[med-svn] [itksnap] 03/07: Merge tag 'upstream/3.6.0'
Gert Wollny
gewo at moszumanska.debian.org
Fri Apr 7 06:37:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
gewo pushed a commit to branch master
in repository itksnap.
commit b6409ed9aabd537c772982e15efbd60fd296c304
Merge: c87886f 1038731
Author: Gert Wollny <gewo at debian.org>
Date: Thu Apr 6 16:14:41 2017 +0000
Merge tag 'upstream/3.6.0'
Upstream version 3.6.0
.gitmodules | 6 +
CMake/standalone.cmake | 5 -
CMakeLists.txt | 208 +-
CTestConfig.cmake | 6 +-
Common/CommandLineArgumentParser.cxx | 2 +-
Common/HistoryManager.cxx | 31 +
Common/HistoryManager.h | 4 +
Common/IPCHandler.cxx | 2 +-
Common/IRISVectorTypesToITKConversion.h | 26 +
...tkBSplineScatteredDataPointSetToImageFilter.txx | 4 +-
.../itkMorphologicalContourInterpolator.h | 413 +++
.../itkMorphologicalContourInterpolator.hxx | 1723 ++++++++++++
...arallelSparseFieldLevelSetImageFilterBugFix.txx | 3 +-
...orTypesToITKConversion.h => ImageFunctions.cxx} | 58 +-
Common/ImageFunctions.h | 93 +
Common/PresetManager.hxx | 3 +-
Common/Registry.cxx | 72 +-
Common/Registry.h | 19 +
Common/SNAPCommon.h | 9 +
Common/SystemInterface.cxx | 8 +-
Common/SystemInterface.h | 2 +-
Common/ThreadSpecificData.cxx | 90 +-
Common/ThreadSpecificData.h | 36 +
GUI/Model/AnnotationModel.cxx | 119 +-
GUI/Model/AnnotationModel.h | 16 +-
GUI/Model/Generic3DModel.cxx | 72 +-
GUI/Model/GenericSliceModel.cxx | 269 +-
GUI/Model/GenericSliceModel.h | 105 +-
GUI/Model/GlobalUIModel.cxx | 22 +-
GUI/Model/GlobalUIModel.h | 24 +
GUI/Model/ImageIOWizardModel.cxx | 158 +-
GUI/Model/ImageIOWizardModel.h | 90 +-
GUI/Model/ImageInfoModel.cxx | 4 +-
GUI/Model/ImageRegistrationManager.cxx | 175 --
GUI/Model/ImageRegistrationManager.h | 70 -
GUI/Model/InteractiveRegistrationModel.cxx | 259 ++
GUI/Model/InteractiveRegistrationModel.h | 101 +
GUI/Model/InterpolateLabelModel.cxx | 119 +
GUI/Model/InterpolateLabelModel.h | 103 +
GUI/Model/LabelEditorModel.cxx | 28 +
GUI/Model/LabelEditorModel.h | 6 +
GUI/Model/LayerGeneralPropertiesModel.cxx | 24 +-
GUI/Model/LayerGeneralPropertiesModel.h | 2 +-
GUI/Model/LayerTableRowModel.cxx | 22 +-
GUI/Model/OrthogonalSliceCursorNavigationModel.cxx | 28 +-
GUI/Model/OrthogonalSliceCursorNavigationModel.h | 12 +-
GUI/Model/PaintbrushModel.cxx | 156 +-
GUI/Model/PaintbrushModel.h | 14 +-
GUI/Model/PolygonDrawingModel.cxx | 46 +-
GUI/Model/PolygonDrawingModel.h | 34 +-
GUI/Model/RegistrationModel.cxx | 1090 ++++++++
GUI/Model/RegistrationModel.h | 270 ++
GUI/Model/SaveModifiedLayersModel.cxx | 14 +-
GUI/Model/SaveModifiedLayersModel.h | 6 +-
GUI/Model/SliceWindowCoordinator.cxx | 151 +-
GUI/Model/SliceWindowCoordinator.h | 44 +-
GUI/Model/SnakeROIModel.cxx | 73 +-
GUI/Model/SnakeROIModel.h | 20 +-
GUI/Model/SnakeROIResampleModel.cxx | 6 +-
GUI/Model/SnakeROIResampleModel.h | 7 +-
GUI/Model/SnakeWizardModel.cxx | 81 +-
GUI/Model/SynchronizationModel.cxx | 10 +-
GUI/Qt/Components/DICOMListingTable.cxx | 68 +
GUI/Qt/Components/DICOMListingTable.h | 21 +
GUI/Qt/Components/FileChooserPanelWithHistory.cxx | 78 +-
GUI/Qt/Components/FileChooserPanelWithHistory.h | 8 +
GUI/Qt/Components/HistoryQListModel.cxx | 2 +-
GUI/Qt/Components/LayerInspectorRowDelegate.ui | 2 +-
GUI/Qt/Components/ProcessEventsITKCommand.h | 41 +
GUI/Qt/Components/QtReporterDelegates.cxx | 9 +
GUI/Qt/Components/SNAPQApplication.cxx | 115 +
GUI/Qt/Components/SNAPQApplication.h | 58 +
GUI/Qt/Components/SNAPQtCommon.cxx | 10 +-
GUI/Qt/Components/SliceViewPanel.cxx | 10 +
GUI/Qt/Components/SliceViewPanel.ui | 9 +
GUI/Qt/Components/ViewPanel3D.ui | 24 +-
GUI/Qt/Components/ZoomInspector.cxx | 8 +-
GUI/Qt/Components/ZoomInspector.ui | 2 +-
GUI/Qt/Coupling/QtRadioButtonCoupling.h | 11 +
GUI/Qt/Resources/SNAPResources.qrc | 2 +
GUI/Qt/Resources/reslice_16.png | Bin 0 -> 726 bytes
GUI/Qt/Resources/reslice_16 at 2x.png | Bin 0 -> 1764 bytes
GUI/Qt/View/CrosshairsInteractionMode.cxx | 55 +-
