pre commit action

.editorconfig

@@ -6,6 +6,6 @@ root = true
 # Apply to any source file
 [*.*]
 
-# Indentation of two spaces 
+# Indentation of two spaces
 indent_style = space
 indent_size = 2

.github/workflows/ElastixGitHubActions.yml

@@ -1,7 +1,7 @@
 name: Elastix
 
 on: [push, pull_request]
-  
+
 jobs:
   build:
     # The CMake configure and build commands are platform agnostic and should work equally
@@ -30,7 +30,7 @@ jobs:
             ANNLib: "ANNlib-5.2.dll"
             vcvars64: "C:/Program Files/Microsoft Visual Studio/2022/Enterprise/VC/Auxiliary/Build/vcvars64.bat"
           - os: macos-13
-            c-compiler: "clang"  
+            c-compiler: "clang"
             cxx-compiler: "clang++"
             itk-git-tag: "v5.4.1"
             cmake-build-type: "Release"
@@ -39,7 +39,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    
+
     - name: Make directory structure
       run: |
         items=(*)
@@ -49,15 +49,15 @@ jobs:
         mv .clang-format Elastix-source
         mv Elastix-source/Dockerfile .
       shell: bash
-      
+
     - uses: actions/cache@v3
       id: cache
       with:
         path: |
           ITK-build
           ITK-source
-        key: ${{ matrix.itk-git-tag }}-${{ matrix.os }}-${{ matrix.cmake-build-type }} 
-        
+        key: ${{ matrix.itk-git-tag }}-${{ matrix.os }}-${{ matrix.cmake-build-type }}
+
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
@@ -67,25 +67,25 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install ninja
-        
+
     - name: Get specific version of CMake, Ninja
       uses: lukka/get-cmake@v3.24.2
-      
+
     - name: Download ITK
       if: steps.cache.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: ${{ steps.cache.outputs.cache-hit != 'true' && !startsWith(matrix.os, 'windows') }}
       run: |
         mkdir ITK-build
         cd ITK-build
         cmake -DCMAKE_C_COMPILER:FILEPATH="${{ 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.outputs.cache-hit != 'true' && startsWith(matrix.os, 'windows')
       run: |
@@ -95,7 +95,7 @@ jobs:
         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
@@ -141,7 +141,7 @@ jobs:
       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: |
@@ -153,15 +153,15 @@ jobs:
       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: |
@@ -183,7 +183,7 @@ jobs:
         set path=${{ github.workspace }}\Elastix-build\bin
         externalproject-build\elastix_translation_example.exe
       shell: cmd
-      
+
     - name: Prepare Artifacts Unix
       if: ${{ !startsWith(matrix.os, 'windows') }}
       shell: bash
@@ -199,7 +199,7 @@ jobs:
         mv Elastix-source/LICENSE uploads
         mv bin uploads
         mv lib uploads
-      
+
     - name: Prepare Artifacts Windows
       if: startsWith(matrix.os, 'windows')
       shell: bash
@@ -210,13 +210,13 @@ jobs:
         mv Elastix-build/bin/elastix.exe uploads
         mv Elastix-build/bin/transformix.exe uploads
         mv Elastix-build/bin/${{ matrix.ANNLib }} uploads
-  
+
     - name: Publish Artifacts
       uses: actions/upload-artifact@v4.4.3
-      with: 
+      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/#-action@v1
@@ -225,11 +225,9 @@ jobs:
         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')     
+      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/}
-
-

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v4
+    - name: Check install of Python, pre-commit
+      run: |
+        ./tools/pre-commit-setup.bash
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - uses: pre-commit/action@v3.0.1

.pre-commit-config.yaml

@@ -32,7 +32,6 @@ repos:
    - id: end-of-file-fixer
      exclude: "\\.(md5|sha|sha512|svg|vtk|vtp)$|^Resources\\/[^\\/]+\\.h$|\\/ColorFiles\\/.+\\.txt$|Data\\/Input\\/.+$|\\/ThirdParty\\/|\\/Data\\/"
    - id: forbid-new-submodules
-   - id: forbid-submodules
    - id: mixed-line-ending
      exclude: "\\.(sha|sha512|svg|vtk|vtp)$|\\/ThirdParty\\/|\\/Data\\/"
    - id: name-tests-test
@@ -42,7 +41,7 @@ repos:
    - id: trailing-whitespace
      exclude: "\\.(sha|sha512|svg|vtk|vtp)$|\\/ThirdParty\\/|\\/Data\\/"
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v19.1.4
+  rev: v19.1.7
   hooks:
   - id: clang-format
     args: ['--style=file']

CMake/FindEigen3.cmake

@@ -78,4 +78,3 @@ else(EIGEN3_INCLUDE_DIR)
   mark_as_advanced(EIGEN3_INCLUDE_DIR)
 
 endif()
-

CMake/elastixVersion.cmake

@@ -3,4 +3,4 @@ set(ELASTIX_VERSION_MAJOR "5")
 set(ELASTIX_VERSION_MINOR "2")
 set(ELASTIX_VERSION_PATCH "0")
 
