├── .github └── workflows │ └── ci.yml ├── .travis.yml ├── CMakeLists.txt ├── CTestConfig.cmake ├── Dockerfile ├── Doxygen ├── CMakeLists.txt ├── DoxygenFooter.html ├── DoxygenHeader.html ├── DoxygenStyle.css ├── MainPage.dox ├── doxygen.config.in ├── itkdoxygen.pl.in ├── itkgroup.pl └── vxl_doxy.pl ├── LICENSE.txt ├── Licence_CeCILL-B_V1-en.txt ├── README.md ├── bw-output ├── build-wrapper-dump.json └── build-wrapper.log ├── clitk.doxygen ├── clitk_tools.md ├── cluster_tools ├── CMakeLists.txt ├── check_tmp_cluster.sh ├── computeEnlapsedTime.py ├── gate_common.sh ├── gate_job_ccin2p3.job ├── gate_job_cluster.job ├── gate_job_cluster_nomove.job ├── gate_make_merge_release.sh ├── gate_make_release.sh ├── gate_merge_merges.sh ├── gate_power_merge.sh ├── gate_run_submit_cluster.sh ├── gate_run_submit_cluster_nomove.sh ├── gate_upload_release.sh ├── mergeDoseByRegions.sh ├── mergeDosePerEnergyFile.sh ├── mergeStatFile.py └── mergeStatFile.sh ├── cmake ├── FindGengetopt.cmake ├── FindROOT.cmake ├── build_opt.cmake ├── common.cmake ├── dependencies.cmake └── deploy.cmake.in ├── common ├── CMakeLists.txt ├── clitkChangeDicomTagGenericFilter.h ├── clitkChangeDicomTagGenericFilter.txx ├── clitkCommon.cxx ├── clitkCommon.h ├── clitkCommon.txx ├── clitkCommonGenericFilter.h ├── clitkConfiguration.h.in ├── clitkDD.h ├── clitkDicomRTDoseIO.cxx ├── clitkDicomRTDoseIO.h ├── clitkDicomRTDoseIOFactory.cxx ├── clitkDicomRTDoseIOFactory.h ├── clitkDicomRTStruct2ImageFilter.cxx ├── clitkDicomRTStruct2ImageFilter.h ├── clitkDicomRT_Contour.cxx ├── clitkDicomRT_Contour.h ├── clitkDicomRT_ROI.cxx ├── clitkDicomRT_ROI.h ├── clitkDicomRT_StructureSet.cxx ├── clitkDicomRT_StructureSet.h ├── clitkElastix.h ├── clitkEsrfHstImageIO.cxx ├── clitkEsrfHstImageIO.h ├── clitkEsrfHstImageIOFactory.cxx ├── clitkEsrfHstImageIOFactory.h ├── clitkEsrfHstXMLFileReader.cxx ├── clitkEsrfHstXMLFileReader.h ├── clitkExceptionObject.cxx ├── clitkExceptionObject.h ├── clitkFilterBase.cxx ├── clitkFilterBase.h ├── clitkFilterBase.txx ├── clitkFilterMacros.txx ├── clitkGateAsciiImageIO.cxx ├── clitkGateAsciiImageIO.h ├── clitkGateAsciiImageIOFactory.cxx ├── clitkGateAsciiImageIOFactory.h ├── clitkIO.cxx ├── clitkIO.h ├── clitkImage2DicomRTStructFilter.h ├── clitkImage2DicomRTStructFilter.txx ├── clitkImageCommon.cxx ├── clitkImageCommon.h ├── clitkImageCommon.txx ├── clitkImageToImageGenericFilter.h ├── clitkImageToImageGenericFilter.txx ├── clitkImageToImageGenericFilterBase.cxx ├── clitkImageToImageGenericFilterBase.h ├── clitkLabelizeParameters.h ├── clitkListOfPair.cxx ├── clitkListOfPair.h ├── clitkListOfPair.txx ├── clitkMatrix.cxx ├── clitkMatrix.h ├── clitkMemoryUsage.cxx ├── clitkMemoryUsage.h ├── clitkOrientation.cxx ├── clitkOrientation.h ├── clitkPortability.h ├── clitkTimer.cxx ├── clitkTimer.h ├── clitkTransformUtilities.cxx ├── clitkTransformUtilities.h ├── clitkVfImageIO.cxx ├── clitkVfImageIO.h ├── clitkVfImageIOFactory.cxx ├── clitkVfImageIOFactory.h ├── clitkVoxImageIO.cxx ├── clitkVoxImageIO.h ├── clitkVoxImageIOFactory.cxx ├── clitkVoxImageIOFactory.h ├── clitkXdrImageIO.h ├── clitkXdrImageIOFactory.cxx ├── clitkXdrImageIOFactory.h ├── clitkXdrImageIOReader.cxx ├── clitkXdrImageIOWriter.cxx ├── clitkXml2DicomRTStructFilter.h ├── clitkXml2DicomRTStructFilter.txx ├── vvFromITK.h ├── vvImage.cxx ├── vvImage.h ├── vvImage.txx ├── vvImageReader.cxx ├── vvImageReader.h ├── vvImageReader.txx ├── vvImageWriter.cxx ├── vvImageWriter.h ├── vvImageWriter.txx └── vvToITK.h ├── docWiki.sh ├── fast_make.sh ├── itk ├── RelativePositionPropImageFilter.h ├── RelativePositionPropImageFilter.txx ├── clitkAddRelativePositionConstraintToLabelImageFilter.h ├── clitkAddRelativePositionConstraintToLabelImageFilter.txx ├── clitkAutoCropFilter.h ├── clitkAutoCropFilter.txx ├── clitkBackProjectImageFilter.h ├── clitkBackProjectImageFilter.txx ├── clitkBinaryImageToMeshFilter.h ├── clitkBinaryImageToMeshFilter.txx ├── clitkBooleanOperatorLabelImageFilter.h ├── clitkBooleanOperatorLabelImageFilter.txx ├── clitkBoundingBoxUtils.h ├── clitkBoundingBoxUtils.txx ├── clitkComposeVFFilter.h ├── clitkComposeVFFilter.txx ├── clitkConditionalBinaryDilateImageFilter.h ├── clitkConditionalBinaryDilateImageFilter.txx ├── clitkConditionalBinaryErodeImageFilter.h ├── clitkConditionalBinaryErodeImageFilter.txx ├── clitkConditionalGrayscaleDilateImageFilter.h ├── clitkConditionalGrayscaleDilateImageFilter.txx ├── clitkCoordinatesOfImageBoundariesCalculator.h ├── clitkCropLikeImageFilter.h ├── clitkCropLikeImageFilter.txx ├── clitkDecomposeAndReconstructImageFilter.h ├── clitkDecomposeAndReconstructImageFilter.txx ├── clitkDecomposeThroughErosionImageFilter.h ├── clitkDecomposeThroughErosionImageFilter.txx ├── clitkExplosionControlledThresholdConnectedImageFilter.h ├── clitkExplosionControlledThresholdConnectedImageFilter.txx ├── clitkExtractImageFilter.h ├── clitkExtractImageFilter.txx ├── clitkExtractSliceFilter.h ├── clitkExtractSliceFilter.txx ├── clitkForwardWarpImageFilter.h ├── clitkForwardWarpImageFilter.txx ├── clitkInvertVFFilter.h ├── clitkInvertVFFilter.txx ├── clitkLabelImageOverlapMeasureFilter.h ├── clitkLabelImageOverlapMeasureFilter.txx ├── clitkLocallyAdaptiveBinaryThresholdImageFunction.h ├── clitkLocallyAdaptiveBinaryThresholdImageFunction.txx ├── clitkLocallyAdaptiveThresholdConnectedImageFilter.h ├── clitkLocallyAdaptiveThresholdConnectedImageFilter.txx ├── clitkMeshToBinaryImageFilter.h ├── clitkMeshToBinaryImageFilter.txx ├── clitkPasteImageFilter.h ├── clitkPasteImageFilter.hxx ├── clitkReconstructThroughDilationImageFilter.h ├── clitkReconstructThroughDilationImageFilter.txx ├── clitkReconstructWithConditionalGrayscaleDilateImageFilter.h ├── clitkReconstructWithConditionalGrayscaleDilateImageFilter.txx ├── clitkResampleImageWithOptionsFilter.h ├── clitkResampleImageWithOptionsFilter.txx ├── clitkSegmentationUtils.h ├── clitkSegmentationUtils.txx ├── clitkSetBackgroundImageFilter.h ├── clitkSliceBySliceRelativePositionFilter.h ├── clitkSliceBySliceRelativePositionFilter.txx ├── clitkVectorBSplineDecompositionImageFilter.h ├── clitkVectorBSplineDecompositionImageFilter.txx ├── clitkVectorBSplineDecompositionImageFilterWithOBD.h ├── clitkVectorBSplineDecompositionImageFilterWithOBD.txx ├── clitkVectorBSplineInterpolateImageFunction.h ├── clitkVectorBSplineInterpolateImageFunction.txx ├── clitkVectorBSplineInterpolateImageFunctionWithLUT.h ├── clitkVectorBSplineInterpolateImageFunctionWithLUT.txx ├── clitkVectorBSplineResampleImageFunction.h ├── clitkVectorBSplineResampleImageFunctionWithLUT.h ├── itkBSplineDecompositionImageFilterWithOBD.h ├── itkBSplineDecompositionImageFilterWithOBD.txx ├── itkBSplineInterpolateImageFunctionWithLUT.h ├── itkBSplineInterpolateImageFunctionWithLUT.h.original ├── itkBSplineInterpolateImageFunctionWithLUT.txx ├── itkBSplineInterpolateImageFunctionWithLUT.txx.original ├── itkBSplineResampleImageFunctionWithLUT.h ├── itkBSplineWeightsCalculator.h ├── itkBSplineWeightsCalculator.txx ├── itkBinaryGuerreroFilter.h ├── itkBinaryThinningImageFilter3D.h ├── itkBinaryThinningImageFilter3D.txx ├── itkFlexibleBinaryFunctorImageFilter.h ├── itkFlexibleBinaryFunctorImageFilter.txx ├── itkFlexibleVectorCastImageFilter.h ├── itkImageToVTKImageFilter.h ├── itkImageToVTKImageFilter.txx ├── itkRayCastInterpolateImageFunctionWithOrigin.h ├── itkRayCastInterpolateImageFunctionWithOrigin.txx ├── itkVTKImageToImageFilter.h └── itkVTKImageToImageFilter.txx ├── license-header.txt ├── make_meta.sh ├── make_new_tool.sh ├── registration ├── AffineReg.txt ├── CMakeLists.txt ├── clitkAffineRegistration.cxx ├── clitkAffineRegistration.ggo ├── clitkAffineRegistrationGenericFilter.cxx ├── clitkAffineRegistrationGenericFilter.h ├── clitkBLUTDIR.cxx ├── clitkBLUTDIR.ggo ├── clitkBLUTDIRCommandIterationUpdateDVF.h ├── clitkBLUTDIRGenericFilter.cxx ├── clitkBLUTDIRGenericFilter.h ├── clitkBSplineDeformableTransform.h ├── clitkBSplineDeformableTransform.txx ├── clitkBSplineDeformableTransformInitializer.h ├── clitkBSplineDeformableTransformInitializer.txx ├── clitkCalculateTRE.cxx ├── clitkCalculateTRE.ggo ├── clitkCalculateTREGenericFilter.cxx ├── clitkCalculateTREGenericFilter.h ├── clitkCalculateTREGenericFilter.txx ├── clitkConvertBLUTCoeffsToVFFilter.h ├── clitkConvertBLUTCoeffsToVFFilter.txx ├── clitkConvertBSplineDeformableTransformToVF.cxx ├── clitkConvertBSplineDeformableTransformToVF.ggo ├── clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx ├── clitkConvertBSplineDeformableTransformToVFGenericFilter.h ├── clitkCorrelationRatioImageToImageMetric.h ├── clitkCorrelationRatioImageToImageMetric.txx ├── clitkDeformationFieldTransform.h ├── clitkDeformationFieldTransform.txx ├── clitkDeformationListStatisticsFilter.h ├── clitkDeformationListStatisticsFilter.txx ├── clitkDemonsDeformableRegistration.cxx ├── clitkDemonsDeformableRegistration.ggo ├── clitkDemonsDeformableRegistrationGenericFilter.cxx ├── clitkDemonsDeformableRegistrationGenericFilter.h ├── clitkDemonsDeformableRegistrationGenericFilter.txx ├── clitkDifferenceImageFilter.h ├── clitkDifferenceImageFilter.txx ├── clitkGenericAffineTransform.cxx ├── clitkGenericAffineTransform.h ├── clitkGenericAffineTransform.txx ├── clitkGenericInterpolator.h ├── clitkGenericInterpolator.txx ├── clitkGenericMetric.h ├── clitkGenericMetric.txx ├── clitkGenericOptimizer.h ├── clitkGenericVectorInterpolator.h ├── clitkGenericVectorInterpolator.txx ├── clitkLBFGSBOptimizer.cxx ├── clitkLBFGSBOptimizer.h ├── clitkLinearCombinationImageFilter.h ├── clitkLinearCombinationImageFilter.txx ├── clitkList.h ├── clitkList.txx ├── clitkLists.h ├── clitkLists.txx ├── clitkMatrixTransformToVF.cxx ├── clitkMatrixTransformToVF.ggo ├── clitkMatrixTransformToVFGenericFilter.cxx ├── clitkMatrixTransformToVFGenericFilter.h ├── clitkMatrixTransformToVFGenericFilter.txx ├── clitkMultiResolutionPDEDeformableRegistration.h ├── clitkMultiResolutionPDEDeformableRegistration.txx ├── clitkMultiResolutionPyramidRegionFilter.h ├── clitkMultiResolutionPyramidRegionFilter.txx ├── clitkMultipleBSplineDeformableTransform.h ├── clitkMultipleBSplineDeformableTransform.txx ├── clitkMultipleBSplineDeformableTransformInitializer.h ├── clitkMultipleBSplineDeformableTransformInitializer.txx ├── clitkNormalizedCorrelationImageToImageMetric.h ├── clitkNormalizedCorrelationImageToImageMetric.txx ├── clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h ├── clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx ├── clitkOptNormalizedCorrelationImageToImageMetric.h ├── clitkOptNormalizedCorrelationImageToImageMetric.txx ├── clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h ├── clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx ├── clitkPointListReader.h ├── clitkPointListReader.txx ├── clitkPointListTransform.h ├── clitkPointListTransform.txx ├── clitkPointListWriter.h ├── clitkPointListWriter.txx ├── clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.h ├── clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.txx ├── clitkResampleBSplineDeformableTransformImageFilter.h ├── clitkResampleBSplineDeformableTransformImageFilter.txx ├── clitkShapedBLUTSpatioTemporalDeformableTransform.h ├── clitkShapedBLUTSpatioTemporalDeformableTransform.txx ├── clitkShapedBLUTSpatioTemporalDeformableTransformInitializer.h ├── clitkShapedBLUTSpatioTemporalDeformableTransformInitializer.txx ├── clitkSpatioTemporalMultiResolutionImageRegistrationMethod.h ├── clitkSpatioTemporalMultiResolutionImageRegistrationMethod.txx ├── clitkSpatioTemporalMultiResolutionPyramidImageFilter.h ├── clitkSpatioTemporalMultiResolutionPyramidImageFilter.txx ├── clitkTransformToDeformationFieldSource.h ├── clitkTransformToDeformationFieldSource.txx ├── itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h ├── itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx ├── itkMeanSquaresImageToImageMetricFor3DBLUTFFD.h ├── itkMeanSquaresImageToImageMetricFor3DBLUTFFD.txx ├── itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h ├── itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx ├── itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h └── itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx ├── segmentation ├── CMakeLists.txt ├── clitkAnatomicalFeatureDatabase.cxx ├── clitkAnatomicalFeatureDatabase.h ├── clitkAnatomicalFeatureDatabase.txx ├── clitkConnectedComponentLabeling.cxx ├── clitkConnectedComponentLabeling.ggo ├── clitkConnectedComponentLabelingGenericFilter.h ├── clitkConnectedComponentLabelingGenericFilter.txx ├── clitkDecomposeAndReconstruct.cxx ├── clitkDecomposeAndReconstruct.ggo ├── clitkDecomposeAndReconstructGenericFilter.cxx ├── clitkDecomposeAndReconstructGenericFilter.h ├── clitkDecomposeAndReconstructGenericFilter.txx ├── clitkExtractBones.cxx ├── clitkExtractBones.ggo ├── clitkExtractBonesFilter.h ├── clitkExtractBonesFilter.txx ├── clitkExtractBonesGenericFilter.h ├── clitkExtractBonesGenericFilter.txx ├── clitkExtractLung.cxx ├── clitkExtractLung.ggo ├── clitkExtractLungFilter.h ├── clitkExtractLungFilter.txx ├── clitkExtractLungGenericFilter.h ├── clitkExtractLungGenericFilter.txx ├── clitkExtractMediastinalVessels.cxx ├── clitkExtractPatient.cxx ├── clitkExtractPatient.ggo ├── clitkExtractPatientFilter.h ├── clitkExtractPatientFilter.txx ├── clitkExtractPatientGenericFilter.cxx ├── clitkExtractPatientGenericFilter.h ├── clitkExtractPatientGenericFilter.txx ├── clitkFillMaskFilter.h ├── clitkFillMaskFilter.txx ├── clitkFilterWithAnatomicalFeatureDatabaseManagement.cxx ├── clitkFilterWithAnatomicalFeatureDatabaseManagement.h ├── clitkMorphoMath.cxx ├── clitkMorphoMath.ggo ├── clitkMorphoMathFilter.h ├── clitkMorphoMathFilter.txx ├── clitkMorphoMathGenericFilter.cxx ├── clitkMorphoMathGenericFilter.h ├── clitkMorphoMathGenericFilter.txx ├── clitkMotionMask.cxx ├── clitkMotionMask.ggo ├── clitkMotionMaskGenericFilter.cxx ├── clitkMotionMaskGenericFilter.h ├── clitkMotionMaskGenericFilter.txx ├── clitkRegionGrowing.cxx ├── clitkRegionGrowing.ggo ├── clitkRegionGrowingGenericFilter.cxx ├── clitkRegionGrowingGenericFilter.h ├── clitkRegionGrowingGenericFilter.txx ├── clitkRelativePositionList.h ├── clitkRelativePositionList.txx ├── clitkSliceBySliceRelativePositionFilter_uchar.cxx ├── clitkStructuresExtractionFilter.h ├── clitkStructuresExtractionFilter.txx ├── clitkTestArtery.cxx ├── clitkTestFilter.ggo ├── tree.hh └── tree.pdf ├── sonar-project.properties ├── superbuild └── CMakeLists.txt ├── tests ├── CMakeLists.txt ├── doc │ └── vvDoc.tex └── tools │ ├── CMakeLists.txt │ └── toolTestRunner.cxx ├── tools ├── CMakeLists.txt ├── GateMergeManager.cc ├── GateMergeManager.hh ├── clitk4DImageToNVectorImage.cxx ├── clitk4DImageToNVectorImage.ggo ├── clitk4DImageToNVectorImageGenericFilter.cxx ├── clitk4DImageToNVectorImageGenericFilter.h ├── clitk4DImageToNVectorImageGenericFilter.txx ├── clitkAffineTransform.cxx ├── clitkAffineTransform.ggo ├── clitkAffineTransformGenericFilter.cxx ├── clitkAffineTransformGenericFilter.h ├── clitkAffineTransformGenericFilter.txx ├── clitkAnisotropicDiffusion.cxx ├── clitkAnisotropicDiffusion.ggo ├── clitkAnisotropicDiffusionGenericFilter.cxx ├── clitkAnisotropicDiffusionGenericFilter.h ├── clitkAutoCrop.cxx ├── clitkAutoCrop.ggo ├── clitkAutoCropGenericFilter.h ├── clitkAutoCropGenericFilter.txx ├── clitkBackProjectImage.cxx ├── clitkBackProjectImage.ggo ├── clitkBackProjectImageGenericFilter.cxx ├── clitkBackProjectImageGenericFilter.h ├── clitkBackProjectImageGenericFilter.txx ├── clitkBinarizeImage.cxx ├── clitkBinarizeImage.ggo ├── clitkBinarizeImageGenericFilter.cxx ├── clitkBinarizeImageGenericFilter.h ├── clitkBinaryImageToMesh.cxx ├── clitkBinaryImageToMesh.ggo ├── clitkBlurImage.cxx ├── clitkBlurImage.ggo ├── clitkBlurImageGenericFilter.h ├── clitkBlurImageGenericFilter.txx ├── clitkCatImage.cxx ├── clitkCatImage.ggo ├── clitkCatImageGenericFilter.h ├── clitkCatImageGenericFilter.txx ├── clitkChangeDicomTag.cxx ├── clitkChangeDicomTag.ggo ├── clitkChangeImageInfo.cxx ├── clitkChangeImageInfo.ggo ├── clitkChangeImageInfoGenericFilter.cxx ├── clitkChangeImageInfoGenericFilter.h ├── clitkComposeVF.cxx ├── clitkComposeVF.ggo ├── clitkComposeVFGenericFilter.cxx ├── clitkComposeVFGenericFilter.h ├── clitkComposeVFGenericFilter.txx ├── clitkCropImage.cxx ├── clitkCropImage.ggo ├── clitkCropImageGenericFilter.cxx ├── clitkCropImageGenericFilter.h ├── clitkDice.cxx ├── clitkDice.ggo ├── clitkDicom2Image.cxx ├── clitkDicom2Image.ggo ├── clitkDicomInfo.cxx ├── clitkDicomInfo.ggo ├── clitkDicomRTPlan2Gate.cxx ├── clitkDicomRTPlan2Gate.ggo ├── clitkDicomRTStruct2Image.cxx ├── clitkDicomRTStruct2Image.ggo ├── clitkDicomWave2Text.cxx ├── clitkDicomWave2Text.ggo ├── clitkDicomWave2Text.h ├── clitkElastixTransformToMatrix.cxx ├── clitkElastixTransformToMatrix.ggo ├── clitkExtractSlice.cxx ├── clitkExtractSlice.ggo ├── clitkExtractSliceGenericFilter.cxx ├── clitkExtractSliceGenericFilter.h ├── clitkExtractSliceGenericFilter.txx ├── clitkExtrude.cxx ├── clitkExtrude.ggo ├── clitkExtrudeGenericFilter.h ├── clitkExtrudeGenericFilter.txx ├── clitkFlipImage.cxx ├── clitkFlipImage.ggo ├── clitkFlipImageGenericFilter.cxx ├── clitkFlipImageGenericFilter.h ├── clitkFlipImageGenericFilter.txx ├── clitkFooImage.cxx ├── clitkFooImage.ggo ├── clitkFooImageGenericFilter.h ├── clitkFooImageGenericFilter.txx ├── clitkGammaIndex.cxx ├── clitkGammaIndex.ggo ├── clitkGateSimulation2Dicom.cxx ├── clitkGateSimulation2Dicom.ggo ├── clitkGateSimulation2DicomGenericFilter.cxx ├── clitkGateSimulation2DicomGenericFilter.h ├── clitkGateSimulation2DicomGenericFilter.txx ├── clitkHistogramImage.cxx ├── clitkHistogramImage.ggo ├── clitkHistogramImageGenericFilter.cxx ├── clitkHistogramImageGenericFilter.h ├── clitkImage2Dicom.cxx ├── clitkImage2Dicom.ggo ├── clitkImage2DicomDose.cxx ├── clitkImage2DicomDose.ggo ├── clitkImage2DicomDoseGenericFilter.cxx ├── clitkImage2DicomDoseGenericFilter.h ├── clitkImage2DicomDoseGenericFilter.txx ├── clitkImage2DicomGenericFilter.cxx ├── clitkImage2DicomGenericFilter.h ├── clitkImage2DicomGenericFilter.txx ├── clitkImage2DicomRTStruct.cxx ├── clitkImage2DicomRTStruct.ggo ├── clitkImageArithm.cxx ├── clitkImageArithm.ggo ├── clitkImageArithmGenericFilter.cxx ├── clitkImageArithmGenericFilter.h ├── clitkImageArithmGenericFilter.txx ├── clitkImageConvert.cxx ├── clitkImageConvert.ggo ├── clitkImageConvertGenericFilter.cxx ├── clitkImageConvertGenericFilter.h ├── clitkImageCreate.cxx ├── clitkImageCreate.ggo ├── clitkImageGradientMagnitude.cxx ├── clitkImageGradientMagnitude.ggo ├── clitkImageGradientMagnitudeGenericFilter.h ├── clitkImageGradientMagnitudeGenericFilter.txx ├── clitkImageInfo.cxx ├── clitkImageInfo.ggo ├── clitkImageIntensityWindowing.cxx ├── clitkImageIntensityWindowing.ggo ├── clitkImageIntensityWindowingGenericFilter.h ├── clitkImageIntensityWindowingGenericFilter.txx ├── clitkImageLaplacian.cxx ├── clitkImageLaplacian.ggo ├── clitkImageLaplacianGenericFilter.h ├── clitkImageLaplacianGenericFilter.txx ├── clitkImageMoment.cxx ├── clitkImageMoment.ggo ├── clitkImageMomentGenericFilter.cxx ├── clitkImageMomentGenericFilter.h ├── clitkImageMomentGenericFilter.txx ├── clitkImageStatistics.cxx ├── clitkImageStatistics.ggo ├── clitkImageStatisticsGenericFilter.cxx ├── clitkImageStatisticsGenericFilter.h ├── clitkImageStatisticsGenericFilter.txx ├── clitkImageToVectorImage.cxx ├── clitkImageToVectorImage.ggo ├── clitkImageToVectorImageGenericFilter.cxx ├── clitkImageToVectorImageGenericFilter.h ├── clitkImageToVectorImageGenericFilter.txx ├── clitkImageUncertainty.cxx ├── clitkImageUncertainty.ggo ├── clitkImageWarp.ggo ├── clitkInvertVF.cxx ├── clitkInvertVF.ggo ├── clitkInvertVFGenericFilter.cxx ├── clitkInvertVFGenericFilter.h ├── clitkInvertVFGenericFilter.txx ├── clitkJacobianImage.cxx ├── clitkJacobianImage.ggo ├── clitkJacobianImageGenericFilter.cxx ├── clitkJacobianImageGenericFilter.h ├── clitkJacobianImageGenericFilter.txx ├── clitkLabelImageOverlapMeasureGenericFilter.h ├── clitkLabelImageOverlapMeasureGenericFilter.txx ├── clitkMIP.cxx ├── clitkMIP.ggo ├── clitkMIPGenericFilter.cxx ├── clitkMIPGenericFilter.h ├── clitkMaskLandmarks.cxx ├── clitkMaskLandmarks.ggo ├── clitkMaskOfIntegratedIntensity.cxx ├── clitkMaskOfIntegratedIntensity.ggo ├── clitkMaskOfIntegratedIntensityGenericFilter.h ├── clitkMaskOfIntegratedIntensityGenericFilter.txx ├── clitkMatrixInverse.cxx ├── clitkMatrixInverse.ggo ├── clitkMatrixMultiply.cxx ├── clitkMatrixMultiply.ggo ├── clitkMatrixToElastixTransform.cxx ├── clitkMatrixToElastixTransform.ggo ├── clitkMedianImageFilter.cxx ├── clitkMedianImageFilter.ggo ├── clitkMedianImageGenericFilter.cxx ├── clitkMedianImageGenericFilter.h ├── clitkMedianImageGenericFilter.txx ├── clitkMedianTemporalDimension.cxx ├── clitkMedianTemporalDimension.ggo ├── clitkMedianTemporalDimensionGenericFilter.cxx ├── clitkMedianTemporalDimensionGenericFilter.h ├── clitkMedianTemporalDimensionGenericFilter.txx ├── clitkMergeAsciiDoseActor.cxx ├── clitkMergeAsciiDoseActor.ggo ├── clitkMergeRootFiles.cxx ├── clitkMergeRootFiles.ggo ├── clitkMergeSequence.cxx ├── clitkMergeSequence.ggo ├── clitkMergeSequenceGenericFilter.cxx ├── clitkMergeSequenceGenericFilter.h ├── clitkMergeSequenceGenericFilter.txx ├── clitkMeshToBinaryImage.cxx ├── clitkMeshToBinaryImage.ggo ├── clitkMeshViewer.cxx ├── clitkMeshViewer.ggo ├── clitkMinMaxMask.cxx ├── clitkMinMaxMask.ggo ├── clitkMirrorPadImage.cxx ├── clitkMirrorPadImage.ggo ├── clitkMirrorPadImageGenericFilter.cxx ├── clitkMirrorPadImageGenericFilter.h ├── clitkMirrorPadImageGenericFilter.txx ├── clitkNVectorImageTo4DImage.cxx ├── clitkNVectorImageTo4DImage.ggo ├── clitkNVectorImageTo4DImageGenericFilter.cxx ├── clitkNVectorImageTo4DImageGenericFilter.h ├── clitkNVectorImageTo4DImageGenericFilter.txx ├── clitkNormalizeImageFilter.cxx ├── clitkNormalizeImageFilter.ggo ├── clitkNormalizeImageFilterGenericFilter.h ├── clitkNormalizeImageFilterGenericFilter.txx ├── clitkPadImage.cxx ├── clitkPadImage.ggo ├── clitkPadImageGenericFilter.cxx ├── clitkPadImageGenericFilter.h ├── clitkPartitionEnergyWindowDicom.cxx ├── clitkPartitionEnergyWindowDicom.ggo ├── clitkPartitionEnergyWindowDicomGenericFilter.cxx ├── clitkPartitionEnergyWindowDicomGenericFilter.h ├── clitkPartitionEnergyWindowDicomGenericFilter.txx ├── clitkPointRigidRegistration.cxx ├── clitkPointRigidRegistration.ggo ├── clitkProfileImage.cxx ├── clitkProfileImage.ggo ├── clitkProfileImageGenericFilter.cxx ├── clitkProfileImageGenericFilter.h ├── clitkRTStructStatistics.cxx ├── clitkRTStructStatistics.ggo ├── clitkRTStructStatisticsGenericFilter.cxx ├── clitkRTStructStatisticsGenericFilter.h ├── clitkRTStructStatisticsGenericFilter.txx ├── clitkSUVPeak.cxx ├── clitkSUVPeak.ggo ├── clitkSUVPeakGenericFilter.cxx ├── clitkSUVPeakGenericFilter.h ├── clitkSUVPeakGenericFilter.txx ├── clitkScintivolStats.cxx ├── clitkScintivolStats.ggo ├── clitkSetBackground.cxx ├── clitkSetBackground.ggo ├── clitkSetBackgroundGenericFilter.cxx ├── clitkSetBackgroundGenericFilter.h ├── clitkSetBackgroundGenericFilter.txx ├── clitkSpect2Dicom.cxx ├── clitkSpect2Dicom.ggo ├── clitkSpect2DicomGenericFilter.cxx ├── clitkSpect2DicomGenericFilter.h ├── clitkSpect2DicomGenericFilter.txx ├── clitkSplitImage.cxx ├── clitkSplitImage.ggo ├── clitkSplitImageGenericFilter.cxx ├── clitkSplitImageGenericFilter.h ├── clitkSum.cxx ├── clitkSum.ggo ├── clitkSumGenericFilter.h ├── clitkSumGenericFilter.txx ├── clitkTransformLandmarks.cxx ├── clitkTransformLandmarks.ggo ├── clitkUnsharpMask.cxx ├── clitkUnsharpMask.ggo ├── clitkUnsharpMaskGenericFilter.h ├── clitkUnsharpMaskGenericFilter.txx ├── clitkUpdateVRTagDicom.cxx ├── clitkUpdateVRTagDicom.ggo ├── clitkUpdateVRTagDicomGenericFilter.cxx ├── clitkUpdateVRTagDicomGenericFilter.h ├── clitkUpdateVRTagDicomGenericFilter.txx ├── clitkVFConvert.cxx ├── clitkVFConvert.ggo ├── clitkVFConvertGenericFilter.cxx ├── clitkVFConvertGenericFilter.h ├── clitkVFConvertGenericFilter.txx ├── clitkVFInterpolate.cxx ├── clitkVFInterpolate.ggo ├── clitkVFInterpolateGenericFilter.cxx ├── clitkVFInterpolateGenericFilter.h ├── clitkVFInterpolateGenericFilter.txx ├── clitkVFResample.cxx ├── clitkVFResample.ggo ├── clitkVFResampleGenericFilter.cxx ├── clitkVFResampleGenericFilter.h ├── clitkVFResampleGenericFilter.txx ├── clitkVectorArithm.cxx ├── clitkVectorArithm.ggo ├── clitkVectorArithmGenericFilter.cxx ├── clitkVectorArithmGenericFilter.h ├── clitkVectorArithmGenericFilter.txx ├── clitkVectorImageToImage.cxx ├── clitkVectorImageToImage.ggo ├── clitkVectorImageToImageFilter.h ├── clitkVectorImageToImageFilter.txx ├── clitkVectorImageToImageGenericFilter.cxx ├── clitkVectorImageToImageGenericFilter.h ├── clitkVectorImageToImageGenericFilter.txx ├── clitkWarpImage.cxx ├── clitkWarpImage.ggo ├── clitkWarpImageGenericFilter.cxx ├── clitkWarpImageGenericFilter.h ├── clitkWarpImageGenericFilter.txx ├── clitkWriteDicomSeries.cxx ├── clitkWriteDicomSeries.ggo ├── clitkWriteDicomSeriesGenericFilter.cxx ├── clitkWriteDicomSeriesGenericFilter.h ├── clitkWriteDicomSeriesGenericFilter.txx ├── clitkXml2DicomRTStruct.cxx ├── clitkXml2DicomRTStruct.ggo ├── clitkZeroVF.cxx ├── clitkZeroVF.ggo ├── clitkZeroVFGenericFilter.cxx ├── clitkZeroVFGenericFilter.h └── clitkZeroVFGenericFilter.txx ├── travis ├── travis_build_itk.sh ├── travis_build_qt.sh ├── travis_build_vtk.sh └── travis_build_vv.sh ├── utilities ├── CxImage │ ├── CMakeLists.txt │ ├── CxImageDLL │ │ ├── CxImageCrtDll.cpp │ │ ├── CxImageCrtDll.dsp │ │ ├── CxImageCrtDll.rc │ │ ├── CxImageDll.dsw │ │ ├── CxImageMfcDll.clw │ │ ├── CxImageMfcDll.cpp │ │ ├── CxImageMfcDll.h │ │ ├── CxImageMfcDll.rc │ │ ├── StdAfx.cpp │ │ ├── StdAfx.h │ │ ├── StdCrt.h │ │ ├── cximagemfcdll.dsp │ │ ├── resource.h │ │ └── resrc1.h │ ├── cximage.dsp │ ├── cximage.dsw │ ├── license.txt │ ├── tif_xfile.cpp │ ├── xfile.h │ ├── ximabmp.cpp │ ├── ximabmp.h │ ├── ximacfg.h │ ├── ximadef.h │ ├── ximadsp.cpp │ ├── ximaenc.cpp │ ├── ximaexif.cpp │ ├── ximage.cpp │ ├── ximage.h │ ├── ximagif.cpp │ ├── ximagif.h │ ├── ximahist.cpp │ ├── ximaico.cpp │ ├── ximaico.h │ ├── ximainfo.cpp │ ├── ximaint.cpp │ ├── ximaiter.h │ ├── ximajas.cpp │ ├── ximajas.h │ ├── ximajbg.cpp │ ├── ximajbg.h │ ├── ximajpg.cpp │ ├── ximajpg.h │ ├── ximalpha.cpp │ ├── ximalyr.cpp │ ├── ximamng.cpp │ ├── ximamng.h │ ├── ximapal.cpp │ ├── ximapcx.cpp │ ├── ximapcx.h │ ├── ximapng.cpp │ ├── ximapng.h │ ├── ximaraw.cpp │ ├── ximaraw.h │ ├── ximasel.cpp │ ├── ximaska.cpp │ ├── ximaska.h │ ├── ximatga.cpp │ ├── ximatga.h │ ├── ximath.cpp │ ├── ximath.h │ ├── ximatif.cpp │ ├── ximatif.h │ ├── ximatran.cpp │ ├── ximawbmp.cpp │ ├── ximawbmp.h │ ├── ximawmf.cpp │ ├── ximawmf.h │ ├── ximawnd.cpp │ ├── xiofile.h │ ├── xmemfile.cpp │ └── xmemfile.h └── pugixml │ ├── pugiconfig.hpp │ ├── pugixml.cpp │ └── pugixml.hpp ├── vv ├── CMakeLists.txt ├── License.txt ├── QTreePushButton.cxx ├── QTreePushButton.h ├── QVTKOpenGLNativeWidget2.cxx ├── QVTKOpenGLNativeWidget2.h ├── ReadMe.txt ├── icons │ ├── 1b.png │ ├── 2b.png │ ├── 4b.png │ ├── 8b.png │ ├── GPSup.png │ ├── NEgrid.png │ ├── NOgrid.png │ ├── SEgrid.png │ ├── SOgrid.png │ ├── adjustsize.png │ ├── arithm.png │ ├── basket_download.png │ ├── binarize-big.png │ ├── binarize.png │ ├── bullet_info.png │ ├── crop.png │ ├── cross.png │ ├── cursor-uparrow.png │ ├── cut.png │ ├── ducky.bmp │ ├── ducky.ico │ ├── ducky.png │ ├── edit.png │ ├── editgrid.png │ ├── exit.png │ ├── fileopen.png │ ├── filesave.png │ ├── fusion.png │ ├── green-arrow.png │ ├── histogram.png │ ├── identity.png │ ├── invertcolor.png │ ├── lung-overlay.png │ ├── lung.png │ ├── mip.png │ ├── open.png │ ├── plastimatch-banner.png │ ├── plastimatch.png │ ├── player_pause.png │ ├── player_play.png │ ├── player_stop.png │ ├── profile.png │ ├── register.png │ ├── resample.png │ ├── rotateright.png │ ├── splashscreen.PNG │ ├── splashscreen.odp │ ├── splashscreen.ppt │ ├── splashscreen2.png │ ├── standardbutton-apply-16.png │ ├── standardbutton-cancel-16.png │ ├── tool-roi.png │ ├── undo.png │ └── weNeedYou.png ├── make_vv_class.sh ├── qt_ui │ ├── vvDeformationDialog.ui │ ├── vvDicomSeriesSelector.ui │ ├── vvDocumentation.ui │ ├── vvDummyWindow.ui │ ├── vvHelpDialog.ui │ ├── vvInfoPanel.ui │ ├── vvIntensityValueSlider.ui │ ├── vvLabelImageLoaderWidget.ui │ ├── vvLandmarksPanel.ui │ ├── vvLinkPanel.ui │ ├── vvMainWindow.ui │ ├── vvMainWindowVTK7.ui │ ├── vvOverlayPanel.ui │ ├── vvPacsConnection.ui │ ├── vvPacsSettingsDialog.ui │ ├── vvProgressDialog.ui │ ├── vvRegisterForm.ui │ ├── vvResamplerDialog.ui │ ├── vvSegmentationDialog.ui │ ├── vvSegmentationDialogVTK7.ui │ ├── vvStructSelector.ui │ ├── vvSurfaceViewerDialog.ui │ ├── vvSurfaceViewerDialogVTK7.ui │ ├── vvToolBinarize.ui │ ├── vvToolConnectedComponentLabeling.ui │ ├── vvToolConvert.ui │ ├── vvToolCropImage.ui │ ├── vvToolExtractLung.ui │ ├── vvToolExtractPatient.ui │ ├── vvToolFoo.ui │ ├── vvToolHistogram.ui │ ├── vvToolHistogramVTK7.ui │ ├── vvToolImageArithm.ui │ ├── vvToolInputSelectorWidget.ui │ ├── vvToolMIP.ui │ ├── vvToolMedianFilter.ui │ ├── vvToolMorphoMath.ui │ ├── vvToolPlastimatch.ui │ ├── vvToolProfile.ui │ ├── vvToolProfileVTK7.ui │ ├── vvToolROIManager.ui │ ├── vvToolResample.ui │ ├── vvToolRigidReg.ui │ ├── vvToolSegmentation.ui │ ├── vvToolSimpleInputSelectorWidget.ui │ ├── vvToolStructureSetManager.ui │ ├── vvToolTest.ui │ ├── vvToolWidgetBase.ui │ └── vvTools.ui ├── vtkVOXImageWriter.cxx ├── vtkVOXImageWriter.h ├── vv.cxx ├── vvAnimatedGIFWriter.cxx ├── vvAnimatedGIFWriter.h ├── vvBinaryImageOverlayActor.cxx ├── vvBinaryImageOverlayActor.h ├── vvBlendImageActor.cxx ├── vvBlendImageActor.h ├── vvClipPolyData.cxx ├── vvClipPolyData.h ├── vvConfiguration.h.in ├── vvCropDialog.cxx ├── vvCropDialog.h ├── vvDefaultLut.h ├── vvDeformableRegistration.cxx ├── vvDeformableRegistration.h ├── vvDeformationDialog.cxx ├── vvDeformationDialog.h ├── vvDicomServerQueryFactory.cxx ├── vvDicomServerQueryFactory.h ├── vvDocumentation.h ├── vvGlyph2D.cxx ├── vvGlyph2D.h ├── vvGlyphSource.cxx ├── vvGlyphSource.h ├── vvHelpDialog.h ├── vvIcon.rc ├── vvIcons.qrc ├── vvImageContour.cxx ├── vvImageContour.h ├── vvImageWarp.cxx ├── vvImageWarp.h ├── vvInfoPanel.cxx ├── vvInfoPanel.h ├── vvIntensityValueSlider.cxx ├── vvIntensityValueSlider.h ├── vvInteractorStyleNavigator.cxx ├── vvInteractorStyleNavigator.h ├── vvLabelImageLoaderWidget.cxx ├── vvLabelImageLoaderWidget.h ├── vvLandmarks.cxx ├── vvLandmarks.h ├── vvLandmarksGlyph.cxx ├── vvLandmarksGlyph.h ├── vvLandmarksPanel.cxx ├── vvLandmarksPanel.h ├── vvLinkPanel.cxx ├── vvLinkPanel.h ├── vvMainWindow.cxx ├── vvMainWindow.h ├── vvMainWindowBase.cxx ├── vvMainWindowBase.h ├── vvMesh.cxx ├── vvMesh.h ├── vvMeshActor.cxx ├── vvMeshActor.h ├── vvMeshReader.cxx ├── vvMeshReader.h ├── vvMidPosition.cxx ├── vvMidPosition.h ├── vvOSXHelper.h ├── vvOSXHelper.mm ├── vvOverlayPanel.cxx ├── vvOverlayPanel.h ├── vvPacsSettingsDialog.cxx ├── vvPacsSettingsDialog.h ├── vvProgressDialog.cxx ├── vvProgressDialog.h ├── vvQDicomSeriesSelector.cxx ├── vvQDicomSeriesSelector.h ├── vvQPacsConnection.cxx ├── vvQPacsConnection.h ├── vvQProgressDialogITKCommand.cxx ├── vvQProgressDialogITKCommand.h ├── vvROIActor.cxx ├── vvROIActor.h ├── vvReadState.cxx ├── vvReadState.h ├── vvRegisterForm.cxx ├── vvRegisterForm.h ├── vvSaveState.cxx ├── vvSaveState.h ├── vvSegmentationDialog.cxx ├── vvSegmentationDialog.h ├── vvSlicer.cxx ├── vvSlicer.h ├── vvSlicerManager.cxx ├── vvSlicerManager.h ├── vvSlicerManagerCommand.cxx ├── vvSlicerManagerCommand.h ├── vvStructSelector.cxx ├── vvStructSelector.h ├── vvStructureSetActor.cxx ├── vvStructureSetActor.h ├── vvSurfaceViewerDialog.cxx ├── vvSurfaceViewerDialog.h ├── vvTemplateFile.cxx ├── vvTemplateFile.h ├── vvToolBase.cxx ├── vvToolBase.h ├── vvToolBase.txx ├── vvToolBaseBase.cxx ├── vvToolBaseBase.h ├── vvToolBinarize.cxx ├── vvToolBinarize.h ├── vvToolConvert.cxx ├── vvToolConvert.h ├── vvToolCreator.h ├── vvToolCreator.txx ├── vvToolCreatorBase.cxx ├── vvToolCreatorBase.h ├── vvToolCreatorBase.txx ├── vvToolCropImage.cxx ├── vvToolCropImage.h ├── vvToolFoo.cxx ├── vvToolFoo.h ├── vvToolFooWithWidgetBase.cxx ├── vvToolFooWithWidgetBase.h ├── vvToolHistogram.cxx ├── vvToolHistogram.h ├── vvToolHistogramCommand.cxx ├── vvToolHistogramCommand.h ├── vvToolImageArithm.cxx ├── vvToolImageArithm.h ├── vvToolInputSelectorWidget.cxx ├── vvToolInputSelectorWidget.h ├── vvToolMIP.cxx ├── vvToolMIP.h ├── vvToolManager.cxx ├── vvToolManager.h ├── vvToolMedianFilter.cxx ├── vvToolMedianFilter.h ├── vvToolPlastimatch.cxx ├── vvToolPlastimatch.h ├── vvToolProfile.cxx ├── vvToolProfile.h ├── vvToolROIManager.cxx ├── vvToolROIManager.h ├── vvToolResample.cxx ├── vvToolResample.h ├── vvToolRigidReg.cxx ├── vvToolRigidReg.h ├── vvToolSegmentation.cxx ├── vvToolSegmentation.h ├── vvToolSimpleInputSelectorWidget.cxx ├── vvToolSimpleInputSelectorWidget.h ├── vvToolStructureSetManager.cxx ├── vvToolStructureSetManager.h ├── vvToolTest.cxx ├── vvToolTest.h ├── vvToolWidgetBase.cxx ├── vvToolWidgetBase.h ├── vvUtils.cxx ├── vvUtils.h └── write.php ├── vv_entete.png ├── vv_helpscreenshot.png ├── vv_popi.gif ├── vv_static.md └── vv_vv1.1Overlay.png /CTestConfig.cmake: -------------------------------------------------------------------------------- 1 | macro(SET_IF_NOT_SET var val) 2 | if(NOT DEFINED "${var}") 3 | set("${var}" "${val}") 4 | endif(NOT DEFINED "${var}") 5 | endmacro(SET_IF_NOT_SET) 6 | 7 | # Those are set for running a classical make Experimental 8 | SET_IF_NOT_SET(CTEST_DROP_METHOD "http") 9 | SET_IF_NOT_SET(CTEST_DROP_SITE "my.cdash.org") 10 | SET_IF_NOT_SET(CTEST_DROP_LOCATION "/submit.php?project=VV") 11 | SET_IF_NOT_SET(CTEST_DROP_SITE_CDASH TRUE) 12 | SET_IF_NOT_SET(CTEST_PROJECT_NAME "vv_itk4") 13 | -------------------------------------------------------------------------------- /Doxygen/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # 2 | # Build the documentation 3 | # 4 | include(${CMAKE_ROOT}/Modules/Documentation.cmake) 5 | 6 | if(BUILD_DOXYGEN) 7 | 8 | # 9 | # Configure the script and the doxyfile, then add target 10 | # 11 | configure_file(${CLITK_SOURCE_DIR}/Doxygen/doxygen.config.in 12 | ${PROJECT_BINARY_DIR}/Doxygen/doxygen.config) 13 | 14 | configure_file(${CLITK_SOURCE_DIR}/Doxygen/itkdoxygen.pl.in 15 | ${PROJECT_BINARY_DIR}/Doxygen/itkdoxygen.pl) 16 | 17 | add_custom_target(Documentation 18 | COMMAND ${DOXYGEN_EXECUTABLE} ${PROJECT_BINARY_DIR}/Doxygen/doxygen.config 19 | MAIN_DEPENDENCY ${PROJECT_BINARY_DIR}/Doxygen/doxygen.config 20 | DEPENDS ${PROJECT_BINARY_DIR}/Doxygen/itkdoxygen.pl 21 | WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/Doxygen 22 | ) 23 | 24 | endif(BUILD_DOXYGEN) 25 | -------------------------------------------------------------------------------- /Doxygen/DoxygenFooter.html: -------------------------------------------------------------------------------- 1 |
2 | Generated at $datetime for $projectname by doxygen 5 | $doxygenversion written by Dimitri van Heesch, 6 | © 1997-2000
7 | 8 | 9 | -------------------------------------------------------------------------------- /Doxygen/DoxygenHeader.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | $title 5 | 6 | 7 | 8 | 9 | 10 |
11 | Main Page   12 | Groups   13 | Namespace List   14 | Class Hierarchy   15 | Alphabetical List   16 | Compound List   17 | File List   18 | Namespace Members   19 | Compound Members   20 | File Members   21 | Concepts
22 | 23 | 24 | -------------------------------------------------------------------------------- /Doxygen/MainPage.dox: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | * \mainpage Command Line Insight Toolkit 4 | * 5 | * \section homepage Home Page 6 | * 7 | * http://vv.creatis.insa-lyon.fr/ 8 | * 9 | * \section howto How to use this documentation 10 | * 11 | */ 12 | 13 | -------------------------------------------------------------------------------- /Doxygen/itkdoxygen.pl.in: -------------------------------------------------------------------------------- 1 | # for vxl files run the vxl_doxy.pl script, and use itkgroup.pl for all other files 2 | if ( $ARGV[0] =~ /(vxl|vcl|vnl)/) 3 | { 4 | system ("perl @ITK_SOURCE_DIR@/Utilities/Doxygen/vxl_doxy.pl $ARGV[0]"); 5 | } 6 | else 7 | { 8 | system ("perl @ITK_SOURCE_DIR@/Utilities/Doxygen/itkgroup.pl $ARGV[0]"); 9 | } 10 | -------------------------------------------------------------------------------- /Licence_CeCILL-B_V1-en.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/Licence_CeCILL-B_V1-en.txt -------------------------------------------------------------------------------- /bw-output/build-wrapper-dump.json: -------------------------------------------------------------------------------- 1 | # (C) SonarSource SA, 2014-2017, info@sonarsource.com 2 | # All SONARSOURCE programs and content are copyright protected. 3 | # SONARSOURCE and SONARQUBE are trademarks of SonarSource SA. All rights are expressly reserved. 4 | # 5 | # This file is designed exclusively for use with the SONARSOURCE C / C++ / Objective-C Plugin. 6 | # It may not be used in connection with any other software. 7 | # Any other use is prohibited by law and may be grounds for immediate termination of your License. 8 | { 9 | "version":0, 10 | "captures":[ 11 | ]} 12 | -------------------------------------------------------------------------------- /cluster_tools/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | if(CLITK_BUILD_TOOLS) 2 | #========================================================= 3 | # Install scripts when running make install 4 | set(SCRIPTS 5 | gate_job_cluster.job 6 | gate_job_ccin2p3.job 7 | gate_make_merge_release.sh 8 | gate_make_release.sh 9 | gate_power_merge.sh 10 | gate_run_submit_cluster.sh 11 | gate_upload_release.sh 12 | mergeDosePerEnergyFile.sh 13 | mergeDoseByRegions.sh 14 | mergeStatFile.py 15 | mergeStatFile.sh 16 | gate_run_submit_cluster_nomove.sh 17 | gate_job_cluster_nomove.job 18 | check_tmp_cluster.sh 19 | computeEnlapsedTime.py 20 | ) 21 | 22 | install(FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE) 23 | 24 | endif(CLITK_BUILD_TOOLS) 25 | -------------------------------------------------------------------------------- /cluster_tools/check_tmp_cluster.sh: -------------------------------------------------------------------------------- 1 | #! /bin/bash 2 | 3 | for i in 1 $(seq 4 20) $(seq 30 36) 4 | do 5 | echo 6 | echo "Files on host linux${i}.dg.creatis.insa-lyon.fr " 7 | #ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "find /tmp -user $1 -exec rm -fr {} \; " 8 | ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "find /tmp -user $1 2>/dev/null" 9 | #ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "rm -fr /tmp/tmp.*/core* /tmp/tmp.*/mac /tmp/tmp.*/data /tmp/tmp.*/output/*root" 10 | #ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "mv /tmp/tmp.* data/gate/hybrid_analog_mc/liver/hybrid_emlivermore/rr/rayleigh/run.O6VN" 11 | done 12 | 13 | -------------------------------------------------------------------------------- /cluster_tools/gate_merge_merges.sh: -------------------------------------------------------------------------------- 1 | mkdir run.merge 2 | for i in $(ls -d results.????) 3 | do 4 | ln -s ../$i run.merge/output_${i} 5 | done 6 | gate_power_merge.sh run.merge 7 | 8 | -------------------------------------------------------------------------------- /cluster_tools/gate_upload_release.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | . gate_common.sh 4 | 5 | releasearchive="${1:?"provide path to release archive"}" 6 | test -f ${releasearchive} || error "file ${releasearchive} doesn't exist" 7 | releasename="${prefix}$(basename "${releasearchive}")" 8 | 9 | ensure_proxy || error "no valid proxy" 10 | 11 | echo "releasearchive=${releasearchive}" 12 | echo "releasename=${releasename}" 13 | echo "lfnrelease=${lfnrelease}" 14 | check_user || exit 2 15 | 16 | upload_file "${releasearchive}" "${lfnrelease}${releasename}" && echo "success" || echo "failed" 17 | -------------------------------------------------------------------------------- /cluster_tools/mergeDosePerEnergyFile.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -u 3 | 4 | function usage { 5 | echo "$0 -i -j -o " 6 | exit 1 7 | } 8 | 9 | if [ $# != 6 ] 10 | then 11 | usage 12 | fi 13 | 14 | IN1=$2 15 | IN2=$4 16 | RESULT=$6 17 | 18 | test -f ${IN1} && test -f ${IN2} || usage 19 | 20 | TMP="$(mktemp)" 21 | echo "merging dose file" 22 | for PARAM in `awk '$1 == "#" {print $3}' ${IN1}` 23 | do 24 | echo "merging ${PARAM}" 25 | V1=`awk -v P=${PARAM} '$3 == P {print $4}' ${IN1} ` 26 | V2=`awk -v P=${PARAM} '$3 == P {print $4}' ${IN2} ` 27 | V1=`echo ${V1} | sed -e 's/[eE]+*/\*10\^/'` 28 | V2=`echo ${V2} | sed -e 's/[eE]+*/\*10\^/'` 29 | R=`echo "scale=30; ${V1} + ${V2}" | bc -l` 30 | test -z "${R}" && continue 31 | echo "# energydose ${PARAM} ${R}" >> ${TMP} 32 | done 33 | mv -f ${TMP} ${RESULT} 34 | -------------------------------------------------------------------------------- /cluster_tools/mergeStatFile.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -u 3 | 4 | function usage { 5 | echo "$0 -i -j -o " 6 | exit 1 7 | } 8 | 9 | if [ $# != 6 ] 10 | then 11 | usage 12 | fi 13 | 14 | IN1=$2 15 | IN2=$4 16 | RESULT=$6 17 | 18 | 19 | test -f ${IN1} && test -f ${IN2} || usage 20 | 21 | TMP="$(mktemp)" 22 | echo "merging stat file" 23 | for PARAM in `awk '$1 == "#" {print $2}' ${IN1}` 24 | do 25 | echo "merging ${PARAM}" 26 | V1=`awk -v P=${PARAM} '$2 == P {print $4}' ${IN1} ` 27 | V2=`awk -v P=${PARAM} '$2 == P {print $4}' ${IN2} ` 28 | R=`echo "${V1} + ${V2}" | bc` 29 | test -z "${R}" && continue 30 | echo "# ${PARAM} = ${R}" >> ${TMP} 31 | done 32 | mv -f ${TMP} ${RESULT} 33 | -------------------------------------------------------------------------------- /common/clitkConfiguration.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef clitk_configuration_h 20 | #define clitk_configuration_h 21 | //This file is interpreted by cmake, to define macros based on the cmake configuration options 22 | // 23 | 24 | #cmakedefine01 CLITK_EXPERIMENTAL 25 | #cmakedefine01 CLITK_MEMORY_INFO 26 | #cmakedefine01 CLITK_PRIVATE_FEATURES 27 | #cmakedefine01 CLITK_USE_SYSTEM_GDCM 28 | #cmakedefine01 CLITK_USE_PACS_CONNECTION 29 | 30 | // Global environment variables 31 | #define OS_NAME "@CMAKE_SYSTEM@" 32 | #define ARCHITECTURE "@CMAKE_SYSTEM_PROCESSOR@" 33 | 34 | #endif 35 | -------------------------------------------------------------------------------- /common/clitkDicomRTDoseIOFactory.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkDicomRTDoseIOFactory_cxx 19 | #define clitkDicomRTDoseIOFactory_cxx 20 | 21 | #include "clitkDicomRTDoseIOFactory.h" 22 | 23 | //==================================================================== 24 | clitk::DicomRTDoseIOFactory::DicomRTDoseIOFactory() 25 | { 26 | this->RegisterOverride("itkImageIOBase", 27 | "DicomRTDoseIO", 28 | "Dicom RT dose IO", 29 | 1, 30 | itk::CreateObjectFunction::New()); 31 | } 32 | 33 | 34 | #endif /* end #define clitkDicomRTDoseIOFactory_cxx */ 35 | 36 | -------------------------------------------------------------------------------- /common/clitkEsrfHstImageIO.cxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstImageIO.cxx -------------------------------------------------------------------------------- /common/clitkEsrfHstImageIO.