├── .ExternalData └── README.rst ├── .circleci ├── circleci.cmake └── config.yml ├── .readthedocs.yml ├── .travis.yml ├── CMake ├── CTestCustom.cmake.in ├── ExternalData_config.cmake.in ├── FindCSharp.cmake ├── FindDotNetFrameworkSdk.cmake ├── FindLuaInterp.cmake ├── FindMono.cmake ├── FindPythonVirtualEnv.cmake ├── FindR.cmake ├── GetGitRevisionDescription.cmake ├── UseCSharp.cmake ├── UseDotNetFrameworkSdk.cmake ├── UseMono.cmake ├── VariableList.cmake ├── configure_file_build_time.cmake ├── pre-commit ├── same_uint64_ulong.cxx ├── sitkAddTest.cmake ├── sitkCheckForITKModuleDependencies.cmake ├── sitkCheckRequiredFlags.cmake ├── sitkCheckSourceTree.cmake ├── sitkCheckTemplateDisambiguation.cmake ├── sitkCheckTemplateDisambiguation.cxx ├── sitkCompilerWarningsSettings.cmake ├── sitkExternalData.cmake ├── sitkForbidDownloadsOption.cmake ├── sitkGenerateFilterSource.cmake ├── sitkLanguageOptions.cmake ├── sitkPreventInBuildInstalls.cmake ├── sitkPreventInSourceBuilds.cmake ├── sitkProjectLanguageCommon.cmake ├── sitkSITKLegacyNaming.cmake ├── sitkSourceVersion.cmake ├── sitkSourceVersionVars.cmake.in ├── sitkStripOption.cmake ├── sitkTargetLinkLibrariesWithDynamicLookup.cmake ├── sitkTargetUseITK.cmake ├── sitkUseCCache.cmake ├── sitkUseGTest.cmake ├── sitkUseGoldLinker.cmake └── sitkUseSWIG.cmake ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CTestConfig.cmake ├── Code ├── BasicFilters │ ├── CMakeLists.txt │ ├── include │ │ ├── itkHashImageFilter.h │ │ ├── itkHashImageFilter.hxx │ │ ├── sitkAdditionalProcedures.h │ │ ├── sitkBSplineTransformInitializerFilter.h │ │ ├── sitkBasicFilters.h │ │ ├── sitkCastImageFilter.h │ │ ├── sitkCenteredTransformInitializerFilter.h │ │ ├── sitkCenteredVersorTransformInitializerFilter.h │ │ ├── sitkHashImageFilter.h │ │ ├── sitkImageFilter.h │ │ ├── sitkImageOperators.h │ │ └── sitkLandmarkBasedTransformInitializerFilter.h │ ├── json │ │ ├── AbsImageFilter.json │ │ ├── AbsoluteValueDifferenceImageFilter.json │ │ ├── AcosImageFilter.json │ │ ├── AdaptiveHistogramEqualizationImageFilter.json │ │ ├── AddImageFilter.json │ │ ├── AdditiveGaussianNoiseImageFilter.json │ │ ├── AggregateLabelMapFilter.json │ │ ├── AndImageFilter.json │ │ ├── AntiAliasBinaryImageFilter.json │ │ ├── ApproximateSignedDistanceMapImageFilter.json │ │ ├── AsinImageFilter.json │ │ ├── Atan2ImageFilter.json │ │ ├── AtanImageFilter.json │ │ ├── BSplineDecompositionImageFilter.json │ │ ├── BilateralImageFilter.json │ │ ├── BinShrinkImageFilter.json │ │ ├── BinaryClosingByReconstructionImageFilter.json │ │ ├── BinaryContourImageFilter.json │ │ ├── BinaryDilateImageFilter.json │ │ ├── BinaryErodeImageFilter.json │ │ ├── BinaryFillholeImageFilter.json │ │ ├── BinaryGrindPeakImageFilter.json │ │ ├── BinaryImageToLabelMapFilter.json │ │ ├── BinaryMagnitudeImageFilter.json │ │ ├── BinaryMedianImageFilter.json │ │ ├── BinaryMinMaxCurvatureFlowImageFilter.json │ │ ├── BinaryMorphologicalClosingImageFilter.json │ │ ├── BinaryMorphologicalOpeningImageFilter.json │ │ ├── BinaryNotImageFilter.json │ │ ├── BinaryOpeningByReconstructionImageFilter.json │ │ ├── BinaryProjectionImageFilter.json │ │ ├── BinaryPruningImageFilter.json │ │ ├── BinaryReconstructionByDilationImageFilter.json │ │ ├── BinaryReconstructionByErosionImageFilter.json │ │ ├── BinaryThinningImageFilter.json │ │ ├── BinaryThresholdImageFilter.json │ │ ├── BinaryThresholdProjectionImageFilter.json │ │ ├── BinomialBlurImageFilter.json │ │ ├── BitwiseNotImageFilter.json │ │ ├── BlackTopHatImageFilter.json │ │ ├── BoundedReciprocalImageFilter.json │ │ ├── BoxMeanImageFilter.json │ │ ├── BoxSigmaImageFilter.json │ │ ├── CannyEdgeDetectionImageFilter.json │ │ ├── CannySegmentationLevelSetImageFilter.json │ │ ├── ChangeLabelImageFilter.json │ │ ├── ChangeLabelLabelMapFilter.json │ │ ├── CheckerBoardImageFilter.json │ │ ├── ClampImageFilter.json │ │ ├── ClosingByReconstructionImageFilter.json │ │ ├── CoherenceEnhancingDiffusionImageFilter.json │ │ ├── CollidingFrontsImageFilter.json │ │ ├── ComplexToImaginaryImageFilter.json │ │ ├── ComplexToModulusImageFilter.json │ │ ├── ComplexToPhaseImageFilter.json │ │ ├── ComplexToRealImageFilter.json │ │ ├── ComposeImageFilter.json │ │ ├── ConfidenceConnectedImageFilter.json │ │ ├── ConnectedComponentImageFilter.json │ │ ├── ConnectedThresholdImageFilter.json │ │ ├── ConstantPadImageFilter.json │ │ ├── ConvolutionImageFilter.json │ │ ├── CosImageFilter.json │ │ ├── CropImageFilter.json │ │ ├── CurvatureAnisotropicDiffusionImageFilter.json │ │ ├── CurvatureFlowImageFilter.json │ │ ├── CyclicShiftImageFilter.json │ │ ├── DanielssonDistanceMapImageFilter.json │ │ ├── DemonsRegistrationFilter.json │ │ ├── DerivativeImageFilter.json │ │ ├── DiffeomorphicDemonsRegistrationFilter.json │ │ ├── DilateObjectMorphologyImageFilter.json │ │ ├── DiscreteGaussianDerivativeImageFilter.json │ │ ├── DiscreteGaussianImageFilter.json │ │ ├── DisplacementFieldJacobianDeterminantFilter.json │ │ ├── DivideFloorImageFilter.json │ │ ├── DivideImageFilter.json │ │ ├── DivideRealImageFilter.json │ │ ├── DoubleThresholdImageFilter.json │ │ ├── EdgePotentialImageFilter.json │ │ ├── EqualImageFilter.json │ │ ├── ErodeObjectMorphologyImageFilter.json │ │ ├── ExpImageFilter.json │ │ ├── ExpNegativeImageFilter.json │ │ ├── ExpandImageFilter.json │ │ ├── ExtractImageFilter.json │ │ ├── FFTConvolutionImageFilter.json │ │ ├── FFTNormalizedCorrelationImageFilter.json │ │ ├── FFTPadImageFilter.json │ │ ├── FFTShiftImageFilter.json │ │ ├── FastApproximateRankImageFilter.json │ │ ├── FastMarchingBaseImageFilter.json │ │ ├── FastMarchingImageFilter.json │ │ ├── FastMarchingUpwindGradientImageFilter.json │ │ ├── FastSymmetricForcesDemonsRegistrationFilter.json │ │ ├── FlipImageFilter.json │ │ ├── ForwardFFTImageFilter.json │ │ ├── GaborImageSource.json │ │ ├── GaussianImageSource.json │ │ ├── GeodesicActiveContourLevelSetImageFilter.json │ │ ├── GradientAnisotropicDiffusionImageFilter.json │ │ ├── GradientImageFilter.json │ │ ├── GradientMagnitudeImageFilter.json │ │ ├── GradientMagnitudeRecursiveGaussianImageFilter.json │ │ ├── GradientRecursiveGaussianImageFilter.json │ │ ├── GrayscaleConnectedClosingImageFilter.json │ │ ├── GrayscaleConnectedOpeningImageFilter.json │ │ ├── GrayscaleDilateImageFilter.json │ │ ├── GrayscaleErodeImageFilter.json │ │ ├── GrayscaleFillholeImageFilter.json │ │ ├── GrayscaleGeodesicDilateImageFilter.json │ │ ├── GrayscaleGeodesicErodeImageFilter.json │ │ ├── GrayscaleGrindPeakImageFilter.json │ │ ├── GrayscaleMorphologicalClosingImageFilter.json │ │ ├── GrayscaleMorphologicalOpeningImageFilter.json │ │ ├── GreaterEqualImageFilter.json │ │ ├── GreaterImageFilter.json │ │ ├── GridImageSource.json │ │ ├── HConcaveImageFilter.json │ │ ├── HConvexImageFilter.json │ │ ├── HMaximaImageFilter.json │ │ ├── HMinimaImageFilter.json │ │ ├── HalfHermitianToRealInverseFFTImageFilter.json │ │ ├── HausdorffDistanceImageFilter.json │ │ ├── HistogramMatchingImageFilter.json │ │ ├── HuangThresholdImageFilter.json │ │ ├── IntensityWindowingImageFilter.json │ │ ├── IntermodesThresholdImageFilter.json │ │ ├── InverseDeconvolutionImageFilter.json │ │ ├── InverseDisplacementFieldImageFilter.json │ │ ├── InverseFFTImageFilter.json │ │ ├── InvertDisplacementFieldImageFilter.json │ │ ├── InvertIntensityImageFilter.json │ │ ├── IsoContourDistanceImageFilter.json │ │ ├── IsoDataThresholdImageFilter.json │ │ ├── IsolatedConnectedImageFilter.json │ │ ├── IsolatedWatershedImageFilter.json │ │ ├── IterativeInverseDisplacementFieldImageFilter.json │ │ ├── JoinSeriesImageFilter.json │ │ ├── KittlerIllingworthThresholdImageFilter.json │ │ ├── LabelContourImageFilter.json │ │ ├── LabelImageToLabelMapFilter.json │ │ ├── LabelIntensityStatisticsImageFilter.json │ │ ├── LabelMapContourOverlayImageFilter.json │ │ ├── LabelMapMaskImageFilter.json │ │ ├── LabelMapOverlayImageFilter.json │ │ ├── LabelMapToBinaryImageFilter.json │ │ ├── LabelMapToLabelImageFilter.json │ │ ├── LabelMapToRGBImageFilter.json │ │ ├── LabelOverlapMeasuresImageFilter.json │ │ ├── LabelOverlayImageFilter.json │ │ ├── LabelSetDilateImageFilter.json │ │ ├── LabelSetErodeImageFilter.json │ │ ├── LabelShapeStatisticsImageFilter.json │ │ ├── LabelStatisticsImageFilter.json │ │ ├── LabelToRGBImageFilter.json │ │ ├── LabelUniqueLabelMapFilter.json │ │ ├── LabelVotingImageFilter.json │ │ ├── LandweberDeconvolutionImageFilter.json │ │ ├── LaplacianImageFilter.json │ │ ├── LaplacianRecursiveGaussianImageFilter.json │ │ ├── LaplacianSegmentationLevelSetImageFilter.json │ │ ├── LaplacianSharpeningImageFilter.json │ │ ├── LessEqualImageFilter.json │ │ ├── LessImageFilter.json │ │ ├── LevelSetMotionRegistrationFilter.json │ │ ├── LiThresholdImageFilter.json │ │ ├── Log10ImageFilter.json │ │ ├── LogImageFilter.json │ │ ├── MagnitudeAndPhaseToComplexImageFilter.json │ │ ├── MaskImageFilter.json │ │ ├── MaskNegatedImageFilter.json │ │ ├── MaskedFFTNormalizedCorrelationImageFilter.json │ │ ├── MaximumEntropyThresholdImageFilter.json │ │ ├── MaximumImageFilter.json │ │ ├── MaximumProjectionImageFilter.json │ │ ├── MeanImageFilter.json │ │ ├── MeanProjectionImageFilter.json │ │ ├── MedianImageFilter.json │ │ ├── MedianProjectionImageFilter.json │ │ ├── MergeLabelMapFilter.json │ │ ├── MinMaxCurvatureFlowImageFilter.json │ │ ├── MinimumImageFilter.json │ │ ├── MinimumMaximumImageFilter.json │ │ ├── MinimumProjectionImageFilter.json │ │ ├── MirrorPadImageFilter.json │ │ ├── ModulusImageFilter.json │ │ ├── MomentsThresholdImageFilter.json │ │ ├── MorphologicalGradientImageFilter.json │ │ ├── MorphologicalWatershedFromMarkersImageFilter.json │ │ ├── MorphologicalWatershedImageFilter.json │ │ ├── MultiLabelSTAPLEImageFilter.json │ │ ├── MultiplyImageFilter.json │ │ ├── N4BiasFieldCorrectionImageFilter.json │ │ ├── NaryAddImageFilter.json │ │ ├── NaryMaximumImageFilter.json │ │ ├── NeighborhoodConnectedImageFilter.json │ │ ├── NoiseImageFilter.json │ │ ├── NormalizeImageFilter.json │ │ ├── NormalizeToConstantImageFilter.json │ │ ├── NormalizedCorrelationImageFilter.json │ │ ├── NotEqualImageFilter.json │ │ ├── NotImageFilter.json │ │ ├── ObjectnessMeasureImageFilter.json │ │ ├── OpeningByReconstructionImageFilter.json │ │ ├── OrImageFilter.json │ │ ├── OtsuMultipleThresholdsImageFilter.json │ │ ├── OtsuThresholdImageFilter.json │ │ ├── PasteImageFilter.json │ │ ├── PatchBasedDenoisingImageFilter.json │ │ ├── PermuteAxesImageFilter.json │ │ ├── PhysicalPointImageSource.json │ │ ├── PowImageFilter.json │ │ ├── ProjectedLandweberDeconvolutionImageFilter.json │ │ ├── RankImageFilter.json │ │ ├── RealAndImaginaryToComplexImageFilter.json │ │ ├── RealToHalfHermitianForwardFFTImageFilter.json │ │ ├── ReconstructionByDilationImageFilter.json │ │ ├── ReconstructionByErosionImageFilter.json │ │ ├── RecursiveGaussianImageFilter.json │ │ ├── RegionOfInterestImageFilter.json │ │ ├── RegionalMaximaImageFilter.json │ │ ├── RegionalMinimaImageFilter.json │ │ ├── RelabelComponentImageFilter.json │ │ ├── RelabelLabelMapFilter.json │ │ ├── RenyiEntropyThresholdImageFilter.json │ │ ├── ResampleImageFilter.json │ │ ├── RescaleIntensityImageFilter.json │ │ ├── RichardsonLucyDeconvolutionImageFilter.json │ │ ├── RoundImageFilter.json │ │ ├── SLICImageFilter.json │ │ ├── STAPLEImageFilter.json │ │ ├── SaltAndPepperNoiseImageFilter.json │ │ ├── ScalarChanAndVeseDenseLevelSetImageFilter.json │ │ ├── ScalarConnectedComponentImageFilter.json │ │ ├── ScalarImageKmeansImageFilter.json │ │ ├── ScalarToRGBColormapImageFilter.json │ │ ├── ShanbhagThresholdImageFilter.json │ │ ├── ShapeDetectionLevelSetImageFilter.json │ │ ├── ShiftScaleImageFilter.json │ │ ├── ShotNoiseImageFilter.json │ │ ├── ShrinkImageFilter.json │ │ ├── SigmoidImageFilter.json │ │ ├── SignedDanielssonDistanceMapImageFilter.json │ │ ├── SignedMaurerDistanceMapImageFilter.json │ │ ├── SimilarityIndexImageFilter.json │ │ ├── SimpleContourExtractorImageFilter.json │ │ ├── SinImageFilter.json │ │ ├── SliceImageFilter.json │ │ ├── SmoothingRecursiveGaussianImageFilter.json │ │ ├── SobelEdgeDetectionImageFilter.json │ │ ├── SpeckleNoiseImageFilter.json │ │ ├── SqrtImageFilter.json │ │ ├── SquareImageFilter.json │ │ ├── SquaredDifferenceImageFilter.json │ │ ├── StandardDeviationProjectionImageFilter.json │ │ ├── StatisticsImageFilter.json │ │ ├── StochasticFractalDimensionImageFilter.json │ │ ├── SubtractImageFilter.json │ │ ├── SumProjectionImageFilter.json │ │ ├── SymmetricForcesDemonsRegistrationFilter.json │ │ ├── TanImageFilter.json │ │ ├── TernaryAddImageFilter.json │ │ ├── TernaryMagnitudeImageFilter.json │ │ ├── TernaryMagnitudeSquaredImageFilter.json │ │ ├── ThresholdImageFilter.json │ │ ├── ThresholdMaximumConnectedComponentsImageFilter.json │ │ ├── ThresholdSegmentationLevelSetImageFilter.json │ │ ├── TikhonovDeconvolutionImageFilter.json │ │ ├── TileImageFilter.json │ │ ├── TobogganImageFilter.json │ │ ├── TransformToDisplacementFieldFilter.json │ │ ├── TriangleThresholdImageFilter.json │ │ ├── UnaryMinusImageFilter.json │ │ ├── UnsharpMaskImageFilter.json │ │ ├── ValuedRegionalMaximaImageFilter.json │ │ ├── ValuedRegionalMinimaImageFilter.json │ │ ├── VectorConfidenceConnectedImageFilter.json │ │ ├── VectorConnectedComponentImageFilter.json │ │ ├── VectorIndexSelectionCastImageFilter.json │ │ ├── VectorMagnitudeImageFilter.json │ │ ├── VotingBinaryHoleFillingImageFilter.json │ │ ├── VotingBinaryImageFilter.json │ │ ├── VotingBinaryIterativeHoleFillingImageFilter.json │ │ ├── WarpImageFilter.json │ │ ├── WhiteTopHatImageFilter.json │ │ ├── WienerDeconvolutionImageFilter.json │ │ ├── WrapPadImageFilter.json │ │ ├── XorImageFilter.json │ │ ├── YenThresholdImageFilter.json │ │ ├── ZeroCrossingBasedEdgeDetectionImageFilter.json │ │ ├── ZeroCrossingImageFilter.json │ │ └── ZeroFluxNeumannPadImageFilter.json │ ├── src │ │ ├── CMakeLists.txt │ │ ├── sitkAdditionalProcedures.cxx │ │ ├── sitkBSplineTransformInitializerFilter.cxx │ │ ├── sitkBoundaryConditions.hxx │ │ ├── sitkCastImageFilter-2.cxx │ │ ├── sitkCastImageFilter-2l.cxx │ │ ├── sitkCastImageFilter-2v.cxx │ │ ├── sitkCastImageFilter-3.cxx │ │ ├── sitkCastImageFilter-3l.cxx │ │ ├── sitkCastImageFilter-3v.cxx │ │ ├── sitkCastImageFilter-4.cxx │ │ ├── sitkCastImageFilter-4l.cxx │ │ ├── sitkCastImageFilter-4v.cxx │ │ ├── sitkCastImageFilter.cxx │ │ ├── sitkCastImageFilter.hxx │ │ ├── sitkCenteredTransformInitializerFilter.cxx │ │ ├── sitkCenteredVersorTransformInitializerFilter.cxx │ │ ├── sitkCreateInterpolator.hxx │ │ ├── sitkCreateKernel.h │ │ ├── sitkHashImageFilter.cxx │ │ ├── sitkHeavisideFunction.hxx │ │ ├── sitkImageFilter.cxx │ │ ├── sitkImageToKernel.hxx │ │ ├── sitkLabelFunctorUtils.hxx │ │ ├── sitkLandmarkBasedTransformInitializerFilter.cxx │ │ ├── sitkPermuteAxis_Static.hxx │ │ └── sitkToPixelType.hxx │ └── templates │ │ ├── sitkBinaryFunctorFilterTemplate.cxx.in │ │ ├── sitkBinaryFunctorFilterTemplate.h.in │ │ ├── sitkDualImageFilterTemplate.cxx.in │ │ ├── sitkDualImageFilterTemplate.h.in │ │ ├── sitkFastMarchingImageFilterTemplate.cxx.in │ │ ├── sitkFastMarchingImageFilterTemplate.h.in │ │ ├── sitkImageFilterTemplate.cxx.in │ │ ├── sitkImageFilterTemplate.h.in │ │ ├── sitkImageSourceTemplate.cxx.in │ │ ├── sitkImageSourceTemplate.h.in │ │ ├── sitkKernelImageFilterTemplate.cxx.in │ │ ├── sitkKernelImageFilterTemplate.h.in │ │ ├── sitkMultiInputImageFilterTemplate.cxx.in │ │ ├── sitkMultiInputImageFilterTemplate.h.in │ │ ├── sitkRegionGrowingImageFilterTemplate.cxx.in │ │ └── sitkRegionGrowingImageFilterTemplate.h.in ├── CMakeLists.txt ├── Common │ ├── CMakeLists.txt │ ├── include │ │ ├── Ancillary │ │ │ ├── FunctionTraits.h │ │ │ ├── TypeList.h │ │ │ ├── hl_sha1.cxx │ │ │ └── hl_sha1.h │ │ ├── SimpleITK.h │ │ ├── sitkAffineTransform.h │ │ ├── sitkBSplineTransform.h │ │ ├── sitkCommand.h │ │ ├── sitkCommon.h │ │ ├── sitkConditional.h │ │ ├── sitkDetail.h │ │ ├── sitkDisplacementFieldTransform.h │ │ ├── sitkDualMemberFunctionFactory.h │ │ ├── sitkDualMemberFunctionFactory.hxx │ │ ├── sitkEuler2DTransform.h │ │ ├── sitkEuler3DTransform.h │ │ ├── sitkEvent.h │ │ ├── sitkExceptionObject.h │ │ ├── sitkFunctionCommand.h │ │ ├── sitkImage.h │ │ ├── sitkImageConvert.h │ │ ├── sitkInterpolator.h │ │ ├── sitkKernel.h │ │ ├── sitkMacro.h │ │ ├── sitkMemberFunctionFactory.h │ │ ├── sitkMemberFunctionFactory.hxx │ │ ├── sitkMemberFunctionFactoryBase.h │ │ ├── sitkNonCopyable.h │ │ ├── sitkPixelIDTokens.h │ │ ├── sitkPixelIDTypeLists.h │ │ ├── sitkPixelIDTypes.h │ │ ├── sitkPixelIDValues.h │ │ ├── sitkProcessObject.h │ │ ├── sitkRandomSeed.h │ │ ├── sitkScaleSkewVersor3DTransform.h │ │ ├── sitkScaleTransform.h │ │ ├── sitkScaleVersor3DTransform.h │ │ ├── sitkSimilarity2DTransform.h │ │ ├── sitkSimilarity3DTransform.h │ │ ├── sitkTemplateFunctions.h │ │ ├── sitkTransform.h │ │ ├── sitkTranslationTransform.h │ │ ├── sitkVersion.h │ │ ├── sitkVersorRigid3DTransform.h │ │ └── sitkVersorTransform.h │ └── src │ │ ├── CMakeLists.txt │ │ ├── sitkAffineTransform.cxx │ │ ├── sitkBSplineTransform.cxx │ │ ├── sitkCommand.cxx │ │ ├── sitkConfigure.h.in │ │ ├── sitkDisplacementFieldTransform.cxx │ │ ├── sitkEuler2DTransform.cxx │ │ ├── sitkEuler3DTransform.cxx │ │ ├── sitkEvent.cxx │ │ ├── sitkExceptionObject.cxx │ │ ├── sitkFunctionCommand.cxx │ │ ├── sitkImage.cxx │ │ ├── sitkImage.hxx │ │ ├── sitkImageExplicit.cxx │ │ ├── sitkInterpolator.cxx │ │ ├── sitkKernel.cxx │ │ ├── sitkPimpleImageBase.h │ │ ├── sitkPimpleImageBase.hxx │ │ ├── sitkPimpleTransform.hxx │ │ ├── sitkPixelIDValues.cxx │ │ ├── sitkProcessObject.cxx │ │ ├── sitkScaleSkewVersor3DTransform.cxx │ │ ├── sitkScaleTransform.cxx │ │ ├── sitkScaleVersor3DTransform.cxx │ │ ├── sitkSimilarity2DTransform.cxx │ │ ├── sitkSimilarity3DTransform.cxx │ │ ├── sitkTransform.cxx │ │ ├── sitkTransformHelper.hxx │ │ ├── sitkTranslationTransform.cxx │ │ ├── sitkVersion.cxx │ │ ├── sitkVersionConfig.h.in │ │ ├── sitkVersorRigid3DTransform.cxx │ │ └── sitkVersorTransform.cxx ├── Elastix │ ├── CMakeLists.txt │ ├── include │ │ ├── sitkElastixImageFilter.h │ │ └── sitkTransformixImageFilter.h │ └── src │ │ ├── CMakeLists.txt │ │ ├── sitkElastixImageFilter.cxx │ │ ├── sitkElastixImageFilterImpl.cxx │ │ ├── sitkElastixImageFilterImpl.h │ │ ├── sitkTransformixImageFilter.cxx │ │ ├── sitkTransformixImageFilterImpl.cxx │ │ └── sitkTransformixImageFilterImpl.h ├── Explicit │ ├── CMakeLists.txt │ ├── include │ │ ├── sitkExplicit.h │ │ ├── sitkExplicitITK.h │ │ ├── sitkExplicitITKComposeImageFilter.h │ │ ├── sitkExplicitITKDefaultPixelAccessor.h │ │ ├── sitkExplicitITKDefaultVectorPixelAccessor.h │ │ ├── sitkExplicitITKImage.h │ │ ├── sitkExplicitITKImageBase.h │ │ ├── sitkExplicitITKImageConstIterator.h │ │ ├── sitkExplicitITKImageRegion.h │ │ ├── sitkExplicitITKImageRegionConstIterator.h │ │ ├── sitkExplicitITKImageScanlineConstIterator.h │ │ ├── sitkExplicitITKImageScanlineIterator.h │ │ ├── sitkExplicitITKImageSource.h │ │ ├── sitkExplicitITKImageToImageFilter.h │ │ ├── sitkExplicitITKImportImageContainer.h │ │ ├── sitkExplicitITKInPlaceImageFilter.h │ │ ├── sitkExplicitITKLabelMap.h │ │ ├── sitkExplicitITKVectorImage.h │ │ └── sitkExplicitITKVectorIndexSelectionCastImageFilter.h │ └── src │ │ ├── CMakeLists.txt │ │ ├── sitkExplicitITKComposeImageFilter.cxx │ │ ├── sitkExplicitITKDefaultPixelAccessor.cxx │ │ ├── sitkExplicitITKDefaultVectorPixelAccessor.cxx │ │ ├── sitkExplicitITKImage.cxx │ │ ├── sitkExplicitITKImageBase.cxx │ │ ├── sitkExplicitITKImageConstIterator.cxx │ │ ├── sitkExplicitITKImageRegion.cxx │ │ ├── sitkExplicitITKImageRegionConstIterator.cxx │ │ ├── sitkExplicitITKImageScanlineConstIterator.cxx │ │ ├── sitkExplicitITKImageScanlineIterator.cxx │ │ ├── sitkExplicitITKImageSource.cxx │ │ ├── sitkExplicitITKImageToImageFilter.cxx │ │ ├── sitkExplicitITKImportImageContainer.cxx │ │ ├── sitkExplicitITKInPlaceImageFilter.cxx │ │ ├── sitkExplicitITKLabelMap.cxx │ │ ├── sitkExplicitITKVectorImage.cxx │ │ └── sitkExplicitITKVectorIndexSelectionCastImageFilter.cxx ├── IO │ ├── CMakeLists.txt │ ├── include │ │ ├── sitkIO.h │ │ ├── sitkImageFileReader.h │ │ ├── sitkImageFileWriter.h │ │ ├── sitkImageReaderBase.h │ │ ├── sitkImageSeriesReader.h │ │ ├── sitkImageSeriesWriter.h │ │ ├── sitkImageViewer.h │ │ ├── sitkImportImageFilter.h │ │ └── sitkShow.h │ └── src │ │ ├── CMakeLists.txt │ │ ├── sitkImageFileReader.cxx │ │ ├── sitkImageFileWriter.cxx │ │ ├── sitkImageIOUtilities.cxx │ │ ├── sitkImageIOUtilities.h │ │ ├── sitkImageReaderBase.cxx │ │ ├── sitkImageSeriesReader.cxx │ │ ├── sitkImageSeriesWriter.cxx │ │ ├── sitkImageViewer.cxx │ │ ├── sitkImportImageFilter.cxx │ │ ├── sitkMetaDataDictionaryCustomCast.hxx │ │ └── sitkShow.cxx └── Registration │ ├── CMakeLists.txt │ ├── include │ ├── sitkImageRegistrationMethod.h │ └── sitkRegistration.h │ └── src │ ├── CMakeLists.txt │ ├── sitkCreateInterpolator.hxx │ ├── sitkImageRegistrationMethod.cxx │ ├── sitkImageRegistrationMethod_CreateMetric.cxx │ ├── sitkImageRegistrationMethod_CreateMetric.hxx │ ├── sitkImageRegistrationMethod_CreateOptimizer.cxx │ └── sitkImageRegistrationMethod_CreateParametersAdaptor.hxx ├── Documentation ├── CMakeLists.txt ├── Doxygen │ ├── MainPage.dox │ └── PythonDownloads.dox ├── Makefile ├── README.md ├── Sphinx │ ├── Acknowledgements.rst │ ├── AffineRegistration.rst │ ├── AtlasBasedSegmentation.rst │ ├── GetDeformationField.rst │ ├── GettingStarted.rst │ ├── GroupwiseRegistration.rst │ ├── HelloWorld.rst │ ├── Introduction.rst │ ├── KnownIssues.rst │ ├── LabelBasedRegistration.rst │ ├── MultiMetricRegularisation.rst │ ├── NonRigidRegistration.rst │ ├── ParameterMaps.rst │ ├── PointBasedRegistration.rst │ ├── RegisterDICOMs.rst │ ├── RigidRegistration.rst │ ├── _static │ │ ├── BrainProtonDensity.png │ │ ├── BrainProtonDensityBSplined.png │ │ ├── BrainProtonDensityTranslated13x17y.png │ │ ├── BrainProtonDensityTranslatedR1013x17y.png │ │ ├── BrainProtonDensityTranslatedR1013x17yS12.png │ │ ├── ImageConcepts.png │ │ ├── ImagePyramidConcept.png │ │ ├── ImageRegistrationConcept.png │ │ ├── IntelliJSetJar.png │ │ ├── IntelliJSetLibrary.png │ │ ├── PostAffine.jpeg │ │ ├── PostGroupwise.jpg │ │ ├── PostNonrigid.jpg │ │ ├── PostRotated.jpeg │ │ ├── PostTranslated.jpeg │ │ ├── PreAffine.jpeg │ │ ├── PreGroupwise.jpg │ │ ├── PreNonrigid.jpg │ │ ├── PreRotated.jpeg │ │ ├── PreTranslated.jpeg │ │ ├── WindowsInstallationBuildSolution.png │ │ ├── WindowsInstallationConfigureCMake.png │ │ ├── WindowsInstallationOpenSolution.png │ │ └── WindowsInstallationSelectCompiler.png │ ├── conf.py │ └── index.rst └── make.bat ├── Examples ├── AdvancedImageReading │ ├── AdvancedImageReading.R │ ├── AdvancedImageReading.py │ ├── CMakeLists.txt │ └── Documentation.rst ├── BufferImportExport.cxx ├── CMakeLists.txt ├── CSharp │ ├── CMakeLists.txt │ ├── CannySegmentationLevelSetImageFilter.cs │ ├── ConnectedThresholdSegmentation.cs │ ├── Documentation.rst │ ├── ImageGetBuffer.cs │ ├── SimpleElastix.cs │ └── SimpleTransformix.cs ├── DemonsRegistration1 │ ├── CMakeLists.txt │ ├── DemonsRegistration1.R │ ├── DemonsRegistration1.cxx │ ├── DemonsRegistration1.py │ └── Documentation.rst ├── DemonsRegistration2 │ ├── CMakeLists.txt │ ├── DemonsRegistration2.R │ ├── DemonsRegistration2.cxx │ ├── DemonsRegistration2.py │ └── Documentation.rst ├── DicomImagePrintTags │ ├── CMakeLists.txt │ ├── DicomImagePrintTags.R │ ├── DicomImagePrintTags.py │ └── Documentation.rst ├── DicomSeriesFromArray │ ├── CMakeLists.txt │ ├── DicomSeriesFromArray.R │ ├── DicomSeriesFromArray.py │ └── Documentation.rst ├── DicomSeriesReadModifyWrite │ ├── CMakeLists.txt │ ├── DicomSeriesReadModifySeriesWrite.R │ ├── DicomSeriesReadModifySeriesWrite.py │ └── Documentation.rst ├── DicomSeriesReader │ ├── CMakeLists.txt │ ├── DicomSeriesReader.R │ ├── DicomSeriesReader.cxx │ ├── DicomSeriesReader.java │ ├── DicomSeriesReader.lua │ ├── DicomSeriesReader.py │ └── Documentation.rst ├── FastMarchingSegmentation │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── FastMarchingSegmentation.cs │ ├── FastMarchingSegmentation.cxx │ └── FastMarchingSegmentation.py ├── FilterProgressReporting │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── FilterProgressReporting.R │ ├── FilterProgressReporting.cs │ ├── FilterProgressReporting.cxx │ ├── FilterProgressReporting.java │ ├── FilterProgressReporting.py │ └── FilterProgressReporting.rb ├── HelloWorld │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── HelloWorld.R │ ├── HelloWorld.cs │ ├── HelloWorld.cxx │ ├── HelloWorld.java │ ├── HelloWorld.lua │ ├── HelloWorld.py │ ├── HelloWorld.rb │ ├── HelloWorld.tcl │ └── Testing │ │ └── Temporary │ │ ├── CTestCostData.txt │ │ └── LastTest.log ├── ITKIntegration │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ElastixFilter.cxx │ ├── ITKIntegration.cxx │ └── TransformixFilter.cxx ├── ImageGridManipulation │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageGridManipulation.R │ └── ImageGridManipulation.py ├── ImageIOSelection │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageIOSelection.R │ └── ImageIOSelection.py ├── ImageRegistrationMethod1 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethod1.R │ ├── ImageRegistrationMethod1.cs │ ├── ImageRegistrationMethod1.cxx │ ├── ImageRegistrationMethod1.java │ ├── ImageRegistrationMethod1.lua │ └── ImageRegistrationMethod1.py ├── ImageRegistrationMethod2 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethod2.R │ ├── ImageRegistrationMethod2.cs │ ├── ImageRegistrationMethod2.cxx │ └── ImageRegistrationMethod2.py ├── ImageRegistrationMethod3 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethod3.R │ └── ImageRegistrationMethod3.py ├── ImageRegistrationMethod4 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethod4.R │ └── ImageRegistrationMethod4.py ├── ImageRegistrationMethodBSpline1 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethodBSpline1.R │ ├── ImageRegistrationMethodBSpline1.cxx │ └── ImageRegistrationMethodBSpline1.py ├── ImageRegistrationMethodBSpline2 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethodBSpline2.R │ └── ImageRegistrationMethodBSpline2.py ├── ImageRegistrationMethodBSpline3 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethodBSpline3.cxx │ └── ImageRegistrationMethodBSpline3.py ├── ImageRegistrationMethodDisplacement1 │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethodDisplacement1.R │ ├── ImageRegistrationMethodDisplacement1.cxx │ └── ImageRegistrationMethodDisplacement1.py ├── ImageRegistrationMethodExhaustive │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageRegistrationMethodExhaustive.R │ └── ImageRegistrationMethodExhaustive.py ├── ImageViewing │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── ImageViewing.R │ └── ImageViewing.py ├── Java │ ├── SimpleElastix.java │ └── SimpleTransformix.java ├── N4BiasFieldCorrection │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── N4BiasFieldCorrection.R │ └── N4BiasFieldCorrection.py ├── Python │ ├── BoarderSegmentation.py │ ├── CMakeLists.txt │ ├── CannyEdge.py │ ├── ConnectedThresholdImageFilter.py │ ├── DicomModifyTags.py │ ├── DicomSeriesReader2.py │ ├── Documentation.rst │ ├── ExtractSlice.py │ ├── FFTConvolution.py │ ├── GeodesicActiceContourSegmentation.py │ ├── ImageCreateAndSet.py │ ├── NeighborhoodConnectedImageFilter.py │ ├── ReadAndShow.py │ ├── SimpleElastix.py │ ├── SimpleGaussianProcedural.py │ └── SimpleTransformix.py ├── R │ └── SimpleElastix.R ├── Segmentation │ ├── CMakeLists.txt │ ├── ConnectedThresholdImageFilter.cxx │ └── NeighborhoodConnectedImageFilter.cxx ├── SimpleGaussian │ ├── CMakeLists.txt │ ├── Documentation.rst │ ├── SimpleGaussian.R │ ├── SimpleGaussian.cs │ ├── SimpleGaussian.cxx │ ├── SimpleGaussian.java │ ├── SimpleGaussian.lua │ ├── SimpleGaussian.py │ ├── SimpleGaussian.rb │ └── SimpleGaussian.tcl ├── SimpleGaussianFunctional.cxx ├── elx.cxx ├── index.rst ├── test │ └── CMakeLists.txt └── tfx.cxx ├── ExpandTemplateGenerator ├── Components │ ├── AddExtraIncludes.cxx.in │ ├── ClassDeclaration.h.in │ ├── ClassEnd.h.in │ ├── ClassNameAndPrint.h.in │ ├── ConstructorInitializeMembers.cxx.in │ ├── ConstructorMemberFunctionSetup.cxx.in │ ├── ConstructorSignature.cxx.in │ ├── ConstructorVectorPixels.cxx.in │ ├── CustomCasts.cxx │ ├── CustomMethods.cxx.in │ ├── CustomMethods.h.in │ ├── DestructorDefinition.cxx.in │ ├── DoNotEditWarning.cxx.in │ ├── DoNotEditWarning.h.in │ ├── ExecuteInternalGetImagePointers.cxx.in │ ├── ExecuteInternalITKFilter.cxx.in │ ├── ExecuteInternalMethod.h.in │ ├── ExecuteInternalSetITKFilterInputs.cxx.in │ ├── ExecuteInternalSetITKFilterParameters.cxx.in │ ├── ExecuteInternalSignature.cxx.in │ ├── ExecuteInternalTypedefs.cxx.in │ ├── ExecuteInternalUpdateAndReturn.cxx.in │ ├── ExecuteInternalVectorImages.cxx.in │ ├── ExecuteMethodNoParameters.h.in │ ├── ExecuteMethodWithParameters.h.in │ ├── ExecuteNoParameters.cxx.in │ ├── ExecuteWithParameters.cxx.in │ ├── FunctionalAPI.cxx.in │ ├── FunctionalAPI.h.in │ ├── ImageParameters.in │ ├── InputParameters.in │ ├── InputParametersInternal.in │ ├── MemberFunctionDispatch.h.in │ ├── MemberGetSetDeclarations.h.in │ ├── MemberParameters.in │ ├── MemberParametersWithDefaults.in │ ├── MemberPointsGetSetDeclarations.h.in │ ├── PrivateMemberDeclarations.h.in │ ├── PublicDeclarations.h.in │ ├── StandardIncludes.cxx.in │ ├── ToStringBody.cxx.in │ ├── ToStringReturn.cxx.in │ └── ToStringSignature.cxx.in ├── ExpandTemplate.lua ├── JSONQuery.lua └── json.lua ├── LICENSE ├── NOTICE ├── Pipfile ├── README ├── README.md ├── SimpleITKConfig.cmake.in ├── SimpleITKConfigVersion.cmake.in ├── SuperBuild ├── CMakeLists.txt ├── CTestConfig.cmake ├── ExternalSource │ ├── lua-5.3.5.tar.gz.sha512 │ ├── pcre-8.43.tar.gz.sha512 │ ├── swig-3.0.12.tar.gz.sha512 │ ├── swigwin-3.0.12.zip.sha512 │ └── virtualenv-15.1.0.tar.gz.sha512 ├── External_Elastix.cmake ├── External_GTest.cmake ├── External_ITK.cmake ├── External_Lua.cmake ├── External_PCRE.cmake ├── External_SimpleITKExamples.cmake ├── External_Swig.cmake ├── External_virtualenv.cmake ├── SuperBuild.cmake ├── lua.cmake ├── pcre_configure_step.cmake.in └── swig_configure_step.cmake.in ├── Testing ├── CI │ └── Azure │ │ ├── azure-pipelines-package.yml │ │ ├── azure-pipelines.yml │ │ ├── azure.cmake │ │ ├── scripts │ │ ├── mac_build_java.sh │ │ ├── mac_build_python.sh │ │ ├── win_build_csharp.sh │ │ ├── win_build_java.sh │ │ └── win_build_python.sh │ │ └── templates │ │ ├── git-download-steps.yml │ │ ├── package-linux-job.yml │ │ ├── package-mac-job.yml │ │ └── package-win-job.yml ├── CMakeLists.txt ├── Data │ ├── Baseline │ │ ├── BasicFilters_AbsImageFilter_float.nrrd.sha512 │ │ ├── BasicFilters_AbsImageFilter_short.nrrd.sha512 │ │ ├── BasicFilters_AbsImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_AcosImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_AcosImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_AdaptiveHistogramEqualizationImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_AdaptiveHistogramEqualizationImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_AdaptiveHistogramEqualizationImageFilter_histo.1.nrrd.sha512 │ │ ├── BasicFilters_AdaptiveHistogramEqualizationImageFilter_histo.nrrd.sha512 │ │ ├── BasicFilters_AdditiveGaussianNoiseImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_AdditiveGaussianNoiseImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_AdditiveGaussianNoiseImageFilter_rgb.nrrd.sha512 │ │ ├── BasicFilters_AntiAliasBinaryImageFilter_cthead.nrrd.sha512 │ │ ├── BasicFilters_ApproximateSignedDistanceMapImageFilter_default.1.nrrd.sha512 │ │ ├── BasicFilters_ApproximateSignedDistanceMapImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_ApproximateSignedDistanceMapImageFilter_modified_parms.nrrd.sha512 │ │ ├── BasicFilters_AsinImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_Atan2ImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_AtanImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_AtanImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_BSplineDecompositionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_BilateralImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_BinaryMagnitudeImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_BinaryMinMaxCurvatureFlowImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_BinaryMinMaxCurvatureFlowImageFilter_longer.nrrd.sha512 │ │ ├── BasicFilters_BoundedReciprocalImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_BoundedReciprocalImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_CannySegmentationLevelSetImageFilter_cthead.nrrd.sha512 │ │ ├── BasicFilters_ClampImageFilter_double.nrrd.sha512 │ │ ├── BasicFilters_CoherenceEnhancingDiffusionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_CollidingFrontsImageFilter_around_dots.nrrd.sha512 │ │ ├── BasicFilters_ComplexToModulusImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ComplexToPhaseImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ConvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_CosImageFilter_float.nrrd.sha512 │ │ ├── BasicFilters_CosImageFilter_short.nrrd.sha512 │ │ ├── BasicFilters_CosImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_CurvatureAnisotropicDiffusionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_CurvatureAnisotropicDiffusionImageFilter_longer.nrrd.sha512 │ │ ├── BasicFilters_CurvatureFlowImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_CurvatureFlowImageFilter_longer.nrrd.sha512 │ │ ├── BasicFilters_DanielssonDistanceMapImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_DemonsRegistrationFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_DemonsRegistrationFilter_2d_with_initial.nrrd.sha512 │ │ ├── BasicFilters_DerivativeImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_DerivativeImageFilter_zsecondorder.nrrd.sha512 │ │ ├── BasicFilters_DiffeomorphicDemonsRegistrationFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_DiffeomorphicDemonsRegistrationFilter_2d_with_initial.nrrd.sha512 │ │ ├── BasicFilters_DilateObjectMorphologyImageFilter_float.nrrd.sha512 │ │ ├── BasicFilters_DilateObjectMorphologyImageFilter_short.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianDerivativeImageFilter_float1.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianDerivativeImageFilter_float_10.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianDerivativeImageFilter_float_dx.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianDerivativeImageFilter_float_dy2.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianImageFilter_float.nrrd.sha512 │ │ ├── BasicFilters_DiscreteGaussianImageFilter_short.nrrd.sha512 │ │ ├── BasicFilters_DisplacementFieldJacobianDeterminantFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_DisplacementFieldJacobianDeterminantFilter_2d_weights.nrrd.sha512 │ │ ├── BasicFilters_DivideRealImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_EdgePotentialImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ErodeObjectMorphologyImageFilter_float.nrrd.sha512 │ │ ├── BasicFilters_ErodeObjectMorphologyImageFilter_short.nrrd.sha512 │ │ ├── BasicFilters_ExpImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ExpImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_ExpNegativeImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ExpNegativeImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_ExpandImageFilter_Expand2x3.nrrd.sha512 │ │ ├── BasicFilters_ExpandImageFilter_Interpolator_BSpline.nrrd.sha512 │ │ ├── BasicFilters_ExpandImageFilter_Interpolator_Gaussian.nrrd.sha512 │ │ ├── BasicFilters_ExpandImageFilter_Vector.nrrd.sha512 │ │ ├── BasicFilters_FFTConvolutionImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_FFTConvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_3D.1.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_3D.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_EvenKernel.1.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_EvenKernel.