spaceGroup_, &NumberLineEdit::newValue, this, [this] {
+        UpdateSpaceGroupName();
+        EmitExperiment();
+    });
 
     // --- Spot finding ---
-    layout->addWidget(new TitleLabel("Spot finding", page));
-    auto *spotGroup = new QGroupBox(page);
-    auto *spot = new QFormLayout(spotGroup);
+    auto *spotSection = new CollapsibleSection("Spot finding", page);
+    auto *spot = new QFormLayout();
     auto *snr = new SliderPlusBox(1.0, 10.0, 0.1, 1, page);
     snr->setValue(spot_.signal_to_noise_threshold);
     auto *count = new SliderPlusBox(0.0, 100.0, 1.0, 0, page);
@@ -126,7 +162,8 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     spot->addRow("Signal/noise", snr);
     spot->addRow("Photon count", count);
     spot->addRow("Min pixels/spot", minPix);
-    layout->addWidget(spotGroup);
+    spotSection->setContentLayout(spot);
+    layout->addWidget(spotSection);
     connect(snr, &SliderPlusBox::valueChanged, this, [this](double v) {
         spot_.signal_to_noise_threshold = static_cast<float>(v); EmitSpotFinding(); });
     connect(count, &SliderPlusBox::valueChanged, this, [this](double v) {
@@ -135,9 +172,8 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
         spot_.min_pix_per_spot = std::lround(v); EmitSpotFinding(); });
 
     // --- Indexing ---
-    layout->addWidget(new TitleLabel("Indexing", page));
-    auto *idxGroup = new QGroupBox(page);
-    auto *idx = new QFormLayout(idxGroup);
+    auto *idxSection = new CollapsibleSection("Indexing", page);
+    auto *idx = new QFormLayout();
     auto *algo = new QComboBox(page);
     algo->addItem("Auto", static_cast<int>(IndexingAlgorithmEnum::Auto));
     algo->addItem("FFBIDX (GPU, known cell)", static_cast<int>(IndexingAlgorithmEnum::FFBIDX));
@@ -153,7 +189,8 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     refine->setCurrentIndex(refine->findData(static_cast<int>(indexing_.GetGeomRefinementAlgorithm())));
     idx->addRow("Algorithm", algo);
     idx->addRow("Refinement", refine);
-    layout->addWidget(idxGroup);
+    idxSection->setContentLayout(idx);
+    layout->addWidget(idxSection);
     connect(algo, &QComboBox::currentIndexChanged, this, [this, algo] {
         indexing_.Algorithm(static_cast<IndexingAlgorithmEnum>(algo->currentData().toInt()));
         EmitSpotFinding();
@@ -163,6 +200,7 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
         EmitSpotFinding();
     });
 
+    layout->addStretch();   // anchor sections to the top so expanding an accordion grows downward
     return page;
 }
 
@@ -171,9 +209,8 @@ QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
     auto *layout = new QVBoxLayout(page);
     layout->setContentsMargins(0, 0, 0, 0);
 
-    layout->addWidget(new TitleLabel("Azimuthal integration", page));
-    auto *azGroup = new QGroupBox(page);
-    auto *az = new QFormLayout(azGroup);
+    auto *azSection = new CollapsibleSection("Azimuthal integration", page);
+    auto *az = new QFormLayout();
     auto *lowQ = new SliderPlusBox(1e-5, 10.0, 0.001, 4, page);
     lowQ->setValue(azint_.GetLowQ_recipA());
     auto *highQ = new SliderPlusBox(2e-5, 10.0, 0.001, 4, page);
@@ -188,7 +225,8 @@ QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
     az->addRow("High Q [Å⁻¹]", highQ);
     az->addRow("Q spacing [Å⁻¹]", spacing);
     az->addRow("Azimuthal bins", azimBins);
-    layout->addWidget(azGroup);
+    azSection->setContentLayout(az);
+    layout->addWidget(azSection);
 
     auto emitAz = [=, this] {
         azint_.QRange_recipA(static_cast<float>(lowQ->value()), static_cast<float>(highQ->value()));
@@ -202,12 +240,17 @@ QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
     connect(azimBins, &QComboBox::currentIndexChanged, this, [emitAz] { emitAz(); });
 
     // Powder calibration (calibrant rings + geometry refinement) - reuse the existing widget.
-    layout->addWidget(new TitleLabel("Powder calibration", page));
+    auto *powderSection = new CollapsibleSection("Powder calibration", page);
+    auto *powderLayout = new QVBoxLayout();
+    powderLayout->setContentsMargins(0, 0, 0, 0);
     powder_ = new PowderCalibrationWidget(page);
     connect(powder_, &PowderCalibrationWidget::findBeamCenter, this, &JFJochViewerSettingsDock::findBeamCenter);
     connect(powder_, &PowderCalibrationWidget::ringsFromCalibration, this, &JFJochViewerSettingsDock::ringsFromCalibration);
-    layout->addWidget(powder_);
+    powderLayout->addWidget(powder_);
+    powderSection->setContentLayout(powderLayout);
+    layout->addWidget(powderSection);
 
+    layout->addStretch();   // anchor sections to the top so expanding an accordion grows downward
     return page;
 }
 
@@ -222,6 +265,8 @@ void JFJochViewerSettingsDock::EmitExperiment() {
     experiment_.DetectorDistance_mm(static_cast<float>(distance_->value()));
     experiment_.BeamX_pxl(static_cast<float>(beamX_->value()));
     experiment_.BeamY_pxl(static_cast<float>(beamY_->value()));
+    experiment_.PoniRot1_rad(static_cast<float>(rot1_->value() * PI / 180.0));
+    experiment_.PoniRot2_rad(static_cast<float>(rot2_->value() * PI / 180.0));
     if (cellKnown_->isChecked()) {
         experiment_.SetUnitCell(UnitCell{
             static_cast<float>(cellA_->value()), static_cast<float>(cellB_->value()),
@@ -243,6 +288,8 @@ void JFJochViewerSettingsDock::RefreshGeometryFields() {
     distance_->setValue(experiment_.GetDetectorDistance_mm());
     beamX_->setValue(experiment_.GetBeamX_pxl());
     beamY_->setValue(experiment_.GetBeamY_pxl());
+    rot1_->setValue(experiment_.GetPoniRot1_rad() * 180.0 / PI);
+    rot2_->setValue(experiment_.GetPoniRot2_rad() * 180.0 / PI);
 
     const auto cell = experiment_.GetUnitCell();
     QSignalBlocker blockKnown(cellKnown_);
@@ -254,6 +301,25 @@ void JFJochViewerSettingsDock::RefreshGeometryFields() {
         cellAlpha_->setValue(cell->alpha); cellBeta_->setValue(cell->beta); cellGamma_->setValue(cell->gamma);
         spaceGroup_->setValue(experiment_.GetSpaceGroupNumber().value_or(0));
     }
+    UpdateSpaceGroupName();
+}
+
+void JFJochViewerSettingsDock::UpdateSpaceGroupName() {
+    if (!cellKnown_->isChecked()) {
+        spaceGroupName_->setText("—");
+        return;
+    }
+    const int n = static_cast<int>(std::lround(spaceGroup_->value()));
+    if (n >= 1 && n <= 230) {
+        try {
+            const auto &sg = gemmi::get_spacegroup_by_number(n);   // Hermann–Mauguin short symbol
+            spaceGroupName_->setText(QString::fromStdString(sg.short_name()));
+        } catch (...) {
+            spaceGroupName_->setText("invalid");
+        }
+    } else {
+        spaceGroupName_->setText(n == 0 ? "—" : "invalid");
+    }
 }
 
 void JFJochViewerSettingsDock::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
diff --git a/viewer/widgets/JFJochViewerSettingsDock.h b/viewer/widgets/JFJochViewerSettingsDock.h
index 4794df21..c41a67bf 100644
--- a/viewer/widgets/JFJochViewerSettingsDock.h
+++ b/viewer/widgets/JFJochViewerSettingsDock.h
@@ -16,6 +16,7 @@
 class QStackedWidget;
 class QCheckBox;
 class QComboBox;
+class QLabel;
 class SliderPlusBox;
 class NumberLineEdit;
 class PowderCalibrationWidget;
@@ -48,21 +49,27 @@ private:
     bool have_experiment_ = false;     // geometry edits only take effect once a dataset is loaded
     int64_t max_spots_ = 1000;
 
-    // MX geometry + crystal fields
+    // Geometry fields (shared by both MX and AzInt, since both need the same geometry)
     NumberLineEdit *energy_ = nullptr;
     NumberLineEdit *distance_ = nullptr;
     NumberLineEdit *beamX_ = nullptr;
     NumberLineEdit *beamY_ = nullptr;
+    NumberLineEdit *rot1_ = nullptr;     // detector tilt (PONI rot1), deg
+    NumberLineEdit *rot2_ = nullptr;     // detector tilt (PONI rot2), deg
+    // Crystal fields
     QCheckBox *cellKnown_ = nullptr;
     NumberLineEdit *cellA_ = nullptr, *cellB_ = nullptr, *cellC_ = nullptr;
     NumberLineEdit *cellAlpha_ = nullptr, *cellBeta_ = nullptr, *cellGamma_ = nullptr;
     NumberLineEdit *spaceGroup_ = nullptr;
+    QLabel *spaceGroupName_ = nullptr;   // resolved Hermann–Mauguin symbol
 
     PowderCalibrationWidget *powder_ = nullptr;
 
+    QWidget *BuildGeometrySection();
     QWidget *BuildMXPage();
     QWidget *BuildAzIntPage();
     void EmitSpotFinding();
     void EmitExperiment();
     void RefreshGeometryFields();
+    void UpdateSpaceGroupName();
 };
-- 
2.52.0


From a7c1560dcbcf46f2b2e82fa34b521f5263583621 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 11:08:14 +0200
Subject: [PATCH 210/228] =?UTF-8?q?viewer:=20toolbar=20rework=20=E2=80=94?=
 =?UTF-8?q?=20icons,=20prominent=20scrubber,=20HTTP=20states=20(g=E2=80=93?=
 =?UTF-8?q?k)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Complete pass over both toolbars (review items g–k), closing the toolbar topic.

New ToolbarIcons: crisp QPainter vector glyphs (Qt SVG is not a build dep), with
white "on" variants for toggles and a shared flat button style (coral hover,
navy checked).

Navigation toolbar, laid out source-first:
- Open (3.5" diskette) · HTTP sync · Movie (reel-on-top camera, distinct from
  the next/play triangle) ║ the scrub slider, which expands to fill the bar
  (coral track, navy handle) so it is the obvious way to move across the data ║
  precise navigation: first/prev/[number]/next/last, Jump, Sum.
- Open and HTTP-sync reach the file / connect dialogs (JFJochViewerMenu
  openSelected and openHttpSelected, now public).
- HTTP-sync has three states via a status dot (grey disconnected / green live /
  amber frozen); clicking with no live source attached opens the connect dialog.
  Removed the separate "Reanalyze" toggle.

Display toolbar:
- Styled foreground slider (matching), Auto/HDR as styled text toggles.

Hero buttons:
- "Reanalyze image" is now a toggle (worker ReanalyzeImages: run now + keep
  re-analysing on image/settings/processing changes; coral = active).

Processing dock:
- Drop the "New job…" toolbar action (the hero button drives it) and parent the
  job dialog to the main window instead of the dock.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                         |   2 +
 viewer/JFJochViewerMenu.h                     |   6 +-
 viewer/JFJochViewerWindow.cpp                 |  21 +-
 viewer/toolbar/JFJochViewerToolbarDisplay.cpp |  37 ++-
 viewer/toolbar/JFJochViewerToolbarDisplay.h   |   9 +-
 viewer/toolbar/JFJochViewerToolbarImage.cpp   | 235 ++++++++----------
 viewer/toolbar/JFJochViewerToolbarImage.h     |  26 +-
 viewer/widgets/ToolbarIcons.cpp               | 173 +++++++++++++
 viewer/widgets/ToolbarIcons.h                 |  26 ++
 viewer/windows/JFJochProcessingJobsWindow.cpp |   4 +-
 10 files changed, 377 insertions(+), 162 deletions(-)
 create mode 100644 viewer/widgets/ToolbarIcons.cpp
 create mode 100644 viewer/widgets/ToolbarIcons.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 85ed9d89..667a9f74 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -64,6 +64,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         widgets/JFJochViewerSettingsDock.h
         widgets/CollapsibleSection.cpp
         widgets/CollapsibleSection.h
+        widgets/ToolbarIcons.cpp
+        widgets/ToolbarIcons.h
         windows/JFJochViewerSpotListWindow.cpp
         windows/JFJochViewerSpotListWindow.h
         image_viewer/JFJochAzIntImage.cpp
diff --git a/viewer/JFJochViewerMenu.h b/viewer/JFJochViewerMenu.h
index 2a07ef2c..50f49ef0 100644
--- a/viewer/JFJochViewerMenu.h
+++ b/viewer/JFJochViewerMenu.h
@@ -29,6 +29,10 @@ public:
     // Adds a dock's show/hide toggle to the Window menu (for docked panels).
     void AddDockEntry(QDockWidget *dock, const QString &name);
 
+public slots:
+    void openSelected();       // also reachable from the toolbar's open-dataset button
+    void openHttpSelected();   // also reachable from the toolbar's HTTP-sync button
+
 signals:
     void fileOpenSelected(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void fileCloseSelected();
@@ -47,8 +51,6 @@ private slots:
     void aboutSelected();
     void licensesSelected();
     void quitSelected();
-    void openSelected();
-    void openHttpSelected();
     void closeSelected();
 
     void saveUserMaskAsTiffSelected();
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index fda87567..09013595 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -168,17 +168,22 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             "QPushButton { background-color:#1F3A5F; color:white; font-weight:bold;"
             " padding:3px 10px; border:none; border-radius:3px; }"
             " QPushButton:hover { background-color:#16314f; }"
+            " QPushButton:checked { background-color:#FA7268; }"
             " QPushButton:disabled { background-color:#9aa6b3; }";
+        // Reanalyze image is a toggle: re-analyse now and keep re-analysing on every image /
+        // settings / processing change while armed (coral = active). Reanalyze dataset is one-shot.
         auto *reanalyzeImageBtn = new QPushButton(FramesIcon(1), " Reanalyze image", this);
         reanalyzeImageBtn->setStyleSheet(heroStyle);
-        reanalyzeImageBtn->setToolTip("Re-run the analysis pipeline on the current image");
+        reanalyzeImageBtn->setCheckable(true);
+        reanalyzeImageBtn->setToolTip("Re-analyse the current image now, and keep re-analysing on"
+                                      " every image / settings / processing change while active");
         auto *reanalyzeDatasetBtn = new QPushButton(FramesIcon(3), " Reanalyze dataset", this);
         reanalyzeDatasetBtn->setStyleSheet(heroStyle);
         reanalyzeDatasetBtn->setToolTip("Re-process the whole dataset (opens a new processing job)");
         toolBarDisplay->addWidget(reanalyzeImageBtn);
         toolBarDisplay->addWidget(reanalyzeDatasetBtn);
-        connect(reanalyzeImageBtn, &QPushButton::clicked,
-                reading_worker, &JFJochImageReadingWorker::Analyze);
+        connect(reanalyzeImageBtn, &QPushButton::toggled,
+                reading_worker, &JFJochImageReadingWorker::ReanalyzeImages);
         connect(reanalyzeDatasetBtn, &QPushButton::clicked,
                 processingJobsWindow, &JFJochProcessingJobsWindow::newJob);
     }
@@ -313,8 +318,14 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::setAutoLoadMode);
     connect(toolBarImage, &JFJochViewerToolbarImage::imageJumpChanged,
             reading_worker, &JFJochImageReadingWorker::setAutoLoadJump);
-    connect(toolBarImage, &JFJochViewerToolbarImage::reanalyzeImages,
-            reading_worker, &JFJochImageReadingWorker::ReanalyzeImages);
+    // HTTP-sync button: reflect the live connection, and open the connect dialog when clicked
+    // while no live source is attached (i.e. a plain file is open).
+    connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
+            toolBarImage, &JFJochViewerToolbarImage::setHttpConnection);
+    connect(toolBarImage, &JFJochViewerToolbarImage::requestHttpConnect,
+            menuBar, &JFJochViewerMenu::openHttpSelected);
+    connect(toolBarImage, &JFJochViewerToolbarImage::requestOpenFile,
+            menuBar, &JFJochViewerMenu::openSelected);
 
     connect(side_panel, &JFJochViewerSidePanel::analyze,
             reading_worker, &JFJochImageReadingWorker::Analyze);
diff --git a/viewer/toolbar/JFJochViewerToolbarDisplay.cpp b/viewer/toolbar/JFJochViewerToolbarDisplay.cpp
index f9cee39b..7048192a 100644
--- a/viewer/toolbar/JFJochViewerToolbarDisplay.cpp
+++ b/viewer/toolbar/JFJochViewerToolbarDisplay.cpp
@@ -4,29 +4,42 @@
 #include "JFJochViewerToolbarDisplay.h"
 #include <QLabel>
 #include "../../common/ColorScale.h"
+#include "../widgets/ToolbarIcons.h"
 
 constexpr double MAX_SLIDER_NO_IMAGE = 65000;
 
 JFJochViewerToolbarDisplay::JFJochViewerToolbarDisplay(QWidget *parent)
     : QToolBar(parent) {
-    addWidget(new QLabel("<b>Foreground </b>&nbsp;&nbsp;"));
+    setWindowTitle("Display");   // shown in the toolbar/dock context menu
+    addWidget(new QLabel(" Foreground  ", this));
 
     foreground_slider = new SliderPlusBox(1, MAX_SLIDER_NO_IMAGE, 1.0, 1, this,
                                           SliderPlusBox::ScaleType::Logarithmic);
     foreground_slider->setValue(10);
-
+    foreground_slider->setToolTip("White point of the colour map (image contrast)");
+    foreground_slider->setStyleSheet(
+        "QSlider::groove:horizontal { height:6px; background:#F3D9D4; border-radius:3px; }"
+        "QSlider::sub-page:horizontal { background:#FA7268; border-radius:3px; }"
+        "QSlider::handle:horizontal { background:#1F3A5F; width:14px; margin:-5px 0; border-radius:7px; }"
+        "QSlider::handle:horizontal:hover { background:#16314F; }");
     addWidget(foreground_slider);
-    auto_foreground_button = new QPushButton("Auto");
-    auto_foreground_button->setCheckable(true);
-    auto_foreground_button->setChecked(false);
-    addWidget(auto_foreground_button);
 
-    hdr_mode_button = new QPushButton("HDR");
-    hdr_mode_button->setCheckable(true);
-    hdr_mode_button->setChecked(false);
+    auto makeToggle = [this](const QString &text, const QString &tip) {
+        auto *b = new QToolButton(this);
+        b->setText(text);
+        b->setToolButtonStyle(Qt::ToolButtonTextOnly);
+        b->setCheckable(true);
+        b->setToolTip(tip);
+        b->setCursor(Qt::PointingHandCursor);
+        b->setStyleSheet(ToolbarIcons::buttonStyle());
+        return b;
+    };
+    auto_foreground_button = makeToggle("Auto", "Auto-contrast to the current image");
+    addWidget(auto_foreground_button);
+    hdr_mode_button = makeToggle("HDR", "High dynamic range: show the full intensity range unclipped");
     addWidget(hdr_mode_button);
 
-    addWidget(new QLabel("&nbsp;&nbsp;<b>Color map</b>&nbsp;&nbsp;"));
+    addWidget(new QLabel("   Colour map  ", this));
 
     // Initialize QComboBox with the options
     color_map_select = new QComboBox(this);
@@ -45,8 +58,8 @@ JFJochViewerToolbarDisplay::JFJochViewerToolbarDisplay(QWidget *parent)
     connect(foreground_slider, &SliderPlusBox::valueChanged, this, &JFJochViewerToolbarDisplay::foregroundSet);
     connect(color_map_select, QOverload<int>::of(&QComboBox::currentIndexChanged),
             this, &JFJochViewerToolbarDisplay::colorComboBoxSet);
-    connect(auto_foreground_button, &QPushButton::clicked, this, &JFJochViewerToolbarDisplay::autoForegroundButtonPressed);
-    connect(hdr_mode_button, &QPushButton::clicked, this, &JFJochViewerToolbarDisplay::HDRModeButtonPressed);
+    connect(auto_foreground_button, &QToolButton::clicked, this, &JFJochViewerToolbarDisplay::autoForegroundButtonPressed);
+    connect(hdr_mode_button, &QToolButton::clicked, this, &JFJochViewerToolbarDisplay::HDRModeButtonPressed);
     auto *stretch = new QWidget(this);
     stretch->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Preferred);
     addWidget(stretch);
diff --git a/viewer/toolbar/JFJochViewerToolbarDisplay.h b/viewer/toolbar/JFJochViewerToolbarDisplay.h
index 4db1efef..673fd39b 100644
--- a/viewer/toolbar/JFJochViewerToolbarDisplay.h
+++ b/viewer/toolbar/JFJochViewerToolbarDisplay.h
@@ -5,18 +5,21 @@
 
 #include <QToolBar>
 #include "../widgets/SliderPlusBox.h"
-#include <QPushButton>
+#include <QToolButton>
 #include <QComboBox>
 #include "../../reader/JFJochReaderImage.h"
 
+// Display toolbar: how the image is rendered — foreground (white-point) slider, auto-contrast,
+// HDR (full dynamic range), and the colour map. The two "Reanalyze" hero buttons are appended
+// to this bar by the main window.
 class JFJochViewerToolbarDisplay : public QToolBar {
     Q_OBJECT
 
     bool auto_foreground = false;
 
     SliderPlusBox *foreground_slider;
-    QPushButton *auto_foreground_button;
-    QPushButton *hdr_mode_button;
+    QToolButton *auto_foreground_button;
+    QToolButton *hdr_mode_button;
     QComboBox *color_map_select;
 public:
     JFJochViewerToolbarDisplay(QWidget *parent = nullptr);
diff --git a/viewer/toolbar/JFJochViewerToolbarImage.cpp b/viewer/toolbar/JFJochViewerToolbarImage.cpp
index 497550d9..1fbddc77 100644
--- a/viewer/toolbar/JFJochViewerToolbarImage.cpp
+++ b/viewer/toolbar/JFJochViewerToolbarImage.cpp
@@ -3,100 +3,95 @@
 
 #include "JFJochViewerToolbarImage.h"
 #include <QTimer>
-#include <QStyle>
+#include "../widgets/ToolbarIcons.h"
 
 JFJochViewerToolbarImage::JFJochViewerToolbarImage(QWidget *parent) : QToolBar(parent) {
+    setWindowTitle("Navigation");   // shown in the toolbar/dock context menu
     image_count_in_dataset = 0;
 
-    leftmost_button = new QPushButton(this);
-    leftmost_button->setIcon(style()->standardIcon(QStyle::SP_MediaSkipBackward));
-    leftmost_button->setToolTip("First image");
-    leftmost_button->setFixedWidth(32);
-    addWidget(leftmost_button);
+    auto makeButton = [this](const QIcon &icon, const QString &tip, bool checkable) {
+        auto *b = new QToolButton(this);
+        b->setIcon(icon);
+        b->setIconSize(QSize(20, 20));
+        b->setToolTip(tip);
+        b->setCheckable(checkable);
+        b->setCursor(Qt::PointingHandCursor);
+        b->setStyleSheet(ToolbarIcons::buttonStyle());
+        return b;
+    };
 
-    left_button = new QPushButton(this);
-    left_button->setIcon(style()->standardIcon(QStyle::SP_MediaSeekBackward));
-    left_button->setToolTip("Previous (by jump)");
-    left_button->setFixedWidth(32);
-    addWidget(left_button);
+    // --- create widgets ---
+    open_button = makeButton(ToolbarIcons::openFile(), "Open dataset…", false);
+    open_button->setShortcut(QKeySequence::Open);
 
-    current_image_edit_validator = new QIntValidator(0, 1000, this);
+    autoload_button = makeButton(ToolbarIcons::httpSync(ToolbarIcons::HttpState::Disconnected),
+                                 "Connect to a live source…", false);
+    autoload_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_S));
 
-    current_image_edit = new QLineEdit("0", this);
-    current_image_edit->setFixedWidth(50);
-    current_image_edit->setAlignment(Qt::AlignmentFlag::AlignRight);
-    current_image_edit->setValidator(current_image_edit_validator);
-
-    addWidget(current_image_edit);
-
-    total_number_label = new QLabel("/0", this);
-    addWidget(total_number_label);
-
-    right_button = new QPushButton(this);
-    right_button->setIcon(style()->standardIcon(QStyle::SP_MediaSeekForward));
-    right_button->setToolTip("Next (by jump)");
-    right_button->setFixedWidth(32);
-    addWidget(right_button);
-
-    rightmost_button = new QPushButton(this);
-    rightmost_button->setIcon(style()->standardIcon(QStyle::SP_MediaSkipForward));
-    rightmost_button->setToolTip("Last image");
-    rightmost_button->setFixedWidth(32);
-    addWidget(rightmost_button);
-
-    addWidget(new QLabel(" Jump:", this));
-
-    jump = new NumericComboBox({1, 2, 5, 10, 20, 100, 500}, 1, 999, this);
-    connect(jump, &NumericComboBox::valueChanged, this, &JFJochViewerToolbarImage::setImageJump);
-    addWidget(jump);
-
-    addWidget(new QLabel(" Sum:", this));
-    auto sum = new NumericComboBox({1, 2, 5, 10, 20, 50, 100}, 1, 10000, this);
-    connect(sum, &NumericComboBox::valueChanged, this, &JFJochViewerToolbarImage::setSummation);
-    addWidget(sum);
+    movie_button = makeButton(ToolbarIcons::movie(), "Play movie", true);
+    movie_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_M));
 
+    // The scrub slider is the prominent way to move across the dataset, so it expands to fill.
     image_number_slider = new QSlider(Qt::Horizontal, this);
-    addWidget(image_number_slider);
-
+    image_number_slider->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
+    image_number_slider->setMinimumWidth(140);
+    image_number_slider->setToolTip("Scrub through the dataset");
+    image_number_slider->setStyleSheet(
+        "QSlider::groove:horizontal { height:6px; background:#F3D9D4; border-radius:3px; }"
+        "QSlider::sub-page:horizontal { background:#FA7268; border-radius:3px; }"
+        "QSlider::handle:horizontal { background:#1F3A5F; width:14px; margin:-5px 0; border-radius:7px; }"
+        "QSlider::handle:horizontal:hover { background:#16314F; }");
     image_number_slider_timer = new QTimer(this);
     image_number_slider_timer->setSingleShot(true);
 
+    leftmost_button = makeButton(ToolbarIcons::first(), "First image", false);
+    left_button = makeButton(ToolbarIcons::prev(), "Previous (by jump)", false);
 
-    movie_button = new QPushButton("&Movie");
-    movie_button->setIcon(style()->standardIcon(QStyle::SP_MediaPlay));
-    movie_button->setCheckable(true);
-    movie_button->setChecked(false);
-    movie_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_M));
-    addWidget(movie_button);
+    current_image_edit_validator = new QIntValidator(0, 1000, this);
+    current_image_edit = new QLineEdit("0", this);
+    current_image_edit->setFixedWidth(54);
+    current_image_edit->setAlignment(Qt::AlignmentFlag::AlignRight);
+    current_image_edit->setValidator(current_image_edit_validator);
+    current_image_edit->setToolTip("Current image — type a number to jump");
 