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstImageIO.h -------------------------------------------------------------------------------- /common/clitkEsrfHstImageIOFactory.cxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstImageIOFactory.cxx -------------------------------------------------------------------------------- /common/clitkEsrfHstImageIOFactory.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstImageIOFactory.h -------------------------------------------------------------------------------- /common/clitkEsrfHstXMLFileReader.cxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstXMLFileReader.cxx -------------------------------------------------------------------------------- /common/clitkEsrfHstXMLFileReader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/common/clitkEsrfHstXMLFileReader.h -------------------------------------------------------------------------------- /common/clitkGateAsciiImageIOFactory.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #include "clitkGateAsciiImageIOFactory.h" 20 | 21 | //==================================================================== 22 | clitk::GateAsciiImageIOFactory::GateAsciiImageIOFactory() 23 | { 24 | this->RegisterOverride("itkImageIOBase", 25 | "GateAsciiImageIO", 26 | "GateAscii Image IO", 27 | 1, 28 | itk::CreateObjectFunction::New()); 29 | } 30 | -------------------------------------------------------------------------------- /common/clitkIO.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKIO_H 19 | #define CLITKIO_H 20 | /** 21 | ------------------------------------------------------------------- 22 | * @file clitkIO.h 23 | * @author David Sarrut 24 | * @date 17 May 2006 07:57:56 25 | 26 | * @brief 27 | 28 | -------------------------------------------------------------------*/ 29 | 30 | //-------------------------------------------------------------------- 31 | // CLITK_INIT 32 | #define CLITK_INIT clitk::RegisterClitkFactories(); 33 | 34 | namespace clitk { 35 | void RegisterClitkFactories(); 36 | } 37 | 38 | #endif /* end #define CLITKIO_H */ 39 | 40 | -------------------------------------------------------------------------------- /common/clitkMatrix.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef clitkMatrix_h 20 | #define clitkMatrix_h 21 | 22 | #include 23 | #define VTK_EXCLUDE_STRSTREAM_HEADERS 24 | #include 25 | #include 26 | 27 | //-------------------------------------------------------------------- 28 | namespace clitk { 29 | std::string 30 | Get4x4MatrixDoubleAsString(vtkMatrix4x4 *matrix, 31 | const int precision=3); 32 | 33 | std::string 34 | Get4x4MatrixDoubleAsString(itk::Matrix m, 35 | const int precision=3); 36 | } 37 | //------------------------------------------------------------------- 38 | 39 | #endif 40 | -------------------------------------------------------------------------------- /common/clitkMemoryUsage.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef CLITKMEMORYUSAGE_H 20 | #define CLITKMEMORYUSAGE_H 21 | 22 | // clitk include 23 | #include "clitkConfiguration.h" 24 | 25 | // statgrab include 26 | #if CLITK_MEMORY_INFO == 1 27 | #include 28 | #endif 29 | 30 | //-------------------------------------------------------------------- 31 | namespace clitk { 32 | 33 | void PrintMemory(bool verbose=true, std::string s="") ; 34 | double GetMemoryUsageInMb() ; 35 | 36 | } // end namespace 37 | //-------------------------------------------------------------------- 38 | 39 | #endif /* end #define CLITKMEMORYUSAGE_H */ 40 | 41 | -------------------------------------------------------------------------------- /common/clitkPortability.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKPORTABILITY_H 19 | #define CLITKPORTABILITY_H 20 | #if defined(_WIN32) 21 | # define _USE_MATH_DEFINES //Before math.h include (i.e. cmath) 22 | #endif 23 | #include 24 | 25 | template 26 | int IsNormal(const T val) { 27 | #if defined(_MSC_VER) 28 | return _finite(val); 29 | #else 30 | return std::isnormal(val); 31 | #endif 32 | } 33 | 34 | #if defined(_MSC_VER) 35 | # include 36 | # define mkstemp(x) _mktemp_s(x, sizeof(x)) 37 | #endif 38 | 39 | #endif /* end #define CLITKPORTABILITY_H */ 40 | -------------------------------------------------------------------------------- /itk/clitkPasteImageFilter.hxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | * 3 | * COPY OF itkPasteImageFilter to remove VerifyInputInformation 4 | * 5 | *=========================================================================*/ 6 | 7 | #ifndef __clitkPasteImageFilter_hxx 8 | #define __clitkPasteImageFilter_hxx 9 | 10 | #include "itkPasteImageFilter.h" 11 | 12 | namespace clitk 13 | { 14 | template< class TInputImage, class TSourceImage, class TOutputImage > 15 | PasteImageFilter< TInputImage, TSourceImage, TOutputImage > 16 | ::PasteImageFilter() 17 | { 18 | //this->ProcessObject::SetNumberOfRequiredInputs(2); 19 | 20 | this->InPlaceOff(); 21 | this->m_DestinationIndex.Fill(0); 22 | } 23 | 24 | } // end namespace clitk 25 | 26 | #endif 27 | -------------------------------------------------------------------------------- /itk/itkBSplineInterpolateImageFunctionWithLUT.h.original: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/itk/itkBSplineInterpolateImageFunctionWithLUT.h.original -------------------------------------------------------------------------------- /itk/itkBSplineWeightsCalculator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/itk/itkBSplineWeightsCalculator.h -------------------------------------------------------------------------------- /itk/itkBSplineWeightsCalculator.txx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/itk/itkBSplineWeightsCalculator.txx -------------------------------------------------------------------------------- /license-header.txt: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ==========================================================================*/ 18 | -------------------------------------------------------------------------------- /make_meta.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #This script creates the files necessary for developement: vim tags files, doxygen documentation, ... 3 | ROOT_DIR="$(pwd)" 4 | echo $ROOT_DIR 5 | #ROOT_DIR=${HOME}/workspace/vv 6 | cd "${ROOT_DIR}" 7 | [ "$1" = "--full" ] && doxygen clitk.doxygen& 8 | 9 | find "$(pwd)" -type d | grep -v "^\.$" | while read i 10 | do 11 | cd "$i" && [ -n "$(find . -maxdepth 1 -name '*.c??')" ] && 12 | { 13 | rm .vimrc 14 | ln -s "${ROOT_DIR}/.vimrc" . 15 | ctags -R --languages=c,c++ --exclude=build --langmap=c++:.c++.cc.cp.cpp.cxx.h.h++.hh.hp.hpp.hxx.C.H.txx --exclude=doc --exclude=tests_jef "${ROOT_DIR}" & 16 | } 17 | done 18 | wait 19 | echo "done!" 20 | -------------------------------------------------------------------------------- /make_new_tool.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ $# -ne 1 ] 4 | then 5 | echo "Usage: `basename $0` ToolName" 6 | exit 1 7 | fi 8 | 9 | find tools -name "clitkFooImage*" | 10 | while read i 11 | do 12 | cp $i ${i/FooImage/$1} 13 | if test "$(uname)" = "Darwin" 14 | then 15 | echo $(pwd) 16 | echo sed -i "" "s/FooImage/$1/g" ${i/FooImage/$1} 17 | sed -i "" "s/FooImage/$1/g" ${i/FooImage/$1} 18 | else 19 | sed -i "s/FooImage/$1/ig" ${i/FooImage/$1} 20 | fi 21 | done 22 | echo "Done!" 23 | echo "Don't forget to add your new tool to the various CMakeLists.txt files." 24 | -------------------------------------------------------------------------------- /registration/AffineReg.txt: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================*/ 18 | threads=3 19 | reference=0 20 | target=0 21 | matrix=/home/bharth/bin/writematrix.txt 22 | interp=1 23 | transform=2 24 | transX=0.0 25 | transY=0.0 26 | transZ=0.0 27 | metric=1 28 | samples=1 29 | intThreshold=0.0 30 | stdDev=0.4 31 | blur=0.0 32 | optimizer=1 33 | step=2.0 34 | relax=0.7 35 | valueTol=0.01 36 | stepTol=0.1 37 | gradTol=1e-5 38 | lineAcc=0.9 39 | convFactor=1e+12 40 | maxIt=500 41 | maxLineIt=50 42 | maxEval=500 43 | maxCorr=5 44 | selectBound=0 45 | rWeight=50.0 46 | tWeight=1.0 47 | levels=2 48 | inc=1.2 49 | dec=4 50 | -------------------------------------------------------------------------------- /registration/clitkAffineRegistration.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk include 20 | #include "clitkIO.h" 21 | #include "clitkAffineRegistration_ggo.h" 22 | #include "clitkAffineRegistrationGenericFilter.h" 23 | 24 | int main( int argc, char *argv[] ) 25 | { 26 | //init command line and check options 27 | GGO(clitkAffineRegistration, args_info); 28 | CLITK_INIT; 29 | 30 | //=========================================================================== 31 | //Set all the options passed through the commandline 32 | typedef clitk::AffineRegistrationGenericFilter FilterType; 33 | FilterType::Pointer genericFilter = FilterType::New(); 34 | genericFilter->SetArgsInfo(args_info); 35 | genericFilter->Update(); 36 | 37 | return 1; 38 | } 39 | -------------------------------------------------------------------------------- /registration/clitkConvertBSplineDeformableTransformToVF.ggo: -------------------------------------------------------------------------------- 1 | #File clitkConvertBSplineDeformableTransformToVF.ggo 2 | package "clitkConvertBSplineDeformableTransformToVF" 3 | version "1.0" 4 | purpose "Convert a BSpline transform to a DVF with given properties" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | 10 | section "IO" 11 | option "input" i "Input BLUT-coefficient image filename" string yes 12 | option "output" o "Output image filename" string yes 13 | 14 | 15 | section "Output Image Properties" 16 | option "like" - "Make output like this image" string no 17 | option "origin" - "Origin for the output image" double multiple no default="0.0" 18 | option "size" - "Size for the output image" int multiple no default="100" 19 | option "spacing" - "Spacing for the output image" double multiple no default="1.0" 20 | 21 | 22 | section "Transform" 23 | option "type" t "Type (0: itk bspline; 1: BLUT)" int no default="0" 24 | option "order" - "1: Spline order" int multiple no 25 | option "mask" - "1: Mask image filename" string no 26 | option "shape" - "1: Transform shape: 0=egg, 1=diamond" int no default="0" 27 | -------------------------------------------------------------------------------- /registration/clitkMatrixTransformToVF.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMatrixTransformToVF.ggo 2 | package "clitkMatrixTransformToVF" 3 | version "1.0" 4 | purpose "Convert a matrix to a DVF with given properties" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "matrix" i "Input matrix filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "dim" d "Dimension" int no default="3" 12 | 13 | section "Output Image Properties" 14 | option "like" - "Make output like this image" string no 15 | option "origin" - "Origin for the output image" double multiple no default="0.0" 16 | option "size" - "Size for the output image" int multiple no default="100" 17 | option "spacing" - "Spacing for the output image" double multiple no default="1.0" 18 | 19 | -------------------------------------------------------------------------------- /registration/clitkNormalizedCorrelationImageToImageMetric.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef _clitkNormalizedCorrelationImageToImageMetric_h 20 | #define _clitkNormalizedCorrelationImageToImageMetric_h 21 | 22 | // First make sure that the configuration is available. 23 | // This line can be removed once the optimized versions 24 | // gets integrated into the main directories. 25 | #include "itkConfigure.h" 26 | #include "clitkOptNormalizedCorrelationImageToImageMetric.h" 27 | 28 | #endif // _clitkNormalizedCorrelationImageToImageMetric.txx 29 | 30 | 31 | -------------------------------------------------------------------------------- /registration/clitkNormalizedCorrelationImageToImageMetric.txx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef _clitkNormalizedCorrelationImageToImageMetric_txx 20 | #define _clitkNormalizedCorrelationImageToImageMetric_txx 21 | 22 | // First make sure that the configuration is available. 23 | // This line can be removed once the optimized versions 24 | // gets integrated into the main directories. 25 | #include "itkConfigure.h" 26 | 27 | #include "clitkOptNormalizedCorrelationImageToImageMetric.txx" 28 | #endif // _clitkNormalizedCorrelationImageToImageMetric.txx 29 | -------------------------------------------------------------------------------- /registration/clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_h 20 | #define _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_h 21 | 22 | // First make sure that the configuration is available. 23 | // This line can be removed once the optimized versions 24 | // gets integrated into the main directories. 25 | #include "itkConfigure.h" 26 | 27 | #include "clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h" 28 | #endif // _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx 29 | 30 | 31 | -------------------------------------------------------------------------------- /registration/clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_txx 20 | #define _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_txx 21 | 22 | // First make sure that the configuration is available. 23 | // This line can be removed once the optimized versions 24 | // gets integrated into the main directories. 25 | #include "itkConfigure.h" 26 | #include "clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx" 27 | #endif // _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx 28 | -------------------------------------------------------------------------------- /segmentation/clitkConnectedComponentLabeling.ggo: -------------------------------------------------------------------------------- 1 | #File clitkConnectedComponentLabeling.ggo 2 | package "clitkConnectedComponentLabeling" 3 | version "1.0" 4 | purpose "Basic segmentation : connected component labeling " 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | option "verboseOption" - "Display options values" flag off 10 | 11 | section "I/O" 12 | 13 | option "input" i "Input image filename" string yes 14 | option "inputBG" - "Input Background" int default="0" no 15 | option "output" o "Output filename" string yes 16 | 17 | section "Labelize" 18 | 19 | option "minSize" - "Minimum component size in voxels" int no default="100" 20 | option "full" - "Full connecticity" flag off 21 | -------------------------------------------------------------------------------- /segmentation/clitkExtractBones.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkExtractBones_ggo.h" 21 | #include "clitkExtractBonesGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkExtractBones, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::ExtractBonesGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | CLITK_TRY_CATCH_EXIT(filter->Update()); 38 | 39 | return EXIT_SUCCESS; 40 | } // This is the end, my friend 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /segmentation/clitkExtractLung.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkExtractLung_ggo.h" 21 | #include "clitkExtractLungGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | // Init command line 27 | GGO(clitkExtractLung, args_info); 28 | CLITK_INIT; 29 | 30 | // Filter 31 | typedef clitk::ExtractLungGenericFilter FilterType; 32 | FilterType::Pointer filter = FilterType::New(); 33 | 34 | filter->SetArgsInfo(args_info); 35 | 36 | CLITK_TRY_CATCH_EXIT(filter->Update()); 37 | 38 | return EXIT_SUCCESS; 39 | } // This is the end, my friend 40 | //-------------------------------------------------------------------- 41 | -------------------------------------------------------------------------------- /segmentation/clitkMorphoMath.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMorphoMath.ggo 2 | #Author: Jef Vandemeulebroucke 3 | #Date : Tue 28 April 2009 16.35 4 | 5 | package "clitk" 6 | version "Perform standard morphological operations" 7 | 8 | option "config" - "Config file" string no 9 | option "verbose" v "Verbose" flag off 10 | option "imagetypes" - "Display allowed image types" flag off 11 | 12 | section "Input" 13 | 14 | option "input" i "Input image filename" string yes 15 | option "output" o "Output image filename" string yes 16 | 17 | 18 | section "Processing Parameters" 19 | 20 | option "type" t "0=Erode, 1=Dilate, 2=Close (erode(dilate(x))), 3=Open (dilate(erode(x))), 4=CondErode, 5=CondDilate" int no default="0" 21 | option "fg" - "Foreground value" float no default="1" 22 | option "bg" - "Background value (0,1,3: filling value)" float no default="0" 23 | option "bound" b "0-1: Set borders to foreground/ 2:safe borders " flag off 24 | option "radius" r "Use binary ball element with given radius" int no multiple default="1" 25 | option "radiusInMM" m "Use binary ball element with given radius in mm (rounded to nearest voxel value), you can give one radius by dimension" double no multiple default="1" 26 | 27 | option "extend" - "Extend the image size according to radius" flag off 28 | 29 | -------------------------------------------------------------------------------- /segmentation/clitkSliceBySliceRelativePositionFilter_uchar.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ======================================================================-====*/ 18 | 19 | #ifndef CLITKSLICEBYSLICERELATIVEPOSITIONFILTER_UCHARH 20 | #define CLITKSLICEBYSLICERELATIVEPOSITIONFILTER_UCHARH 21 | 22 | // clitk 23 | #include "clitkSliceBySliceRelativePositionFilter.h" 24 | 25 | typedef unsigned char PixelType_uchar; 26 | typedef itk::Image ImageType_uchar; 27 | template class clitk::SliceBySliceRelativePositionFilter; 28 | 29 | #endif 30 | -------------------------------------------------------------------------------- /segmentation/clitkTestArtery.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ======================================================================-====*/ 18 | 19 | // clitk 20 | #include "clitkCommon.h" 21 | 22 | //-------------------------------------------------------------------- 23 | int main(int argc, char * argv[]) 24 | { 25 | // Typedef 26 | typedef uchar MaskImagePixelType; 27 | typedef short ImagePixelType; 28 | typedef itk::Image ImageType; 29 | typedef itk::Image MaskImageType; 30 | 31 | // Input 32 | 33 | 34 | 35 | 36 | 37 | return EXIT_SUCCESS; 38 | } // This is the end, my friend 39 | //-------------------------------------------------------------------- 40 | -------------------------------------------------------------------------------- /segmentation/clitkTestFilter.ggo: -------------------------------------------------------------------------------- 1 | #File clitkTestFilter.ggo 2 | package "clitkTestFilter" 3 | version "1.0" 4 | purpose "Test a filter" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input1" i "Input 1 image filename" string no 10 | option "input2" j "Input 2 image filename" string no 11 | option "input3" k "Input 3 image filename" string no 12 | option "output" o "Output image filename" string no 13 | 14 | option "angle1" a "First angle (degree)" float default = "0" no 15 | option "angle2" b "Second angle (degree)" float default = "0" no 16 | 17 | -------------------------------------------------------------------------------- /segmentation/tree.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/segmentation/tree.pdf -------------------------------------------------------------------------------- /sonar-project.properties: -------------------------------------------------------------------------------- 1 | sonar.projectKey=vv 2 | sonar.projectName=vv 3 | sonar.projectVersion=1.4 4 | 5 | # ===================================================== 6 | # Meta-data for the project 7 | # ===================================================== 8 | 9 | sonar.links.homepage=https://github.com/open-vv/vv 10 | sonar.links.ci=https://travis-ci.org/open-vv/vv 11 | sonar.links.scm=https://github.com/open-vv/vv 12 | sonar.links.issue=https://github.com/open-vv/vv/issues 13 | sonar.host.url=https://sonarcloud.io 14 | 15 | 16 | # ===================================================== 17 | # Properties that will be shared amongst all modules 18 | # ===================================================== 19 | 20 | # SQ standard properties 21 | sonar.sources=. 