Merge branch '2509.rc.87' into 'main'

1.0.0-rc.87

See merge request jungfraujoch/nextgendcu!176

.gitattributes

@@ -1,2 +0,0 @@
-*.mcs filter=lfs diff=lfs merge=lfs -text
-*.mcs.gz filter=lfs diff=lfs merge=lfs -text

.gitea/workflows/build_and_test.yml

@@ -12,7 +12,6 @@ on:
 jobs:
   build-rpm:
     name: build:rpm (${{ matrix.distro }})
-    if: github.ref_type == 'tag'
     runs-on: ${{ matrix.runner }}
     strategy:
       fail-fast: false
@@ -21,30 +20,48 @@ jobs:
           - runner: jfjoch_rocky8
             distro: rocky8
             cmake_flags: -DJFJOCH_USE_CUDA=ON
+            pkg_glob: "*.rpm"
+            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12/upload
           - runner: jfjoch_rocky8
             distro: rocky8_sls9
             cmake_flags: -DJFJOCH_USE_CUDA=ON -DSLS9=ON
+            pkg_glob: "*.rpm"
+            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12/upload
           - runner: jfjoch_rocky8
             distro: rocky8_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
+            pkg_glob: "*.rpm"
+            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda/upload
           - runner: jfjoch_rocky9
             distro: rocky9
             cmake_flags: -DJFJOCH_USE_CUDA=ON
+            pkg_glob: "*.rpm"
+            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-cuda13/upload
           - runner: jfjoch_rocky9
             distro: rocky9_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
+            pkg_glob: "*.rpm"
+            upload_url: https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda/upload
           - runner: jfjoch_ubuntu2204
             distro: ubuntu2204
             cmake_flags: -DJFJOCH_USE_CUDA=ON
+            pkg_glob: "*.deb"
+            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/cuda13/upload
           - runner: jfjoch_ubuntu2204
             distro: ubuntu2204_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
+            pkg_glob: "*.deb"
+            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/nocuda/upload
           - runner: jfjoch_ubuntu2404
             distro: ubuntu2404
             cmake_flags: -DJFJOCH_USE_CUDA=ON
+            pkg_glob: "*.deb"
+            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/noble/cuda13/upload
           - runner: jfjoch_ubuntu2404
             distro: ubuntu2404_nocuda
             cmake_flags: -DJFJOCH_USE_CUDA=OFF
+            pkg_glob: "*.deb"
+            upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/noble/nocuda/upload
     steps:
       - uses: actions/checkout@v4
       - name: Build packages
@@ -58,74 +75,21 @@ jobs:
       - name: Upload packages
         if: github.ref_type == 'tag'
         shell: bash
+        env:
+          TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
         run: |
+          set -euo pipefail
           cd build
-          if [ "${{ matrix.distro }}" = "rocky8" ]; then
-            for file in *.rpm; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "rocky8_nocuda" ]; then
-            for file in *.rpm; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "rocky8_sls9" ]; then
-            for file in *.rpm; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "rocky9_nocuda" ]; then
-            for file in *.rpm; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "ubuntu2204_nocuda" ]; then
-            for file in *.deb; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/nocuda/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "ubuntu2204" ]; then
-            for file in *.deb; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/debian/pool/jammy/cuda13/upload
-              fi
-            done
-          elif [ "${{ matrix.distro }}" = "ubuntu2404" ]; then
-            for file in *.deb; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/debian/pool/noble/cuda13/upload
-              fi
-            done
-          fi
-          elif [ "${{ matrix.distro }}" = "ubuntu2404_nocuda" ]; then
-            for file in *.deb; do
-              if [ -f "$file" ]; then
-                curl --user __token__:${{ secrets.PIP_REPOSITORY_API_TOKEN }} \
-                     --upload-file "$file" \
-                     https://gitea.psi.ch/api/packages/mx/debian/pool/noble/nocuda/upload
-              fi
-            done
+          shopt -s nullglob
+          files=(${{ matrix.pkg_glob }})
+          if [ ${#files[@]} -eq 0 ]; then
+            echo "No package files found for pattern: ${{ matrix.pkg_glob }}"
+            exit 1
           fi
+          for file in "${files[@]}"; do
+            echo "Uploading $file -> ${{ matrix.upload_url }}"
+            curl --fail --user __token__:"$TOKEN" --upload-file "$file" "${{ matrix.upload_url }}"
+          done
   python-client:
     name: Generate python client
     runs-on: jfjoch_rocky8
@@ -139,30 +103,7 @@ jobs:
         run: |
           twine upload -u __token__ -p ${{ secrets.CI_PYPI_TOKEN }} --skip-existing dist/*
           twine upload -u __token__ -p ${{ secrets.PIP_REPOSITORY_API_TOKEN }} --repository-url https://gitea.psi.ch/api/packages/mx/pypi dist/*
-  create-release:
-    name: Create release
-    runs-on: jfjoch_rocky8
-    # if: github.ref_type == 'tag'
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          persist-credentials: 'true' # Optional; should be the default
-      - 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: Create release
-        env:
-          GITEA_TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
-        shell: bash
-        run: |
-          python3 gitea_create_release.py
+
   documentation:
     name: Build documentation
     runs-on: jfjoch_rocky8
@@ -192,7 +133,6 @@ jobs:
   unit-tests:
     name: Unit tests
     runs-on: jfjoch_rocky8
-    if: github.ref_type == 'tag'
     container:
       image: gitea.psi.ch/leonarski_f/jfjoch_rocky8:2509
       options: --gpus all

common/JFJochMessages.h

@@ -133,9 +133,11 @@ struct DataMessage {
     std::optional<int64_t> original_number;
     std::vector<Reflection> reflections;
 