-    autoload_button = new QPushButton("HTTP Sync");
-    autoload_button->setCheckable(true);
-    autoload_button->setChecked(false);
-    // Fixed width so the tri-state glyph prefix never reflows the toolbar.
-    autoload_button->setFixedWidth(120);
-    autoload_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_S));
+    total_number_label = new QLabel("/0", this);
+
+    right_button = makeButton(ToolbarIcons::next(), "Next (by jump)", false);
+    rightmost_button = makeButton(ToolbarIcons::last(), "Last image", false);
+
+    jump = new NumericComboBox({1, 2, 5, 10, 20, 100, 500}, 1, 999, this);
+    connect(jump, &NumericComboBox::valueChanged, this, &JFJochViewerToolbarImage::setImageJump);
+    auto sum_box = new NumericComboBox({1, 2, 5, 10, 20, 50, 100}, 1, 10000, this);
+    connect(sum_box, &NumericComboBox::valueChanged, this, &JFJochViewerToolbarImage::setSummation);
+
+    // --- lay out: source actions, then the scrubber, then precise navigation ---
+    addWidget(open_button);
     addWidget(autoload_button);
+    addWidget(movie_button);
+    addSeparator();
+    addWidget(image_number_slider);
+    addSeparator();
+    addWidget(leftmost_button);
+    addWidget(left_button);
+    addWidget(current_image_edit);
+    addWidget(total_number_label);
+    addWidget(right_button);
+    addWidget(rightmost_button);
+    addWidget(new QLabel(" Jump ", this));
+    addWidget(jump);
+    addWidget(new QLabel(" Sum ", this));
+    addWidget(sum_box);
 
-    reanalyze_button = new QPushButton("&Reanalyze");
-    reanalyze_button->setCheckable(true);
-    reanalyze_button->setChecked(false);
-    reanalyze_button->setShortcut(QKeySequence(Qt::CTRL | Qt::Key_R));
-    addWidget(reanalyze_button);
-
-    connect(movie_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::movieButtonPressed);
-    connect(autoload_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::autoloadButtonPressed);
-    connect(reanalyze_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::reanalyzeButtonPressed);
-
-    auto *stretch = new QWidget(this);
-    stretch->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Preferred);
-    addWidget(stretch);
+    connect(movie_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::movieButtonPressed);
+    connect(open_button, &QToolButton::clicked, this, [this] { emit requestOpenFile(); });
+    connect(autoload_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::autoloadButtonPressed);
 
     setImageNumber(0, 0);
 
-    connect(left_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::leftButtonPressed);
-    connect(right_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::rightButtonPressed);
-    connect(leftmost_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::leftmostButtonPressed);
-    connect(rightmost_button, &QPushButton::clicked, this, &JFJochViewerToolbarImage::rightmostButtonPressed);
+    connect(left_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::leftButtonPressed);
+    connect(right_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::rightButtonPressed);
+    connect(leftmost_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::leftmostButtonPressed);
+    connect(rightmost_button, &QToolButton::clicked, this, &JFJochViewerToolbarImage::rightmostButtonPressed);
 
     connect(current_image_edit, &QLineEdit::editingFinished, this, &JFJochViewerToolbarImage::editFinalized);
     connect(image_number_slider, &QSlider::sliderPressed, this, &JFJochViewerToolbarImage::imageNumberSliderPressed);
@@ -135,22 +130,42 @@ void JFJochViewerToolbarImage::updateButtons() {
         total_number_label->setText("/" + QString::number(image_count_in_dataset));
 }
 
+void JFJochViewerToolbarImage::updateHttpButton() {
+    ToolbarIcons::HttpState s;
+    QString tip;
+    if (!http_connected) {
+        s = ToolbarIcons::HttpState::Disconnected;
+        tip = "Connect to a live source…";
+    } else if (autoload_mode == JFJochImageReadingWorker::AutoloadMode::HTTPSync) {
+        s = ToolbarIcons::HttpState::Live;
+        tip = "Following live (image + data) — click to stop";
+    } else {
+        s = ToolbarIcons::HttpState::Frozen;
+        tip = "Connected, not following — click to follow live";
+    }
+    autoload_button->setIcon(ToolbarIcons::httpSync(s));
+    autoload_button->setToolTip(tip);
+}
+
 void JFJochViewerToolbarImage::setImageNumber(int64_t total_images, int64_t current_image) {
     image_count_in_dataset = total_images;
     curr_image = current_image;
     updateButtons();
 }
 
+void JFJochViewerToolbarImage::setHttpConnection(bool connected, QString) {
+    http_connected = connected;
+    updateHttpButton();
+}
+
 void JFJochViewerToolbarImage::leftButtonPressed() {
-    if (curr_image >= jump_value) {
+    if (curr_image >= jump_value)
         emit loadImage(curr_image - jump_value, sum);
-    }
 }
 
 void JFJochViewerToolbarImage::rightButtonPressed() {
-    if (curr_image < image_count_in_dataset - jump_value) {
+    if (curr_image < image_count_in_dataset - jump_value)
         emit loadImage(curr_image + jump_value, sum);
-    }
 }
 
 void JFJochViewerToolbarImage::rightmostButtonPressed() {
@@ -167,8 +182,7 @@ void JFJochViewerToolbarImage::imageNumberSliderPressed() {
 
 void JFJochViewerToolbarImage::imageNumberSliderReleased() {
     image_number_slider_manual = false;
-    int val = image_number_slider->value();
-    emit loadImage(val, sum);
+    emit loadImage(image_number_slider->value(), sum);
 }
 
 void JFJochViewerToolbarImage::imageNumberSliderMoved(int val) {
@@ -181,13 +195,10 @@ void JFJochViewerToolbarImage::imageNumberSliderMoved(int val) {
 void JFJochViewerToolbarImage::editFinalized() {
     bool ok;
     int editedValue = current_image_edit->text().toInt(&ok);
-
-    if (ok && editedValue >= 1 && editedValue <= image_count_in_dataset) {
+    if (ok && editedValue >= 1 && editedValue <= image_count_in_dataset)
         emit loadImage(editedValue - 1, sum);
-    }
 }
 
-
 void JFJochViewerToolbarImage::setImageJump(int val) {
     jump_value = val;
     updateButtons();
@@ -198,24 +209,20 @@ void JFJochViewerToolbarImage::setSummation(int val) {
     sum = val;
     jump_value = val;
     jump->setValue(val);
-
     updateButtons();
     emit loadImage(curr_image, sum);
 }
 
 void JFJochViewerToolbarImage::autoloadButtonPressed() {
-    // The button either starts/resumes live following or stops it; the data-only "frozen" state
-    // is entered automatically by manually selecting an image while following.
-    switch (autoload_mode) {
-        case JFJochImageReadingWorker::AutoloadMode::HTTPSync:
-            emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::None);
-            break;
-        case JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset:
-        case JFJochImageReadingWorker::AutoloadMode::Movie:
-        case JFJochImageReadingWorker::AutoloadMode::None:
-            emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::HTTPSync);
-            break;
+    // Not connected: ask the window to open the connection dialog. Connected: toggle live following.
+    if (!http_connected) {
+        emit requestHttpConnect();
+        return;
     }
+    if (autoload_mode == JFJochImageReadingWorker::AutoloadMode::HTTPSync)
+        emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::None);
+    else
+        emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::HTTPSync);
 }
 
 void JFJochViewerToolbarImage::movieButtonPressed() {
@@ -225,36 +232,10 @@ void JFJochViewerToolbarImage::movieButtonPressed() {
         emit autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode::None);
 }
 
-void JFJochViewerToolbarImage::reanalyzeButtonPressed() {
-    emit reanalyzeImages(reanalyze_button->isChecked());
-}
-
 void JFJochViewerToolbarImage::setAutoloadMode(JFJochImageReadingWorker::AutoloadMode input) {
     autoload_mode = input;
-    switch (input) {
-        case JFJochImageReadingWorker::AutoloadMode::HTTPSync:
-            autoload_button->setText("▣ HTTP Sync");
-            autoload_button->setToolTip("Following live (image + data)");
-            autoload_button->setChecked(true);
-            movie_button->setChecked(false);
-            break;
-        case JFJochImageReadingWorker::AutoloadMode::HTTPSyncDataset:
-            autoload_button->setText("◐ HTTP Sync");
-            autoload_button->setToolTip("Following data only — image frozen (click to resume live)");
-            autoload_button->setChecked(true);
-            movie_button->setChecked(false);
-            break;
-        case JFJochImageReadingWorker::AutoloadMode::Movie:
-            autoload_button->setText("HTTP Sync");
-            autoload_button->setToolTip("");
-            autoload_button->setChecked(false);
-            movie_button->setChecked(true);
-            break;
-        case JFJochImageReadingWorker::AutoloadMode::None:
-            autoload_button->setText("HTTP Sync");
-            autoload_button->setToolTip("");
-            autoload_button->setChecked(false);
-            movie_button->setChecked(false);
-            break;
-    }
+    const bool playing = (input == JFJochImageReadingWorker::AutoloadMode::Movie);
+    movie_button->setChecked(playing);   // checked (navy) = movie running; icon stays the camera
+    movie_button->setToolTip(playing ? "Stop movie" : "Play movie");
+    updateHttpButton();
 }
diff --git a/viewer/toolbar/JFJochViewerToolbarImage.h b/viewer/toolbar/JFJochViewerToolbarImage.h
index c7679865..93792ef2 100644
--- a/viewer/toolbar/JFJochViewerToolbarImage.h
+++ b/viewer/toolbar/JFJochViewerToolbarImage.h
@@ -5,7 +5,7 @@
 
 #include <QToolBar>
 #include <QLabel>
-#include <QPushButton>
+#include <QToolButton>
 #include <QSlider>
 #include <QTimer>
 
@@ -13,10 +13,13 @@
 #include "../widgets/NumericComboBox.h"
 #include "../JFJochImageReadingWorker.h"
 
+// Navigation / acquisition toolbar: which image is shown (first/prev/next/last, an editable
+// number, and a prominent scrub slider), Jump/Sum, movie playback, and live HTTP sync.
 class JFJochViewerToolbarImage : public QToolBar {
     Q_OBJECT
 
     JFJochImageReadingWorker::AutoloadMode autoload_mode = JFJochImageReadingWorker::AutoloadMode::None;
+    bool http_connected = false;
     size_t image_count_in_dataset;
     int64_t curr_image;
 
@@ -27,32 +30,35 @@ class JFJochViewerToolbarImage : public QToolBar {
     QLineEdit *current_image_edit;
     QIntValidator *current_image_edit_validator;
 
-    QPushButton *leftmost_button;
-    QPushButton *left_button;
-    QPushButton *right_button;
-    QPushButton *rightmost_button;
+    QToolButton *leftmost_button;
+    QToolButton *left_button;
+    QToolButton *right_button;
+    QToolButton *rightmost_button;
 
     QSlider *image_number_slider;
     QTimer *image_number_slider_timer;
     bool image_number_slider_manual = false;
 
-    QPushButton *movie_button;
-    QPushButton *autoload_button;
-    QPushButton *reanalyze_button;
+    QToolButton *movie_button;
+    QToolButton *open_button;
+    QToolButton *autoload_button;
 
     NumericComboBox *jump;
 
     void updateButtons();
+    void updateHttpButton();
 signals:
     void loadImage(int64_t number, int summation);
     void autoLoadButtonPressed(JFJochImageReadingWorker::AutoloadMode mode);
     void imageJumpChanged(int64_t val);
-    void reanalyzeImages(bool input);
+    void requestHttpConnect();   // clicked while not connected: ask the window to open the dialog
+    void requestOpenFile();      // open-dataset button: ask the window to open the file dialog
 public:
     explicit JFJochViewerToolbarImage(QWidget *parent = nullptr);
 public slots:
     void setImageNumber(int64_t total_images, int64_t current_image);
     void setAutoloadMode(JFJochImageReadingWorker::AutoloadMode input);
+    void setHttpConnection(bool connected, QString addr);
 private slots:
     void leftButtonPressed();
     void rightButtonPressed();
@@ -69,6 +75,4 @@ private slots:
 
     void movieButtonPressed();
     void autoloadButtonPressed();
-    void reanalyzeButtonPressed();
 };
-
diff --git a/viewer/widgets/ToolbarIcons.cpp b/viewer/widgets/ToolbarIcons.cpp
new file mode 100644
index 00000000..fe24de1c
--- /dev/null
+++ b/viewer/widgets/ToolbarIcons.cpp
@@ -0,0 +1,173 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "ToolbarIcons.h"
+
+#include <QPainter>
+#include <QPainterPath>
+#include <QPolygonF>
+#include <functional>
+
+namespace {
+    constexpr int S = 32;
+    const QColor INK("#2B2B2B");
+    const QColor DISABLED("#9AA6B3");
+
+    using DrawFn = std::function<void(QPainter &, const QColor &)>;
+
+    QPixmap render(const DrawFn &fn, const QColor &color) {
+        QPixmap pm(S, S);
+        pm.fill(Qt::transparent);
+        QPainter p(&pm);
+        p.setRenderHint(QPainter::Antialiasing);
+        fn(p, color);
+        return pm;
+    }
+
+    // Toggle-capable icon: ink when off, white when on (checked, navy background), grey when disabled.
+    QIcon toggleIcon(const DrawFn &fn) {
+        QIcon ic;
+        ic.addPixmap(render(fn, INK), QIcon::Normal, QIcon::Off);
+        ic.addPixmap(render(fn, Qt::white), QIcon::Normal, QIcon::On);
+        ic.addPixmap(render(fn, Qt::white), QIcon::Active, QIcon::On);
+        ic.addPixmap(render(fn, DISABLED), QIcon::Disabled, QIcon::Off);
+        return ic;
+    }
+
+    void fillTriangle(QPainter &p, const QColor &c, QPointF a, QPointF b, QPointF tip) {
+        p.setPen(Qt::NoPen);
+        p.setBrush(c);
+        p.drawPolygon(QPolygonF({a, b, tip}));
+    }
+
+    void bar(QPainter &p, const QColor &c, double x) {
+        p.setPen(Qt::NoPen);
+        p.setBrush(c);
+        p.drawRoundedRect(QRectF(x, 9, 3.2, 14), 1.2, 1.2);
+    }
+
+    // A pair of curved arrows forming a refresh/sync ring.
+    void syncArrows(QPainter &p, const QColor &c) {
+        QPen pen(c, 2.4, Qt::SolidLine, Qt::RoundCap);
+        p.setPen(pen);
+        p.setBrush(Qt::NoBrush);
+        const QRectF r(9, 9, 14, 14);
+        p.drawArc(r, 40 * 16, 230 * 16);
+        p.drawArc(r, (40 + 180) * 16, 230 * 16);
+        // arrowheads at the two open ends
+        p.setPen(Qt::NoPen);
+        p.setBrush(c);
+        p.drawPolygon(QPolygonF({QPointF(22, 7.5), QPointF(22, 13.5), QPointF(17.5, 11)}));
+        p.drawPolygon(QPolygonF({QPointF(10, 24.5), QPointF(10, 18.5), QPointF(14.5, 21)}));
+    }
+}
+
+namespace ToolbarIcons {
+
+QIcon first() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        bar(p, c, 9);
+        fillTriangle(p, c, {24, 9}, {24, 23}, {14, 16});
+    });
+}
+
+QIcon prev() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        fillTriangle(p, c, {22, 8}, {22, 24}, {11, 16});
+    });
+}
+
+QIcon next() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        fillTriangle(p, c, {10, 8}, {10, 24}, {21, 16});
+    });
+}
+
+QIcon last() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        fillTriangle(p, c, {8, 9}, {8, 23}, {18, 16});
+        bar(p, c, 19.8);
+    });
+}
+
+QIcon movie() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        // Two reels on top of a camera body with a lens barrel — an old-fashioned movie camera.
+        p.setBrush(Qt::NoBrush);
+        p.setPen(QPen(c, 1.8));
+        p.drawEllipse(QPointF(10, 11.5), 3.0, 3.0);
+        p.drawEllipse(QPointF(16.5, 11.5), 3.0, 3.0);
+        p.setPen(Qt::NoPen);
+        p.setBrush(c);
+        p.drawRoundedRect(QRectF(5, 15, 16, 10), 2, 2);
+        p.drawRoundedRect(QRectF(21, 17, 5, 6), 1, 1);   // lens barrel
+    });
+}
+
+QIcon openFile() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        // 3.5" diskette ("save" floppy): square jacket with a cut top-right corner, the metal
+        // shutter across the top, and a label panel below.
+        p.setPen(QPen(c, 1.8));
+        p.setBrush(Qt::NoBrush);
+        QPolygonF body({{6, 6}, {20, 6}, {26, 12}, {26, 26}, {6, 26}});
+        p.drawPolygon(body);                              // jacket
+        p.setPen(Qt::NoPen);
+        p.setBrush(c);
+        p.drawRect(QRectF(10, 6, 8, 5.5));                // metal shutter (top)
+        p.setBrush(Qt::NoBrush);
+        p.setPen(QPen(c, 1.6));
+        p.drawRect(QRectF(9.5, 15.5, 13, 8.5));           // label panel
+    });
+}
+
+QIcon reanalyzeImage() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        p.setPen(QPen(c, 2.0));
+        p.setBrush(Qt::NoBrush);
+        p.drawRoundedRect(QRectF(8, 8, 16, 16), 2.5, 2.5);
+        p.setBrush(c);
+        p.drawEllipse(QPointF(16, 16), 2.2, 2.2);
+    });
+}
+
+QIcon reanalyzeDataset() {
+    return toggleIcon([](QPainter &p, const QColor &c) {
+        p.setPen(QPen(c, 2.0));
+        p.setBrush(Qt::NoBrush);
+        for (int i = 2; i >= 0; --i)
+            p.drawRoundedRect(QRectF(5 + i * 4.0, 5 + i * 4.0, 14, 14), 2.0, 2.0);
+        p.setBrush(c);
+        p.drawEllipse(QPointF(12, 12), 2.0, 2.0);
+    });
+}
+
+QIcon httpSync(HttpState state) {
+    QColor dot;
+    switch (state) {
+        case HttpState::Disconnected: dot = QColor("#9AA6B3"); break;   // grey
+        case HttpState::Live:         dot = QColor("#5CB85C"); break;   // green
+        case HttpState::Frozen:       dot = QColor("#E9A23B"); break;   // amber
+    }
+    auto draw = [dot](QPainter &p, const QColor &c) {
+        syncArrows(p, c);
+        p.setPen(QPen(Qt::white, 1.2));
+        p.setBrush(dot);
+        p.drawEllipse(QPointF(24, 24), 4.2, 4.2);   // status dot
+    };
+    QIcon ic;
+    ic.addPixmap(render(draw, INK), QIcon::Normal, QIcon::Off);
+    ic.addPixmap(render(draw, DISABLED), QIcon::Disabled, QIcon::Off);
+    return ic;
+}
+
+QString buttonStyle() {
+    return QStringLiteral(
+        "QToolButton { border:none; border-radius:4px; padding:4px 6px; color:#2B2B2B;"
+        " background:transparent; }"
+        " QToolButton:hover { background:rgba(250,114,104,0.20); }"
+        " QToolButton:checked { background:#1F3A5F; color:white; }"
+        " QToolButton:disabled { color:#9AA6B3; }");
+}
+
+}  // namespace ToolbarIcons
diff --git a/viewer/widgets/ToolbarIcons.h b/viewer/widgets/ToolbarIcons.h
new file mode 100644
index 00000000..81a8316d
--- /dev/null
+++ b/viewer/widgets/ToolbarIcons.h
@@ -0,0 +1,26 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QIcon>
+
+// Vector toolbar glyphs drawn with QPainter (Qt SVG module is not a build dependency). Toggle
+// icons carry a white "On" variant so they read on the navy checked-button background; momentary
+// icons are ink with a greyed disabled variant. Colours match the viewer palette.
+namespace ToolbarIcons {
+    QIcon first();
+    QIcon prev();
+    QIcon next();
+    QIcon last();
+    QIcon movie();              // reel-on-top movie camera (distinct from the next/play triangle)
+    QIcon openFile();           // 5.25" diskette with an outward arrow
+    QIcon reanalyzeImage();     // single diffraction frame
+    QIcon reanalyzeDataset();   // a stack of frames
+
+    enum class HttpState { Disconnected, Live, Frozen };
+    QIcon httpSync(HttpState state);   // sync arrows + a status dot (grey / green / amber)
+
+    // Shared stylesheet for flat toolbar buttons (coral hover, navy checked + white content).
+    QString buttonStyle();
+}
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index ad41f9fa..0fc02790 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -57,7 +57,7 @@ JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker
 
     toolbar_ = new QToolBar("Jobs", this);
     toolbar_->setMovable(false);
-    toolbar_->addAction("New job…", this, &JFJochProcessingJobsWindow::newJob);
+    // "New job" is launched by the "Reanalyze dataset" hero button, not from this dock's toolbar.
     toolbar_->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
     toolbar_->addAction("Remove result", this, &JFJochProcessingJobsWindow::removeResult);
     toolbar_->addSeparator();
@@ -110,7 +110,7 @@ void JFJochProcessingJobsWindow::onHttpConnectionChanged(bool connected, QString
 }
 
 int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec &spec) {
-    QDialog dlg(this);
+    QDialog dlg(window());   // centre on the main window, not inside the processing dock
     dlg.setWindowTitle("New processing job");
 
     auto *mode = new QComboBox(&dlg);
-- 
2.52.0


From c62cd995662e05720fe8f6f1b4624913d899886d Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 11:49:54 +0200
Subject: [PATCH 211/228] viewer: thumbnail hit feed (image strip)

A dockable strip of thumbnails for a handful of representative images, with
spots overlaid so a real pattern reads like a constellation; click opens that
image.

- JFJochViewerImageStrip: mode selector (evenly spaced / most spots / indexed,
  computed from the dataset's per-image metrics) + a Spots toggle; a scrollable
  row of thumbnail buttons; click emits imageSelected.
- The reading worker renders thumbnails off-thread and non-disruptively: load
  each image via its reader, downsample by block-maximum (keeps Bragg spots),
  map through the colour-scale LUT, optionally paint spots (coral indexed /
  teal not), and emit thumbnailReady(image_number, QImage). File mode only.
- Docked in the bottom area, shown in the Processing perspective; the colour map
  follows the display toolbar.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/CMakeLists.txt                     |   2 +
 viewer/JFJochImageReadingWorker.cpp       |  92 +++++++++++++++
 viewer/JFJochImageReadingWorker.h         |  12 ++
 viewer/JFJochViewerWindow.cpp             |  20 ++++
 viewer/JFJochViewerWindow.h               |   1 +
 viewer/widgets/JFJochViewerImageStrip.cpp | 132 ++++++++++++++++++++++
 viewer/widgets/JFJochViewerImageStrip.h   |  42 +++++++
 7 files changed, 301 insertions(+)
 create mode 100644 viewer/widgets/JFJochViewerImageStrip.cpp
 create mode 100644 viewer/widgets/JFJochViewerImageStrip.h

diff --git a/viewer/CMakeLists.txt b/viewer/CMakeLists.txt
index 667a9f74..8e51d412 100644
--- a/viewer/CMakeLists.txt
+++ b/viewer/CMakeLists.txt
@@ -66,6 +66,8 @@ ADD_EXECUTABLE(jfjoch_viewer jfjoch_viewer.cpp JFJochViewerWindow.cpp JFJochView
         widgets/CollapsibleSection.h
         widgets/ToolbarIcons.cpp
         widgets/ToolbarIcons.h
+        widgets/JFJochViewerImageStrip.cpp
+        widgets/JFJochViewerImageStrip.h
         windows/JFJochViewerSpotListWindow.cpp
         windows/JFJochViewerSpotListWindow.h
         image_viewer/JFJochAzIntImage.cpp
diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index b9d6725a..a22862d5 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -21,6 +21,8 @@
 #include <QVector>
 #include <QMutexLocker>
 #include <QFileInfo>
+#include <QPainter>
+#include <algorithm>
 
 #include "../preview/JFJochTIFF.h"
 
@@ -99,11 +101,13 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
     qRegisterMetaType<ScalingSettings>("ScalingSettings");
     qRegisterMetaType<RunData>("RunData");
     qRegisterMetaType<QVector<RunData>>("QVector<RunData>");
+    qRegisterMetaType<QVector<qint64>>("QVector<qint64>");
     spot_finding_settings = settings;
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings);
     http_reader.Experiment(experiment);
     file_reader.Experiment(experiment);
+    thumb_color_scale_.Select(ColorScaleEnum::Indigo);
 
     autoload_timer = new QTimer(this);
     autoload_timer->setInterval(autoload_interval);
@@ -1025,3 +1029,91 @@ void JFJochImageReadingWorker::SetActiveSnapshot(QString name) {
     }
 }
 
+
+void JFJochImageReadingWorker::SetThumbnailColorMap(int color_map) {
+    QMutexLocker locker(&m);
+    thumb_color_scale_.Select(static_cast<ColorScaleEnum>(color_map));
+}
+
+void JFJochImageReadingWorker::RenderThumbnails(QVector<qint64> image_numbers, bool show_spots) {
+    // File mode only; live HTTP cannot address arbitrary images cheaply.
+    if (http_mode)
+        return;
+    for (qint64 n : image_numbers) {
+        QImage thumb = RenderThumbnail_i(n, show_spots);
+        if (!thumb.isNull())
+            emit thumbnailReady(n, thumb);
+    }
+}
+
+QImage JFJochImageReadingWorker::RenderThumbnail_i(int64_t image_number, bool show_spots) {
+    std::shared_ptr<JFJochReaderImage> img;
+    try {
+        QMutexLocker locker(&m);
+        if (http_mode || image_number < 0 || image_number >= total_images)
+            return {};
+        img = file_reader.LoadImage(image_number, 1);
+    } catch (const std::exception &e) {
+        logger.Debug("Thumbnail load failed for image {}: {}", image_number, e.what());
+        return {};
+    }
+    if (!img)
+        return {};
+
+    const int W = static_cast<int>(img->Dataset().experiment.GetXPixelsNum());
+    const int H = static_cast<int>(img->Dataset().experiment.GetYPixelsNum());
+    const auto &px = img->Image();
+    if (W <= 0 || H <= 0 || static_cast<int64_t>(px.size()) < static_cast<int64_t>(W) * H)
+        return {};
+
+    // Downsample by block-maximum (keeps sharp Bragg spots), then map through the colour-scale LUT.
+    constexpr int maxDim = 120;
+    const double s = static_cast<double>(maxDim) / std::max(W, H);
+    const int tw = std::max(1, static_cast<int>(W * s));
+    const int th = std::max(1, static_cast<int>(H * s));
+    const int bx = std::max(1, W / tw);
+    const int by = std::max(1, H / th);
+
+    const float fg = std::max(1.0f, static_cast<float>(img->GetAutoContrastValue()));
+    const auto &lut = thumb_color_scale_.LUTData();
+    const int lutSize = static_cast<int>(lut.size());
+    const float invRange = fg > 0 ? (lutSize - 1) / fg : 0.0f;
+    const rgb gap = thumb_color_scale_.Apply(ColorScaleSpecial::Gap);
+
+    QImage out(tw, th, QImage::Format_RGB32);
+    for (int ty = 0; ty < th; ++ty) {
+        QRgb *line = reinterpret_cast<QRgb *>(out.scanLine(ty));
+        const int y1 = std::min(H, ty * by + by);
+        for (int tx = 0; tx < tw; ++tx) {
+            const int x1 = std::min(W, tx * bx + bx);
+            int32_t best = 0;
+            bool any = false;
+            for (int yy = ty * by; yy < y1; ++yy)
+                for (int xx = tx * bx; xx < x1; ++xx) {
+                    const int32_t v = px[yy * W + xx];
+                    if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE) continue;
+                    if (v == SATURATED_PXL_VALUE) { best = static_cast<int32_t>(fg); any = true; continue; }
+                    if (!any || v > best) { best = v; any = true; }
+                }
+            rgb c;
+            if (!any) {
+                c = gap;
+            } else {
+                int idx = static_cast<int>(std::max(0, best) * invRange + 0.5f);
+                idx = std::clamp(idx, 0, lutSize - 1);
+                c = lut[idx];
+            }
+            line[tx] = qRgb(c.r, c.g, c.b);
+        }
+    }
+
+    if (show_spots) {
+        QPainter p(&out);
+        p.setRenderHint(QPainter::Antialiasing);
+        for (const auto &sp : img->ImageData().spots) {
+            p.setPen(QPen(sp.indexed ? QColor(0xFA, 0x72, 0x68) : QColor(0x2A, 0x9D, 0x8F), 1.0));
+            p.drawEllipse(QPointF(sp.x * s, sp.y * s), 1.6, 1.6);
+        }
+    }
+    return out;
+}
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 6cc50558..352739ca 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -10,6 +10,9 @@
 #include <QMutex>
 #include <QTimer>
 #include <QElapsedTimer>
+#include <QImage>
+
+#include "../common/ColorScale.h"
 
