jfjoch_hdf5_test: A bit more functions

This reverts commit b31ca511f6.

.gitea/workflows/build_and_test.yml

@@ -76,27 +76,16 @@ jobs:
             upload_url: https://gitea.psi.ch/api/packages/mx/debian/pool/noble/nocuda/upload
     steps:
       - uses: actions/checkout@v4
-      - name: Install CMake 3.26 on Ubuntu 22.04
-        if: matrix.distro == 'ubuntu2204' || matrix.distro == 'ubuntu2204_nocuda'
-        shell: bash
-        run: |
-          set -euo pipefail
-          apt-get update
-          apt-get install -y wget gpg ca-certificates
-          wget -qO- https://apt.kitware.com/keys/kitware-archive-latest.asc \
-            | gpg --dearmor \
-            | tee /usr/share/keyrings/kitware-archive-keyring.gpg > /dev/null
-          echo "deb [signed-by=/usr/share/keyrings/kitware-archive-keyring.gpg] https://apt.kitware.com/ubuntu/ jammy main" \
-            | tee /etc/apt/sources.list.d/kitware.list > /dev/null
-          apt-get update
-          apt-get install -y cmake=3.26.* cmake-data=3.26.* kitware-archive-keyring
-          cmake --version
-      - name: Build packages
+      - name: Setup build (cmake)
         shell: bash
         run: |
           mkdir -p build
           cd build
           cmake -G Ninja -DJFJOCH_INSTALL_DRIVER_SOURCE=ON -DJFJOCH_VIEWER_BUILD=ON -DCMAKE_BUILD_TYPE=Release ${{ matrix.cmake_flags }} ..
+      - name: Build packages
+        shell: bash
+        run: |
+          cd build
           ninja frontend
           ninja -j16 package
       - name: Upload packages
@@ -133,6 +122,32 @@ jobs:
                  python3 gitea_upload_file.py "$file"
             done
           fi
+  dials-test:
+    name: DIALS processing test
+    runs-on: jfjoch_rocky9
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build processing test
+        shell: bash
+        run: |
+          mkdir -p build
+          cd build
+          cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ..
+          ninja -j16 jfjoch_hdf5_test
+      - name: Generate test data (with virtual data set and 4 linked image files)
+        shell: bash
+        run: |
+          set -euo pipefail
+          mkdir -p dials_test
+          cd dials_test
+          ../build/tools/jfjoch_hdf5_test ../tests/test_data/compression_benchmark.h5 -n100 -f25 -V
+      - name: Run DIALS processing
+        shell: bash
+        run: |
+          source /opt/dials-v3-27-0/dials_env.sh
+          set -euo pipefail
+          cd dials_test
+          xia2.ssx image=writing_test_master.h5 space_group=P43212 unit_cell=78.551,78.551,36.914,90.000,90.000,90.000
   python-client:
     name: Generate python client
     runs-on: jfjoch_rocky8

CMakeLists.txt

@@ -175,7 +175,7 @@ ENDIF()
 
 IF (NOT JFJOCH_WRITER_ONLY)
     ADD_CUSTOM_COMMAND(OUTPUT frontend/dist/index.html
-            COMMAND npm install
+            COMMAND npm ci
             COMMAND npm run build
             COMMAND npm run redocly
             WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/frontend)

docker/rocky9/Dockerfile

@@ -8,6 +8,9 @@ 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"
+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
 
 # Update base, enable CRB (RHEL/Rocky 9), and install toolchain + Qt deps
 RUN dnf -y update && \
@@ -65,6 +68,8 @@ RUN dnf -y update && \
       libdrm-devel \
       libglvnd-core-devel \
       libglvnd-devel \
+      glibc-langpack-en \
+      glibc-locale-source \
       freetype-devel && \
     dnf clean all && rm -rf /var/cache/dnf
 
@@ -185,9 +190,23 @@ RUN set -eux; \
     cmake --install .; \
     cd /; rm -rf /tmp/qt-everywhere-src-${QT_VERSION} /tmp/qt-everywhere-src-${QT_VERSION}.tar.xz
 
