change Poisson log-likelihood truncation/thresholding strategy #1250
Workflow file for this run
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| name: Build and ctest and recon_test_pack CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - tof_sino_UCL | |
| paths-ignore: | |
| - '.appveyor.yml' | |
| - 'CITATION.cff' | |
| - '**/*.md' | |
| - '**/*.html' | |
| - '**/*.htm' | |
| - '**/*.tex' | |
| pull_request: | |
| branches: | |
| - master | |
| - tof_sino_UCL | |
| paths-ignore: | |
| - '.appveyor.yml' | |
| - 'CITATION.cff' | |
| - '**/*.md' | |
| - '**/*.html' | |
| - '**/*.htm' | |
| - '**/*.tex' | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 9 | |
| cuda_version: "0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=ON" | |
| BUILD_TYPE: "Release" | |
| parallelproj: "ON" | |
| ROOT: "ON" | |
| ITK: "OFF" | |
| - os: ubuntu-latest | |
| compiler: clang | |
| #compiler_version: | |
| cuda_version: "0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=ON" | |
| BUILD_TYPE: "Release" | |
| parallelproj: "ON" | |
| ROOT: "OFF" | |
| # currently using ITK 5.2 which doesn't like clang 14 | |
| ITK: "OFF" | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 10 | |
| cuda_version: "0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17" | |
| BUILD_TYPE: "Debug" | |
| parallelproj: "OFF" | |
| ROOT: "OFF" | |
| ITK: "ON" | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 12 | |
| cuda_version: "0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=20" | |
| BUILD_TYPE: "RelWithDebInfo" | |
| parallelproj: "ON" | |
| ROOT: "OFF" | |
| ITK: "ON" | |
| - os: ubuntu-latest | |
| compiler: gcc | |
| compiler_version: 12 | |
| cuda_version: "12.1.0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17" | |
| BUILD_TYPE: "Release" | |
| parallelproj: "ON" | |
| ROOT: "OFF" | |
| ITK: "ON" | |
| - os: macOS-latest | |
| compiler: gcc | |
| compiler_version: 11 | |
| cuda_version: "0" | |
| BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | |
| parallelproj: "OFF" | |
| BUILD_TYPE: "Debug" | |
| ROOT: "OFF" | |
| ITK: "OFF" | |
| # Currently disabled due to problems with listmode recon, see https://github.com/UCL/STIR/issues/1200 | |
| #- os: macOS-latest | |
| # compiler: clang | |
| # compiler_version: 16 | |
| # BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | |
| # parallelproj: "OFF" | |
| # BUILD_TYPE: "Release" | |
| # ROOT: "OFF" | |
| # ITK: "OFF" | |
| # let's run all of them, as opposed to aborting when one fails | |
| fail-fast: false | |
| name: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
| steps: | |
| - name: disk space | |
| shell: bash | |
| run: | | |
| case ${{matrix.os}} in | |
| (ubuntu* | macOS*) | |
| df -h | |
| # saves about 2GB | |
| echo removing dotnet | |
| sudo rm -rf /usr/share/dotnet | |
| # saves about 10 GB | |
| echo removing agent_tools | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| # saves about 10 GB | |
| echo removing android files | |
| sudo rm -rf /usr/local/lib/android | |
| df -h | |
| ;; | |
| (windows*) | |
| # no idea how to do this | |
| ;; | |
| esac | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: disk space | |
| shell: bash | |
| run: | | |
| case ${{matrix.os}} in | |
| (ubuntu* | macOS*) | |
| sudo .github/workflows/GHA_increase_disk_space.sh | |
| ;; | |
| (windows*) | |
| # no idea what to do here | |
| ;; | |
| esac | |
| - name: set_compiler_variables | |
| shell: bash | |
| run: | | |
| set -ex | |
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
| CC="clang" | |
| CXX="clang++" | |
| elif test 'XX${{ matrix.compiler }}' = 'XXgcc'; then | |
| CC="gcc" | |
| CXX="g++" | |
| fi | |
| if test 'XX${{ matrix.compiler_version }}' != 'XX'; then | |
| CC=${CC}-${{ matrix.compiler_version }} | |
| CXX=${CXX}-${{ matrix.compiler_version }} | |
| fi | |
| if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then | |
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
| brew install llvm@${{ matrix.compiler_version }} | |
| if test XX${HOMEBREW_PREFIX} = XX; then | |
| HOMEBREW_PREFIX=/usr/local | |
| fi | |
| LDFLAGS="-L$HOMEBREW_PREFIX/opt/llvm/lib/c++ -Wl,-rpath,$HOMEBREW_PREFIX/opt/llvm/lib/c++" | |
| # make available to jobs below | |
| echo LDFLAGS="$LDFLAGS" >> $GITHUB_ENV | |
| CC="$HOMEBREW_PREFIX/opt/llvm/bin/clang" | |
| CXX="$HOMEBREW_PREFIX/opt/llvm/bin/clang++" | |
| fi | |
| fi | |
| export CC CXX | |
| # make available to jobs below | |
| echo CC="$CC" >> $GITHUB_ENV | |
| echo CXX="$CXX" >> $GITHUB_ENV | |
| - if: matrix.cuda_version != '0' | |
| uses: Jimver/[email protected] | |
| id: cuda-toolkit | |
| with: | |
| cuda: ${{ matrix.cuda_version }} | |
| linux-local-args: '["--toolkit"]' | |
| - name: install_dependencies | |
| shell: bash | |
| run: | | |
| set -ex | |
| # We will install some external dependencies here | |
| CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | |