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_FFTNormalizedCorrelationImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_FastMarchingBaseImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_FastMarchingImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_FastMarchingUpwindGradientImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_FastSymmetricForcesDemonsRegistrationFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_FastSymmetricForcesDemonsRegistrationFilter_2d_with_initial.nrrd.sha512 │ │ ├── BasicFilters_ForwardFFTImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_GaborImageSource_default.nrrd.sha512 │ │ ├── BasicFilters_GaborSourceImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GaussianImageSource_default.nrrd.sha512 │ │ ├── BasicFilters_GaussianSourceImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GeodesicActiveContourLevelSetImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_GradientAnisotropicDiffusionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_GradientAnisotropicDiffusionImageFilter_longer.nrrd.sha512 │ │ ├── BasicFilters_GradientImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GradientImageFilter_default_float.nrrd.sha512 │ │ ├── BasicFilters_GradientMagnitudeImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GradientMagnitudeRecursiveGaussianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GradientRecursiveGaussianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_GradientRecursiveGaussianImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_GridImageSource_default.nrrd.sha512 │ │ ├── BasicFilters_GridSourceImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_HalfHermitianToRealInverseFFTImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_HistogramMatchingImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_InverseDeconvolutionImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_InverseDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_InverseDisplacementFieldImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_InverseFFTImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_InvertDisplacementFieldImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_IsoContourDistanceImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_IterativeInverseDisplacementFieldImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_LandweberDeconvolutionImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_LandweberDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_LaplacianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_LaplacianRecursiveGaussianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_LaplacianSegmentationLevelSetImageFilter_cthead.nrrd.sha512 │ │ ├── BasicFilters_LaplacianSharpeningImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_LevelSetMotionRegistrationFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_Log10ImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_LogImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_LogImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_MagnitudeAndPhaseToComplexImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.1.nrrd.sha512 │ │ ├── BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.nrrd.sha512 │ │ ├── BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_MeanProjectionImageFilter_z_projection.nrrd.sha512 │ │ ├── BasicFilters_MinMaxCurvatureFlowImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_MinMaxCurvatureFlowImageFilter_longer.nrrd.sha512 │ │ ├── BasicFilters_MirrorPadImageFilter_decay.nrrd.sha512 │ │ ├── BasicFilters_N4BiasFieldCorrectionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_NeighborhoodConnectedImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_NormalizeImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_NormalizeImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_NormalizeToConstantImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_NormalizeToConstantImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_NormalizedCorrelationImageFilter_EvenKernel.nrrd.sha512 │ │ ├── BasicFilters_NormalizedCorrelationImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ObjectnessMeasureImageFilter_dark_dots.nrrd.sha512 │ │ ├── BasicFilters_ObjectnessMeasureImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_PatchBasedDenoisingImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_PowImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_PowToConstantImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_PowToConstantImageFilter_setting_constant.nrrd.sha512 │ │ ├── BasicFilters_ProjectedLandweberDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_RealToHalfHermitianForwardFFTImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_RecursiveGaussianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_RecursiveGaussianImageFilter_rgb_image.nrrd.sha512 │ │ ├── BasicFilters_ResampleImageFilter_NearestNeighborExtrapolator.nrrd.sha512 │ │ ├── BasicFilters_ResampleImageFilter_bspline_resample.nrrd.sha512 │ │ ├── BasicFilters_ResampleImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ResampleImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_ResampleImageFilter_wCastwInterpolator.nrrd.sha512 │ │ ├── BasicFilters_RescaleIntensityImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_RichardsonLucyDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_SLICImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_SLICImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_SLICImageFilter_gray_scale.nrrd.sha512 │ │ ├── BasicFilters_SLICImageFilter_minimum.nrrd.sha512 │ │ ├── BasicFilters_STAPLEImageFilter_basic.nrrd.sha512 │ │ ├── BasicFilters_SaltAndPepperNoiseImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_SaltAndPepperNoiseImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_SaltAndPepperNoiseImageFilter_rgb.nrrd.sha512 │ │ ├── BasicFilters_ScalarChanAndVeseDenseLevelSetImageFilter_cthead.nrrd.sha512 │ │ ├── BasicFilters_ShapeDetectionLevelSetImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ShotNoiseImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_ShotNoiseImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_ShotNoiseImageFilter_rgb.nrrd.sha512 │ │ ├── BasicFilters_SignedDanielssonDistanceMapImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_SignedMaurerDistanceMapImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_SinImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_SinImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_SmoothingRecursiveGaussianImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_SmoothingRecursiveGaussianImageFilter_rgb_image.nrrd.sha512 │ │ ├── BasicFilters_SobelEdgeDetectionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_SpeckleNoiseImageFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_SpeckleNoiseImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_SpeckleNoiseImageFilter_rgb.nrrd.sha512 │ │ ├── BasicFilters_SqrtImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_SqrtImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_SquaredDifferenceImageFilter_2DStapleImages.nrrd.sha512 │ │ ├── BasicFilters_SquaredDifferenceImageFilter_Ramp_Short1.nrrd.sha512 │ │ ├── BasicFilters_SquaredDifferenceImageFilter_Ramp_Short2.nrrd.sha512 │ │ ├── BasicFilters_StandardDeviationProjectionImageFilter_z_projection.nrrd.sha512 │ │ ├── BasicFilters_StochasticFractalDimensionImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_StochasticFractalDimensionImageFilter_mask.nrrd.sha512 │ │ ├── BasicFilters_SumProjectionImageFilter_z_projection.nrrd.sha512 │ │ ├── BasicFilters_SymmetricForcesDemonsRegistrationFilter_2d.nrrd.sha512 │ │ ├── BasicFilters_SymmetricForcesDemonsRegistrationFilter_2d_with_initial.nrrd.sha512 │ │ ├── BasicFilters_TanImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_TanImageFilter_vector.nrrd.sha512 │ │ ├── BasicFilters_TernaryMagnitudeImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_TernaryMagnitudeSquaredImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_ThresholdSegmentationLevelSetImageFilter_cthead.nrrd.sha512 │ │ ├── BasicFilters_TikhonovDeconvolutionImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_TikhonovDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_TransformToDisplacementFieldFilter_32.nrrd.sha512 │ │ ├── BasicFilters_TransformToDisplacementFieldFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_UnsharpMaskImageFilter_default.nrrd.sha512 │ │ ├── BasicFilters_UnsharpMaskImageFilter_local_contrast.nrrd.sha512 │ │ ├── BasicFilters_VectorMagnitudeImageFilter_3d.nrrd.sha512 │ │ ├── BasicFilters_WarpImageFilter_cthead1.nrrd.sha512 │ │ ├── BasicFilters_WarpImageFilter_vm.nrrd.sha512 │ │ ├── BasicFilters_WienerDeconvolutionImageFilter_defaults.1.nrrd.sha512 │ │ ├── BasicFilters_WienerDeconvolutionImageFilter_defaults.nrrd.sha512 │ │ ├── BasicFilters_ZeroCrossingBasedEdgeDetectionImageFilter_defaults.nrrd.sha512 │ │ ├── DemonsRegistration1Test_displacement.mha.sha512 │ │ ├── DemonsRegistration2Test_displacement.mha.sha512 │ │ ├── Example_SimpleDerivative.nrrd.sha512 │ │ ├── Example_SimpleGaussian_2.0.nrrd.sha512 │ │ ├── FastMarchingSegmentation1.mha.sha512 │ │ ├── ImageRegistrationMethod3Test1.mha.sha512 │ │ ├── ImageRegistrationMethod3Test2.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline1.1.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline1.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline2.1.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline2.2.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline2.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline3.1.mha.sha512 │ │ ├── ImageRegistrationMethodBSpline3.mha.sha512 │ │ ├── ImageRegistrationMethodDisplacement1.1.mha.sha512 │ │ ├── ImageRegistrationMethodDisplacement1.mha.sha512 │ │ ├── ImageRegistrationMethodDisplacement1Test2.1.mha.sha512 │ │ ├── ImageRegistrationMethodDisplacement1Test2.mha.sha512 │ │ ├── ImageRegistrationMethodExhaustiveTest1.mha.sha512 │ │ ├── Registration_Resample_Resample.nrrd.sha512 │ │ ├── displacement_-13x-17y.mha.sha512 │ │ └── displacement_13x17y.mha.sha512 │ └── Input │ │ ├── 2th_cthead1.mha.sha512 │ │ ├── 2th_cthead1.png.sha512 │ │ ├── 2th_cthead1_distance.nrrd.sha512 │ │ ├── 4D.nii.gz.sha512 │ │ ├── BlackDots.png.sha512 │ │ ├── BrainProtonDensitySlice.png.sha512 │ │ ├── BrainProtonDensitySlice20InitialDisplacement.mha.sha512 │ │ ├── BrainProtonDensitySliceBSplined10.png.sha512 │ │ ├── BrainProtonDensitySliceBorder20.png.sha512 │ │ ├── BrainProtonDensitySliceBorder20Mask.png.sha512 │ │ ├── BrainProtonDensitySliceR10X13Y17.png.sha512 │ │ ├── BrainProtonDensitySliceR10X13Y17S12.png.sha512 │ │ ├── BrainProtonDensitySliceShifted13x17y.png.sha512 │ │ ├── BrainT1SliceBorder20.png.sha512 │ │ ├── DeconvolutionInput.nrrd.sha512 │ │ ├── DeconvolutionKernel.nrrd.sha512 │ │ ├── DicomSeries │ │ ├── Image0075.dcm.sha512 │ │ ├── Image0076.dcm.sha512 │ │ └── Image0077.dcm.sha512 │ │ ├── Gaussian_1.5.nrrd.sha512 │ │ ├── LargeWhiteCircle.nrrd.sha512 │ │ ├── LargeWhiteCircle_Float.nrrd.sha512 │ │ ├── OAS1_0001_MR1_mpr-1_anon.nrrd.sha512 │ │ ├── OAS1_0002_MR1_mpr-1_anon.nrrd.sha512 │ │ ├── RA-FFT-Complex.nrrd.sha512 │ │ ├── RA-Float.nrrd.sha512 │ │ ├── RA-Gradient.nrrd.sha512 │ │ ├── RA-HalfFFT-Complex.nrrd.sha512 │ │ ├── RA-Short.nrrd.sha512 │ │ ├── RA-Slice-Float.nrrd.sha512 │ │ ├── RA-Slice-Short.nrrd.sha512 │ │ ├── RA-Slice-Short.png.sha512 │ │ ├── Ramp-Down-Short.nrrd.sha512 │ │ ├── Ramp-One-Zero-Float.nrrd.sha512 │ │ ├── Ramp-Up-Short.nrrd.sha512 │ │ ├── Ramp-Zero-One-Float.nrrd.sha512 │ │ ├── STAPLE1-binary.png.sha512 │ │ ├── STAPLE1.png.sha512 │ │ ├── STAPLE2-binary.png.sha512 │ │ ├── STAPLE2.png.sha512 │ │ ├── SmallWhiteCircle.nrrd.sha512 │ │ ├── SmallWhiteCircle_Float.nrrd.sha512 │ │ ├── ThresholdSegmentationLevelSetVentricle.png.sha512 │ │ ├── VM1111Shrink-RGB.png.sha512 │ │ ├── VM1111Shrink-RGBFloat.nrrd.sha512 │ │ ├── VM1111Shrink-RGBNorm.nrrd.sha512 │ │ ├── VM1111Shrink-dis1.nrrd.sha512 │ │ ├── VM1111Shrink-mask.png.sha512 │ │ ├── WhiteDots.png.sha512 │ │ ├── branchy-lines.png.sha512 │ │ ├── cthead1-Float.mha.sha512 │ │ ├── cthead1-dis1.nrrd.sha512 │ │ ├── cthead1-grad-mag.mha.sha512 │ │ ├── cthead1-grad-mag.nrrd.sha512 │ │ ├── cthead1-ls-seed.nrrd.sha512 │ │ ├── cthead1-marker.png.sha512 │ │ ├── cthead1-mask.png.sha512 │ │ ├── cthead1-seed.png.sha512 │ │ ├── cthead1.png.sha512 │ │ ├── displacement.mha.sha512 │ │ ├── fruit.png.sha512 │ │ ├── noisy-vector-grid.nrrd.sha512 │ │ ├── points_5d.mha.sha512 │ │ ├── r16slice.nii.gz │ │ ├── r16slice_rigid.nii.gz │ │ ├── r64slice.nii.gz │ │ ├── simple-label-b.png.sha512 │ │ ├── simple-label-c.png.sha512 │ │ ├── simple-label-d.png.sha512 │ │ ├── simple-label-e.png.sha512 │ │ └── xforms │ │ ├── affine_i_3.txt.sha512 │ │ ├── bspline_ceoff0.mha.sha512 │ │ ├── composite_i_3.txt.sha512 │ │ ├── displacement_-13x-17y.txt.sha512 │ │ ├── i_3.txt.sha512 │ │ ├── quaternion_rigid_i_3.txt.sha512 │ │ ├── scale_i_3.txt.sha512 │ │ ├── scale_logarithmic_i_3.txt.sha512 │ │ ├── translation_-13x-17y.txt.sha512 │ │ ├── translation_i_3.txt.sha512 │ │ └── versor_i_3.txt.sha512 └── Unit │ ├── CMakeLists.txt │ ├── CSharp │ ├── CMakeLists.txt │ └── CSharpImageTest.cs │ ├── CSharpImageFilterTestTemplate.cs.in │ ├── IOTests.cxx │ ├── ImageFilterCTestTemplate.cmake.in │ ├── Java │ ├── CMakeLists.txt │ ├── sitkImageTests.java │ └── sitkProcessObjectTest.java │ ├── JavaImageFilterTestTemplate.java.in │ ├── LuaImageFilterTestTemplate.lua.in │ ├── Python │ ├── CMakeLists.txt │ ├── ConcurrentImageRead.py │ ├── IOTest.py │ ├── ImageReadWriteInt64.py │ ├── sitkGetArrayViewFromImageTest.py │ ├── sitkImageIndexingTest.py │ ├── sitkImageTests.py │ ├── sitkNumpyArrayConversionTest.py │ ├── sitkProcessObjectTest.py │ ├── sitkTransformTests.py │ └── sitkTransformixImageFilterTest.py │ ├── PythonImageFilterTestTemplate.py.in │ ├── R │ ├── CMakeLists.txt │ ├── R2Img2R.R │ ├── RArithmeticTest.R │ ├── RImageListArguments.R │ ├── RImageSlicingTests.R │ ├── RPixelAccess.R │ ├── RSwigVectorConversionTests.R │ └── RTransformTests.R │ ├── RImageFilterTestTemplate.R.in │ ├── RubyImageFilterTestTemplate.rb.in │ ├── SimpleITKUnitTestDriver.cxx │ ├── TclImageFilterTestTemplate.tcl.in │ ├── TestBase │ ├── CMakeLists.txt │ ├── SimpleITKTestHarness.cxx │ ├── SimpleITKTestHarness.h │ ├── SimpleITKTestHarnessPaths.h.in │ ├── sitkCompareDriver.cxx │ ├── sitkImageCompare.cxx │ ├── sitkImageCompare.h │ ├── sitkTransformCompare.cxx │ └── sitkTransformCompare.h │ ├── itkHashImageFilterTest.cxx │ ├── itkSliceImageFilterTest.cxx │ ├── sitkBasicFiltersTests.cxx │ ├── sitkCommonTests.cxx │ ├── sitkElastixFilterTests.cxx │ ├── sitkElastixImageFilterTests.cxx │ ├── sitkExceptionsTests.cxx │ ├── sitkImage4DTests.cxx │ ├── sitkImageFilterTestTemplate.cxx.in │ ├── sitkImageIOTests.cxx │ ├── sitkImageRegistrationMethodTests.cxx │ ├── sitkImageTests.cxx │ ├── sitkImageViewerTest.cxx │ ├── sitkImageViewerTest.h.in │ ├── sitkImportImageTest.cxx │ ├── sitkLabelStatisticsTest.cxx │ ├── sitkOperatorTests.cxx │ ├── sitkParameterMapTests.cxx │ ├── sitkShowTest.cxx │ ├── sitkSystemInformationTest.cxx │ ├── sitkTransformTests.cxx │ ├── sitkTransformToDisplacementFieldFilterTest.cxx │ ├── sitkTransformixFilterTests.cxx │ ├── sitkTransformixImageFilterTests.cxx │ └── sitkTypeListsTests.cxx ├── UseSimpleITK.cmake.in ├── Utilities ├── ApplyApacheLicense.sh ├── CMakeLists.txt ├── CSVtoTable.py ├── CompareITKandSITKFilters.py ├── Distribution │ └── manylinux │ │ ├── Dockerfile-i686 │ │ ├── Dockerfile-x86_64 │ │ ├── imagefiles │ │ ├── cmd.sh │ │ └── install.sh │ │ └── run.sh ├── Doxygen │ ├── Doxygen.cmake │ ├── GenerateExamplesDox.cmake │ ├── ITKDoxygenTags.cmake │ ├── docker │ │ ├── Dockerfile │ │ ├── README │ │ └── run.sh │ └── doxygen.config.in ├── GenerateDocs │ ├── GenerateDoc.py │ ├── JSONDocUpdate.sh │ ├── README │ ├── SwigDocUpdate.sh │ ├── config_vars.sh │ ├── docker │ │ ├── Dockerfile │ │ ├── cmd.sh │ │ ├── config_vars.sh │ │ ├── entrypoint.sh │ │ └── run.sh │ ├── doxy2swig.py │ └── doxyall.py ├── Hooks │ ├── pre-commit │ ├── pre-commit-style.bash │ └── prepare-commit-msg ├── JSON │ ├── JSONBeautify.py │ ├── JSONGenerateSphinxFiltersDoc.py │ ├── JSONInputAtoInputs.py │ ├── JSONUpdateITKModules.py │ └── JSONValidate.py ├── KWStyle │ ├── CMakeLists.txt │ ├── KWStyle.cmake │ ├── SITK.kws.xml.in │ ├── SITKFiles.txt.in │ └── SITKOverwrite.txt ├── Maintenance │ ├── ContentLinkSynchronization.sh │ ├── GeneratePythonDownloadsPage.py │ ├── JIRAHTMLReleaseNoteToWiki.py │ └── SourceTarball.bash ├── ParseForExplicitInstantiation.py ├── SetupForDevelopment.sh ├── Statistics │ ├── download_stats.py │ └── environment.yml ├── UploadBinaryData.sh ├── filters.csv ├── pypi.sh.in └── valgrind.sh.in ├── Version.cmake ├── Wrapping ├── CMakeLists.txt ├── CSharp │ ├── AssemblyInfo.cs.in │ ├── CMakeLists.txt │ ├── CSharp.i │ ├── CSharpTypemapHelper.i │ ├── SimpleITK.i │ └── dist │ │ └── CMakeLists.txt ├── Common │ └── SimpleITK_Common.i ├── Java │ ├── CMakeLists.txt │ ├── Java.i │ ├── JavaDoc.i │ ├── SimpleITK.i │ └── dist │ │ └── CMakeLists.txt ├── Lua │ ├── CMakeLists.txt │ ├── Lua.i │ ├── SimpleITK.i │ └── SimpleITKLuaMain.cxx ├── Python │ ├── CMakeLists.txt │ ├── LegacyPackaging.cmake │ ├── Packaging │ │ ├── __init__.py │ │ ├── setup.py.in │ │ └── setupegg.py │ ├── Python.i │ ├── PythonDocstrings.i │ ├── PythonVirtualEnvInstall.cmake.in │ ├── SimpleITK.i │ ├── dist │ │ └── CMakeLists.txt │ ├── sitkNumpyArrayConversion.cxx │ ├── sitkPyCommand.cxx │ ├── sitkPyCommand.h │ └── sitkPython.h ├── R │ ├── CMakeLists.txt │ ├── Packaging │ │ └── SimpleITK │ │ │ ├── DESCRIPTION.in │ │ │ ├── NAMESPACE │ │ │ ├── R │ │ │ ├── zA.R │ │ │ ├── zFixes.R │ │ │ └── zOps.R │ │ │ ├── inst │ │ │ ├── doc │ │ │ │ └── SimpleITK_tutorial.pdf │ │ │ └── extdata │ │ │ │ ├── cthead1-Float.mha.sha512 │ │ │ │ └── cthead1.png.sha512 │ │ │ ├── man │ │ │ ├── ImageSeriesReader_GetGDCMSeriesFileNames.Rd │ │ │ ├── SimpleITK_Image-class.Rd │ │ │ ├── hidden_aliases.Rd │ │ │ └── sitkRdfiles.tar.gz.sha512 │ │ │ ├── src │ │ │ └── Makefile │ │ │ └── vignettes │ │ │ ├── InsightArticle.cls │ │ │ ├── InsightJournal.sty │ │ │ ├── SimpleITK_tutorial.Rnw │ │ │ ├── algorithm.sty │ │ │ ├── algorithmic.sty │ │ │ ├── amssymb.sty │ │ │ ├── fancyhdr.sty │ │ │ ├── floatflt.sty │ │ │ ├── fncychap.sty │ │ │ ├── times.sty │ │ │ └── upquote.sty │ ├── R.i │ ├── SimpleITK.i │ ├── mkNamespace.R │ ├── processSwigCode.R │ ├── rrun.swg │ ├── sitkRArray.cxx │ ├── sitkRCommand.cxx │ └── sitkRCommand.h ├── Ruby │ ├── CMakeLists.txt │ ├── Ruby.i │ └── SimpleITK.i └── Tcl │ ├── CMakeLists.txt │ ├── SimpleITK.i │ └── Tcl.i ├── docs ├── Makefile ├── _static │ └── style.css ├── _templates │ └── breadcrumbs.html ├── images │ ├── BuildPathConfiguration.jpg.sha512 │ ├── CMakeLists.txt │ ├── EclipseConfigureBuildPath.jpg.sha512 │ ├── ImageOriginAndSpacing.svg.sha512 │ ├── ManagedLibrary.jpg.sha512 │ ├── NativeLibraryProperties.jpg.sha512 │ ├── NewVisualStudioProject.jpg.sha512 │ ├── Readme.md │ ├── SimpleITKCSharpUnzip.jpg.sha512 │ ├── VisualStudioConfigurationManager.jpg.sha512 │ ├── VisualStudioExample.jpg.sha512 │ ├── imageJ.png.sha512 │ ├── isbi.png.sha512 │ ├── miccai.png.sha512 │ ├── nonisotropicVsIsotropic.svg.sha512 │ ├── simpleitk_logo.png.sha512 │ ├── spatialRelationship.svg.sha512 │ └── spie.png.sha512 ├── make.bat ├── requirements.txt └── source │ ├── CMakeLists.txt │ ├── FilterTemplates.rst │ ├── IO.rst │ ├── _static │ └── style.css │ ├── about.rst │ ├── building.rst │ ├── cmake_cplusplus.rst │ ├── conf.py │ ├── conventions.rst │ ├── faq.rst │ ├── filters.rst │ ├── fundamentalConcepts.rst │ ├── history.rst │ ├── index.rst │ ├── installation.rst │ ├── license.rst │ ├── link_AdvancedImageReading_docs.rst │ ├── link_CSharp_docs.rst │ ├── link_DemonsRegistration1_docs.rst │ ├── link_DemonsRegistration2_docs.rst │ ├── link_DicomImagePrintTags_docs.rst │ ├── link_DicomSeriesFromArray_docs.rst │ ├── link_DicomSeriesReadModifyWrite_docs.rst │ ├── link_DicomSeriesReader_docs.rst │ ├── link_FastMarchingSegmentation_docs.rst │ ├── link_FilterProgressReporting_docs.rst │ ├── link_HelloWorld_docs.rst │ ├── link_ITKIntegration_docs.rst │ ├── link_ImageGridManipulation_docs.rst │ ├── link_ImageIOSelection_docs.rst │ ├── link_ImageRegistrationMethod1_docs.rst │ ├── link_ImageRegistrationMethod2_docs.rst │ ├── link_ImageRegistrationMethod3_docs.rst │ ├── link_ImageRegistrationMethod4_docs.rst │ ├── link_ImageRegistrationMethodBSpline1_docs.rst │ ├── link_ImageRegistrationMethodBSpline2_docs.rst │ ├── link_ImageRegistrationMethodBSpline3_docs.rst │ ├── link_ImageRegistrationMethodDisplacement1_docs.rst │ ├── link_ImageRegistrationMethodExhaustive_docs.rst │ ├── link_ImageViewing_docs.rst │ ├── link_N4BiasFieldCorrection_docs.rst │ ├── link_SimpleGaussian_docs.rst │ ├── link_examples.rst │ ├── registrationExamplePrefix.rst │ ├── registrationOverview.rst │ ├── setUp.rst │ ├── sitk_example.cxx │ └── tutorialsAndCourses.rst ├── git-gerrit-push ├── git-gitlab-push ├── git-gitlab-sync ├── setup-gerrit ├── setup-gitlab ├── setup-hooks ├── setup-lfs ├── setup-ssh ├── setup-stage ├── setup-upstream └── setup-user /.ExternalData/README.rst: -------------------------------------------------------------------------------- 1 | .ExternalData 2 | ============= 3 | 4 | The ITK ``.ExternalData`` directory is an object store for the 5 | CMake ExternalData module that ITK uses to manage test input 6 | and baseline data. 7 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Optionally build your docs in additional formats such as PDF and ePub 9 | formats: all 10 | 11 | # Build documentation in the docs/ directory with Sphinx 12 | sphinx: 13 | configuration: docs/source/conf.py 14 | 15 | # Optionally set the version of Python and requirements required to build your docs 16 | python: 17 | version: 3.7 18 | install: 19 | - requirements: docs/requirements.txt 20 | -------------------------------------------------------------------------------- /CMake/ExternalData_config.cmake.in: -------------------------------------------------------------------------------- 1 | set(ExternalData_OBJECT_STORES "@ExternalData_OBJECT_STORES@") 2 | set(ExternalData_URL_TEMPLATES "@ExternalData_URL_TEMPLATES@") 3 | set(ExternalData_TIMEOUT_INACTIVITY "@ExternalData_TIMEOUT_INACTIVITY@") 4 | set(ExternalData_TIMEOUT_ABSOLUTE "@ExternalData_TIMEOUT_ABSOLUTE@") 5 | set(ExternalData_NO_SYMLINKS "@ExternalData_NO_SYMLINKS@") 6 | @_ExternalData_CONFIG_CODE@ 7 | -------------------------------------------------------------------------------- /CMake/UseDotNetFrameworkSdk.