-    std::vector<float> integration_logI;
-    std::vector<float> integration_one_over_d;
+    std::vector<float> integration_B_logI;
+    std::vector<float> integration_B_one_over_d;
+
     std::vector<float> integration_Isigma;
+    std::vector<float> integration_Isigma_one_over_d;
 
     std::optional<float> beam_corr_x;
     std::optional<float> beam_corr_y;

docker/rocky8/Dockerfile

@@ -14,7 +14,6 @@ RUN dnf -y update && \
       dnf-plugins-core \
       epel-release \
       git \
-      git-lfs \
       which \
       ca-certificates \
       wget \
@@ -61,15 +60,12 @@ RUN dnf -y update && \
       python3-pip \
       python3-setuptools \
       python3-wheel \
-      python3-requests \
       twine \
       openblas \
       openblas-devel \
       freetype-devel && \
     dnf clean all && rm -rf /var/cache/dnf
 
-RUN git lfs install
-
 RUN set -eux; \
     cd /tmp; \
     curl -LO https://www.openssl.org/source/openssl-${OPENSSL_VERSION}.tar.gz; \

docker/rocky9/Dockerfile

@@ -15,7 +15,6 @@ RUN dnf -y update && \
       dnf-plugins-core \
       epel-release \
       git \
-      git-lfs \
       which \
       ca-certificates \
       wget \
@@ -33,7 +32,6 @@ RUN dnf -y update && \
       redhat-rpm-config \
       ninja-build \
       python3 \
-      python3-requests \
       perl \
       pkgconf-pkg-config \
       libxcb-devel \
@@ -63,8 +61,6 @@ RUN dnf -y update && \
       freetype-devel && \
     dnf clean all && rm -rf /var/cache/dnf
 
-RUN git lfs install
-
 RUN set -eux; \
     cd /tmp; \
     curl -LO https://www.openssl.org/source/openssl-${OPENSSL_VERSION}.tar.gz; \

docs/CHANGELOG.md

@@ -1,4 +1,11 @@
 # Changelog
+## 1.0.0.rc.87
+This is an UNSTABLE release.
+
+* jfjoch_viewer: Display more image metadata (angle / exposure time)
+* jfjoch_viewer: Improve I/sigma and B-factor plots
+* jfjoch_broker: Estimate resolution based on visible spots
+
 ## 1.0.0.rc.86
 This is an UNSTABLE release.
 