-set(ELASTIX_VERSION "${ELASTIX_VERSION_MAJOR}.${ELASTIX_VERSION_MINOR}.${ELASTIX_VERSION_PATCH}")
+set(ELASTIX_VERSION "${ELASTIX_VERSION_MAJOR}.${ELASTIX_VERSION_MINOR}.${ELASTIX_VERSION_PATCH}")

CMakeLists.txt

@@ -16,7 +16,7 @@ cmake_policy(SET CMP0042 NEW) # "MACOSX_RPATH is enabled by default."
 include(CTest)
 
 #---------------------------------------------------------------------
-# Allow specifying whether or not the executables are built. 
+# Allow specifying whether or not the executables are built.
 option( ELASTIX_BUILD_EXECUTABLE "Build elastix and transformix as executable? (The libraries are always built as well anyway.)" ON )
 
   # The following may make smaller and quicker loading libraries,

CODE_OF_CONDUCT.md

@@ -74,4 +74,3 @@ available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.ht
 
 For answers to common questions about this code of conduct, see
 https://www.contributor-covenant.org/faq
-

Common/CMakeLists.txt

@@ -214,4 +214,3 @@ endif()
 target_link_libraries(elxCommon
   ${ITK_LIBRARIES}
 )
-

Common/GTesting/itkImageFullSamplerGTest.cxx

@@ -187,4 +187,4 @@ GTEST_TEST(ImageFullSampler, ExactlyEqualVersusSlightlyDifferentMaskImageDomain)
   EXPECT_FALSE(samplesOnExactlyEqualImageDomains.empty());
 
   EXPECT_EQ(samplesOnExactlyEqualImageDomains, samplesOnSlightlyDifferentImageDomains);
-}
+}

Common/OpenCL/Kernels/GPUBSplineInterpolateImageFunction.cl

@@ -347,7 +347,7 @@ void set_interpolation_weights_3d( const float3 cindex, float * weights,
   // function pointers to reference the correct spline order. Left as is for
   // now for readability use following float per different spline order:
   // float w, w2, w4, t, t0, t1, t2;
-  
+
   // create float x[3] from float3, makes it easy to use in loops
   float x[3];
   x[0] = cindex.x;

Components/CMakeLists.txt

@@ -234,4 +234,3 @@ foreach(userComponentDir ${ELASTIX_USER_COMPONENT_DIRS})
 
   endforeach()
 endforeach()
-

Components/FixedImagePyramids/FixedGenericPyramid/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( FixedGenericPyramid
  elxFixedGenericPyramid.h
  elxFixedGenericPyramid.hxx
  elxFixedGenericPyramid.cxx)
-

Components/FixedImagePyramids/FixedRecursivePyramid/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( FixedRecursivePyramid
  elxFixedRecursivePyramid.h
  elxFixedRecursivePyramid.hxx
  elxFixedRecursivePyramid.cxx)
-

Components/FixedImagePyramids/FixedShrinkingPyramid/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( FixedShrinkingPyramid # Was OFF by default before elastix 5.0.
  elxFixedShrinkingPyramid.h
  elxFixedShrinkingPyramid.hxx
  elxFixedShrinkingPyramid.cxx)
-

Components/FixedImagePyramids/FixedSmoothingPyramid/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( FixedSmoothingPyramid
  elxFixedSmoothingPyramid.h
  elxFixedSmoothingPyramid.hxx
  elxFixedSmoothingPyramid.cxx)
-

Components/ImageSamplers/Full/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( FullSampler
  elxFullSampler.h
  elxFullSampler.hxx
  elxFullSampler.cxx)
-

Components/ImageSamplers/Grid/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( GridSampler
  elxGridSampler.h
  elxGridSampler.hxx
  elxGridSampler.cxx)
-

Components/ImageSamplers/MultInputRandomCoordinate/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( MultiInputRandomCoordinateSampler
  elxMultiInputRandomCoordinateSampler.h
  elxMultiInputRandomCoordinateSampler.hxx
  elxMultiInputRandomCoordinateSampler.cxx)
-

Components/ImageSamplers/Random/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( RandomSampler
  elxRandomSampler.h
  elxRandomSampler.hxx
  elxRandomSampler.cxx)
-

Components/ImageSamplers/RandomCoordinate/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( RandomCoordinateSampler
  elxRandomCoordinateSampler.h
  elxRandomCoordinateSampler.hxx
  elxRandomCoordinateSampler.cxx)
-

Components/ImageSamplers/RandomSparseMask/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( RandomSamplerSparseMask
  elxRandomSamplerSparseMask.h
  elxRandomSamplerSparseMask.hxx
  elxRandomSamplerSparseMask.cxx)
-

