Paths

Table of Contentst

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CMake/PackageDepends/
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PackageDepends/
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MITK_GDCM_Config.cmake
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CMakeExternals/
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ITK-4.13.3.patch
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ITK-5.2.1.patch
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ITK.cmake
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MatchPoint.cmake
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CMakeLists.txt
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Documentation/Doxygen/3-DeveloperManual/Concepts/
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Doxygen/
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3-DeveloperManual/
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Concepts/
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BasicDataTypes.dox
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Examples/
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Plugins/
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org.mitk.example.gui.imaging/src/internal/colourimageprocessing/
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src/
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internal/
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colourimageprocessing/
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mitkColourImageProcessor.cpp
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org.mitk.example.gui.regiongrowing/
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CMakeLists.txt
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Tutorial/
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Step6/
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CMakeLists.txt
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Step7/
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CMakeLists.txt
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Step8/
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CMakeLists.txt
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Modules/
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AlgorithmsExt/
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include/
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mitkCropTimestepsImageFilter.h
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mitkNonBlockingAlgorithm.h
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src/
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mitkAnisotropicRegistrationCommon.cpp
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mitkAutoCropImageFilter.cpp
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mitkCovarianceMatrixCalculator.cpp
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mitkCropTimestepsImageFilter.cpp
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mitkMaskImageFilter.cpp
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mitkNonBlockingAlgorithm.cpp
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mitkPlaneFit.cpp
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mitkSimpleHistogram.cpp
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mitkWeightedPointTransform.cpp
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BasicImageProcessing/src/
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src/
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mitkTransformationOperation.cpp
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BoundingShape/
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include/
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mitkBoundingShapeInteractor.h
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src/Interactions/
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Interactions/
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mitkBoundingShapeInteractor.cpp
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CameraCalibration/
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mitkCameraIntrinsics.cpp
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mitkCameraIntrinsics.h
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mitkEndoDebug.cpp
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mitkTransform.cpp
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Classification/
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CLMiniApps/
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CMakeLists.txt
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CLUtilities/
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CMakeLists.txt
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include/
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itkEnhancedScalarImageToRunLengthMatrixFilter.hxx
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itkLocalIntensityFilter.hxx
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itkLocalStatisticFilter.hxx
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itkMultiHistogramFilter.cpp
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itkNeighborhoodFunctorImageFilter.h
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src/Features/
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Features/
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itkLineHistogramBasedMassImageFilter.cpp
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CLVigraRandomForest/
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include/
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mitkPURFClassifier.h
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mitkVigraRandomForestClassifier.h
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src/Classifier/
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Classifier/
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mitkPURFClassifier.cpp
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mitkVigraRandomForestClassifier.cpp
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ContourModel/
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DataManagement/
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mitkContourElement.cpp
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mitkContourElement.h
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mitkContourModel.cpp
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mitkContourModel.h
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IO/
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mitkContourModelWriter.h
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Core/
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CMakeLists.txt
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files.cmake
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include/
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itkImportMitkImageContainer.h
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itkVtkAbstractTransform.h
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itkVtkAbstractTransform.txx
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mitkAbstractTransformGeometry.h
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mitkAffineTransform3D.h
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mitkArray.h
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mitkBaseData.h
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mitkBaseGeometry.h
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mitkBaseRenderer.h
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mitkDataInteractor.h
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mitkDataNode.h
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mitkDataStorage.h
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mitkEqual.h
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mitkExtractSliceFilter2.h
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mitkIOUtil.h
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mitkImage.h
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mitkImageAccessorBase.h
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mitkImageGenerator.h
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mitkImageSource.h
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mitkImageToItk.txx
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mitkInteractionSchemeSwitcher.h
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mitkLimitedLinearUndo.h
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mitkMessage.h
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mitkPixelType.h
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mitkPixelTypeMultiplex.h
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mitkPixelTypeTraits.h
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mitkPointSet.h
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mitkPropertyList.h
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mitkRenderingManager.h
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mitkSliceNavigationController.h
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mitkSlicesCoordinator.h
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mitkStandaloneDataStorage.h
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mitkUtf8Util.h
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src/
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Algorithms/
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mitkExtractSliceFilter2.cpp
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mitkHistogramGenerator.cpp
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mitkImageSource.cpp
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mitkMultiComponentImageDataComparisonFilter.cpp
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mitkRGBToRGBACastImageFilter.cpp
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Controllers/
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mitkLimitedLinearUndo.cpp
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mitkRenderingManager.cpp
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mitkSlicesCoordinator.cpp
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DataManagement/
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mitkAbstractTransformGeometry.cpp
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mitkBaseData.cpp
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mitkBaseGeometry.cpp
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mitkDataNode.cpp
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mitkDataStorage.cpp
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mitkGeometryTransformHolder.cpp