gitea_create_release.py

@@ -1,122 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from typing import Optional
-try:
-    import requests
-except ModuleNotFoundError:
-    print("ERROR: Python 'requests' package is required. Please install it (e.g., pip install requests).")
-    sys.exit(1)
-
-gitea_api_url = "https://gitea.psi.ch/api/v1/"
-repo_owner = "mx"
-repo_name = "jungfraujoch"
-
-gitea_token = os.getenv('GITEA_TOKEN')
-if gitea_token is None:
-    print("ERROR: Required environment variables not set")
-    sys.exit(1)
-
-def read_version():
-    try:
-        with open('VERSION', 'r') as f:
-            return f.readline().strip()
-    except FileNotFoundError:
-        print("ERROR: VERSION file not found")
-        sys.exit(1)
-
-def create_release(version):
-    headers = {
-        'Authorization': f'token {gitea_token}',
-        'Content-Type': 'application/json',
-    }
-
-    data = {
-        'tag_name': version,
-        'name': f'Release {version}',
-        'draft': False,
-        'prerelease': '-rc.' in version or '-alpha.' in version or '-beta.' in version
-    }
-
-    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases'
-
-    response = requests.post(url, headers=headers, json=data)
-    if response.status_code != 201:
-        print(f"ERROR: Failed to create release. Status code: {response.status_code}")
-        print(response.text)
-        sys.exit(1)
-
-    release = response.json()
-    print(f"Successfully created release {version}")
-    return release
-
-def get_release_by_tag(version: str):
-    """
-    Fetch release information by tag name.
-    Returns the release object (dict) or exits on error.
-    """
-    headers = {
-        'Authorization': f'token {gitea_token}',
-        'Content-Type': 'application/json',
-    }
-    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases/tags/{version}'
-    resp = requests.get(url, headers=headers)
-    if resp.status_code != 200:
-        print(f"ERROR: Failed to fetch release {version}. Status code: {resp.status_code}")
-        print(resp.text)
-        sys.exit(1)
-    return resp.json()
-
-def upload_file_to_release(version: str, file_path: str, name: Optional[str] = None, label: Optional[str] = None):
-    """
-    Upload a file as an asset to the release identified by the given version tag.
-
-    :param version: Tag name of the release (e.g., '1.2.3' or '1.2.3-rc.1')
-    :param file_path: Local file path to upload
-    :param name: Optional asset name to display in release (defaults to filename)
-    :param label: Optional asset label (display name)
-    """
-    if not os.path.isfile(file_path):
-        print(f"ERROR: File not found: {file_path}")
-        sys.exit(1)
-
-    # Ensure the release exists and get its ID
-    release = get_release_by_tag(version)
-    release_id = release.get('id')
-    if release_id is None:
-        print("ERROR: Release ID not found in response")
-        sys.exit(1)
-
-    headers = {
-        'Authorization': f'token {gitea_token}',
-    }
-
-    asset_name = name if name else os.path.basename(file_path)
-    data = {'name': asset_name}
-    if label:
-        data['label'] = label
-
-    url = f'{gitea_api_url}/repos/{repo_owner}/{repo_name}/releases/{release_id}/assets'
-
-    with open(file_path, 'rb') as f:
-        files = {
-            'attachment': (asset_name, f, 'application/octet-stream'),
-        }
-        resp = requests.post(url, headers=headers, data=data, files=files)
-
-    if resp.status_code not in (201, 200):
-        print(f"ERROR: Failed to upload asset. Status code: {resp.status_code}")
-        print(resp.text)
-        sys.exit(1)
-
-    asset = resp.json()
-    browser_download_url = asset.get('browser_download_url') or asset.get('browser_url') or asset.get('url')
-    print(f"Uploaded asset '{asset_name}' to release {version}: {browser_download_url}")
-
-if __name__ == '__main__':
-    version = read_version()
-    release = create_release(version)
-
-    upload_file_to_release(version, 'fpga/images/jfjoch_fpga_pcie_8x10g.mcs.gz', 'jfjoch_fpga_pcie_8x10g.mcs.gz', '8x10G FPGA image')
-    upload_file_to_release(version, 'fpga/images/jfjoch_fpga_pcie_100g.mcs.gz', 'jfjoch_fpga_pcie_100g.mcs.gz', '100G FPGA image')

image_analysis/SpotAnalyze.cpp

@@ -8,7 +8,7 @@
 #include "spot_finding/StrongPixelSet.h"
 #include "bragg_integration/BraggIntegrate2D.h"
 #include "indexing/AnalyzeIndexing.h"
-
+#include "bragg_integration/CalcISigma.h"
 
 void SpotAnalyze(const DiffractionExperiment &experiment,
                  const SpotFindingSettings &spot_finding_settings,
@@ -86,16 +86,13 @@ void SpotAnalyze(const DiffractionExperiment &experiment,
                                                 ewald_dist_cutoff, output.number);
 
                     constexpr size_t kMaxReflections = 10000;
-                    if (res.reflections.size() > kMaxReflections) {
-                        output.reflections.assign(res.reflections.begin(),
-                                                  res.reflections.begin() + kMaxReflections);
+                    if (res.size() > kMaxReflections) {
+                        output.reflections.assign(res.begin(), res.begin() + kMaxReflections);
                     } else
-                        output.reflections = res.reflections;
+                        output.reflections = res;
 
-                    output.b_factor = res.b_factor;
-                    output.integration_Isigma = res.Isigma;
-                    output.integration_logI = res.logI;
-                    output.integration_one_over_d = res.one_over_d;
+                    CalcISigma(output);
+                    CalcWilsonBFactor(output);
                 }
             }
         }

image_analysis/bragg_integration/BraggIntegrate2D.cpp

@@ -4,13 +4,10 @@
 #include "BraggIntegrate2D.h"
 #include "BraggPrediction.h"
 
-#include "BraggIntegrationStats.h"
-
 template<class T>
 bool IntegrateReflection(Reflection &r, const T *image, size_t xpixel, size_t ypixel,
                          int64_t special_value, int64_t saturation,
                          float r_3, float r_1_sq, float r_2_sq, float r_3_sq) {
-
     r.I = 0;
     r.bkg = 0;
 