| case ${{matrix.os}} in | |
| (ubuntu*) | |
| sudo apt update | |
| # install compiler | |
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
| # package is called clang, need libomp-dev for OpenMP support | |
| sudo apt install $CC libomp-dev | |
| else | |
| sudo apt install $CXX | |
| fi | |
| # other dependencies | |
| sudo apt install libboost-dev libhdf5-serial-dev swig python3-dev nlohmann-json3-dev | |
| if test "${{matrix.ITK}}XX" == "ONXX"; then | |
| sudo apt install libinsighttoolkit5-dev | |
| fi | |
| # free up some disk space | |
| apt autoremove --purge && sudo apt clean | |
| PYTHON_EXECUTABLE=$(which python3) | |
| ;; | |
| (macOS*) | |
| brew install boost swig python nlohmann-json | |
| PYTHON_EXECUTABLE=$(which python3) | |
| ;; | |
| (windows*) | |
| # this compiles the whole thing so takes ages | |
| vcpkg install boost-core hdf5 nlohmann-json | |
| # swig is preinstalled and is currently not in vcpcg | |
| vcpkg list | |
| PYTHON_EXECUTABLE=$(which python3) | |
| ;; | |
| esac | |
| echo PYTHON_EXECUTABLE="$PYTHON_EXECUTABLE" >> $GITHUB_ENV | |
| ${PYTHON_EXECUTABLE} -m venv ${GITHUB_WORKSPACE}/my-env | |
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
| #python -m pip install -U pip | |
| case ${{matrix.os}} in | |
| (macOS*) | |
| # attempt to get round buggy Accelerate builds, see https://github.com/numpy/numpy/issues/15947 | |
| # but it didn't work, so commented out | |
| # brew install openblas | |
| # export OPENBLAS=$(brew --prefix openblas) | |
| #python -m pip install --no-cache-dir --no-binary numpy numpy # avoid the cached .whl! | |
| python -m pip install numpy | |
| ;; | |
| (*) | |
| python -m pip install numpy | |
| ;; | |
| esac | |
| python -m pip install pytest | |
| if test "${{matrix.parallelproj}}XX" == "ONXX"; then | |
| git clone --depth 1 --branch v1.7.3 https://github.com/gschramm/parallelproj | |
| mkdir parallelproj/build | |
| cd parallelproj/build | |
| if test "${{matrix.cuda_version}}" == "0"; then | |
| extra_args="-DSKIP_CUDA_LIB:BOOL=ON" | |
| fi | |
| cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} ${extra_args} | |
| cmake --build . --target install --config Release | |
| cd ../.. | |
| rm -rf parallelproj | |
| fi | |
| # Install ROOT (warning: currently only valid on Ubuntu) | |
| if test "${{matrix.ROOT}}XX" == "ONXX"; then | |
| ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz | |
| wget https://root.cern/download/"$ROOT_file" | |
| tar -xzvf "$ROOT_file" | |
| rm "$ROOT_file" | |
| source root/bin/thisroot.sh | |
| fi | |
| # we'll install some dependencies with shared libraries, so need to let the OS know | |
| # thisroot.sh also modified the path, so save that for the recon_test_pack | |
| case ${{matrix.os}} in | |
| (ubuntu*) | |
| echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo PATH="$PATH" >> $GITHUB_ENV | |
| ;; | |
| (macOS*) | |
| echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo PATH="$PATH" >> $GITHUB_ENV | |
| ;; | |
| (windows*) | |
| echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV | |
| ;; | |
| esac | |
| - name: ccache | |
| uses: hendrikmuhs/ccache-action@v1 | |
| with: | |
| key: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }} | |
| max-size: "2G" | |
| - name: configure | |
| shell: bash | |
| env: | |
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
| BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | |
| run: | | |
| set -ex | |
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
| #export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH" | |
| cmake --version | |
| if test "XX$CC" != "XX"; then | |
| $CC --version | |
| $CXX --version | |
| fi | |
| CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | |
| # make available to jobs below | |
| echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV | |
| EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`" | |
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}" | |
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON" | |
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL" | |
| echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS" | |
| mkdir build | |
| cd build | |
| cmake -S .. ${BUILD_FLAGS} ${EXTRA_BUILD_FLAGS} | |
| # report disk space | |
| case ${{matrix.os}} in | |
| (ubuntu* | macOS*) | |
| df -h | |
| ;; | |
| (windows*) | |
| # no idea how to do this | |
| ;; | |
| esac | |
| - name: build | |
| shell: bash | |
| env: | |
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/build; | |
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
| cmake --build . -j 2 --config ${BUILD_TYPE}} --target install | |
| # Enable tmate debugging of manually-triggered workflows if the input option was provided | |
| - name: Setup tmate session if triggered | |
| uses: mxschmitt/action-tmate@v3 | |
| timeout-minutes: 15 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }} | |