 #include "../reader/JFJochHDF5Reader.h"
 #include "../common/Logger.h"
@@ -88,6 +91,9 @@ private:
 
     SpotFindingSettings spot_finding_settings;
 
+    ColorScale thumb_color_scale_;   // colour map used for the image-strip thumbnails
+    QImage RenderThumbnail_i(int64_t image_number, bool show_spots);
+
     std::optional<int64_t> current_image;
     int64_t current_summation = 1;
     int64_t total_images = 0;
@@ -160,6 +166,7 @@ signals:
     void snapshotsChanged(QStringList names, QString active);
     void runsChanged(QVector<RunData> runs, QString active_id);
     void fileOpened();   // a new file/stream was loaded - listeners should reset per-file state
+    void thumbnailReady(qint64 image_number, QImage thumb);   // for the image-strip / hit feed
 
 public:
     JFJochImageReadingWorker(const SpotFindingSettings &settings, const DiffractionExperiment& experiment, QObject *parent = nullptr);
@@ -212,4 +219,9 @@ public slots:
     void SetActiveSnapshot(QString name);
     void RenameRun(QString id, QString label);   // change a run's display label (legend)
     void RemoveRun(QString id);                  // drop a reprocessing snapshot (not "Original")
+
+    // Render downsampled thumbnails for the given images (file mode only), emitting thumbnailReady
+    // for each; non-disruptive (does not change the displayed image).
+    void RenderThumbnails(QVector<qint64> image_numbers, bool show_spots);
+    void SetThumbnailColorMap(int color_map);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 09013595..8983d93e 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -20,6 +20,7 @@
 #include "image_viewer/JFJochDiffractionImage.h"
 #include "JFJochViewerSidePanel.h"
 #include "widgets/JFJochViewerSettingsDock.h"
+#include "widgets/JFJochViewerImageStrip.h"
 #include "JFJochViewerStatusBar.h"
 #include "../common/CUDAWrapper.h"
 #include "windows/JFJochViewerImageListWindow.h"
@@ -534,6 +535,24 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     }
     menuBar->AddDockEntry(processingDock, "Processing");
 
+    // Image strip / hit feed: thumbnails of representative images, rendered off-thread; click opens.
+    auto *imageStrip = new JFJochViewerImageStrip(this);
+    imageStripDock = new QDockWidget("Image strip", this);
+    imageStripDock->setObjectName("imageStripDock");
+    imageStripDock->setWidget(imageStrip);
+    addDockWidget(Qt::BottomDockWidgetArea, imageStripDock);
+    menuBar->AddDockEntry(imageStripDock, "Image strip");
+    connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
+            imageStrip, &JFJochViewerImageStrip::datasetLoaded);
+    connect(imageStrip, &JFJochViewerImageStrip::requestThumbnails,
+            reading_worker, &JFJochImageReadingWorker::RenderThumbnails);
+    connect(reading_worker, &JFJochImageReadingWorker::thumbnailReady,
+            imageStrip, &JFJochViewerImageStrip::thumbnailReady);
+    connect(imageStrip, &JFJochViewerImageStrip::imageSelected,
+            reading_worker, &JFJochImageReadingWorker::LoadImage);
+    connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
+            reading_worker, &JFJochImageReadingWorker::SetThumbnailColorMap);
+
     connect(menuBar, &JFJochViewerMenu::imageLayoutSelected, this,
             [this] { ApplyPerspective(Perspective::Image); });
     connect(menuBar, &JFJochViewerMenu::processingLayoutSelected, this,
@@ -565,6 +584,7 @@ void JFJochViewerWindow::ApplyPerspective(Perspective p) {
     if (inspectorDock) inspectorDock->setVisible(true);
     if (settingsDock) settingsDock->setVisible(processing);
     if (processingDock) processingDock->setVisible(processing);
+    if (imageStripDock) imageStripDock->setVisible(processing);
     for (auto *d : findChildren<QDockWidget *>())
         if (d->objectName().startsWith("datasetInfoDock"))
             d->setVisible(processing);
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 3c5960fb..6562ca4f 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -42,6 +42,7 @@ private:
     QDockWidget *inspectorDock = nullptr;         // image inspector (former right-hand side panel)
     QDockWidget *settingsDock = nullptr;          // inline MX/AzInt settings panel
     QDockWidget *processingDock = nullptr;        // processing jobs panel
+    QDockWidget *imageStripDock = nullptr;        // thumbnail strip / hit feed
     QByteArray defaultLayoutState;                // captured after construction, for "Reset layout"
     int datasetInfoCounter = 0;                   // gives each dataset-info dock a unique objectName
 
diff --git a/viewer/widgets/JFJochViewerImageStrip.cpp b/viewer/widgets/JFJochViewerImageStrip.cpp
new file mode 100644
index 00000000..8fc38461
--- /dev/null
+++ b/viewer/widgets/JFJochViewerImageStrip.cpp
@@ -0,0 +1,132 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "JFJochViewerImageStrip.h"
+
+#include <QComboBox>
+#include <QCheckBox>
+#include <QHBoxLayout>
+#include <QVBoxLayout>
+#include <QScrollArea>
+#include <QToolButton>
+#include <QLabel>
+#include <QPixmap>
+
+#include <algorithm>
+#include <numeric>
+
+JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent) {
+    auto *layout = new QVBoxLayout(this);
+    layout->setContentsMargins(4, 2, 4, 2);
+
+    auto *controls = new QHBoxLayout();
+    controls->addWidget(new QLabel("Show", this));
+    mode_ = new QComboBox(this);
+    mode_->addItem("Evenly spaced", 0);
+    mode_->addItem("Most spots", 1);
+    mode_->addItem("Indexed", 2);
+    controls->addWidget(mode_);
+    spots_ = new QCheckBox("Spots", this);
+    spots_->setChecked(true);
+    spots_->setToolTip("Overlay found spots — a real pattern reads like a constellation");
+    controls->addWidget(spots_);
+    controls->addStretch();
+    layout->addLayout(controls);
+
+    auto *scroll = new QScrollArea(this);
+    scroll->setWidgetResizable(true);
+    scroll->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
+    scroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAsNeeded);
+    auto *stripWidget = new QWidget(scroll);
+    strip_ = new QHBoxLayout(stripWidget);
+    strip_->setContentsMargins(0, 0, 0, 0);
+    strip_->addStretch();
+    scroll->setWidget(stripWidget);
+    layout->addWidget(scroll);
+
+    connect(mode_, &QComboBox::currentIndexChanged, this, [this] { Rebuild(); });
+    connect(spots_, &QCheckBox::toggled, this, [this] { Rebuild(); });
+}
+
+void JFJochViewerImageStrip::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
+    dataset_ = std::move(dataset);
+    Rebuild();
+}
+
+void JFJochViewerImageStrip::thumbnailReady(qint64 image_number, QImage thumb) {
+    auto it = slots_.find(image_number);
+    if (it != slots_.end())
+        it.value()->setIcon(QPixmap::fromImage(thumb));
+}
+
+QVector<qint64> JFJochViewerImageStrip::ComputeRepresentatives() const {
+    QVector<qint64> result;
+    if (!dataset_)
+        return result;
+    const int64_t total = dataset_->experiment.GetImageNum();
+    if (total <= 0)
+        return result;
+    const int N = static_cast<int>(std::min<int64_t>(8, total));
+    const int mode = mode_->currentIndex();
+    const auto &sc = dataset_->spot_count;
+    const auto &sci = dataset_->spot_count_indexed;
+
+    auto evenly = [&] {
+        for (int i = 0; i < N; ++i)
+            result.push_back(N == 1 ? 0 : static_cast<int64_t>(i) * (total - 1) / (N - 1));
+    };
+
+    if (mode == 1 && !sc.empty()) {                 // most spots
+        std::vector<int64_t> idx(sc.size());
+        std::iota(idx.begin(), idx.end(), 0);
+        const size_t n = std::min<size_t>(N, idx.size());
+        std::partial_sort(idx.begin(), idx.begin() + n, idx.end(),
+                          [&](int64_t a, int64_t b) { return sc[a] > sc[b]; });
+        idx.resize(n);
+        std::sort(idx.begin(), idx.end());
+        for (int64_t i : idx) result.push_back(i);
+    } else if (mode == 2 && !sci.empty()) {         // indexed images, evenly sampled
+        std::vector<int64_t> indexed;
+        for (size_t i = 0; i < sci.size(); ++i)
+            if (sci[i] > 0) indexed.push_back(static_cast<int64_t>(i));
+        if (indexed.empty()) {
+            evenly();
+        } else {
+            const int n = static_cast<int>(std::min<size_t>(N, indexed.size()));
+            for (int i = 0; i < n; ++i)
+                result.push_back(indexed[n == 1 ? 0 : static_cast<size_t>(i) * (indexed.size() - 1) / (n - 1)]);
+        }
+    } else {
+        evenly();
+    }
+    return result;
+}
+
+void JFJochViewerImageStrip::Rebuild() {
+    // Clear the strip (keep the trailing stretch).
+    slots_.clear();
+    while (strip_->count() > 1) {
+        QLayoutItem *item = strip_->takeAt(0);
+        if (item->widget())
+            item->widget()->deleteLater();
+        delete item;
+    }
+    if (!dataset_)
+        return;
+
+    const QVector<qint64> reps = ComputeRepresentatives();
+    int pos = 0;
+    for (qint64 n : reps) {
+        auto *btn = new QToolButton(this);
+        btn->setToolButtonStyle(Qt::ToolButtonTextUnderIcon);
+        btn->setIconSize(QSize(120, 120));
+        btn->setText(QString::number(n + 1));
+        btn->setAutoRaise(true);
+        btn->setCursor(Qt::PointingHandCursor);
+        btn->setToolTip(QStringLiteral("Open image %1").arg(n + 1));
+        connect(btn, &QToolButton::clicked, this, [this, n] { emit imageSelected(n, 1); });
+        strip_->insertWidget(pos++, btn);
+        slots_[n] = btn;
+    }
+    emit requestThumbnails(reps, spots_->isChecked());
+}
diff --git a/viewer/widgets/JFJochViewerImageStrip.h b/viewer/widgets/JFJochViewerImageStrip.h
new file mode 100644
index 00000000..fae90657
--- /dev/null
+++ b/viewer/widgets/JFJochViewerImageStrip.h
@@ -0,0 +1,42 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <QWidget>
+#include <QMap>
+#include <memory>
+
+#include "../../reader/JFJochReaderDataset.h"
+
+class QComboBox;
+class QCheckBox;
+class QHBoxLayout;
+class QToolButton;
+
+// A strip of thumbnails for a handful of representative images (evenly spaced, most spots, or
+// indexed), optionally overlaid with spots so a real pattern reads like a constellation. Clicking
+// a thumbnail opens that image. Thumbnails are rendered off-thread by the reading worker.
+class JFJochViewerImageStrip : public QWidget {
+    Q_OBJECT
+public:
+    explicit JFJochViewerImageStrip(QWidget *parent = nullptr);
+
+public slots:
+    void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
+    void thumbnailReady(qint64 image_number, QImage thumb);
+
+signals:
+    void requestThumbnails(QVector<qint64> image_numbers, bool show_spots);
+    void imageSelected(int64_t image_number, int64_t summation);
+
+private:
+    std::shared_ptr<const JFJochReaderDataset> dataset_;
+    QComboBox *mode_ = nullptr;
+    QCheckBox *spots_ = nullptr;
+    QHBoxLayout *strip_ = nullptr;
+    QMap<qint64, QToolButton *> slots_;   // image number -> its thumbnail button
+
+    QVector<qint64> ComputeRepresentatives() const;
+    void Rebuild();
+};
-- 
2.52.0


From 7d24cdba4f48e645e703dddf516d1aafbf5c5724 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 12:07:44 +0200
Subject: [PATCH 212/228] =?UTF-8?q?viewer:=20hit-feed=20polish=20=E2=80=94?=
 =?UTF-8?q?=20stacked=20docks,=20hidden=20processing,=20resolution=20mode?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Follow-up to the image strip, addressing the review:

- Composition: stack the plots and the thumbnail strip vertically (plots on top
  with more height, strip below) instead of sharing horizontal space — both
  benefit from width, and the strip needs less height.
- Processing dock is hidden by default and narrower; it reveals itself only when
  a reprocessing job starts (new jobStarted signal), and the Processing
  perspective no longer force-shows it.
- Thumbnail spot overlays now use the same feature (indexed) / spot colours as
  the main viewer, and follow the side-panel colour pickers.
- New strip selection modes "Resolution" and "Background": pick images that span
  that metric's distribution (a quick histogram-representative selection).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp           | 12 +++++++++-
 viewer/JFJochImageReadingWorker.h             |  5 ++++
 viewer/JFJochViewerWindow.cpp                 | 24 ++++++++++++++-----
 viewer/widgets/JFJochViewerImageStrip.cpp     | 21 ++++++++++++++++
 viewer/windows/JFJochProcessingJobsWindow.cpp |  1 +
 viewer/windows/JFJochProcessingJobsWindow.h   |  1 +
 6 files changed, 57 insertions(+), 7 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index a22862d5..6a7e2f70 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -1035,6 +1035,16 @@ void JFJochImageReadingWorker::SetThumbnailColorMap(int color_map) {
     thumb_color_scale_.Select(static_cast<ColorScaleEnum>(color_map));
 }
 
+void JFJochImageReadingWorker::SetThumbnailFeatureColor(QColor c) {
+    QMutexLocker locker(&m);
+    thumb_feature_color_ = c;
+}
+
+void JFJochImageReadingWorker::SetThumbnailSpotColor(QColor c) {
+    QMutexLocker locker(&m);
+    thumb_spot_color_ = c;
+}
+
 void JFJochImageReadingWorker::RenderThumbnails(QVector<qint64> image_numbers, bool show_spots) {
     // File mode only; live HTTP cannot address arbitrary images cheaply.
     if (http_mode)
@@ -1111,7 +1121,7 @@ QImage JFJochImageReadingWorker::RenderThumbnail_i(int64_t image_number, bool sh
         QPainter p(&out);
         p.setRenderHint(QPainter::Antialiasing);
         for (const auto &sp : img->ImageData().spots) {
-            p.setPen(QPen(sp.indexed ? QColor(0xFA, 0x72, 0x68) : QColor(0x2A, 0x9D, 0x8F), 1.0));
+            p.setPen(QPen(sp.indexed ? thumb_feature_color_ : thumb_spot_color_, 1.0));
             p.drawEllipse(QPointF(sp.x * s, sp.y * s), 1.6, 1.6);
         }
     }
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 352739ca..94a982e7 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -11,6 +11,7 @@
 #include <QTimer>
 #include <QElapsedTimer>
 #include <QImage>
+#include <QColor>
 
 #include "../common/ColorScale.h"
 
@@ -92,6 +93,8 @@ private:
     SpotFindingSettings spot_finding_settings;
 
     ColorScale thumb_color_scale_;   // colour map used for the image-strip thumbnails
+    QColor thumb_feature_color_ = Qt::magenta;   // indexed-spot overlay (matches the main viewer)
+    QColor thumb_spot_color_ = Qt::green;        // non-indexed spot overlay
     QImage RenderThumbnail_i(int64_t image_number, bool show_spots);
 
     std::optional<int64_t> current_image;
@@ -224,4 +227,6 @@ public slots:
     // for each; non-disruptive (does not change the displayed image).
     void RenderThumbnails(QVector<qint64> image_numbers, bool show_spots);
     void SetThumbnailColorMap(int color_map);
+    void SetThumbnailFeatureColor(QColor c);
+    void SetThumbnailSpotColor(QColor c);
 };
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 8983d93e..7e5d219a 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -518,7 +518,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(settingsPanel, &JFJochViewerSettingsDock::ringsFromCalibration,
             side_panel, &JFJochViewerSidePanel::SetRings);
 
-    // Dock the processing panel in the bottom-right corner, next to the dataset-info plots.
+    // Processing panel: hidden by default and narrower; it reveals itself (to the right of the
+    // plots) only when a reprocessing job starts.
     processingDock = new QDockWidget("Processing", this);
     processingDock->setObjectName("processingDock");
     processingDock->setAllowedAreas(Qt::BottomDockWidgetArea);
@@ -528,19 +529,26 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     addDockWidget(Qt::BottomDockWidgetArea, processingDock);
     if (lastDatasetInfoDock) {
         splitDockWidget(lastDatasetInfoDock, processingDock, Qt::Horizontal);
-        resizeDocks({lastDatasetInfoDock, processingDock}, {650, 350}, Qt::Horizontal);
-        // Give the bottom area generous height: the per-dataset plot is a headline feature, so it
-        // gets real room rather than a thin strip.
-        resizeDocks({lastDatasetInfoDock, processingDock}, {420, 420}, Qt::Vertical);
+        resizeDocks({lastDatasetInfoDock, processingDock}, {900, 280}, Qt::Horizontal);
     }
+    processingDock->hide();
     menuBar->AddDockEntry(processingDock, "Processing");
+    connect(processingJobsWindow, &JFJochProcessingJobsWindow::jobStarted, this, [this] {
+        processingDock->show();
+        processingDock->raise();
+    });
 
     // Image strip / hit feed: thumbnails of representative images, rendered off-thread; click opens.
+    // Stacked below the plots — both want vertical room, and the strip needs less of it.
     auto *imageStrip = new JFJochViewerImageStrip(this);
     imageStripDock = new QDockWidget("Image strip", this);
     imageStripDock->setObjectName("imageStripDock");
     imageStripDock->setWidget(imageStrip);
     addDockWidget(Qt::BottomDockWidgetArea, imageStripDock);
+    if (lastDatasetInfoDock) {
+        splitDockWidget(lastDatasetInfoDock, imageStripDock, Qt::Vertical);
+        resizeDocks({lastDatasetInfoDock, imageStripDock}, {340, 180}, Qt::Vertical);
+    }
     menuBar->AddDockEntry(imageStripDock, "Image strip");
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             imageStrip, &JFJochViewerImageStrip::datasetLoaded);
@@ -552,6 +560,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::LoadImage);
     connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
             reading_worker, &JFJochImageReadingWorker::SetThumbnailColorMap);
+    connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
+            reading_worker, &JFJochImageReadingWorker::SetThumbnailFeatureColor);
+    connect(side_panel, &JFJochViewerSidePanel::setSpotColor,
+            reading_worker, &JFJochImageReadingWorker::SetThumbnailSpotColor);
 
     connect(menuBar, &JFJochViewerMenu::imageLayoutSelected, this,
             [this] { ApplyPerspective(Perspective::Image); });
@@ -583,8 +595,8 @@ void JFJochViewerWindow::ApplyPerspective(Perspective p) {
     const bool processing = (p == Perspective::Processing);
     if (inspectorDock) inspectorDock->setVisible(true);
     if (settingsDock) settingsDock->setVisible(processing);
-    if (processingDock) processingDock->setVisible(processing);
     if (imageStripDock) imageStripDock->setVisible(processing);
+    if (processingDock && !processing) processingDock->hide();   // shows only when a job starts
     for (auto *d : findChildren<QDockWidget *>())
         if (d->objectName().startsWith("datasetInfoDock"))
             d->setVisible(processing);
diff --git a/viewer/widgets/JFJochViewerImageStrip.cpp b/viewer/widgets/JFJochViewerImageStrip.cpp
index 8fc38461..607aaa34 100644
--- a/viewer/widgets/JFJochViewerImageStrip.cpp
+++ b/viewer/widgets/JFJochViewerImageStrip.cpp
@@ -14,6 +14,7 @@
 
 #include <algorithm>
 #include <numeric>
+#include <cmath>
 
 JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent) {
     auto *layout = new QVBoxLayout(this);
@@ -25,6 +26,8 @@ JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent
     mode_->addItem("Evenly spaced", 0);
     mode_->addItem("Most spots", 1);
     mode_->addItem("Indexed", 2);
+    mode_->addItem("Resolution", 3);     // representatives across the resolution range
+    mode_->addItem("Background", 4);      // representatives across the background range
     controls->addWidget(mode_);
     spots_ = new QCheckBox("Spots", this);
     spots_->setChecked(true);
@@ -76,6 +79,20 @@ QVector<qint64> JFJochViewerImageStrip::ComputeRepresentatives() const {
             result.push_back(N == 1 ? 0 : static_cast<int64_t>(i) * (total - 1) / (N - 1));
     };
 
+    // Pick N images that span a metric's distribution (sort by value, sample evenly across it) —
+    // a quick "histogram representative" selection.
+    auto spread = [&](const std::vector<float> &metric) {
+        std::vector<std::pair<float, int64_t>> vals;
+        for (size_t i = 0; i < metric.size(); ++i)
+            if (std::isfinite(metric[i]))
+                vals.push_back({metric[i], static_cast<int64_t>(i)});
+        if (vals.empty()) { evenly(); return; }
+        std::sort(vals.begin(), vals.end());
+        const int n = static_cast<int>(std::min<size_t>(N, vals.size()));
+        for (int i = 0; i < n; ++i)
+            result.push_back(vals[n == 1 ? 0 : static_cast<size_t>(i) * (vals.size() - 1) / (n - 1)].second);
+    };
+
     if (mode == 1 && !sc.empty()) {                 // most spots
         std::vector<int64_t> idx(sc.size());
         std::iota(idx.begin(), idx.end(), 0);
@@ -96,6 +113,10 @@ QVector<qint64> JFJochViewerImageStrip::ComputeRepresentatives() const {
             for (int i = 0; i < n; ++i)
                 result.push_back(indexed[n == 1 ? 0 : static_cast<size_t>(i) * (indexed.size() - 1) / (n - 1)]);
         }
+    } else if (mode == 3 && !dataset_->resolution_estimate.empty()) {   // resolution spread
+        spread(dataset_->resolution_estimate);
+    } else if (mode == 4 && !dataset_->bkg_estimate.empty()) {          // background spread
+        spread(dataset_->bkg_estimate);
     } else {
         evenly();
     }
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 0fc02790..6f5cf5be 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -295,6 +295,7 @@ void JFJochProcessingJobsWindow::newJob() {
 
     job_timer_.start();
     controller_->start(inputs.file, experiment, inputs.pixel_mask, config);
+    emit jobStarted();
     emit writeStatusBar("Started processing job " + label);
 }
 
diff --git a/viewer/windows/JFJochProcessingJobsWindow.h b/viewer/windows/JFJochProcessingJobsWindow.h
index 653dd3a8..dc65f74c 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.h
+++ b/viewer/windows/JFJochProcessingJobsWindow.h
@@ -34,6 +34,7 @@ signals:
     void writeStatusBar(QString message, int timeout_ms = 0);
     // Live per-image results while a job runs, for the dataset-info plots (nullptr clears it).
     void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
+    void jobStarted();   // a reprocessing job was launched — reveal the (hidden-by-default) panel
 
 public slots:
     void onHttpConnectionChanged(bool connected, QString addr);
-- 
2.52.0


From 164c03f1cef084b8ef7e06d944f653ee4245cad2 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 14:07:31 +0200
Subject: [PATCH 213/228] viewer: soften heights, stochastic strip selection,
 stable on live sync
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Address the review on the image strip / hit feed:

- Height constraints: JFJochSimpleChartView used a hard setFixedHeight(300) and,
  being a page in the dataset-info stack, forced the whole plot dock (and thus
  the window) taller than the screen once the strip was stacked below. Make it a
  soft minimum (120). Wrap the settings dock in a QScrollArea so its content can
  scroll instead of forcing window height. Smaller strip thumbnails (96) and
  lower default bottom-dock heights. The window no longer grows past its
  requested size.
- Stochastic selection: representatives are now picked at random within N equal
  bins (over image index, or a metric's sorted order), and a Refresh button
  re-rolls a fresh set — avoiding deterministic-spacing artefacts. "Most spots"
  stays deterministic; "Indexed" becomes spaced-random.
- Live stability: the strip stores dataset updates but only rebuilds on file
  open (worker fileOpened) / mode / Spots / Refresh, so HTTP sync image updates
  no longer trigger constant thumbnail refetching.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp             | 11 ++-
 viewer/charts/JFJochSimpleChartView.cpp   |  2 +-
 viewer/widgets/JFJochViewerImageStrip.cpp | 81 +++++++++++++++--------
 viewer/widgets/JFJochViewerImageStrip.h   |  1 +
 4 files changed, 63 insertions(+), 32 deletions(-)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 7e5d219a..6d8daabb 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -496,10 +496,15 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     // into the running analysis so edits re-run on the current image / dataset.
     auto *settingsPanel = new JFJochViewerSettingsDock(spot_finding_settings, indexing_settings,
                                                        experiment.GetAzimuthalIntegrationSettings(), this);
+    auto *settingsScroll = new QScrollArea(this);
+    settingsScroll->setWidget(settingsPanel);
+    settingsScroll->setWidgetResizable(true);
+    settingsScroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
+    settingsScroll->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded);
     settingsDock = new QDockWidget("Settings", this);
     settingsDock->setObjectName("settingsDock");
     settingsDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
-    settingsDock->setWidget(settingsPanel);
+    settingsDock->setWidget(settingsScroll);   // scrollable: don't force the window taller than the screen
     addDockWidget(Qt::LeftDockWidgetArea, settingsDock);
     menuBar->AddDockEntry(settingsDock, "Settings");
 