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mitkImage.cpp
-
mitkImageAccessorBase.cpp
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mitkImageDataItem.cpp
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mitkImageReadAccessor.cpp
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mitkImageStatisticsHolder.cpp
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mitkImageVtkReadAccessor.cpp
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mitkImageVtkWriteAccessor.cpp
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mitkImageWriteAccessor.cpp
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mitkLevelWindow.cpp
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mitkPlaneGeometry.cpp
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mitkPointSet.cpp
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mitkPropertyList.cpp
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mitkStandaloneDataStorage.cpp
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IO/
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mitkAbstractFileReader.cpp
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mitkAbstractFileWriter.cpp
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mitkCustomMimeType.cpp
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mitkFileReaderSelector.cpp
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mitkFileWriterSelector.cpp
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mitkIOMimeTypes.cpp
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mitkIOUtil.cpp
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mitkItkImageIO.cpp
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mitkLog.cpp
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mitkPixelType.cpp
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mitkRawImageFileReader.h
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mitkStandardFileLocations.cpp
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mitkSurfaceVtkIO.cpp
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mitkUtf8Util.cpp
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Interactions/
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mitkDataInteractor.cpp
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mitkDisplayActionEventBroadcast.cpp
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mitkDisplayInteractor.cpp
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mitkInteractionSchemeSwitcher.cpp
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Rendering/
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mitkBaseRenderer.cpp
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mitkImageVtkMapper2D.cpp
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mitkCoreServices.cpp
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test/
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mitkArbitraryTimeGeometryTest.cpp
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mitkBaseGeometryTest.cpp
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mitkIOUtilTest.cpp
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mitkImageAccessorTest.cpp
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mitkImageDimensionConverterTest.cpp
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mitkImageGeneratorTest.cpp
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mitkImportItkImageTest.cpp
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mitkItkImageIOTest.cpp
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mitkLogTest.cpp
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mitkPixelTypeTest.cpp
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mitkPlanePositionManagerTest.cpp
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mitkSurfaceToImageFilterTest.cpp
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mitkTinyXMLTest.cpp
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DICOM/
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CMakeLists.txt
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autoload/DICOMImageIO/include/
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DICOMImageIO/
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include/
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mitkDICOMTagsOfInterestService.h
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include/
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mitkDICOMITKSeriesGDCMReader.h
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mitkDICOMTagScanner.h
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src/
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legacy/
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mitkDicomSR_LoadDICOMRGBPixel.cpp
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mitkDicomSR_LoadDICOMRGBPixel4D.cpp
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mitkDicomSR_LoadDICOMScalar.cpp
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mitkDicomSR_LoadDICOMScalar4D.cpp
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mitkDicomSeriesReader.cpp
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mitkDICOMITKSeriesGDCMReader.cpp
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mitkDICOMTagScanner.cpp
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mitkITKDICOMSeriesReaderHelper.cpp
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DICOMTesting/
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include/
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mitkTestDICOMLoading.h
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src/
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mitkTestDICOMLoading.cpp
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DataTypesExt/
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include/
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mitkAffineBaseDataInteractor3D.h
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src/
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mitkAffineBaseDataInteractor3D.cpp
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IGT/
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Algorithms/
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mitkNavigationDataToPointSetFilter.cpp
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mitkPivotCalibration.cpp
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IO/
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mitkNavigationDataPlayer.h
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Rendering/
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mitkNavigationDataSliceVisualization.cpp
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Testing/
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mitkTrackingDeviceTest.cpp
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TrackingDevices/
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mitkClaronTool.h
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mitkClaronTrackingDevice.cpp
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mitkClaronTrackingDevice.h
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mitkNDITrackingDevice.cpp
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mitkNDITrackingDevice.h
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mitkOpenIGTLinkTrackingDevice.cpp
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mitkOpenIGTLinkTrackingDevice.h
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mitkOpenIGTLinkTrackingTool.h
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mitkOptitrackTrackingDevice.cpp
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mitkOptitrackTrackingDevice.h
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mitkOptitrackTrackingTool.h
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mitkTrackingDevice.cpp
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mitkTrackingDevice.h
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mitkTrackingTool.cpp
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mitkTrackingTool.h
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mitkVirtualTrackingDevice.cpp
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mitkVirtualTrackingDevice.h
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mitkVirtualTrackingTool.cpp
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mitkVirtualTrackingTool.h
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ImageDenoising/
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Testing/
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itkTotalVariationDenoisingImageFilterTest.cpp
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itkLocalVariationImageFilter.txx
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itkTotalVariationDenoisingImageFilter.txx
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itkTotalVariationSingleIterationImageFilter.txx
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ImageExtraction/
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mitkExtractImageFilter.cpp
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ImageStatistics/
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Testing/
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mitkImageStatisticsCalculatorTest.cpp
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mitkImageStatisticsTextureAnalysisTest.cpp
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files.cmake
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itkMultiGaussianImageSource.hxx
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mitkExtendedLabelStatisticsImageFilter.h
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mitkExtendedLabelStatisticsImageFilter.hxx
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mitkExtendedStatisticsImageFilter.h
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mitkExtendedStatisticsImageFilter.hxx
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mitkHotspotMaskGenerator.cpp
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mitkImageStatisticsCalculator.cpp
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mitkLabelStatisticsImageFilter.h
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mitkLabelStatisticsImageFilter.hxx
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mitkMinMaxImageFilterWithIndex.h
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mitkMinMaxImageFilterWithIndex.hxx
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mitkMinMaxLabelmageFilterWithIndex.h
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mitkMinMaxLabelmageFilterWithIndex.hxx
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mitkPlanarFigureMaskGenerator.cpp
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mitkStatisticsImageFilter.h