@@ -68,24 +65,23 @@ bool IntegrateReflection(Reflection &r, const T *image, size_t xpixel, size_t yp
 
 
 template<class T>
-QuickIntegrateResult IntegrateInternal(const DiffractionExperiment &experiment,
-                                       const CompressedImage &image,
-                                       const CrystalLattice &latt,
-                                       float dist_from_ewald_sphere,
-                                       int64_t special_value,
-                                       int64_t saturation,
-                                       int64_t image_number) {
+std::vector<Reflection> IntegrateInternal(const DiffractionExperiment &experiment,
+                                          const CompressedImage &image,
+                                          const CrystalLattice &latt,
+                                          float dist_from_ewald_sphere,
+                                          int64_t special_value,
+                                          int64_t saturation,
+                                          int64_t image_number) {
     auto settings = experiment.GetBraggIntegrationSettings();
     auto geom = experiment.GetDiffractionGeometry();
 
     auto start = std::chrono::high_resolution_clock::now();
     std::vector<uint8_t> buffer;
-    auto ptr = reinterpret_cast<const T*>(image.GetUncompressedPtr(buffer));
+    auto ptr = reinterpret_cast<const T *>(image.GetUncompressedPtr(buffer));
 
     auto refl = CalcBraggPredictions(experiment, latt, settings.GetDMinLimit_A(), dist_from_ewald_sphere);
 
-    QuickIntegrateResult ret;
-    BraggIntegrationStats stats(6.0, settings.GetDMinLimit_A(), 20); // Wilson statistics is only linear in certain resolution range
+    std::vector<Reflection> ret;
     float r_3 = settings.GetR3();
     float r_1_sq = settings.GetR1() * settings.GetR1();
     float r_2_sq = settings.GetR2() * settings.GetR2();
@@ -94,51 +90,52 @@ QuickIntegrateResult IntegrateInternal(const DiffractionExperiment &experiment,
     for (const auto &[x, r_in]: refl) {
         Reflection r = r_in;
         if (IntegrateReflection(r, ptr, image.GetWidth(), image.GetHeight(), special_value, saturation,
-                              r_3, r_1_sq, r_2_sq, r_3_sq)) {
+                                r_3, r_1_sq, r_2_sq, r_3_sq)) {
             if (experiment.GetPolarizationFactor()) {
-                float pol = geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y, experiment.GetPolarizationFactor().value());
+                float pol = geom.CalcAzIntPolarizationCorr(r.predicted_x, r.predicted_y,
+                                                           experiment.GetPolarizationFactor().value());
                 r.I /= pol;
                 r.bkg /= pol;
                 r.sigma /= pol;
             }
 
             r.image_number = static_cast<int>(image_number);
-            ret.reflections.push_back(r);
-            stats.AddReflection(r);
+            ret.push_back(r);
         }
     }
-    ret.b_factor = stats.BFactor();
-    ret.logI = stats.GetWilsonPlot();
-    ret.one_over_d = stats.GetWilsonPlotLegend();
-    ret.Isigma = stats.GetISigmaPlot();
 
     return ret;
 }
 
-QuickIntegrateResult BraggIntegrate2D(const DiffractionExperiment &experiment,
-                                      const CompressedImage &image,
-                                      const CrystalLattice &latt,
-                                      float dist_from_ewald_sphere,
-                                      int64_t image_number) {
+std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
+                                         const CompressedImage &image,
+                                         const CrystalLattice &latt,
+                                         float dist_from_ewald_sphere,
+                                         int64_t image_number) {
     if (image.GetCompressedSize() == 0)
         return {};
 
     switch (image.GetMode()) {
         case CompressedImageMode::Int8:
-            return IntegrateInternal<int8_t>(experiment, image, latt, dist_from_ewald_sphere, INT8_MIN, INT8_MAX, image_number);
+            return IntegrateInternal<int8_t>(experiment, image, latt, dist_from_ewald_sphere, INT8_MIN, INT8_MAX,
+                                             image_number);
         case CompressedImageMode::Int16:
-            return IntegrateInternal<int16_t>(experiment, image, latt, dist_from_ewald_sphere, INT16_MIN, INT16_MAX, image_number);
+            return IntegrateInternal<int16_t>(experiment, image, latt, dist_from_ewald_sphere, INT16_MIN, INT16_MAX,
+                                              image_number);
         case CompressedImageMode::Int32:
-            return IntegrateInternal<int32_t>(experiment, image, latt, dist_from_ewald_sphere, INT32_MIN, INT32_MAX, image_number);
+            return IntegrateInternal<int32_t>(experiment, image, latt, dist_from_ewald_sphere, INT32_MIN, INT32_MAX,
+                                              image_number);
         case CompressedImageMode::Uint8:
-            return IntegrateInternal<uint8_t>(experiment, image, latt, dist_from_ewald_sphere, UINT8_MAX, UINT8_MAX, image_number);
+            return IntegrateInternal<uint8_t>(experiment, image, latt, dist_from_ewald_sphere, UINT8_MAX, UINT8_MAX,
+                                              image_number);
         case CompressedImageMode::Uint16:
-            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT16_MAX, UINT16_MAX, image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT16_MAX, UINT16_MAX,
+                                               image_number);
         case CompressedImageMode::Uint32:
-            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT32_MAX, UINT32_MAX, image_number);
+            return IntegrateInternal<uint16_t>(experiment, image, latt, dist_from_ewald_sphere, UINT32_MAX, UINT32_MAX,
+                                               image_number);
         default:
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                   "Image mode not supported");
     }
 }
-

image_analysis/bragg_integration/BraggIntegrate2D.h

@@ -9,18 +9,10 @@
 #include "../../common/CrystalLattice.h"
 #include "../../common/Reflection.h"
 