GUI/Qt/View/GenericView3D.cxx | 9 +-
GUI/Qt/View/PaintbrushInteractionMode.cxx | 8 +-
GUI/Qt/View/QtAbstractOpenGLBox.cxx | 21 +-
GUI/Qt/View/QtVTKRenderWindowBox.cxx | 28 +-
GUI/Qt/View/RegistrationInteractionMode.cxx | 98 +
GUI/Qt/View/RegistrationInteractionMode.h | 65 +
.../View/SliceWindowInteractionDelegateWidget.cxx | 4 +-
GUI/Qt/View/TestOpenGLDialog.h | 246 ++
GUI/Qt/Windows/DropActionDialog.cxx | 81 +-
GUI/Qt/Windows/DropActionDialog.h | 15 +-
GUI/Qt/Windows/DropActionDialog.ui | 6 +-
GUI/Qt/Windows/ImageIOWizard.cxx | 198 +-
GUI/Qt/Windows/ImageIOWizard.h | 19 +-
GUI/Qt/Windows/ImageIOWizard/RegistrationPage.cxx | 92 -
GUI/Qt/Windows/ImageIOWizard/RegistrationPage.h | 58 -
GUI/Qt/Windows/ImageIOWizard/RegistrationPage.ui | 154 --
GUI/Qt/Windows/InterpolateLabelsDialog.cxx | 63 +
GUI/Qt/Windows/InterpolateLabelsDialog.h | 36 +
GUI/Qt/Windows/InterpolateLabelsDialog.ui | 290 +++
GUI/Qt/Windows/LabelEditorDialog.cxx | 30 +
GUI/Qt/Windows/LabelEditorDialog.h | 8 +
GUI/Qt/Windows/LabelEditorDialog.ui | 20 +
GUI/Qt/Windows/LayerInspectorDialog.cxx | 22 +-
GUI/Qt/Windows/MainControlPanel.cxx | 6 +-
GUI/Qt/Windows/MainControlPanel.ui | 50 +-
GUI/Qt/Windows/MainImageWindow.cxx | 364 ++-
GUI/Qt/Windows/MainImageWindow.h | 37 +-
GUI/Qt/Windows/MainImageWindow.ui | 112 +-
GUI/Qt/Windows/PreferencesDialog.cxx | 5 +
GUI/Qt/Windows/PreferencesDialog.ui | 8 +-
GUI/Qt/Windows/Registration/RegistrationDialog.cxx | 309 +++
GUI/Qt/Windows/Registration/RegistrationDialog.h | 68 +
GUI/Qt/Windows/Registration/RegistrationDialog.ui | 931 +++++++
GUI/Qt/Windows/ReorientImageDialog.ui | 88 +-
GUI/Qt/Windows/ResampleDialog.cxx | 2 +-
GUI/Qt/Windows/SaveModifiedLayersDialog.cxx | 2 +-
GUI/Qt/Windows/SimpleFileDialogWithHistory.cxx | 23 +-
GUI/Qt/Windows/SimpleFileDialogWithHistory.h | 10 +-
GUI/Qt/Windows/SpeedImageDialog.cxx | 7 +-
GUI/Qt/Windows/SpeedImageDialog.ui | 177 +-
GUI/Qt/Windows/SplashPanel.ui | 2 +-
GUI/Qt/main.cxx | 277 +-
GUI/Renderer/AnnotationRenderer.cxx | 40 +-
GUI/Renderer/AnnotationRenderer.h | 4 +-
GUI/Renderer/CrosshairsRenderer.cxx | 12 +-
GUI/Renderer/Generic3DRenderer.cxx | 2 +-
GUI/Renderer/GenericSliceRenderer.cxx | 397 ++-
GUI/Renderer/GenericSliceRenderer.h | 59 +-
GUI/Renderer/IntensityCurveVTKRenderer.cxx | 6 +-
GUI/Renderer/OpenGLSliceTexture.cxx | 99 +-
GUI/Renderer/OpenGLSliceTexture.h | 45 +-
GUI/Renderer/OptimizationProgressRenderer.cxx | 60 +-
GUI/Renderer/OptimizationProgressRenderer.h | 15 +-
GUI/Renderer/OrientationGraphicRenderer.cxx | 2 +-
.../OrientationWidget/Reorient/ScanningROI.cxx | 16 +-
.../OrientationWidgetGUI.cxx | 24 +-
GUI/Renderer/PaintbrushRenderer.cxx | 2 +-
GUI/Renderer/PolygonDrawingRenderer.cxx | 48 +-
GUI/Renderer/PolygonDrawingRenderer.h | 10 +-
GUI/Renderer/RegistrationRenderer.cxx | 161 ++
GUI/Renderer/RegistrationRenderer.h | 29 +
GUI/Renderer/SliceWindowDecorationRenderer.cxx | 6 +-
GUI/Renderer/SnakeModeRenderer.cxx | 8 +-
GUI/Renderer/SnakeParameterPreviewRenderer.cxx | 3 +-
GUI/Renderer/SnakeParameterPreviewRenderer.h | 3 +-
GUI/Renderer/SnakeROIRenderer.cxx | 8 +-
GUI/Renderer/Window3DPicker.cxx | 10 +-
GUI/Renderer/Window3DPicker.h | 2 +-
Logic/Common/ImageCoordinateGeometry.cxx | 24 +-
Logic/Common/ImageCoordinateGeometry.h | 16 +-
Logic/Common/ImageCoordinateTransform.cxx | 116 +-
Logic/Common/ImageCoordinateTransform.h | 43 +-
Logic/Common/ImageRayIntersectionFinder.h | 20 +-
Logic/Common/ImageRayIntersectionFinder.txx | 24 +-
Logic/Common/MetaDataAccess.cxx | 5 +
Logic/Common/MetaDataAccess.h | 2 +
Logic/Common/SNAPAppearanceSettings.cxx | 39 +-
Logic/Common/SNAPAppearanceSettings.h | 1 +
Logic/Common/SNAPRegistryIO.cxx | 14 +-
Logic/Common/SNAPRegistryIO.h | 4 +-
Logic/Common/SNAPSegmentationROISettings.h | 4 -
Logic/Framework/GenericImageData.cxx | 219 +-
Logic/Framework/GenericImageData.h | 44 +-
Logic/Framework/GlobalState.h | 3 +-
Logic/Framework/IRISApplication.cxx | 845 ++++--
Logic/Framework/IRISApplication.h | 140 +-