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mitkStatisticsImageFilter.hxx
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ImageStatisticsUI/
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Qmitk/
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QmitkImageStatisticsTreeModel.cpp
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QmitkImageStatisticsTreeModel.h
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test/
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QmitkImageStatisticsDataGeneratorTest.cpp
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LegacyIO/
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mitkImageWriter.cpp
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mitkItkImageFileReader.cpp
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MatchPointRegistration/
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include/
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itkStitchImageFilter.h
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itkStitchImageFilter.tpp
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src/Helper/
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Helper/
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mitkImageStitchingHelper.cpp
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ModelFit/
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include/
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itkMaskedStatisticsImageFilter.hxx
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itkMultiOutputNaryFunctorImageFilter.tpp
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mitkBinaryImageToLabelSetImageFilter.h
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mitkModelFitFunctorBase.h
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mitkModelFitInfo.h
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src/
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Common/
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mitkBinaryImageToLabelSetImageFilter.cpp
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mitkTimeGridHelper.cpp
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Functors/
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mitkModelFitFunctorBase.cpp
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test/
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itkMaskedStatisticsImageFilterTest.cpp
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itkMultiOutputNaryFunctorImageFilterTest.cpp
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Multilabel/
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CMakeLists.txt
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autoload/IO/
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IO/
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mitkLabelSetImageIO.cpp
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mitkLabelSetImageConverter.cpp
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OpenCVVideoSupport/
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Commands/
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mitkGrabCutOpenCVImageFilter.cpp
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mitkGrabCutOpenCVImageFilter.h
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Testing/
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mitkOpenCVToMitkImageFilterTest.cpp
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mitkOpenCVToMitkImageFilter.cpp
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mitkOpenCVToMitkImageFilter.h
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OpenIGTLink/
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Filters/
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mitkImageToIGTLMessageFilter.cpp
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mitkIGTLClient.cpp
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mitkIGTLDevice.cpp
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mitkIGTLDevice.h
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mitkIGTLMessageProvider.cpp
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mitkIGTLMessageProvider.h
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mitkIGTLMessageQueue.cpp
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mitkIGTLMessageQueue.h
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mitkIGTLMessageSource.cpp
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mitkIGTLMessageSource.h
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mitkIGTLServer.cpp
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mitkIGTLServer.h
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PlanarFigure/
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include/
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mitkPlanarFigureInteractor.h
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src/Interactions/
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Interactions/
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mitkPlanarFigureInteractor.cpp
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Python/autoload/PythonService/
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autoload/
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PythonService/
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mitkPythonService.cpp
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RT/src/
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src/
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mitkDoseImageVtkMapper2D.cpp
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Segmentation/
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Algorithms/
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itkAdaptiveThresholdIterator.h
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itkAdaptiveThresholdIterator.txx
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itkContourExtractor2DImageFilter.h
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itkContourExtractor2DImageFilter.txx
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mitkCorrectorAlgorithm.cpp
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mitkDiffImageApplier.cpp
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mitkSurfaceStampImageFilter.cpp
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CMakeLists.txt
-
DataManagement/
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mitkExtrudedContour.cpp
-
mitkExtrudedContour.h
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Interactions/
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mitkBinaryThresholdBaseTool.cpp
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mitkTool.cpp
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mitkToolEvents.h
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mitkWatershedTool.cpp
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SegmentationUtilities/BooleanOperations/
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BooleanOperations/
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mitkBooleanOperation.cpp
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SegmentationUI/Qmitk/
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Qmitk/
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QmitkSlicesInterpolator.cpp
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SurfaceInterpolation/
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mitkComputeContourSetNormalsFilter.cpp
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ToFHardware/
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mitkToFCameraDevice.cpp
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mitkToFCameraDevice.h
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mitkToFCameraMITKPlayerDevice.cpp
-
mitkToFCameraMITKPlayerDevice.h
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mitkToFImageRecorder.cpp
-
mitkToFImageRecorder.h
-
mitkToFNrrdImageWriter.cpp
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TubeGraph/
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include/
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mitkTubeGraphDataInteractor.h
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src/Interactions/
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Interactions/
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mitkTubeGraphDataInteractor.cpp
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US/
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USFilters/
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mitkUSImageSource.cpp
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mitkUSImageSource.h
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USModel/
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mitkUSDevice.cpp
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mitkUSDevice.h
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mitkUSIGTLDevice.cpp
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mitkUSVideoDevice.cpp
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Plugins/
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org.mitk.gui.qt.basicimageprocessing/
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CMakeLists.txt
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org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/
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CMakeLists.txt
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org.mitk.gui.qt.imagecropper/src/internal/
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src/
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internal/
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QmitkImageCropperView.cpp
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org.mitk.gui.qt.imagenavigator/src/internal/
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src/
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internal/
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QmitkImageNavigatorView.cpp
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org.mitk.gui.qt.matchpoint.visualizer/src/internal/
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src/
-
internal/
-
QmitkMatchPointRegistrationVisualizer.cpp
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org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/
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src/
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internal/
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SegmentationUtilities/
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ImageMasking/
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QmitkImageMaskingWidget.cpp