22 | 23 | # Properties specific to the C/C++ analyzer: 24 | sonar.cfamily.build-wrapper-output=bw-output 25 | sonar.cfamily.gcov.reportsPath=. -------------------------------------------------------------------------------- /tests/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_policy(SET CMP0005 NEW) 2 | #========================================================= 3 | #========================================================= 4 | # Data tests path 5 | find_path(CLITK_TEST_DATA_PATH Lung3D.mhd) 6 | if(NOT ${CLITK_TEST_DATA_PATH} MATCHES "NOTFOUND$") 7 | set(CLITK_TEST_DATA_PATH "${CLITK_TEST_DATA_PATH}/") 8 | endif() 9 | add_definitions(-DCLITK_TEST_DATA_PATH="${CLITK_TEST_DATA_PATH}") 10 | #========================================================= 11 | #========================================================= 12 | set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/tests/bin) 13 | set(BUILDNAME ${CMAKE_SYSTEM_NAME}${CMAKE_OSX_ARCHITECTURES} CACHE INTERNAL DOCSTRING) 14 | #========================================================= 15 | #========================================================= 16 | # Enabled options to test 17 | if(CLITK_BUILD_TOOLS) 18 | add_subdirectory(tools) 19 | endif() 20 | #if(CLITK_BUILD_VV) 21 | # add_subdirectory(vv) 22 | #endif() 23 | # if(CLITK_BUILD_SEGMENTATION) 24 | # add_subdirectory(segmentation) 25 | # endif() 26 | # 27 | # if(CLITK_BUILD_REGISTATION) 28 | # add_subdirectory(registration) 29 | # endif() 30 | #add_subdirectory(common) 31 | #========================================================= 32 | 33 | -------------------------------------------------------------------------------- /tools/clitk4DImageToNVectorImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitk4DImageToNVectorImage.ggo 2 | package "clitk4DImageToNVectorImage" 3 | version "1.0" 4 | purpose "Convert the 4th dimension of a 4D Image into a VectorPixel 3D Image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | 12 | -------------------------------------------------------------------------------- /tools/clitkAffineTransformGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkAffineTransformGenericFilter_cxx 19 | #define clitkAffineTransformGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkAffineTransformGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkAffineTransformGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | 38 | } //end clitk 39 | 40 | #endif //#define clitkAffineTransformGenericFilter_cxx 41 | -------------------------------------------------------------------------------- /tools/clitkAnisotropicDiffusion.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkAnisotropicDiffusion_ggo.h" 21 | #include "clitkAnisotropicDiffusionGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkAnisotropicDiffusion, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::AnisotropicDiffusionGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | CLITK_TRY_CATCH_EXIT(filter->Update()); 38 | 39 | return EXIT_SUCCESS; 40 | } // This is the end, my friend 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /tools/clitkAnisotropicDiffusion.ggo: -------------------------------------------------------------------------------- 1 | #File clitkAnisotropicDiffusion.ggo 2 | package "clitkAnisotropicDiffusion" 3 | version "1.0" 4 | purpose "Performs gradient or curvature anisotropic diffusion filtering" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output image filename" string yes 12 | option "type" - "Type of filtering" values="Gradient","Curvature" enum no default="Gradient" 13 | option "niterations" n "Number of iterations" int no default="5" 14 | option "conductance" c "Conductance" double no default="3" 15 | option "timestep" t "Time step" double no default="0.01" 16 | -------------------------------------------------------------------------------- /tools/clitkAutoCrop.ggo: -------------------------------------------------------------------------------- 1 | #File clitkAutoCrop.ggo 2 | package "clitkAutoCrop" 3 | version "1.0" 4 | purpose "Crop a mask image" 5 | 6 | option "config" - "Config file" string no 7 | option "imagetypes" - "Display allowed image types" flag off 8 | option "verbose" v "Verbose" flag off 9 | option "verboseOption" - "Display options values" flag off 10 | option "verboseWarningOff" - "Do not display warning" flag off 11 | 12 | section "I/O" 13 | 14 | option "input" i "Input image filename" string yes 15 | option "output" o "Output image filename" string yes 16 | 17 | option "BG" - "Background value in input." double default="0" no 18 | -------------------------------------------------------------------------------- /tools/clitkBinarizeImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkBinarizeImage_ggo.h" 21 | #include "clitkBinarizeImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkBinarizeImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::BinarizeImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | CLITK_TRY_CATCH_EXIT(filter->Update()); 38 | 39 | return EXIT_SUCCESS; 40 | } // This is the end, my friend 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /tools/clitkBinarizeImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkBinarizeImage.ggo 2 | package "clitkBinarizeImage" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output image filename" string yes 12 | option "lower" l "Lower intensity (default=min), fg is greater than this value" double no 13 | option "upper" u "Upper intensity (default=max), fg is lower than this value" double no 14 | 15 | option "fg" - "Foreground (FG) or 'inside' value" double no default="1" 16 | option "bg" - "Background (BG) or 'ouside' value" double no default="0" 17 | option "mode" - "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both" no default="both" 18 | 19 | 20 | option "percentage" p "Percentage of total pixels values (in %)" double no 21 | -------------------------------------------------------------------------------- /tools/clitkBinaryImageToMesh.ggo: -------------------------------------------------------------------------------- 1 | #File clitkBinaryImageToMesh.ggo 2 | package "clitkBinaryImageToMesh" 3 | version "1.0" 4 | purpose "Converts a binary image into a mesh object." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image" string yes 10 | option "output" o "Output mesh file prefix (if empty, use input file's base name as prefix; if a directoy, output to it using input file's base name as prefix; otherwise, use given name as prefix ; if names ends with .vtk the output is written as a vtkPolyData file" string no 11 | option "decimate" d "Decimate mesh (value in [0-1] is the target reduction percentage, outside this range means NO decimation)" double no default="-1" 12 | option "view" - "View result" flag off 13 | -------------------------------------------------------------------------------- /tools/clitkBlurImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkBlurImage.ggo 2 | package "clitkBlurImage" 3 | version "1.0" 4 | purpose "Filter the input image with a Gaussian" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "output" o "Output image filename" string required 13 | 14 | option "variance" - "value of the gaussian variance (multiple values=number of image dimension) in mm² - default=1.0" double optional multiple 15 | -------------------------------------------------------------------------------- /tools/clitkCatImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkCatImage_ggo.h" 21 | #include "clitkCatImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkCatImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::CatImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | CLITK_TRY_CATCH_EXIT(filter->Update()); 37 | 38 | 39 | return EXIT_SUCCESS; 40 | }// end main 41 | 42 | //-------------------------------------------------------------------- 43 | -------------------------------------------------------------------------------- /tools/clitkCatImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkCatImage.ggo 2 | package "clitkCatImage" 3 | version "1.0" 4 | purpose "Concatenate two images along chosen direction" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input1" i "First input image filename" string required 12 | option "input2" j "Second input image filename" string required 13 | option "output" o "Output image filename" string required 14 | option "dimension" d "Dimension on which to concatenate" int required 15 | -------------------------------------------------------------------------------- /tools/clitkChangeDicomTag.ggo: -------------------------------------------------------------------------------- 1 | #File clitkChangeDicomTag.ggo 2 | package "clitkChangeDicomTag" 3 | version "1.0" 4 | description "Change Dicom tag -k value to -t" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input dicom file" string yes 10 | option "output" o "Output dicom file" string yes 11 | option "key" k "Keys of tags to modify" string no multiple default="0008|103e" 12 | option "tag" t "Tags values" string no multiple default="MIDPOSITION" 13 | -------------------------------------------------------------------------------- /tools/clitkChangeImageInfo.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkChangeImageInfo_ggo.h" 21 | #include "clitkChangeImageInfoGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | // Init command line 27 | GGO(clitkChangeImageInfo, args_info); 28 | CLITK_INIT; 29 | 30 | // Filter 31 | typedef clitk::ChangeImageInfoGenericFilter FilterType; 32 | FilterType::Pointer filter = FilterType::New(); 33 | 34 | filter->SetArgsInfo(args_info); 35 | 36 | CLITK_TRY_CATCH_EXIT(filter->Update()); 37 | 38 | return EXIT_SUCCESS; 39 | } // This is the end, my friend 40 | //-------------------------------------------------------------------- 41 | -------------------------------------------------------------------------------- /tools/clitkChangeImageInfo.ggo: -------------------------------------------------------------------------------- 1 | #File clitkChangeImageInfo.ggo 2 | package "clitkChangeImageInfo" 3 | version "1.0" 4 | purpose "Change the information (spacing, origin, direction...) of an image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output image filename" string yes 12 | option "spacing" s "Spacing" double multiple no 13 | option "origin" - "Origin" double multiple no 14 | option "direction" d "Direction" double multiple no 15 | -------------------------------------------------------------------------------- /tools/clitkComposeVF.ggo: -------------------------------------------------------------------------------- 1 | #File clitkComposeVF.ggo 2 | #Author: Jef Vandemeulebroucke 3 | #Date : Tue 20 August 16.35 4 | 5 | package "clitk" 6 | version "Read two vector fields (.mhd, .vf, ..) and compose them using linear interpolation" 7 | 8 | option "config" - "Config file" string no 9 | option "input1" i "Input1 VF filename" string yes 10 | option "input2" j "Input2 VF filename" string yes 11 | option "output" o "Output VF filename" string yes 12 | option "type" t "Type of input images (0: DVF, 1: b-spline coefficient images)" int no default="0" 13 | option "like" l "Image to read output parameters from (obligatory if type=1)" string no 14 | option "pad" p "Edgepadding value" float multiple no default="0.0" 15 | option "verbose" v "Verbose" flag off 16 | 17 | -------------------------------------------------------------------------------- /tools/clitkCropImage.cxx: -------------------------------------------------------------------------------- 1 | 2 | /*========================================================================= 3 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 4 | 5 | Authors belong to: 6 | - University of LYON http://www.universite-lyon.fr/ 7 | - Léon Bérard cancer center http://www.centreleonberard.fr 8 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 9 | 10 | This software is distributed WITHOUT ANY WARRANTY; without even 11 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 12 | PURPOSE. See the copyright notices for more information. 13 | 14 | It is distributed under dual licence 15 | 16 | - BSD See included LICENSE.txt file 17 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 18 | ===========================================================================**/ 19 | 20 | // clitk 21 | #include "clitkCropImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkCropImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::CropImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | try { 38 | filter->Update(); 39 | } catch(std::runtime_error e) { 40 | std::cout << e.what() << std::endl; 41 | } 42 | 43 | return EXIT_SUCCESS; 44 | } // This is the end, my friend 45 | //-------------------------------------------------------------------- 46 | -------------------------------------------------------------------------------- /tools/clitkDice.ggo: -------------------------------------------------------------------------------- 1 | #File clitkDice.ggo 2 | package "clitkDice" 3 | version "1.0" 4 | purpose "Compute Dice between labeled images. Background must be 0." 5 | 6 | section "General options" 7 | option "config" - "Config file" string no 8 | option "verbose" v "Verbose" flag off 9 | option "imagetypes" - "Display allowed image types" flag off 10 | option "long" l "Long display (not only dice)" flag off 11 | 12 | section "Input" 13 | option "input1" i "Input mask 1" string yes 14 | option "input2" j "Input mask 2" string yes 15 | 16 | option "label1" - "Label in input1" int no default="1" 17 | option "label2" - "Label in input2" int no default="1" 18 | -------------------------------------------------------------------------------- /tools/clitkDicom2Image.ggo: -------------------------------------------------------------------------------- 1 | # file clitkDicom2Image.ggo 2 | package "clitk" 3 | version "Try to convert a DICOM into an image (.hdr, .vox...) identifying all available series" 4 | 5 | option "config" - "Config file" string no 6 | option "verbose" v "Verbose" flag off 7 | option "tolerance" t "Tolerance for slice position" double default="0" no 8 | option "output" o "Output image filename" string yes 9 | option "std_input" - "Take the like of input file from stdin, to support huge lists of filenames" flag off 10 | option "focal_origin" - "Output files with FOCAL-like origin, instead of the origin present in the dicom files" flag off 11 | option "patientSystem" p "Open the image with patient coordinate system" flag off 12 | option "instanceNumber" n "Sort the images regarding instance number in dicom tag" flag off 13 | option "reverse" r "Reverse the slice order" flag off 14 | -------------------------------------------------------------------------------- /tools/clitkDicomInfo.ggo: -------------------------------------------------------------------------------- 1 | # file DicomInfos.ggo 2 | package "clitk" 3 | version "read and print Dicom header" 4 | 5 | option "config" - "Config file" string no 6 | option "studyID" s "Only display Study UID" flag off 7 | option "uniq" u "Do not display if same study UID" flag off 8 | option "filename" f "Display filename" flag off 9 | -------------------------------------------------------------------------------- /tools/clitkDicomRTPlan2Gate.ggo: -------------------------------------------------------------------------------- 1 | # file DicomRTPlan2Gate 2 | package "clitk" 3 | version "1.0" 4 | purpose "Convert DicomRTPlan to Gate compatible file" 5 | option "config" - "config file" string no 6 | option "input" i "Input dicom file name" string yes 7 | option "output" o "Output text file name" string yes 8 | option "verbose" v "verbose" flag off 9 | -------------------------------------------------------------------------------- /tools/clitkDicomWave2Text.ggo: -------------------------------------------------------------------------------- 1 | # file DicomWave2Text 2 | package "clitk" 3 | version "1.2" 4 | purpose "Extract data from a Dicom wave file to a text file" 5 | option "config" - "config file" string no 6 | option "InputFile" i "Dicom inputfile name" string yes 7 | option "OutputFile" o "Text outputfile name" string yes 8 | option "Verbose" v "verbose" int no 9 | -------------------------------------------------------------------------------- /tools/clitkDicomWave2Text.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef CLITKDICOMWAVE2TEXT_H 20 | #define CLITKDICOMWAVE2TEXT_H 21 | 22 | namespace clitk { 23 | 24 | //--------------------------------------------------------------------- 25 | class DicomWave2Text 26 | { 27 | 28 | public: 29 | //constructor; 30 | DicomWave2Text(); 31 | //destructor; 32 | ~DicomWave2Text(); 33 | 34 | }; 35 | 36 | } // end namespace 37 | 38 | #endif 39 | -------------------------------------------------------------------------------- /tools/clitkElastixTransformToMatrix.ggo: -------------------------------------------------------------------------------- 1 | #File clitkElastixTransformToMatrix.ggo 2 | package "clitkElastixTransformToMatrix" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | option "input" i "Input elastix filename" string required 9 | option "output" o "Output matrix filename" string required 10 | -------------------------------------------------------------------------------- /tools/clitkExtractSlice.ggo: -------------------------------------------------------------------------------- 1 | #File clitkExtractSlice.ggo 2 | package "clitkExtractSlice" 3 | version "1.0" 4 | purpose "Extract a slice: will collapse the dimension given by axe, retaining only the index given by slice." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "axe" a "Axe (0,1, ...)" int no default="0" 12 | option "slice" s "Slice index (0,1,....)" int no default="0" 13 | 14 | -------------------------------------------------------------------------------- /tools/clitkExtrude.ggo: -------------------------------------------------------------------------------- 1 | #File clitkExtrude.ggo 2 | package "clitkExtrude" 3 | version "1.0" 4 | purpose "Extrude an image i along the last+1 dimension repeating the image N times. So the output has 1 dimension more than the input." 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string required 10 | option "output" o "Output image filename" string required 11 | option "size" N "Size in pixel of extrusion" int no default="1" 12 | option "spacing" s "Spacing of the new dimension" double no default="1.0" 13 | option "origin" - "Origin of the new dimension" double no default="0.0" 14 | option "like" l "Size, spacing and origin like this image" string no 15 | -------------------------------------------------------------------------------- /tools/clitkFlipImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkFlipImage.ggo 2 | package "clitkFlipImage" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "axe" a "Axe" int no default="0" 12 | option "origin" - "Flip around origin" flag off 13 | -------------------------------------------------------------------------------- /tools/clitkFooImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkFooImage_ggo.h" 21 | #include "clitkFooImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkFooImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::FooImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | filter->Update(); 37 | 38 | return EXIT_SUCCESS; 39 | }// end main 40 | 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /tools/clitkFooImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkFooImage.ggo 2 | package "clitkFooImage" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "output" o "Output image filename" string required 13 | 14 | -------------------------------------------------------------------------------- /tools/clitkGammaIndex.ggo: -------------------------------------------------------------------------------- 1 | #File clitkGammaIndex.ggo 2 | package "clitkGammaIndex" 3 | version "1.1" 4 | purpose "Compute the gamma index map for target dose map vs reference dose map. If verbose is given, the ratio of gamma>1 pixels of the total pixel in the image is computed. Absolute dose margin has priority over relative dose margin. The relative dose margin is relative to the maximum dose in the reference image.\n\nclitkGammaIndex -v -i ref.mhd -j disp.mhd -o gamma.mhd -s 3 -r 0.04\nthis will compute the 3mm 4% gamma index between ref and disp." 5 | 6 | option "verbose" v "Verbose" flag off 7 | 8 | option "reference" i "Reference dose map" string yes 9 | option "target" j "Target dose map" string yes 10 | option "output" o "Output image filename" string yes 11 | 12 | option "spatial-margin" s "Spatial margin [mm]" double yes 13 | option "relative-dose-margin" r "Dose margin relative to max dose in reference [%]" double no 14 | option "absolute-dose-margin" d "Absolute dose margin [Gray]" double no 15 | option "translation-x" x "Target relative position x [mm]" double default="0" no 16 | option "translation-y" y "Target relative position y [mm]" double default="0" no 17 | option "translation-z" z "Target relative position z [mm]" double default="0" no 18 | 19 | -------------------------------------------------------------------------------- /tools/clitkGateSimulation2Dicom.ggo: -------------------------------------------------------------------------------- 1 | #File clitkGateSimulation2Dicom.ggo 2 | package "clitkGateSimulation2Dicom" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "inputModelFilename" d "Input dicom model" string yes 11 | option "outputFilename" o "Output dicom directory/filename" string yes 12 | -------------------------------------------------------------------------------- /tools/clitkGateSimulation2DicomGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkGateSimulation2DicomGenericFilter_cxx 19 | #define clitkGateSimulation2DicomGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkGateSimulation2DicomGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkGateSimulation2DicomGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkGateSimulation2DicomGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkHistogramImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkHistogramImage_ggo.h" 21 | #include "clitkHistogramImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkHistogramImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::HistogramImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | CLITK_TRY_CATCH_EXIT(filter->Update()); 38 | filter->SaveAs(); 39 | 40 | return EXIT_SUCCESS; 41 | } // This is the end, my friend 42 | //-------------------------------------------------------------------- 43 | -------------------------------------------------------------------------------- /tools/clitkHistogramImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkHistogramImage.ggo 2 | package "clitkHistogramImage" 3 | version "1.0" 4 | purpose "Save the histogram of the input image in the output text file" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output texte filename" string yes 12 | option "size" s "size of the bin" double no 13 | 14 | 15 | 16 | -------------------------------------------------------------------------------- /tools/clitkImage2Dicom.