+# Install DIALS using the official binary tarball workflow
+RUN set -eux; \
+    cd /tmp; \
+    curl -fL -o dials.tar.xz "${DIALS_TARBALL_URL}"; \
+    tar -xJf dials.tar.xz; \
+    cd dials-installer; \
+    ./install --prefix="${DIALS_PREFIX}"; \
+    cd /; \
+    rm -rf /tmp/dials.tar.xz /tmp/dials-*-linux-x86_64
+
 # Make Qt and Eigen discoverable by CMake
 ENV CMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}:/opt/hdf5-${HDF5_TAG}-static:/opt/qt-${QT_VERSION}-static
 
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
+
 # Set workdir for your project
 WORKDIR /workspace
 

docker/ubuntu2204/Dockerfile

@@ -22,11 +22,11 @@ RUN set -eux; \
       ca-certificates \
       curl \
       wget \
+      gpg \
       git \
       tar \
       xz-utils \
       build-essential \
-      cmake \
       ninja-build \
       python3 \
       python3-requests \
@@ -78,10 +78,25 @@ RUN set -eux; \
       libassimp-dev \
       libglvnd-dev \
       libfreetype6-dev; \
+    wget -qO- https://apt.kitware.com/keys/kitware-archive-latest.asc \
+      | gpg --dearmor \
+      | tee /usr/share/keyrings/kitware-archive-keyring.gpg > /dev/null; \
+    echo "deb [signed-by=/usr/share/keyrings/kitware-archive-keyring.gpg] https://apt.kitware.com/ubuntu/ jammy main" \
+      | tee /etc/apt/sources.list.d/kitware.list > /dev/null; \
+    apt-get update; \
+    apt-get install -y --no-install-recommends \
+      cmake=3.26.* \
+      cmake-data=3.26.* \
+      kitware-archive-keyring; \
     apt-get -y install gcc-12 g++-12; \
     apt-get clean; \
     rm -rf /var/lib/apt/lists/*
 
+# Use GCC/G++ 12 for builds
+ENV CC=/usr/bin/gcc-12
+ENV CXX=/usr/bin/g++-12
+ENV PATH=/usr/bin:${PATH}
+
 # Build a static OpenSSL
 RUN set -eux; \
     cd /tmp; \
@@ -166,11 +181,6 @@ RUN set -eux; \
 ENV CMAKE_PREFIX_PATH=/opt/libtiff-${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
 
-# Use GCC/G++ 12 for builds
-ENV CC=/usr/bin/gcc-12
-ENV CXX=/usr/bin/g++-12
-ENV PATH=/usr/bin:${PATH}
-
 # Build and install static Qt 6.9 with Core, Gui, Widgets, Charts, DBus
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \

make_doc.sh

@@ -1,6 +1,8 @@
 #!/bin/bash
 
-python3.12 -m venv tmp_venv/
+set -euo pipefail
+
+python3.11 -m venv tmp_venv/
 source tmp_venv/bin/activate
 
 pip install -r docs/requirements.txt

tools/jfjoch_hdf5_test.cpp

@@ -18,26 +18,48 @@ int main(int argc, char **argv) {
 
     RegisterHDF5Filter();
 