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # A CMake Module for using C# .NET. 3 | # 4 | # The following variables are set: 5 | # (none) 6 | # 7 | # This file is based on the work of GDCM: 8 | # http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/UseDotNETFrameworkSDK.cmake 9 | # Copyright (c) 2006-2010 Mathieu Malaterre 10 | # 11 | 12 | message( STATUS "Using .NET compiler version ${CSHARP_DOTNET_VERSION}" ) 13 | -------------------------------------------------------------------------------- /CMake/UseMono.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # A CMake Module for using Mono. 3 | # 4 | # The following variables are set: 5 | # (none) 6 | # 7 | # Additional references can be found here: 8 | # http://www.mono-project.com/Main_Page 9 | # http://www.mono-project.com/CSharp_Compiler 10 | # 11 | # This file is based on the work of GDCM: 12 | # http://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMake/FindMono.cmake 13 | # Copyright (c) 2006-2010 Mathieu Malaterre 14 | # 15 | 16 | message( STATUS "Using Mono compiler version ${CSHARP_MONO_VERSION}" ) -------------------------------------------------------------------------------- /CMake/configure_file_build_time.cmake: -------------------------------------------------------------------------------- 1 | configure_file( "${CONFIGUREBUILDTIME_filename}" "${CONFIGUREBUILDTIME_out_filename}" ) 2 | -------------------------------------------------------------------------------- /CMake/pre-commit: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | echo 'Your work tree has not been configured for SimpleITK development. 3 | Paste the following commands into a shell: 4 | 5 | ./Utilities/SetupForDevelopment.sh 6 | 7 | See https://www.itk.org/Wiki/ITK/Git/Develop for more details.' 8 | exit 1 9 | -------------------------------------------------------------------------------- /CMake/same_uint64_ulong.cxx: -------------------------------------------------------------------------------- 1 | #include 2 | 3 | // This program compiles when unsignedlong and uint64_t are the same type 4 | 5 | template struct IsSame; 6 | template< typename T > 7 | struct IsSame { }; 8 | 9 | int main( void ) 10 | { 11 | IsSame FailsWhenNotSameTypes; 12 | return 0; 13 | } 14 | -------------------------------------------------------------------------------- /CMake/sitkCheckSourceTree.cmake: -------------------------------------------------------------------------------- 1 | # Install a pre-commit hook to bootstrap commit hooks. 2 | if(EXISTS "${SimpleITK_SOURCE_DIR}/.git/config" AND 3 | NOT EXISTS "${SimpleITK_SOURCE_DIR}/.git/hooks/pre-commit") 4 | # Silently ignore the error if the hooks directory is read-only. 5 | execute_process( 6 | COMMAND ${CMAKE_COMMAND} -E copy ${SimpleITK_SOURCE_DIR}/CMake/pre-commit 7 | ${SimpleITK_SOURCE_DIR}/.git/hooks/pre-commit 8 | OUTPUT_VARIABLE _output 9 | ERROR_VARIABLE _output 10 | RESULT_VARIABLE _result 11 | ) 12 | if(_result AND NOT "${_output}" MATCHES "Error copying file") 13 | message("${_output}") 14 | endif() 15 | endif() 16 | -------------------------------------------------------------------------------- /CMake/sitkCheckTemplateDisambiguation.cmake: -------------------------------------------------------------------------------- 1 | # CMake Module to check for usage of the `template` keyword to 2 | # disambiguate dependent name look ups. 3 | # 4 | # More information can be found about this usage case here: 5 | # http://en.cppreference.com/w/cpp/language/dependent_name Under the 6 | # heading "The typename disambiguator for dependent names". 7 | 8 | 9 | 10 | try_compile(SITK_HAS_TEMPLATE_DISAMBIGUATOR_DEPENDENT_NAME 11 | "${PROJECT_BINARY_DIR}" 12 | "${CMAKE_CURRENT_LIST_DIR}/sitkCheckTemplateDisambiguation.cxx") 13 | -------------------------------------------------------------------------------- /CMake/sitkCheckTemplateDisambiguation.cxx: -------------------------------------------------------------------------------- 1 | template 2 | struct A 3 | { 4 | template 5 | void operator()( ) {}; 6 | }; 7 | 8 | 9 | template 10 | void g( ) 11 | { 12 | A obj; 13 | 14 | // The following `template` keyword is required by C++. But with 15 | // MSVC (); 17 | } 18 | 19 | 20 | int main(void) 21 | { 22 | g(); 23 | 24 | return 0; 25 | } 26 | -------------------------------------------------------------------------------- /CMake/sitkForbidDownloadsOption.cmake: -------------------------------------------------------------------------------- 1 | 2 | include(sitkSITKLegacyNaming) 3 | 4 | #----------------------------------------------------------------------------- 5 | # Forbid downloading resources from the network during a build. This helps 6 | # when building on systems without network connectivity to determine which 7 | # resources much be obtained manually and made available to the build. 8 | option(SimpleITK_FORBID_DOWNLOADS "Do not download source code or data from the network" OFF) 9 | mark_as_advanced(SimpleITK_FORBID_DOWNLOADS) 10 | sitk_legacy_naming(SimpleITK_FORBID_DOWNLOADS) 11 | 12 | macro(sitk_enforce_forbid_downloads _name) 13 | if(SimpleITK_FORBID_DOWNLOADS) 14 | message(SEND_ERROR "Attempted to download ${_name} when SimpleITK_FORBID_DOWNLOADS is ON") 15 | endif() 16 | endmacro() 17 | -------------------------------------------------------------------------------- /CMake/sitkPreventInBuildInstalls.cmake: -------------------------------------------------------------------------------- 1 | string(TOLOWER "${CMAKE_INSTALL_PREFIX}" _PREFIX) 2 | string(TOLOWER "${ITK_BINARY_DIR}" _BUILD) 3 | if("${_PREFIX}" STREQUAL "${_BUILD}") 4 | message(FATAL_ERROR 5 | "The current CMAKE_INSTALL_PREFIX points at the build tree:\n" 6 | " ${CMAKE_INSTALL_PREFIX}\n" 7 | "This is not supported." 8 | ) 9 | endif() 10 | -------------------------------------------------------------------------------- /CMake/sitkPreventInSourceBuilds.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # This function will prevent in-source builds 3 | function(AssureOutOfSourceBuilds) 4 | # make sure the user doesn't play dirty with symlinks 5 | get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH) 6 | get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) 7 | 8 | # disallow in-source builds 9 | if("${srcdir}" STREQUAL "${bindir}") 10 | message("######################################################") 11 | message("# SimpleITK should not be configured & built in the SimpleITK source directory") 12 | message("# You must run cmake in a build directory.") 13 | message("######################################################") 14 | message(FATAL_ERROR "Quitting configuration") 15 | endif() 16 | endfunction() 17 | 18 | AssureOutOfSourceBuilds() 19 | -------------------------------------------------------------------------------- /CMake/sitkSourceVersionVars.cmake.in: -------------------------------------------------------------------------------- 1 | macro( _set_if_not_empty var value ) 2 | if( NOT "${value}" STREQUAL "" ) 3 | set( ${var} "${value}" ) 4 | endif() 5 | endmacro() 6 | 7 | set( _GIT_VERSION_MAJOR "@_GIT_VERSION_MAJOR@" ) 8 | set( _GIT_VERSION_MINOR "@_GIT_VERSION_MINOR@" ) 9 | _set_if_not_empty( _GIT_VERSION_PATCH "@_GIT_VERSION_PATCH@" ) 10 | _set_if_not_empty( _GIT_VERSION_TWEAK "@_GIT_VERSION_TWEAK@" ) 11 | _set_if_not_empty( _GIT_VERSION_RC "@_GIT_VERSION_RC@" ) 12 | _set_if_not_empty( _GIT_VERSION_POST "@_GIT_VERSION_POST@" ) 13 | _set_if_not_empty( _GIT_VERSION_DEV "@_GIT_VERSION_DEV@" ) 14 | _set_if_not_empty( _GIT_VERSION_HASH "@_GIT_VERSION_HASH@" ) 15 | -------------------------------------------------------------------------------- /CMake/sitkUseCCache.cmake: -------------------------------------------------------------------------------- 1 | # Add CMake option to automatically use ccache. 2 | # 3 | # The ccache in CMAKE_CXX_COMPILER_LAUNCHER and 4 | # CMAKE_C_COMPILER_LAUNCHER variables. 5 | 6 | option(USE_CCACHE "Use ccache to expedite re-compilations. Recommended for development" OFF) 7 | if(USE_CCACHE) 8 | find_program(CCACHE_PROGRAM ccache) 9 | if(CCACHE_PROGRAM) 10 | message(STATUS "Enabling ccache") 11 | set(CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE_PROGRAM}) 12 | set(CMAKE_C_COMPILER_LAUNCHER ${CCACHE_PROGRAM}) 13 | endif() 14 | endif() 15 | -------------------------------------------------------------------------------- /CTestConfig.cmake: -------------------------------------------------------------------------------- 1 | set(CTEST_PROJECT_NAME "SimpleITK") 2 | set(CTEST_NIGHTLY_START_TIME "1:00:00 UTC") 3 | 4 | set(CTEST_DROP_METHOD "http") 5 | set(CTEST_DROP_SITE "open.cdash.org") 6 | set(CTEST_DROP_LOCATION "/submit.php?project=SimpleITK") 7 | set(CTEST_DROP_SITE_CDASH TRUE) 8 | -------------------------------------------------------------------------------- /Code/BasicFilters/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | # Set up code generation 4 | include(sitkGenerateFilterSource) 5 | generate_filter_source() 6 | 7 | add_subdirectory( src ) 8 | 9 | 10 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ComplexToImaginaryImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ComplexToImaginaryImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "ComplexPixelIDTypeList", 8 | "output_pixel_type" : "typename InputImageType::PixelType::value_type", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Test Complex to imaginary", 14 | "md5hash" : "3be155009ce0f99e56293002c4ba1b2a", 15 | "settings" : [], 16 | "inputs" : [ 17 | "Input/RA-FFT-Complex.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes pixel-wise the imaginary part of a complex image.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ComplexToModulusImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ComplexToModulusImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "ComplexPixelIDTypeList", 8 | "output_pixel_type" : "typename InputImageType::PixelType::value_type", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Test Complex to modulus", 14 | "tolerance" : "0.01", 15 | "settings" : [], 16 | "inputs" : [ 17 | "Input/RA-FFT-Complex.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes pixel-wise the Modulus of a complex image.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ComplexToPhaseImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ComplexToPhaseImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "ComplexPixelIDTypeList", 8 | "output_pixel_type" : "typename InputImageType::PixelType::value_type", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Test Complex to Phase", 14 | "tolerance" : "0.0001", 15 | "settings" : [], 16 | "inputs" : [ 17 | "Input/RA-FFT-Complex.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes pixel-wise the modulus of a complex image.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ComplexToRealImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ComplexToRealImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "ComplexPixelIDTypeList", 8 | "output_pixel_type" : "typename InputImageType::PixelType::value_type", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Test Complex to real", 14 | "md5hash" : "3278e36babb23c17fecc09d2e1b3f575", 15 | "settings" : [], 16 | "inputs" : [ 17 | "Input/RA-FFT-Complex.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes pixel-wise the real(x) part of a complex image.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ExpImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ExpImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the exponential function of each pixel.", 22 | "detaileddescription" : "The computation is performed using std::exp(x).", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ExpNegativeImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ExpNegativeImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the function exp(-K.x) for each input pixel.", 22 | "detaileddescription" : "Every output pixel is equal to std::exp(-K.x ). where x is the intensity of the homologous input pixel, and K is a user-provided constant.", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/Log10ImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "Log10ImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the log10 of each pixel.", 22 | "detaileddescription" : "The computation is performed using std::log10(x).", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/LogImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "LogImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the log() of each pixel.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/ModulusImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "ModulusImageFilter", 3 | "template_code_filename" : "BinaryFunctorFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "constant_type" : "uint32_t", 6 | "number_of_inputs" : 2, 7 | "pixel_types" : "IntegerPixelIDTypeList", 8 | "members" : [], 9 | "tests" : [ 10 | { 11 | "tag" : "defaults", 12 | "description" : "Simply run with default settings", 13 | "settings" : [], 14 | "md5hash" : "12fd4fb023059d4659d30ee449bb6599", 15 | "inputs" : [ 16 | "Input/STAPLE1.png", 17 | "Input/STAPLE2.png" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the modulus (x % dividend) pixel-wise.", 22 | "detaileddescription" : "The input pixel type must support the c++ modulus operator (%).\n\nIf the dividend is zero, the maximum value will be returned.\n\n\\author Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/RoundImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "RoundImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "doc" : "", 6 | "number_of_inputs" : 1, 7 | "pixel_types" : "RealPixelIDTypeList", 8 | "members" : [], 9 | "tests" : [ 10 | { 11 | "tag" : "default", 12 | "description" : "Simply run with default settings", 13 | "settings" : [], 14 | "md5hash" : "3ccccde44efaa3d688a86e94335c1f16", 15 | "inputs" : [ 16 | "Input/RA-Float.nrrd" 17 | ] 18 | } 19 | ], 20 | "briefdescription" : "Rounds the value of each pixel.", 21 | "detaileddescription" : "The computations are performed using itk::Math::Round(x).", 22 | "itk_module" : "ITKImageIntensity", 23 | "itk_group" : "ImageIntensity" 24 | } 25 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/SinImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "SinImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the sine of each pixel.", 22 | "detaileddescription" : "The computations are performed using std::sin(x).", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/SqrtImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "SqrtImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the square root of each pixel.", 22 | "detaileddescription" : "The computations are performed using std::sqrt(x).", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/SquareImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "SquareImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "md5hash" : "314065b457b66e102b9cafd7c49be6b3", 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the square of the intensity values pixel-wise.", 22 | "detaileddescription" : "", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/BasicFilters/json/TanImageFilter.json: -------------------------------------------------------------------------------- 1 | { 2 | "name" : "TanImageFilter", 3 | "template_code_filename" : "ImageFilter", 4 | "template_test_filename" : "ImageFilter", 5 | "number_of_inputs" : 1, 6 | "doc" : "Some global documentation", 7 | "pixel_types" : "BasicPixelIDTypeList", 8 | "vector_pixel_types_by_component" : "VectorPixelIDTypeList", 9 | "members" : [], 10 | "tests" : [ 11 | { 12 | "tag" : "defaults", 13 | "description" : "Simply run with default settings", 14 | "settings" : [], 15 | "tolerance" : 0.01, 16 | "inputs" : [ 17 | "Input/Ramp-Zero-One-Float.nrrd" 18 | ] 19 | } 20 | ], 21 | "briefdescription" : "Computes the tangent of each input pixel.", 22 | "detaileddescription" : "The computations are performed using std::tan(x).", 23 | "itk_module" : "ITKImageIntensity", 24 | "itk_group" : "ImageIntensity" 25 | } 26 | -------------------------------------------------------------------------------- /Code/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | if (SimpleITK_EXPLICIT_INSTANTIATION) 2 | add_subdirectory(Explicit) 3 | endif() 4 | add_subdirectory(Common) 5 | add_subdirectory(Elastix) 6 | add_subdirectory(BasicFilters) 7 | add_subdirectory(IO) 8 | add_subdirectory(Registration) 9 | -------------------------------------------------------------------------------- /Code/Common/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_subdirectory( src ) 3 | 4 | # CMake option variable are prefixes with the project name "SimpleITK" 5 | # while C++ preprocess defines only have SITK. These variable need the 6 | # prefix translation. 7 | set( SITK_INT64_PIXELIDS ${SimpleITK_INT64_PIXELIDS} ) 8 | set( SITK_4D_IMAGES ${SimpleITK_4D_IMAGES} ) 9 | set( SITK_EXPLICIT_INSTANTIATION ${SimpleITK_EXPLICIT_INSTANTIATION} ) 10 | 11 | include(sitkCheckTemplateDisambiguation) 12 | 13 | configure_file( "src/sitkConfigure.h.in" "include/sitkConfigure.h" ) 14 | install(FILES "${CMAKE_CURRENT_BINARY_DIR}/include/sitkConfigure.h" 15 | DESTINATION "${SimpleITK_INSTALL_INCLUDE_DIR}" 16 | COMPONENT Development) 17 | 18 | configure_file("src/sitkVersionConfig.h.in" "include/sitkVersionConfig.h" @ONLY) 19 | install(FILES "${CMAKE_CURRENT_BINARY_DIR}/include/sitkVersionConfig.h" 20 | DESTINATION "${SimpleITK_INSTALL_INCLUDE_DIR}" 21 | COMPONENT Development) 22 | -------------------------------------------------------------------------------- /Code/Common/include/Ancillary/hl_sha1.cxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Code/Common/include/Ancillary/hl_sha1.cxx -------------------------------------------------------------------------------- /Code/Common/include/Ancillary/hl_sha1.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Code/Common/include/Ancillary/hl_sha1.h -------------------------------------------------------------------------------- /Code/Elastix/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory( src ) 2 | -------------------------------------------------------------------------------- /Code/Explicit/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_subdirectory( src ) 3 | -------------------------------------------------------------------------------- /Code/IO/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_subdirectory( src ) 3 | -------------------------------------------------------------------------------- /Code/Registration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory( src ) 2 | -------------------------------------------------------------------------------- /Documentation/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Documentation/CMakeLists.txt -------------------------------------------------------------------------------- /Documentation/README.md: -------------------------------------------------------------------------------- 1 | Documentation 2 | ============= 3 | 4 | This is the source code for the project documentation at [simpleelastix.readthedocs.org](http://simpleelastix.readthedocs.org/). If you want to contribute, you can build the documentation locally by installing sphinx: 5 | 6 | ```bash 7 | $ sudo apt-get install python-sphinx 8 | ``` 9 | 10 | and run the following make command in `Documentation/`: 11 | 12 | ```bash 13 | $ make html 14 | ``` 15 | 16 | The docs will be generated and the output files will be placed in the `build/html/` directory which can be browsed (locally) with your favorite browser. The documentation can be automatically regenerated whenever a file changes (useful for development) using `sphinx-autobuild`: 17 | 18 | ```bash 19 | make livehtml 20 | ``` 21 | 22 | To enable this behaviour, install `sphinx-autobuild` with `pip install sphinx-autobuild`. 