| - name: ctest | |
| shell: bash | |
| env: | |
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
| run: | | |
| set -vx | |
| cd ${GITHUB_WORKSPACE}/build | |
| # find test exclusions. Complicated due to need of single -E argument and | pattern | |
| if test ${{matrix.cuda_version}} != "0"; then | |
| # No CUDA drivers on GitHub Actions | |
| EXCLUDE="parallelproj|test_blocks_on_cylindrical_projectors" | |
| fi | |
| # don't run all of them in Debug mode as it takes too long | |
| if test ${BUILD_TYPE} = Debug; then | |
| # Also excluding test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin | |
| # as it is a bit slow. Moreover it fails on MacOS (Debug) | |
| # https://github.com/UCL/STIR/pull/1418#issuecomment-2109518132 | |
| EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection|test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin" | |
| EXCLUDE="${EXCLUDE_Debug}${EXCLUDE:+"|"}${EXCLUDE}" | |
| fi | |
| # prepend -E | |
| if [ ! -z "${EXCLUDE}" ]; then | |
| EXCLUDE="-E ${EXCLUDE}" | |
| fi | |
| # execute tests | |
| ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE} | |
| - name: Upload ctest log files for debugging | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: ctest_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
| path: | | |
| ${{ github.workspace }}/build/**/*.log | |
| ${{ github.workspace }}/build/**/*.hv | |
| ${{ github.workspace }}/build/**/*.v | |
| ${{ github.workspace }}/build/**/*.hs | |
| ${{ github.workspace }}/build/**/*.s | |
| retention-days: 7 | |
| - name: C++ examples with STIR_LOCAL | |
| shell: bash | |
| run: | | |
| set -ex; | |
| PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
| # Run examples to see if they work | |
| cd ${GITHUB_WORKSPACE}/examples/PET_simulation | |
| ./run_simulation.sh 1> /dev/null | |
| # Run the Demo executables | |
| EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++/using_STIR_LOCAL | |
| cd ${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL | |
| generate_image generate_image.par | |
| forward_project sino.hs image.hv small.hs | |
| # Cannot test demo1 or demo2 as they require interactivity. Piping does not work. | |
| ${EXE_LOC}/demo3 demo.par --display_off | |
| ${EXE_LOC}/demo3 demoPM.par --display_off | |
| ${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par | |
| ${EXE_LOC}/demo5_line_search demo5_line_search.par | |
| - name: remove build | |
| shell: bash | |
| # remove to create some disk space | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| df -h . | |
| rm -rf ./build | |
| df -h . | |
| - name: C++ examples with installed STIR | |
| shell: bash | |
| run: | | |
| set -ex; | |
| # build and run C++/using_installed_STIR | |
| PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
| cd ${GITHUB_WORKSPACE}/examples/C++/using_installed_STIR | |
| cmake -S . -B build/ -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX} | |
| cmake --build build/ --config Release --target install | |
| # run demo | |
| demo_create_image | |
| # just check if its output makes sense | |
| list_image_info test.hv | |
| rm -rf build | |
| - name: recon_test_pack | |
| shell: bash | |
| env: | |
| BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | |
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
| run: | | |
| set -ex; | |
| PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
| cd ${GITHUB_WORKSPACE}/recon_test_pack | |
| ./run_tests.sh --nointbp | |
| # don't run all of them in Debug mode as it takes too long | |
| if test ${BUILD_TYPE} != Debug; then | |
| ./run_test_simulate_and_recon.sh | |
| ./run_test_listmode_recon.sh | |
| ./run_test_simulate_and_recon_with_motion.sh | |
| ./run_scatter_tests.sh | |
| ./run_test_zoom_image.sh | |
| ./run_ML_norm_tests.sh | |
| if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi | |
| ./run_tests_modelling.sh | |
| cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT | |
| ./run_SPECT_tests.sh | |
| fi | |
| - name: Upload recon_test_pack log files for debugging | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
| path: | | |
| ${{ github.workspace }}/recon_test_pack/**/*.log | |
| ${{ github.workspace }}/recon_test_pack/**/my_*v | |
| ${{ github.workspace }}/recon_test_pack/**/my_*s | |
| retention-days: 7 | |
| - name: remove recon_test_pack | |
| shell: bash | |
| run: | | |
| rm -rf ${GITHUB_WORKSPACE}/recon_test_pack | |
| - name: Python | |
| shell: bash | |
| run: | | |
| set -ex | |
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
| # Run Python tests, making sure we're using the correct Python interpreter | |
| which python | |
| export PYTHONPATH=${CMAKE_INSTALL_PREFIX}/python | |
| cd ${GITHUB_WORKSPACE}/src | |
| case ${{matrix.os}} in | |
| (macOS*) | |
| echo skipping pytest due to numpy problem for now. | |
| ;; | |
| (*) | |
| python -m pytest . | |
| ;; | |
| esac |