Components/Interpolators/BSplineInterpolator/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( BSplineInterpolator
  elxBSplineInterpolator.h
  elxBSplineInterpolator.hxx
  elxBSplineInterpolator.cxx)
-

Components/Interpolators/BSplineInterpolatorFloat/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( BSplineInterpolatorFloat # Was OFF by default before elastix 5
  elxBSplineInterpolatorFloat.h
  elxBSplineInterpolatorFloat.hxx
  elxBSplineInterpolatorFloat.cxx)
-

Components/Interpolators/LinearInterpolator/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( LinearInterpolator
  elxLinearInterpolator.h
  elxLinearInterpolator.hxx
  elxLinearInterpolator.cxx)
-

Components/Interpolators/NearestNeighborInterpolator/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( NearestNeighborInterpolator # Was OFF by default before elasti
  elxNearestNeighborInterpolator.h
  elxNearestNeighborInterpolator.hxx
  elxNearestNeighborInterpolator.cxx)
-

Components/Interpolators/RayCastInterpolator/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( RayCastInterpolator # Was OFF by default before elastix 5.0.1
  elxRayCastInterpolator.h
  elxRayCastInterpolator.hxx
  elxRayCastInterpolator.cxx)
-

Components/Interpolators/ReducedDimensionBSplineInterpolator/CMakeLists.txt

@@ -3,4 +3,3 @@ ADD_ELXCOMPONENT( ReducedDimensionBSplineInterpolator
  elxReducedDimensionBSplineInterpolator.h
  elxReducedDimensionBSplineInterpolator.hxx
  elxReducedDimensionBSplineInterpolator.cxx)
-

Components/Metrics/AdvancedKappaStatistic/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( AdvancedKappaStatisticMetric # Was OFF by default before elast
  elxAdvancedKappaStatisticMetric.cxx
  itkAdvancedKappaStatisticImageToImageMetric.h
  itkAdvancedKappaStatisticImageToImageMetric.hxx)
-

Components/Metrics/AdvancedMattesMutualInformation/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( AdvancedMattesMutualInformationMetric
  elxAdvancedMattesMutualInformationMetric.cxx
  itkParzenWindowMutualInformationImageToImageMetric.h
  itkParzenWindowMutualInformationImageToImageMetric.hxx)
-

Components/Metrics/AdvancedMeanSquares/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( AdvancedMeanSquaresMetric
  elxAdvancedMeanSquaresMetric.cxx
  itkAdvancedMeanSquaresImageToImageMetric.h
  itkAdvancedMeanSquaresImageToImageMetric.hxx)
-

Components/Metrics/AdvancedNormalizedCorrelation/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( AdvancedNormalizedCorrelationMetric
  elxAdvancedNormalizedCorrelationMetric.cxx
  itkAdvancedNormalizedCorrelationImageToImageMetric.h
  itkAdvancedNormalizedCorrelationImageToImageMetric.hxx)
-

Components/Metrics/BendingEnergyPenalty/CMakeLists.txt

@@ -6,4 +6,3 @@ ADD_ELXCOMPONENT( TransformBendingEnergyPenalty
  itkTransformBendingEnergyPenaltyTerm.h
  itkTransformBendingEnergyPenaltyTerm.hxx
 )
-

Components/Metrics/CorrespondingPointsEuclideanDistanceMetric/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( CorrespondingPointsEuclideanDistanceMetric
  elxCorrespondingPointsEuclideanDistanceMetric.hxx
  itkCorrespondingPointsEuclideanDistancePointMetric.h
  itkCorrespondingPointsEuclideanDistancePointMetric.hxx)
-

Components/Metrics/DisplacementMagnitudePenalty/CMakeLists.txt

@@ -6,4 +6,3 @@ ADD_ELXCOMPONENT( DisplacementMagnitudePenalty # Was OFF by default before elast
  itkDisplacementMagnitudePenaltyTerm.h
  itkDisplacementMagnitudePenaltyTerm.hxx
 )
-

Components/Metrics/DistancePreservingRigidityPenalty/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( DistancePreservingRigidityPenalty
  elxDistancePreservingRigidityPenaltyTerm.cxx
  itkDistancePreservingRigidityPenaltyTerm.h
  itkDistancePreservingRigidityPenaltyTerm.hxx)
-

Components/Metrics/GradientDifference/CMakeLists.txt

@@ -5,4 +5,3 @@ ADD_ELXCOMPONENT( GradientDifferenceMetric # Was OFF by default before elastix 5
  elxGradientDifferenceMetric.cxx
  itkGradientDifferenceImageToImageMetric2.h
  itkGradientDifferenceImageToImageMetric2.hxx)
-

Components/Metrics/KNNGraphAlphaMutualInformation/CMakeLists.txt

@@ -18,4 +18,3 @@ if(USE_KNNGraphAlphaMutualInformationMetric)
   elastix_export_target(KNNlib)
   elastix_export_target(ANNlib)
 endif()
-