Logic/Framework/ImageAnnotationData.cxx | 18 +-
Logic/Framework/ImageAnnotationData.h | 20 +-
Logic/Framework/ImageIODelegates.cxx | 43 +-
Logic/Framework/ImageIODelegates.h | 37 +-
Logic/Framework/SNAPImageData.cxx | 5 +-
Logic/Framework/SegmentationUpdateIterator.h | 287 ++
Logic/Framework/UndoDataManager.h | 90 +-
Logic/Framework/UndoDataManager.txx | 137 +-
Logic/ImageWrapper/DisplayMappingPolicy.cxx | 89 +-
Logic/ImageWrapper/DisplayMappingPolicy.h | 20 +-
Logic/ImageWrapper/GuidedNativeImageIO.cxx | 227 +-
Logic/ImageWrapper/GuidedNativeImageIO.h | 68 +-
Logic/ImageWrapper/ImageWrapper.cxx | 683 ++++-
Logic/ImageWrapper/ImageWrapper.h | 108 +-
Logic/ImageWrapper/ImageWrapperBase.h | 85 +-
Logic/ImageWrapper/ImageWrapperTraits.h | 12 +-
Logic/ImageWrapper/ScalarImageWrapper.cxx | 265 +-
Logic/ImageWrapper/ScalarImageWrapper.h | 27 +-
Logic/ImageWrapper/VectorImageWrapper.cxx | 70 +-
Logic/ImageWrapper/VectorImageWrapper.h | 7 +-
Logic/ImageWrapper/VectorToScalarImageAccessor.h | 32 +-
Logic/LevelSet/LevelSetExtensionFilter.h | 22 +-
Logic/LevelSet/SNAPAdvectionFieldImageFilter.h | 22 +-
Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx | 22 +-
Logic/LevelSet/SNAPLevelSetDriver.h | 25 +-
Logic/LevelSet/SNAPLevelSetDriver.txx | 25 +-
Logic/LevelSet/SNAPLevelSetFunction.h | 32 +-
Logic/LevelSet/SNAPLevelSetFunction.txx | 23 +-
Logic/LevelSet/SignedDistanceFilter.h | 131 -
Logic/LevelSet/SignedDistanceFilter.txx | 108 -
Logic/LevelSet/SnakeParameters.cxx | 22 +-
Logic/LevelSet/SnakeParameters.h | 135 +-
Logic/LevelSet/SnakeParametersPreviewPipeline.cxx | 64 +-
Logic/LevelSet/SnakeParametersPreviewPipeline.h | 1 -
Logic/Mesh/MultiLabelMeshPipeline.cxx | 61 +-
Logic/Mesh/MultiLabelMeshPipeline.h | 55 +-
Logic/Preprocessing/ImageCollectionToImageFilter.h | 2 +-
.../PreprocessingFilterConfigTraits.cxx | 2 +-
.../PreprocessingFilterConfigTraits.h | 8 +-
.../{RandomForest => }/RFClassificationEngine.cxx | 71 +-
.../{RandomForest => }/RFClassificationEngine.h | 20 +-
.../RandomForest/RandomForestClassifier.cxx | 37 -
.../RandomForest/RandomForestClassifier.h | 93 -
Logic/Preprocessing/SlicePreviewFilterWrapper.h | 8 +-
Logic/Preprocessing/SlicePreviewFilterWrapper.txx | 4 +-
Logic/RLEImage/RLEImage.h | 253 ++
Logic/RLEImage/RLEImage.txx | 260 ++
Logic/RLEImage/RLEImageConstIterator.h | 407 +++
Logic/RLEImage/RLEImageIterator.h | 154 ++
Logic/RLEImage/RLEImageRegionConstIterator.h | 220 ++
Logic/RLEImage/RLEImageRegionIterator.h | 139 +
Logic/RLEImage/RLEImageScanlineConstIterator.h | 144 +
Logic/RLEImage/RLEImageScanlineIterator.h | 80 +
Logic/RLEImage/RLERegionOfInterestImageFilter.h | 282 ++
Logic/RLEImage/RLERegionOfInterestImageFilter.txx | 533 ++++
Logic/Slicing/AdaptiveSlicingPipeline.h | 187 ++
Logic/Slicing/AdaptiveSlicingPipeline.txx | 287 ++
Logic/Slicing/FastLinearInterpolator.h | 886 +++++++
Logic/Slicing/IRISSlicer.h | 180 +-
Logic/Slicing/IRISSlicer.txx | 268 +-
Logic/Slicing/IRISSlicer_RLE.txx | 353 +++
.../ImageRegionConstIteratorWithIndexOverride.h | 74 +
.../IntensityToColorLookupTableImageFilter.cxx | 10 +
.../IntensityToColorLookupTableImageFilter.h | 9 +-
.../Slicing/LookupTableIntensityMappingFilter.cxx | 81 +-
Logic/Slicing/LookupTableIntensityMappingFilter.h | 3 +
Logic/Slicing/NonOrthogonalSlicer.h | 285 ++
Logic/Slicing/NonOrthogonalSlicer.txx | 431 +++
.../RGBALookupTableIntensityMappingFilter.cxx | 75 +-
.../RGBALookupTableIntensityMappingFilter.h | 4 +
README.git | 9 +
README.html | 98 +-
README.md | 67 +
ReleaseNotes.txt => ReleaseNotes.md | 241 +-
Submodules/c3d/.gitignore | 16 +
Submodules/c3d/CMakeLists.txt | 219 ++
Submodules/c3d/COPYING.txt | 674 +++++
.../c3d/CTestConfig.cmake | 13 +-
Submodules/c3d/Convert2DMain.cxx | 39 +
Submodules/c3d/Convert3DMain.cxx | 38 +
Submodules/c3d/Convert4DMain.cxx | 38 +
Submodules/c3d/ConvertException.h | 63 +
Submodules/c3d/ConvertImageND.cxx | 2609 +++++++++++++++++++