23 | -------------------------------------------------------------------------------- /Documentation/Sphinx/Acknowledgements.rst: -------------------------------------------------------------------------------- 1 | Acknowledgements 2 | ================ 3 | 4 | `SimpleElastix `_ is developed and maintained by `Kasper Marstal `_. `Elastix `_ is developed and maintained by Stefan Klein, Erasmus Medical Center, Rotterdam, Netherlands, and Marius Staring, Leiden University Medical Center, Leiden, Netherlands. `SimpleITK `_ is developed and maintained by Bradley Lowekamp and fellow Kitware developers. -------------------------------------------------------------------------------- /Documentation/Sphinx/AtlasBasedSegmentation.rst: -------------------------------------------------------------------------------- 1 | Atlas-based Segmentation 2 | ======================== 3 | 4 | .. In the past decade a significant amount of research has focused on strategies for combining multiple atlases and even automatic atlas selection strategies. -------------------------------------------------------------------------------- /Documentation/Sphinx/GetDeformationField.rst: -------------------------------------------------------------------------------- 1 | GetDeformationField 2 | =================== -------------------------------------------------------------------------------- /Documentation/Sphinx/KnownIssues.rst: -------------------------------------------------------------------------------- 1 | Known Issues 2 | ============ 3 | 4 | - Assigning a parameter in a parameter map list silently fails (e.g. `plist[1]['Transform'] = ['BSplineTransform']`). A workaround is to assign the value directly to the parameter map before adding the map to the list. -------------------------------------------------------------------------------- /Documentation/Sphinx/LabelBasedRegistration.rst: -------------------------------------------------------------------------------- 1 | Label-based Registration 2 | ======================== -------------------------------------------------------------------------------- /Documentation/Sphinx/MultiMetricRegularisation.rst: -------------------------------------------------------------------------------- 1 | Multi-Metric Regularisation 2 | =========================== -------------------------------------------------------------------------------- /Documentation/Sphinx/RegisterDICOMs.rst: -------------------------------------------------------------------------------- 1 | Registering DICOM images -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Documentation/Sphinx/_static/WindowsInstallationSelectCompiler.png -------------------------------------------------------------------------------- /Examples/AdvancedImageReading/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | sitk_add_python_test( Example.AdvancedImageReading 7 | "${CMAKE_CURRENT_SOURCE_DIR}/AdvancedImageReading.py" 8 | DATA{${SimpleITK_DATA_ROOT}/Input/BrainProtonDensitySlice.png} ) 9 | 10 | sitk_add_python_test( Example.AdvancedImageReading 11 | "${CMAKE_CURRENT_SOURCE_DIR}/AdvancedImageReading.R" 12 | DATA{${SimpleITK_DATA_ROOT}/Input/BrainProtonDensitySlice.png} ) 13 | -------------------------------------------------------------------------------- /Examples/CSharp/Documentation.rst: -------------------------------------------------------------------------------- 1 | CSharp Integration 2 | ================== 3 | 4 | 5 | Overview 6 | -------- 7 | 8 | 9 | Code 10 | ---- 11 | 12 | 13 | .. literalinclude:: ../../Examples/CSharp/ImageGetBuffer.cs 14 | :language: c# 15 | :lines: 18- 16 | -------------------------------------------------------------------------------- /Examples/DicomImagePrintTags/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | sitk_add_python_test( Example.DicomImagePrintTags 7 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomImagePrintTags.py" 8 | DATA{${SimpleITK_DATA_ROOT}/Input/DicomSeries/Image0075.dcm} 9 | ) 10 | if( WRAP_PYTHON ) 11 | set_tests_properties( Python.Example.DicomImagePrintTags 12 | PROPERTIES PASS_REGULAR_EXPRESSION "\\(0008|0060\\) = = \"MR\"") 13 | endif() 14 | 15 | sitk_add_r_test( Example.DicomImagePrintTags 16 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomImagePrintTags.R" 17 | DATA{${SimpleITK_DATA_ROOT}/Input/DicomSeries/Image0075.dcm} 18 | ) 19 | if(WRAP_R) 20 | set_tests_properties( R.Example.DicomImagePrintTags 21 | PROPERTIES PASS_REGULAR_EXPRESSION "\\(0008|0060\\) = = \"MR\"") 22 | endif() 23 | -------------------------------------------------------------------------------- /Examples/DicomSeriesFromArray/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | set(out_dir "${SimpleITK_TEST_OUTPUT_DIR}/Python.DicomSeriesFromArray") 7 | file(MAKE_DIRECTORY ${out_dir}) 8 | sitk_add_python_test( Example.DicomSeriesFromArray 9 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomSeriesFromArray.py" 10 | "${out_dir}" 11 | ) 12 | 13 | set(out_dir "${SimpleITK_TEST_OUTPUT_DIR}/R.DicomSeriesFromArray") 14 | file(MAKE_DIRECTORY ${out_dir}) 15 | sitk_add_r_test( Example.DicomSeriesFromArray 16 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomSeriesFromArray.R" 17 | "${out_dir}" 18 | ) 19 | -------------------------------------------------------------------------------- /Examples/DicomSeriesReadModifyWrite/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | set(out_dir "${SimpleITK_TEST_OUTPUT_DIR}/Python.DicomSeriesReadModifySeriesWrite") 7 | file(MAKE_DIRECTORY ${out_dir}) 8 | sitk_add_python_test( Example.DicomSeriesReadModifySeriesWrite 9 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomSeriesReadModifySeriesWrite.py" 10 | DATA{${SimpleITK_DATA_ROOT}/Input/DicomSeries/,REGEX:Image[0-9]+.dcm} 11 | "${out_dir}" 12 | ) 13 | 14 | sitk_add_r_test( Example.DicomSeriesReadModifySeriesWrite 15 | "${CMAKE_CURRENT_SOURCE_DIR}/DicomSeriesReadModifySeriesWrite.R" 16 | DATA{${SimpleITK_DATA_ROOT}/Input/DicomSeries/,REGEX:Image[0-9]+.dcm} 17 | "${out_dir}" 18 | ) 19 | -------------------------------------------------------------------------------- /Examples/HelloWorld/Testing/Temporary/CTestCostData.txt: -------------------------------------------------------------------------------- 1 | --- 2 | -------------------------------------------------------------------------------- /Examples/HelloWorld/Testing/Temporary/LastTest.log: -------------------------------------------------------------------------------- 1 | Start testing: Sep 14 13:41 EDT 2 | ---------------------------------------------------------- 3 | End testing: Sep 14 13:41 EDT 4 | -------------------------------------------------------------------------------- /Examples/ITKIntegration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | if(NOT CMAKE_PROJECT_NAME STREQUAL "SimpleITK") 2 | find_package ( ITK ) 3 | include( ${ITK_USE_FILE} ) 4 | find_package ( Elastix ) 5 | include ( ${ELASTIX_USE_FILE} ) 6 | endif() 7 | 8 | add_executable ( ITKIntegration ITKIntegration.cxx ) 9 | target_link_libraries ( ITKIntegration ${SimpleITK_LIBRARIES} ${ITK_LIBRARIES} ) 10 | 11 | add_executable ( ElastixFilter ElastixFilter.cxx ) 12 | target_link_libraries( ElastixFilter ${ELASTIX_LIBRARIES} ${ITK_LIBRARIES} ) 13 | 14 | add_executable ( TransformixFilter TransformixFilter.cxx ) 15 | target_link_libraries( TransformixFilter ${ELASTIX_LIBRARIES} ${ITK_LIBRARIES} ) 16 | -------------------------------------------------------------------------------- /Examples/ITKIntegration/Documentation.rst: -------------------------------------------------------------------------------- 1 | Integration with ITK 2 | ==================== 3 | 4 | 5 | Overview 6 | -------- 7 | 8 | 9 | Code 10 | ---- 11 | 12 | .. tabs :: 13 | 14 | .. tab:: C++ 15 | 16 | .. literalinclude:: ../../Examples/ITKIntegration/ITKIntegration.cxx 17 | :language: c++ 18 | :lines: 18- 19 | -------------------------------------------------------------------------------- /Examples/ImageGridManipulation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if ( NOT BUILD_TESTING ) 3 | return () 4 | endif () 5 | 6 | sitk_add_python_test( Example.ImageGridManipulation 7 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageGridManipulation.py" 8 | ) 9 | 10 | sitk_add_r_test( Example.ImageGridManipulation 11 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageGridManipulation.R" 12 | ) 13 | -------------------------------------------------------------------------------- /Examples/ImageIOSelection/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | sitk_add_python_test( Example.ImageIOSelection 7 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageIOSelection.py" 8 | DATA{${SimpleITK_DATA_ROOT}/Input/BrainProtonDensitySlice.png} ) 9 | 10 | sitk_add_python_test( Example.IOSelection 11 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageIOSelection.R" 12 | DATA{${SimpleITK_DATA_ROOT}/Input/BrainProtonDensitySlice.png} ) 13 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethod2/Documentation.rst: -------------------------------------------------------------------------------- 1 | Image Registration Method 2 2 | =========================== 3 | 4 | .. include:: registrationExamplePrefix.rst 5 | 6 | Overview 7 | -------- 8 | 9 | 10 | Code 11 | ---- 12 | 13 | .. tabs:: 14 | 15 | .. tab:: C# 16 | 17 | .. literalinclude:: ../../Examples/ImageRegistrationMethod2/ImageRegistrationMethod2.cs 18 | :language: c# 19 | :lines: 18- 20 | 21 | .. tab:: C++ 22 | 23 | .. literalinclude:: ../../Examples/ImageRegistrationMethod2/ImageRegistrationMethod2.cxx 24 | :language: c++ 25 | :lines: 18- 26 | 27 | .. tab:: Python 28 | 29 | .. literalinclude:: ../../Examples/ImageRegistrationMethod2/ImageRegistrationMethod2.py 30 | :language: python 31 | :lines: 1,19- 32 | 33 | .. tab:: R 34 | 35 | .. literalinclude:: ../../Examples/ImageRegistrationMethod2/ImageRegistrationMethod2.R 36 | :language: R 37 | :lines: 18- 38 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethod3/Documentation.rst: -------------------------------------------------------------------------------- 1 | Image Registration Method 3 2 | =========================== 3 | 4 | .. include:: registrationExamplePrefix.rst 5 | 6 | Overview 7 | -------- 8 | 9 | Code 10 | ---- 11 | 12 | .. tabs:: 13 | 14 | .. tab:: Python 15 | 16 | .. literalinclude:: ../../Examples/ImageRegistrationMethod3/ImageRegistrationMethod3.py 17 | :language: python 18 | :lines: 1,19- 19 | 20 | .. tab:: R 21 | 22 | .. literalinclude:: ../../Examples/ImageRegistrationMethod3/ImageRegistrationMethod3.R 23 | :language: R 24 | :lines: 18- 25 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethod4/Documentation.rst: -------------------------------------------------------------------------------- 1 | Image Registration Method 4 2 | =========================== 3 | 4 | .. include:: registrationExamplePrefix.rst 5 | 6 | Overview 7 | -------- 8 | 9 | Code 10 | ---- 11 | 12 | .. tabs:: 13 | 14 | .. tab:: Python 15 | 16 | .. literalinclude:: ../../Examples/ImageRegistrationMethod4/ImageRegistrationMethod4.py 17 | :language: python 18 | :lines: 1,19- 19 | 20 | .. tab:: R 21 | 22 | .. literalinclude:: ../../Examples/ImageRegistrationMethod4/ImageRegistrationMethod4.R 23 | :language: R 24 | :lines: 18- 25 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethodBSpline1/Documentation.rst: -------------------------------------------------------------------------------- 1 | .. _lbl_image_registration_method_bspline1: 2 | 3 | Image Registration Method BSpline 1 4 | =================================== 5 | 6 | .. include:: registrationExamplePrefix.rst 7 | 8 | Overview 9 | -------- 10 | 11 | 12 | Code 13 | ---- 14 | 15 | .. tabs:: 16 | 17 | .. tab:: C++ 18 | 19 | .. literalinclude:: ../../Examples/ImageRegistrationMethodBSpline1/ImageRegistrationMethodBSpline1.cxx 20 | :language: c++ 21 | :lines: 18- 22 | 23 | .. tab:: Python 24 | 25 | .. literalinclude:: ../../Examples/ImageRegistrationMethodBSpline1/ImageRegistrationMethodBSpline1.py 26 | :language: python 27 | :lines: 1,19- 28 | 29 | .. tab:: R 30 | 31 | .. literalinclude:: ../../Examples/ImageRegistrationMethodBSpline1/ImageRegistrationMethodBSpline1.R 32 | :language: R 33 | :lines: 18- 34 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethodBSpline2/Documentation.rst: -------------------------------------------------------------------------------- 1 | .. _lbl_image_registration_method_bspline2: 2 | 3 | Image Registration Method BSpline 2 4 | =================================== 5 | 6 | .. include:: registrationExamplePrefix.rst 7 | 8 | 9 | Overview 10 | -------- 11 | 12 | 13 | Code 14 | ---- 15 | 16 | .. tabs:: 17 | 18 | .. tab:: Python 19 | 20 | .. literalinclude:: ../../Examples/ImageRegistrationMethodBSpline2/ImageRegistrationMethodBSpline2.py 21 | :language: python 22 | :lines: 1,19- 23 | 24 | .. tab:: R 25 | 26 | .. literalinclude:: ../../Examples/ImageRegistrationMethodBSpline2/ImageRegistrationMethodBSpline2.R 27 | :language: R 28 | :lines: 18- 29 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethodDisplacement1/Documentation.rst: -------------------------------------------------------------------------------- 1 | Image Registration Method Displacement 1 2 | ======================================== 3 | 4 | 5 | Overview 6 | -------- 7 | 8 | 9 | Code 10 | ---- 11 | 12 | .. tabs:: 13 | 14 | .. tab:: C++ 15 | 16 | .. literalinclude:: ../../Examples/ImageRegistrationMethodDisplacement1/ImageRegistrationMethodDisplacement1.cxx 17 | :language: c++ 18 | :lines: 18- 19 | 20 | .. tab:: Python 21 | 22 | .. literalinclude:: ../../Examples/ImageRegistrationMethodDisplacement1/ImageRegistrationMethodDisplacement1.py 23 | :language: python 24 | :lines: 1,19- 25 | 26 | .. tab:: R 27 | 28 | .. literalinclude:: ../../Examples/ImageRegistrationMethodDisplacement1/ImageRegistrationMethodDisplacement1.R 29 | :language: R 30 | :lines: 18- 31 | -------------------------------------------------------------------------------- /Examples/ImageRegistrationMethodExhaustive/Documentation.rst: -------------------------------------------------------------------------------- 1 | Image Registration Method Exhaustive 2 | ==================================== 3 | 4 | 5 | Overview 6 | -------- 7 | 8 | 9 | Code 10 | ---- 11 | 12 | .. tabs:: 13 | 14 | .. tab:: Python 15 | 16 | .. literalinclude:: ../../Examples/ImageRegistrationMethodExhaustive/ImageRegistrationMethodExhaustive.py 17 | :language: python 18 | :lines: 1,19- 19 | 20 | .. tab:: R 21 | 22 | .. literalinclude:: ../../Examples/ImageRegistrationMethodExhaustive/ImageRegistrationMethodExhaustive.R 23 | :language: R 24 | :lines: 18- 25 | -------------------------------------------------------------------------------- /Examples/ImageViewing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | if ( NOT SimpleITK_TESTING_NOSHOW ) 7 | 8 | sitk_add_python_test( Example.ImageViewing 9 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageViewing.py" 10 | ) 11 | 12 | sitk_add_r_test( Example.ImageViewing 13 | "${CMAKE_CURRENT_SOURCE_DIR}/ImageViewing.R" 14 | ) 15 | 16 | endif() 17 | -------------------------------------------------------------------------------- /Examples/N4BiasFieldCorrection/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | if(NOT BUILD_TESTING) 3 | return() 4 | endif() 5 | 6 | sitk_add_python_test( Example.N4BiasFieldCorrection 7 | "${CMAKE_CURRENT_SOURCE_DIR}/N4BiasFieldCorrection.py" 8 | DATA{${SimpleITK_DATA_ROOT}/Input/OAS1_0001_MR1_mpr-1_anon.nrrd} 9 | "${SimpleITK_TEST_OUTPUT_DIR}/Python.Example.N4BiasFieldCorrection.nrrd" 10 | "1" ) 11 | 12 | sitk_add_r_test( Example.N4BiasFieldCorrection 13 | "${CMAKE_CURRENT_SOURCE_DIR}/N4BiasFieldCorrection.R" 14 | DATA{${SimpleITK_DATA_ROOT}/Input/OAS1_0001_MR1_mpr-1_anon.nrrd} 15 | "${SimpleITK_TEST_OUTPUT_DIR}/R.Example.N4BiasFieldCorrection.nrrd" 16 | "1" ) 17 | -------------------------------------------------------------------------------- /Examples/Python/SimpleElastix.py: -------------------------------------------------------------------------------- 1 | import SimpleITK as sitk 2 | import sys 3 | 4 | # Instantiate SimpleElastix 5 | elastixImageFilter = sitk.ElastixImageFilter() 6 | 7 | # Read Input 8 | elastixImageFilter.SetFixedImage(sitk.ReadImage(str(sys.argv[1]))) 9 | elastixImageFilter.SetMovingImage(sitk.ReadImage(str(sys.argv[2]))) 10 | elastixImageFilter.SetParameterMap(sitk.ReadParameterFile(str(sys.argv[3]))) 11 | 12 | # Perform registration 13 | elastixImageFilter.LogToConsoleOn() 14 | elastixImageFilter.Execute() 15 | 16 | # Write result image 17 | elastixImageFilter.WriteImage(elastixImageFilter.GetResultImage(), str(sys.argv[4])) 18 | -------------------------------------------------------------------------------- /Examples/Python/SimpleTransformix.py: -------------------------------------------------------------------------------- 1 | import SimpleITK as sitk 2 | import sys 3 | 4 | # Make transform 5 | elastixImageFilter = sitk.ElastixImageFilter() 6 | elastixImageFilter.SetFixedImage(sitk.ReadImage(str(sys.argv[1]))) 7 | elastixImageFilter.SetMovingImage(sitk.ReadImage(str(sys.argv[2]))) 8 | elastixImageFilter.SetParameterMap(sitk.ReadParameterFile(str(sys.argv[3]))) 9 | elastixImageFilter.LogToConsoleOn() 10 | elastixImageFilter.Execute() 11 | 12 | # Instantiate SimpleTransformix 13 | transformixImageFilter = sitk.TransformixImageFilter() 14 | 15 | # Read Input 16 | transformixImageFilter.SetMovingImage(sitk.ReadImage(str(sys.argv[4]))) 17 | transformixImageFilter.SetParameterMap(elastixImageFilter.GetTransformParameterMap()) 18 | 19 | # Perform warp 20 | transformixImageFilter.LogToConsoleOn() 21 | transformixImageFilter.Execute() 22 | 23 | # Write result image 24 | sitk.WriteImage(transformixImageFilter.GetResultImage(), str(sys.argv[5])) 25 | -------------------------------------------------------------------------------- /Examples/R/SimpleElastix.R: -------------------------------------------------------------------------------- 1 | library(SimpleITK) 2 | 3 | elastixImageFilter <- ElastixImageFilter() 4 | elastixImageFilter$SetFixedImage(ReadImage("fixedImage.nii")) 5 | elastixImageFilter$SetMovingImage(ReadImage("movingImage.nii")) 6 | elastixImageFilter$Execute() 7 | resultImage <- elastixImageFilter.GetResultImage() 8 | -------------------------------------------------------------------------------- /Examples/Segmentation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | # Add executable example targets 3 | add_executable ( ConnectedThresholdImageFilter ConnectedThresholdImageFilter.cxx ) 4 | target_link_libraries ( ConnectedThresholdImageFilter ${SimpleITK_LIBRARIES} ) 5 | 6 | add_executable ( NeighborhoodConnectedImageFilter NeighborhoodConnectedImageFilter.cxx ) 7 | target_link_libraries ( NeighborhoodConnectedImageFilter ${SimpleITK_LIBRARIES} ) 8 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/AddExtraIncludes.cxx.in: -------------------------------------------------------------------------------- 1 | $(if include_files and #include_files > 0 then 2 | OUT = [[// Additional include files 3 | $(for i=1,#include_files do OUT = OUT .. '#include "' .. include_files[i] .. '"' if i < #include_files then OUT = OUT .. '\n' end end) 4 | // Done with additional include files]] 5 | end) 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ClassEnd.h.in: -------------------------------------------------------------------------------- 1 | }; 2 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ClassNameAndPrint.h.in: -------------------------------------------------------------------------------- 1 | /** Name of this class */ 2 | std::string GetName() const { return std::string ("${name}"); } 3 | 4 | /** Print ourselves out */ 5 | std::string ToString() const; 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ConstructorInitializeMembers.cxx.in: -------------------------------------------------------------------------------- 1 | $(if measurements then 2 | temp=false 3 | for i = 1,#measurements do 4 | if measurements[i].active then 5 | temp=true 6 | else 7 | OUT=OUT..'