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImage2Dicom.ggo 2 | package "clitkImage2Dicom" 3 | version "1.0" 4 | purpose "Convert the 3D mhd input image (int image) into a 3D dicom (outputDcm) based on the dictionary of the dicoms in inputDcm. The number of slice between the input and the inputDcm could be different" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string no 10 | option "inputDcm" d "Input dicom filename" string no 11 | option "outputDcm" o "Output dicom folder" string no 12 | option "nameDicom" n "Output dicom filename" string no 13 | option "newUID" u "Write output with new UID" flag off 14 | option "volume" - "Save a dicom volume" flag off 15 | option "key" k "Keys of tags to modify" string no multiple 16 | option "tag" t "Tags values" string no multiple 17 | 18 | -------------------------------------------------------------------------------- /tools/clitkImage2DicomDose.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImage2DicomDose.ggo 2 | package "clitkImage2DicomDose" 3 | version "1.0" 4 | purpose "Convert mhd file into Dicom RTDose fil using a model" 5 | 6 | option "config" - "Config file" string no 7 | option "input" i "inputfile name" string yes 8 | option "DicomInputFile" m "dicom model name" string no 9 | option "output" o "output directory/filename" string yes 10 | option "verbose" v "Verbose" flag off 11 | 12 | -------------------------------------------------------------------------------- /tools/clitkImage2DicomDoseGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkImage2DicomDoseGenericFilter_cxx 19 | #define clitkImage2DicomDoseGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkImage2DicomDoseGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkImage2DicomDoseGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkImage2DicomDoseGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkImage2DicomGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkImage2DicomGenericFilter_cxx 19 | #define clitkImage2DicomGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkImage2DicomGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkImage2DicomGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkImage2DicomGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkImage2DicomRTStruct.ggo: -------------------------------------------------------------------------------- 1 | # file clitkImage2DicomRTStruct.ggo 2 | package "clitk" 3 | version "Add a (binary) image inside a DICOM RT Structure Set (contours)" 4 | 5 | option "config" - "Config file" string no 6 | option "verbose" v "Verbose" flag off 7 | 8 | option "input" i "Input image file (binary image) to be converted into contours" string multiple yes 9 | option "rtstruct" r "Input rt struct" string yes 10 | option "dicom" d "Input folder where the initial dicom ct is" string yes 11 | option "output" o "Output DicomRT filename" string yes 12 | 13 | option "threshold" t "Threshold for binary image" float no default = "0.5" 14 | option "skip" s "Do not write in output the structures that was in input" flag off 15 | option "roitype" - "Name of the type of roi added into the rt-struct" string no default = "ORGAN" 16 | 17 | -------------------------------------------------------------------------------- /tools/clitkImageArithm.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageArithm.ggo 2 | package "clitkImageArithm" 3 | version "1.0" 4 | purpose "Perform an arithmetic operation (+-*/ ...) using two images or using an image and a scalar value." 5 | 6 | 7 | option "config" - "Config file" string no 8 | option "verbose" v "Verbose" flag off 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input1" i "Input first image filename" string yes 12 | option "input2" j "Input second image filename" string no 13 | option "output" o "Output image filename" string yes 14 | 15 | option "scalar" s "Scalar value" double no 16 | option "operation" t "Type of operation : \n With another image : 0=add*, 1=multiply, 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff\n; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=ln 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; \n* operations supported with vector fields as inputs. \n** for fluence image, if pixel value == 0, consider value=0.5" int default="0" no 17 | option "pixelValue" - "Default value for NaN/Inf" double default="0.0" no 18 | 19 | option "setFloatOutput" f "Set output to float pixel type" flag off 20 | 21 | #option "binary" b "Mask for binary operation" string no 22 | -------------------------------------------------------------------------------- /tools/clitkImageArithmGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKIMAGEARITHMGENERICFILTER_CXX 19 | #define CLITKIMAGEARITHMGENERICFILTER_CXX 20 | 21 | #include "clitkImageArithmGenericFilter.h" 22 | 23 | namespace clitk { 24 | // Specialisation 25 | // template<> 26 | // class ImageArithmGenericFilter; 27 | 28 | 29 | } 30 | 31 | #endif //define CLITKIMAGEARITHMGENERICFILTER_CXX 32 | -------------------------------------------------------------------------------- /tools/clitkImageConvert.ggo: -------------------------------------------------------------------------------- 1 | # file clitkImageConvert.ggo 2 | package "clitkImageConvert" 3 | version "1.0" 4 | purpose "Convert an image into another image.\n\tAllow to change the file format and/or the pixel type. \n\tKnown file formats 2D: jpeg png bmp tif mhd hdr vox dcm \n\tKnown file formats 3D: mhd vox hdr dcm\n\tKnown file formats 4D: mhd \n\tKnown images: 2D 3D or 4D, schar, uchar, short, ushort, int, float and double\n\nIf the -o option is not given, the last parameter of the command line is used as output." 5 | 6 | option "config" - "Config file" string no 7 | option "input" i "Input image filename" string no 8 | option "output" o "Output image filename" string no 9 | option "type" t "Output type (float, ushort ...)" string no 10 | option "verbose" v "Verbose" flag off 11 | option "compression" c "Compress output" flag off 12 | option "vv" - "Read image as in vv and save transform in meta information" flag off 13 | option "correct" - "Correct dicom with negative Z spacing" flag off 14 | option "noniimeta" - "Multiply 1st and 2nd coordinate of Direction and Origin by -1" flag off 15 | -------------------------------------------------------------------------------- /tools/clitkImageCreate.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageCreate.ggo 2 | package "clitkImageCreate" 3 | version "1.0" 4 | purpose "Create a new singled value filled image (pixeltype is float, use clitkImageConvert to change)." 5 | 6 | option "config" - "Config file" string no 7 | option "output" o "Output image filename" string yes 8 | 9 | option "like" l "Size/spacing like this other image" string no 10 | 11 | option "size" - "Number of pixels of each coordinate" int no multiple 12 | option "spacing" - "Spacing in mm between pixels" float no multiple 13 | option "origin" - "Origin in mm" double no multiple 14 | option "transformMatrix" - "Rotation matrix" double no multiple 15 | 16 | option "value" - "Value for all voxels" float default="0.0" no 17 | option "verbose" v "Verbose" flag off 18 | 19 | #option "random" r "Random fill" flag off 20 | #option "max" - "Max random fill" double default="100.0" no 21 | #option "min" - "Min random fill" double default="0.0" no 22 | 23 | -------------------------------------------------------------------------------- /tools/clitkImageGradientMagnitude.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageGradientMagnitude.ggo 2 | package "clitkImageGradientMagnitude" 3 | version "1.0" 4 | purpose "Compute the gradient magnitude of the input image" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "mask" m "Mask input image filename" string optional 13 | option "output" o "Output image filename" string required 14 | option "normalize" n "Normalize the output image between 0 and 1" flag off 15 | option "gaussian_filter" g "Gaussian filtering - default sigma value=1.0" flag off 16 | -------------------------------------------------------------------------------- /tools/clitkImageInfo.ggo: -------------------------------------------------------------------------------- 1 | # file clitkImageInfo.ggo 2 | package "clitkImageInfo" 3 | version "1.0" 4 | purpose "Display information on images." 5 | 6 | option "config" - "Config file" string no 7 | option "long" l "Long line output (1 or 2)" int default = "1" no 8 | option "verbose" v "Same as -l 1" flag off 9 | option "name" n "Display filename" flag off 10 | option "matrix" m "Display matrix" flag off 11 | -------------------------------------------------------------------------------- /tools/clitkImageIntensityWindowing.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageIntensityWindowing.ggo 2 | package "clitkImageIntensityWindowing" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "output" o "Output image filename" string required 13 | option "mask" m "Mask input image filename" string optional 14 | -------------------------------------------------------------------------------- /tools/clitkImageLaplacian.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageLaplacian.ggo 2 | package "clitkImageLaplacian" 3 | version "1.0" 4 | purpose "Compute the laplacian of the input image" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "mask" m "Mask input image filename" string optional 13 | option "output" o "Output image filename" string required 14 | option "normalize" n "Normalize the output image between 0 and 1" flag off 15 | option "gaussian_filter" g "Gaussian filtering - default sigma value=1.0" flag on 16 | -------------------------------------------------------------------------------- /tools/clitkImageMoment.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageMoment.ggo 2 | package "clitkImageMoment" 3 | version "1.0" 4 | purpose "Calculate the image moment: the center of gravity" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "center" c "Compute center of gravity" flag on 11 | option "second" s "Compute second order moments" flag off 12 | option "axes" a "Compute the principal axes" flag off 13 | -------------------------------------------------------------------------------- /tools/clitkImageStatistics.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkImageStatistics_ggo.h" 21 | #include "clitkIO.h" 22 | #include "clitkImageStatisticsGenericFilter.h" 23 | 24 | 25 | //-------------------------------------------------------------------- 26 | int main(int argc, char * argv[]) { 27 | 28 | // Init command line 29 | GGO(clitkImageStatistics, args_info); 30 | CLITK_INIT; 31 | 32 | // Filter 33 | clitk::ImageStatisticsGenericFilter::Pointer genericFilter=clitk::ImageStatisticsGenericFilter::New(); 34 | 35 | genericFilter->SetArgsInfo(args_info); 36 | CLITK_TRY_CATCH_EXIT(genericFilter->Update()); 37 | 38 | return EXIT_SUCCESS; 39 | }// end main 40 | 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /tools/clitkImageToVectorImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageToVectorImage.ggo 2 | package "clitkImageToVectorImage" 3 | version "1.0" 4 | purpose "Compose 3 images to 1 vector image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "output" o "Output image filename" string yes 10 | 11 | 12 | -------------------------------------------------------------------------------- /tools/clitkImageUncertainty.ggo: -------------------------------------------------------------------------------- 1 | # file clitkImageRescaleIntensity.ggo 2 | package "clitk" 3 | version "Compute the uncertainty of simulation outputs using Chetty's history-by-history's method" 4 | 5 | option "config" - "Config file" string no 6 | option "input" i "Input image filename" string yes 7 | option "inputSquared" s "Input squared image filename" string yes 8 | option "output" o "Output image filename" string yes 9 | option "NumberOfEvents" n "Number of events" int yes 10 | option "verbose" v "Verbose" flag off 11 | option "absolute" a "Absolute instead of the relative" flag off 12 | option "default" d "Default when input is 0." double no default="1." 13 | -------------------------------------------------------------------------------- /tools/clitkImageWarp.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageWarp.ggo 2 | #Author: Jef Vandemeulebroucke 3 | #Date : Tue 13 August 19.35 4 | 5 | package "clitk" 6 | version "Read an Image (short, char or float; 2D or 3D) and a vector field (float, 2D or 3D) and deform the input through backward or forward mapping." 7 | 8 | option "config" - "Config file" string no 9 | option "verbose" v "Verbose" flag off 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output image filename" string yes 12 | option "vf" - "Vector field filename" string yes 13 | option "forward" f "Use forward warping (only linear interp)" flag off 14 | option "spacing" s "The output spacing: 0=like the VF, 1= like the input image (linear interpolation of the VF prior to warp)" int no default="0" 15 | option "interp" - "Type of interpolation used for the warping: 0=nearest neighbor, 1= linear, 2= cubic Bspline" int no default="1" 16 | option "pad" - "Edge padding value" float no default="0.0" 17 | -------------------------------------------------------------------------------- /tools/clitkInvertVF.ggo: -------------------------------------------------------------------------------- 1 | #File clitkInvertVF.ggo 2 | #Author: Jef Vandemeulebroucke 3 | #Date : Tue 15 June 16.35 4 | 5 | package "clitk" 6 | version "Read a DVF and invert it using a linear splat to the target, or by subsumpling the input grid and matching it to the output grid" 7 | 8 | option "config" - "Config file" string no 9 | option "verbose" v "Verbose" flag off 10 | option "threads" - "Number of threads (default=min(8, #CPU))" int no 11 | 12 | option "input" i "Input VF filename" string yes 13 | option "output" o "Output VF filename" string yes 14 | option "type" t "Type of filter: 0=clitk (fast forward splat using linear kernels), 1=clitk (like 0, but input images are B-Spline coefficients), 2= itk (grid subsumpling with controllable precision)" int no default="0" 15 | option "threadSafe" - "Clitk: use thread safe algorithm" flag off 16 | option "pad" p "Clitk: edge padding value (1 or N number of values!, defautls to zeros)" double multiple no 17 | option "sampling" s "Itk: subsampling factor" int no default="20" 18 | option "like" l "Image whose grid (spacing and size) will be used for output" string no 19 | -------------------------------------------------------------------------------- /tools/clitkInvertVFGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkInvertVFGenericFilter_cxx 19 | #define clitkInvertVFGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkInvertVFGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkInvertVFGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkInvertVFGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkJacobianImage.cxx: -------------------------------------------------------------------------------- 1 | #include "clitkJacobianImage_ggo.h" 2 | #include "clitkJacobianImageGenericFilter.h" 3 | 4 | int main(int argc, char** argv) { 5 | // Init command line 6 | GGO(clitkJacobianImage, args_info); 7 | 8 | // Filter 9 | typedef clitk::JacobianImageGenericFilter FilterType; 10 | FilterType::Pointer genericFilter = FilterType::New(); 11 | 12 | genericFilter->SetArgsInfo(args_info); 13 | genericFilter->Update(); 14 | 15 | return EXIT_SUCCESS; 16 | } -------------------------------------------------------------------------------- /tools/clitkJacobianImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkJacobianImage.ggo 2 | #Author: Rômulo Pinho 3 | #Date : Tue 21 June 16.10 4 | 5 | package "clitk" 6 | version "Read a DVF and calculate the corresponding jacobian image." 7 | 8 | option "config" - "Config file" string no 9 | option "verbose" v "Verbose" flag off 10 | 11 | option "input" i "Input VF filename" string yes 12 | option "output" o "Output VF filename" string yes 13 | -------------------------------------------------------------------------------- /tools/clitkJacobianImageGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================*/ 18 | #include "clitkJacobianImageGenericFilter.h" 19 | 20 | namespace clitk 21 | { 22 | 23 | } -------------------------------------------------------------------------------- /tools/clitkMIP.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkMIP_ggo.h" 21 | #include "clitkMIPGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkMIP, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::MIPGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | try { 38 | filter->Update(); 39 | } catch(std::runtime_error e) { 40 | std::cout << e.what() << std::endl; 41 | } 42 | 43 | return EXIT_SUCCESS; 44 | } // This is the end, my friend 45 | //-------------------------------------------------------------------- 46 | -------------------------------------------------------------------------------- /tools/clitkMIP.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMIP.ggo 2 | package "clitkMIP" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output image filename" string yes 12 | option "dimension" d "Dimension along which to project" int yes 13 | -------------------------------------------------------------------------------- /tools/clitkMaskLandmarks.ggo: -------------------------------------------------------------------------------- 1 | package "clitkMaskLandmarks" 2 | version "1.0" 3 | purpose "Remove landmarks outside of a given mask also remove their corresponding points if multiple input are given." 4 | 5 | option "config" - "Config file" string no 6 | option "verbose" v "Verbose" flag off 7 | 8 | option "input" i "Input landmarks filename" string yes multiple 9 | option "mask" m "Input mask" string yes 10 | option "output" o "Output landmarks filename" string yes multiple 11 | -------------------------------------------------------------------------------- /tools/clitkMaskOfIntegratedIntensity.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMaskOfIntegratedIntensity.ggo 2 | package "clitkMaskOfIntegratedIntensity" 3 | version "1.0" 4 | purpose "Compute a mask that represent X% of the total pixels values" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string required 11 | option "output" o "Output image filename" string required 12 | option "percentage" p "Percentage of total pixels values (in %)" double required 13 | -------------------------------------------------------------------------------- /tools/clitkMatrixInverse.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMatrixToElastixTransform.ggo 2 | package "clitkMatrixInverse" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "input" i "Input matrix filename" string required 8 | option "output" o "Output matrix filename" string required 9 | -------------------------------------------------------------------------------- /tools/clitkMatrixMultiply.ggo: -------------------------------------------------------------------------------- 1 | package "clitkMatrixMultiply" 2 | version "1.0" 3 | purpose "Multiply two 4x4 matrices. In matrice notations, does input2*input" 4 | 5 | option "config" - "Config file" string optional 6 | option "input1" i "Input matrix filename" string required 7 | option "input2" j "Input matrix filename" string required 8 | option "output" o "Output matrix filename" string required 9 | -------------------------------------------------------------------------------- /tools/clitkMatrixToElastixTransform.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMatrixToElastixTransform.ggo 2 | package "clitkMatrixToElastixTransform" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | option "input" i "Input matrix filename" string required 9 | option "output" o "Output elastix filename" string required 10 | option "center" - "Rotation center" float no multiple(3) 11 | -------------------------------------------------------------------------------- /tools/clitkMedianImageFilter.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMedianImageFilter.ggo 2 | package "clitkMedianImageFilter" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "input" i "Input image filename" string yes 9 | option "output" o "Output image filename" string yes 10 | option "radius" r "Radius in each Direction" int multiple no default="1" 11 | 12 | 13 | -------------------------------------------------------------------------------- /tools/clitkMedianImageGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================*/ 18 | #ifndef clitkMedianImageGenericFilter_cxx 19 | #define clitkMedianImageGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkMedianImageGenericFilter.cxx 23 | * @author Bharath Navalpakkam 24 | * @date 20.03.2010 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkMedianImageGenericFilter.h" 31 | 32 | #endif //#define clitkMedianImageGenericFilter_cxx 33 | -------------------------------------------------------------------------------- /tools/clitkMedianTemporalDimension.