-struct QuickIntegrateResult {
-    std::vector<Reflection> reflections;
-    std::optional<float> b_factor;
-    std::vector<float> logI;
-    std::vector<float> one_over_d;
-    std::vector<float> Isigma;
-};
-
-QuickIntegrateResult BraggIntegrate2D(const DiffractionExperiment &experiment,
-                                      const CompressedImage &image,
-                                      const CrystalLattice &latt,
-                                      float dist_from_ewald_sphere,
-                                      int64_t image_number);
+std::vector<Reflection> BraggIntegrate2D(const DiffractionExperiment &experiment,
+                                         const CompressedImage &image,
+                                         const CrystalLattice &latt,
+                                         float dist_from_ewald_sphere,
+                                         int64_t image_number);
 
 #endif //JFJOCH_BRAGGINTEGRATE2D_H

image_analysis/bragg_integration/BraggIntegrationStats.cpp

@@ -39,12 +39,12 @@ std::optional<float> BraggIntegrationStats::BFactor() {
                            + (static_cast<float>(i) + 0.5) * (one_over_dmin - one_over_dmax) / static_cast<float>(nshells);
         wilson_plot_legend.push_back(one_over_d);
         if (count[i] == 0 )
-            plot_Isigma.push_back(NAN);
+            plot_Isigma.push_back(0);
         else
             plot_Isigma.push_back(I_sigma[i] / count[i]);
 
         if (count[i] == 0 || I[i] < 0.0 || I_sigma[i] < 0.2f * count[i])
-            wilson_plot.push_back(NAN);
+            wilson_plot.push_back(0);
         else
             wilson_plot.push_back(log(I[i] / count[i]));
     }
@@ -60,7 +60,7 @@ std::vector<float> BraggIntegrationStats::GetWilsonPlot() {
     return wilson_plot;
 }
 
-std::vector<float> BraggIntegrationStats::GetWilsonPlotLegend() {
+std::vector<float> BraggIntegrationStats::GetOneOverDPlot() {
     return wilson_plot_legend;
 }
 

image_analysis/bragg_integration/BraggIntegrationStats.h

@@ -23,11 +23,11 @@ class BraggIntegrationStats {
     std::vector<float> wilson_plot_legend;
     std::vector<float> plot_Isigma;
 public:
-    explicit BraggIntegrationStats(float d_max_A = 6.0, float d_min_A = 1.5, int32_t nshells = 20);
+    explicit BraggIntegrationStats(float d_max_A, float d_min_A, int32_t nshells);
     void AddReflection(const Reflection &r);
     std::optional<float> BFactor();
     std::vector<float> GetWilsonPlot();
-    std::vector<float> GetWilsonPlotLegend();
+    std::vector<float> GetOneOverDPlot();
     std::vector<float> GetISigmaPlot();
 };
 

image_analysis/bragg_integration/CMakeLists.txt

@@ -6,6 +6,8 @@ ADD_LIBRARY(JFJochBraggIntegration STATIC
         BraggIntegrationStats.cpp
         BraggIntegrationStats.h
         Regression.h
+        CalcISigma.cpp
+        CalcISigma.h
 )
 
 TARGET_LINK_LIBRARIES(JFJochBraggIntegration JFJochCommon)

image_analysis/bragg_integration/CalcISigma.cpp

@@ -0,0 +1,32 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "CalcISigma.h"
+#include "BraggIntegrationStats.h"
+
+void CalcISigma(DataMessage &msg) {
+    if (msg.reflections.empty())
+        return;
+
+    BraggIntegrationStats stats(50.0, 1.5, 20);
+    for (const auto &r: msg.reflections)
+        stats.AddReflection(r);
+
+    stats.BFactor(); // need to do it to generate plots...
+
+    msg.integration_Isigma = stats.GetISigmaPlot();
+    msg.integration_Isigma_one_over_d = stats.GetOneOverDPlot();
+}
+
+void CalcWilsonBFactor(DataMessage &msg) {
+    if (msg.reflections.empty())
+        return;
+
+    BraggIntegrationStats stats(6.0, 3.0, 10); // Wilson statistics is only linear in certain resolution range
+    for (const auto &r: msg.reflections)
+        stats.AddReflection(r);
+
+    msg.b_factor = stats.BFactor();
+    msg.integration_B_logI = stats.GetWilsonPlot();
+    msg.integration_B_one_over_d = stats.GetOneOverDPlot();
+}

image_analysis/bragg_integration/CalcISigma.h

@@ -0,0 +1,12 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#ifndef JFJOCH_CALCISIGMA_H
+#define JFJOCH_CALCISIGMA_H
+
+#include "../../common/JFJochMessages.h"
+
+void CalcISigma(DataMessage &msg);
+void CalcWilsonBFactor(DataMessage &msg);
+
+#endif //JFJOCH_CALCISIGMA_H

image_analysis/spot_finding/SpotFindingSettings.h

@@ -19,7 +19,7 @@ struct SpotFindingSettings {
     float ice_ring_width_Q_recipA = 0.02;
 
     bool indexing = true;
-    bool quick_integration = false;
+    bool quick_integration = true;
 };
 