\ 8 | this->m_'..measurements[i].name..' = '..measurements[i].default..';\ 9 | ' 10 | end 11 | end 12 | if temp then 13 | OUT=OUT..[[ 14 | this->m_Filter = NULL;]] 15 | end 16 | end) 17 | $(foreach members 18 | $(if (default ~= nil) then 19 | OUT = [[ 20 | this->m_${name} = ${default}; 21 | ]] 22 | end)) 23 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ConstructorMemberFunctionSetup.cxx.in: -------------------------------------------------------------------------------- 1 | this->m_MemberFactory.reset( new detail::MemberFunctionFactory( this ) ); 2 | 3 | $(if custom_register then 4 | OUT=' ${custom_register}' 5 | else 6 | OUT = [[ 7 | this->m_MemberFactory->RegisterMemberFunctions< PixelIDTypeList, 3 > (); 8 | this->m_MemberFactory->RegisterMemberFunctions< PixelIDTypeList, 2 > (); 9 | ]] 10 | end) 11 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ConstructorSignature.cxx.in: -------------------------------------------------------------------------------- 1 | ${name}::${name} () 2 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ConstructorVectorPixels.cxx.in: -------------------------------------------------------------------------------- 1 | $(if vector_pixel_types_by_component then 2 | OUT=[[ typedef ${vector_pixel_types_by_component} VectorByComponentsPixelIDTypeList; 3 | typedef detail::ExecuteInternalVectorImageAddressor VectorAddressorType; 4 | this->m_MemberFactory->RegisterMemberFunctions< VectorByComponentsPixelIDTypeList, 3, VectorAddressorType> (); 5 | this->m_MemberFactory->RegisterMemberFunctions< VectorByComponentsPixelIDTypeList, 2, VectorAddressorType> ();]] 6 | end) 7 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/CustomMethods.cxx.in: -------------------------------------------------------------------------------- 1 | $(if custom_methods and #custom_methods > 0 then 2 | OUT = [[ 3 | 4 | // 5 | // Custom Methods 6 | // 7 | ]] 8 | for i=1,#custom_methods do 9 | OUT=OUT..'\n' 10 | OUT=OUT..custom_methods[i].return_type..[[ ${name}::]]..custom_methods[i].name..'(' 11 | if custom_methods[i].parameters then 12 | for pnum=1,#custom_methods[i].parameters do 13 | if pnum > 1 then 14 | OUT=OUT..', ' 15 | end 16 | OUT=OUT..custom_methods[i].parameters[pnum].type ..' '.. custom_methods[i].parameters[pnum].var_name 17 | end 18 | end 19 | OUT=OUT..[[ ) 20 | { 21 | ]]..custom_methods[i].body..[[ 22 | 23 | } 24 | ]] 25 | end end) 26 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/CustomMethods.h.in: -------------------------------------------------------------------------------- 1 | $(if custom_methods and #custom_methods > 0 then 2 | OUT=OUT..'\n' 3 | for i=1,#custom_methods do 4 | OUT=OUT..'\n' 5 | if custom_methods[i].doc then 6 | OUT=OUT..' /** '..custom_methods[i].doc..' */\n' 7 | end 8 | OUT=OUT..' '..custom_methods[i].return_type..' '..custom_methods[i].name..'(' 9 | if custom_methods[i].parameters then 10 | for pnum=1,#custom_methods[i].parameters do 11 | if pnum > 1 then 12 | OUT=OUT..', ' 13 | end 14 | OUT=OUT..custom_methods[i].parameters[pnum].type ..' '.. custom_methods[i].parameters[pnum].var_name 15 | end 16 | end 17 | OUT=OUT..[[ ); 18 | ]] 19 | end end) 20 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/DestructorDefinition.cxx.in: -------------------------------------------------------------------------------- 1 | // 2 | // Destructor 3 | // 4 | ${name}::~${name} () 5 | { 6 | $(if measurements then 7 | temp=false 8 | for i = 1,#measurements do 9 | if measurements[i].active then 10 | temp=true 11 | end 12 | end 13 | if temp then 14 | OUT=[[ 15 | if (this->m_Filter != NULL) 16 | { 17 | m_Filter->UnRegister(); 18 | } 19 | ]] 20 | end 21 | end) 22 | } 23 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/DoNotEditWarning.cxx.in: -------------------------------------------------------------------------------- 1 | /* 2 | * WARNING: DO NOT EDIT THIS FILE! 3 | * THIS FILE IS AUTOMATICALLY GENERATED BY THE SIMPLEITK BUILD PROCESS. 4 | * Please look at sitkImageFilterTemplate.cxx.in to make changes. 5 | */ 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/DoNotEditWarning.h.in: -------------------------------------------------------------------------------- 1 | /* 2 | * WARNING: DO NOT EDIT THIS FILE! 3 | * THIS FILE IS AUTOMATICALLY GENERATED BY THE SIMPLEITK BUILD PROCESS. 4 | * Please look at sitk${template_code_filename}Template.h.in to make changes. 5 | */ 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalGetImagePointers.cxx.in: -------------------------------------------------------------------------------- 1 | $(if number_of_inputs > 0 then 2 | OUT=[[ 3 | // Get the pointer to the ITK image contained in image1 4 | typename InputImageType::ConstPointer image1 = this->CastImageToITK( inImage1 ); 5 | ]] end)$(for nimg=2,number_of_inputs do 6 | OUT = OUT .. ' // Get the a pointer to the ITK image contained in image' .. nimg .. '\n' 7 | OUT = OUT .. ' typename InputImageType' .. nimg .. '::ConstPointer image' .. nimg .. ' =' 8 | .. ' this->CastImageToITK( inImage' .. nimg .. ' );\n' 9 | end) 10 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalITKFilter.cxx.in: -------------------------------------------------------------------------------- 1 | $(if filter_type then 2 | OUT=[[typedef ${filter_type} FilterType;]] 3 | else 4 | if itk_name then 5 | OUT=[[typedef itk::${itk_name} FilterType;]] 16 | end) 17 | // Set up the ITK filter 18 | typename FilterType::Pointer filter = FilterType::New(); 19 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalMethod.h.in: -------------------------------------------------------------------------------- 1 | private: 2 | 3 | /** Setup for member function dispatching */ 4 | 5 | typedef $(if no_return_image then OUT="void" else OUT="Image" end) (Self::*MemberFunctionType)( $(include ImageParameters.in)$(include InputParametersInternal.in) ); 6 | template $(if no_return_image then OUT="void" else OUT="Image" end) ExecuteInternal ( $(include ImageParameters.in)$(include InputParametersInternal.in) ); 7 | $(if vector_pixel_types_by_component then 8 | if number_of_inputs > 1 then 9 | throw 'number_of_inputs must be 1 to use vector_pixel_types_by_component' 10 | end 11 | OUT=[[ 12 | /** Dispatched methods which calls ExecuteInteral on each component */ 13 | template ]] if no_return_image then OUT=OUT..[[void]] else OUT=OUT..[[Image]] end OUT=OUT..[[ ExecuteInternalVectorImage ( const Image& image );]] 14 | end) 15 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalSetITKFilterParameters.cxx.in: -------------------------------------------------------------------------------- 1 | 2 | $(foreach members 3 | $(if custom_itk_cast then 4 | OUT = ' ${custom_itk_cast}' 5 | elseif dim_vec and dim_vec == 1 then 6 | OUT = [[ 7 | ${itk_type} itkVec${name} = sitkSTLVectorToITK<${itk_type}>( this->Get${name}() ); 8 | filter->Set${name}( itkVec${name} );]] 9 | elseif pixeltype then 10 | OUT = ' filter->Set${name} ( static_cast< typename ${pixeltype}ImageType::PixelType> ( this->m_${name} ) );' 11 | elseif enum then 12 | OUT = ' filter->Set${name} ( ${itk_type} ( int( this->m_${name} ) ) );' 13 | else 14 | OUT = ' filter->Set${name} ( this->m_${name} );' 15 | end) 16 | ) 17 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalSignature.cxx.in: -------------------------------------------------------------------------------- 1 | template 2 | $(if no_return_image then OUT=[[void]] else OUT=[[Image]] end) ${name}::ExecuteInternal ( $(for inum=1,number_of_inputs do 3 | if inum>1 then 4 | OUT=OUT.. ', ' 5 | end 6 | OUT= OUT .. 'const Image& inImage' .. inum 7 | end )$(if inputs then 8 | for i = 1,#inputs do 9 | if (number_of_inputs > 0 or i > 1) then 10 | OUT = OUT .. ", " 11 | end 12 | if not inputs[i].type and inputs[i].enum then 13 | OUT = OUT .. name .. '::' .. inputs[i].name .. 'Type' 14 | elseif inputs[i].dim_vec and (inputs[i].dim_vec == 1) then 15 | OUT = OUT..'const std::vector<'..inputs[i].type..'> *' 16 | elseif inputs[i].point_vec and (inputs[i].point_vec == 1) then 17 | OUT = OUT..'const std::vector< std::vector<'..inputs[i].type..'> > *' 18 | else 19 | OUT = OUT .. 'const ' .. inputs[i].type .. ' *' 20 | end 21 | OUT = OUT .. ' in' .. inputs[i].name 22 | end 23 | end) ) 24 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteInternalTypedefs.cxx.in: -------------------------------------------------------------------------------- 1 | $(if (number_of_inputs) > 0 or (inputs and #inputs > 0 ) then 2 | OUT=[[ 3 | // Define the input and output image types 4 | typedef TImageType InputImageType; 5 | ]] end) 6 | $(for nimg=2,number_of_inputs do 7 | OUT=OUT .. ' typedef TImageType InputImageType' .. nimg .. ';\n' 8 | end) 9 | $(if output_image_type then 10 | OUT=[[//Define output image type 11 | typedef ${output_image_type} OutputImageType;]] 12 | elseif output_pixel_type then 13 | OUT=[[// Define output image type 14 | typedef itk::Image< ${output_pixel_type}, InputImageType::ImageDimension > OutputImageType;]] 15 | else 16 | OUT=[[typedef InputImageType OutputImageType;]] 17 | end) 18 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteMethodNoParameters.h.in: -------------------------------------------------------------------------------- 1 | $(if inputs then 2 | for i =1,#inputs do 3 | if inputs[i].optional then 4 | has_optional_inputs=inputs[i].optional 5 | end 6 | end 7 | end 8 | ) 9 | /** Execute the filter on the input image$(if number_of_inputs == 2 then OUT=[[s]]end) */ 10 | $(if no_return_image then OUT="void" else OUT="Image" end) Execute ( $(include ImageParameters.in)$(include InputParameters.in) ); 11 | $(if has_optional_inputs then 12 | no_optional=1 13 | OUT=[[ ]] if no_return_image then OUT=OUT..[[void]] else OUT=OUT..[[Image]] end OUT=OUT..[[ Execute ( $(include ImageParameters.in)$(include InputParameters.in) ); 14 | ]] 15 | end)$(if inputs then no_optional=nil end) 16 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ExecuteMethodWithParameters.h.in: -------------------------------------------------------------------------------- 1 | $(if members and #members > 0 then 2 | OUT=[[ 3 | 4 | 5 | /** Execute the filter on the input image$(if number_of_inputs == 2 then OUT='s'end) with the given parameters */ 6 | ]] 7 | if no_return_image then 8 | OUT=OUT..[[void]] 9 | else 10 | OUT=OUT..[[Image]] 11 | end 12 | OUT=OUT..[[ Execute ( $(include ImageParameters.in)$(include InputParameters.in)$(include MemberParameters.in) );]] 13 | end)$(if members and #members > 0 then 14 | if has_optional_inputs then 15 | no_optional=1 16 | OUT=OUT..[[ 17 | 18 | ]] 19 | if no_return_image then 20 | OUT=OUT..[[void]] 21 | else 22 | OUT=OUT..[[Image]] 23 | end 24 | OUT=OUT..[[ Execute ( $(include ImageParameters.in)$(include InputParameters.in)$(include MemberParameters.in) );]] 25 | end 26 | end) 27 | $(if inputs then no_optional=nil end) 28 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ImageParameters.in: -------------------------------------------------------------------------------- 1 | $(for inum=1,number_of_inputs do 2 | if inum>1 then 3 | OUT=OUT.. ', ' 4 | end 5 | OUT= OUT .. 'const Image& image' .. inum 6 | end ) 7 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/InputParameters.in: -------------------------------------------------------------------------------- 1 | $(if inputs then 2 | local count=1 3 | for i = 1,#inputs do 4 | if not (inputs[i].optional and no_optional) then 5 | if (number_of_inputs > 0 or count > 1) then 6 | OUT = OUT .. ", " 7 | end 8 | count = count + 1 9 | if not inputs[i].type and inputs[i].enum then 10 | OUT = OUT .. name .. '::' .. inputs[i].name .. 'Type' 11 | elseif inputs[i].dim_vec and (inputs[i].dim_vec == 1) then 12 | OUT = OUT..'const std::vector<'..inputs[i].type..'> &' 13 | elseif inputs[i].point_vec and (inputs[i].point_vec == 1) then 14 | OUT = OUT..'const std::vector< std::vector<'..inputs[i].type..'> > &' 15 | else 16 | OUT = OUT .. 'const ' .. inputs[i].type .. ' &' 17 | end 18 | OUT = OUT .. ' ' .. inputs[i].name:sub(1,1):lower() .. inputs[i].name:sub(2,-1) 19 | end 20 | end 21 | end) 22 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/InputParametersInternal.in: -------------------------------------------------------------------------------- 1 | $(if inputs then 2 | for i = 1,#inputs do 3 | if (number_of_inputs > 0 or i > 1) then 4 | OUT = OUT .. ", " 5 | end 6 | if not inputs[i].type and inputs[i].enum then 7 | OUT = OUT .. name .. '::' .. inputs[i].name .. 'Type' 8 | elseif inputs[i].dim_vec and (inputs[i].dim_vec == 1) then 9 | OUT = OUT..'const std::vector<'..inputs[i].type..'> *' 10 | elseif inputs[i].point_vec and (inputs[i].point_vec == 1) then 11 | OUT = OUT..'const std::vector< std::vector<'..inputs[i].type..'> > *' 12 | else 13 | OUT = OUT .. 'const ' .. inputs[i].type .. ' *' 14 | end 15 | OUT = OUT .. ' ' .. inputs[i].name:sub(1,1):lower() .. inputs[i].name:sub(2,-1) 16 | end 17 | end) 18 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/MemberFunctionDispatch.h.in: -------------------------------------------------------------------------------- 1 | friend struct detail::MemberFunctionAddressor; 2 | $(if vector_pixel_types_by_component then 3 | OUT=[[ friend struct detail::ExecuteInternalVectorImageAddressor;]] 4 | end) 5 | std::unique_ptr > m_MemberFactory; 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/MemberParameters.in: -------------------------------------------------------------------------------- 1 | $(for i = 1,#members do 2 | temp = number_of_inputs 3 | if inputs then 4 | temp = temp + #inputs 5 | end 6 | if (temp > 0 or i > 1) then 7 | OUT = OUT .. ", " 8 | end 9 | if not members[i].type and members[i].enum then 10 | OUT = OUT .. name .. '::' .. members[i].name .. 'Type' 11 | elseif members[i].dim_vec and (members[i].dim_vec == 1) then 12 | OUT = OUT..'const std::vector<'..members[i].type..'> &' 13 | elseif members[i].point_vec and (members[i].point_vec == 1) then 14 | OUT = OUT..'const std::vector< std::vector<'..members[i].type..'> > &' 15 | else 16 | OUT = OUT .. members[i].type 17 | end 18 | OUT = OUT .. ' ' .. members[i].name:sub(1,1):lower() .. members[i].name:sub(2,-1) 19 | end) 20 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/MemberParametersWithDefaults.in: -------------------------------------------------------------------------------- 1 | $(for i = 1,#members do 2 | local count = number_of_inputs 3 | if inputs then 4 | for j = 1,#inputs do 5 | if not (inputs[j].optional and no_optional) then 6 | count = count + 1 7 | end 8 | end 9 | end 10 | if (count > 0 or i > 1) then 11 | OUT = OUT .. ", " 12 | end 13 | if not type and members[i].enum then 14 | OUT = OUT .. name .. '::' .. members[i].name .. 'Type' 15 | elseif members[i].dim_vec and (members[i].dim_vec == 1) then 16 | OUT = OUT..'const std::vector<'..members[i].type..'> &' 17 | elseif members[i].point_vec and (members[i].point_vec == 1) then 18 | OUT = OUT..'const std::vector< std::vector<'..members[i].type..'> > &' 19 | else 20 | OUT = OUT .. members[i].type 21 | end 22 | OUT= OUT .." ".. members[i].name:sub(1,1):lower() .. members[i].name:sub(2,-1) .. " = " .. members[i].default 23 | end) 24 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/MemberPointsGetSetDeclarations.h.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/ExpandTemplateGenerator/Components/MemberPointsGetSetDeclarations.h.in -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/PublicDeclarations.h.in: -------------------------------------------------------------------------------- 1 | $(if public_declarations then 2 | OUT=[[ 3 | /** Custom public declarations */ 4 | ${public_declarations} 5 | ]]end) 6 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/StandardIncludes.cxx.in: -------------------------------------------------------------------------------- 1 | #include "itkImage.h" 2 | #include "itkVectorImage.h" 3 | #include "itkLabelMap.h" 4 | #include "itkLabelObject.h" 5 | #include "itkNumericTraits.h" 6 | #include "itkNumericTraitsVariableLengthVectorPixel.h" 7 | #include "itkVectorIndexSelectionCastImageFilter.h" 8 | #include "itkComposeImageFilter.h" 9 | 10 | #include "sitk${name}.h" 11 | $(if itk_name then 12 | OUT=[[ 13 | #include "itk${itk_name}.h"]] 14 | else 15 | OUT=[[ 16 | #include "itk${name}.h"]] 17 | end) 18 | 19 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ToStringReturn.cxx.in: -------------------------------------------------------------------------------- 1 | return out.str(); 2 | -------------------------------------------------------------------------------- /ExpandTemplateGenerator/Components/ToStringSignature.cxx.in: -------------------------------------------------------------------------------- 1 | std::string ${name}::ToString() const 2 | -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- 1 | SimpleElastix 2 | Copyright 2015-2018 Kasper Marstal 3 | 4 | Elastix 5 | Copyright 2014 University Medical Center Utrecht and contributors 6 | 7 | SimpleITK 8 | Copyright 2010-2019 Insight Software Consortium 9 | Copyright 2020 NumFOCUS 10 | 11 | Kitware Local Git Setup Scripts 12 | Copyright 2010-2012 Kitware, Inc. 13 | 14 | This product includes software developed at Kitware, Inc. 15 | (http://www.kitware.com/). 16 | 17 | This software is distributed under the Apache 2.0 License. 18 | 19 | See LICENSE file for details. 