ENH: Add IMPACT Similarity Metric to Elastix #4368
Workflow file for this run
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| name: Elastix | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| # The CMake configure and build commands are platform agnostic and should work equally | |
| # well on Windows or Mac. You can convert this to a matrix build if you need | |
| # cross-platform coverage. | |
| # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 3 | |
| matrix: | |
| os: [ubuntu-22.04, windows-2022, macos-13] | |
| include: | |
| - os: ubuntu-22.04 | |
| c-compiler: "gcc" | |
| cxx-compiler: "g++" | |
| libtorch_url: https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.6.0%2Bcpu.zip | |
| itk-git-tag: "v5.4.1" | |
| cmake-build-type: "Release" | |
| ANNLib: "libANNlib-5.2.so" | |
| ANNLib2: "libANNlib-5.2.so.1" | |
| TORCH_LIBS: | |
| - libtorch/libtorch/lib/libc10.so | |
| - libtorch/libtorch/lib/libgomp-98b21ff3.so.1 | |
| - libtorch/libtorch/lib/libtorch.so | |
| - libtorch/libtorch/lib/libtorch_cpu.so | |
| - os: windows-2022 | |
| c-compiler: "cl.exe" | |
| cxx-compiler: "cl.exe" | |
| libtorch_url: https://download.pytorch.org/libtorch/cpu/libtorch-win-shared-with-deps-2.6.0%2Bcpu.zip | |
| itk-git-tag: "v5.4.1" | |
| cmake-build-type: "Release" | |
| ANNLib: "ANNlib-5.2.dll" | |
| TORCH_LIBS: | |
| - libtorch/libtorch/lib/c10.dll | |
| - libtorch/libtorch/lib/torch_cpu.dll | |
| - libtorch/libtorch/lib/torch.dll | |
| vcvars64: "C:/Program Files/Microsoft Visual Studio/2022/Enterprise/VC/Auxiliary/Build/vcvars64.bat" | |
| - os: macos-13 | |
| c-compiler: "clang" | |
| cxx-compiler: "clang++" | |
| libtorch_url: https://download.pytorch.org/libtorch/cpu/libtorch-macos-arm64-2.6.0.zip | |
| itk-git-tag: "v5.4.1" | |
| cmake-build-type: "Release" | |
| ANNLib: "libANNlib-5.2.1.dylib" | |
| ANNLib2: "libANNlib-5.2.dylib" | |
| TORCH_LIBS: | |
| - libtorch/libtorch/lib/libtorch.dylib | |
| - libtorch/libtorch/lib/libc10.dylib | |
| - libtorch/libtorch/lib/libtorch_cpu.dylib | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Make directory structure | |
| run: | | |
| items=(*) | |
| mkdir Elastix-source | |
| mv ${items[*]} Elastix-source | |
| mv .editorconfig Elastix-source | |
| mv .clang-format Elastix-source | |
| mv Elastix-source/Dockerfile . | |
| shell: bash | |
| - uses: actions/cache@v3 | |
| id: cache_ITK | |
| with: | |
| path: | | |
| ITK-build | |
| ITK-source | |
| key: ${{ matrix.itk-git-tag }}-${{ matrix.os }}-${{ matrix.cmake-build-type }}-v2 | |
| - name: Save libtorch URL to file | |
| shell: bash | |
| run: | | |
| echo "${{ matrix.libtorch_url }}" > libtorch_url.txt | |
| - uses: actions/cache@v3 | |
| id: cache_libtorch | |
| with: | |
| path: | | |
| libtorch | |
| key: libtorch-${{ hashFiles('libtorch_url.txt') }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install ninja | |
| - name: Get specific version of CMake, Ninja | |
| uses: lukka/get-cmake@latest | |
| - name: Download libtorch CPU | |
| if: ${{ steps.cache_libtorch.outputs.cache-hit != 'true' && !startsWith(matrix.os, 'mac') }} | |
| shell: bash | |
| run: | | |
| curl -L ${{matrix.libtorch_url}} -o libtorch.zip | |
| - name: Download libtorch CPU | |
| if: steps.cache_libtorch.outputs.cache-hit != 'true' && startsWith(matrix.os, 'mac') | |
| shell: bash | |
| run: | | |
| git clone --recursive https://github.com/pytorch/pytorch.git | |
| - name: Extract libtorch | |
| if: ${{ steps.cache_libtorch.outputs.cache-hit != 'true' && !startsWith(matrix.os, 'mac') }} | |
| shell: bash | |
| run: | | |