 #endif //JUNGFRAUJOCH_SPOTFINDINGSETTINGS_H

reader/JFJochHDF5Reader.cpp

@@ -4,6 +4,7 @@
 #include "JFJochHDF5Reader.h"
 #include "spdlog/fmt/fmt.h"
 #include "../image_analysis/bragg_integration/BraggIntegrationStats.h"
+#include "../image_analysis/bragg_integration/CalcISigma.h"
 
 std::vector<hsize_t> GetDimension(HDF5Object& object, const std::string& path) {
     const auto dim = object.GetDimension(path);
@@ -542,8 +543,6 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
             || 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");
-        BraggIntegrationSettings settings;
-        BraggIntegrationStats stats(6.0, settings.GetDMinLimit_A(), 10); // Wilson statistics is only linear in certain resolution range
 
         for (size_t i = 0; i < h.size(); i++) {
             Reflection r{
@@ -557,13 +556,10 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
                 .bkg = bkg.at(i),
                 .sigma = int_err.at(i)
             };
-            stats.AddReflection(r);
             message.reflections.emplace_back(r);
         }
-
-        message.integration_logI = stats.GetWilsonPlot();
-        message.integration_one_over_d = stats.GetWilsonPlotLegend();
-        message.integration_Isigma = stats.GetISigmaPlot();
+        CalcISigma(message);
+        CalcWilsonBFactor(message);
     }
 
     return true;

reader/JFJochHttpReader.cpp

@@ -8,6 +8,7 @@
 #include "../frame_serialize/CBORStream2Deserializer.h"
 #include "../broker/gen/model/Image_buffer_status.h"
 #include "../broker/gen/model/Plots.h"
+#include "../image_analysis/bragg_integration/CalcISigma.h"
 
 void JFJochHttpReader::Close_i() {
     addr = "";
@@ -155,6 +156,10 @@ bool JFJochHttpReader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
             return false;
 
         message = *msg->data_message;
+
+        CalcISigma(message);
+        CalcWilsonBFactor(message);
+
         return true;
     } catch (std::exception &e) {
         return false;

viewer/JFJochViewerImageStatistics.cpp

@@ -3,6 +3,7 @@
 
 #include "JFJochViewerImageStatistics.h"
 #include <QFormLayout>
+#include <QRegularExpression>
 
 static QString mkSourceInstrumentText(const DiffractionExperiment& exp) {
     QString src, inst;
@@ -61,11 +62,11 @@ JFJochViewerImageStatistics::JFJochViewerImageStatistics(QWidget *parent) : QWid
     sample_name = new QLabel(this);
     layout->addRow("Sample:", sample_name);
 
-    error_pixels = new QLabel(this);
-    layout->addRow(new QLabel("Error pixels:"), error_pixels);
+    exposure_time = new QLabel(this);
+    layout->addRow(new QLabel("Exposure Time:"), exposure_time);
 
-    sat_pixels = new QLabel(this);
-    layout->addRow(new QLabel("Sat. pixels:"), sat_pixels);
+    rotation_angle = new QLabel(this);
+    layout->addRow(new QLabel("Image angle:"), rotation_angle);
 
     valid_values = new QLabel(this);
     layout->addRow(new QLabel("Valid values:"), valid_values);
@@ -99,6 +100,17 @@ JFJochViewerImageStatistics::JFJochViewerImageStatistics(QWidget *parent) : QWid
 
 }
 
+QString TrimZeros(double number, int precision) {
+    auto s = QString::number(number, 'f', precision);
+    s.remove(QRegularExpression("\\.?0+$"));
+    if (s.isEmpty()) s = "0";
+    return s;
+}
+
+QString FormatTime(std::chrono::microseconds time) {
+    return TrimZeros(time.count()/1e6, 6);
+}
+
 void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
     if (!image) {
         source_name->setText("");
@@ -107,9 +119,12 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
         dataset_name->setToolTip("");
         detector_name->setText("");
         detector_name->setToolTip("");
-        error_pixels->setText("");
-        sat_pixels->setText("");
+        exposure_time->setText("");
+        exposure_time->setToolTip("");
+        rotation_angle->setText("");
+        rotation_angle->setToolTip("");
         valid_values->setText("");
+        valid_values->setToolTip("");
         spots->setText("");
         bkg_estimate->setText("");
         indexed->setText("");
@@ -146,16 +161,24 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
     detector_name->setText(text);
 
     source_name->setText(mkSourceInstrumentText(exp));
-    source_name->setToolTip(mkSampleTooltip(exp));
+    source_name->setToolTip(mkSourceInstrumentTooltip(exp));
 
     sample_name->setText(mkSampleText(exp));
     sample_name->setToolTip(mkSampleTooltip(exp));
 