20 | -------------------------------------------------------------------------------- /Pipfile: -------------------------------------------------------------------------------- 1 | [[source]] 2 | url = "https://pypi.org/simple" 3 | verify_ssl = true 4 | name = "pypi" 5 | 6 | [packages] 7 | 8 | [dev-packages] 9 | 10 | [requires] 11 | python_version = "3.6" 12 | -------------------------------------------------------------------------------- /SimpleITKConfigVersion.cmake.in: -------------------------------------------------------------------------------- 1 | set(PACKAGE_VERSION "@SimpleITK_VERSION@") 2 | 3 | if("${PACKAGE_FIND_VERSION_MAJOR}" EQUAL "@SimpleITK_VERSION_MAJOR@" 4 | AND NOT "${PACKAGE_FIND_VERSION}" VERSION_GREATER "${PACKAGE_VERSION}") 5 | set(PACKAGE_VERSION_COMPATIBLE 1) # compatible with older 6 | if("${PACKAGE_FIND_VERSION}" VERSION_EQUAL "${PACKAGE_VERSION}") 7 | set(PACKAGE_VERSION_EXACT 1) # exact match for this version 8 | endif() 9 | endif() 10 | -------------------------------------------------------------------------------- /SuperBuild/CTestConfig.cmake: -------------------------------------------------------------------------------- 1 | set(CTEST_PROJECT_NAME "SuperBuildSimpleITK") 2 | set(CTEST_NIGHTLY_START_TIME "1:00:00 UTC") 3 | 4 | set(CTEST_DROP_METHOD "http") 5 | set(CTEST_DROP_SITE "open.cdash.org") 6 | set(CTEST_DROP_LOCATION "/submit.php?project=SimpleITK") 7 | set(CTEST_DROP_SITE_CDASH TRUE) 8 | -------------------------------------------------------------------------------- /SuperBuild/ExternalSource/lua-5.3.5.tar.gz.sha512: -------------------------------------------------------------------------------- 1 | 4f9516acc4659dfd0a9e911bfa00c0788f0ad9348e5724fe8fb17aac59e9c0060a64378f82be86f8534e49c6c013e7488ad17321bafcc787831d3d67406bd0f4 2 | -------------------------------------------------------------------------------- /SuperBuild/ExternalSource/pcre-8.43.tar.gz.sha512: -------------------------------------------------------------------------------- 1 | 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-------------------------------------------------------------------------------- 1 | d7e95b8c017ec076210f30b6fd4bb44be2f7dc0257492c25bb00fee597d3ade34226d03539180f1edaf2d27b361f8efdabb92d3476e13785b890878ee1295cb2 2 | -------------------------------------------------------------------------------- /Testing/CI/Azure/azure-pipelines-package.yml: -------------------------------------------------------------------------------- 1 | 2 | trigger: 3 | tags: 4 | include: 5 | - '*' 6 | branches: 7 | exclude: 8 | - '*' 9 | pr: none 10 | schedules: 11 | - cron: "0 3 * * *" # 10 pm EST->UTC 12 | displayName: Daily build 13 | branches: 14 | include: 15 | - develop 16 | always: false 17 | 18 | variables: 19 | ExternalDataVersion: 1.2.0 20 | jobs: 21 | - job: Configure 22 | displayName: Configure Variables 23 | pool: 24 | vmImage: 'Ubuntu-16.04' 25 | steps: 26 | - checkout: none 27 | - bash: | 28 | echo "##vso[task.setvariable variable=BuildHash;isOutput=true]${CONFIGURE_BUILDHASH:-release}" 29 | name: configure 30 | - template: templates/package-linux-job.yml 31 | parameters: 32 | ARCH: x86_64 33 | - template: templates/package-mac-job.yml 34 | - template: templates/package-win-job.yml 35 | parameters: 36 | PYTHON_ARCH: x64 37 | CMAKE_PLATFORM: x64 38 | VCVAR_OPTIONS: amd64 39 | -------------------------------------------------------------------------------- /Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Unit) 2 | -------------------------------------------------------------------------------- /Testing/Data/Baseline/BasicFilters_AbsImageFilter_float.nrrd.sha512: -------------------------------------------------------------------------------- 1 | 0fef8b24aba7b5177934909c136fae870d84797ea953f636a91d38dfe233c4a93272c7fd98e5128722c19430eaddcca2a8495fe9f7518a395e360316391dd4ed 2 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 009083f12a6a5a906e92b4872593842d6405a84228749850a539285421ee3b357e8664f5680454a3d713b56de744303f418d1809761d43e48faca4edb2f068bc 2 | -------------------------------------------------------------------------------- /Testing/Data/Input/xforms/versor_i_3.txt.sha512: -------------------------------------------------------------------------------- 1 | 972b0002e86ec2248ba30469375c46edefffb17df83e0eb9e4bacaa47ee610b982a80b3ee6d55620a67ce4d13ae412dc956b817a53ffa7b034c5cd773f3e43d8 2 | -------------------------------------------------------------------------------- /Testing/Unit/CSharp/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | # 4 | # CSharp Tests 5 | # 6 | sitk_add_csharp_test( Test.ImageTest 7 | "${CMAKE_CURRENT_SOURCE_DIR}/CSharpImageTest.cs" ) 8 | -------------------------------------------------------------------------------- /Testing/Unit/Java/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | # 3 | # Java Tests 4 | # 5 | sitk_add_java_test( ProcessObjectTest 6 | "${CMAKE_CURRENT_SOURCE_DIR}/sitkProcessObjectTest.java" ) 7 | 8 | sitk_add_java_test( ImageTests 9 | "${CMAKE_CURRENT_SOURCE_DIR}/sitkImageTests.java" ) 10 | -------------------------------------------------------------------------------- /Testing/Unit/R/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # R Tests 3 | # 4 | sitk_add_r_test( Arithmetic 5 | "${CMAKE_CURRENT_SOURCE_DIR}/RArithmeticTest.R" 6 | ) 7 | sitk_add_r_test( PixelIndexing 8 | "${CMAKE_CURRENT_SOURCE_DIR}/RPixelAccess.R" 9 | ) 10 | sitk_add_r_test( ImageListArguments 11 | "${CMAKE_CURRENT_SOURCE_DIR}/RImageListArguments.R" 12 | ) 13 | sitk_add_r_test( SwigVectorConversion 14 | "${CMAKE_CURRENT_SOURCE_DIR}/RSwigVectorConversionTests.R" 15 | ) 16 | sitk_add_r_test( ImageSlicing 17 | "${CMAKE_CURRENT_SOURCE_DIR}/RImageSlicingTests.R" 18 | ) 19 | sitk_add_r_test( Transform 20 | "${CMAKE_CURRENT_SOURCE_DIR}/RTransformTests.R" 21 | ) 22 | sitk_add_r_test( Image2Array2Image 23 | "${CMAKE_CURRENT_SOURCE_DIR}/R2Img2R.R" 24 | ) 25 | -------------------------------------------------------------------------------- /Testing/Unit/R/RImageListArguments.R: -------------------------------------------------------------------------------- 1 | ## tests of image pixel access. 2 | ## helps to check whether the rtype entries for std:vector in R.i are OK. 3 | library(SimpleITK) 4 | 5 | imsize <- 64 6 | img1 = Image(imsize, imsize, "sitkFloat32") 7 | img2 = Image(imsize, imsize, "sitkFloat32") 8 | 9 | arglist <- list(img1, img2, img1) 10 | 11 | h<-Tile(arglist, c(length(arglist),1)) 12 | sz <- h$GetSize() 13 | 14 | if (any(sz != c(imsize*length(arglist), imsize))) 15 | { 16 | cat("Failure in tiling with image list arguments\n") 17 | quit(save="no", status=1) 18 | } 19 | -------------------------------------------------------------------------------- /Testing/Unit/sitkImageViewerTest.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * Copyright NumFOCUS 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0.txt 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *=========================================================================*/ 18 | #ifndef __sitkImageViewerTest_h 19 | #define __sitkImageViewerTest_h 20 | 21 | #define CMAKE_COMMAND "@CMAKE_COMMAND@" 22 | 23 | #endif 24 | -------------------------------------------------------------------------------- /UseSimpleITK.cmake.in: -------------------------------------------------------------------------------- 1 | # 2 | # This file sets up include directories, link directories, and 3 | # compiler settings for a project to use SimpleITK. It should not be 4 | # included directly, but rather through the SimpleITK_USE_FILE setting 5 | # obtained from SimpleITKConfig.cmake. 6 | # 7 | 8 | # Add include directories needed to use SimpleITK. 9 | include_directories(${SimpleITK_INCLUDE_DIRS}) 10 | 11 | # Add link directories needed to use SimpleITK. 12 | link_directories(${SimpleITK_LIBRARY_DIRS}) 13 | -------------------------------------------------------------------------------- /Utilities/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | configure_file( 2 | ${CMAKE_CURRENT_SOURCE_DIR}/pypi.sh.in 3 | ${CMAKE_CURRENT_BINARY_DIR}/pypi.sh 4 | ) 5 | 6 | configure_file( 7 | ${CMAKE_CURRENT_SOURCE_DIR}/valgrind.sh.in 8 | ${CMAKE_CURRENT_BINARY_DIR}/valgrind.sh 9 | ) 10 | -------------------------------------------------------------------------------- /Utilities/Distribution/manylinux/Dockerfile-i686: -------------------------------------------------------------------------------- 1 | FROM quay.io/pypa/manylinux1_i686 2 | MAINTAINER Insight Software Consortium 3 | 4 | ADD https://github.com/Kitware/CMake/releases/download/v3.11.4/cmake-3.11.4.tar.gz \ 5 | https://www.openssl.org/source/openssl-1.0.2q.tar.gz \ 6 | /tmp/ 7 | 8 | WORKDIR /tmp/ 9 | COPY ./imagefiles/install.sh ./ 10 | RUN /usr/bin/linux32 bash -v install.sh && rm -rf /tmp/* 11 | 12 | # User is expected to mount directory to "/work" 13 | ENTRYPOINT [ "/usr/bin/linux32", "bash", "-c", "groupadd -o -g $_GROUPID $_USER && useradd -m -o -g $_GROUPID $_USER -u $_USERID && su $_USER /work/io/imagefiles/cmd.sh" ] 14 | -------------------------------------------------------------------------------- /Utilities/Distribution/manylinux/Dockerfile-x86_64: -------------------------------------------------------------------------------- 1 | FROM quay.io/pypa/manylinux1_x86_64 2 | MAINTAINER Insight Software Consortium 3 | 4 | ADD https://github.com/Kitware/CMake/releases/download/v3.11.4/cmake-3.11.4.tar.gz \ 5 | https://www.openssl.org/source/openssl-1.0.2q.tar.gz \ 6 | /tmp/ 7 | 8 | WORKDIR /tmp/ 9 | COPY ./imagefiles/install.sh ./ 10 | RUN bash -v install.sh && rm -rf /tmp/* 11 | 12 | # User is expected to mount directory to "/work" 13 | ENTRYPOINT ["bash", "-c", "groupadd -o -g $_GROUPID $_USER && useradd -m -o -g $_GROUPID $_USER -u $_USERID && su $_USER /work/io/imagefiles/cmd.sh" ] 14 | -------------------------------------------------------------------------------- /Utilities/Doxygen/docker/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:18.04 as simpleitk-doxygen 2 | 3 | RUN apt-get update && \ 4 | DEBIAN_FRONTEND=noninteractive apt-get install -y \ 5 | cmake \ 6 | bison \ 7 | build-essential \ 8 | curl \ 9 | flex \ 10 | git \ 11 | ninja-build \ 12 | graphviz \ 13 | python \ 14 | && apt-get clean 15 | 16 | RUN git clone https://github.com/doxygen/doxygen.git && \ 17 | ( cd doxygen && \ 18 | git checkout Release_1_8_17 && \ 19 | mkdir bld && cd bld && \ 20 | cmake -G Ninja -DCMAKE_BUILD_TYPE=Release .. && \ 21 | ninja install) && \ 22 | rm -rf ./doxygen 23 | 24 | RUN git config --global url."https://github.com/InsightSoftwareConsortium/".insteadOf "https://itk.org/" 25 | 26 | COPY run.sh /tmp 27 | 28 | WORKDIR /work 29 | 30 | ENTRYPOINT ["/tmp/run.sh"] 31 | -------------------------------------------------------------------------------- /Utilities/Doxygen/docker/README: -------------------------------------------------------------------------------- 1 | This dockerfile has been created to facilitate the creation of SimpleITK html 2 | doxygen documentation. 3 | 4 | Run the following commands: 5 | 6 | #docker build --build-arg TAG=v1.1.0 . -f Dockerfile -t simpleitk-doxygen 7 | docker build -f Dockerfile -t simpleitk-doxygen . 8 | 9 | export TAG=v1.2.0 10 | docker run --env TAG --name sitk-dox simpleitk-doxygen 11 | -or- 12 | docker run \ 13 | --env TAG \ 14 | --mount type=bind,source=/home/blowekamp/src/SimpleITK,destination=/work/SimpleITK,readonly \ 15 | --name sitk-dox simpleitk-doxygen 16 | 17 | docker cp sitk-dox:/SimpleITKDoxygen.tar.gz SimpleITKDoxygen${TAG:+-${TAG}}.tar.gz 18 | docker rm sitk-dox 19 | -------------------------------------------------------------------------------- /Utilities/Doxygen/docker/run.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | TAG=${TAG:-"master"} 4 | set -xe 5 | if [ ! -d SimpleITK ]; then 6 | git clone https://github.com/SimpleITK/SimpleITK.git && 7 | (cd SimpleITK && git checkout ${TAG}) 8 | fi 9 | 10 | mkdir SimpleITK-build && \ 11 | cd SimpleITK-build && \ 12 | cmake -G Ninja\ 13 | -DBUILD_DOXYGEN=ON\ 14 | -DWRAP_DEFAULT=OFF\ 15 | -DSimpleITK_BUILD_DISTRIBUTE:BOOL=ON\ 16 | ../SimpleITK/SuperBuild/ && \ 17 | cmake --build . --target SimpleITK-doc && \ 18 | cd SimpleITK-build/Documentation/ && \ 19 | tar --exclude=\*.md5 -zcvf /SimpleITKDoxygen.tar.gz ./html 20 | -------------------------------------------------------------------------------- /Utilities/GenerateDocs/config_vars.sh: -------------------------------------------------------------------------------- 1 | #! /bin/sh 2 | 3 | SIMPLEITK="${HOME}/src/SimpleITK" 4 | 5 | ITK_XML="${HOME}/temp/xml" 6 | 7 | SITK_BUILD_DIR="/dev/shm/SimpleITK/SimpleITK-build" 8 | 9 | PYTHON_EXECUTABLE="python" 10 | -------------------------------------------------------------------------------- /Utilities/GenerateDocs/docker/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:18.04 2 | 3 | RUN apt-get update && \ 4 | DEBIAN_FRONTEND=noninteractive apt-get install -y cmake cmake-curses-gui gcc g++ git python python-dev python-regex doxygen ninja-build gnuplot wget texlive-full 5 | 6 | WORKDIR /tmp/ 7 | COPY ./cmd.sh /work/bin/ 8 | COPY ./entrypoint.sh /work/bin/ 9 | COPY ./config_vars.sh /work/bin/ 10 | RUN chmod o+rx /work/bin/*.sh 11 | 12 | 13 | ENTRYPOINT ["/work/bin/entrypoint.sh"] 14 | CMD ["/work/bin/cmd.sh"] 15 | -------------------------------------------------------------------------------- /Utilities/GenerateDocs/docker/config_vars.sh: -------------------------------------------------------------------------------- 1 | #! /bin/sh 2 | 3 | SIMPLEITK="/tmp/SimpleITK" 4 | 5 | ITK_XML="${HOME}/temp/xml" 6 | 7 | SITK_BUILD_DIR="/tmp/bld/SimpleITK-build" 8 | 9 | PYTHON_EXECUTABLE="python" 10 | -------------------------------------------------------------------------------- /Utilities/GenerateDocs/docker/entrypoint.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | set -eux 4 | umask 000 5 | groupadd -o -g $_GROUPID $_USER 6 | useradd -m -o -g $_GROUPID $_USER -u $_USERID 7 | unset _GROUPID _USERID 8 | su $_USER $@ 9 | -------------------------------------------------------------------------------- /Utilities/JSON/JSONBeautify.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | import json 3 | import sys 4 | try: 5 | from collections import OrderedDict 6 | except ImportError: 7 | import ordereddict as OrderedDict 8 | 9 | # This script takes one argument the name of a json file. 10 | # 11 | 12 | 13 | fname = sys.argv[1] 14 | 15 | print( "Processing ", fname) 16 | 17 | with open( fname, "r" ) as fp: 18 | j = json.load( fp, object_pairs_hook=OrderedDict ) 19 | 20 | with open( fname, "w" ) as fp: 21 | json.dump( j, fp, indent=2, separators=(',',' : ') ) 22 | print("", file=fp) 23 | -------------------------------------------------------------------------------- /Utilities/JSON/JSONValidate.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import print_function 3 | import json, sys 4 | 5 | try: 6 | json.load( open( sys.argv[1], "r" )) 7 | except ValueError as e: 8 | print( "ValueError: {0}".format( e ) ) 9 | print( "{0}:0:0: error: validating json file.".format( sys.argv[1] ) ) 10 | sys.exit(1) 11 | except TypeError as e: 12 | print( "TypeError: {0}".format( e ) ) 13 | print( "{0}:0:0: error: validating json file.".format( sys.argv[1] ) ) 14 | sys.exit(1) 15 | -------------------------------------------------------------------------------- /Utilities/KWStyle/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Utilities/KWStyle/CMakeLists.txt -------------------------------------------------------------------------------- /Utilities/KWStyle/SITK.kws.xml.in: -------------------------------------------------------------------------------- 1 | 2 | 3 | 200 4 | [A-Z] 5 | m_[A-Z] 6 | 0 7 | 1 8 | 1 9 | 3 10 | /**, *, */,true 11 | itk 12 | [NameOfClass],itk 13 | [NameOfClass]_[Extension] 14 | 2 15 | 16 | 1,1 17 | 18 | -------------------------------------------------------------------------------- /Utilities/KWStyle/SITKFiles.txt.in: -------------------------------------------------------------------------------- 1 | @PROJECT_SOURCE_DIR@/Code/Common/include/*.h 2 | @PROJECT_SOURCE_DIR@/Code/Common/include/*.hxx 3 | @PROJECT_SOURCE_DIR@/Code/Common/src/*.cxx 4 | @PROJECT_SOURCE_DIR@/Code/Common/src/*.hxx 5 | @PROJECT_SOURCE_DIR@/Code/IO/include/*.h 6 | @PROJECT_SOURCE_DIR@/Code/IO/include/*.hxx 7 | @PROJECT_SOURCE_DIR@/Code/IO/src/*.cxx 8 | @PROJECT_SOURCE_DIR@/Code/IO/src/*.hxx 9 | @PROJECT_SOURCE_DIR@/Code/BasicFilters/include/*.h 10 | @PROJECT_SOURCE_DIR@/Code/BasicFilters/include/*.hxx 11 | @PROJECT_SOURCE_DIR@/Code/BasicFilters/src/*.cxx 12 | @PROJECT_SOURCE_DIR@/Code/BasicFilters/src/*.hxx 13 | @PROJECT_BINARY_DIR@/Code/BasicFilters/*.h 14 | @PROJECT_BINARY_DIR@/Code/BasicFilters/*.cxx 15 | @PROJECT_BINARY_DIR@/Code/BasicFilters/*.hxx 16 | -------------------------------------------------------------------------------- /Utilities/KWStyle/SITKOverwrite.txt: -------------------------------------------------------------------------------- 1 | sitkVersionConfig.h LineLength 300 2 | -------------------------------------------------------------------------------- /Utilities/Statistics/environment.yml: -------------------------------------------------------------------------------- 1 | name: sitk_stats 2 | 3 | channels: 4 | - conda-forge 5 | 6 | dependencies: 7 | - matplotlib 8 | - numpy 9 | - cartopy 10 | - pandas 11 | - requests 12 | -------------------------------------------------------------------------------- /Utilities/pypi.sh.in: -------------------------------------------------------------------------------- 1 | sudo python @CMAKE_BINARY_DIR@/Wrapping/Python/Packaging/setup.py bdist upload -r pypi 2 | -------------------------------------------------------------------------------- /Wrapping/CSharp/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | %include "sitkImportImageFilter.h" 3 | -------------------------------------------------------------------------------- /Wrapping/Java/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | -------------------------------------------------------------------------------- /Wrapping/Lua/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | -------------------------------------------------------------------------------- /Wrapping/Python/Packaging/__init__.py: -------------------------------------------------------------------------------- 1 | from .SimpleITK import * 2 | -------------------------------------------------------------------------------- /Wrapping/Python/Packaging/setupegg.py: -------------------------------------------------------------------------------- 1 | """ 2 | A setup.py script to use setuptools, which gives wheel and egg goodness, etc. 3 | """ 4 | try: 5 | from setuptools import setup 6 | except ImportError: 7 | # SimpleITK no longer provides ez_setup, but a copy may be around 8 | # so we give it a try. It's intended that setuptools be install in 9 | # a constructed virtualenv during the make process. 10 | from ez_setup import use_setuptools 11 | use_setuptools() 12 | import os 13 | 14 | from setuptools import setup 15 | 16 | fn = os.path.dirname(os.path.realpath(__file__)) + '/setup.py' 17 | exec(open(fn).read()) 18 | -------------------------------------------------------------------------------- /Wrapping/Python/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | 3 | %include "sitkPyCommand.h" 4 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/DESCRIPTION.in: -------------------------------------------------------------------------------- 1 | Package: SimpleITK 2 | Version: @SimpleITKR_VERSION@ 3 | Date: @DATE@ 4 | Title: Bindings to SimpleITK Image Segmentation and Registration toolkit 5 | Authors@R: c(person("Richard", "Beare", role = c("aut", "cre"), 6 | email = "Richard.Beare@ieee.org"), 7 | person("Bradley", "Lowekamp", role = "aut", 8 | email = "blowekamp@mail.nih.gov"), 9 | person("Ziv", "Yaniv", role="aut", 10 | email = "zivrafael.yaniv@nih.gov")) 11 | Depends: R (>= 3.3) 12 | Imports: methods 13 | Description: An interface to SimpleITK, which is a simplified 14 | interface to the Insight Toolkit (ITKv@ITK_VERSION_MAJOR@.