Submodules/c3d/ConvertImageND.h | 204 ++
Submodules/c3d/ConvertImageVersion.cxx.in | 2 +
Submodules/c3d/ConvertNDLibrary.cmake | 145 ++
Submodules/c3d/ImageStack.h | 103 +
Submodules/c3d/README.txt | 19 +
Submodules/c3d/adapters/.ResliceImage.cxx.swp | Bin 0 -> 16384 bytes
Submodules/c3d/adapters/AddImages.cxx | 65 +
Submodules/c3d/adapters/AddImages.h | 48 +
Submodules/c3d/adapters/AlignByLandmarks.cxx | 243 ++
Submodules/c3d/adapters/AlignByLandmarks.h | 54 +
Submodules/c3d/adapters/AntiAliasImage.cxx | 64 +
Submodules/c3d/adapters/AntiAliasImage.h | 48 +
Submodules/c3d/adapters/ApplyMetric.cxx | 470 ++++
Submodules/c3d/adapters/ApplyMetric.h | 73 +
Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx | 220 ++
Submodules/c3d/adapters/BiasFieldCorrectionN4.h | 48 +
Submodules/c3d/adapters/BinaryHoleFill.cxx | 58 +
Submodules/c3d/adapters/BinaryHoleFill.h | 48 +
Submodules/c3d/adapters/BinaryImageCentroid.cxx | 68 +
Submodules/c3d/adapters/BinaryImageCentroid.h | 48 +
Submodules/c3d/adapters/BinaryMathOperation.cxx | 99 +
Submodules/c3d/adapters/BinaryMathOperation.h | 60 +
Submodules/c3d/adapters/Canny.cxx | 86 +
Submodules/c3d/adapters/Canny.h | 48 +
Submodules/c3d/adapters/ClipImageIntensity.cxx | 55 +
Submodules/c3d/adapters/ClipImageIntensity.h | 48 +
Submodules/c3d/adapters/ComputeFFT.cxx | 85 +
Submodules/c3d/adapters/ComputeFFT.h | 48 +
Submodules/c3d/adapters/ComputeMoments.cxx | 101 +
Submodules/c3d/adapters/ComputeMoments.h | 48 +
Submodules/c3d/adapters/ComputeOverlaps.cxx | 97 +
Submodules/c3d/adapters/ComputeOverlaps.h | 48 +
Submodules/c3d/adapters/ConnectedComponents.cxx | 95 +
Submodules/c3d/adapters/ConnectedComponents.h | 48 +
Submodules/c3d/adapters/ConvertAdapter.h | 63 +
Submodules/c3d/adapters/CoordinateMap.cxx | 83 +
Submodules/c3d/adapters/CoordinateMap.h | 48 +
Submodules/c3d/adapters/CopyTransform.cxx | 67 +
Submodules/c3d/adapters/CopyTransform.h | 48 +
Submodules/c3d/adapters/CreateImage.cxx | 59 +
Submodules/c3d/adapters/CreateImage.h | 48 +
Submodules/c3d/adapters/CreateInterpolator.cxx | 96 +
Submodules/c3d/adapters/CreateInterpolator.h | 61 +
Submodules/c3d/adapters/DicomSeriesList.cxx | 124 +
Submodules/c3d/adapters/DicomSeriesList.h | 48 +
Submodules/c3d/adapters/ExtractRegion.cxx | 61 +
Submodules/c3d/adapters/ExtractRegion.h | 48 +
Submodules/c3d/adapters/ExtractSlice.cxx | 216 ++
Submodules/c3d/adapters/ExtractSlice.h | 51 +
Submodules/c3d/adapters/FlipImage.cxx | 65 +
Submodules/c3d/adapters/FlipImage.h | 48 +
Submodules/c3d/adapters/GeneralLinearModel.cxx | 91 +
Submodules/c3d/adapters/GeneralLinearModel.h | 48 +
Submodules/c3d/adapters/HessianObjectness.cxx | 87 +
Submodules/c3d/adapters/HessianObjectness.h | 48 +
Submodules/c3d/adapters/HistogramMatch.cxx | 69 +
Submodules/c3d/adapters/HistogramMatch.h | 48 +
Submodules/c3d/adapters/ImageERF.cxx | 58 +
Submodules/c3d/adapters/ImageERF.h | 48 +
Submodules/c3d/adapters/ImageGradient.cxx | 84 +
Submodules/c3d/adapters/ImageGradient.h | 48 +
Submodules/c3d/adapters/ImageLaplacian.cxx | 55 +
Submodules/c3d/adapters/ImageLaplacian.h | 48 +
Submodules/c3d/adapters/LabelOverlapMeasures.cxx | 135 +
Submodules/c3d/adapters/LabelOverlapMeasures.h | 48 +
Submodules/c3d/adapters/LabelStatistics.cxx | 106 +
Submodules/c3d/adapters/LabelStatistics.h | 48 +
Submodules/c3d/adapters/LandmarksToSpheres.cxx | 175 ++
Submodules/c3d/adapters/LandmarksToSpheres.h | 48 +
Submodules/c3d/adapters/LaplacianSharpening.cxx | 53 +
Submodules/c3d/adapters/LaplacianSharpening.h | 48 +
Submodules/c3d/adapters/LevelSetSegmentation.cxx | 192 ++
Submodules/c3d/adapters/LevelSetSegmentation.h | 60 +
Submodules/c3d/adapters/MRFVote.cxx | 189 ++
Submodules/c3d/adapters/MRFVote.h | 48 +
Submodules/c3d/adapters/MathematicalMorphology.cxx | 81 +
Submodules/c3d/adapters/MathematicalMorphology.h | 48 +
Submodules/c3d/adapters/MeanFilter.cxx | 61 +
Submodules/c3d/adapters/MeanFilter.h | 48 +
Submodules/c3d/adapters/MedianFilter.cxx | 58 +