-    if ((argc < 2) || (argc > 4)) {
-        std::cout << "Usage: ./jfjoch_hdf5_test <JF4M hdf5 file> {{<#images>} <rate in Hz>}" << std::endl;
-        std::cout << std::endl;
-        std::cout << "Env. variables:" << std::endl;
-        std::cout << "HDF5DATASET_WRITE_TEST_PREFIX" << std::endl;
-        std::cout << "HDF5MASTER_NEW_FORMAT" << std::endl;
+    int64_t nimages_out = 100;
+
+    std::string prefix = "writing_test";
+    FileWriterFormat format = FileWriterFormat::NXmxLegacy;
+    std::optional<int64_t> images_per_file;
+    std::optional<float> rotation;
+
+    int opt;
+    while ((opt = getopt(argc, argv, "o:n:Vf:R:")) != -1) {
+        switch (opt) {
+            case 'o':
+                prefix = optarg;
+                break;
+            case 'n':
+                nimages_out = atoll(optarg);
+                break;
+            case 'V':
+                format = FileWriterFormat::NXmxVDS;
+                break;
+            case 'R':
+                rotation = atof(optarg);
+                break;
+            case 'f':
+                images_per_file = atoll(optarg);
+                if (images_per_file.value() <= 0) {
+                    std::cerr << "Invalid number of images per file: " << optarg << std::endl;
+                    exit(EXIT_FAILURE);
+                }
+                images_per_file = atoll(optarg);
+                break;
+            default:
+                std::cout << "Usage: ./jfjoch_hdf5_test <JF4M hdf5 file> [-o <prefix>] [-n <num images>] [-V] [-f <num images per file>] [-R<rotation angle>]" << std::endl;
+                exit(EXIT_FAILURE);
+        }
+    }
+
+    if (optind >= argc) {
+        std::cout << "Usage: ./jfjoch_hdf5_test <JF4M hdf5 file> [-o <prefix>] [-n <num images>] [-V] [-f <num images per file>] [-R<rotation angle>]" << std::endl;
         exit(EXIT_FAILURE);
     }
 
-    int64_t nimages_out = 100;
-    double rate = 2200;
-
-    if (argc >= 3)
-        nimages_out = atoi(argv[2]);
-    if (argc >= 4)
-        rate = atof(argv[3]);
-
-    std::chrono::microseconds period_us((rate == 0) ? 0 : (int64_t) (1.0e6 / rate));
-
-    HDF5ReadOnlyFile data(argv[1]);
+    HDF5ReadOnlyFile data(argv[optind]);
     HDF5DataSet dataset(data, "/entry/data/data");
     HDF5DataSpace file_space(dataset);
 
@@ -53,6 +75,8 @@ int main(int argc, char **argv) {
     x.BeamX_pxl(1090).BeamY_pxl(1136).DetectorDistance_mm(75).IncidentEnergy_keV(WVL_1A_IN_KEV);
     x.MaskModuleEdges(true);
     x.MaskChipEdges(true);
+    if (rotation && rotation.value() != 0.0)
+        x.Goniometer(GoniometerAxis("omega", 0, rotation.value(), Coord(-1,0,0), std::nullopt));
 
     if ((file_space.GetDimensions()[1] == 2164) && (file_space.GetDimensions()[2] == 2068)) {
         std::cout << "JF4M with gaps detected (2068 x 2164)" << std::endl;
@@ -64,16 +88,12 @@ int main(int argc, char **argv) {
     logger.Info("Number of images in the original dataset: " + std::to_string(nimages));
 
     // Set file name
-    if (std::getenv("HDF5DATASET_WRITE_TEST_PREFIX") == nullptr)
-        x.FilePrefix("writing_test");
-    else
-        x.FilePrefix(std::getenv("HDF5DATASET_WRITE_TEST_PREFIX"));
+    x.FilePrefix(prefix);
+    x.SetFileWriterFormat(format);
+    x.OverwriteExistingFiles(true);
 
-    if (std::getenv("HDF5MASTER_NEW_FORMAT") != nullptr) {
-        std::cout << "Using new format for HDF5 master file" << std::endl;
-        x.SetFileWriterFormat(FileWriterFormat::NXmxVDS);
-    } else
-        x.SetFileWriterFormat(FileWriterFormat::NXmxLegacy);
+    if (images_per_file.has_value())
+        x.ImagesPerFile(images_per_file.value());
 
     x.ImagesPerTrigger(nimages);
 
@@ -127,8 +147,6 @@ int main(int argc, char **argv) {
 
     size_t total_image_size = 0;
     for (int i = 0; i < nimages_out; i++) {
-        std::this_thread::sleep_until(start_time + i * period_us);
-
         DataMessage message{};
         message.image = CompressedImage(output[i % nimages], x.GetXPixelsNum(), x.GetYPixelsNum(),
                                         x.GetImageMode(), x.GetCompressionAlgorithm());