@ITK_VERSION_MINOR@.@ITK_VERSION_PATCH@) for medical image segmentation 15 | and registration. 16 | License: Apache License 2.0 17 | URL: http://www.simpleitk.org, https://www.itk.org 18 | BugReports: https://issues.itk.org 19 | Maintainer: Richard Beare 20 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | useDynLib(SimpleITK) 3 | exportPattern( "." ) 4 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/R/zFixes.R: -------------------------------------------------------------------------------- 1 | ## File containing manual fixes for code generated by swig 2 | ## that is wrong. 3 | ## This file will get shorter and disappear as we improve swig. 4 | 5 | PermuteAxesImageFilter_DefaultOrder = 6 | function(value, .copy = FALSE) 7 | { 8 | PermuteAxesImageFilter_DefaultOrder_get(.copy) 9 | } 10 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/inst/doc/SimpleITK_tutorial.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuperElastix/SimpleElastix/1eec0227efd13d312b1c99df38b4647add47378a/Wrapping/R/Packaging/SimpleITK/inst/doc/SimpleITK_tutorial.pdf -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/inst/extdata/cthead1-Float.mha.sha512: -------------------------------------------------------------------------------- 1 | 6a99d4f3edaf5238ab585f9b8445720a8d71157157acb0a461ca568e10ece671fb8f2af3d348d6cbe5b43560536f149cc1a4102ce9a4b8b4936ae23e3d9101b8 2 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/inst/extdata/cthead1.png.sha512: -------------------------------------------------------------------------------- 1 | 07fde89ac38926e4cd1746282071c8d3fb0b6222aed9d70f5fdcabb10a8caee3ad8c040d103924e55aa484d6f8ab5310cde52a6a0ecf83a9d87f0501f23c0cc1 2 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/man/sitkRdfiles.tar.gz.sha512: -------------------------------------------------------------------------------- 1 | e26fd5c57ba45d6871ab2bd4e78ef8b7558036a5e30b40235f616e478d3997f3084e20c33033f132abe48ca7095239a195a9408a8bb6268d230f7cbd55e6d78b 2 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/src/Makefile: -------------------------------------------------------------------------------- 1 | all: 2 | echo "Dummy makefile for binary package" 3 | clean: 4 | 5 | # don't clean, otherwise R CMD build doesn't work as 6 | # this isn't really a source package 7 | -------------------------------------------------------------------------------- /Wrapping/R/Packaging/SimpleITK/vignettes/times.sty: -------------------------------------------------------------------------------- 1 | %% 2 | %% This is file `times.sty', 3 | %% generated with the docstrip utility. 4 | %% 5 | %% The original source files were: 6 | %% 7 | %% psfonts.dtx (with options: `times') 8 | %% 9 | %% IMPORTANT NOTICE: 10 | %% 11 | %% For the copyright see the source file. 12 | %% 13 | %% Any modified versions of this file must be renamed 14 | %% with new filenames distinct from times.sty. 15 | %% 16 | %% For distribution of the original source see the terms 17 | %% for copying and modification in the file psfonts.dtx. 18 | %% 19 | %% This generated file may be distributed as long as the 20 | %% original source files, as listed above, are part of the 21 | %% same distribution. (The sources need not necessarily be 22 | %% in the same archive or directory.) 23 | \ProvidesPackage{times} 24 | [2002/09/08 PSNFSS-v9.0a 25 | (SPQR) 26 | ] 27 | \renewcommand{\sfdefault}{phv} 28 | \renewcommand{\rmdefault}{ptm} 29 | \renewcommand{\ttdefault}{pcr} 30 | \endinput 31 | %% 32 | %% End of file `times.sty'. 33 | -------------------------------------------------------------------------------- /Wrapping/R/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | 3 | %include "sitkRCommand.h" 4 | -------------------------------------------------------------------------------- /Wrapping/Ruby/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | -------------------------------------------------------------------------------- /Wrapping/Tcl/SimpleITK.i: -------------------------------------------------------------------------------- 1 | %include SimpleITK_Common.i 2 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = -aE 6 | SPHINXBUILD = sphinx-build 7 | SOURCEDIR = source 8 | BUILDDIR = build 9 | 10 | # Put it first so that "make" without argument is like "make help". 11 | help: 12 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 13 | 14 | .PHONY: help Makefile 15 | 16 | # Catch-all target: route all unknown targets to Sphinx using the new 17 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 18 | %: Makefile 19 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 20 | -------------------------------------------------------------------------------- /docs/_templates/breadcrumbs.html: -------------------------------------------------------------------------------- 1 | {%- extends "sphinx_rtd_theme/breadcrumbs.html" %} 2 | 3 | {% block breadcrumbs_aside %} 4 | {% endblock %} 5 | {% block breadcrumbs %} 6 | {% endblock %} 7 | -------------------------------------------------------------------------------- /docs/images/BuildPathConfiguration.jpg.sha512: -------------------------------------------------------------------------------- 1 | d65ffefbb60eedfbbc41952031132e14c1b7a5e453d64d7181fac410844b6b8a626e4a871e43577c180ad24db29b79d2907672df3cbb83c0a6ed87cd19d62f06 2 | -------------------------------------------------------------------------------- /docs/images/EclipseConfigureBuildPath.jpg.sha512: -------------------------------------------------------------------------------- 1 | 8b4da5222b05623221b4e25e06032ba0690120470574b1a035b999d29c4c8a5a2ea28ada5a34c03509eb3e4d8c0f0b66718eba9a0cf2be891d25017a5ffefd55 2 | -------------------------------------------------------------------------------- /docs/images/ImageOriginAndSpacing.svg.sha512: -------------------------------------------------------------------------------- 1 | 0fb1f6d53e6ea5d5a29127402197bebdeb955f186cedbedae16aebc0780437734cd3d814a0390d752d2e1c8b99593f3b6ffbf4a6c6b7de9cd885fcc2178b98f8 2 | -------------------------------------------------------------------------------- /docs/images/ManagedLibrary.jpg.sha512: -------------------------------------------------------------------------------- 1 | c5901a52f9ed0e76fffb7d49d20371ecfccd5f9e1902523605876ffe8ec1e5ff0dd34d4d9f1bc1722ca250b17bd3cd228d22799fd97fa91e42f35f961f050fbf 2 | -------------------------------------------------------------------------------- /docs/images/NativeLibraryProperties.jpg.sha512: -------------------------------------------------------------------------------- 1 | 3daf16a95895670234fe0dfda72cc24f0a0bb8bff68f33aa9abbaf28855f6c5dacc115f27bf7b6d9245cc3894652637b320a1efeee83901bccabddeb989847f9 2 | -------------------------------------------------------------------------------- /docs/images/NewVisualStudioProject.jpg.sha512: -------------------------------------------------------------------------------- 1 | ca73f82f9c7f05588701b63980c15dfcb0fe2e77637de4f378bd8e8aae7698c49d4a9c83c70bdec1181aeae99ff64f867f5da2284cd0bd4021e2ee4d289cc48d 2 | -------------------------------------------------------------------------------- /docs/images/Readme.md: -------------------------------------------------------------------------------- 1 | Readme 2 | ====== 3 | 4 | This directory is for images used by for the Sphinx 5 | documentation. Because images are relatively large files compared to 6 | source code, they are not stored in the git repository. Instead we 7 | just store SHA512 hashed of the files then utilize [CMake's 8 | ExternalData](https://cmake.org/cmake/help/v3.10/module/ExternalData.html) 9 | module to download the data. 10 | 11 | To add data to this directory, the file must be uploaded to one of the 12 | binary data stores, and the sha512 files are committed to the repository. 13 | -------------------------------------------------------------------------------- /docs/images/SimpleITKCSharpUnzip.jpg.sha512: -------------------------------------------------------------------------------- 1 | 4245ad122ce2427c011250009876471aa557289ac5791233d24469d9af7e5a4a46b50705cdce9b6b149aae78558df2eb80fb70b1fd17e32eec42b02735db7e4e 2 | -------------------------------------------------------------------------------- /docs/images/VisualStudioConfigurationManager.jpg.sha512: -------------------------------------------------------------------------------- 1 | c38d62ddaeff8062d765ff9f1de158d894dce9d8316097810708e202f981687471845d67ab956a5542cd6536b71d8d1700665f632d07856519223dcbc4ed0dc2 2 | -------------------------------------------------------------------------------- /docs/images/VisualStudioExample.jpg.sha512: -------------------------------------------------------------------------------- 1 | 52db7a7a2755c82e0f57dcfede19c0bfc78649fb01d909ecc228b8176dc6951d0031d5675b4de461458599b5f7d9ac1018ee000408a2b7dc7db4031f8d951df0 2 | -------------------------------------------------------------------------------- /docs/images/imageJ.png.sha512: -------------------------------------------------------------------------------- 1 | e6a0aeacdf34f38c3960b07ba2ec223005d44fd54b49318ac214e846eb4e0934345f9e474e95c8ace5a02681fd4b776b790e63fe3ab05174ed89a55a31e5ce3e 2 | -------------------------------------------------------------------------------- /docs/images/isbi.png.sha512: -------------------------------------------------------------------------------- 1 | 151d461cc8d560aa4022d9eb95359dba764d582d979a211091e4e613f816d417d427564233273424e9548a9c323a42dac344f0d70b1d89f76a2fcd691ceadec8 2 | -------------------------------------------------------------------------------- /docs/images/miccai.png.sha512: -------------------------------------------------------------------------------- 1 | e27aa2547352c3d9ab4476a3b77f0e2d3f3779722562202303a5f49308206db21aef9539303fb96abaa08fc55122d40f11a3f50f76c450e7ff74d1dafefabd87 2 | -------------------------------------------------------------------------------- /docs/images/nonisotropicVsIsotropic.svg.sha512: -------------------------------------------------------------------------------- 1 | c189aeac49e642b2fd616b9a8a717a4c51f7e53f5d8f0a704d4a10204437ca69bdf27d353cf1cc70a9553c1ef32edba603ed85af305345d8121fdf736d0e81ce 2 | -------------------------------------------------------------------------------- /docs/images/simpleitk_logo.png.sha512: -------------------------------------------------------------------------------- 1 | 285be26989b554eb4d4a4e7b293e9e5bcad712b676a2cdae11e462256a5c98b5345500bf2a8ed515e6d19085d565307123f2b879f32d8ca523b2b0bb7cabba57 2 | -------------------------------------------------------------------------------- /docs/images/spatialRelationship.svg.sha512: -------------------------------------------------------------------------------- 1 | d602f10ab1916d1a28fb14b13d9a50e24be1a9435aefc0341998c47ab7690e2cf1582e077c4cf1949fdbf4c50837469fc2c796493e3e878e994646e835ed4e8c 2 | -------------------------------------------------------------------------------- /docs/images/spie.png.sha512: -------------------------------------------------------------------------------- 1 | cfb3a4cc3a9629e13ca425984edac45ee28f2658050455cbe92a7e3f0bf146a7d8c54846ed322dbd8a748eeba51e9058a2220884e5d62b1f44cd59aabb27c643 2 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=../.. 11 | set BUILDDIR=../../build 12 | set SPHINXPROJ=SimpleITK 13 | 14 | if "%1" == "" goto help 15 | 16 | %SPHINXBUILD% >NUL 2>NUL 17 | if errorlevel 9009 ( 18 | echo. 19 | echo.The Sphinx module was not found. Make sure you have Sphinx installed, 20 | echo.then set the SPHINXBUILD environment variable to point to the full 21 | echo.path of the 'sphinx-build' executable. Alternatively you may add the 22 | echo.Sphinx directory to PATH. 23 | echo. 24 | echo.If you don't have Sphinx installed, grab it from 25 | echo.http://sphinx-doc.org/ 26 | exit /b 1 27 | ) 28 | 29 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 30 | goto end 31 | 32 | :help 33 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 34 | 35 | :end 36 | popd 37 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx-tabs 2 | cmake 3 | sphinx_rtd_theme 4 | -------------------------------------------------------------------------------- /docs/source/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 3.14) 2 | 3 | project(sitk_example) 4 | 5 | find_package(SimpleITK) 6 | add_executable ( sitk_example sitk_example.cxx ) 7 | target_link_libraries ( sitk_example ${SimpleITK_LIBRARIES} ) 8 | -------------------------------------------------------------------------------- /docs/source/about.rst: -------------------------------------------------------------------------------- 1 | .. _lbl_about: 2 | 3 | About 4 | ===== 5 | 6 | SimpleITK is a simplified programming interface to the algorithms and data structures of the `Insight Toolkit `_ (ITK). It supports bindings for multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and TCL. These bindings enable scientists to develop image analysis workflows in the programming language they are most familiar with. The toolkit supports more than 15 different image file formats, provides over 280 image analysis filters, and implements a unified interface to the ITK intensity-based registration framework. 7 | 8 | .. toctree:: 9 | :maxdepth: 1 10 | 11 | history 12 | license 13 | -------------------------------------------------------------------------------- /docs/source/license.rst: -------------------------------------------------------------------------------- 1 | .. _lbl_license: 2 | 3 | License 4 | ************ 5 | 6 | .. include:: ../../LICENSE 7 | :literal: 8 | -------------------------------------------------------------------------------- /docs/source/link_AdvancedImageReading_docs.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../../Examples/AdvancedImageReading/Documentation.rst 2 | -------------------------------------------------------------------------------- /docs/source/link_CSharp_docs.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../../Examples/CSharp/Documentation.rst 2 | -------------------------------------------------------------------------------- /docs/source/link_DemonsRegistration1_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DemonsRegistration1/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_DemonsRegistration2_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DemonsRegistration2/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_DicomImagePrintTags_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DicomImagePrintTags/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_DicomSeriesFromArray_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DicomSeriesFromArray/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_DicomSeriesReadModifyWrite_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DicomSeriesReadModifyWrite/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_DicomSeriesReader_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/DicomSeriesReader/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_FastMarchingSegmentation_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/FastMarchingSegmentation/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_FilterProgressReporting_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/FilterProgressReporting/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_HelloWorld_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/HelloWorld/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ITKIntegration_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ITKIntegration/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageGridManipulation_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageGridManipulation/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageIOSelection_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageIOSelection/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethod1_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethod1/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethod2_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethod2/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethod3_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethod3/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethod4_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethod4/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethodBSpline1_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethodBSpline1/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethodBSpline2_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethodBSpline2/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethodBSpline3_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethodBSpline3/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethodDisplacement1_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethodDisplacement1/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageRegistrationMethodExhaustive_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageRegistrationMethodExhaustive/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_ImageViewing_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/ImageViewing/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_N4BiasFieldCorrection_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/N4BiasFieldCorrection/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_SimpleGaussian_docs.rst: -------------------------------------------------------------------------------- 1 | 2 | .. include:: ../../Examples/SimpleGaussian/Documentation.rst 3 | -------------------------------------------------------------------------------- /docs/source/link_examples.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../../Examples/index.rst 2 | -------------------------------------------------------------------------------- /docs/source/registrationExamplePrefix.rst: -------------------------------------------------------------------------------- 1 | If you are not familiar with the SimpleITK registration framework we recommend 2 | that you read the :ref:`registration overview ` 3 | before continuing with the example. 4 | -------------------------------------------------------------------------------- /docs/source/sitk_example.cxx: -------------------------------------------------------------------------------- 1 | // This one header will include all SimpleITK filters and external objects. 2 | #include 3 | #include 4 | 5 | // create convenient namespace alias 6 | namespace sitk = itk::simple; 7 | 8 | int main ( int argc, char* argv[] ) { 9 | 10 | sitk::PixelIDValueEnum pixelType = sitk::sitkUInt8; 11 | std::vector imageSize ( 2, 128 ); 12 | 13 | // Create a black image 14 | sitk::Image image( imageSize, pixelType ); 15 | 16 | // Add a Gaussian blob to the image 17 | std::vector blobSize ( 2, 64.0 ); 18 | std::vector blobCenter ( 2, 64.0 ); 19 | image = image + sitk::GaussianSource( pixelType, imageSize, blobSize, blobCenter ); 20 | 21 | // Write the image as a PNG file 22 | sitk::WriteImage(image, "blob.png" ); 23 | 24 | } 25 | --------------------------------------------------------------------------------