Submodules/c3d/adapters/MedianFilter.h | 48 +
Submodules/c3d/adapters/MixtureModel.cxx | 124 +
Submodules/c3d/adapters/MixtureModel.h | 48 +
Submodules/c3d/adapters/MultiplyImages.cxx | 66 +
Submodules/c3d/adapters/MultiplyImages.h | 48 +
Submodules/c3d/adapters/NormalizeLocalWindow.cxx | 128 +
Submodules/c3d/adapters/NormalizeLocalWindow.h | 48 +
.../c3d/adapters/NormalizedCrossCorrelation.cxx | 131 +
.../c3d/adapters/NormalizedCrossCorrelation.h | 48 +
Submodules/c3d/adapters/OverlayLabelImage.cxx | 90 +
Submodules/c3d/adapters/OverlayLabelImage.h | 48 +
Submodules/c3d/adapters/PadImage.cxx | 78 +
Submodules/c3d/adapters/PadImage.h | 48 +
Submodules/c3d/adapters/PeronaMalik.cxx | 57 +
Submodules/c3d/adapters/PeronaMalik.h | 48 +
Submodules/c3d/adapters/PrintImageInfo.cxx | 260 ++
Submodules/c3d/adapters/PrintImageInfo.h | 49 +
Submodules/c3d/adapters/RFApply.cxx | 82 +
Submodules/c3d/adapters/RFApply.h | 48 +
Submodules/c3d/adapters/RFTrain.cxx | 176 ++
Submodules/c3d/adapters/RFTrain.h | 68 +
Submodules/c3d/adapters/Rank.cxx | 86 +
Submodules/c3d/adapters/Rank.h | 48 +
Submodules/c3d/adapters/ReadImage.cxx | 201 ++
Submodules/c3d/adapters/ReadImage.h | 58 +
Submodules/c3d/adapters/ReciprocalImage.cxx | 63 +
Submodules/c3d/adapters/ReciprocalImage.h | 48 +
Submodules/c3d/adapters/ReorderStack.cxx | 62 +
Submodules/c3d/adapters/ReorderStack.h | 48 +
Submodules/c3d/adapters/ReplaceIntensities.cxx | 79 +
Submodules/c3d/adapters/ReplaceIntensities.h | 48 +
Submodules/c3d/adapters/ResampleImage.cxx | 90 +
Submodules/c3d/adapters/ResampleImage.h | 48 +
Submodules/c3d/adapters/ResliceImage.cxx | 182 ++
Submodules/c3d/adapters/ResliceImage.h | 48 +
Submodules/c3d/adapters/SLICSuperVoxel.cxx | 79 +
Submodules/c3d/adapters/SLICSuperVoxel.h | 48 +
Submodules/c3d/adapters/SampleImage.cxx | 60 +
Submodules/c3d/adapters/SampleImage.h | 52 +
Submodules/c3d/adapters/ScalarToRGB.cxx | 96 +
Submodules/c3d/adapters/ScalarToRGB.h | 48 +
Submodules/c3d/adapters/ScaleShiftImage.cxx | 63 +
Submodules/c3d/adapters/ScaleShiftImage.h | 48 +
Submodules/c3d/adapters/SetOrientation.cxx | 86 +
Submodules/c3d/adapters/SetOrientation.h | 48 +
Submodules/c3d/adapters/SetSform.cxx | 89 +
Submodules/c3d/adapters/SetSform.h | 48 +
.../c3d/adapters/SignedDistanceTransform.cxx | 68 +
Submodules/c3d/adapters/SignedDistanceTransform.h | 48 +
.../c3d/adapters/SimpleElasticRegistration.cxx | 733 ++++++
.../c3d/adapters/SimpleElasticRegistration.h | 133 +
Submodules/c3d/adapters/SmoothImage.cxx | 88 +
Submodules/c3d/adapters/SmoothImage.h | 48 +
Submodules/c3d/adapters/SplitMultilabelImage.cxx | 85 +
Submodules/c3d/adapters/SplitMultilabelImage.h | 48 +
Submodules/c3d/adapters/StapleAlgorithm.cxx | 71 +
Submodules/c3d/adapters/StapleAlgorithm.h | 48 +
Submodules/c3d/adapters/TestImage.cxx | 94 +
Submodules/c3d/adapters/TestImage.h | 48 +
Submodules/c3d/adapters/ThresholdImage.cxx | 59 +
Submodules/c3d/adapters/ThresholdImage.h | 48 +
Submodules/c3d/adapters/TileImages.cxx | 94 +
Submodules/c3d/adapters/TileImages.h | 48 +
Submodules/c3d/adapters/TrimImage.cxx | 104 +
Submodules/c3d/adapters/TrimImage.h | 52 +
Submodules/c3d/adapters/UnaryMathOperation.cxx | 48 +
Submodules/c3d/adapters/UnaryMathOperation.h | 48 +
Submodules/c3d/adapters/UpdateMetadataKey.cxx | 53 +
Submodules/c3d/adapters/UpdateMetadataKey.h | 48 +
Submodules/c3d/adapters/Vote.cxx | 104 +
Submodules/c3d/adapters/Vote.h | 48 +
.../c3d/adapters/VoxelwiseComponentFunction.cxx | 186 ++
.../c3d/adapters/VoxelwiseComponentFunction.h | 51 +
Submodules/c3d/adapters/VoxelwiseRegression.cxx | 73 +
Submodules/c3d/adapters/VoxelwiseRegression.h | 48 +
Submodules/c3d/adapters/WarpImage.cxx | 105 +
Submodules/c3d/adapters/WarpImage.h | 48 +
Submodules/c3d/adapters/WarpLabelImage.cxx | 154 ++
Submodules/c3d/adapters/WarpLabelImage.h | 48 +
Submodules/c3d/adapters/WeightedSum.cxx | 76 +
Submodules/c3d/adapters/WeightedSum.h | 48 +