| unzip -q libtorch.zip -d libtorch | |
| - name: Extract libtorch | |
| if: steps.cache_libtorch.outputs.cache-hit != 'true' && startsWith(matrix.os, 'mac') | |
| shell: bash | |
| run: | | |
| python -m pip install -r pytorch/requirements.txt | |
| mkdir libtorch-build | |
| mkdir libtorch | |
| mkdir libtorch/libtorch | |
| cd libtorch-build | |
| cmake ../pytorch -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../libtorch/libtorch -DPython_EXECUTABLE=$(which python) -DBUILD_PYTHON=OFF -DBUILD_TEST=OFF -DUSE_CUDA=OFF -DUSE_MPS=OFF -DUSE_MKLDNN=OFF -DUSE_QNNPACK=OFF -DUSE_XNNPACK=OFF -DUSE_FBGEMM=OFF | |
| ninja install | |
| - name: Download ITK | |
| if: steps.cache_ITK.outputs.cache-hit != 'true' | |
| run: | | |
| git clone https://github.com/InsightSoftwareConsortium/ITK.git ITK-source | |
| cd ITK-source | |
| git checkout ${{ matrix.itk-git-tag }} | |
| - name: Build ITK | |
| if: ${{ steps.cache_ITK.outputs.cache-hit != 'true' && !startsWith(matrix.os, 'windows') }} | |
| run: | | |
| mkdir ITK-build | |
| cd ITK-build | |
| cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -DITK_LEGACY_REMOVE=ON -GNinja ../ITK-source | |
| ninja | |
| - name: Build ITK | |
| if: steps.cache_ITK.outputs.cache-hit != 'true' && startsWith(matrix.os, 'windows') | |
| run: | | |
| mkdir ITK-build | |
| cd ITK-build | |
| call "${{ matrix.vcvars64 }}" | |
| cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK-source | |
| ninja | |
| shell: cmd | |
| - name: Install requirements of PythonTests | |
| run: | | |
| python -m pip install -r ${{ github.workspace }}/Elastix-source/Testing/PythonTests/requirements.txt | |
| - name: Configure CTest script | |
| shell: bash | |
| run: | | |
| operating_system="${{ matrix.os }}" | |
| cat > dashboard.cmake << EOF | |
| set(CTEST_SITE "GitHubActions") | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}" CTEST_DASHBOARD_ROOT) | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/Elastix-source" CTEST_SOURCE_DIRECTORY) | |
| file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/Elastix-build" CTEST_BINARY_DIRECTORY) | |
| set(dashboard_source_name "${GITHUB_REPOSITORY}") | |
| set(branch "${GITHUB_REF#refs/heads/}") | |
| set(sha "${GITHUB_SHA}") | |
| set(dashboard_model "Experimental") | |
| set(CTEST_BUILD_NAME "${GITHUB_REPOSITORY}-${operating_system}-\${branch}-\${sha}") | |
| set(CTEST_UPDATE_VERSION_ONLY 1) | |
| set(CTEST_TEST_ARGS \${CTEST_TEST_ARGS} PARALLEL_LEVEL \${PARALLEL_LEVEL}) | |
| set(CTEST_BUILD_CONFIGURATION "Release") | |
| set(CTEST_CMAKE_GENERATOR "Ninja") | |
| set(dashboard_no_clean 1) | |
| set(ENV{CC} ${{ matrix.c-compiler }}) | |
| set(ENV{CXX} ${{ matrix.cxx-compiler }}) | |
| if(WIN32) | |
| set(ENV{PATH} "\${CTEST_DASHBOARD_ROOT}/ITK-build/bin;\${CTEST_DASHBOARD_ROOT}/libtorch/libtorch/lib;\$ENV{PATH}") | |
| endif() | |
| set(dashboard_cache " | |
| ITK_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/ITK-build | |
| Torch_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/libtorch/libtorch/share/cmake/Torch | |
| ELASTIX_USE_GTEST:BOOL=ON | |
| USE_ALL_COMPONENTS:BOOL=ON | |
| BUILD_TESTING:BOOL=ON | |
| ") | |
| string(TIMESTAMP build_date "%Y-%m-%d") | |
| message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}") | |
| message("CTEST_SITE= \${CTEST_SITE}") | |
| include(\${CTEST_SOURCE_DIRECTORY}/Testing/Dashboard/elxCommonCDash.cmake) | |
| EOF | |
| cat dashboard.cmake | |
| - name: Test MacOs | |
| if: startsWith(matrix.os, 'macos') | |
| run: | | |
| ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP|elastix_run_3DCT_lung.NMI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake | |
| - name: Test Windows | |
| if: startsWith(matrix.os, 'windows') | |
| run: | | |
| call "${{ matrix.vcvars64 }}" | |
| ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake | |
| shell: cmd | |
| - name: Test Ubuntu | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| ctest --output-on-failure -VV -j 2 -E "elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP" -S dashboard.cmake | |
| - name: Build externalproject example | |
| if: ${{ !startsWith(matrix.os, 'windows') }} | |
| run: | | |
| mkdir externalproject-build | |
| cd externalproject-build | |
| cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject | |
| ninja | |
| - name: Build externalproject example | |
| if: startsWith(matrix.os, 'windows') | |
| run: | | |
| mkdir externalproject-build | |
| cd externalproject-build | |
| call "${{ matrix.vcvars64 }}" | |
| cmake -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DElastix_DIR=${{ github.workspace }}/Elastix-build -GNinja ../Elastix-source/dox/externalproject | |
| ninja | |
| shell: cmd | |
| - name: Run externalproject example | |
| if: ${{ !startsWith(matrix.os, 'windows') }} | |
| run: | | |
| cd externalproject-build | |
| ./elastix_impact_metric_example | |
| - name: Run externalproject example | |
| if: startsWith(matrix.os, 'windows') | |
| run: | | |
| set PATH=${{ github.workspace }}\Elastix-build\bin;${{ github.workspace }}\libtorch\libtorch\lib;%PATH% | |
| cd externalproject-build | |
| .\elastix_impact_metric_example.exe | |
| shell: cmd | |
| - name: Prepare Artifacts Unix | |
| if: ${{ !startsWith(matrix.os, 'windows') }} | |
| shell: bash | |
| env: | |
| TORCH_LIBS: ${{ join(matrix.TORCH_LIBS, ' ') }} | |
| run: | | |
| mkdir bin | |
| mkdir lib | |
| mkdir uploads | |
| mv Elastix-build/bin/elastix bin | |
| mv Elastix-build/bin/transformix bin | |
| mv Elastix-build/bin/${{ matrix.ANNLib }} lib | |
| mv Elastix-build/bin/${{ matrix.ANNLib2 }} lib | |
| for lib in $TORCH_LIBS; do | |
| cp "$lib" lib | |
| done | |
| mv Elastix-source/NOTICE uploads | |
| mv Elastix-source/LICENSE uploads | |
| mv bin uploads | |
| mv lib uploads | |
| - name: Prepare Artifacts Windows | |
| if: startsWith(matrix.os, 'windows') | |
| shell: bash | |
| env: | |
| TORCH_LIBS: ${{ join(matrix.TORCH_LIBS, ' ') }} | |
| run: | | |
| mkdir uploads | |
| mv Elastix-source/NOTICE uploads | |
| mv Elastix-source/LICENSE uploads | |
| mv Elastix-build/bin/elastix.exe uploads | |
| mv Elastix-build/bin/transformix.exe uploads | |
| mv Elastix-build/bin/${{ matrix.ANNLib }} uploads | |
| for lib in $TORCH_LIBS; do | |
| echo "Copying $lib" | |
| cp "$lib" uploads | |
| done | |
| - name: Publish Artifacts | |
| uses: actions/[email protected] | |
| with: | |
| name: "${{ matrix.os }}" | |
| path: uploads | |
| - name: Login to Docker Hub | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && startsWith(matrix.os, 'ubuntu') | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Build and push | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| mkdir output | |
| docker build -t superelastix/elastix:${GITHUB_REF#refs/tags/} . | |
| docker run -u $UID:$GROUPS --mount type=bind,source="$(pwd)"/output,target=/out -v "$(pwd)"/Elastix-source/Testing/Data:/elastix/ superelastix/elastix:${GITHUB_REF#refs/tags/} elastix -out /out/ -p /elastix/parameters.3D.NC.euler.ASGD.001.txt -f /elastix/3DCT_lung_baseline.mha -m /elastix/3DCT_lung_followup.mha | |
| docker push superelastix/elastix:${GITHUB_REF#refs/tags/} |