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMedianTemporalDimension.ggo 2 | package "clitkMedianTemporalDimension" 3 | version "1.0" 4 | purpose "Average the last dimension to an (n-1)D image. Input is either nD or multiple (n-1)D image or DVF" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes multiple 10 | option "output" o "Output image filename" string yes 11 | 12 | 13 | -------------------------------------------------------------------------------- /tools/clitkMedianTemporalDimensionGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkMedianTemporalDimensionGenericFilter_cxx 19 | #define clitkMedianTemporalDimensionGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkMedianTemporalDimensionGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkMedianTemporalDimensionGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | 38 | 39 | } //end clitk 40 | 41 | #endif //#define clitkMedianTemporalDimensionGenericFilter_cxx 42 | -------------------------------------------------------------------------------- /tools/clitkMergeAsciiDoseActor.ggo: -------------------------------------------------------------------------------- 1 | # file clitkMergeAsciiDoseActor.ggo 2 | package "clitk" 3 | version "Add values from two ASCII files (must contains list of numbers)" 4 | 5 | option "config" - "Config file" string no 6 | option "input1" i "Input ASCII file" string yes 7 | option "input2" j "Input ASCII file" string yes 8 | option "output" o "Output ASCII file" string yes 9 | 10 | 11 | -------------------------------------------------------------------------------- /tools/clitkMergeRootFiles.ggo: -------------------------------------------------------------------------------- 1 | # -------------------------------------------- 2 | # file clitkMergeRootFiles.ggo 3 | package "clitkMergeRootFiles" 4 | version "1.0" 5 | purpose "Merge several ROOT files" 6 | # -------------------------------------------- 7 | 8 | option "config" - "Config file" string no 9 | option "input" i "Input ROOT filenames" string multiple yes 10 | option "output" o "Output ROOT filename" string yes 11 | option "fastmerge" f "Fast merge" optional 12 | option "verbose" v "Verbose level" int optional 13 | 14 | -------------------------------------------------------------------------------- /tools/clitkMergeSequence.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMergeSequence.ggo 2 | #Author: Jef Vandemeulebroucke 3 | #Date : Tue 15 June 16.35 4 | 5 | package "clitkMergeSequence" 6 | version "1.0" 7 | purpose "Read a series of nD images (unnamed inputs) and merge them to a (n+1)D image. 8 | The spacing of the (n+1)th dimension is given by the option spacing." 9 | 10 | option "config" - "Config file" string no 11 | option "spacing" s "Spacing for the new dimension" double no default="1" 12 | option "output" o "Output filename" string yes 13 | option "verbose" v "Verbose" flag off 14 | -------------------------------------------------------------------------------- /tools/clitkMeshToBinaryImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkBinaryImageToMesh.ggo 2 | package "clitkMeshToBinaryImage" 3 | version "1.0" 4 | purpose "Transform a vtk obj file into a binary mask" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input obj file" string yes 10 | option "output" o "Output binary image" string yes 11 | option "like" l "Output image will be like this one (size, spacing)" string yes 12 | -------------------------------------------------------------------------------- /tools/clitkMeshViewer.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMeshViewer.ggo 2 | package "clitkMeshViewer" 3 | version "1.0" 4 | purpose "Visualize a set of meshes" 5 | usage "clitkMeshViewer FILE1 FILE2 ... [OPTIONS]" 6 | 7 | option "config" - "Config file" string no 8 | option "verbose" v "Verbose" flag off 9 | 10 | option "animate" - "Enable animation mode (type p/m to start/stop animation)" flag off 11 | option "fps" - "Set the animation's frame rate (in fps)" double default="4.0" no 12 | -------------------------------------------------------------------------------- /tools/clitkMinMaxMask.ggo: -------------------------------------------------------------------------------- 1 | #File clitkExtractLungs.ggo 2 | package "clitkMinMaxMask" 3 | version "1.0" 4 | purpose "ssdfgsfg ssdf g." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input1" i "Input mask image filename" string yes 10 | option "input2" j "Input mask image filename" string yes 11 | -------------------------------------------------------------------------------- /tools/clitkMirrorPadImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkMirrorPadImage.ggo 2 | package "clitkMirrorPadImage" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "mirror" m "Mirror the entire image along given axis" int no 12 | option "pad" p "Mirror pad with given size" int multiple no 13 | option "lower" l "Pad on lower end (else upper)" flag off 14 | option "origin" - "Set new origin to 0" flag off 15 | -------------------------------------------------------------------------------- /tools/clitkNVectorImageTo4DImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkNVectorImageTo4DImage.ggo 2 | package "clitkNVectorImageTo4DImage" 3 | version "1.0" 4 | purpose "Convert all pixel channels of the image into a 4D image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | 12 | -------------------------------------------------------------------------------- /tools/clitkNormalizeImageFilter.ggo: -------------------------------------------------------------------------------- 1 | #File clitkNormalizeImageFilter.ggo 2 | package "clitkNormalizeImageFilter" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "output" o "Output image filename" string required 13 | option "mask" m "Mask input image filename" string optional 14 | option "total_normalisation" n "Normalise such as the total is = 1.0" flag off -------------------------------------------------------------------------------- /tools/clitkPadImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkPadImage.ggo 2 | package "clitkPadImage" 3 | version "1.0" 4 | purpose "Pad an image according to a given extends or like another image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | section "I/O" 10 | 11 | option "input" i "Input image filename" string yes 12 | option "output" o "Output image filename" string yes 13 | 14 | section "Used determined padding" 15 | option "lower" l "Size of the lower bound padding (multiple values=number of image dimension)" int no multiple 16 | option "upper" u "Size of the upper bound padding (multiple values=number of image dimension)" int no multiple 17 | 18 | 19 | section "Pad like another image" 20 | option "like" - "Pad like this image (must have the same spacing and bounding box must be larger)" string no 21 | 22 | section "Extra parameters" 23 | option "value" - "Value to be set in padded area" float default="0" no 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /tools/clitkPartitionEnergyWindowDicom.ggo: -------------------------------------------------------------------------------- 1 | #File clitkPartitionEnergyWindowDicom.ggo 2 | package "clitkPartitionEnergyWindowDicom" 3 | version "1.0" 4 | purpose "From one Dicom with different energy windows (eg with SPECT), the tool create new dicoms for each energy window and copy the correct dicom tag" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input Dicom image filename" string yes 10 | option "output" o "Output dicom directory" string yes 11 | -------------------------------------------------------------------------------- /tools/clitkPartitionEnergyWindowDicomGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkPartitionEnergyWindowDicomGenericFilter_cxx 19 | #define clitkPartitionEnergyWindowDicomGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkPartitionEnergyWindowDicomGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkPartitionEnergyWindowDicomGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkPartitionEnergyWindowDicomGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkPointRigidRegistration.ggo: -------------------------------------------------------------------------------- 1 | #File clitkPointRigidRegistration.ggo 2 | package "clitkPointRigidRegistration" 3 | version "1.0" 4 | purpose "Finding the rigid transformation between two cartesian coordinate systems\n 5 | based on corresponding points positions" 6 | 7 | option "config" - "Config file" string optional 8 | option "verbose" v "Verbose" flag off 9 | 10 | 11 | 12 | option "input" i "Corresponding points' positions filename" string required 13 | option "output" o "Output transformation filename" string required 14 | option "error" e "Output error filename" string optional 15 | -------------------------------------------------------------------------------- /tools/clitkProfileImage.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkProfileImage_ggo.h" 21 | #include "clitkProfileImageGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkProfileImage, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::ProfileImageGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | 37 | CLITK_TRY_CATCH_EXIT(filter->Update()); 38 | 39 | return EXIT_SUCCESS; 40 | } // This is the end, my friend 41 | //-------------------------------------------------------------------- 42 | -------------------------------------------------------------------------------- /tools/clitkProfileImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkProfileImage.ggo 2 | package "clitkProfileImage" 3 | version "1.0" 4 | purpose "Save the profile between 2 points of the input image in the output text file" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | option "imagetypes" - "Display allowed image types" flag off 9 | 10 | option "input" i "Input image filename" string yes 11 | option "output" o "Output texte filename" string yes 12 | option "point1" f "First point (vox)" double yes multiple(-4) 13 | option "point2" s "Second point (vox)" double yes multiple(-4) 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tools/clitkRTStructStatistics.ggo: -------------------------------------------------------------------------------- 1 | #File clitkRTStructStatistics.ggo 2 | package "clitkRTStructStatistics" 3 | version "2.0" 4 | purpose "Find the centroid (in mm) and roundness of a binarized image." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename (mask)" string yes 10 | -------------------------------------------------------------------------------- /tools/clitkRTStructStatisticsGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKRTSTRUCTSTATISTICSGENERICFILTER_CXX 19 | #define CLITKRTSTRUCTSTATISTICSGENERICFILTER_CXX 20 | 21 | #include "clitkRTStructStatisticsGenericFilter.h" 22 | 23 | namespace clitk { 24 | // Specialisation 25 | // template<> 26 | // class RTStructStatisticsGenericFilter; 27 | 28 | 29 | } 30 | 31 | #endif //define CLITKRTSTRUCTSTATISTICSGENERICFILTER_CXX 32 | -------------------------------------------------------------------------------- /tools/clitkSUVPeak.ggo: -------------------------------------------------------------------------------- 1 | #File clitkSUVPeak.ggo 2 | package "clitkSUVPeak" 3 | version "2.0" 4 | purpose "This tool Compute the SUV Peak. 5 | The output is the position of the SUV Peak (in mm) and its value. 6 | The filter use a normalized sphere of 1 cc with 1 for voxel inside, 0 for outside. 7 | And for voxels that intercepted the sphere, it computes the intersection volume using Monte Carlo simulation." 8 | 9 | option "config" - "Config file" string no 10 | option "verbose" v "Verbose" flag off 11 | 12 | option "input" i "Input first image filename" string yes 13 | option "mask" m "Mask image filename (uchar)" string no 14 | option "allow_resize" r "Resize mask if different from input" flag off 15 | option "volume" - "Volume of the filter in cc" double default="1" no 16 | -------------------------------------------------------------------------------- /tools/clitkSUVPeakGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKSUVPEAKGENERICFILTER_CXX 19 | #define CLITKSUVPEAKGENERICFILTER_CXX 20 | 21 | #include "clitkSUVPeakGenericFilter.h" 22 | 23 | namespace clitk { 24 | // Specialisation 25 | // template<> 26 | // class SUVPeakGenericFilter; 27 | 28 | 29 | } 30 | 31 | #endif //define CLITKSUVPEAKGENERICFILTER_CXX 32 | -------------------------------------------------------------------------------- /tools/clitkSetBackground.ggo: -------------------------------------------------------------------------------- 1 | #File clitkSetBackground.ggo 2 | package "clitkSetBackground" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "mask" m "Mask image filename" string yes 12 | option "outsideValue" p "Outside value" double no default="0.0" 13 | option "maskValue" l "Mask value" double no default="0.0" 14 | option "fg" - "Foreground mode" flag off 15 | -------------------------------------------------------------------------------- /tools/clitkSpect2Dicom.ggo: -------------------------------------------------------------------------------- 1 | #File clitkSpect2Dicom.ggo 2 | package "clitkSpect2Dicom" 3 | version "1.0" 4 | purpose "Convert the 3D mhd input SPECT image (int image) into a 3D dicom (outputDcm) based on the dictionary of the dicoms in inputDcm." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string no 10 | option "inputDcm" d "Input dicom filename" string no 11 | option "outputDcm" o "Output dicom filename" string no 12 | 13 | -------------------------------------------------------------------------------- /tools/clitkSpect2DicomGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkSpect2DicomGenericFilter_cxx 19 | #define clitkSpect2DicomGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkSpect2DicomGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkSpect2DicomGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkSpect2DicomGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkSplitImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkSplitImage.ggo 2 | package "clitkSplitImage" 3 | version "1.0" 4 | purpose "Split an image into n images along a dimension" 5 | 6 | 7 | option "config" - "Config file" string no 8 | option "input" i "Input image filename" string yes 9 | option "output" o "Output image base filename" string yes 10 | option "verbose" v "Verbose" flag off 11 | 12 | option "dimension" d "Dimension to split on" int yes 13 | option "png" p "Png file format" flag off 14 | option "window" w "Window" double no 15 | option "level" l "Level" double no 16 | -------------------------------------------------------------------------------- /tools/clitkSum.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | // clitk 20 | #include "clitkSum_ggo.h" 21 | #include "clitkSumGenericFilter.h" 22 | 23 | //-------------------------------------------------------------------- 24 | int main(int argc, char * argv[]) 25 | { 26 | 27 | // Init command line 28 | GGO(clitkSum, args_info); 29 | CLITK_INIT; 30 | 31 | // Filter 32 | typedef clitk::SumGenericFilter FilterType; 33 | FilterType::Pointer filter = FilterType::New(); 34 | 35 | filter->SetArgsInfo(args_info); 36 | try { 37 | filter->Update(); 38 | } catch(std::runtime_error e) { 39 | std::cout << e.what() << std::endl; 40 | } 41 | 42 | return EXIT_SUCCESS; 43 | }// end main 44 | 45 | //-------------------------------------------------------------------- 46 | -------------------------------------------------------------------------------- /tools/clitkSum.ggo: -------------------------------------------------------------------------------- 1 | #File clitkSum.ggo 2 | package "clitkSum" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string optional 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string required 12 | option "output" o "Output image filename" string required 13 | option "dimension" d "Dimension along which to sum" int yes 14 | -------------------------------------------------------------------------------- /tools/clitkTransformLandmarks.ggo: -------------------------------------------------------------------------------- 1 | #File clitkTransformLandmarks.ggo 2 | package "clitkTransformLandmarks" 3 | version "1.0" 4 | purpose "Trasnform a set of landmarks with the given 4x4 matrix. Output to stdout." 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input landmarks filename" string yes 10 | option "matrix" m "Input 4x4 matrix filename ('.mat' file)" string no 11 | option "spacing" s "If given, applies the given spacing (x,y,z) to the input points." double no multiple default="1" 12 | option "output" o "Output landmarks filename" string yes 13 | option "type" t "Landmarks type ('pts' for Jef; 'txt' for VV ; 'vtk' for vtk meshes)" string no default="txt" 14 | 15 | 16 | -------------------------------------------------------------------------------- /tools/clitkUnsharpMask.ggo: -------------------------------------------------------------------------------- 1 | #File clitkUnsharpMask.ggo 2 | package "clitkUnsharpMask" 3 | version "1.0" 4 | purpose "Image sharpening technique. It computes Image - blurred(Image). Here blurred(Image) is the output of a gaussian filtering with a sigma measured in world coordinates" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input" i "Input image filename" string yes 12 | option "output" o "Output image filename" string yes 13 | option "sigma" s "Sigma of the gaussian" double required 14 | -------------------------------------------------------------------------------- /tools/clitkUpdateVRTagDicom.ggo: -------------------------------------------------------------------------------- 1 | #File clitkUpdateVRTagDicom.ggo 2 | package "clitkUpdateVRTagDicom" 3 | version "1.0" 4 | purpose "Fix VR Dicom tag mistakes with gdcm" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input Dicom image filename" string yes 10 | option "output" o "Output dicom filename" string yes 11 | option "model" m "Model dicom filename" string yes 12 | -------------------------------------------------------------------------------- /tools/clitkUpdateVRTagDicomGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkUpdateVRTagDicomGenericFilter_cxx 19 | #define clitkUpdateVRTagDicomGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkUpdateVRTagDicomGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkUpdateVRTagDicomGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkUpdateVRTagDicomGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkVFConvert.ggo: -------------------------------------------------------------------------------- 1 | #File clitkVFConvert.ggo 2 | package "clitkVFConvert" 3 | version "1.0" 4 | purpose "Convert file format" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | 12 | 13 | -------------------------------------------------------------------------------- /tools/clitkVFInterpolate.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageInterpolate.ggo 2 | package "clitkImageInterpolate" 3 | version "1.0" 4 | purpose "Interpolate an image. You can specify the interpolation, you can apply a Gaussian filter before." 5 | 6 | option "config" - "Config file" string no 7 | option "input1" i "Input image filename" string yes 8 | option "input2" j "Input image filename" string yes 9 | option "output" o "Output image filename" string yes 10 | option "distance" d "Distance (d in [0,1])" float yes 11 | option "verbose" v "Verbose" flag off 12 | option "interp" - "Interpolation type: {nn, linear}" string no default="nn" 13 | #option "order" b "BSpline ordre (range 0-5)" int no default="3" 14 | #option "sampling" s "BLUT sampling value" int no default="30" 15 | 16 | -------------------------------------------------------------------------------- /tools/clitkVFInterpolateGenericFilter.txx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKVFRESAMPLEGENERICFILTER_TXX 19 | #define CLITKVFRESAMPLEGENERICFILTER_TXX 20 | /** 21 | ------------------------------------------------= 22 | * @file clitkVFInterpolateGenericFilter.txx 23 | * @author David Sarrut 24 | * @date 23 Feb 2008 08:40:11 25 | * 26 | * @brief 27 | * 28 | * 29 | ------------------------------------------------=*/ 30 | 31 | //-------------------------------------------------------------------- 32 | 33 | #endif /* end #define CLITKVFRESAMPLEGENERICFILTER_TXX */ 34 | 35 | -------------------------------------------------------------------------------- /tools/clitkVFResample.ggo: -------------------------------------------------------------------------------- 1 | #File clitkImageResample.ggo 2 | package "clitkImageResample" 3 | version "1.0" 4 | purpose "Resample an image. You can specify the interpolation, you can apply a Gaussian filter before." 