Submodules/c3d/adapters/WeightedSumVoxelwise.cxx | 74 +
Submodules/c3d/adapters/WeightedSumVoxelwise.h | 48 +
Submodules/c3d/adapters/WrapDimension.cxx | 90 +
Submodules/c3d/adapters/WrapDimension.h | 48 +
Submodules/c3d/adapters/WriteImage.cxx | 247 ++
Submodules/c3d/adapters/WriteImage.h | 58 +
.../generator/ConvertAdapterTemplate.cxx.in | 47 +
.../adapters/generator/ConvertAdapterTemplate.h.in | 48 +
Submodules/c3d/adapters/generator/runme.sh | 4 +
Submodules/c3d/api/ConvertAPI.cxx | 220 ++
Submodules/c3d/api/ConvertAPI.h | 98 +
Submodules/c3d/cmake/Package.cmake | 124 +
Submodules/c3d/doc/c3d.md | 1503 +++++++++++
Submodules/c3d/gui/CMake/DeployQt5.cmake | 337 +++
Submodules/c3d/gui/CommandEditor.cxx | 503 ++++
Submodules/c3d/gui/CommandEditor.h | 91 +
Submodules/c3d/gui/ConvertSyntaxHighlighter.cxx | 91 +
Submodules/c3d/gui/ConvertSyntaxHighlighter.h | 50 +
Submodules/c3d/gui/HistoryDialog.cxx | 177 ++
Submodules/c3d/gui/HistoryDialog.h | 51 +
Submodules/c3d/gui/HistoryDialog.ui | 107 +
Submodules/c3d/gui/MainWindow.cxx | 499 ++++
Submodules/c3d/gui/MainWindow.h | 92 +
Submodules/c3d/gui/MainWindow.ui | 210 ++
Submodules/c3d/gui/SettingsDialog.cxx | 88 +
Submodules/c3d/gui/SettingsDialog.h | 35 +
Submodules/c3d/gui/SettingsDialog.ui | 115 +
.../c3d/gui/Utilities/Forwarding/CMakeLists.txt | 19 +
.../gui/Utilities/Forwarding/SharedForwardExe.c.in | 27 +
Submodules/c3d/gui/main.cxx | 109 +
Submodules/c3d/gui/resources/macos/Info.plist | 29 +
Submodules/c3d/gui/resources/macos/c3dgui.icns | Bin 0 -> 142873 bytes
Submodules/c3d/gui/resources/macos/icon.graffle | 331 +++
.../c3d/gui/resources/macos/icon_256x256.png | Bin 0 -> 25300 bytes
.../c3d/gui/resources/macos/icon_512x512.png | Bin 0 -> 53630 bytes
Submodules/c3d/itkextras/CMakeLists.txt | 3 +
.../c3d/itkextras}/ImageCollectionToImageFilter.h | 1 +
.../ImageRegionConstIteratorWithIndexOverride.h | 78 +
.../OneDimensionalInPlaceAccumulateFilter.h | 123 +
.../OneDimensionalInPlaceAccumulateFilter.txx | 565 ++++
Submodules/c3d/itkextras/PovRayIO/CMakeLists.txt | 7 +
.../c3d/itkextras/PovRayIO/itkPovRayDF3ImageIO.cxx | 121 +
.../c3d/itkextras/PovRayIO/itkPovRayDF3ImageIO.h | 95 +
.../PovRayIO/itkPovRayDF3ImageIOFactory.cxx | 52 +
.../PovRayIO/itkPovRayDF3ImageIOFactory.h | 67 +
.../c3d/itkextras/RandomForest/CMakeLists.txt | 1 +
.../RandomForest/Library/classification.h | 0
.../itkextras}/RandomForest/Library/classifier.h | 1 +
.../c3d/itkextras}/RandomForest/Library/data.h | 0
.../c3d/itkextras}/RandomForest/Library/forest.h | 0
.../c3d/itkextras}/RandomForest/Library/imageio.h | 3 +-
.../RandomForest/Library/linearalgebra.h | 0
.../c3d/itkextras}/RandomForest/Library/node.h | 0
.../c3d/itkextras}/RandomForest/Library/random.h | 0
.../itkextras}/RandomForest/Library/statistics.h | 5 +-
.../c3d/itkextras}/RandomForest/Library/trainer.h | 0
.../RandomForest/Library/trainingcontext.h | 0
.../c3d/itkextras}/RandomForest/Library/tree.h | 6 +-
.../c3d/itkextras}/RandomForest/Library/type.h | 0
.../c3d/itkextras}/RandomForest/Library/utility.h | 0
.../RandomForest/RandomForestClassifier.cxx | 0
.../RandomForest/RandomForestClassifier.h | 197 ++
.../RandomForestClassifyImageFilter.h | 28 +-
.../RandomForestClassifyImageFilter.txx | 177 +-
Submodules/c3d/itkextras/VectorImageTools.h | 59 +
Submodules/c3d/itkextras/VoxBoIO/CMakeLists.txt | 7 +
.../c3d/itkextras/VoxBoIO/itkVoxBoCUBImageIO.cxx | 792 ++++++
.../c3d/itkextras/VoxBoIO/itkVoxBoCUBImageIO.h | 128 +
.../VoxBoIO/itkVoxBoCUBImageIOFactory.cxx | 52 +
.../itkextras/VoxBoIO/itkVoxBoCUBImageIOFactory.h | 67 +
Submodules/c3d/itkextras/gsGSAffine3DTransform.h | 159 ++
Submodules/c3d/itkextras/gsGSAffine3DTransform.txx | 501 ++++
.../itkGaussianInterpolateImageFunction.h | 267 ++
.../itkHessianToObjectnessMeasureImageFilter.h | 173 ++
.../itkHessianToObjectnessMeasureImageFilter.hxx | 206 ++
.../c3d/itkextras/itkLabelContourImageFilter.h | 226 ++
.../c3d/itkextras/itkLabelContourImageFilter.txx | 449 ++++
