mx/Jungfraujoch
0
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases 38 Wiki Activity

v1.0.0-rc.124 (#31)
All checks were successful
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 11m23s
Details
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 10m32s
Details
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 9m15s
Details
Build Packages / Generate python client (push) Successful in 19s
Details
Build Packages / Build documentation (push) Successful in 49s
Details
Build Packages / Create release (push) Has been skipped
Details
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 9m13s
Details
Build Packages / build:rpm (rocky8) (push) Successful in 9m10s
Details
Build Packages / build:rpm (rocky9) (push) Successful in 9m58s
Details
Build Packages / build:rpm (ubuntu2204) (push) Successful in 8m52s
Details
Build Packages / build:rpm (ubuntu2404) (push) Successful in 8m42s
Details
Build Packages / Unit tests (push) Successful in 1h12m44s
Details
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 11m30s
Details

Browse Source 
This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them,
especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123.

* jfjoch_broker: Improve refection position prediction and Bragg integration code.
* jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation.
* jfjoch_writer: Fix saving mosaicity properly in HDF5 file.
* jfjoch_viewer: Introduce high-dynamic range mode for images
* jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%)
* jfjoch_viewer: Zoom-in numbers have better readability

Reviewed-on: #31
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This commit was merged in pull request #31.
This commit is contained in:
leonarski_f
2026-02-01 13:29:33 +01:00
committed by leonarski_f
parent 1c4dfd03e2
commit 07fe4dd3bb
212 changed files with 2861 additions and 905 deletions
Download Patch File Download Diff File Expand all files Collapse all files

121
tests/XtalOptimizerTest.cpp
View File

@@ -5,7 +5,7 @@
#include <iostream>
#include "../image_analysis/geom_refinement/XtalOptimizer.h"
#include "../image_analysis/bragg_integration/BraggPrediction.h"
#include "../image_analysis/bragg_prediction/BraggPrediction.h"
TEST_CASE("XtalOptimizer") {
DiffractionExperiment exp_i;
@@ -203,15 +203,15 @@ TEST_CASE("XtalOptimizer_triclinic") {
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.5);
CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.05);
CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.05);
CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.05);
CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
}
@@ -361,15 +361,15 @@ TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta
<< " " << uc_o.gamma << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.3);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.3);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - 90) < 0.01);
CHECK(fabs(uc_o.gamma - 120) < 0.01);
CHECK(fabs(uc_o.alpha - 90) < 0.1);
CHECK(fabs(uc_o.beta - 90) < 0.1);
CHECK(fabs(uc_o.gamma - 120) < 0.1);
}
TEST_CASE("XtalOptimizer_cubic") {
@@ -469,15 +469,15 @@ TEST_CASE("XtalOptimizer_monoclinic") {
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta << " " << uc_o.gamma << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - uc_i.beta) < 0.02);
CHECK(fabs(uc_o.gamma - 90) < 0.02);
CHECK(fabs(uc_o.alpha - 90) < 0.05);
CHECK(fabs(uc_o.beta - uc_i.beta) < 0.05);
CHECK(fabs(uc_o.gamma - 90) < 0.05);
}
TEST_CASE("LatticeToRodrigues") {
@@ -576,7 +576,8 @@ TEST_CASE("XtalOptimizer_rotation") {
// Predict reflections for images at 0-30 deg.
for (int img = 0; img < 10; ++img) {
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
const RotMatrix rot = axis.GetTransformation(img);
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
@@ -626,3 +627,89 @@ TEST_CASE("XtalOptimizer_rotation") {
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
}
TEST_CASE("XtalOptimizer_refine_rotation_axis") {
// Geometry
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
// Base lattice (non-pathological)
CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
auto uc_ref = latt_base.GetUnitCell();
// Rotation axis: around X with 3 deg per image
GoniometerAxis axis("omega", 0.0f, 3.0f, Coord(1,0,0), std::nullopt);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.002
};
std::vector<SpotToSave> spots;
BraggPrediction prediction;
// Predict reflections for images at 0-30 deg.
for (int img = 0; img < 10; ++img) {
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
for (int i = 0; i < n; ++i) {
const auto& r = prediction.GetReflections().at(i);
SpotToSave s{};
s.x = r.predicted_x;
s.y = r.predicted_y;
s.image = img; // provide image index for rotation-aware refinement
s.intensity = 1.0f; // minimal positive value
s.ice_ring = false;
s.indexed = true;
spots.push_back(s);
}
}
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement
XtalOptimizerData xtal_opt;
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
xtal_opt.geom.BeamX_pxl(1003).BeamY_pxl(997).DetectorDistance_mm(200.0)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.axis = GoniometerAxis("omega", 0.0f, 3.0f,
Coord(0.8, 0.05, 0.05).Normalize(),
std::nullopt);
xtal_opt.min_spots = 200;
xtal_opt.refine_beam_center = true;
xtal_opt.refine_distance_mm = false;
xtal_opt.refine_detector_angles = false;
xtal_opt.refine_rotation_axis = true;
auto t0 = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto t1 = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer (rotation 4 images) took "
<< std::chrono::duration_cast<std::chrono::microseconds>(t1 - t0).count()
<< " microseconds" << std::endl;
const auto uc_out = xtal_opt.latt.GetUnitCell();
// Geometry checks
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2f);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2f);
// Lattice checks
CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
CHECK(fabsf(uc_ref.c - uc_out.c) < 0.3f);
CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
CHECK(fabsf(xtal_opt.axis->GetAxis().x - 1.0) < 0.01f);
CHECK(fabsf(xtal_opt.axis->GetAxis().y) < 0.01f);
CHECK(fabsf(xtal_opt.axis->GetAxis().z) < 0.01f);
}