5 | 6 | option "config" - "Config file" string no 7 | option "input" i "Input image filename" string yes 8 | option "output" o "Output image filename" string yes 9 | option "verbose" v "Verbose" flag off 10 | option "interp" - "Interpolation type: {nn, linear, bspline, blut}" string no default="nn" 11 | option "order" b "BSpline ordre (range 0-5)" int no default="3" 12 | option "sampling" s "BLUT sampling value" int no default="30" 13 | option "size" - "Number of pixels of each coordonate" int no multiple default="0" 14 | option "spacing" - "Spacing in mm between pixels" float no multiple default="0.0" 15 | option "gauss" g "Apply Gaussian before (sigma in mm) ; no Gaussian if not given" float no multiple default="1.0" 16 | option "default" d "Default pixel value" float no default = "0.0" 17 | 18 | -------------------------------------------------------------------------------- /tools/clitkVFResampleGenericFilter.txx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKVFRESAMPLEGENERICFILTER_TXX 19 | #define CLITKVFRESAMPLEGENERICFILTER_TXX 20 | /** 21 | ------------------------------------------------= 22 | * @file clitkVFResampleGenericFilter.txx 23 | * @author David Sarrut 24 | * @date 23 Feb 2008 08:40:11 25 | * 26 | * @brief 27 | * 28 | * 29 | ------------------------------------------------=*/ 30 | 31 | //-------------------------------------------------------------------- 32 | 33 | #endif /* end #define CLITKVFRESAMPLEGENERICFILTER_TXX */ 34 | 35 | -------------------------------------------------------------------------------- /tools/clitkVectorArithm.ggo: -------------------------------------------------------------------------------- 1 | #File clitkVectorArithm.ggo 2 | package "clitkVectorArithm" 3 | version "1.0" 4 | purpose "Perform an arithmetic operation (+-*/ ...) using two images or using an image and a scalar value." 5 | 6 | 7 | option "config" - "Config file" string no 8 | option "verbose" v "Verbose" flag off 9 | option "imagetypes" - "Display allowed image types" flag off 10 | 11 | option "input1" i "Input first image filename" string yes 12 | option "input2" j "Input second image filename" string no 13 | option "output" o "Output image filename" string yes 14 | 15 | option "scalar" s "Scalar value" double no 16 | option "operation" t "Type of operation : \n With another image : 0=add, 1=multiply, 2=dotproduct, 7=difference, 9=crossproduct\n; For 'scalar' : 0=add, 1=multiply, 5=absval (magnitude), 6=squared magnitude, 11=divide, 12=normalize" int default="0" no 17 | option "pixelValue" - "Default value for NaN/Inf" double default="0.0" no 18 | 19 | option "setFloatOutput" f "Set output to float pixel type" flag off 20 | 21 | #option "binary" b "Mask for binary operation" string no 22 | -------------------------------------------------------------------------------- /tools/clitkVectorArithmGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef CLITKVECTORARITHMGENERICFILTER_CXX 19 | #define CLITKVECTORARITHMGENERICFILTER_CXX 20 | 21 | #include "clitkVectorArithmGenericFilter.h" 22 | 23 | namespace clitk { 24 | // Specialisation 25 | // template<> 26 | // class VectorArithmGenericFilter; 27 | 28 | 29 | } 30 | 31 | #endif //define CLITKVECTORARITHMGENERICFILTER_CXX 32 | -------------------------------------------------------------------------------- /tools/clitkVectorImageToImage.ggo: -------------------------------------------------------------------------------- 1 | #File clitkVectorImageToImage.ggo 2 | package "clitkVectorImageToImage" 3 | version "1.0" 4 | purpose "Extract a component image from a vector image" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "output" o "Output image filename" string yes 11 | option "componentIndex" c "Component index to extract" int no default="0" 12 | 13 | -------------------------------------------------------------------------------- /tools/clitkWriteDicomSeries.ggo: -------------------------------------------------------------------------------- 1 | #File clitkWriteDicomSeries.ggo 2 | package "clitkWriteDicomSeries" 3 | version "1.0" 4 | purpose "" 5 | 6 | option "config" - "Config file" string no 7 | option "verbose" v "Verbose" flag off 8 | 9 | option "input" i "Input image filename" string yes 10 | option "inputDir" d "Input dicom directory" string yes 11 | option "outputDir" o "Output dicom directory" string yes 12 | option "key" k "Keys of tags to modify" string no multiple default="0008|103e" 13 | option "tag" t "Tags values" string no multiple default="MIDPOSITION" 14 | option "newSeriesUID" e "Write the series with a new series UID (ignored if given in key/tag option)" flag off 15 | option "newStudyUID" u "Write the series with a new study UID (ignored if given in key/tag option; forces newSeriesUID = true)" flag off 16 | option "useSizeAsReference" s "Use the size of the dicom image as reference for an occasional resampling" flag off 17 | option "preserve" p "Preserve private tags and keep original UID (eg: Xio)" flag off 18 | -------------------------------------------------------------------------------- /tools/clitkWriteDicomSeriesGenericFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef clitkWriteDicomSeriesGenericFilter_cxx 19 | #define clitkWriteDicomSeriesGenericFilter_cxx 20 | 21 | /* ================================================= 22 | * @file clitkWriteDicomSeriesGenericFilter.cxx 23 | * @author 24 | * @date 25 | * 26 | * @brief 27 | * 28 | ===================================================*/ 29 | 30 | #include "clitkWriteDicomSeriesGenericFilter.h" 31 | 32 | 33 | namespace clitk 34 | { 35 | 36 | 37 | } //end clitk 38 | 39 | #endif //#define clitkWriteDicomSeriesGenericFilter_cxx 40 | -------------------------------------------------------------------------------- /tools/clitkXml2DicomRTStruct.ggo: -------------------------------------------------------------------------------- 1 | # file clitkXml2DicomRTStruct.ggo 2 | package "clitk" 3 | version "1.0" 4 | description "Convert a Structure from XML to DICOM RT Structure Set (contours) 5 | The structure of the xml has to be like this: 6 | " 7 | 8 | option "config" - "Config file" string no 9 | option "verbose" v "Verbose" flag off 10 | 11 | option "input" i "Input xml file with struct to be converted into DicomRTStruct" string yes 12 | option "rtstruct" r "Input rt struct" string yes 13 | option "dicom" d "Input folder where the initial dicom used for the input is" string yes 14 | option "output" o "Output DicomRT filename" string yes 15 | option "pixel" p "Use pixel coordinates instead of mm coordinates (Usefull with transformation matrix)" flag off 16 | option "image" j "If pixel is set, path to the mhd image converted from dicom" string no 17 | -------------------------------------------------------------------------------- /tools/clitkZeroVF.ggo: -------------------------------------------------------------------------------- 1 | #File clitkZeroVF.ggo 2 | #Author: Joel Schaerer 3 | ##Date : Tue 15 March 16.35 4 | 5 | package "clitk" 6 | version "Read a vector fields (.mhd, .vf, ..) and zero it" 7 | 8 | option "config" - "Config file" string no 9 | option "input" i "Input VF filename" string yes 10 | option "output" o "Output VF filename" string yes 11 | option "verbose" v "Verbose" flag off 12 | -------------------------------------------------------------------------------- /travis/travis_build_itk.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -ev 3 | MAKE="make --jobs=$NUM_THREADS --keep-going" 4 | 5 | #Prepare cmake arguments following the ITK version 6 | if [ "$C11" == "true" ]; then 7 | itk_repo_str=" --branch "$ITK_VERSION" https://github.com/InsightSoftwareConsortium/ITK.git --depth 1" 8 | cmake_arg_str=" -DCMAKE_CXX_FLAGS=-std=c++11 -DModule_ITKVtkGlue=ON -DVTK_DIR=$VTK_DIR -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF " 9 | else 10 | itk_repo_str=" --branch "$ITK_VERSION" https://github.com/InsightSoftwareConsortium/ITK.git --depth 1" 11 | cmake_arg_str=" -DModule_ITKVtkGlue=ON -DVTK_DIR=$VTK_DIR -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF " 12 | fi 13 | 14 | if [ -d $ITK_SOURCE_DIR ]; then 15 | echo $ITK_SOURCE_DIR exists 16 | if [ ! -f $ITK_SOURCE_DIR/CMakeLists.txt ]; then 17 | echo $ITK_SOURCE_DIR does not contain CMakeList.txt 18 | rm -rf $ITK_SOURCE_DIR 19 | fi 20 | fi 21 | 22 | #git clone in the ITK source folder 23 | if [ ! -d $ITK_SOURCE_DIR ]; then 24 | git clone $itk_repo_str $ITK_SOURCE_DIR 25 | fi 26 | 27 | #CMAKE and MAKE 28 | mkdir -p $ITK_DIR 29 | cd $ITK_DIR 30 | cmake $cmake_arg_str $ITK_SOURCE_DIR 31 | $MAKE 32 | cd - 33 | 34 | cd $cwd 35 | -------------------------------------------------------------------------------- /travis/travis_build_qt.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -ev 3 | 4 | #Install the correct Qt Version 5 | if [ "$QT_VERSION" == "4.8.7" ]; then 6 | if test $TRAVIS_OS_NAME == linux ; then sudo apt-get -y --force-yes install qt4-dev-tools; fi 7 | elif [ "$QT_VERSION" == "5.5.1" ]; then 8 | if test $TRAVIS_OS_NAME == linux ; then sudo add-apt-repository --yes ppa:beineri/opt-qt551-trusty; fi 9 | if test $TRAVIS_OS_NAME == linux ; then sudo apt-get update -qq; fi 10 | if test $TRAVIS_OS_NAME == linux ; then sudo apt-get -y --force-yes install qt55tools qt55x11extras; fi 11 | fi 12 | if test $TRAVIS_OS_NAME == osx ; then brew install qt5; fi 13 | if test $TRAVIS_OS_NAME == osx ; then brew link qt5 --force; fi 14 | 15 | 16 | -------------------------------------------------------------------------------- /travis/travis_build_vv.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -ev 3 | MAKE="make --jobs=$NUM_THREADS --keep-going" 4 | 5 | #Prepare cmake arguments following the vv version 6 | if [ "$C11" == "true" ]; then 7 | cmake_arg_str=" -DCMAKE_CXX_FLAGS=-std=c++11 8 | -DCLITK_BUILD_REGISTRATION=OFF 9 | -DCLITK_BUILD_SEGMENTATION=OFF 10 | -DCLITK_BUILD_TOOLS=OFF 11 | -DCLITK_BUILD_VV=ON 12 | -DCLITK_EXPERIMENTAL=OFF" 13 | else 14 | cmake_arg_str=" -DCLITK_BUILD_REGISTRATION=OFF 15 | -DCLITK_BUILD_SEGMENTATION=OFF 16 | -DCLITK_BUILD_TOOLS=OFF 17 | -DCLITK_BUILD_VV=ON 18 | -DCLITK_EXPERIMENTAL=OFF" 19 | fi 20 | 21 | #CMAKE and MAKE 22 | mkdir -p $BUILD_DIR 23 | cd $BUILD_DIR 24 | cmake $cmake_arg_str .. 25 | $MAKE 26 | cd .. 27 | #build-wrapper-linux-x86-64 --out-dir bw-output make clean all 28 | #sonar-scanner 29 | cd $cwd 30 | -------------------------------------------------------------------------------- /utilities/CxImage/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | include(../../cmake/common.cmake) 2 | 3 | add_library(clitkCxImage STATIC 4 | ximaenc.cpp 5 | ximatran.cpp 6 | ximath.cpp 7 | ximaint.cpp 8 | ximage.cpp 9 | ximagif.cpp 10 | ximainfo.cpp 11 | ximalpha.cpp 12 | ximalyr.cpp 13 | ximapal.cpp 14 | ximasel.cpp 15 | xmemfile.cpp 16 | ) 17 | include_directories(.) 18 | 19 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/CxImageCrtDll.cpp: -------------------------------------------------------------------------------- 1 | // CxImageCrtDll.cpp : Defines the entry point for the CxImageCrtDll application. 2 | // 3 | 4 | #include "stdcrt.h" 5 | 6 | BOOL APIENTRY DllMain( HANDLE /*hModule*/, 7 | DWORD /*ul_reason_for_call*/, 8 | LPVOID /*lpReserved*/ 9 | ) 10 | { 11 | return TRUE; 12 | } 13 | 14 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/CxImageCrtDll.rc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/utilities/CxImage/CxImageDLL/CxImageCrtDll.rc -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/CxImageMfcDll.clw: -------------------------------------------------------------------------------- 1 | ; CLW file contains information for the MFC ClassWizard 2 | 3 | [General Info] 4 | Version=1 5 | ClassCount=1 6 | Class1=CcximagemfcdllApp 7 | LastClass=CcximagemfcdllApp 8 | NewFileInclude2=#include "cximagemfcdll.h" 9 | ResourceCount=0 10 | NewFileInclude1=#include "stdafx.h" 11 | 12 | [CLS:CcximagemfcdllApp] 13 | Type=0 14 | HeaderFile=cximagemfcdll.h 15 | ImplementationFile=cximagemfcdll.cpp 16 | Filter=N 17 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/CxImageMfcDll.h: -------------------------------------------------------------------------------- 1 | // cximagemfcdll.h : main header file for the cximagemfcdll DLL 2 | // 3 | 4 | #if !defined(AFX_cximagemfcdll_H__E98F71A6_B361_11D6_BB83_CAEE2E1CB77B__INCLUDED_) 5 | #define AFX_cximagemfcdll_H__E98F71A6_B361_11D6_BB83_CAEE2E1CB77B__INCLUDED_ 6 | 7 | #if _MSC_VER > 1000 8 | #pragma once 9 | #endif // _MSC_VER > 1000 10 | 11 | #ifndef __AFXWIN_H__ 12 | #error include 'stdafx.h' before including this file for PCH 13 | #endif 14 | 15 | #include "resource.h" // main symbols 16 | 17 | ///////////////////////////////////////////////////////////////////////////// 18 | // CcximagemfcdllApp 19 | // See cximagemfcdll.cpp for the implementation of this class 20 | // 21 | 22 | class CcximagemfcdllApp : public CWinApp 23 | { 24 | public: 25 | CcximagemfcdllApp(); 26 | 27 | // Overrides 28 | // ClassWizard generated virtual function overrides 29 | //{{AFX_VIRTUAL(CcximagemfcdllApp) 30 | //}}AFX_VIRTUAL 31 | 32 | //{{AFX_MSG(CcximagemfcdllApp) 33 | // NOTE - the ClassWizard will add and remove member functions here. 34 | // DO NOT EDIT what you see in these blocks of generated code ! 35 | //}}AFX_MSG 36 | DECLARE_MESSAGE_MAP() 37 | }; 38 | 39 | 40 | ///////////////////////////////////////////////////////////////////////////// 41 | 42 | //{{AFX_INSERT_LOCATION}} 43 | // Microsoft Visual C++ will insert additional declarations immediately before the previous line. 44 | 45 | #endif // !defined(AFX_cximagemfcdll_H__E98F71A6_B361_11D6_BB83_CAEE2E1CB77B__INCLUDED_) 46 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/CxImageMfcDll.rc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/utilities/CxImage/CxImageDLL/CxImageMfcDll.rc -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/StdAfx.cpp: -------------------------------------------------------------------------------- 1 | // stdafx.cpp : source file that includes just the standard includes 2 | // cximagemfcdll.pch will be the pre-compiled header 3 | // stdafx.obj will contain the pre-compiled type information 4 | 5 | #include "stdafx.h" 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/StdCrt.h: -------------------------------------------------------------------------------- 1 | // stdafx.h : include file for standard system include files, 2 | // or project specific include files that are used frequently, but 3 | // are changed infrequently 4 | // 5 | 6 | #if !defined(AFX_STDAFX_H__F30A8A60_284F_4DF6_9431_6283105686F6__INCLUDED_) 7 | #define AFX_STDAFX_H__F30A8A60_284F_4DF6_9431_6283105686F6__INCLUDED_ 8 | 9 | #if _MSC_VER > 1000 10 | #pragma once 11 | #endif // _MSC_VER > 1000 12 | 13 | 14 | // Insert your headers here 15 | #define WIN32_LEAN_AND_MEAN // Exclude rarely-used stuff from Windows headers 16 | 17 | #include 18 | 19 | // TODO: reference additional headers your program requires here 20 | 21 | //{{AFX_INSERT_LOCATION}} 22 | // Microsoft Visual C++ will insert additional declarations immediately before the previous line. 23 | 24 | #endif // !defined(AFX_STDAFX_H__F30A8A60_284F_4DF6_9431_6283105686F6__INCLUDED_) 25 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/resource.h: -------------------------------------------------------------------------------- 1 | //{{NO_DEPENDENCIES}} 2 | // Microsoft Developer Studio generated include file. 3 | // Used by CxImageMFCdll.rc 4 | // 5 | 6 | // Next default values for new objects 7 | // 8 | #ifdef APSTUDIO_INVOKED 9 | #ifndef APSTUDIO_READONLY_SYMBOLS 10 | #define _APS_NEXT_RESOURCE_VALUE 6000 11 | #define _APS_NEXT_COMMAND_VALUE 32771 12 | #define _APS_NEXT_CONTROL_VALUE 6000 13 | #define _APS_NEXT_SYMED_VALUE 6000 14 | #endif 15 | #endif 16 | -------------------------------------------------------------------------------- /utilities/CxImage/CxImageDLL/resrc1.h: -------------------------------------------------------------------------------- 1 | //{{NO_DEPENDENCIES}} 2 | // Microsoft Developer Studio generated include file. 3 | // Used by CxImageCrtDll.rc 4 | // 5 | 6 | // Next default values for new objects 7 | // 8 | #ifdef APSTUDIO_INVOKED 9 | #ifndef APSTUDIO_READONLY_SYMBOLS 10 | #define _APS_NEXT_RESOURCE_VALUE 6000 11 | #define _APS_NEXT_COMMAND_VALUE 32771 12 | #define _APS_NEXT_CONTROL_VALUE 6000 13 | #define _APS_NEXT_SYMED_VALUE 6000 14 | #endif 15 | #endif 16 | -------------------------------------------------------------------------------- /utilities/CxImage/cximage.dsw: -------------------------------------------------------------------------------- 1 | Microsoft Developer Studio Workspace File, Format Version 6.00 2 | # WARNING: DO NOT EDIT OR DELETE THIS WORKSPACE FILE! 3 | 4 | ############################################################################### 5 | 6 | Project: "CxImage"=.\CxImage.dsp - Package Owner=<4> 7 | 8 | Package=<5> 9 | {{{ 10 | }}} 11 | 12 | Package=<4> 13 | {{{ 14 | }}} 15 | 16 | ############################################################################### 17 | 18 | Global: 19 | 20 | Package=<5> 21 | {{{ 22 | }}} 23 | 24 | Package=<3> 25 | {{{ 26 | }}} 27 | 28 | ############################################################################### 29 | 30 | -------------------------------------------------------------------------------- /utilities/CxImage/ximadsp.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/utilities/CxImage/ximadsp.cpp -------------------------------------------------------------------------------- /utilities/CxImage/ximainfo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/utilities/CxImage/ximainfo.cpp -------------------------------------------------------------------------------- /utilities/CxImage/ximajbg.h: -------------------------------------------------------------------------------- 1 | /* 2 | * File: ximajbg.h 3 | * Purpose: JBG Image Class Loader and Writer 4 | */ 5 | /* ========================================================== 6 | * CxImageJBG (c) 18/Aug/2002 Davide Pizzolato - www.xdp.it 7 | * For conditions of distribution and use, see copyright notice in ximage.h 8 | * 9 | * based on LIBJBG Copyright (c) 2002, Markus Kuhn - All rights reserved. 10 | * ========================================================== 11 | */ 12 | #if !defined(__ximaJBG_h) 13 | #define __ximaJBG_h 14 | 15 | #include "ximage.h" 16 | 17 | #if CXIMAGE_SUPPORT_JBG 18 | 19 | extern "C" { 20 | #include "../jbig/jbig.h" 21 | }; 22 | 23 | class CxImageJBG: public CxImage 24 | { 25 | public: 26 | CxImageJBG(): CxImage(CXIMAGE_FORMAT_JBG) {} 27 | 28 | // bool Load(const TCHAR * imageFileName){ return CxImage::Load(imageFileName,CXIMAGE_FORMAT_JBG);} 29 | // bool Save(const TCHAR * imageFileName){ return CxImage::Save(imageFileName,CXIMAGE_FORMAT_JBG);} 30 | bool Decode(CxFile * hFile); 31 | bool Decode(FILE *hFile) { CxIOFile file(hFile); return Decode(&file); } 32 | 33 | #if CXIMAGE_SUPPORT_ENCODE 34 | bool Encode(CxFile * hFile); 35 | bool Encode(FILE *hFile) { CxIOFile file(hFile); return Encode(&file); } 36 | #endif // CXIMAGE_SUPPORT_ENCODE 37 | protected: 38 | static void jbig_data_out(BYTE *buffer, unsigned int len, void *file) 39 | {((CxFile*)file)->Write(buffer,len,1);} 40 | }; 41 | 42 | #endif 43 | 44 | #endif 45 | -------------------------------------------------------------------------------- /utilities/CxImage/ximaska.h: -------------------------------------------------------------------------------- 1 | /* 2 | * File: ximaska.h 3 | * Purpose: SKA Image Class Loader and Writer 4 | */ 5 | /* ========================================================== 6 | * CxImageSKA (c) 25/Sep/2007 Davide Pizzolato - www.xdp.it 7 | * For conditions of distribution and use, see copyright notice in ximage.h 8 | * ========================================================== 9 | */ 10 | #if !defined(__ximaSKA_h) 11 | #define __ximaSKA_h 12 | 13 | #include "ximage.h" 14 | 15 | #if CXIMAGE_SUPPORT_SKA 16 | 17 | class CxImageSKA: public CxImage 18 | { 19 | #pragma pack(1) 20 | typedef struct tagSkaHeader { 21 | unsigned short Width; 22 | unsigned short Height; 23 | BYTE BppExp; 24 | DWORD dwUnknown; 25 | } SKAHEADER; 26 | #pragma pack() 27 | 28 | public: 29 | CxImageSKA(): CxImage(CXIMAGE_FORMAT_SKA) {} 30 | 31 | // bool Load(const char * imageFileName){ return CxImage::Load(imageFileName,CXIMAGE_FORMAT_ICO);} 32 | // bool Save(const char * imageFileName){ return CxImage::Save(imageFileName,CXIMAGE_FORMAT_ICO);} 33 | bool Decode(CxFile * hFile); 34 | bool Decode(FILE *hFile) { CxIOFile file(hFile); return Decode(&file); } 35 | 36 | #if CXIMAGE_SUPPORT_ENCODE 37 | bool Encode(CxFile * hFile); 38 | bool Encode(FILE *hFile) { CxIOFile file(hFile); return Encode(&file); } 39 | #endif // CXIMAGE_SUPPORT_ENCODE 40 | }; 41 | 42 | #endif 43 | 44 | #endif 45 | -------------------------------------------------------------------------------- /utilities/CxImage/ximath.h: -------------------------------------------------------------------------------- 1 | #if !defined(__ximath_h) 2 | #define __ximath_h 3 | 4 | #include "ximadef.h" 5 | 6 | //***bd*** simple floating point point 7 | class DLL_EXP CxPoint2 8 | { 9 | public: 10 | CxPoint2(); 11 | CxPoint2(float const x_, float const y_); 12 | CxPoint2(CxPoint2 const &p); 13 | 14 | float Distance(CxPoint2 const p2); 15 | float Distance(float const x_, float const y_); 16 | 17 | float x,y; 18 | }; 19 | 20 | //and simple rectangle 21 | class DLL_EXP CxRect2 22 | { 23 | public: 24 | CxRect2(); 25 | CxRect2(float const x1_, float const y1_, float const x2_, float const y2_); 26 | CxRect2(CxPoint2 const &bl, CxPoint2 const &tr); 27 | CxRect2(CxRect2 const &p); 28 | 29 | float Surface() const; 30 | CxRect2 CrossSection(CxRect2 const &r2) const; 31 | CxPoint2 Center() const; 32 | float Width() const; 33 | float Height() const; 34 | 35 | CxPoint2 botLeft; 36 | CxPoint2 topRight; 37 | }; 38 | 39 | #endif 40 | -------------------------------------------------------------------------------- /utilities/CxImage/ximawbmp.h: -------------------------------------------------------------------------------- 1 | /* 2 | * File: ximawbmp.h 3 | * Purpose: WBMP Image Class Loader and Writer 4 | */ 5 | /* ========================================================== 6 | * CxImageWBMP (c) 12/Jul/2002 Davide Pizzolato - www.xdp.it 7 | * For conditions of distribution and use, see copyright notice in ximage.h 8 | * ========================================================== 9 | */ 10 | #if !defined(__ximaWBMP_h) 11 | #define __ximaWBMP_h 12 | 13 | #include "ximage.h" 14 | 15 | #if CXIMAGE_SUPPORT_WBMP 16 | 17 | class CxImageWBMP: public CxImage 18 | { 19 | #pragma pack(1) 20 | typedef struct tagWbmpHeader 21 | { 22 | DWORD Type; // 0 23 | BYTE FixHeader; // 0 24 | DWORD ImageWidth; // Image Width 25 | DWORD ImageHeight; // Image Height 26 | } WBMPHEADER; 27 | #pragma pack() 28 | public: 29 | CxImageWBMP(): CxImage(CXIMAGE_FORMAT_WBMP) {} 30 | 31 | // bool Load(const TCHAR * imageFileName){ return CxImage::Load(imageFileName,CXIMAGE_FORMAT_WBMP);} 32 | // bool Save(const TCHAR * imageFileName){ return CxImage::Save(imageFileName,CXIMAGE_FORMAT_WBMP);} 33 | bool Decode(CxFile * hFile); 34 | bool Decode(FILE *hFile) { CxIOFile file(hFile); return Decode(&file); } 35 | protected: 36 | bool ReadOctet(CxFile * hFile, DWORD *data); 37 | 38 | public: 39 | #if CXIMAGE_SUPPORT_ENCODE 40 | bool Encode(CxFile * hFile); 41 | bool Encode(FILE *hFile) { CxIOFile file(hFile); return Encode(&file); } 42 | protected: 43 | bool WriteOctet(CxFile * hFile, const DWORD data); 44 | #endif // CXIMAGE_SUPPORT_ENCODE 45 | }; 46 | 47 | #endif 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /utilities/CxImage/ximawnd.