...itkLabelImageGaussianInterpolateImageFunction.h | 262 ++
.../itkextras/itkLabelOverlapMeasuresImageFilter.h | 208 ++
.../itkLabelOverlapMeasuresImageFilter.txx | 437 ++++
.../itkMultiScaleHessianBasedMeasureImageFilter.h | 225 ++
...itkMultiScaleHessianBasedMeasureImageFilter.hxx | 435 ++++
Submodules/c3d/itkextras/itkOrientedRASImage.h | 271 ++
.../c3d/itkextras/itkSLICSuperVoxelImageFilter.h | 111 +
.../c3d/itkextras/itkSLICSuperVoxelImageFilter.hxx | 285 ++
Submodules/c3d/utilities/AffineTransformTool.cxx | 785 ++++++
Submodules/c3d/utilities/CMakeLists.txt | 5 +
Submodules/c3d/utilities/bashcomp.sh | 120 +
Submodules/c3d/utilities/doc/Documentation.cxx | 194 ++
Submodules/c3d/utilities/doc/Documentation.h | 93 +
Submodules/c3d/utilities/hexdump.c | 2109 +++++++++++++++
Submodules/c3d/utilities/hexdump.h | 215 ++
Submodules/greedy/.CMakeLists.txt.un~ | Bin 0 -> 30805 bytes
Submodules/greedy/.gitignore | 5 +
Submodules/greedy/CMake/FindFFTW.cmake | 68 +
Submodules/greedy/CMake/Package.cmake | 123 +
Submodules/greedy/CMakeLists.txt | 88 +
Submodules/greedy/src/.SimpleWarpImageFilter.h.un~ | Bin 0 -> 609 bytes
.../greedy/src/.SimpleWarpImageFilter.txx.un~ | Bin 0 -> 555 bytes
Submodules/greedy/src/.greedy_main.cxx.un~ | Bin 0 -> 9909 bytes
Submodules/greedy/src/.lddmm_data.cxx.un~ | Bin 0 -> 195729 bytes
Submodules/greedy/src/.lddmm_data.h.un~ | Bin 0 -> 35112 bytes
Submodules/greedy/src/CommandLineHelper.h | 316 +++
Submodules/greedy/src/FastLinearInterpolator.h | 893 +++++++
.../greedy/src/FastWarpCompositeImageFilter.h | 142 +
.../greedy/src/FastWarpCompositeImageFilter.txx | 147 ++
Submodules/greedy/src/GreedyAPI.cxx | 2745 ++++++++++++++++++++
Submodules/greedy/src/GreedyAPI.h | 318 +++
Submodules/greedy/src/GreedyException.h | 60 +
Submodules/greedy/src/GreedyParameters.cxx | 69 +
Submodules/greedy/src/GreedyParameters.h | 221 ++
.../ImageRegionConstIteratorWithIndexOverride.h | 78 +
.../greedy/src/LinearTransformToWarpFilter.h | 106 +
.../greedy/src/LinearTransformToWarpFilter.txx | 104 +
.../src/MultiComponentApproximateNCCImageMetric.h | 242 ++
.../MultiComponentApproximateNCCImageMetric.txx | 496 ++++
.../greedy/src/MultiComponentImageMetricBase.h | 378 +++
.../greedy/src/MultiComponentImageMetricBase.txx | 512 ++++
.../src/MultiComponentMutualInfoImageMetric.h | 367 +++
.../src/MultiComponentMutualInfoImageMetric.txx | 592 +++++
.../greedy/src/MultiComponentNCCImageMetric.h | 271 ++
.../greedy/src/MultiComponentNCCImageMetric.txx | 641 +++++
.../greedy/src/MultiImageAffineMSDMetricFilter.h | 220 ++
.../greedy/src/MultiImageAffineMSDMetricFilter.txx | 258 ++
.../greedy/src/MultiImageOpticalFlowImageFilter.h | 142 +
.../src/MultiImageOpticalFlowImageFilter.txx | 174 ++
.../greedy/src/MultiImageRegistrationHelper.h | 238 ++
.../greedy/src/MultiImageRegistrationHelper.txx | 1210 +++++++++
.../greedy/src/MultiImageSimpleWarpImageFilter.h | 903 +++++++
.../greedy/src/MultiImageSimpleWarpImageFilter.txx | 1429 ++++++++++
.../src/OneDimensionalInPlaceAccumulateFilter.h | 123 +
.../src/OneDimensionalInPlaceAccumulateFilter.txx | 585 +++++
Submodules/greedy/src/SimpleWarpImageFilter.h | 208 ++
Submodules/greedy/src/SimpleWarpImageFilter.txx | 246 ++
Submodules/greedy/src/bk/SimpleWarpImageFilter.h | 195 ++
Submodules/greedy/src/bk/SimpleWarpImageFilter.txx | 236 ++
Submodules/greedy/src/bk/greedy_main.cxx | 295 +++
.../src/bk/itkGaussianInterpolateImageFunction.h | 267 ++
.../src/bk/itkOptLinearInterpolateImageFunction.h | 520 ++++
.../bk/itkOptLinearInterpolateImageFunction.txx | 160 ++
.../itkOptVectorLinearInterpolateImageFunction.h | 520 ++++
.../itkOptVectorLinearInterpolateImageFunction.txx | 160 ++
Submodules/greedy/src/bk/lddmm_common.h | 10 +
Submodules/greedy/src/bk/lddmm_data.cxx | 871 +++++++
Submodules/greedy/src/bk/lddmm_data.h | 172 ++
Submodules/greedy/src/bk/lddmm_main.cxx | 326 +++
Submodules/greedy/src/bk/lddmm_temp.cxx | 0