@@ -547,11 +552,13 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     addDockWidget(Qt::BottomDockWidgetArea, imageStripDock);
     if (lastDatasetInfoDock) {
         splitDockWidget(lastDatasetInfoDock, imageStripDock, Qt::Vertical);
-        resizeDocks({lastDatasetInfoDock, imageStripDock}, {340, 180}, Qt::Vertical);
+        resizeDocks({lastDatasetInfoDock, imageStripDock}, {260, 140}, Qt::Vertical);
     }
     menuBar->AddDockEntry(imageStripDock, "Image strip");
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             imageStrip, &JFJochViewerImageStrip::datasetLoaded);
+    connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
+            imageStrip, &JFJochViewerImageStrip::resetForNewFile);
     connect(imageStrip, &JFJochViewerImageStrip::requestThumbnails,
             reading_worker, &JFJochImageReadingWorker::RenderThumbnails);
     connect(reading_worker, &JFJochImageReadingWorker::thumbnailReady,
diff --git a/viewer/charts/JFJochSimpleChartView.cpp b/viewer/charts/JFJochSimpleChartView.cpp
index d964d821..d8622dd1 100644
--- a/viewer/charts/JFJochSimpleChartView.cpp
+++ b/viewer/charts/JFJochSimpleChartView.cpp
@@ -12,7 +12,7 @@
 JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
     : QChartView(new QChart(), parent) {
     chart()->legend()->hide();
-    setFixedHeight(300);
+    setMinimumHeight(120);   // soft floor: let the host dock/window decide the height
     setRenderHint(QPainter::Antialiasing);
     setMouseTracking(true);
     //setRubberBand(QChartView::RubberBand::HorizontalRubberBand);
diff --git a/viewer/widgets/JFJochViewerImageStrip.cpp b/viewer/widgets/JFJochViewerImageStrip.cpp
index 607aaa34..785daf13 100644
--- a/viewer/widgets/JFJochViewerImageStrip.cpp
+++ b/viewer/widgets/JFJochViewerImageStrip.cpp
@@ -11,6 +11,8 @@
 #include <QToolButton>
 #include <QLabel>
 #include <QPixmap>
+#include <QStyle>
+#include <QRandomGenerator>
 
 #include <algorithm>
 #include <numeric>
@@ -33,8 +35,15 @@ JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent
     spots_->setChecked(true);
     spots_->setToolTip("Overlay found spots — a real pattern reads like a constellation");
     controls->addWidget(spots_);
+    auto *refresh = new QToolButton(this);
+    refresh->setIcon(style()->standardIcon(QStyle::SP_BrowserReload));
+    refresh->setAutoRaise(true);
+    refresh->setCursor(Qt::PointingHandCursor);
+    refresh->setToolTip("Re-roll the representative selection");
+    controls->addWidget(refresh);
     controls->addStretch();
     layout->addLayout(controls);
+    connect(refresh, &QToolButton::clicked, this, [this] { Rebuild(); });
 
     auto *scroll = new QScrollArea(this);
     scroll->setWidgetResizable(true);
@@ -52,8 +61,14 @@ JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent
 }
 
 void JFJochViewerImageStrip::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
+    // Store the latest dataset (metrics may update during live sync / re-analysis) but do NOT
+    // rebuild here — that would refetch thumbnails on every HTTP image update. Rebuilding happens
+    // on file open (resetForNewFile, which fires just after this) and on mode / Spots / Refresh.
     dataset_ = std::move(dataset);
-    Rebuild();
+}
+
+void JFJochViewerImageStrip::resetForNewFile() {
+    Rebuild();   // a new file/stream opened; dataset_ was just set by datasetLoaded
 }
 
 void JFJochViewerImageStrip::thumbnailReady(qint64 image_number, QImage thumb) {
@@ -71,29 +86,43 @@ QVector<qint64> JFJochViewerImageStrip::ComputeRepresentatives() const {
         return result;
     const int N = static_cast<int>(std::min<int64_t>(8, total));
     const int mode = mode_->currentIndex();
-    const auto &sc = dataset_->spot_count;
-    const auto &sci = dataset_->spot_count_indexed;
+    auto *rng = QRandomGenerator::global();
 
-    auto evenly = [&] {
-        for (int i = 0; i < N; ++i)
-            result.push_back(N == 1 ? 0 : static_cast<int64_t>(i) * (total - 1) / (N - 1));
+    // Pick one random image from each of N equal bins over an ordered candidate list. Stochastic,
+    // so Refresh re-rolls a fresh set and deterministic-spacing artefacts are avoided.
+    auto binnedRandom = [&](const std::vector<int64_t> &candidates) {
+        const size_t M = candidates.size();
+        if (M == 0)
+            return;
+        const int n = static_cast<int>(std::min<size_t>(N, M));
+        for (int i = 0; i < n; ++i) {
+            const size_t lo = static_cast<size_t>(i) * M / n;
+            size_t hi = static_cast<size_t>(i + 1) * M / n;
+            if (hi <= lo) hi = lo + 1;
+            result.push_back(candidates[lo + rng->bounded(static_cast<quint32>(hi - lo))]);
+        }
     };
 
-    // Pick N images that span a metric's distribution (sort by value, sample evenly across it) —
-    // a quick "histogram representative" selection.
-    auto spread = [&](const std::vector<float> &metric) {
+    // Image indices ordered by a metric (finite values only), low to high.
+    auto orderedByMetric = [](const std::vector<float> &metric) {
         std::vector<std::pair<float, int64_t>> vals;
         for (size_t i = 0; i < metric.size(); ++i)
             if (std::isfinite(metric[i]))
                 vals.push_back({metric[i], static_cast<int64_t>(i)});
-        if (vals.empty()) { evenly(); return; }
         std::sort(vals.begin(), vals.end());
-        const int n = static_cast<int>(std::min<size_t>(N, vals.size()));
-        for (int i = 0; i < n; ++i)
-            result.push_back(vals[n == 1 ? 0 : static_cast<size_t>(i) * (vals.size() - 1) / (n - 1)].second);
+        std::vector<int64_t> idx;
+        idx.reserve(vals.size());
+        for (const auto &v : vals) idx.push_back(v.second);
+        return idx;
     };
 
-    if (mode == 1 && !sc.empty()) {                 // most spots
+    std::vector<int64_t> allIndices(total);
+    std::iota(allIndices.begin(), allIndices.end(), 0);
+
+    const auto &sc = dataset_->spot_count;
+    const auto &sci = dataset_->spot_count_indexed;
+
+    if (mode == 1 && !sc.empty()) {                 // most spots (deterministic top-N)
         std::vector<int64_t> idx(sc.size());
         std::iota(idx.begin(), idx.end(), 0);
         const size_t n = std::min<size_t>(N, idx.size());
@@ -102,23 +131,17 @@ QVector<qint64> JFJochViewerImageStrip::ComputeRepresentatives() const {
         idx.resize(n);
         std::sort(idx.begin(), idx.end());
         for (int64_t i : idx) result.push_back(i);
-    } else if (mode == 2 && !sci.empty()) {         // indexed images, evenly sampled
+    } else if (mode == 2 && !sci.empty()) {         // indexed images, spaced random
         std::vector<int64_t> indexed;
         for (size_t i = 0; i < sci.size(); ++i)
             if (sci[i] > 0) indexed.push_back(static_cast<int64_t>(i));
-        if (indexed.empty()) {
-            evenly();
-        } else {
-            const int n = static_cast<int>(std::min<size_t>(N, indexed.size()));
-            for (int i = 0; i < n; ++i)
-                result.push_back(indexed[n == 1 ? 0 : static_cast<size_t>(i) * (indexed.size() - 1) / (n - 1)]);
-        }
-    } else if (mode == 3 && !dataset_->resolution_estimate.empty()) {   // resolution spread
-        spread(dataset_->resolution_estimate);
-    } else if (mode == 4 && !dataset_->bkg_estimate.empty()) {          // background spread
-        spread(dataset_->bkg_estimate);
-    } else {
-        evenly();
+        binnedRandom(indexed.empty() ? allIndices : indexed);
+    } else if (mode == 3 && !dataset_->resolution_estimate.empty()) {
+        binnedRandom(orderedByMetric(dataset_->resolution_estimate));
+    } else if (mode == 4 && !dataset_->bkg_estimate.empty()) {
+        binnedRandom(orderedByMetric(dataset_->bkg_estimate));
+    } else {                                        // evenly spaced (random within each bin)
+        binnedRandom(allIndices);
     }
     return result;
 }
@@ -140,7 +163,7 @@ void JFJochViewerImageStrip::Rebuild() {
     for (qint64 n : reps) {
         auto *btn = new QToolButton(this);
         btn->setToolButtonStyle(Qt::ToolButtonTextUnderIcon);
-        btn->setIconSize(QSize(120, 120));
+        btn->setIconSize(QSize(96, 96));
         btn->setText(QString::number(n + 1));
         btn->setAutoRaise(true);
         btn->setCursor(Qt::PointingHandCursor);
diff --git a/viewer/widgets/JFJochViewerImageStrip.h b/viewer/widgets/JFJochViewerImageStrip.h
index fae90657..2a8df93d 100644
--- a/viewer/widgets/JFJochViewerImageStrip.h
+++ b/viewer/widgets/JFJochViewerImageStrip.h
@@ -25,6 +25,7 @@ public:
 public slots:
     void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
     void thumbnailReady(qint64 image_number, QImage thumb);
+    void resetForNewFile();   // a new file/stream opened: rebuild once, then stay put on live updates
 
 signals:
     void requestThumbnails(QVector<qint64> image_numbers, bool show_spots);
-- 
2.52.0


From 94b66348c55598d8107e585d9d5f15d64b7de85b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 14:55:47 +0200
Subject: [PATCH 214/228] viewer: fix thumbnail render crash (worker-thread
 exception / LUT UB)

The image-strip thumbnail renderer could take the whole viewer down:

- Only the image load was wrapped in try/catch; the rest of RenderThumbnail_i
  (pixel access, LUT mapping, QPainter) ran unguarded on the worker thread, so
  any exception there called std::terminate. Wrap the entire function.
- std::clamp(idx, 0, lutSize - 1) is undefined behaviour when the colour LUT is
  empty (lo > hi). Bail out early if the LUT has no entries.

A click landing while a later thumbnail is still rendering surfaced this.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp | 123 +++++++++++++++-------------
 1 file changed, 66 insertions(+), 57 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 6a7e2f70..4658cf4d 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -1057,73 +1057,82 @@ void JFJochImageReadingWorker::RenderThumbnails(QVector<qint64> image_numbers, b
 }
 
 QImage JFJochImageReadingWorker::RenderThumbnail_i(int64_t image_number, bool show_spots) {
-    std::shared_ptr<JFJochReaderImage> img;
+    // Everything runs inside one try: an uncaught exception here would be on the worker thread and
+    // would std::terminate the whole app. On any failure we just skip this thumbnail.
     try {
-        QMutexLocker locker(&m);
-        if (http_mode || image_number < 0 || image_number >= total_images)
+        std::shared_ptr<JFJochReaderImage> img;
+        {
+            QMutexLocker locker(&m);
+            if (http_mode || image_number < 0 || image_number >= total_images)
+                return {};
+            img = file_reader.LoadImage(image_number, 1);
+        }
+        if (!img)
             return {};
-        img = file_reader.LoadImage(image_number, 1);
-    } catch (const std::exception &e) {
-        logger.Debug("Thumbnail load failed for image {}: {}", image_number, e.what());
-        return {};
-    }
-    if (!img)
-        return {};
 
-    const int W = static_cast<int>(img->Dataset().experiment.GetXPixelsNum());
-    const int H = static_cast<int>(img->Dataset().experiment.GetYPixelsNum());
-    const auto &px = img->Image();
-    if (W <= 0 || H <= 0 || static_cast<int64_t>(px.size()) < static_cast<int64_t>(W) * H)
-        return {};
+        const int W = static_cast<int>(img->Dataset().experiment.GetXPixelsNum());
+        const int H = static_cast<int>(img->Dataset().experiment.GetYPixelsNum());
+        const auto &px = img->Image();
+        if (W <= 0 || H <= 0 || static_cast<int64_t>(px.size()) < static_cast<int64_t>(W) * H)
+            return {};
 
-    // Downsample by block-maximum (keeps sharp Bragg spots), then map through the colour-scale LUT.
-    constexpr int maxDim = 120;
-    const double s = static_cast<double>(maxDim) / std::max(W, H);
-    const int tw = std::max(1, static_cast<int>(W * s));
-    const int th = std::max(1, static_cast<int>(H * s));
-    const int bx = std::max(1, W / tw);
-    const int by = std::max(1, H / th);
+        const auto &lut = thumb_color_scale_.LUTData();
+        const int lutSize = static_cast<int>(lut.size());
+        if (lutSize <= 0)
+            return {};
 
-    const float fg = std::max(1.0f, static_cast<float>(img->GetAutoContrastValue()));
-    const auto &lut = thumb_color_scale_.LUTData();
-    const int lutSize = static_cast<int>(lut.size());
-    const float invRange = fg > 0 ? (lutSize - 1) / fg : 0.0f;
-    const rgb gap = thumb_color_scale_.Apply(ColorScaleSpecial::Gap);
+        // Downsample by block-maximum (keeps sharp Bragg spots), then map through the LUT.
+        constexpr int maxDim = 120;
+        const double s = static_cast<double>(maxDim) / std::max(W, H);
+        const int tw = std::max(1, static_cast<int>(W * s));
+        const int th = std::max(1, static_cast<int>(H * s));
+        const int bx = std::max(1, W / tw);
+        const int by = std::max(1, H / th);
 
-    QImage out(tw, th, QImage::Format_RGB32);
-    for (int ty = 0; ty < th; ++ty) {
-        QRgb *line = reinterpret_cast<QRgb *>(out.scanLine(ty));
-        const int y1 = std::min(H, ty * by + by);
-        for (int tx = 0; tx < tw; ++tx) {
-            const int x1 = std::min(W, tx * bx + bx);
-            int32_t best = 0;
-            bool any = false;
-            for (int yy = ty * by; yy < y1; ++yy)
-                for (int xx = tx * bx; xx < x1; ++xx) {
-                    const int32_t v = px[yy * W + xx];
-                    if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE) continue;
-                    if (v == SATURATED_PXL_VALUE) { best = static_cast<int32_t>(fg); any = true; continue; }
-                    if (!any || v > best) { best = v; any = true; }
+        const float fg = std::max(1.0f, static_cast<float>(img->GetAutoContrastValue()));
+        const float invRange = (lutSize - 1) / fg;
+        const rgb gap = thumb_color_scale_.Apply(ColorScaleSpecial::Gap);
+
+        QImage out(tw, th, QImage::Format_RGB32);
+        for (int ty = 0; ty < th; ++ty) {
+            QRgb *line = reinterpret_cast<QRgb *>(out.scanLine(ty));
+            const int y1 = std::min(H, ty * by + by);
+            for (int tx = 0; tx < tw; ++tx) {
+                const int x1 = std::min(W, tx * bx + bx);
+                int32_t best = 0;
+                bool any = false;
+                for (int yy = ty * by; yy < y1; ++yy)
+                    for (int xx = tx * bx; xx < x1; ++xx) {
+                        const int32_t v = px[yy * W + xx];
+                        if (v == GAP_PXL_VALUE || v == ERROR_PXL_VALUE) continue;
+                        if (v == SATURATED_PXL_VALUE) { best = static_cast<int32_t>(fg); any = true; continue; }
+                        if (!any || v > best) { best = v; any = true; }
+                    }
+                rgb c;
+                if (!any) {
+                    c = gap;
+                } else {
+                    int idx = static_cast<int>(std::max(0, best) * invRange + 0.5f);
+                    idx = std::clamp(idx, 0, lutSize - 1);
+                    c = lut[idx];
                 }
-            rgb c;
-            if (!any) {
-                c = gap;
-            } else {
-                int idx = static_cast<int>(std::max(0, best) * invRange + 0.5f);
-                idx = std::clamp(idx, 0, lutSize - 1);
-                c = lut[idx];
+                line[tx] = qRgb(c.r, c.g, c.b);
             }
-            line[tx] = qRgb(c.r, c.g, c.b);
         }
-    }
 
-    if (show_spots) {
-        QPainter p(&out);
-        p.setRenderHint(QPainter::Antialiasing);
-        for (const auto &sp : img->ImageData().spots) {
-            p.setPen(QPen(sp.indexed ? thumb_feature_color_ : thumb_spot_color_, 1.0));
-            p.drawEllipse(QPointF(sp.x * s, sp.y * s), 1.6, 1.6);
+        if (show_spots) {
+            QPainter p(&out);
+            p.setRenderHint(QPainter::Antialiasing);
+            for (const auto &sp : img->ImageData().spots) {
+                p.setPen(QPen(sp.indexed ? thumb_feature_color_ : thumb_spot_color_, 1.0));
+                p.drawEllipse(QPointF(sp.x * s, sp.y * s), 1.6, 1.6);
+            }
         }
+        return out;
+    } catch (const std::exception &e) {
+        logger.Debug("Thumbnail render failed for image {}: {}", image_number, e.what());
+        return {};
+    } catch (...) {
+        return {};
     }
-    return out;
 }
-- 
2.52.0


From c5457e2e270c1abcf4eab9c48dc4e30a37a3d155 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 15:11:24 +0200
Subject: [PATCH 215/228] viewer: keep plot axis labels readable when
 compressed

When the plot dock was short, Qt Charts dropped the axis labels first, making
the plot hard to read.

- Reclaim Qt Charts' outer graphics-layout padding and trim the inner margins
  (both chart views) so the plot and its labels get the available space.
- Raise the chart minimum height (dataset-info 80 -> 140, per-image 120 -> 140)
  so the dock can't be squeezed below the point where the axis labels fit.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp           | 2 +-
 viewer/charts/JFJochDatasetInfoChartView.cpp | 6 ++++++
 viewer/charts/JFJochSimpleChartView.cpp      | 5 ++++-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index bc0cb932..774ce884 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -52,7 +52,7 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
 
     stack = new QStackedWidget(this);
     chart_view = new JFJochDatasetInfoChartView(this);
-    chart_view->setMinimumHeight(80);   // low floor so the bottom dock resizes freely (default is set via resizeDocks)
+    chart_view->setMinimumHeight(140);   // keep enough room for the axis labels even when compressed
     grid_scan_image = new JFJochGridScanImage(this);
     image_chart = new JFJochViewerSidePanelChart(this);   // per-image profiles, folded in from the side panel
 
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index 77806db2..46486046 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -6,12 +6,18 @@
 #include <QClipboard>
 #include <QCategoryAxis>
 #include <QtCharts/QLegendMarker>
+#include <QGraphicsLayout>
 
 #include "JFJochDatasetInfoChartView.h"
 
 JFJochDatasetInfoChartView::JFJochDatasetInfoChartView(QWidget *parent)
     : QChartView(new QChart(), parent) {
     chart()->legend()->hide();
+    // Reclaim Qt Charts' outer layout padding and trim the inner margins so the axis labels keep
+    // their room even when the dock is short (otherwise they are the first thing Qt drops).
+    chart()->layout()->setContentsMargins(0, 0, 0, 0);
+    chart()->setMargins(QMargins(2, 2, 6, 2));
+    chart()->setBackgroundRoundness(0);
     setRenderHint(QPainter::Antialiasing);
    // setRubberBand(QChartView::RubberBand::RectangleRubberBand);
     setMouseTracking(true);
diff --git a/viewer/charts/JFJochSimpleChartView.cpp b/viewer/charts/JFJochSimpleChartView.cpp
index d8622dd1..35b582fa 100644
--- a/viewer/charts/JFJochSimpleChartView.cpp
+++ b/viewer/charts/JFJochSimpleChartView.cpp
@@ -8,11 +8,14 @@
 #include <QApplication>
 #include <QCategoryAxis>
 #include <QRegularExpression>
+#include <QGraphicsLayout>
 
 JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
     : QChartView(new QChart(), parent) {
     chart()->legend()->hide();
-    setMinimumHeight(120);   // soft floor: let the host dock/window decide the height
+    chart()->layout()->setContentsMargins(0, 0, 0, 0);   // reclaim padding for the plot + labels
+    chart()->setMargins(QMargins(2, 2, 6, 2));
+    setMinimumHeight(140);   // soft floor: enough for the axis labels to stay readable
     setRenderHint(QPainter::Antialiasing);
     setMouseTracking(true);
     //setRubberBand(QChartView::RubberBand::HorizontalRubberBand);
-- 
2.52.0


From 83d006e79baad649c32a0c5d90a150f51518ed89 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 15:31:16 +0200
Subject: [PATCH 216/228] viewer: "+ Plot" button + strip fits height with
 in-bitmap numbers

Plots:
- A "+ Plot" button on the dataset-info panel spawns another plot dock, placed
  beside the previous one (horizontal split) so several metrics can be watched
  side by side. Same path as the Charts menu, now one click away.

Image strip:
- The image number is painted into the thumbnail bitmap (coral badge, top-left)
  instead of a text label under the icon, so no height is lost to it.
- Thumbnails are icon-only and scale to the available dock height (resizeEvent),
  so the strip never needs more room than it has; lowered its minimum.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp       | 19 ++++++++++++
 viewer/JFJochViewerDatasetInfo.cpp        | 11 ++++++-
 viewer/JFJochViewerDatasetInfo.h          |  1 +
 viewer/JFJochViewerWindow.cpp             |  4 +++
 viewer/widgets/JFJochViewerImageStrip.cpp | 36 ++++++++++++++++-------
 viewer/widgets/JFJochViewerImageStrip.h   |  7 +++++
 6 files changed, 67 insertions(+), 11 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index 4658cf4d..f304df4e 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -22,6 +22,7 @@
 #include <QMutexLocker>
 #include <QFileInfo>
 #include <QPainter>
+#include <QFontMetrics>
 #include <algorithm>
 
 #include "../preview/JFJochTIFF.h"
@@ -1128,6 +1129,24 @@ QImage JFJochImageReadingWorker::RenderThumbnail_i(int64_t image_number, bool sh
                 p.drawEllipse(QPointF(sp.x * s, sp.y * s), 1.6, 1.6);
             }
         }
+
+        // Image-number badge in the top-left, so the strip needs no text label (and loses no height).
+        {
+            QPainter p(&out);
+            p.setRenderHint(QPainter::Antialiasing);
+            QFont f = p.font();
+            f.setBold(true);
+            f.setPixelSize(11);
+            p.setFont(f);
+            const QString label = QString::number(image_number + 1);
+            const QRect tb = QFontMetrics(f).boundingRect(label);
+            const QRect badge(2, 2, tb.width() + 8, tb.height() + 2);
+            p.setPen(Qt::NoPen);
+            p.setBrush(QColor(0xFA, 0x72, 0x68));        // coral
+            p.drawRoundedRect(badge, 3, 3);
+            p.setPen(Qt::white);
+            p.drawText(badge, Qt::AlignCenter, label);
+        }
         return out;
     } catch (const std::exception &e) {
         logger.Debug("Thumbnail render failed for image {}: {}", image_number, e.what());
diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 774ce884..57f999c7 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -46,9 +46,18 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
     image_button->setFixedWidth(100);
     image_button->setCheckable(true);
 
+    auto add_plot_button = new QPushButton("+ Plot", this);
+    add_plot_button->setFixedWidth(80);
+    add_plot_button->setToolTip("Open another dataset-info plot, side by side");
+    add_plot_button->setStyleSheet(
+        "QPushButton { background-color:#1F3A5F; color:white; font-weight:bold; border:none;"
+        " border-radius:3px; padding:3px 8px; } QPushButton:hover { background-color:#16314F; }");
+    connect(add_plot_button, &QPushButton::clicked, this, &JFJochViewerDatasetInfo::addPlot);
+
     layout->addWidget(reset_button, 0, 2);
     layout->addWidget(grid_button, 0, 3);
     layout->addWidget(image_button, 0, 4);
+    layout->addWidget(add_plot_button, 0, 5);
 
     stack = new QStackedWidget(this);
     chart_view = new JFJochDatasetInfoChartView(this);
@@ -60,7 +69,7 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
     stack->addWidget(grid_scan_image);
     stack->addWidget(image_chart);
 
-    layout->addWidget(stack, 1, 0, 1, 5);
+    layout->addWidget(stack, 1, 0, 1, 6);
 
     connect(chart_view, &JFJochDatasetInfoChartView::imageSelected,
             this, &JFJochViewerDatasetInfo::imageSelectedInChart);
diff --git a/viewer/JFJochViewerDatasetInfo.h b/viewer/JFJochViewerDatasetInfo.h
index e3d21d1d..5a48e03c 100644
--- a/viewer/JFJochViewerDatasetInfo.h
+++ b/viewer/JFJochViewerDatasetInfo.h
@@ -41,6 +41,7 @@ class JFJochViewerDatasetInfo : public QWidget {
 signals:
     void imageSelected(int64_t number, int64_t summation);
     void writeStatusBar(QString string, int timeout_ms = 0);
+    void addPlot();   // request another dataset-info plot dock
 
 public:
     explicit JFJochViewerDatasetInfo(QWidget *parent = nullptr);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 6d8daabb..041e3fa0 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -640,6 +640,9 @@ void JFJochViewerWindow::NewDatasetInfo() {
     dock->setAttribute(Qt::WA_DeleteOnClose);
     dock->setWidget(info);
     addDockWidget(Qt::BottomDockWidgetArea, dock);
+    // Place additional plots beside the previous one so "+ Plot" gives a visible row of plots.
+    if (lastDatasetInfoDock)
+        splitDockWidget(lastDatasetInfoDock, dock, Qt::Horizontal);
     lastDatasetInfoDock = dock;
 
     // Wire signals like the initial dataset_info
@@ -655,6 +658,7 @@ void JFJochViewerWindow::NewDatasetInfo() {
             info, &JFJochViewerDatasetInfo::liveRunUpdated);
     connect(info, &JFJochViewerDatasetInfo::imageSelected,
             reading_worker, &JFJochImageReadingWorker::LoadImage);
+    connect(info, &JFJochViewerDatasetInfo::addPlot, this, &JFJochViewerWindow::NewDatasetInfo);
     connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
             info, &JFJochViewerDatasetInfo::setColorMap);
     connect(info, &JFJochViewerDatasetInfo::writeStatusBar,
diff --git a/viewer/widgets/JFJochViewerImageStrip.cpp b/viewer/widgets/JFJochViewerImageStrip.cpp
index 785daf13..1c845715 100644
--- a/viewer/widgets/JFJochViewerImageStrip.cpp
+++ b/viewer/widgets/JFJochViewerImageStrip.cpp
@@ -13,10 +13,12 @@
 #include <QPixmap>
 #include <QStyle>
 #include <QRandomGenerator>
+#include <QResizeEvent>
 
 #include <algorithm>
 #include <numeric>
 #include <cmath>
+#include <utility>
 
 JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent) {
     auto *layout = new QVBoxLayout(this);
@@ -45,16 +47,17 @@ JFJochViewerImageStrip::JFJochViewerImageStrip(QWidget *parent) : QWidget(parent
     layout->addLayout(controls);
     connect(refresh, &QToolButton::clicked, this, [this] { Rebuild(); });
 