Diffusion MITK 145223cf223f

Migrate from ITK v4.13.3 to v5.2.1
145223cf223f
Actions

Description

Migrate from ITK v4.13.3 to v5.2.1

Summary:
Upgrade MatchPoint to an ITK v5.1 compatible version

Migrate MitkCore to ITK v5.1

Migrate Core test driver to ITK v5.2

Refactor UTF-8 conversion from IOUtil into Utf8Util

itksys::SystemTools is now based on UTF-8.

Fix error introduced during ITK 5 migration

Continue ITK v5 migration

Migrate MinMax(Label)ImageFilterWithIndex to ITK v5

Use ITK v5.2.1 instead of v5.2.0

Fix errors reported by Visual Studio 2022

Continue migration to ITK v5

Building the whole solution in WorkbenchRelease configuration works
now except for the image statistics calculation filter, which needs
a more sophisticated upgrade.

Complete first version of migrated image statistics filter

Fix event definition

Fix missing dependency

Set measurement vector size of histogram before its initialization

Migrate label statistics image filter to ITK v5

Add patch to make ITK 5 compatible to itself

Migrate more classes to ITK v5

Migrate legacy ITK threading to C++ standard library threading

I isolated the migration of threading involving the replacement of
itk::MultiThreader with std::thread in this commit as it has a high
potential of unwanted/unexpected runtime changes or bugs.

Complete compile-time ITK v5 migration in All configuration

This is a major milestone of the ITK v5 migration. It is supposed to
result in successful builds of the Differential build clients.
Platform-related fixes may be necessary.

Several tests including critical image statistics tests fail and hence
potential bugs introduced with the migration must be fixed before the
migration is ready for the develop branch.

Ref T27437

Test Plan: No test plan. This Differential is meant as a preview and to facilitate the Differential build clients.

Reviewers: O1 MITK Reviewer Group I, O3 MITK Reviewer Group II, floca

Reviewed By: O1 MITK Reviewer Group I, O3 MITK Reviewer Group II, floca

Tags: Breaking Change

Maniphest Tasks: T27437

Differential Revision: https://phabricator.mitk.org/D595