Submodules/greedy/src/greedy_main.cxx | 473 ++++
.../src/itkGaussianInterpolateImageFunction.h | 290 +++
.../itkOptVectorLinearInterpolateImageFunction.h | 520 ++++
.../itkOptVectorLinearInterpolateImageFunction.txx | 160 ++
.../itkVectorImageCentralDifferenceImageFunction.h | 150 ++
...tkVectorImageCentralDifferenceImageFunction.hxx | 93 +
Submodules/greedy/src/lddmm_common.h | 74 +
Submodules/greedy/src/lddmm_data.cxx | 1433 ++++++++++
Submodules/greedy/src/lddmm_data.h | 285 ++
Submodules/greedy/src/lddmm_main.cxx | 354 +++
.../greedy/src/macf/macf_fixed_point_inverse.cxx | 75 +
Submodules/greedy/src/macf/macf_gradient.cxx | 126 +
.../greedy/src/macf/macf_objective_and_delta.cxx | 108 +
.../src/macf/macf_objective_and_gradient.cxx | 94 +
Submodules/greedy/src/macf/macf_pyramid.cxx | 86 +
.../data/lddmm/test01_expected_result.nii.gz | Bin 0 -> 120766 bytes
.../greedy/testing/data/lddmm/test01_input.nii.gz | Bin 0 -> 18580 bytes
.../greedy/testing/data/phantom01_fixed.nii.gz | Bin 0 -> 7086 bytes
.../greedy/testing/data/phantom01_mask.nii.gz | Bin 0 -> 3689 bytes
.../greedy/testing/data/phantom01_moving.nii.gz | Bin 0 -> 60132 bytes
.../greedy/testing/data/phantom01_readme.txt | 9 +
Submodules/greedy/testing/data/phantom01_rigid.mat | 4 +
.../greedy/testing/data/phantom01_source.nii.gz | Bin 0 -> 3073 bytes
.../greedy/testing/data/phantom02_fixed.nii.gz | Bin 0 -> 7573 bytes
.../greedy/testing/data/phantom02_moving.nii.gz | Bin 0 -> 61666 bytes
.../greedy/testing/data/phantom03_fixed.nii.gz | Bin 0 -> 379368 bytes
.../greedy/testing/data/phantom03_moving.nii.gz | Bin 0 -> 7059886 bytes
Submodules/greedy/testing/data/runpair.sh | 32 +
Submodules/greedy/testing/data/src/phantoms.sh | 35 +
.../TestOneDimensionalInPlaceAccumulateFilter.cxx | 68 +
Testing/GUI/Qt/SNAPTestQt.cxx | 45 +-
Testing/GUI/Qt/SNAPTestQt.h | 6 +
Testing/GUI/Qt/Scripts/test_DiffSpace.js | 49 +
Testing/GUI/Qt/Scripts/test_Library.js | 17 +-
Testing/GUI/Qt/Scripts/test_Workspace.js | 2 +-
Testing/GUI/Qt/TestingScripts.qrc | 11 +-
Testing/Logic/SNAPTestDriver.cxx | 256 --
Testing/Logic/SNAPTestDriver.h | 63 -
Testing/Logic/SlicingPerformanceTest.cxx | 331 +++
Testing/Logic/TestBase.h | 100 -
Testing/Logic/TestCompareLevelSets.cxx | 850 ------
Testing/Logic/TestCompareLevelSets.h | 73 -
Testing/Logic/TestImageWrapper.h | 93 -
Testing/Logic/TestMain.cxx | 25 -
Testing/Logic/TutorialTest.cxx | 373 ---
Testing/Logic/iteratorTests.cxx | 25 +
Testing/Logic/itkImageIteratorTest.cxx | 280 ++
Testing/Logic/itkImageIteratorWithIndexTest.cxx | 399 +++
.../Logic/itkImageIteratorsForwardBackwardTest.cxx | 172 ++
...tkImageRegionConstIteratorWithOnlyIndexTest.cxx | 230 ++
Testing/Logic/itkImageRegionIteratorTest.cxx | 246 ++
Testing/Logic/itkImageScanlineIteratorTest1.cxx | 235 ++
Testing/Logic/itkIteratorTests.cxx | 124 +
.../Logic/itkRegionOfInterestImageFilterTest.cxx | 144 +
Testing/Logic/testRLE.cxx | 145 ++
Testing/TestData/X300.mha | Bin 0 -> 1684 bytes
Testing/TestData/X39.nii.gz | Bin 0 -> 465 bytes
Testing/TestData/Y300.mha | Bin 0 -> 1132 bytes
Testing/TestData/Y55.nii.gz | Bin 0 -> 284 bytes
Testing/TestData/Z150.mha | Bin 0 -> 1522 bytes
Testing/TestData/Z32.nii.gz | Bin 0 -> 426 bytes
Testing/TestData/diffspace.itksnap | 328 +++
Testing/TestData/fixed_image.nii.gz | Bin 0 -> 1268 bytes
Testing/TestData/moving_image.nii.gz | Bin 0 -> 1069 bytes
Testing/TestData/multi_chunk.nii.gz | Bin 0 -> 277681 bytes
Testing/TestData/reslice_image.nii.gz | Bin 0 -> 7479 bytes
Testing/TestData/t1_chunk.nii.gz | Bin 0 -> 97937 bytes
Testing/TestData/t2_chunk.nii.gz | Bin 0 -> 62091 bytes
Testing/TestData/vb-seg.mha | Bin 0 -> 180716 bytes
Testing/TestData/warp_image.nii.gz | Bin 0 -> 163728 bytes
Testing/TestData/warpfield.itksnap | 349 +++
Utilities/MacOS/BundleResources/Info.plist | 15 +-
632 files changed, 77698 insertions(+), 6213 deletions(-)
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