-    auto *scroll = new QScrollArea(this);
-    scroll->setWidgetResizable(true);
-    scroll->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
-    scroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAsNeeded);
-    auto *stripWidget = new QWidget(scroll);
+    scroll_ = new QScrollArea(this);
+    scroll_->setWidgetResizable(true);
+    scroll_->setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
+    scroll_->setHorizontalScrollBarPolicy(Qt::ScrollBarAsNeeded);
+    scroll_->setMinimumHeight(48);   // let the dock shrink; thumbnails scale to fit
+    auto *stripWidget = new QWidget(scroll_);
     strip_ = new QHBoxLayout(stripWidget);
     strip_->setContentsMargins(0, 0, 0, 0);
     strip_->addStretch();
-    scroll->setWidget(stripWidget);
-    layout->addWidget(scroll);
+    scroll_->setWidget(stripWidget);
+    layout->addWidget(scroll_);
 
     connect(mode_, &QComboBox::currentIndexChanged, this, [this] { Rebuild(); });
     connect(spots_, &QCheckBox::toggled, this, [this] { Rebuild(); });
@@ -162,9 +165,7 @@ void JFJochViewerImageStrip::Rebuild() {
     int pos = 0;
     for (qint64 n : reps) {
         auto *btn = new QToolButton(this);
-        btn->setToolButtonStyle(Qt::ToolButtonTextUnderIcon);
-        btn->setIconSize(QSize(96, 96));
-        btn->setText(QString::number(n + 1));
+        btn->setToolButtonStyle(Qt::ToolButtonIconOnly);   // the image number is drawn in the bitmap
         btn->setAutoRaise(true);
         btn->setCursor(Qt::PointingHandCursor);
         btn->setToolTip(QStringLiteral("Open image %1").arg(n + 1));
@@ -172,5 +173,20 @@ void JFJochViewerImageStrip::Rebuild() {
         strip_->insertWidget(pos++, btn);
         slots_[n] = btn;
     }
+    UpdateThumbnailSize();
     emit requestThumbnails(reps, spots_->isChecked());
 }
+
+void JFJochViewerImageStrip::UpdateThumbnailSize() {
+    if (!scroll_)
+        return;
+    // Scale the thumbnails to the available height so the strip never needs more room than it has.
+    const int h = std::clamp(scroll_->viewport()->height() - 4, 40, 240);
+    for (auto *btn : std::as_const(slots_))
+        btn->setIconSize(QSize(h, h));
+}
+
+void JFJochViewerImageStrip::resizeEvent(QResizeEvent *event) {
+    QWidget::resizeEvent(event);
+    UpdateThumbnailSize();
+}
diff --git a/viewer/widgets/JFJochViewerImageStrip.h b/viewer/widgets/JFJochViewerImageStrip.h
index 2a8df93d..f1b5404b 100644
--- a/viewer/widgets/JFJochViewerImageStrip.h
+++ b/viewer/widgets/JFJochViewerImageStrip.h
@@ -13,6 +13,8 @@ class QComboBox;
 class QCheckBox;
 class QHBoxLayout;
 class QToolButton;
+class QScrollArea;
+class QResizeEvent;
 
 // A strip of thumbnails for a handful of representative images (evenly spaced, most spots, or
 // indexed), optionally overlaid with spots so a real pattern reads like a constellation. Clicking
@@ -31,13 +33,18 @@ signals:
     void requestThumbnails(QVector<qint64> image_numbers, bool show_spots);
     void imageSelected(int64_t image_number, int64_t summation);
 
+protected:
+    void resizeEvent(QResizeEvent *event) override;
+
 private:
     std::shared_ptr<const JFJochReaderDataset> dataset_;
     QComboBox *mode_ = nullptr;
     QCheckBox *spots_ = nullptr;
+    QScrollArea *scroll_ = nullptr;
     QHBoxLayout *strip_ = nullptr;
     QMap<qint64, QToolButton *> slots_;   // image number -> its thumbnail button
 
     QVector<qint64> ComputeRepresentatives() const;
     void Rebuild();
+    void UpdateThumbnailSize();   // scale thumbnails to the available dock height
 };
-- 
2.52.0


From 6ead87fcce6bf3cebcfcb36b085e7c98da28d869 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:07:35 +0200
Subject: [PATCH 217/228] viewer: per-image plot reuses the dataset-info combo
 (no second combo)

In per-image mode the embedded chart brought its own combo box, so the plot
panel showed two. Drop the per-image chart's combo and drive it from the one
dataset-info combo:

- JFJochViewerSidePanelChart loses its combo; it exposes PlotTypes() (the
  available profiles) and a setPlotType(code) slot, driven externally.
- JFJochViewerDatasetInfo fills its single combo with the per-image plot types
  while in per-image mode (per-dataset metrics otherwise) and routes the
  selection to the chart; dataset/runs/live updates leave the per-image combo
  and plot untouched.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerDatasetInfo.cpp            |  29 ++++-
 viewer/widgets/JFJochViewerSidePanelChart.cpp | 113 ++++++++----------
 viewer/widgets/JFJochViewerSidePanelChart.h   |  23 ++--
 3 files changed, 90 insertions(+), 75 deletions(-)

diff --git a/viewer/JFJochViewerDatasetInfo.cpp b/viewer/JFJochViewerDatasetInfo.cpp
index 57f999c7..cd426c11 100644
--- a/viewer/JFJochViewerDatasetInfo.cpp
+++ b/viewer/JFJochViewerDatasetInfo.cpp
@@ -105,7 +105,9 @@ JFJochViewerDatasetInfo::JFJochViewerDatasetInfo(QWidget *parent) : QWidget(pare
             [this]() {
                 if (image_button->isChecked())
                     grid_button->setChecked(false);
-                combo_box->setEnabled(!image_button->isChecked());   // the metric combo is for the dataset plot
+                UpdateLabels();                  // swap the one combo's contents for the mode
+                combo_box->setCurrentIndex(0);
+                comboBoxSelected(0);             // apply the first option of the new mode
                 UpdateView();
             });
     connect(image_chart, &JFJochViewerSidePanelChart::writeStatusBar,
@@ -121,6 +123,13 @@ void JFJochViewerDatasetInfo::UpdateLabels() {
 
     combo_box->clear();
 
+    // In per-image mode the one combo selects which per-image profile to show (no second combo).
+    if (image_button && image_button->isChecked()) {
+        for (const auto &pt : JFJochViewerSidePanelChart::PlotTypes())
+            combo_box->addItem(pt.first, pt.second);
+        return;
+    }
+
     if (this->dataset) {
         combo_box->addItem("Background estimate", 0);
         combo_box->addItem("Resolution estimate", 7);
@@ -173,6 +182,12 @@ void JFJochViewerDatasetInfo::UpdateLabels() {
 
 void JFJochViewerDatasetInfo::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
     this->dataset = dataset;
+    // Per-image mode: the combo holds plot types and the chart follows the displayed image, so a
+    // new dataset must not repopulate the combo or run the per-dataset plot.
+    if (image_button && image_button->isChecked()) {
+        UpdateView();
+        return;
+    }
     if (dataset) {
         UpdateLabels();
         if (last_selection < combo_box->count())
@@ -312,6 +327,8 @@ void JFJochViewerDatasetInfo::UpdateView() {
 void JFJochViewerDatasetInfo::runsChanged(QVector<RunData> runs, QString active_id) {
     runs_ = std::move(runs);
     active_id_ = std::move(active_id);
+    if (image_button && image_button->isChecked())
+        return;   // per-image mode: runs/overlays are a per-dataset concern
     UpdateLabels();
     if (last_selection < combo_box->count())
         combo_box->setCurrentIndex(last_selection);
@@ -320,11 +337,19 @@ void JFJochViewerDatasetInfo::runsChanged(QVector<RunData> runs, QString active_
 
 void JFJochViewerDatasetInfo::liveRunUpdated(std::shared_ptr<const JFJochReaderDataset> in_dataset) {
     live_run_ = std::move(in_dataset);
+    if (image_button && image_button->isChecked())
+        return;
     UpdatePlot();   // lightweight refresh; no combo rebuild on every live tick
 }
 
 void JFJochViewerDatasetInfo::comboBoxSelected(int index) {
-    UpdatePlot();
+    // The one combo means per-dataset metrics in normal mode, per-image plot types in image mode.
+    if (image_button && image_button->isChecked()) {
+        if (image_chart && index >= 0 && index < combo_box->count())
+            image_chart->setPlotType(combo_box->itemData(index).toInt());
+    } else {
+        UpdatePlot();
+    }
 }
 
 void JFJochViewerDatasetInfo::setColorMap(int color_map) {
diff --git a/viewer/widgets/JFJochViewerSidePanelChart.cpp b/viewer/widgets/JFJochViewerSidePanelChart.cpp
index ed3cea47..a4cb3c79 100644
--- a/viewer/widgets/JFJochViewerSidePanelChart.cpp
+++ b/viewer/widgets/JFJochViewerSidePanelChart.cpp
@@ -6,78 +6,71 @@
 
 JFJochViewerSidePanelChart::JFJochViewerSidePanelChart(QWidget *parent) : QWidget(parent) {
     auto layout = new QVBoxLayout(this);
-
-    combo_box = new QComboBox(this);
-    combo_box->addItem("Azimuthal integration (1D)", 0);
-    combo_box->addItem("Wilson plot", 1);
-    combo_box->addItem("I/sigma", 2);
-    combo_box->addItem("Spots (count)", 5);
-    combo_box->addItem("Spots (intensity)", 6);
-    combo_box->addItem("X-ray fluorescence spectrum", 4);
-
-    layout->addWidget(combo_box);
-
-    connect(combo_box, &QComboBox::currentIndexChanged,
-            this, &JFJochViewerSidePanelChart::comboBoxSelected);
+    layout->setContentsMargins(0, 0, 0, 0);
 
     azint_plot = new JFJochSimpleChartView(this);
-
-    layout->addWidget(azint_plot); // index 0
+    layout->addWidget(azint_plot);
     setLayout(layout);
+
     connect(azint_plot, &JFJochSimpleChartView::writeStatusBar,
-      [&](QString string, int timeout_ms) {
-          emit writeStatusBar(string, timeout_ms);
-      });
+            [&](QString string, int timeout_ms) { emit writeStatusBar(string, timeout_ms); });
 }
 
-void JFJochViewerSidePanelChart::comboBoxSelected(int val) {
+QList<QPair<QString, int>> JFJochViewerSidePanelChart::PlotTypes() {
+    return {
+        {"Azimuthal integration (1D)", 0},
+        {"Wilson plot", 1},
+        {"I/sigma", 2},
+        {"Spots (count)", 5},
+        {"Spots (intensity)", 6},
+        {"X-ray fluorescence spectrum", 4},
+    };
+}
+
+void JFJochViewerSidePanelChart::setPlotType(int code) {
+    plot_type_ = code;
     redrawPlot();
 }
 
 void JFJochViewerSidePanelChart::redrawPlot() {
+    if (!image)
+        return;
+
     std::vector<float> x, y;
-
-    if (image) {
-        auto index = combo_box->currentIndex();
-        switch (combo_box->itemData(index).toInt()) {
-            case 0:
-                x = image->GetAzInt1D_BinToQ();
-                y = image->GetAzInt1D();
-                azint_plot->UpdateData(x, y, "Q [Å^-1]", "", false);
-                break;
-            case 1:
-                x = image->ImageData().integration_B_one_over_d_square;
-                y = image->ImageData().integration_B_logI;
-                azint_plot->UpdateData(x, y, "d [Å]", "ln(&lt;I&gt;)", true);
-
-                break;
-            case 2:
-                x = image->ImageData().integration_Isigma_one_over_d_square;
-                y = image->ImageData().integration_Isigma;
-                azint_plot->UpdateData(x, y, "d [Å]", "I/sigma", true);
-
-                break;
-            case 4:
-                x = image->Dataset().experiment.GetFluorescenceSpectrum().GetEnergy_eV();
-                y = image->Dataset().experiment.GetFluorescenceSpectrum().GetData();
-                for (auto &iter: x)
-                    iter /= 1000.0; // Convert eV to keV
-                azint_plot->UpdateData(x, y, "E [keV]", "", false);
-                break;
-            case 5:
-                x = image->ImageData().spot_plot_one_over_d_square;
-                y = image->ImageData().spot_plot_count;
-                azint_plot->UpdateData(x, y, "d [Å]", "Count", true);
-
-                break;
-            case 6:
-                x = image->ImageData().spot_plot_one_over_d_square;
-                y = image->ImageData().spot_plot_intensity;
-                azint_plot->UpdateData(x, y, "d [Å]", "Count", true);
-                break;
-        }
+    switch (plot_type_) {
+        case 0:
+            x = image->GetAzInt1D_BinToQ();
+            y = image->GetAzInt1D();
+            azint_plot->UpdateData(x, y, "Q [Å^-1]", "", false);
+            break;
+        case 1:
+            x = image->ImageData().integration_B_one_over_d_square;
+            y = image->ImageData().integration_B_logI;
+            azint_plot->UpdateData(x, y, "d [Å]", "ln(&lt;I&gt;)", true);
+            break;
+        case 2:
+            x = image->ImageData().integration_Isigma_one_over_d_square;
+            y = image->ImageData().integration_Isigma;
+            azint_plot->UpdateData(x, y, "d [Å]", "I/sigma", true);
+            break;
+        case 4:
+            x = image->Dataset().experiment.GetFluorescenceSpectrum().GetEnergy_eV();
+            y = image->Dataset().experiment.GetFluorescenceSpectrum().GetData();
+            for (auto &iter: x)
+                iter /= 1000.0; // Convert eV to keV
+            azint_plot->UpdateData(x, y, "E [keV]", "", false);
+            break;
+        case 5:
+            x = image->ImageData().spot_plot_one_over_d_square;
+            y = image->ImageData().spot_plot_count;
+            azint_plot->UpdateData(x, y, "d [Å]", "Count", true);
+            break;
+        case 6:
+            x = image->ImageData().spot_plot_one_over_d_square;
+            y = image->ImageData().spot_plot_intensity;
+            azint_plot->UpdateData(x, y, "d [Å]", "Count", true);
+            break;
     }
-
 }
 
 void JFJochViewerSidePanelChart::loadImage(std::shared_ptr<const JFJochReaderImage> in_image) {
diff --git a/viewer/widgets/JFJochViewerSidePanelChart.h b/viewer/widgets/JFJochViewerSidePanelChart.h
index 42e2ad4a..74141bd2 100644
--- a/viewer/widgets/JFJochViewerSidePanelChart.h
+++ b/viewer/widgets/JFJochViewerSidePanelChart.h
@@ -4,35 +4,32 @@
 #pragma once
 
 #include <QWidget>
-#include <QComboBox>
-#include <QStackedWidget>
+#include <QList>
+#include <QPair>
+#include <QString>
 
 #include "../../reader/JFJochReaderImage.h"
 #include "../charts/JFJochSimpleChartView.h"
-#include "../image_viewer/JFJochAzIntImage.h"
 
+// Per-image profile plot (azimuthal 1D, Wilson, I/sigma, spots, fluorescence). It has no selector
+// of its own — the host (dataset-info dock) drives the plot type via setPlotType, reusing its one
+// combo box.
 class JFJochViewerSidePanelChart : public QWidget {
     Q_OBJECT
-    QStackedWidget *stack = nullptr;
-
     JFJochSimpleChartView *azint_plot = nullptr;
-
     std::shared_ptr<const JFJochReaderImage> image;
-    QComboBox *combo_box;
+    int plot_type_ = 0;
     void redrawPlot();
 
 signals:
     void writeStatusBar(QString string, int timeout_ms = 0);
 
-private slots:
-    void comboBoxSelected(int val);
-
 public:
     JFJochViewerSidePanelChart(QWidget *parent);
+    // The available per-image plots as (label, code), so the host can fill its own combo.
+    static QList<QPair<QString, int>> PlotTypes();
 
 public slots:
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
+    void setPlotType(int code);
 };
-
-
-
-- 
2.52.0


From 9ba8096c0b625b7205cb7da614f8f08eec5dab60 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:13:26 +0200
Subject: [PATCH 218/228] viewer: chart top margin + settings dock width bounds
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- The chart top margin was too tight (2 px), so the highest Y-axis label
  overlapped the top edge; give it 10 px of room (both chart views).
- The settings dock had no width constraints (unlike the inspector), so it
  stretched ugly when widened and would not fold back narrowly. Cap it to
  330–480 px like the inspector.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochViewerWindow.cpp                | 4 ++++
 viewer/charts/JFJochDatasetInfoChartView.cpp | 2 +-
 viewer/charts/JFJochSimpleChartView.cpp      | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 041e3fa0..2a496cec 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -501,6 +501,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     settingsScroll->setWidgetResizable(true);
     settingsScroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
     settingsScroll->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded);
+    // Constrain the width like the inspector, so it neither stretches ugly when widened nor
+    // refuses to fold back narrow.
+    settingsScroll->setMinimumWidth(330);
+    settingsScroll->setMaximumWidth(480);
     settingsDock = new QDockWidget("Settings", this);
     settingsDock->setObjectName("settingsDock");
     settingsDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
diff --git a/viewer/charts/JFJochDatasetInfoChartView.cpp b/viewer/charts/JFJochDatasetInfoChartView.cpp
index 46486046..1e65b1b8 100644
--- a/viewer/charts/JFJochDatasetInfoChartView.cpp
+++ b/viewer/charts/JFJochDatasetInfoChartView.cpp
@@ -16,7 +16,7 @@ JFJochDatasetInfoChartView::JFJochDatasetInfoChartView(QWidget *parent)
     // Reclaim Qt Charts' outer layout padding and trim the inner margins so the axis labels keep
     // their room even when the dock is short (otherwise they are the first thing Qt drops).
     chart()->layout()->setContentsMargins(0, 0, 0, 0);
-    chart()->setMargins(QMargins(2, 2, 6, 2));
+    chart()->setMargins(QMargins(2, 10, 8, 2));   // top room so the highest Y label is not clipped
     chart()->setBackgroundRoundness(0);
     setRenderHint(QPainter::Antialiasing);
    // setRubberBand(QChartView::RubberBand::RectangleRubberBand);
diff --git a/viewer/charts/JFJochSimpleChartView.cpp b/viewer/charts/JFJochSimpleChartView.cpp
index 35b582fa..e5f7524f 100644
--- a/viewer/charts/JFJochSimpleChartView.cpp
+++ b/viewer/charts/JFJochSimpleChartView.cpp
@@ -14,7 +14,7 @@ JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
     : QChartView(new QChart(), parent) {
     chart()->legend()->hide();
     chart()->layout()->setContentsMargins(0, 0, 0, 0);   // reclaim padding for the plot + labels
-    chart()->setMargins(QMargins(2, 2, 6, 2));
+    chart()->setMargins(QMargins(2, 10, 8, 2));   // top room so the highest Y label is not clipped
     setMinimumHeight(140);   // soft floor: enough for the axis labels to stay readable
     setRenderHint(QPainter::Antialiasing);
     setMouseTracking(true);
-- 
2.52.0


From e3bd1a3529a74ae3153239da22aae03265bbcff4 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:21:03 +0200
Subject: [PATCH 219/228] viewer: settings fields fill the panel width (form
 growth policy)

The settings content stopped resizing past ~360 px, leaving dead space when the
dock was widened. Cause: QFormLayout's default field growth policy keeps fields
at their size hint. Set AllNonFixedFieldsGrow on all five forms (geometry, unit
cell, spot finding, indexing, azint) so the fields grow to fill the dock width.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/widgets/JFJochViewerSettingsDock.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/viewer/widgets/JFJochViewerSettingsDock.cpp b/viewer/widgets/JFJochViewerSettingsDock.cpp
index f130c717..7cf819aa 100644
--- a/viewer/widgets/JFJochViewerSettingsDock.cpp
+++ b/viewer/widgets/JFJochViewerSettingsDock.cpp
@@ -62,6 +62,7 @@ JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &sp
 QWidget *JFJochViewerSettingsDock::BuildGeometrySection() {
     auto *section = new CollapsibleSection("Geometry", this);
     auto *geom = new QFormLayout();
+    geom->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);   // fields fill the panel width
 
     energy_ = new NumberLineEdit(1.0, 200.0, 12.4, 4, "keV", this);
     distance_ = new NumberLineEdit(10.0, 5000.0, 100.0, 2, "mm", this);
@@ -108,6 +109,7 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     // --- Unit cell + space group (new: no input existed before) ---
     auto *cellSection = new CollapsibleSection("Unit cell", page);
     auto *cell = new QFormLayout();
+    cell->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
     cellKnown_ = new QCheckBox("Known unit cell", page);
     cell->addRow("", cellKnown_);
     cellA_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
@@ -153,6 +155,7 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     // --- Spot finding ---
     auto *spotSection = new CollapsibleSection("Spot finding", page);
     auto *spot = new QFormLayout();
+    spot->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
     auto *snr = new SliderPlusBox(1.0, 10.0, 0.1, 1, page);
     snr->setValue(spot_.signal_to_noise_threshold);
     auto *count = new SliderPlusBox(0.0, 100.0, 1.0, 0, page);
@@ -174,6 +177,7 @@ QWidget *JFJochViewerSettingsDock::BuildMXPage() {
     // --- Indexing ---
     auto *idxSection = new CollapsibleSection("Indexing", page);
     auto *idx = new QFormLayout();
+    idx->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
     auto *algo = new QComboBox(page);
     algo->addItem("Auto", static_cast<int>(IndexingAlgorithmEnum::Auto));
     algo->addItem("FFBIDX (GPU, known cell)", static_cast<int>(IndexingAlgorithmEnum::FFBIDX));
@@ -211,6 +215,7 @@ QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
 
     auto *azSection = new CollapsibleSection("Azimuthal integration", page);
     auto *az = new QFormLayout();
+    az->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
     auto *lowQ = new SliderPlusBox(1e-5, 10.0, 0.001, 4, page);
     lowQ->setValue(azint_.GetLowQ_recipA());
     auto *highQ = new SliderPlusBox(2e-5, 10.0, 0.001, 4, page);
-- 
2.52.0


From 8eee3dc7856773172e4663f3a2e9d4dd522544df Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 15:04:38 +0200
Subject: [PATCH 220/228] Support providing trimming energies

---
 broker/JFJochBrokerParser.cpp           |  6 ++++++
 common/DetectorSetup.cpp                | 10 ++++++++++
 common/DetectorSetup.h                  |  3 +++
 detector_control/SLSDetectorWrapper.cpp |  5 +++--
 4 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/broker/JFJochBrokerParser.cpp b/broker/JFJochBrokerParser.cpp
index ffb3d092..0dc117cb 100644
--- a/broker/JFJochBrokerParser.cpp
+++ b/broker/JFJochBrokerParser.cpp
@@ -8,6 +8,7 @@
 #include "../image_pusher/HDF5FilePusher.h"
 #include "OpenAPIConvert.h"
 #include "Detector_type.h"
+#include "../cmake-build-release-nogpu/_deps/catch2-src/src/catch2/internal/catch_string_manip.hpp"
 #include "../image_pusher/NonePusher.h"
 #include "../image_pusher/TCPStreamPusher.h"
 
@@ -91,10 +92,15 @@ DetectorSetup ParseDetectorSetup(const org::openapitools::server::model::Detecto
     DetectorSetup setup(geom, detector_type, d.getDescription(), d.getHostname());
 
     auto calib = d.getCalibrationFile();
+    auto trim_energies = d.getTrimEnergiesEV();
     if (!calib.empty()) {
         switch (detector_type) {
             case DetectorType::EIGER:
                 setup.SetTrimFiles(calib);
+                if (trim_energies.empty())
+                    throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                          "Trimming energies not provided");
+                setup.TrimEnergies_eV(trim_energies);
                 break;
             case DetectorType::JUNGFRAU:
                 setup.LoadGain(calib);
diff --git a/common/DetectorSetup.cpp b/common/DetectorSetup.cpp
index a982f693..f6b2b3cc 100644
--- a/common/DetectorSetup.cpp
+++ b/common/DetectorSetup.cpp
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include <filesystem>
+#include <utility>
 
 #include "DetectorSetup.h"
 #include "JFJochException.h"
@@ -449,3 +450,12 @@ DetectorSetup &DetectorSetup::TempThreshold_degC(int64_t input) {
     temperature_thresold_degC = static_cast<int32_t>(input);
     return *this;
 }
+
+DetectorSetup &DetectorSetup::TrimEnergies_eV(std::vector<int> input) {
+    trim_energy_eV_values = std::move(input);
+    return *this;
+}
+
+std::vector<int> DetectorSetup::GetTrimEnergies_eV() const {
+    return trim_energy_eV_values;
+}
diff --git a/common/DetectorSetup.h b/common/DetectorSetup.h
index 0b082fdc..4a2472b2 100644
--- a/common/DetectorSetup.h
+++ b/common/DetectorSetup.h
@@ -25,6 +25,7 @@ class DetectorSetup {
     std::vector<std::string> gain_file_names;
     std::vector<std::string> trim_file_names;
     std::string trim_file_directory;
+    std::vector<int> trim_energy_eV_values;
     std::shared_ptr<JFGainCalibration> gain_calibration;
     int64_t udp_interface_count = 2;
     float pixel_size_um = 75.0f;
@@ -85,6 +86,7 @@ public:
     DetectorSetup& DECTRISROI(const std::string &input);
     DetectorSetup& DefaultSettings(const std::optional<DetectorSettings> &input);
     DetectorSetup& TempThreshold_degC(int64_t input);
+    DetectorSetup& TrimEnergies_eV(std::vector<int> input);
 
     [[nodiscard]] DetectorType GetDetectorType() const;
     [[nodiscard]] const DetectorGeometry& GetGeometry() const;
@@ -116,6 +118,7 @@ public:
     [[nodiscard]] std::string GetDECTRISROI() const;
     [[nodiscard]] std::optional<DetectorSettings> GetDefaultSettings() const;
     [[nodiscard]] int32_t GetTempThreshold_degC() const;
+    [[nodiscard]] std::vector<int> GetTrimEnergies_eV() const;
 };
 
 DetectorSetup DetJF4M(const std::string &description = "Detector",
diff --git a/detector_control/SLSDetectorWrapper.cpp b/detector_control/SLSDetectorWrapper.cpp
index 81187860..c8ad5c95 100644
--- a/detector_control/SLSDetectorWrapper.cpp
+++ b/detector_control/SLSDetectorWrapper.cpp
@@ -145,10 +145,11 @@ void SLSDetectorWrapper::Initialize(DiffractionExperiment& experiment,
             auto trim_directory = experiment.GetDetectorSetup().GetTrimFileDirectory();
             if (!trim_directory.empty()) {
                 // Hardcoded for now - need to make it nicer
-                std::vector<int> trim_en = {4500, 5400, 6400, 8000, 9900, 15800};
+                std::vector<int> trim_en = experiment.GetDetectorSetup().GetTrimEnergies_eV();
+                if (trim_en.empty())
+                    throw JFJochException(JFJochExceptionCategory::Detector, "Trimming energies not provided");
                 det.setTrimEnergies(trim_en);
                 det.setSettingsPath(trim_directory);
-
             }
             auto trim_files = experiment.GetDetectorSetup().GetTrimFileNames();
 
-- 
2.52.0


From 2df1035518331ff1b06d11bc62dc5e9173886435 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:31:23 +0200
Subject: [PATCH 221/228] OpenAPI: update