-    text = QString("<b>%1</b>").arg(image->ErrorPixels().size());
-    error_pixels->setText(text);
-
-    text = QString("<b>%1</b>").arg(image->SaturatedPixels().size());
-    sat_pixels->setText(text);
+    if (exp.GetGoniometer()) {
+        rotation_angle->setText(QString("<b>%1°</b>")
+            .arg(TrimZeros(exp.GetGoniometer()->GetIncrement_deg(), 3)));
+        rotation_angle->setToolTip(QString("Start angle: <b>%1°</b><br/>This image: <b>%2°</b>")
+            .arg(TrimZeros(exp.GetGoniometer()->GetStart_deg(), 3))
+            .arg(TrimZeros(exp.GetGoniometer()->GetAngle_deg(image->ImageData().number), 3))
+            );
+    } else {
+        rotation_angle->setText(QString("-"));
+        rotation_angle->setToolTip("");
+    }
+    exposure_time->setText(QString("<b>%1</b> s").arg(FormatTime(exp.GetImageTime())));
+    exposure_time->setToolTip(QString("Count time: <b>%1</b> s<br/>").arg(FormatTime(exp.GetImageCountTime())));
 
     text = QString("<b>%1</b>").arg(image->ImageData().spots.size());
     spots->setText(text);
@@ -170,6 +193,8 @@ void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderIm
             .arg(image->ValidPixels().begin()->first)
             .arg(image->ValidPixels().rbegin()->first);
     valid_values->setText(text);
+    valid_values->setToolTip(QString("Error pixels: <b>%1</b><br/>Saturated pixels: <b>%2</b>")
+        .arg(image->ErrorPixels().size()).arg(image->SaturatedPixels().size()));
 
     if (!image->Dataset().bkg_estimate.empty()) {
         text = QString("<b>%1</b>").arg(image->ImageData().bkg_estimate.value_or(0));

viewer/JFJochViewerImageStatistics.h

@@ -15,8 +15,8 @@ class JFJochViewerImageStatistics : public QWidget {
     QLabel *sample_name;
     QLabel *dataset_name;
     QLabel *detector_name;
-    QLabel *error_pixels;
-    QLabel *sat_pixels;
+    QLabel *exposure_time;
+    QLabel *rotation_angle;
     QLabel *spots;
     QLabel *valid_values;
     QLabel *indexed;

viewer/JFJochViewerSidePanelChart.cpp

@@ -24,8 +24,8 @@ JFJochViewerSidePanelChart::JFJochViewerSidePanelChart(QWidget *parent) : QWidge
     azint_image = new JFJochAzIntImageView(this);
 
     stack = new QStackedWidget(this);
-    stack->addWidget(azint_plot);   // index 0
-    stack->addWidget(azint_image);  // index 1
+    stack->addWidget(azint_plot); // index 0
+    stack->addWidget(azint_image); // index 1
     layout->addWidget(stack);
 
     setLayout(layout);
@@ -44,7 +44,8 @@ void JFJochViewerSidePanelChart::comboBoxSelected(int val) {
 }
 
 void JFJochViewerSidePanelChart::redrawPlot() {
-    std::vector<float> x,y;
+    std::vector<float> x, y;
+    bool one_over_x = false;
     if (image) {
         auto index = combo_box->currentIndex();
         switch (combo_box->itemData(index).toInt()) {
@@ -53,12 +54,14 @@ void JFJochViewerSidePanelChart::redrawPlot() {
                 y = image->GetAzInt1D();
                 break;
             case 1:
-                x = image->ImageData().integration_one_over_d;
-                y = image->ImageData().integration_logI;
+                x = image->ImageData().integration_B_one_over_d;
+                y = image->ImageData().integration_B_logI;
+                one_over_x = true;
                 break;
             case 2:
-                x = image->ImageData().integration_one_over_d;
+                x = image->ImageData().integration_Isigma_one_over_d;
                 y = image->ImageData().integration_Isigma;
+                one_over_x = true;
                 break;
             case 4:
                 x = image->Dataset().experiment.GetFluorescenceSpectrum().GetEnergy_eV();
@@ -83,7 +86,7 @@ void JFJochViewerSidePanelChart::redrawPlot() {
         }
     }
     if (!x.empty() && !y.empty()) {
-        azint_plot->UpdateData(x,y);
+        azint_plot->UpdateData(x, y, one_over_x);
     } else {
         azint_plot->ClearData();
     }
@@ -92,4 +95,4 @@ void JFJochViewerSidePanelChart::redrawPlot() {
 void JFJochViewerSidePanelChart::loadImage(std::shared_ptr<const JFJochReaderImage> in_image) {
     image = in_image;
     redrawPlot();
-}
+}

viewer/widgets/JFJochSimpleChartView.cpp

@@ -6,6 +6,7 @@
 #include <QMenu>
 #include <QClipboard>
 #include <QApplication>
+#include <QCategoryAxis>
 
 JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
         : QChartView(new QChart(), parent) {
@@ -15,16 +16,58 @@ JFJochSimpleChartView::JFJochSimpleChartView(QWidget *parent)
     //setRubberBand(QChartView::RubberBand::HorizontalRubberBand);
 }
 
-void JFJochSimpleChartView::UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y) {
-    x = in_x;
-    y = in_y;
+void JFJochSimpleChartView::UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y, bool one_over_x) {
+    x = in_x; y = in_y;
     chart()->removeAllSeries();
-    if (!x.empty() && x.size() == y.size()) {
-        series = new QLineSeries(this);
-        for (int i = 0; i < x.size(); i++)
-            series->append(x[i], in_y[i]);
-        chart()->addSeries(series);
-        chart()->createDefaultAxes();
+    // Remove all axes to avoid duplicates
+    for (auto ax : chart()->axes()) chart()->removeAxis(ax);
+
+    if (x.empty() || x.size() != y.size()) return;
+
+    auto* series = new QLineSeries(this);
+    for (size_t i = 0; i < x.size(); ++i) series->append(x[i], y[i]);
+    chart()->addSeries(series);
+
+    auto* axY = new QValueAxis();
+    chart()->addAxis(axY, Qt::AlignLeft);
+    series->attachAxis(axY);
+
+    // Build X range
+    auto [minXIt, maxXIt] = std::minmax_element(x.begin(), x.end());
+    const double xmin = *minXIt, xmax = *maxXIt;
+
+    if (one_over_x) {
+        // Hidden X value axis on top for grid/range
+        auto* axXTop = new QValueAxis();
+        axXTop->setRange(xmin, xmax);
+        axXTop->setTickCount(5);
+        axXTop->setLabelsVisible(false);
+        chart()->addAxis(axXTop, Qt::AlignTop);
+        series->attachAxis(axXTop);
+
+        // Visible category axis at bottom for 1/x labels
+        auto* axXcat = new QCategoryAxis();
+        axXcat->setLabelsPosition(QCategoryAxis::AxisLabelsPositionOnValue);
+        axXcat->setGridLineVisible(false);
+        axXcat->setMinorGridLineVisible(false);
+
+        const int tickCount = axXTop->tickCount();
+        const double step = (tickCount > 1) ? (xmax - xmin) / (tickCount - 1) : 0.0;
+        for (int i = 0; i < tickCount; ++i) {
+            const double xv = xmin + i * step;
+            const QString lab = (std::abs(xv) < 1e-12)
+                                ? QStringLiteral("∞")
+                                : QString::number(1.0 / xv, 'g', 4);
+            axXcat->append(lab, xv);
+        }
+        chart()->addAxis(axXcat, Qt::AlignBottom);
+        series->attachAxis(axXcat);
+    } else {
+        // Normal value axis at bottom
+        auto* axX = new QValueAxis();
+        axX->setRange(xmin, xmax);
+        chart()->addAxis(axX, Qt::AlignBottom);
+        series->attachAxis(axX);
     }
 }
 
@@ -51,3 +94,31 @@ void JFJochSimpleChartView::contextMenuEvent(QContextMenuEvent *event) {
         cb->setText(out);
     }
 }
+
+void JFJochSimpleChartView::applyInverseXLabels(QValueAxis* axX, QLineSeries* s) {
+    axX->setTickCount(5); // adjust as needed
+    axX->setLabelsVisible(false); // hide default numeric labels
+
+    auto* axXcat = new QCategoryAxis();
+    axXcat->setLabelsPosition(QCategoryAxis::AxisLabelsPositionOnValue);
+    axXcat->setGridLineVisible(false);
+    axXcat->setMinorGridLineVisible(false);
+
+    const int tickCount = axX->tickCount();
+    const double min = axX->min();
+    const double max = axX->max();
+    const double step = (tickCount > 1) ? (max - min) / (tickCount - 1) : 0.0;
+
+    for (int i = 0; i < tickCount; ++i) {
+        const double xv = min + i * step;
+        if (std::abs(xv) < 1e-12) {
+            axXcat->append("∞", xv);
+        } else {
+            const double inv = 1.0 / xv;
+            axXcat->append(QString::number(inv, 'g', 4), xv);
+        }
+    }
+
+    chart()->addAxis(axXcat, Qt::AlignBottom);
+    s->attachAxis(axXcat);
+}

viewer/widgets/JFJochSimpleChartView.h

@@ -11,15 +11,16 @@
 class JFJochSimpleChartView  : public QChartView {
     Q_OBJECT
 
-    QLineSeries *series = nullptr;
     std::vector<float> x, y;
 
+    void applyInverseXLabels(QValueAxis* axX, QLineSeries* s);
     void Plot();
 protected:
     void contextMenuEvent(QContextMenuEvent *event) override;
 public:
     JFJochSimpleChartView(QWidget *parent = nullptr);
-    void UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y);
+    void UpdateData(const std::vector<float> &in_x, const std::vector<float> &in_y, bool one_over_x);
+
     void ClearData();
 };