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/utilities/CxImage/ximawnd.cpp -------------------------------------------------------------------------------- /utilities/CxImage/xmemfile.h: -------------------------------------------------------------------------------- 1 | #if !defined(__xmemfile_h) 2 | #define __xmemfile_h 3 | 4 | #include "xfile.h" 5 | 6 | ////////////////////////////////////////////////////////// 7 | class DLL_EXP CxMemFile : public CxFile 8 | { 9 | public: 10 | CxMemFile(BYTE* pBuffer = NULL, DWORD size = 0); 11 | ~CxMemFile(); 12 | 13 | bool Open(); 14 | BYTE* GetBuffer(bool bDetachBuffer = true); 15 | 16 | virtual bool Close(); 17 | virtual size_t Read(void *buffer, size_t size, size_t count); 18 | virtual size_t Write(const void *buffer, size_t size, size_t count); 19 | virtual bool Seek(long offset, int origin); 20 | virtual long Tell(); 21 | virtual long Size(); 22 | virtual bool Flush(); 23 | virtual bool Eof(); 24 | virtual long Error(); 25 | virtual bool PutC(unsigned char c); 26 | virtual long GetC(); 27 | virtual char * GetS(char *string, int n); 28 | virtual long Scanf(const char *format, void* output); 29 | 30 | protected: 31 | bool Alloc(DWORD nBytes); 32 | void Free(); 33 | 34 | BYTE* m_pBuffer; 35 | DWORD m_Size; 36 | bool m_bFreeOnClose; 37 | long m_Position; //current position 38 | long m_Edge; //buffer size 39 | }; 40 | 41 | #endif 42 | -------------------------------------------------------------------------------- /vv/License.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/License.txt -------------------------------------------------------------------------------- /vv/QTreePushButton.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #include "QTreePushButton.h" 19 | 20 | QTreePushButton::QTreePushButton():QPushButton() 21 | { 22 | m_item = NULL; 23 | m_index = 0; 24 | m_column = 0; 25 | connect(this,SIGNAL(clicked()),this, SLOT(clickedIntoATree())); 26 | } 27 | 28 | void QTreePushButton::clickedIntoATree() 29 | { 30 | emit clickedInto(m_item,m_column); 31 | emit clickedInto(m_index,m_column); 32 | } 33 | -------------------------------------------------------------------------------- /vv/QVTKOpenGLNativeWidget2.cxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/QVTKOpenGLNativeWidget2.cxx -------------------------------------------------------------------------------- /vv/QVTKOpenGLNativeWidget2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/QVTKOpenGLNativeWidget2.h -------------------------------------------------------------------------------- /vv/ReadMe.txt: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================*/ 18 | For information, help and more: 19 | http://www.creatis.insa-lyon.fr/rio/vv 20 | -------------------------------------------------------------------------------- /vv/icons/1b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/icons/1b.png -------------------------------------------------------------------------------- /vv/icons/2b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/icons/2b.png 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https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv/icons/weNeedYou.png -------------------------------------------------------------------------------- /vv/make_vv_class.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | if [ -z "$1" ] 3 | then 4 | echo "Usage: make_vv_class.sh classname" 5 | exit 1 6 | fi 7 | if [ -e vv"$1".cxx ] 8 | then 9 | echo "Error: vv$1.cxx already exists classname" 10 | exit 1 11 | fi 12 | 13 | cp vvTemplateFile.cxx vv$1.cxx 14 | cp vvTemplateFile.h vv$1.h 15 | sed -i "s/XXX/$1/g" vv$1.* 16 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolConvert.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 400 10 | 300 11 | 12 | 13 | 14 | Form 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolFoo.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | vvToolFoo 4 | 5 | 6 | 7 | 0 8 | 0 9 | 358 10 | 213 11 | 12 | 13 | 14 | Form 15 | 16 | 17 | 18 | 19 | 20 | Foo ! 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolInputSelectorWidget.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | vvToolInputSelectorWidget 4 | 5 | 6 | 7 | 0 8 | 0 9 | 676 10 | 381 11 | 12 | 13 | 14 | 15 | 8 16 | 17 | 18 | 19 | Form 20 | 21 | 22 | false 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolMIP.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | vvToolMIP 4 | 5 | 6 | 7 | 0 8 | 0 9 | 319 10 | 86 11 | 12 | 13 | 14 | Form 15 | 16 | 17 | 18 | 19 | 20 | Projection Dimension 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolPlastimatch.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | vvToolPlastimatch 4 | 5 | 6 | 7 | 0 8 | 0 9 | 400 10 | 300 11 | 12 | 13 | 14 | Form 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 0 24 | 0 25 | 26 | 27 | 28 | Plastimatch 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 0 37 | 0 38 | 39 | 40 | 41 | Put options here ... 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | -------------------------------------------------------------------------------- /vv/qt_ui/vvToolTest.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | vvToolTest 4 | 5 | 6 | 7 | 0 8 | 0 9 | 433 10 | 222 11 | 12 | 13 | 14 | Test sphere 15 | 16 | 17 | 18 | 19 | 20 | Qt::Horizontal 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /vv/vvAnimatedGIFWriter.h: -------------------------------------------------------------------------------- 1 | #ifndef __vvAnimatedGIFWriter_h 2 | #define __vvAnimatedGIFWriter_h 3 | 4 | #include 5 | 6 | #include 7 | #include 8 | 9 | class vtkImageAppend; 10 | 11 | class vvAnimatedGIFWriter : public vtkGenericMovieWriter //test this if link error... 12 | { 13 | public: 14 | static vvAnimatedGIFWriter *New(); 15 | vtkTypeMacro(vvAnimatedGIFWriter,vtkGenericMovieWriter); 16 | void PrintSelf(ostream& os, vtkIndent indent) override; 17 | 18 | // Description: 19 | // These methods start writing an Movie file, write a frame to the file 20 | // and then end the writing process. 21 | void Start() override; 22 | void Write() override; 23 | void End() override; 24 | 25 | // Description: 26 | // Set/Get the frame rate, in frame/s. 27 | vtkSetClampMacro(Rate, int, 1, 5000); 28 | vtkGetMacro(Rate, int); 29 | 30 | // Description: 31 | // Set/Get the number of loops, 0 means infinite 32 | vtkSetClampMacro(Loops, int, 0, 5000); 33 | vtkGetMacro(Loops, int); 34 | 35 | // Description: 36 | // Set/Get the dithering 37 | vtkSetMacro(Dither, bool); 38 | vtkGetMacro(Dither, bool); 39 | 40 | protected: 41 | vvAnimatedGIFWriter(); 42 | ~vvAnimatedGIFWriter(); 43 | 44 | int Rate; 45 | int Loops; 46 | bool Dither; 47 | 48 | vtkSmartPointer RGBvolume; 49 | std::vector< vtkSmartPointer > RGBslices; 50 | 51 | private: 52 | vvAnimatedGIFWriter(const vvAnimatedGIFWriter&); // Not implemented 53 | void operator=(const vvAnimatedGIFWriter&); // Not implemented 54 | }; 55 | 56 | #endif 57 | -------------------------------------------------------------------------------- /vv/vvClipPolyData.h: -------------------------------------------------------------------------------- 1 | #ifndef VVCLIPPOLYDATA_H 2 | #define VVCLIPPOLYDATA_H 3 | 4 | #include "vtkClipPolyData.h" 5 | 6 | class vvClipPolyData : public vtkClipPolyData 7 | { 8 | public: 9 | vtkTypeMacro(vvClipPolyData,vtkClipPolyData); 10 | void PrintSelf(ostream& os, vtkIndent indent) override; 11 | 12 | static vvClipPolyData *New(); 13 | 14 | protected: 15 | vvClipPolyData(); 16 | ~vvClipPolyData(); 17 | 18 | int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *) override; 19 | 20 | private: 21 | vvClipPolyData(const vvClipPolyData&); // Not implemented. 22 | void operator=(const vvClipPolyData&); // Not implemented. 23 | }; 24 | 25 | #endif // VVCLIPPOLYDATA_H 26 | -------------------------------------------------------------------------------- /vv/vvConfiguration.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef vv_configuration_h 20 | #define vv_configuration_h 21 | 22 | #define VV_VERSION "v@CPACK_PACKAGE_VERSION_MAJOR@.@CPACK_PACKAGE_VERSION_MINOR@.@CPACK_PACKAGE_VERSION_PATCH@" 23 | 24 | #endif 25 | -------------------------------------------------------------------------------- /vv/vvCropDialog.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef vvCropDialog_h 19 | #define vvCropDialog_h 20 | #include 21 | #include 22 | class vvSlicerManager; 23 | #include "vvImage.h" 24 | #include "ui_vvCropDialog.h" 25 | 26 | ///Allows the user to create a new image by cropping an existing one 27 | class vvCropDialog : public QDialog,private Ui::vvCropDialog 28 | { 29 | Q_OBJECT 30 | public: 31 | vvCropDialog(std::vector sms,int current=0); 32 | vvImage::Pointer GetOutput() {return mResult;} 33 | 34 | protected: 35 | std::vector mSlicerManagers; 36 | vvImage::Pointer mResult; 37 | 38 | private slots: 39 | void ImageChanged(int newindex); 40 | void ComputeCroppedImage(); 41 | }; 42 | 43 | #endif 44 | -------------------------------------------------------------------------------- /vv/vvDocumentation.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef vvDocumentation_h 19 | #define vvDocumentation_h 20 | #include 21 | #include 22 | 23 | #include "ui_vvDocumentation.h" 24 | 25 | class vvDocumentation : public QDialog, private Ui::vvDocumentation 26 | { 27 | Q_OBJECT 28 | 29 | public: 30 | vvDocumentation() { 31 | setupUi(this); 32 | } 33 | ~vvDocumentation() {} 34 | 35 | public slots: 36 | 37 | private: 38 | 39 | }; 40 | 41 | #endif 42 | -------------------------------------------------------------------------------- /vv/vvHelpDialog.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef vvHelpDialog_h 19 | #define vvHelpDialog_h 20 | #include 21 | #include 22 | 23 | #include "ui_vvHelpDialog.h" 24 | 25 | class vvHelpDialog : public QDialog, private Ui::vvHelpDialog 26 | { 27 | Q_OBJECT 28 | 29 | public: 30 | vvHelpDialog() { 31 | setupUi(this); 32 | } 33 | ~vvHelpDialog() {} 34 | 35 | public slots: 36 | 37 | private: 38 | 39 | }; 40 | 41 | #endif 42 | -------------------------------------------------------------------------------- /vv/vvIcon.rc: -------------------------------------------------------------------------------- 1 | // Icon with lowest ID value placed first to ensure application icon 2 | // remains consistent on all systems. 3 | IDI_ICON1 ICON "icons/ducky.ico" 4 | 5 | -------------------------------------------------------------------------------- /vv/vvMainWindowBase.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #include "vvMainWindowBase.h" 20 | 21 | //------------------------------------------------------------------------------ 22 | QMenu * vvMainWindowBase::GetMenu(std::string menuName) const 23 | { 24 | if (menuName == "Tools") return mMenuTools; 25 | if (menuName == "Segmentation") return mMenuSegmentation; 26 | std::cerr << "Error in vvMainWindowBase::GetMenu: menu '" << menuName << "' is unknown." << std::endl; 27 | exit(0); 28 | } 29 | //------------------------------------------------------------------------------ 30 | 31 | 32 | -------------------------------------------------------------------------------- /vv/vvOSXHelper.h: -------------------------------------------------------------------------------- 1 | #ifndef _OSX_HELPER_ 2 | #define _OSX_HELPER_ 3 | 4 | // For retina displays, see 5 | // http://public.kitware.com/pipermail/vtkusers/2015-February/090117.html 6 | void disableGLHiDPI( long a_id ); 7 | 8 | #endif 9 | 10 | -------------------------------------------------------------------------------- /vv/vvOSXHelper.mm: -------------------------------------------------------------------------------- 1 | #include 2 | #include "vvOSXHelper.h" 3 | 4 | // For retina displays, see 5 | // http://public.kitware.com/pipermail/vtkusers/2015-February/090117.html 6 | void disableGLHiDPI( long a_id ){ 7 | NSView *view = reinterpret_cast( a_id ); 8 | [view setWantsBestResolutionOpenGLSurface:NO]; 9 | } 10 | 11 | -------------------------------------------------------------------------------- /vv/vvPacsSettingsDialog.cxx: -------------------------------------------------------------------------------- 1 | #include "vvPacsSettingsDialog.h" 2 | #include "vvQPacsConnection.h" 3 | #include "vvUtils.h" 4 | 5 | vvPacsSettingsDialog::vvPacsSettingsDialog(QWidget *i_parent) 6 | : QDialog(i_parent) 7 | { 8 | mparent = i_parent; 9 | ui.setupUi(this); 10 | update(); 11 | } 12 | 13 | void vvPacsSettingsDialog::accept() 14 | { 15 | 16 | AddDicomServer(ui.NameEdit->text().toStdString(),ui.AETitleEdit->text().toStdString(),ui.AdressEdit->text().toStdString(), ui.PortEdit->text().toStdString()); 17 | ((vvQPacsConnection*)this->parent())->refreshNetworks(); 18 | close(); 19 | } -------------------------------------------------------------------------------- /vv/vvPacsSettingsDialog.h: -------------------------------------------------------------------------------- 1 | #ifndef __vvPacsSettingsDialog_H 2 | #define __vvPacsSettingsDialog_H 3 | #include "ui_vvPacsSettingsDialog.h" 4 | #include 5 | #include 6 | 7 | class vvPacsSettingsDialog : public QDialog 8 | { 9 | Q_OBJECT 10 | public: 11 | 12 | vvPacsSettingsDialog(QWidget *parent=0); 13 | 14 | ~vvPacsSettingsDialog(){} 15 | private: 16 | QWidget *mparent; 17 | Ui::vvPacsSettingsDialog ui; 18 | private slots: 19 | void accept(); 20 | 21 | }; 22 | #endif //__vvPacsSettingsDialog_H 23 | -------------------------------------------------------------------------------- /vv/vvProgressDialog.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef VVPROGRESSDIALOG_H 20 | #define VVPROGRESSDIALOG_H 21 | 22 | // vv 23 | #include "ui_vvProgressDialog.h" 24 | 25 | //------------------------------------------------------------------------------ 26 | class vvProgressDialog : 27 | public QDialog, 28 | private Ui::vvProgressDialog 29 | { 30 | Q_OBJECT 31 | 32 | public: 33 | vvProgressDialog(std::string message,bool show_progress=false); 34 | ~vvProgressDialog() {} 35 | void SetCancelButtonEnabled(bool b); 36 | void SetText(std::string message); 37 | void AddToText(std::string message); 38 | void SetProgress(unsigned int current,unsigned int max); 39 | }; 40 | //------------------------------------------------------------------------------ 41 | 42 | #endif 43 | -------------------------------------------------------------------------------- /vv/vvReadState.h: -------------------------------------------------------------------------------- 1 | #ifndef VVREADSTATE_H 2 | #define VVREADSTATE_H 3 | 4 | #include 5 | #include 6 | 7 | class vvMainWindow; 8 | class QXmlStreamReader; 9 | class QFile; 10 | 11 | class vvReadState 12 | { 13 | public: 14 | vvReadState(); 15 | virtual ~vvReadState(); 16 | 17 | virtual void Run(vvMainWindow* vvWindow, const std::string& file); 18 | int GetNumberOfImages() { return m_NumImages; } 19 | 20 | protected: 21 | 22 | void ReadGUI(); 23 | void ReadTree(); 24 | void ReadTools(); 25 | void ReadTool(const std::string & toolname); 26 | std::string ReadImage(); 27 | std::string ReadFusion(int index); 28 | std::string ReadOverlay(int index); 29 | std::string ReadVector(int index); 30 | std::string ReadLink(); 31 | 32 | #if __cplusplus > 199711L 33 | std::shared_ptr m_XmlReader; 34 | std::shared_ptr m_File; 35 | #else 36 | std::auto_ptr m_XmlReader; 37 | std::auto_ptr m_File; 38 | #endif 39 | vvMainWindow* m_Window; 40 | int m_TreeItemCount; 41 | int m_NumImages; 42 | }; 43 | 44 | #endif // VVREADSTATE_H 45 | -------------------------------------------------------------------------------- /vv/vvRegisterForm.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef vvRegisterForm_h 19 | #define vvRegisterForm_h 20 | 21 | #include "ui_vvRegisterForm.h" 22 | #include 23 | #include 24 | #include 25 | class vvRegisterForm : public QDialog, private Ui::vvRegisterForm 26 | { 27 | Q_OBJECT 28 | 29 | public: 30 | vvRegisterForm(QUrl url, QString path, QSettings::Format format); 31 | void sendData(); 32 | ~vvRegisterForm() {} 33 | virtual bool canPush(); 34 | virtual void acquitPushed(); 35 | public slots: 36 | virtual void accept(); 37 | virtual void show(); 38 | protected: 39 | QUrl url; 40 | QSettings settings; 41 | QNetworkAccessManager* manager; 42 | }; 43 | 44 | #endif 45 | -------------------------------------------------------------------------------- /vv/vvSaveState.h: -------------------------------------------------------------------------------- 1 | #ifndef VVSAVESTATE_H 2 | #define VVSAVESTATE_H 3 | 4 | #include 5 | #include 6 | #include "vvSlicerManager.h" 7 | 8 | class vvMainWindow; 9 | class QXmlStreamWriter; 10 | class QFile; 11 | class QTreeWidgetItem; 12 | 13 | class vvSaveState 14 | { 15 | public: 16 | vvSaveState(); 17 | virtual ~vvSaveState(); 18 | 19 | virtual void Run(vvMainWindow* vvWindow, const std::string& file); 20 | 21 | protected: 22 | 23 | void SaveGlobals(); 24 | void SaveGUI(); 25 | void SaveTree(); 26 | void SaveTools(); 27 | void SaveImage(const QTreeWidgetItem* item, int index); 28 | void SaveFusion(const QTreeWidgetItem* item, const vvSlicerManager* slicerManager); 29 | void SaveOverlay(const QTreeWidgetItem* item, const vvSlicerManager* slicerManager); 30 | void SaveVector(const QTreeWidgetItem* item); 31 | void SaveLink(const vvSlicerManager* slicerManager); 32 | 33 | #if __cplusplus > 199711L 34 | std::shared_ptr m_XmlWriter; 35 | std::shared_ptr m_File; 36 | #else 37 | std::auto_ptr m_XmlWriter; 38 | std::auto_ptr m_File; 39 | #endif 40 | vvMainWindow* m_Window; 41 | }; 42 | 43 | #endif // VVSAVESTATE_H 44 | -------------------------------------------------------------------------------- /vv/vvTemplateFile.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #include "vvXXX.h" 19 | -------------------------------------------------------------------------------- /vv/vvTemplateFile.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef vvXXX_h 19 | #define vvXXX_h 20 | #endif 21 | -------------------------------------------------------------------------------- /vv/vvToolBase.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | 19 | #ifndef VVTOOLBASE_CXX 20 | #define VVTOOLBASE_CXX 21 | #include "vvToolBase.h" 22 | 23 | #endif 24 | 25 | -------------------------------------------------------------------------------- /vv/vvToolFoo.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | Program: vv http://www.creatis.insa-lyon.fr/rio/vv 3 | 4 | Authors belong to: 5 | - University of LYON http://www.universite-lyon.fr/ 6 | - Léon Bérard cancer center http://www.centreleonberard.fr 7 | - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without even 10 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 11 | PURPOSE. See the copyright notices for more information. 12 | 13 | It is distributed under dual licence 14 | 15 | - BSD See included LICENSE.txt file 16 | - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 17 | ===========================================================================**/ 18 | #ifndef VVTOOLFOO_H 19 | #define VVTOOLFOO_H 20 | 21 | #include 22 | 23 | #include "vvToolBase.h" 24 | #include "ui_vvToolFoo.h" 25 | 26 | //------------------------------------------------------------------------------ 27 | class vvToolFoo: 28 | public QDialog, 29 | public vvToolBase, 30 | private Ui::vvToolFoo 31 | { 32 | Q_OBJECT 33 | public: 34 | vvToolFoo(vvMainWindowBase* parent = nullptr, Qt::WindowFlags f = Qt::WindowFlags{}); 35 | ~vvToolFoo(); 36 | 37 | static void Initialize(); 38 | 39 | protected: 40 | Ui::vvToolFoo ui; 41 | 42 | }; // end class vvToolFoo 43 | //------------------------------------------------------------------------------ 44 | 45 | #endif 46 | 47 | -------------------------------------------------------------------------------- /vv_entete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv_entete.png -------------------------------------------------------------------------------- /vv_helpscreenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv_helpscreenshot.png -------------------------------------------------------------------------------- /vv_popi.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv_popi.gif -------------------------------------------------------------------------------- /vv_vv1.1Overlay.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open-vv/vv/d74e0d414c7331763ccd823af28c84f6d9e8a3ab/vv_vv1.1Overlay.png --------------------------------------------------------------------------------