---
 broker/redoc-static.html                | 8 ++++----
 docs/python_client/docs/RoiAzimuthal.md | 4 +++-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 73cd15d5..2fceca1b 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -806,16 +806,16 @@ This can only be done when detector is <code>Idle</code>, <code>Error</code> or
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/detector/status</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/detector/status</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pkq_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pkq_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pkq_0" aria-labelledby="tab_R_9pkq_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"powerchip"</span>: <span class="token string">&quot;PowerOn&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"server_version"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"number_of_triggers_left"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"fpga_temp_degC"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"high_voltage_V"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1config~1roi/get" data-section-id="/paths/~1config~1roi/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1config~1roi/get" aria-label="/paths/~1config~1roi/get"></a>Get ROI definitions<!-- --> </h2><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>OK</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/config/roi</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
-</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/config/roi</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pla_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pla_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pla_0" aria-labelledby="tab_R_9pla_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"box"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"circle"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"azim"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1config~1roi/put" data-section-id="/paths/~1config~1roi/put" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1config~1roi/put" aria-label="/paths/~1config~1roi/put"></a>Upload ROI definitions<!-- --> </h2><h5 class="sc-dAlyuH jbQuod">Request Body schema: <span class="sc-cWSHoV fzNksy">application/json</span></h5><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"></div><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="box"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand box"><span class="property-name">box</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->roi_box_list<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>List of box ROIs</p>
+</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/config/roi</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pla_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pla_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pla_0" aria-labelledby="tab_R_9pla_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"box"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"circle"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"azim"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_min_deg"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_max_deg"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1config~1roi/put" data-section-id="/paths/~1config~1roi/put" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1config~1roi/put" aria-label="/paths/~1config~1roi/put"></a>Upload ROI definitions<!-- --> </h2><h5 class="sc-dAlyuH jbQuod">Request Body schema: <span class="sc-cWSHoV fzNksy">application/json</span></h5><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"></div><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="box"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand box"><span class="property-name">box</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->roi_box_list<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>List of box ROIs</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="circle"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand circle"><span class="property-name">circle</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->roi_circle_list<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>List of circular ROIs</p>
 </div></div></div></td></tr><tr class="last "><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="azim"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand azim"><span class="property-name">azim</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div class="sc-Nxspf sc-hRJfrW cXxAXt kYVhSL">required</div></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->roi_azim_list<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>List of azimuthal ROIs</p>
 </div></div></div></td></tr></tbody></table><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jkjMMR" disabled=""><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Input parsing or validation error</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">500<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Error within Jungfraujoch code - see output message.</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="put" class="sc-eZYNyq cnqpVw http-verb put">put</span><span class="sc-iEXKAA gUNSDu">/config/roi</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
-</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/config/roi</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Request samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="react-tabs__tab react-tabs__tab--selected" role="tab" id="tab_R_99lq_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_99lq_0" tabindex="0" data-rttab="true">Payload</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_99lq_0" aria-labelledby="tab_R_99lq_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"box"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"circle"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"azim"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-error react-tabs__tab--selected" role="tab" id="tab_R_9plq_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9plq_0" tabindex="0" data-rttab="true">500</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9plq_0" aria-labelledby="tab_R_9plq_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"msg"</span>: <span class="token string">&quot;Detector in wrong state&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"reason"</span>: <span class="token string">&quot;WrongDAQState&quot;</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1statistics/get" data-section-id="/paths/~1statistics/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1statistics/get" aria-label="/paths/~1statistics/get"></a>Get general statistics<!-- --> </h2><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
+</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/config/roi</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Request samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="react-tabs__tab react-tabs__tab--selected" role="tab" id="tab_R_99lq_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_99lq_0" tabindex="0" data-rttab="true">Payload</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_99lq_0" aria-labelledby="tab_R_99lq_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"box"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"circle"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"azim"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_min_deg"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_max_deg"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-error react-tabs__tab--selected" role="tab" id="tab_R_9plq_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9plq_0" tabindex="0" data-rttab="true">500</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9plq_0" aria-labelledby="tab_R_9plq_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"msg"</span>: <span class="token string">&quot;Detector in wrong state&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"reason"</span>: <span class="token string">&quot;WrongDAQState&quot;</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1statistics/get" data-section-id="/paths/~1statistics/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1statistics/get" aria-label="/paths/~1statistics/get"></a>Get general statistics<!-- --> </h2><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/statistics</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
-</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/statistics</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pma_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pma_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pma_0" aria-labelledby="tab_R_9pma_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"detector"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"powerchip"</span>: <span class="token string">&quot;PowerOn&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"server_version"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"number_of_triggers_left"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fpga_temp_degC"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_voltage_V"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"detector_list"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"detectors"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"id"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"description"</span>: <span class="token string">&quot;JUNGFRAU 4 Mpixel&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"serial_number"</span>: <span class="token string">&quot;JF17T16V01&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"base_ipv4_addr"</span>: <span class="token string">&quot;10.10.10.1&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"udp_interface_count"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"nmodules"</span>: <span class="token number">18</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"width"</span>: <span class="token number">2068</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"height"</span>: <span class="token number">2164</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pixel_size_mm"</span>: <span class="token number">0.075</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"readout_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_frame_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_count_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"type"</span>: <span class="token string">&quot;EIGER&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"current_id"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"detector_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"frame_time_us"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"count_time_us"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"internal_frame_generator"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"internal_frame_generator_images"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_trigger_delay_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"timing"</span>: <span class="token string">&quot;auto&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eiger_threshold_keV"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eiger_bit_depth"</span>: <span class="token number">8</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g0_frames"</span>: <span class="token number">2000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g1_frames"</span>: <span class="token number">300</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g2_frames"</span>: <span class="token number">300</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_min_image_count"</span>: <span class="token number">128</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_storage_cell_count"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_storage_cell_delay_ns"</span>: <span class="token number">5000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_fixed_gain_g1"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_use_gain_hg0"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"image_format_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"summation"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"geometry_transform"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_conversion"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_conversion_factor_keV"</span>: <span class="token number">0.001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"bit_depth_image"</span>: <span class="token number">8</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"signed_output"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mask_module_edges"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mask_chip_edges"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_mask_pixels_without_g0"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"apply_mask"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g0_rms_limit"</span>: <span class="token number">100</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"instrument_metadata"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"source_name"</span>: <span class="token string">&quot;Swiss Light Source&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"source_type"</span>: <span class="token string">&quot;Synchrotron X-ray Source&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"instrument_name"</span>: <span class="token string">&quot;CristallinaMX&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pulsed_source"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"electron_source"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"file_writer_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"overwrite"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"format"</span>: <span class="token string">&quot;NXmxOnlyData&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"data_processing_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enable"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"indexing"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"signal_to_noise_threshold"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"photon_count_threshold"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_pix_per_spot"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_pix_per_spot"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_resolution_limit"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"low_resolution_limit"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_resolution_limit_for_spot_count_low_res"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"quick_integration"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"ice_ring_width_q_recipA"</span>: <span class="token number">0.02</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_res_gap_Q_recipA"</span>: <span class="token number">1.5</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"measurement"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"file_prefix"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"run_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"experiment_group"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_collected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_sent"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_written"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_discarded_lossy_compression"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_image_number_sent"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"collection_efficiency"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"compression_ratio"</span>: <span class="token number">5.3</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"cancelled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_receiver_delay"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"indexing_rate"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_width"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_height"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_pixel_depth"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"bkg_estimate"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"unit_cell"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"error_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"saturated_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"roi_beam_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"roi_beam_sum"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"broker"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"state"</span>: <span class="token string">&quot;Inactive&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"message_severity"</span>: <span class="token string">&quot;success&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"gpu_count"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"broker_version"</span>: <span class="token string">&quot;1.0.0-rc.128&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"fpga"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"pci_dev_id"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"serial_number"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fw_version"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"base_mac_addr"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eth_link_count"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eth_link_status"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"power_usage_W"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fpga_temp_C"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"hbm_temp_C"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"packets_udp"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"packets_sls"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"idle"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pcie_link_speed"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pcie_link_width"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"calibration"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"module_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"storage_cell_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g0_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g1_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g2_mean"</span>: <span class="token number">0.1</span><span class="token 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aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enabled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"period_ms"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"socket_address"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"zeromq_metadata"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enabled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"period_ms"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"socket_address"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"dark_mask"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"detector_threshold_keV"</span>: <span class="token number">3.5</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"frame_time_us"</span>: <span class="token number">10000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"number_of_frames"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_allowed_pixel_count"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_frames_with_signal"</span>: <span class="token number">10</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"pixel_mask"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"user_mask"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"too_high_pedestal_rms"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"wrong_gain"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"roi"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"box"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"circle"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"azim"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"az_int"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"polarization_corr"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"solid_angle_corr"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_q_recipA"</span>: <span class="token number">0.00002</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"low_q_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_spacing"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"azimuthal_bins"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"force_cpu"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"buffer"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"min_image_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_image_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"image_numbers"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"total_slots"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"available_slots"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"in_preparation_slots"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"in_sending_slots"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"current_counter"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"indexing"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"algorithm"</span>: <span class="token string">&quot;FFBIDX&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fft_max_unit_cell_A"</span>: <span class="token number">250</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fft_min_unit_cell_A"</span>: <span class="token number">10</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fft_high_resolution_A"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fft_num_vectors"</span>: <span class="token number">16384</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"tolerance"</span>: <span class="token number">0.5</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"thread_count"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"geom_refinement_algorithm"</span>: <span class="token string">&quot;BeamCenter&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"unit_cell_dist_tolerance"</span>: <span class="token number">0.05</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"viable_cell_min_spots"</span>: <span class="token number">10</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"index_ice_rings"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rotation_indexing"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rotation_indexing_min_angular_range_deg"</span>: <span class="token number">20</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rotation_indexing_angular_stride_deg"</span>: <span class="token number">0.5</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"blocking"</span>: <span class="token boolean">true</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"image_pusher"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"pusher_type"</span>: <span class="token string">&quot;ZeroMQ&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"addr"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;tcp://1.2.3.4:5000&quot;</span>,</div></li><li><div class="hoverable collapsed"><span class="token string">&quot;tcp://1.2.3.4:5001&quot;</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"connected_writers"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_written"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_write_error"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"writer_fifo_utilization"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1statistics~1data_collection/get" data-section-id="/paths/~1statistics~1data_collection/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1statistics~1data_collection/get" aria-label="/paths/~1statistics~1data_collection/get"></a>Get data collection statistics<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>Results of the last data collection</p>
+</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/statistics</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_9pma_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_9pma_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_9pma_0" aria-labelledby="tab_R_9pma_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"detector"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"powerchip"</span>: <span class="token string">&quot;PowerOn&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"server_version"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"number_of_triggers_left"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fpga_temp_degC"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_voltage_V"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"detector_list"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"detectors"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"id"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"description"</span>: <span class="token string">&quot;JUNGFRAU 4 Mpixel&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"serial_number"</span>: <span class="token string">&quot;JF17T16V01&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"base_ipv4_addr"</span>: <span class="token string">&quot;10.10.10.1&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"udp_interface_count"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"nmodules"</span>: <span class="token number">18</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"width"</span>: <span class="token number">2068</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"height"</span>: <span class="token number">2164</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pixel_size_mm"</span>: <span class="token number">0.075</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"readout_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_frame_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_count_time_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"type"</span>: <span class="token string">&quot;EIGER&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"current_id"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"detector_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"frame_time_us"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"count_time_us"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"internal_frame_generator"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"internal_frame_generator_images"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_trigger_delay_ns"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"timing"</span>: <span class="token string">&quot;auto&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eiger_threshold_keV"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eiger_bit_depth"</span>: <span class="token number">8</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g0_frames"</span>: <span class="token number">2000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g1_frames"</span>: <span class="token number">300</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g2_frames"</span>: <span class="token number">300</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_min_image_count"</span>: <span class="token number">128</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_storage_cell_count"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_storage_cell_delay_ns"</span>: <span class="token number">5000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_fixed_gain_g1"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_use_gain_hg0"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"image_format_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"summation"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"geometry_transform"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_conversion"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_conversion_factor_keV"</span>: <span class="token number">0.001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"bit_depth_image"</span>: <span class="token number">8</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"signed_output"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mask_module_edges"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mask_chip_edges"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_mask_pixels_without_g0"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"apply_mask"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"jungfrau_pedestal_g0_rms_limit"</span>: <span class="token number">100</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"instrument_metadata"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"source_name"</span>: <span class="token string">&quot;Swiss Light Source&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"source_type"</span>: <span class="token string">&quot;Synchrotron X-ray Source&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"instrument_name"</span>: <span class="token string">&quot;CristallinaMX&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pulsed_source"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"electron_source"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"file_writer_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"overwrite"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"format"</span>: <span class="token string">&quot;NXmxOnlyData&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"data_processing_settings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enable"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"indexing"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"signal_to_noise_threshold"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"photon_count_threshold"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_pix_per_spot"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_pix_per_spot"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_resolution_limit"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"low_resolution_limit"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_resolution_limit_for_spot_count_low_res"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"quick_integration"</span>: <span class="token boolean">false</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"ice_ring_width_q_recipA"</span>: <span class="token number">0.02</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"high_res_gap_Q_recipA"</span>: <span class="token number">1.5</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"measurement"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"file_prefix"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"run_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"experiment_group"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_collected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_sent"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_written"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_discarded_lossy_compression"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_image_number_sent"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"collection_efficiency"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"compression_ratio"</span>: <span class="token number">5.3</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"cancelled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_receiver_delay"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"indexing_rate"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_width"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_height"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"detector_pixel_depth"</span>: <span class="token number">2</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"bkg_estimate"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"unit_cell"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"error_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"saturated_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"roi_beam_pixels"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"roi_beam_sum"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"broker"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"state"</span>: <span class="token string">&quot;Inactive&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"message_severity"</span>: <span class="token string">&quot;success&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"gpu_count"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"broker_version"</span>: <span class="token string">&quot;1.0.0-rc.128&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"fpga"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"pci_dev_id"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"serial_number"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fw_version"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"base_mac_addr"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eth_link_count"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"eth_link_status"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"power_usage_W"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fpga_temp_C"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"hbm_temp_C"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"packets_udp"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"packets_sls"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"idle"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pcie_link_speed"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pcie_link_width"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"calibration"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"module_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"storage_cell_number"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g0_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g1_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"pedestal_g2_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"gain_g0_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"gain_g1_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"gain_g2_mean"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"masked_pixels"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"zeromq_preview"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enabled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"period_ms"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"socket_address"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"zeromq_metadata"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"enabled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"period_ms"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"socket_address"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"dark_mask"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"detector_threshold_keV"</span>: <span class="token number">3.5</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"frame_time_us"</span>: <span class="token number">10000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"number_of_frames"</span>: <span class="token number">1000</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_allowed_pixel_count"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_frames_with_signal"</span>: <span class="token number">10</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"pixel_mask"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"user_mask"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"too_high_pedestal_rms"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"wrong_gain"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"roi"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"box"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_x_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"min_y_pxl"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"max_y_pxl"</span>: <span class="token number">0</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"circle"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_x_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"center_y_pxl"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"radius_pxl"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"azim"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"rois"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_min_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_max_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_min_deg"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"phi_max_deg"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token 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class="hoverable collapsed"><span class="property token string">"low_q_recipA"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"q_spacing"</span>: <span class="token number">0.00001</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"azimuthal_bins"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"force_cpu"</span>: <span class="token boolean">false</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"buffer"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul 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class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"connected_writers"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_written"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"images_write_error"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"writer_fifo_utilization"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token number">0</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1statistics~1data_collection/get" data-section-id="/paths/~1statistics~1data_collection/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1statistics~1data_collection/get" aria-label="/paths/~1statistics~1data_collection/get"></a>Get data collection statistics<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>Results of the last data collection</p>
 </div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
 </div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>No data collection performed so far</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/statistics/data_collection</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
@@ -937,7 +937,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
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The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.153","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","image_scale_b","compression_ratio"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. 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[pixels]"},"center_y_pxl":{"type":"number","format":"float","description":"Y coordinate of center of the circle [pixels]"},"radius_pxl":{"type":"number","format":"float","minimum":0,"exclusiveMinimum":true,"description":"Radius of the circle [pixels]"}}},"roi_box":{"type":"object","description":"Box ROI","required":["name","min_x_pxl","max_x_pxl","min_y_pxl","max_y_pxl"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"min_x_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in X coordinate for the box","minimum":0},"max_x_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in X coordinate for the box","minimum":0},"min_y_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in Y coordinate for the box","minimum":0},"max_y_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in Y coordinate for the box","minimum":0}}},"roi_circle_list":{"type":"object","description":"List of circular ROIs","required":["rois"],"properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_circle"}}}},"roi_box_list":{"type":"object","description":"List of box ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_box"}}}},"roi_azim_list":{"type":"object","description":"List of azimuthal ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_azimuthal"}}}},"roi_definitions":{"type":"object","required":["box","circle","azim"],"description":"ROI defintions","properties":{"box":{"$ref":"#/components/schemas/roi_box_list"},"circle":{"$ref":"#/components/schemas/roi_circle_list"},"azim":{"$ref":"#/components/schemas/roi_azim_list"}}},"dark_mask_settings":{"type":"object","description":"Settings for collection of dark images to be used for mask calculation","required":["detector_threshold_keV","frame_threshold_keV","max_allowed_pixel_count","max_frames_with_signal","frame_time_us","number_of_frames"],"properties":{"detector_threshold_keV":{"type":"number","format":"float","description":"Energy threshold for dark image collection","minimum":2.5,"default":3.5,"maximum":100},"frame_time_us":{"type":"integer","format":"int64","description":"Time between frames for dark image collection","minimum":500,"default":10000,"maximum":100000},"number_of_frames":{"type":"integer","format":"int64","description":"Number of frames for dark image collection; zero means no dark collection","minimum":0,"default":1000},"max_allowed_pixel_count":{"type":"integer","format":"int64","description":"Maximum count in a pixel considered normal (not-masked)","minimum":0,"default":1},"max_frames_with_signal":{"type":"integer","format":"int64","description":"Maximum number of frames with signal in a pixel considered normal (not-masked)","minimum":0,"default":10}}},"indexing_settings":{"type":"object","description":"Settings for crystallography indexing","required":["algorithm","geom_refinement_algorithm","fft_high_resolution_A","fft_max_unit_cell_A","fft_min_unit_cell_A","fft_num_vectors","tolerance","thread_count","unit_cell_dist_tolerance","index_ice_rings","viable_cell_min_spots","rotation_indexing","rotation_indexing_min_angular_range_deg","rotation_indexing_angular_stride_deg","blocking"],"properties":{"algorithm":{"$ref":"#/components/schemas/indexing_algorithm"},"fft_max_unit_cell_A":{"type":"number","format":"float","default":250,"maximum":500,"minimum":50,"description":"Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT"},"fft_min_unit_cell_A":{"type":"number","format":"float","default":10,"minimum":5,"maximum":40,"description":"Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT"},"fft_high_resolution_A":{"type":"number","format":"float","default":2,"minimum":0.5,"maximum":6,"description":"Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT.\nThere is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.\n"},"fft_num_vectors":{"type":"integer","format":"int64","minimum":128,"default":16384,"description":"Number of search directions for the FFT algorithm; parameter value affects execution time of FFT."},"tolerance":{"type":"number","format":"float","minimum":0,"maximum":0.5,"description":"Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted"},"thread_count":{"type":"integer","format":"int64","minimum":1,"maximum":64,"description":"Thread count for indexing algorithm"},"geom_refinement_algorithm":{"$ref":"#/components/schemas/geom_refinement_algorithm"},"unit_cell_dist_tolerance":{"type":"number","format":"float","minimum":0.0001,"maximum":0.2001,"default":0.05,"description":"Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored"},"viable_cell_min_spots":{"type":"integer","format":"int64","minimum":5,"default":10,"description":"Minimum number of indexed spots required for a cell to be considered viable"},"index_ice_rings":{"type":"boolean","default":false,"description":"Include spots marked as ice rings in the indexing run. \nIf `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.\n"},"rotation_indexing":{"type":"boolean","default":false},"rotation_indexing_min_angular_range_deg":{"type":"number","format":"float","default":20,"minimum":1},"rotation_indexing_angular_stride_deg":{"type":"number","format":"float","default":0.5,"minimum":0},"blocking":{"type":"boolean","default":true,"description":"Indexing in Jungfraujoch goes with a dedicated thread pool.\nIf set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates.\nIf set to true, the thread pool will block until a thread is available.\n"}}},"instrument_metadata":{"type":"object","description":"Metadata for a measurement instrument","required":["source_name","instrument_name"],"properties":{"source_name":{"type":"string","example":"Swiss Light Source"},"source_type":{"type":"string","description":"Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. \nhttps://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource\nNXsource allows the following:\n\nSpallation Neutron Source\nPulsed Reactor Neutron Source\nReactor Neutron Source\nSynchrotron X-ray Source\nPulsed Muon Source\nRotating Anode X-ray\nFixed Tube X-ray\nUV Laser\nFree-Electron Laser\nOptical Laser\nIon Source\nUV Plasma Source\nMetal Jet X-ray\n","example":"Synchrotron X-ray Source","default":""},"instrument_name":{"type":"string","example":"CristallinaMX"},"pulsed_source":{"type":"boolean","description":"Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)\n","default":false},"electron_source":{"type":"boolean","description":"Settings specific to electron source (e.g., wavelength definition)\n","default":false}}},"detector_module_direction":{"type":"string","enum":["Xp","Xn","Yp","Yn"]},"detector_type":{"type":"string","enum":["EIGER","JUNGFRAU","DECTRIS"]},"image_pusher_type":{"type":"string","default":"None","enum":["ZeroMQ","HDF5","CBOR","TCP","None"]},"standard_detector_geometry":{"type":"object","description":"Regular rectangular geometry, first module is in the bottom left corner of the detector","required":["nmodules"],"properties":{"nmodules":{"type":"integer","minimum":1,"description":"Number of modules in the detector"},"gap_x":{"type":"integer","default":8,"minimum":0,"description":"Gap size in X direction [pixels]"},"gap_y":{"type":"integer","minimum":0,"default":36,"description":"Gap size in Y direction [pixels]"},"modules_in_row":{"type":"integer","minimum":1,"default":1,"description":"Number of modules in one row"}}},"detector_module":{"type":"object","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number"},"y0":{"type":"number"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER)."},"sensor_thickness_um":{"type":"number","format":"float","minimum":0,"default":320},"readout_time_ns":{"type":"integer","format":"int64","minimum":1,"description":"Minimum difference between frame time and count time in microseconds\nDefaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU\n"},"min_count_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum count time available for the detector."},"min_frame_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum frame time available for the detector."},"calibration_file":{"type":"array","description":"Can be empty for all detectors - default calibration used.\nFor JUNGFRAU: list of gain files, one entry per module.\nFor EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.\n","items":{"type":"string"}},"hostname":{"type":"array","description":"Hostname for detector module. One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - 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One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; 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       var container = document.getElementById('redoc');
       Redoc.hydrate(__redoc_state, container);
diff --git a/docs/python_client/docs/RoiAzimuthal.md b/docs/python_client/docs/RoiAzimuthal.md
index b736ad68..33f6e8cb 100644
--- a/docs/python_client/docs/RoiAzimuthal.md
+++ b/docs/python_client/docs/RoiAzimuthal.md
@@ -1,6 +1,6 @@
 # RoiAzimuthal
 
-ROI as Q-range (or resolution range)
+ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
 
 ## Properties
 
@@ -9,6 +9,8 @@ Name | Type | Description | Notes
 **name** | **str** | Name for the ROI; used in the plots | 
 **q_min_recip_a** | **float** | Minimum Q-range for the ROI | 
 **q_max_recip_a** | **float** | Maximum Q-range for the ROI | 
+**phi_min_deg** | **float** | Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit both for a full ring. A sector with phi_min_deg &gt; phi_max_deg wraps across 0.  | [optional] 
+**phi_max_deg** | **float** | Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.  | [optional] 
 
 ## Example
 
-- 
2.52.0


From bcf01c28f425fbded1ab542f768f650546d353ca Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 15:38:36 +0200
Subject: [PATCH 222/228] jfjoch_broker: Fix

---
 broker/JFJochBrokerParser.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/broker/JFJochBrokerParser.cpp b/broker/JFJochBrokerParser.cpp
index 0dc117cb..54f4ada9 100644
--- a/broker/JFJochBrokerParser.cpp
+++ b/broker/JFJochBrokerParser.cpp
@@ -8,7 +8,6 @@
 #include "../image_pusher/HDF5FilePusher.h"
 #include "OpenAPIConvert.h"
 #include "Detector_type.h"
-#include "../cmake-build-release-nogpu/_deps/catch2-src/src/catch2/internal/catch_string_manip.hpp"
 #include "../image_pusher/NonePusher.h"
 #include "../image_pusher/TCPStreamPusher.h"
 
-- 
2.52.0


From 066c0dfa90fd1d581333a5f9075e59ff5fb8fac9 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:52:16 +0200
Subject: [PATCH 223/228] OpenAPI: fix missing trim_energie_eV

---
 broker/gen/model/Detector.cpp       | 54 +++++++++++++++++++++++++++++
 broker/gen/model/Detector.h         |  9 +++++
 broker/jfjoch_api.yaml              |  9 +++++
 broker/redoc-static.html            |  2 +-
 docs/python_client/docs/Detector.md |  1 +
 frontend/src/client/types.gen.ts    |  6 ++++
 frontend/src/client/zod.gen.ts      |  1 +
 7 files changed, 81 insertions(+), 1 deletion(-)

diff --git a/broker/gen/model/Detector.cpp b/broker/gen/model/Detector.cpp
index e7bbd72d..0b686db6 100644
--- a/broker/gen/model/Detector.cpp
+++ b/broker/gen/model/Detector.cpp
@@ -40,6 +40,7 @@ Detector::Detector()
     m_Min_frame_time_ns = 0L;
     m_Min_frame_time_nsIsSet = false;
     m_Calibration_fileIsSet = false;
+    m_Trim_energies_eVIsSet = false;
     m_HostnameIsSet = false;
     m_Sensor_material = "Si";
     m_Sensor_materialIsSet = false;
@@ -221,6 +222,32 @@ bool Detector::validate(std::stringstream& msg, const std::string& pathPrefix) c
 
     }
          
+    if (trimEnergiesEVIsSet())
+    {
+        const std::vector<int32_t>& value = m_Trim_energies_eV;
+        const std::string currentValuePath = _pathPrefix + ".trimEnergiesEV";
+                
+        
+        { // Recursive validation of array elements
+            const std::string oldValuePath = currentValuePath;
+            int i = 0;
+            for (const int32_t& value : value)
+            { 
+                const std::string currentValuePath = oldValuePath + "[" + std::to_string(i) + "]";
+                        
+        
+        if (value < 100)
+        {
+            success = false;
+            msg << currentValuePath << ": must be greater than or equal to 100;";
+        }
+ 
+                i++;
+            }
+        }
+
+    }
+         
     if (hostnameIsSet())
     {
         const std::vector<std::string>& value = m_Hostname;
@@ -345,6 +372,9 @@ bool Detector::operator==(const Detector& rhs) const
     ((!calibrationFileIsSet() && !rhs.calibrationFileIsSet()) || (calibrationFileIsSet() && rhs.calibrationFileIsSet() && getCalibrationFile() == rhs.getCalibrationFile())) &&
     
     
+    ((!trimEnergiesEVIsSet() && !rhs.trimEnergiesEVIsSet()) || (trimEnergiesEVIsSet() && rhs.trimEnergiesEVIsSet() && getTrimEnergiesEV() == rhs.getTrimEnergiesEV())) &&
+    
+    
     ((!hostnameIsSet() && !rhs.hostnameIsSet()) || (hostnameIsSet() && rhs.hostnameIsSet() && getHostname() == rhs.getHostname())) &&
     
     
@@ -406,6 +436,8 @@ void to_json(nlohmann::json& j, const Detector& o)
         j["min_frame_time_ns"] = o.m_Min_frame_time_ns;
     if(o.calibrationFileIsSet() || !o.m_Calibration_file.empty())
         j["calibration_file"] = o.m_Calibration_file;
+    if(o.trimEnergiesEVIsSet() || !o.m_Trim_energies_eV.empty())
+        j["trim_energies_eV"] = o.m_Trim_energies_eV;
     if(o.hostnameIsSet() || !o.m_Hostname.empty())
         j["hostname"] = o.m_Hostname;
     if(o.sensorMaterialIsSet())
@@ -482,6 +514,11 @@ void from_json(const nlohmann::json& j, Detector& o)
         j.at("calibration_file").get_to(o.m_Calibration_file);
         o.m_Calibration_fileIsSet = true;
     } 
+    if(j.find("trim_energies_eV") != j.end())
+    {
+        j.at("trim_energies_eV").get_to(o.m_Trim_energies_eV);
+        o.m_Trim_energies_eVIsSet = true;
+    } 
     if(j.find("hostname") != j.end())
     {
         j.at("hostname").get_to(o.m_Hostname);
@@ -713,6 +750,23 @@ void Detector::unsetCalibration_file()
 {
     m_Calibration_fileIsSet = false;
 }
+std::vector<int32_t> Detector::getTrimEnergiesEV() const
+{
+    return m_Trim_energies_eV;
+}
+void Detector::setTrimEnergiesEV(std::vector<int32_t> const value)
+{
+    m_Trim_energies_eV = value;
+    m_Trim_energies_eVIsSet = true;
+}
+bool Detector::trimEnergiesEVIsSet() const
+{
+    return m_Trim_energies_eVIsSet;
+}
+void Detector::unsetTrim_energies_eV()
+{
+    m_Trim_energies_eVIsSet = false;
+}
 std::vector<std::string> Detector::getHostname() const
 {
     return m_Hostname;
diff --git a/broker/gen/model/Detector.h b/broker/gen/model/Detector.h
index 999949c4..ee24d86d 100644
--- a/broker/gen/model/Detector.h
+++ b/broker/gen/model/Detector.h
@@ -139,6 +139,13 @@ public:
     bool calibrationFileIsSet() const;
     void unsetCalibration_file();
     /// <summary>
+    /// List of energies at which trimming calibration is provided. Only needed for PSI EIGER and compulsory in this case 
+    /// </summary>
+    std::vector<int32_t> getTrimEnergiesEV() const;
+    void setTrimEnergiesEV(std::vector<int32_t> const value);
+    bool trimEnergiesEVIsSet() const;
+    void unsetTrim_energies_eV();
+    /// <summary>
     /// Hostname for detector module. One entry per module One entry per module. Either empty or number of module entries. 
     /// </summary>
     std::vector<std::string> getHostname() const;
@@ -234,6 +241,8 @@ protected:
     bool m_Min_frame_time_nsIsSet;
     std::vector<std::string> m_Calibration_file;
     bool m_Calibration_fileIsSet;
+    std::vector<int32_t> m_Trim_energies_eV;
+    bool m_Trim_energies_eVIsSet;
     std::vector<std::string> m_Hostname;
     bool m_HostnameIsSet;
     std::string m_Sensor_material;
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 31a53a89..00e70e80 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -2121,6 +2121,15 @@ components:
             For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.
           items:
             type: string
+        trim_energies_eV:
+          type: array
+          description: |
+            List of energies at which trimming calibration is provided.
+            Only needed for PSI EIGER and compulsory in this case
+          items:
+            type: integer
+            format: int32
+            minimum: 100
         hostname:
           type: array
           description: |
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 2fceca1b..0bc418af 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -937,7 +937,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
-      const __redoc_state = {"menu":{"activeItemIdx":-1},"spec":{"data":{"openapi":"3.0.3","info":{"title":"Jungfraujoch","description":"API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).\nJungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.\nJungfraujoch uses FPGA boards to acquire data at high data rates.\n\n# License Clarification\n\nWhile this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**\nwhen this file is used solely to generate OpenAPI clients or when implementing applications that\ninteract with the API. Generated client code and applications using this API definition are not\nsubject to the GPL license requirements and may be distributed under terms of your choosing.\n\nThis exception is similar in spirit to the Linux Kernel's approach to userspace API headers and\nthe GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.153","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","image_scale_b","compression_ratio"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"},"saturation":{"in":"query","name":"saturation","required":false,"schema":{"type":"number","format":"float","minimum":-32767,"maximum":32767},"description":"Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"},"background":{"in":"query","name":"background","required":false,"schema":{"type":"number","format":"float","default":0,"minimum":-32767,"maximum":32767},"description":"Background value to set contrast in the preview image"},"show_spots":{"in":"query","name":"show_spots","schema":{"type":"boolean","default":true},"description":"Show spot finding results on the image"},"show_beam_center":{"in":"query","name":"show_beam_center","schema":{"type":"boolean","default":true},"description":"Show beam center on the image"},"show_roi":{"in":"query","name":"show_roi","schema":{"type":"boolean","default":false},"description":"Show ROI areas on the image"},"jpeg_quality":{"in":"query","name":"jpeg_quality","description":"Quality of JPEG image (100 - highest; 0 - lowest)","schema":{"type":"integer","format":"int64","default":100,"minimum":0,"maximum":100}},"show_user_mask":{"in":"query","name":"show_user_mask","schema":{"type":"boolean","default":false},"description":"Show user mask"},"resolution_ring":{"in":"query","name":"show_res_ring","description":"Show resolution ring, provided in Angstrom","schema":{"type":"number","format":"float","default":0.1,"minimum":0.1,"maximum":100}},"resolution_estimate":{"in":"query","name":"show_res_est","description":"Show resolution estimation as a ring","schema":{"type":"boolean","default":false}},"color_scale":{"in":"query","name":"color","description":"Color scale for preview image","schema":{"type":"string","enum":["indigo","viridis","bw","wb","green","heat","magma","inferno"],"default":"indigo"}}},"schemas":{"grid_scan":{"description":"Definition of a grid scan (mutually exclusive with `rotation_axis`)","type":"object","required":["n_fast","step_x_um","step_y_um"],"properties":{"n_fast":{"type":"integer","format":"int64","minimum":1,"example":20,"description":"Number of elements in the fast direction"},"step_x_um":{"type":"number","format":"float","example":5,"description":"Step in grid along the fast direction. Can be negative. \nPositive number: left to right\nNegative number: right to left\n"},"step_y_um":{"type":"number","format":"float","example":-3,"description":"Step in grid along the slow direction. Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\n","enum":["BeamCenter","OrientationOnly","None"]},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. If left empty, no file will be saved."},"images_per_file":{"type":"integer","format":"int64","minimum":0,"default":1000,"description":"Number of files in a single HDF5 data file (0 = write all images to a single data file)."},"space_group_number":{"type":"integer","format":"int64","minimum":1,"maximum":194,"description":"Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments\nand to turn off for other experiments.\n"},"save_calibration":{"type":"boolean","description":"Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.\nIf parameter is not provided calibration will be saved only if more than 4 images are recorded.\n"},"polarization_factor":{"type":"number","description":"Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization","format":"float","minimum":-1,"maximum":1},"ring_current_mA":{"type":"number","format":"float","description":"Ring current at the beginning of the data collection","minimum":0},"sample_temperature_K":{"type":"number","format":"float","description":"Sample temperature in Kelvin","minimum":0},"poni_rot1_rad":{"type":"number","description":"PONI angle rot1 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot2_rad":{"type":"number","description":"PONI angle rot2 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot3_rad":{"type":"number","description":"PONI angle rot3 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"unit_cell":{"$ref":"#/components/schemas/unit_cell"},"spot_finding":{"type":"boolean","description":"Enable spot finding and save spots","default":true},"max_spot_count":{"type":"integer","minimum":10,"maximum":2000,"default":250,"description":"Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected"},"detect_ice_rings":{"type":"boolean","description":"Flag spots as ice rings and reduce their effect on indexing"},"async_start":{"type":"boolean","default":false,"description":"When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement."},"xray_fluorescence_spectrum":{"type":"object","required":["energy_eV","data"],"properties":{"energy_eV":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan energy for each measurement point"},"data":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV"}}}}},"crystal_lattice":{"type":"array","items":{"type":"number","format":"float"},"minItems":9,"maxItems":9,"description":"Real-space crystal lattice 3D vectors in Angstrom.\nOrder is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)\n"},"unit_cell":{"type":"object","description":"Unit cell parameters. Necessary to run indexing. Units of angstrom and degree","required":["a","b","c","alpha","beta","gamma"],"properties":{"a":{"type":"number","format":"float","example":37,"minimum":0},"b":{"type":"number","format":"float","example":37,"minimum":0},"c":{"type":"number","format":"float","example":78,"minimum":0},"alpha":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"beta":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"gamma":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360}}},"file_writer_format":{"type":"string","enum":["NXmxOnlyData","NXmxLegacy","NXmxVDS","NXmxIntegrated","CBF","TIFF","NoFileWritten"],"default":"NXmxLegacy","description":"NoFileWritten - no files are written at all\nNXmxOnlyData - only data files are written, no master file\nNXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia  \nNXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling\nNXmxIntegrated - single HDF5 per dataset\nCBF - CBF format (limited metadata)\nTIFF - TIFF format (no metadata)\n"},"file_writer_settings":{"type":"object","properties":{"overwrite":{"type":"boolean","default":false,"description":"Inform jfjoch_write to overwrite existing files. 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Optional: provide both phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit both for a full ring. A sector with phi_min_deg > phi_max_deg wraps across 0.\n"},"phi_max_deg":{"type":"number","format":"float","description":"Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.\n"}}},"roi_circle":{"type":"object","description":"Circular ROI","required":["name","center_x_pxl","center_y_pxl","radius_pxl"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"center_x_pxl":{"type":"number","format":"float","description":"X coordinate of center of the circle [pixels]"},"center_y_pxl":{"type":"number","format":"float","description":"Y coordinate of center of the circle [pixels]"},"radius_pxl":{"type":"number","format":"float","minimum":0,"exclusiveMinimum":true,"description":"Radius of the circle [pixels]"}}},"roi_box":{"type":"object","description":"Box ROI","required":["name","min_x_pxl","max_x_pxl","min_y_pxl","max_y_pxl"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"min_x_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in X coordinate for the box","minimum":0},"max_x_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in X coordinate for the box","minimum":0},"min_y_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in Y coordinate for the box","minimum":0},"max_y_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in Y coordinate for the box","minimum":0}}},"roi_circle_list":{"type":"object","description":"List of circular ROIs","required":["rois"],"properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_circle"}}}},"roi_box_list":{"type":"object","description":"List of box ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_box"}}}},"roi_azim_list":{"type":"object","description":"List of azimuthal ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_azimuthal"}}}},"roi_definitions":{"type":"object","required":["box","circle","azim"],"description":"ROI defintions","properties":{"box":{"$ref":"#/components/schemas/roi_box_list"},"circle":{"$ref":"#/components/schemas/roi_circle_list"},"azim":{"$ref":"#/components/schemas/roi_azim_list"}}},"dark_mask_settings":{"type":"object","description":"Settings for collection of dark images to be used for mask calculation","required":["detector_threshold_keV","frame_threshold_keV","max_allowed_pixel_count","max_frames_with_signal","frame_time_us","number_of_frames"],"properties":{"detector_threshold_keV":{"type":"number","format":"float","description":"Energy threshold for dark image collection","minimum":2.5,"default":3.5,"maximum":100},"frame_time_us":{"type":"integer","format":"int64","description":"Time between frames for dark image collection","minimum":500,"default":10000,"maximum":100000},"number_of_frames":{"type":"integer","format":"int64","description":"Number of frames for dark image collection; zero means no dark collection","minimum":0,"default":1000},"max_allowed_pixel_count":{"type":"integer","format":"int64","description":"Maximum count in a pixel considered normal (not-masked)","minimum":0,"default":1},"max_frames_with_signal":{"type":"integer","format":"int64","description":"Maximum number of frames with signal in a pixel considered normal (not-masked)","minimum":0,"default":10}}},"indexing_settings":{"type":"object","description":"Settings for crystallography indexing","required":["algorithm","geom_refinement_algorithm","fft_high_resolution_A","fft_max_unit_cell_A","fft_min_unit_cell_A","fft_num_vectors","tolerance","thread_count","unit_cell_dist_tolerance","index_ice_rings","viable_cell_min_spots","rotation_indexing","rotation_indexing_min_angular_range_deg","rotation_indexing_angular_stride_deg","blocking"],"properties":{"algorithm":{"$ref":"#/components/schemas/indexing_algorithm"},"fft_max_unit_cell_A":{"type":"number","format":"float","default":250,"maximum":500,"minimum":50,"description":"Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT"},"fft_min_unit_cell_A":{"type":"number","format":"float","default":10,"minimum":5,"maximum":40,"description":"Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT"},"fft_high_resolution_A":{"type":"number","format":"float","default":2,"minimum":0.5,"maximum":6,"description":"Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT.\nThere is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.\n"},"fft_num_vectors":{"type":"integer","format":"int64","minimum":128,"default":16384,"description":"Number of search directions for the FFT algorithm; parameter value affects execution time of FFT."},"tolerance":{"type":"number","format":"float","minimum":0,"maximum":0.5,"description":"Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted"},"thread_count":{"type":"integer","format":"int64","minimum":1,"maximum":64,"description":"Thread count for indexing algorithm"},"geom_refinement_algorithm":{"$ref":"#/components/schemas/geom_refinement_algorithm"},"unit_cell_dist_tolerance":{"type":"number","format":"float","minimum":0.0001,"maximum":0.2001,"default":0.05,"description":"Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored"},"viable_cell_min_spots":{"type":"integer","format":"int64","minimum":5,"default":10,"description":"Minimum number of indexed spots required for a cell to be considered viable"},"index_ice_rings":{"type":"boolean","default":false,"description":"Include spots marked as ice rings in the indexing run. \nIf `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.\n"},"rotation_indexing":{"type":"boolean","default":false},"rotation_indexing_min_angular_range_deg":{"type":"number","format":"float","default":20,"minimum":1},"rotation_indexing_angular_stride_deg":{"type":"number","format":"float","default":0.5,"minimum":0},"blocking":{"type":"boolean","default":true,"description":"Indexing in Jungfraujoch goes with a dedicated thread pool.\nIf set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates.\nIf set to true, the thread pool will block until a thread is available.\n"}}},"instrument_metadata":{"type":"object","description":"Metadata for a measurement instrument","required":["source_name","instrument_name"],"properties":{"source_name":{"type":"string","example":"Swiss Light Source"},"source_type":{"type":"string","description":"Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. \nhttps://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource\nNXsource allows the following:\n\nSpallation Neutron Source\nPulsed Reactor Neutron Source\nReactor Neutron Source\nSynchrotron X-ray Source\nPulsed Muon Source\nRotating Anode X-ray\nFixed Tube X-ray\nUV Laser\nFree-Electron Laser\nOptical Laser\nIon Source\nUV Plasma Source\nMetal Jet X-ray\n","example":"Synchrotron X-ray Source","default":""},"instrument_name":{"type":"string","example":"CristallinaMX"},"pulsed_source":{"type":"boolean","description":"Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)\n","default":false},"electron_source":{"type":"boolean","description":"Settings specific to electron source (e.g., wavelength definition)\n","default":false}}},"detector_module_direction":{"type":"string","enum":["Xp","Xn","Yp","Yn"]},"detector_type":{"type":"string","enum":["EIGER","JUNGFRAU","DECTRIS"]},"image_pusher_type":{"type":"string","default":"None","enum":["ZeroMQ","HDF5","CBOR","TCP","None"]},"standard_detector_geometry":{"type":"object","description":"Regular rectangular geometry, first module is in the bottom left corner of the detector","required":["nmodules"],"properties":{"nmodules":{"type":"integer","minimum":1,"description":"Number of modules in the detector"},"gap_x":{"type":"integer","default":8,"minimum":0,"description":"Gap size in X direction [pixels]"},"gap_y":{"type":"integer","minimum":0,"default":36,"description":"Gap size in Y direction [pixels]"},"modules_in_row":{"type":"integer","minimum":1,"default":1,"description":"Number of modules in one row"}}},"detector_module":{"type":"object","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number"},"y0":{"type":"number"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER)."},"sensor_thickness_um":{"type":"number","format":"float","minimum":0,"default":320},"readout_time_ns":{"type":"integer","format":"int64","minimum":1,"description":"Minimum difference between frame time and count time in microseconds\nDefaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU\n"},"min_count_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum count time available for the detector."},"min_frame_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum frame time available for the detector."},"calibration_file":{"type":"array","description":"Can be empty for all detectors - default calibration used.\nFor JUNGFRAU: list of gain files, one entry per module.\nFor EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.\n","items":{"type":"string"}},"hostname":{"type":"array","description":"Hostname for detector module. One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. 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One entry per module\nOne entry per module. Either empty or number of module entries.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["addr"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"}}},"pcie_devices":{"type":"array","minLength":1,"items":{"type":"object","required":["block_device"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minLength":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; 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--- a/docs/python_client/docs/Detector.md
+++ b/docs/python_client/docs/Detector.md
@@ -16,6 +16,7 @@ Name | Type | Description | Notes
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index a8b818e8..eaab66ba 100644
--- a/frontend/src/client/types.gen.ts
+++ b/frontend/src/client/types.gen.ts
@@ -1389,6 +1389,12 @@ export type detector = {
      *
      */
     calibration_file?: Array<string>;
+    /**
+     * List of energies at which trimming calibration is provided.
+     * Only needed for PSI EIGER and compulsory in this case
+     *
+     */
+    trim_energies_eV?: Array<number>;
     /**
      * Hostname for detector module. One entry per module
      * One entry per module. Either empty or number of module entries.
diff --git a/frontend/src/client/zod.gen.ts b/frontend/src/client/zod.gen.ts
index c6095998..f07a9f3f 100644
--- a/frontend/src/client/zod.gen.ts
+++ b/frontend/src/client/zod.gen.ts
@@ -612,6 +612,7 @@ export const zDetector = z.object({
     min_count_time_ns: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
     min_frame_time_ns: z.coerce.bigint().gte(BigInt(0)).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
     calibration_file: z.array(z.string()).optional(),
+    trim_energies_eV: z.array(z.int().gte(100).max(2147483647, { error: 'Invalid value: Expected int32 to be <= 2147483647' })).optional(),
     hostname: z.array(z.string()).optional(),
     sensor_material: z.string().optional().default('Si'),
     tx_delay: z.array(z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' })).optional(),
-- 
2.52.0


From 97c3008c399a165aeabec6f6076076f40b2fcc9b Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 16:55:59 +0200
Subject: [PATCH 224/228] TCP stream: tolerate writer backpressure via BUSY
 heartbeats

A slow filesystem could stall the writer's consume pipeline, propagating
TCP backpressure to the pusher. The pusher then treated that backpressure
as a dead peer and force-closed the connection mid-run; the writer
reconnected as a brand-new connection outside the active session, so the
rest of the run was silently dropped and the half-written HDF5 file was
later finalized with holes.

Replace the throughput/progress-based send timeout with a peer-liveness
timeout:

- Add TCPFrameType::BUSY (wire version 2 -> 3).
- TCPImagePuller runs a heartbeat thread that sends BUSY every 250ms on a
  thread independent of the (possibly stalled) write path, so liveness
  keeps flowing during deep stalls. A send_mutex serializes
  ACK/pong/heartbeat writes.
- TCPStreamPusher refreshes last_peer_activity_ns on every inbound frame
  and only declares a connection dead after peer_liveness_timeout (15s) of
  complete silence, tolerating arbitrarily long backpressure while still
  catching a genuinely dead peer (and immediate EPIPE/ECONNRESET).
- Re-key both backpressure waits (the SendAll data path and the post-END
  WaitForEndAck) onto this liveness signal instead of byte-progress /
  DATA-ACK-progress, so a slow final flush at END is tolerated too.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 common/JfjochTCP.h               |  7 +++-
 image_puller/TCPImagePuller.cpp  | 43 ++++++++++++++++++++-
 image_puller/TCPImagePuller.h    |  7 ++++
 image_pusher/TCPStreamPusher.cpp | 65 +++++++++++++++++++++-----------
 image_pusher/TCPStreamPusher.h   | 13 ++++++-
 5 files changed, 109 insertions(+), 26 deletions(-)

diff --git a/common/JfjochTCP.h b/common/JfjochTCP.h
index e945613b..f43709d7 100644
--- a/common/JfjochTCP.h
+++ b/common/JfjochTCP.h
@@ -6,7 +6,7 @@
 #include <cstdint>
 
 constexpr uint32_t JFJOCH_TCP_MAGIC = 0x4A464A54; // JFJT
-constexpr uint32_t JFJOCH_TCP_VERSION = 2;
+constexpr uint32_t JFJOCH_TCP_VERSION = 3;
 
 enum class TCPFrameType : uint16_t {
     START = 1,
@@ -16,6 +16,11 @@ enum class TCPFrameType : uint16_t {
     ACK = 5,
     CANCEL = 6,
     KEEPALIVE   = 7,
+    // Writer -> pusher liveness/backpressure heartbeat. Tells the pusher the writer
+    // is alive but busy (e.g. stalled on a slow filesystem) and that it should keep
+    // waiting for a proper ACK rather than declaring the connection dead. Carries the
+    // writer's current FIFO occupancy in the ack_fifo_* fields.
+    BUSY = 8,
 };
 
 enum class TCPAckCode : uint16_t {
diff --git a/image_puller/TCPImagePuller.cpp b/image_puller/TCPImagePuller.cpp
index f1e83ee2..7f93b561 100644
--- a/image_puller/TCPImagePuller.cpp
+++ b/image_puller/TCPImagePuller.cpp
@@ -54,6 +54,7 @@ TCPImagePuller::TCPImagePuller(const std::string &tcp_addr,
 
     receiver_thread = std::thread(&TCPImagePuller::ReceiverThread, this);
     cbor_thread = std::thread(&TCPImagePuller::CBORThread, this);
+    heartbeat_thread = std::thread(&TCPImagePuller::HeartbeatThread, this);
 
     if (!repub_address.empty()) {
         repub_socket = std::make_unique<ZMQSocket>(ZMQSocketType::Push);
@@ -91,6 +92,8 @@ bool TCPImagePuller::SendAll(const void *buf, size_t len) {
 }
 
 bool TCPImagePuller::SendAck(const PullerAckMessage &ack) {
+    std::lock_guard lg(send_mutex);
+
     TcpFrameHeader h{};
     h.type = static_cast<uint16_t>(TCPFrameType::ACK);
     h.run_number = ack.run_number;
@@ -319,7 +322,12 @@ void TCPImagePuller::ReceiverThread() {
                 TcpFrameHeader pong{};
                 pong.type = static_cast<uint16_t>(TCPFrameType::KEEPALIVE);
                 pong.payload_size = 0;
-                if (!SendAll(&pong, sizeof(pong))) {
+                bool pong_ok;
+                {
+                    std::lock_guard lg(send_mutex);
+                    pong_ok = SendAll(&pong, sizeof(pong));
+                }
+                if (!pong_ok) {
                     logger.Info("Keepalive pong send failed, reconnecting to " + addr);
                     CloseSocket();
                     std::this_thread::sleep_for(std::chrono::milliseconds(20));
@@ -365,6 +373,37 @@ void TCPImagePuller::ReceiverThread() {
     cbor_fifo.PutBlocking(ImagePullerOutput{});
 }
 
+void TCPImagePuller::HeartbeatThread() {
+    // While connected, periodically tell the pusher we are alive even if the
+    // consuming pipeline is stalled (e.g. blocked on a slow filesystem). This lets
+    // the pusher distinguish a busy-but-healthy writer from a dead one and keep
+    // waiting through arbitrarily long backpressure instead of dropping the run.
+    while (!disconnect) {
+        // Sleep in small slices so shutdown stays prompt.
+        for (int i = 0; i < 5 && !disconnect; i++)
+            std::this_thread::sleep_for(HeartbeatInterval / 5);
+        if (disconnect)
+            break;
+
+        {
+            std::unique_lock ul(fd_mutex);
+            if (fd < 0)
+                continue; // Not connected; ReceiverThread is (re)establishing the link.
+        }
+
+        TcpFrameHeader h{};
+        h.type = static_cast<uint16_t>(TCPFrameType::BUSY);
+        h.payload_size = 0;
+        h.ack_fifo_occupancy = cbor_fifo.GetCurrentUtilization();
+        h.ack_fifo_max_occupancy = cbor_fifo.Size();
+
+        // Best effort: a failure here just means the socket is gone, which
+        // ReceiverThread will detect and reconnect on its own.
+        std::lock_guard lg(send_mutex);
+        SendAll(&h, sizeof(h));
+    }
+}
+
 void TCPImagePuller::Disconnect() {
     if (disconnect.exchange(true))
         return;
@@ -377,4 +416,6 @@ void TCPImagePuller::Disconnect() {
         cbor_thread.join();
     if (repub_thread.joinable())
         repub_thread.join();
+    if (heartbeat_thread.joinable())
+        heartbeat_thread.join();
 }
diff --git a/image_puller/TCPImagePuller.h b/image_puller/TCPImagePuller.h
index 5b5f444f..3a0c795e 100644
--- a/image_puller/TCPImagePuller.h
+++ b/image_puller/TCPImagePuller.h
@@ -29,11 +29,17 @@ class TCPImagePuller : public ImagePuller {
     std::thread receiver_thread;
     std::thread cbor_thread;
     std::thread repub_thread;
+    std::thread heartbeat_thread;
+
+    // Serializes all writer->pusher sends (ACKs, keepalive pongs, busy heartbeats)
+    // so that concurrently-sent frames cannot interleave on the socket.
+    std::mutex send_mutex;
 
     Logger logger{"TCPImagePuller"};
 
     static constexpr uint32_t default_repub_watermark = 220;
     static constexpr auto RepubTimeout = std::chrono::milliseconds(100);
+    static constexpr auto HeartbeatInterval = std::chrono::milliseconds(250);
 
     bool ReadExact(void *buf, size_t size);
     bool SendAll(const void *buf, size_t len);
@@ -42,6 +48,7 @@ class TCPImagePuller : public ImagePuller {
     void ReceiverThread();
     void CBORThread();
     void RepubThread();
+    void HeartbeatThread();
 public:
     explicit TCPImagePuller(const std::string &tcp_addr,
                             std::optional<int32_t> rcv_buffer_size = {},
diff --git a/image_pusher/TCPStreamPusher.cpp b/image_pusher/TCPStreamPusher.cpp
index 892b1bbc..88678d3b 100644
--- a/image_pusher/TCPStreamPusher.cpp
+++ b/image_pusher/TCPStreamPusher.cpp
@@ -15,6 +15,13 @@
 #include <linux/errqueue.h>
 #endif
 
+namespace {
+int64_t SteadyNowNs() {
+    return std::chrono::duration_cast<std::chrono::nanoseconds>(
+        std::chrono::steady_clock::now().time_since_epoch()).count();
+}
+}
+
 std::pair<std::string, std::optional<uint16_t>> TCPStreamPusher::ParseTcpAddress(const std::string& addr) {
     const std::string prefix = "tcp://";
     if (addr.rfind(prefix, 0) != 0)
@@ -197,10 +204,6 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
     bool zc_used = false;
     uint32_t zc_first = 0;
     uint32_t zc_last = 0;
-    // Watchdog on *lack of progress*, not total time: a slow but advancing transfer
-    // (a writer applying back-pressure) must not be torn down, only a socket that
-    // stops moving bytes altogether. Reset on every byte actually handed to the kernel.
-    auto last_progress = std::chrono::steady_clock::now();
 
     bool try_zerocopy = false;
 #if defined(MSG_ZEROCOPY)
@@ -216,7 +219,13 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
             return false;
         }
 
-        if (std::chrono::steady_clock::now() - last_progress >= send_total_timeout) {
+        // Treat backpressure as fatal only if the peer shows NO sign of life. A busy
+        // writer keeps refreshing last_peer_activity_ns via BUSY heartbeats / ACKs, so
+        // we wait through arbitrarily long stalls; only a silent peer trips the timeout.
+        const int64_t silent_ns = SteadyNowNs() - c.last_peer_activity_ns.load(std::memory_order_relaxed);
+        if (silent_ns > std::chrono::duration_cast<std::chrono::nanoseconds>(peer_liveness_timeout).count()) {
+            logger.Warning("No liveness from writer on socket " + std::to_string(c.socket_number) +
+                           " for " + std::to_string(silent_ns / 1000000) + " ms while sending; marking broken");
             c.broken = true;
             CloseFd(c.fd);
             if (zc_used_out) *zc_used_out = zc_used;
@@ -291,9 +300,6 @@ bool TCPStreamPusher::SendAll(Connection& c, const void* buf, size_t len, bool a
         }
 #endif
 
-        if (rc > 0)
-            last_progress = std::chrono::steady_clock::now();
-
         sent += static_cast<size_t>(rc);
     }
 
@@ -584,6 +590,9 @@ void TCPStreamPusher::PersistentAckThread(Connection* c) {
             break;
         }
 
+        // Any well-formed frame from the peer is a sign of life.
+        c->last_peer_activity_ns.store(SteadyNowNs(), std::memory_order_relaxed);
+
         const auto frame_type = static_cast<TCPFrameType>(h.type);
 
         // Keepalive pong from the writer
@@ -596,6 +605,17 @@ void TCPStreamPusher::PersistentAckThread(Connection* c) {
             continue;
         }
 
+        // Busy/backpressure heartbeat: the writer is alive but stalled. The liveness
+        // timestamp update above is all we need; just record reported FIFO occupancy.
+        if (frame_type == TCPFrameType::BUSY) {
+            c->last_ack_fifo_occupancy.store(h.ack_fifo_occupancy, std::memory_order_relaxed);
+            if (h.payload_size > 0) {
+                std::vector<uint8_t> discard(h.payload_size);
+                ReadExactPersistent(*c, discard.data(), discard.size());
+            }
+            continue;
+        }
+
         if (frame_type != TCPFrameType::ACK) {
             c->broken = true;
             logger.Error("Unexpected frame type " + std::to_string(h.type) + " on socket " + std::to_string(c->socket_number));
@@ -737,6 +757,7 @@ void TCPStreamPusher::SetupNewConnection(int new_fd, uint32_t socket_number) {
     auto now = std::chrono::steady_clock::now();
     c->last_keepalive_sent = now;
     c->last_keepalive_recv = now;
+    c->last_peer_activity_ns.store(SteadyNowNs(), std::memory_order_relaxed);
 
     auto* raw = c.get();
     c->persistent_ack_future = std::async(std::launch::async, &TCPStreamPusher::PersistentAckThread, this, raw);
@@ -910,26 +931,26 @@ bool TCPStreamPusher::WaitForAck(Connection& c, TCPFrameType ack_for, std::chron
     return ack_ok;
 }
 
-bool TCPStreamPusher::WaitForEndAck(Connection& c, std::chrono::milliseconds no_progress_timeout, std::string* error_text) {
+bool TCPStreamPusher::WaitForEndAck(Connection& c, std::chrono::milliseconds liveness_timeout, std::string* error_text) {
     std::unique_lock ul(c.ack_mutex);
 
-    // After END is sent the writer may still be draining a backlog of DATA frames.
-    // Each DATA ACK that arrives is forward progress, so the END timer is effectively
-    // armed only once the writer falls silent: the timeout fires when neither a DATA
-    // ACK nor the END ACK is seen for the whole window, not while images still drain.
-    uint64_t last_acked = c.data_acked_total.load(std::memory_order_relaxed);
-
+    // After END is sent the writer may still be flushing a backlog to a slow filesystem.
+    // It keeps proving it is alive via BUSY heartbeats and DATA ACKs (both refresh
+    // last_peer_activity_ns), so we wait through arbitrarily long stalls and only give up
+    // if the peer falls completely silent for the whole liveness window.
     while (!c.end_ack_received && !c.broken) {
-        const bool progressed = c.ack_cv.wait_for(ul, no_progress_timeout, [&] {
-            return c.end_ack_received || c.broken.load()
-                   || c.data_acked_total.load(std::memory_order_relaxed) != last_acked;
+        c.ack_cv.wait_for(ul, liveness_timeout, [&] {
+            return c.end_ack_received || c.broken.load();
         });
 
-        if (!progressed) {
-            if (error_text) *error_text = "END ACK timeout (writer stalled)";
+        if (c.end_ack_received || c.broken)
+            break;
+
+        const int64_t silent_ns = SteadyNowNs() - c.last_peer_activity_ns.load(std::memory_order_relaxed);
+        if (silent_ns > std::chrono::duration_cast<std::chrono::nanoseconds>(liveness_timeout).count()) {
+            if (error_text) *error_text = "END ACK timeout (writer silent)";
             return false;
         }
-        last_acked = c.data_acked_total.load(std::memory_order_relaxed);
     }
 
     if (c.broken) {
@@ -1121,7 +1142,7 @@ bool TCPStreamPusher::EndDataCollection(const EndMessage& message) {
         }
 
         std::string ack_err;
-        if (!WaitForEndAck(c, std::chrono::seconds(10), &ack_err))
+        if (!WaitForEndAck(c, peer_liveness_timeout, &ack_err))
             ret = false;
     }
 
diff --git a/image_pusher/TCPStreamPusher.h b/image_pusher/TCPStreamPusher.h
index dfa62c03..2ae61271 100644
--- a/image_pusher/TCPStreamPusher.h
+++ b/image_pusher/TCPStreamPusher.h
@@ -95,6 +95,11 @@ class TCPStreamPusher : public ImagePusher {
 
         std::chrono::steady_clock::time_point last_keepalive_sent{};
         std::chrono::steady_clock::time_point last_keepalive_recv{};
+
+        // Last time ANY frame (ACK / keepalive pong / busy heartbeat) was received from
+        // the peer, as steady_clock nanoseconds. Used to keep a healthy-but-busy writer
+        // alive through long backpressure while still detecting a genuinely dead peer.
+        std::atomic<int64_t> last_peer_activity_ns{0};
     };
 
     std::string endpoint;
@@ -116,7 +121,11 @@ class TCPStreamPusher : public ImagePusher {
     std::future<void> keepalive_future;
 
     std::chrono::milliseconds send_poll_timeout{250};
-    std::chrono::milliseconds send_total_timeout{3000};
+    // Maximum time a send (or the post-END ACK wait) may block with NO sign of life from
+    // the peer before the connection is declared dead. A busy writer refreshes its liveness
+    // every ~250 ms via BUSY heartbeats (and via DATA ACKs), so genuine backpressure of any
+    // duration is tolerated; only a truly silent (frozen/dead) peer trips this.
+    std::chrono::milliseconds peer_liveness_timeout{15000};
 
     int64_t images_per_file = 1;
     uint64_t run_number = 0;
@@ -161,7 +170,7 @@ class TCPStreamPusher : public ImagePusher {
     bool WaitForZeroCopyDrain(Connection& c, std::chrono::milliseconds timeout);
 
     bool WaitForAck(Connection& c, TCPFrameType ack_for, std::chrono::milliseconds timeout, std::string* error_text);
-    bool WaitForEndAck(Connection& c, std::chrono::milliseconds no_progress_timeout, std::string* error_text);
+    bool WaitForEndAck(Connection& c, std::chrono::milliseconds liveness_timeout, std::string* error_text);
 public:
     explicit TCPStreamPusher(const std::string& addr,
                              size_t in_max_connections,
-- 
2.52.0


From d156dfa2e8d3f501ffccfa10874fff7b1bdc05c6 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 18:09:37 +0200
Subject: [PATCH 225/228] TCP stream: gate SendImage enqueue on writer liveness
 too

The broker logs for the dropped runs show the connection torn down ~2s into
a collection (not 3s), via "TCP send failed -> Removed dead connection ->
Accepted (new socket)". That is too early for the SendAll send deadline:
the real gate was the fixed 2-second enqueue deadline in the zerocopy
SendImage path. At the start of a large dataset the writer briefly stalls
draining the socket while it creates the master file and writes the large
START metadata + calibration frames to GPFS; the per-connection queue fills,
and after 2s SendImage marked the connection broken. The writer then
reconnected outside the active session, so the rest of the run was dropped
and the half-written file was finalized at the next START.

Replace the fixed 2s enqueue deadline with the same peer-liveness condition
used on the send path: keep applying backpressure while the writer proves it
is alive (BUSY heartbeats / ACKs refresh last_peer_activity_ns from a thread
independent of the stalled write path), and only declare it dead after the
liveness window of complete silence. A transient startup stall is now ridden
out instead of dropping the run.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 image_pusher/TCPStreamPusher.cpp | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/image_pusher/TCPStreamPusher.cpp b/image_pusher/TCPStreamPusher.cpp
index 88678d3b..7c2656ba 100644
--- a/image_pusher/TCPStreamPusher.cpp
+++ b/image_pusher/TCPStreamPusher.cpp
@@ -1094,23 +1094,28 @@ bool TCPStreamPusher::SendImage(ZeroCopyReturnValue &z) {
         return false;
     }
 
-    const auto deadline = std::chrono::steady_clock::now() + std::chrono::seconds(2);
-    while (std::chrono::steady_clock::now() < deadline) {
-        if (target->broken || !target->active) {
-            z.release();
-            return false;
-        }
-
+    // A full queue means the writer is applying backpressure (e.g. briefly stalled on a
+    // freshly-created file at startup). Keep waiting as long as it proves it is alive —
+    // BUSY heartbeats / ACKs refresh last_peer_activity_ns from a thread independent of
+    // its stalled write path — so a slow-but-healthy writer is held back, not dropped.
+    // Only a peer that has gone completely silent for the liveness window is declared dead.
+    while (!target->broken && target->active) {
         if (target->queue.PutTimeout(ImagePusherQueueElement{
                 .image_data = static_cast<uint8_t *>(z.GetImage()),
                 .z = &z,
                 .end = false
-            }, std::chrono::milliseconds(50))) {
+            }, std::chrono::milliseconds(50)))
             return true;
-            }
+
+        const int64_t silent_ns = SteadyNowNs() - target->last_peer_activity_ns.load(std::memory_order_relaxed);
+        if (silent_ns > std::chrono::duration_cast<std::chrono::nanoseconds>(peer_liveness_timeout).count()) {
+            logger.Warning("No liveness from writer on socket " + std::to_string(target->socket_number) +
+                           " for " + std::to_string(silent_ns / 1000000) + " ms while enqueuing; marking broken");
+            target->broken = true;
+            break;
+        }
     }
 
-    target->broken = true;
     z.release();
     return false;
 }
-- 
2.52.0


From 145b300fa2a4e82cd4b02e6c8e6288239548ba03 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 18:27:04 +0200
Subject: [PATCH 226/228] broker: fail the run loudly when the writer breaks
 mid-acquisition

A writer connection that dropped mid-run left a truncated file, yet the
acquisition was still logged as "finished with success": the writer error
returned by ImagePusher::Finalize() (set via transmission_error on a broken
session connection) was captured into receiver_output.writer_err but never
acted upon.

Treat a non-empty writer_err as a failed acquisition: throw so it is reported
as "finished with error" and surfaced to the caller, instead of silently
succeeding with incomplete data. Applies to both the Lite and FPGA workflows,
which share this stop/finalize path. Combined with the liveness changes (which
no longer tear a connection down for a transient stall), this fires only on a
genuine writer break.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 broker/JFJochServices.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/broker/JFJochServices.cpp b/broker/JFJochServices.cpp
index 1d30ed54..b5913a81 100644
--- a/broker/JFJochServices.cpp
+++ b/broker/JFJochServices.cpp
@@ -122,6 +122,14 @@ JFJochServicesOutput JFJochServices::Stop() {
                                     ret.receiver_output.received_packets[i], ret.receiver_output.expected_packets[i]);
                 }
             }
+
+            // A writer that broke mid-run (e.g. a lost connection) leaves a truncated file.
+            // Surface that as a failed acquisition instead of silently reporting success.
+            if (!ret.receiver_output.writer_err.empty())
+                throw JFJochException(JFJochExceptionCategory::FileWriteError,
+                                      "Writer error, written data may be incomplete: "
+                                      + ret.receiver_output.writer_err);
+
             logger.Info("    ... finished with success");
         } catch (const JFJochException &e) {
             logger.Error("   ... finished with error {}", e.what());
-- 
2.52.0


From e121918f55e31c25001f062c6d6de7b6f1ee0881 Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 19:03:40 +0200
Subject: [PATCH 227/228] docs/CHANGELOG.md: round out the rc.153 entry

Add the biggest user-facing changes the entry was missing: the trimming-energies
config change for PSI EIGER (now compulsory), ROI definitions/bitmap in the master
file with azimuthal phi sectors, and the viewer redesign + in-GUI jfjoch_process jobs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 docs/CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index cae444e1..291950ba 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -9,6 +9,10 @@ This is an UNSTABLE release. It includes many experimental features, as well as
 * jfjoch_broker: Fixes to TCP image pusher
 * jfjoch_broker: Remove NUMA bindings
 * jfjoch_broker: Improvements to indexing
+* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
+* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
+* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
+* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results
 
 ### 1.0.0-rc.152
 * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5)
-- 
2.52.0


From 50b08388d154b55aa3cd71ad87253d4dda890c1c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Tue, 23 Jun 2026 20:15:51 +0200
Subject: [PATCH 228/228] viewer: bound live-monitor memory with
 frame-in-flight backpressure
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The image-reading worker (on its own thread) posted imageLoaded — a full
~40 MB JFJochReaderImage on a 9 Mpix detector — to ~13 GUI consumers over
queued connections, paced only by its own load+analysis time. When the GUI
render (image + azimuthal integration + plots) was the bottleneck, those
queued events piled up without bound and memory blew up.

Funnel every consumer through one window signal: the worker's imageLoaded
crosses the thread boundary exactly once, into JFJochViewerWindow::
OnImageReady, which re-emits imageReady to all GUI consumers synchronously
(same thread) and then acks the worker (imageConsumed). The worker tracks
images_in_flight and AutoLoadTimerExpired stops producing once the cap
(max_images_in_flight = 4) is reached — applied to every auto mode.

Live follow drops intermediate frames (next fetch grabs the newest image);
movie playback paces down to GUI speed without skipping. The existing
adaptive autoload interval is unchanged.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 viewer/JFJochImageReadingWorker.cpp | 38 ++++++++++++++++++++++-------
 viewer/JFJochImageReadingWorker.h   | 11 +++++++++
 viewer/JFJochViewerWindow.cpp       | 38 ++++++++++++++++++++---------
 viewer/JFJochViewerWindow.h         | 11 +++++++++
 4 files changed, 77 insertions(+), 21 deletions(-)

diff --git a/viewer/JFJochImageReadingWorker.cpp b/viewer/JFJochImageReadingWorker.cpp
index f304df4e..81c3def1 100644
--- a/viewer/JFJochImageReadingWorker.cpp
+++ b/viewer/JFJochImageReadingWorker.cpp
@@ -312,7 +312,7 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
         ResetFileOpenRetry_i();
 
         emit datasetLoaded({});
-        emit imageLoaded({});
+        EmitImageLoaded_i({});
     }
 }
 
@@ -342,7 +342,7 @@ void JFJochImageReadingWorker::CloseFile() {
     current_summation = 1;
     total_images = 0;
     current_file = "";
-    emit imageLoaded({});
+    EmitImageLoaded_i({});
     emit datasetLoaded({});
 }
 
@@ -397,7 +397,7 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
         }
 
         if (!current_image_ptr) {
-            emit imageLoaded({});
+            EmitImageLoaded_i({});
             return;
         }
 
@@ -446,7 +446,7 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
 
         logger.Info("Loaded image {} in {}/{} ms Autoload timer set to {} ms", image_number, duration_1, duration_2, autoload_interval);
         emit imageNumberChanged(total_images, current_image.value());
-        emit imageLoaded(current_image_ptr);
+        EmitImageLoaded_i(current_image_ptr);
     } catch (std::exception &e) {
         logger.Error("Error loading image {}: {}", image_number, e.what());
     }
@@ -488,7 +488,7 @@ void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionEx
 
     if (auto_reanalyze)
         ReanalyzeImage_i();
-    emit imageLoaded(current_image_ptr);
+    EmitImageLoaded_i(current_image_ptr);
 }
 
 void JFJochImageReadingWorker::UpdateDataset(const DiffractionExperiment &experiment) {
@@ -525,7 +525,7 @@ void JFJochImageReadingWorker::ReanalyzeImage_i() {
 void JFJochImageReadingWorker::Analyze() {
     QMutexLocker locker(&m);
     ReanalyzeImage_i();
-    emit imageLoaded(current_image_ptr);
+    EmitImageLoaded_i(current_image_ptr);
 }
 
 void JFJochImageReadingWorker::FindCenter(const UnitCell& calibrant, bool guess) {
@@ -582,7 +582,7 @@ void JFJochImageReadingWorker::UpdateSpotFindingSettings(const SpotFindingSettin
 
     if (auto_reanalyze) {
         ReanalyzeImage_i();
-        emit imageLoaded(current_image_ptr);
+        EmitImageLoaded_i(current_image_ptr);
     }
 }
 
@@ -592,7 +592,7 @@ void JFJochImageReadingWorker::ReanalyzeImages(bool input) {
 
     if (auto_reanalyze) {
         ReanalyzeImage_i();
-        emit imageLoaded(current_image_ptr);
+        EmitImageLoaded_i(current_image_ptr);
     }
 }
 
@@ -703,7 +703,7 @@ void JFJochImageReadingWorker::SetROIDefinition_i(const ROIDefinition &rois) {
     }
 
     emit datasetLoaded(dataset);
-    emit imageLoaded(current_image_ptr);
+    EmitImageLoaded_i(current_image_ptr);
 }
 
 void JFJochImageReadingWorker::ApplyROIOverrideToImage_i() {
@@ -821,6 +821,14 @@ void JFJochImageReadingWorker::LoadCalibration(QString dataset) {
 
 void JFJochImageReadingWorker::AutoLoadTimerExpired() {
     QMutexLocker locker(&m);
+
+    // Backpressure (all auto modes): don't hand the GUI more frames than it has rendered - it acks
+    // each one via ImageConsumed(). Without this a fast producer (live follow or movie playback)
+    // outruns rendering and the queued imageLoaded events pile up unbounded. Intermediate frames are
+    // skipped, which for a live monitor is exactly right (the next fetch grabs the newest image).
+    if (images_in_flight >= max_images_in_flight)
+        return;
+
     switch (autoload_mode) {
         case AutoloadMode::HTTPSync:
             if (http_mode)
@@ -842,6 +850,18 @@ void JFJochImageReadingWorker::AutoLoadTimerExpired() {
     }
 }
 
+void JFJochImageReadingWorker::EmitImageLoaded_i(const std::shared_ptr<const JFJochReaderImage>& image) {
+    // Assumes m locked! Count every frame handed to the GUI; ImageConsumed() decrements it once the
+    // frame has been rendered. AutoLoadTimerExpired caps how many frames may be in flight at once.
+    ++images_in_flight;
+    emit imageLoaded(image);
+}
+
+void JFJochImageReadingWorker::ImageConsumed() {
+    QMutexLocker locker(&m);
+    --images_in_flight;
+}
+
 void JFJochImageReadingWorker::SetHttpConnected_i(bool connected, const QString &addr) {
     // Assumes m locked! Only signals on a real change so the status bar does not flicker.
     if (connected == http_connected)
diff --git a/viewer/JFJochImageReadingWorker.h b/viewer/JFJochImageReadingWorker.h
index 94a982e7..efe6f395 100644
--- a/viewer/JFJochImageReadingWorker.h
+++ b/viewer/JFJochImageReadingWorker.h
@@ -119,6 +119,12 @@ private:
     int autoload_interval_max_ms = 2000;      // 0.5 Hz as bottom limit
     float autoload_safety_factor = 2.0f;
 
+    // Backpressure: cap how many frames may be "in flight" to the GUI (emitted but not yet rendered
+    // and acked via ImageConsumed). The autoload timer won't produce another frame while the cap is
+    // reached, so a fast producer can't grow the queued-event backlog without bound.
+    int images_in_flight = 0;
+    int max_images_in_flight = 4;
+
     // File open retry/back-off (GPFS via NFSv4 visibility lag)
     struct PendingLoadRequest {
         QString filename;
@@ -140,6 +146,7 @@ private:
 
     void LoadFile_i(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void LoadImage_i(int64_t image_number, int64_t summation);
+    void EmitImageLoaded_i(const std::shared_ptr<const JFJochReaderImage>& image);
     void RefreshDatasetOnly_i();
     void SetHttpConnected_i(bool connected, const QString &addr);
     void ReanalyzeImage_i();
@@ -216,6 +223,10 @@ public slots:
     void setAutoLoadMode(AutoloadMode mode);
     void setAutoLoadJump(int64_t val);
 
+    // GUI acks that it has consumed (rendered) one frame, freeing an in-flight slot. Drives the
+    // autoload backpressure so the reader can't outrun the viewer (see images_in_flight).
+    void ImageConsumed();
+
     // Register a reprocessing result (_process.h5) as a metadata snapshot over the same images and
     // make it the active dataset; SetActiveSnapshot switches between registered snapshots.
     void RegisterProcessingSnapshot(QString id, QString label, QString master_path);
diff --git a/viewer/JFJochViewerWindow.cpp b/viewer/JFJochViewerWindow.cpp
index 2a496cec..1f195b58 100644
--- a/viewer/JFJochViewerWindow.cpp
+++ b/viewer/JFJochViewerWindow.cpp
@@ -230,10 +230,19 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(menuBar, &JFJochViewerMenu::fileCloseSelected,
             reading_worker, &JFJochImageReadingWorker::CloseFile);
 
+    // The worker runs in its own thread; its imageLoaded crosses the thread boundary exactly once,
+    // into OnImageReady, which re-emits imageReady to every GUI consumer synchronously (same thread)
+    // and then acks the worker (imageConsumed). Routing all consumers through one window signal makes
+    // the ack land after they have all run, and lets the worker cap how many frames are in flight.
     connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+            this, &JFJochViewerWindow::OnImageReady);
+    connect(this, &JFJochViewerWindow::imageConsumed,
+            reading_worker, &JFJochImageReadingWorker::ImageConsumed);
+
+    connect(this, &JFJochViewerWindow::imageReady,
             viewer, &JFJochDiffractionImage::loadImage);
 
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             side_panel, &JFJochViewerSidePanel::loadImage);
 
     connect(reading_worker, &JFJochImageReadingWorker::imageStatsUpdated,
@@ -262,7 +271,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged, azintImageWindow,
             &JFJoch2DAzintImageWindow::setColorMap);
 
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             azintImageWindow, &JFJoch2DAzintImageWindow::imageLoaded);
 
     connect(viewer, &JFJochDiffractionImage::foregroundChanged,
@@ -304,10 +313,10 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             metadataWindow, &JFJochViewerMetadataWindow::datasetLoaded);
 
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             tableWindow, &JFJochViewerImageListWindow::imageLoaded);
 
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             spotWindow, &JFJochViewerSpotListWindow::imageLoaded);
 
     connect(tableWindow, &JFJochViewerImageListWindow::imageSelected,
@@ -338,7 +347,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             reflectionWindow, &JFJochViewerReflectionListWindow::datasetLoaded);
 
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             reflectionWindow, &JFJochViewerReflectionListWindow::imageLoaded);
 
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
@@ -414,7 +423,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::datasetLoaded);
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::imageLoaded);
 
     connect(reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::loadSpotsRequest,
@@ -437,7 +446,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             viewer, &JFJochDiffractionImage::centerOnSpot);
 
     // --- Magnifier ---
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             magnifierWindow, &JFJochHelperWindow::imageLoaded);
     connect(viewer, &JFJochImage::hoverScenePos,
             magnifierWindow, &JFJochMagnifierWindow::centerAt);
@@ -447,10 +456,9 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
 
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded, this,
             [this](std::shared_ptr<const JFJochReaderDataset> ds) { lastDataset = std::move(ds); });
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded, this,
-            [this](std::shared_ptr<const JFJochReaderImage> im) { lastImage = std::move(im); });
+    // lastImage is captured in OnImageReady, which sees every frame before fanning it out.
 
-        connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+        connect(this, &JFJochViewerWindow::imageReady,
             toolBarDisplay, &JFJochViewerToolbarDisplay::imageLoaded);
 
     connect(reading_worker, &JFJochImageReadingWorker::fileLoadError,
@@ -522,7 +530,7 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::FindCenter);
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             settingsPanel, &JFJochViewerSettingsDock::datasetLoaded);
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             settingsPanel, &JFJochViewerSettingsDock::loadImage);
     connect(settingsPanel, &JFJochViewerSettingsDock::ringsFromCalibration,
             side_panel, &JFJochViewerSidePanel::SetRings);
@@ -629,6 +637,12 @@ void JFJochViewerWindow::LoadImage(qint64 image_number, qint64 summation) {
     emit LoadImageRequest(image_number, summation);
 }
 
+void JFJochViewerWindow::OnImageReady(std::shared_ptr<const JFJochReaderImage> image) {
+    lastImage = image;          // newest frame, for dataset-info docks opened later
+    emit imageReady(image);     // fan out to every GUI consumer synchronously (same thread)
+    emit imageConsumed();       // ack the worker so it may fetch/produce the next frame
+}
+
 void JFJochViewerWindow::NewDatasetInfo() {
     auto info = new JFJochViewerDatasetInfo(this);
     info->datasetLoaded(lastDataset);
@@ -652,7 +666,7 @@ void JFJochViewerWindow::NewDatasetInfo() {
     // Wire signals like the initial dataset_info
     connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
             info, &JFJochViewerDatasetInfo::datasetLoaded);
-    connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
+    connect(this, &JFJochViewerWindow::imageReady,
             info, &JFJochViewerDatasetInfo::imageLoaded);
     // All runs (original + reprocessing snapshots) overlay as separate lines.
     connect(reading_worker, &JFJochImageReadingWorker::runsChanged,
diff --git a/viewer/JFJochViewerWindow.h b/viewer/JFJochViewerWindow.h
index 6562ca4f..e2ec806a 100644
--- a/viewer/JFJochViewerWindow.h
+++ b/viewer/JFJochViewerWindow.h
@@ -55,6 +55,12 @@ private:
     void keyPressEvent(QKeyEvent *event) override;
     void keyReleaseEvent(QKeyEvent *event) override;
     void closeEvent(QCloseEvent *event) override;
+
+private slots:
+    // Single cross-thread sink for the worker's imageLoaded: fans out to every GUI consumer
+    // (synchronously, same thread) via imageReady, then acks the worker so it may produce the next.
+    void OnImageReady(std::shared_ptr<const JFJochReaderImage> image);
+
 public slots:
     void LoadFile(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void LoadImage(qint64 image_number, qint64 summation);
@@ -63,6 +69,11 @@ public slots:
     void OnFileLoadRetryStatus(bool active, QString message);
 
 signals:
+    // Internal GUI-thread fan-out of the newest frame: OnImageReady re-emits this to every GUI
+    // consumer synchronously, then acks via imageConsumed (see OnImageReady).
+    void imageReady(std::shared_ptr<const JFJochReaderImage> image);
+    void imageConsumed();   // ack to the worker that one frame has been consumed (backpressure)
+
     void LoadFileRequest(const QString &filename, qint64 image_number, qint64 summation, bool retry);
     void LoadImageRequest(int64_t image_number, int64_t summation);
     void adjustForegroundButton(bool input);
-- 
2.52.0