├── AnisotropicDiffusionImageFilter ├── CMakeLists.txt ├── README.txt └── itk2DAnisotropicDiffusionImageFilter.cxx ├── AntiAliasBinaryImageFilter ├── CMakeLists.txt ├── README.txt ├── ViewOutputVTK.tcl ├── ViewOutputVTK4.1.1.tcl ├── itkAntiAliasBinaryImageFilterExample.cxx ├── itkSampleDataGenerator.cxx └── sample.parameters ├── Auxiliary ├── .NoDartCoverage ├── CMakeLists.txt ├── FltkImageViewer │ ├── CMakeLists.txt │ ├── GLColorSliceView.h │ ├── GLSliceView.h │ ├── GLTwoImageSliceView.h │ ├── README │ ├── SliceView.h │ ├── fltkBox3D.cxx │ ├── fltkBox3D.h │ ├── fltkClippingPlane3DDrawer.cxx │ ├── fltkClippingPlane3DDrawer.h │ ├── fltkClippingPlane3DDrawerGUI.fl │ ├── fltkCommandEvents.h │ ├── fltkCone3D.cxx │ ├── fltkCone3D.h │ ├── fltkCylinder3D.cxx │ ├── fltkCylinder3D.h │ ├── fltkDisplayGlWindowFlatGUI.fl │ ├── fltkDisplayGlWindowGUI.fl │ ├── fltkDrawer.h │ ├── fltkFrustum3D.cxx │ ├── fltkFrustum3D.h │ ├── fltkFrustumFunctionControl.h │ ├── fltkFrustumFunctionControl.txx │ ├── fltkFrustumFunctionControlGUI.fl │ ├── fltkGlDrawer.h │ ├── fltkGlWindow.cxx │ ├── fltkGlWindow.h │ ├── fltkGlWindowInteractive.cxx │ ├── fltkGlWindowInteractive.h │ ├── fltkGlWindowInteractiveFlat.cxx │ ├── fltkGlWindowInteractiveFlat.h │ ├── fltkImage2DViewer.h │ ├── fltkImage2DViewer.txx │ ├── fltkImage2DViewerGUI.fl │ ├── fltkImage2DViewerWindow.cxx │ ├── fltkImage2DViewerWindow.h │ ├── fltkImageViewer.h │ ├── fltkImageViewer.txx │ ├── fltkImageViewerGUI.fl │ ├── fltkLightButton.cxx │ ├── fltkLightButton.h │ ├── fltkPointSet2D.h │ ├── fltkPointSet2D.txx │ ├── fltkPointSet3D.h │ ├── fltkPointSet3D.txx │ ├── fltkProgressBar.cxx │ ├── fltkProgressBar.h │ ├── fltkRGBImage2DViewer.h │ ├── fltkRGBImage2DViewer.txx │ ├── fltkRGBImage2DViewerGUI.fl │ ├── fltkRGBImage2DViewerWindow.cxx │ ├── fltkRGBImage2DViewerWindow.h │ ├── fltkRegularStepGradientDescent.h │ ├── fltkRegularStepGradientDescentGUI.fl │ ├── fltkShape3D.cxx │ ├── fltkShape3D.h │ ├── fltkSlice2DDrawer.h │ ├── fltkSlice2DDrawer.txx │ ├── fltkSlice2DDrawerGUI.fl │ ├── fltkSlice3DDrawer.h │ ├── fltkSlice3DDrawer.txx │ ├── fltkSlice3DDrawerGUI.fl │ ├── fltkSphere3D.cxx │ ├── fltkSphere3D.h │ ├── fltkSphereFunctionControl.h │ ├── fltkSphereFunctionControl.txx │ ├── fltkSphereFunctionControlGUI.fl │ ├── fltkTimeProbeGUI.cxx │ ├── fltkTimeProbeGUI.h │ ├── fltkTimeProbesCollector.cxx │ ├── fltkTimeProbesCollector.h │ ├── fltkTimeProbesCollectorGUI.fl │ ├── fltkUtils.cxx │ ├── fltkUtils.h │ ├── fltkVectorImage3D.h │ ├── fltkVectorImage3D.txx │ ├── fltkWidgetRedrawCommand.h │ ├── fltkWidgetRedrawCommand.txx │ ├── fltkWindowInteractive.cxx │ └── fltkWindowInteractive.h ├── ITKFlFileWriter │ ├── CMakeLists.txt │ ├── Fl_File_ChooserModified.H │ ├── Fl_File_ChooserModified.cxx │ ├── Fl_File_ChooserModified2.cxx │ ├── ITKFlFileWriter.h │ ├── flstring.c │ ├── flstring.h │ └── vsnprintf.c ├── QtImageViewer │ ├── CMakeLists.txt │ ├── QtGlSliceView.cxx │ ├── QtGlSliceView.h │ ├── QtSlicer.cxx │ ├── QtSlicer.h │ ├── QtSlicerGUI.ui │ ├── QtSlicerHelpGUI.ui │ ├── QtSlicerTest.cxx │ └── itkLogoSmall.png ├── README.txt ├── VtkFltk │ ├── CMakeLists.txt │ ├── COPYING.LGPL │ ├── README.txt │ ├── fltkVTKImageViewer.h │ ├── fltkVTKImageViewer.txx │ ├── fltkVTKImageViewerBase.cxx │ ├── fltkVTKImageViewerBase.h │ ├── fltkVTKImageViewerGUI.fl │ ├── vtkFlRenderWindowInteractor.cxx │ ├── vtkFlRenderWindowInteractor.h │ └── vtkFlRenderWindowInteractorExample.cxx ├── vispack │ ├── itkVispackImageContainer.h │ ├── itkVispackSource.h │ └── itkVispackSource.txx └── vtk │ ├── CMakeLists.txt │ ├── ExtractIsoSurface.cxx │ ├── README.txt │ ├── ScreenShotGenerator.cxx │ ├── TkImageViewerInteractor.tcl │ ├── ViewVTKImage.tcl │ ├── WidgetObject.tcl │ ├── itkCurvatureFlowToVTK.cxx │ ├── itkImageToVTKImageFilter.h │ ├── itkImageToVTKImageFilter.txx │ ├── itkPNGVTKtoITKtoVTK.cxx │ ├── itkReadITKImage3DExtractContourVTK.cxx │ ├── itkReadITKImage3DSegmentShowVTK.cxx │ ├── itkReadITKImageSegmentShowVTK.cxx │ ├── itkReadITKImageShowSplineVTK.cxx │ ├── itkReadITKImageShowVTK.cxx │ ├── itkRegisterITKMonitorVTK.cxx │ ├── itkVTKImageToImageFilter.h │ ├── itkVTKImageToImageFilter.txx │ ├── itkVTKtoITKtoVTK.cxx │ ├── vtk2itk.cxx │ ├── vtk2itkDouble.cxx │ ├── vtkImageInclude.tcl │ ├── vtkInt.tcl │ ├── vtkKWImage.cxx │ ├── vtkKWImage.h │ ├── vtkKWImageIO.cxx │ ├── vtkKWImageIO.h │ ├── vtkPolyDataToITKMesh.cxx │ ├── vtkRegistrationMonitor.cxx │ └── vtkRegistrationMonitor.h ├── CMakeLists.txt ├── CTestConfig.cmake ├── CannyLevelSet ├── CMakeLists.txt ├── CannySegmentationLevelSet.cxx ├── CannySegmentationLevelSet.h ├── CannySegmentationLevelSetBase.cxx ├── CannySegmentationLevelSetBase.h └── CannySegmentationLevelSetGUI.fl ├── CellularSegmentation ├── CMakeLists.txt ├── CellularAggregateViewer.cxx ├── CellularAggregateViewer.h ├── CellularSegmentationApplication.cxx ├── CellularSegmentationApplication.h ├── CellularSegmentationApplicationBase.cxx ├── CellularSegmentationApplicationBase.h ├── CellularSegmentationApplicationGUI.fl ├── ClickedPointEvent.h ├── ImageSliceViewer.cxx ├── ImageSliceViewer.h ├── InteractorObserver.cxx ├── InteractorObserver.h └── main.cxx ├── ConvertBetweenFileFormats ├── CMakeLists.txt ├── ImageCompareTests.cxx ├── Testing │ └── Data │ │ ├── BigEndian.mhd │ │ ├── BigEndian.raw │ │ ├── image_in.mhd │ │ └── image_in.raw ├── castconvert.cxx ├── castconvertConfigure.h.in ├── castconvertDicomScalar.cxx ├── castconvertDicomScalarA.cxx ├── castconvertScalar.cxx ├── castconvertScalar2D.cxx ├── castconvertScalar2DA.cxx ├── castconvertScalar3D.cxx ├── castconvertScalar3DA.cxx ├── castconvertScalar4D.cxx ├── castconvertScalar4DA.cxx ├── castconverthelpers.h └── itkTestMain.h ├── Curves2DExtractor ├── CMakeLists.txt ├── README ├── ceExtractorConsole.cxx ├── ceExtractorConsole.h ├── ceExtractorConsoleBase.cxx ├── ceExtractorConsoleBase.h ├── ceExtractorConsoleGUI.fl └── main.cxx ├── Curves3DExtractor ├── CMakeLists.txt ├── PixelAccessors.h ├── ceExtractorConsole.cxx ├── ceExtractorConsole.h ├── ceExtractorConsoleBase.cxx ├── ceExtractorConsoleBase.h ├── ceExtractorConsoleGUI.fl └── main.cxx ├── DICOMApp ├── CMakeLists.txt └── main.cxx ├── DartConfig.cmake ├── DeformableModelSimplexMesh ├── CMakeLists.txt ├── ClickedPointEvent.h ├── DeformableModelApplication.cxx ├── DeformableModelApplication.h ├── DeformableModelApplicationBase.cxx ├── DeformableModelApplicationBase.h ├── DeformableModelApplicationGUI.fl ├── ImageSliceViewer.cxx ├── ImageSliceViewer.h ├── ImageSurfaceViewer.cxx ├── ImageSurfaceViewer.h ├── InteractorObserver.cxx ├── InteractorObserver.h ├── how_to_use.html ├── itkMeshTovtkPolyData.cxx ├── itkMeshTovtkPolyData.h ├── main.cxx ├── vtkPolyDataToitkMesh.cxx └── vtkPolyDataToitkMesh.h ├── DeformableRegistration3DTimeSeries ├── CMakeLists.txt ├── DeformableRegistration3DTimeSeries.cxx ├── DeformableRegistration3DTimeSeries.h ├── DeformableRegistration3DTimeSeriesBase.cxx ├── DeformableRegistration3DTimeSeriesBase.h ├── DeformableRegistration3DTimeSeriesGUI.fl ├── DicomImageReader.h ├── DicomImageReader.txx ├── DicomImageReaderBase.cxx ├── DicomImageReaderBase.h ├── DicomImageReaderGUI.fl ├── FEMRParameters1.txt ├── InteractorObserver.cxx ├── InteractorObserver.h ├── TransferFunctionEditor.cxx ├── TransferFunctionEditor.h ├── caimr.bmp └── main.cxx ├── DicomImageViewer ├── CMakeLists.txt └── DicomImageViewer.cxx ├── DigitalArchive ├── CMakeLists.txt ├── DSpaceMediaFilters │ ├── DicomFilter.java │ ├── GzipFilter.java │ ├── ITKFilter.java │ ├── LICENSE │ └── ZipFilter.java ├── FlDicomQueryChooser │ ├── ActionsHelp.html │ ├── CMakeLists.txt │ ├── FindDCMTK.cmake │ ├── FindITKApps.cmake │ ├── FlDicomQueryChooser.cxx │ ├── FlDicomQueryChooser.h │ ├── FlDicomQueryChooserGUI.fl │ ├── ImageViewerGUI.fl │ ├── fldqcDatatypes.h │ ├── fldqcLocalDirectoryQuery.cxx │ ├── fldqcLocalDirectoryQuery.h │ ├── fldqcNet.cxx │ ├── fldqcNet.h │ ├── fldqcPreferences.cxx │ ├── fldqcPreferences.h │ ├── fldqcPreferencesGUI.fl │ ├── fldqcRemoteNetworkQuery.cxx │ ├── fldqcRemoteNetworkQuery.h │ └── main.cxx └── ThumbnailGenerator │ ├── CMakeLists.txt │ ├── DicomGenerateThumbnail.cxx │ └── GenerateThumbnail.cxx ├── DistanceMapFilter ├── CMakeLists.txt ├── DistanceMapFilter.cxx ├── DistanceMapFilter.h ├── DistanceMapFilterBase.cxx ├── DistanceMapFilterBase.h ├── DistanceMapFilterGUI.fl └── main.cxx ├── DuctExtractor ├── CMakeLists.txt ├── DuctExtractor.cxx ├── DuctExtractor.h ├── DuctExtractorConsole.cxx ├── DuctExtractorConsole.h ├── DuctExtractorConsoleBase.cxx ├── DuctExtractorConsoleBase.h ├── DuctExtractorConsoleGUI.fl └── DuctExtractorConsoleGUI.txt ├── EdgeDetection ├── CMakeLists.txt ├── README ├── itk2DEdgeDetectionSample.cxx ├── itk3DEdgeDetectionSample.cxx ├── itkSWSRawFileReader.h ├── itkSWSRawFileReader.txx ├── itkmyRawFileWriter.h └── itkmyRawFileWriter.txx ├── EllipsoidInteriorExteriorSpatialFunction ├── CMakeLists.txt ├── README.doc ├── README.htm ├── README.pdf ├── README.tex ├── README_files │ ├── filelist.xml │ ├── image001.png │ ├── image002.gif │ ├── image003.wmz │ ├── image004.gif │ ├── image005.jpg │ ├── image006.jpg │ └── oledata.mso ├── ellipsoid.eps ├── ellipsoid.jpg ├── itkEllipsoidInteriorExteriorSpatialFunctionExample.cxx └── itkLogo.eps ├── FEM ├── CMakeLists.txt ├── FEMImageRegLMEx.cxx ├── FEMInputFileGenerator.cxx ├── FEMRead.cxx ├── FEMSolverHyperbolicExample.cxx ├── FEMTruss.cxx └── truss.meta ├── FORCEBUILD ├── FastMarchingLevelSet ├── CMakeLists.txt ├── FastMarchingLevelSet.cxx ├── FastMarchingLevelSet.h ├── FastMarchingLevelSetBase.cxx ├── FastMarchingLevelSetBase.h └── FastMarchingLevelSetGUI.fl ├── FindFLTK.cmake ├── FindFltkImageViewer.cmake ├── FindInsightApplications.cmake ├── FloodFilledSpatialFunction ├── CMakeLists.txt └── itkFloodFilledSpatialFunctionExample.cxx ├── FuzzyConnectedness ├── CMakeLists.txt ├── FuzzyConnectApp.cxx ├── FuzzyConnectApp.h ├── FuzzyConnectedness.cxx ├── ReadMe.doc └── ReadMe.pdf ├── GPDM2DTest ├── CMakeLists.txt ├── GPDM2DTest.cpp ├── MySegmentation.cxx ├── MySegmentation.h ├── MyTestAppUI.cxx ├── MyTestAppUI.fl └── MyTestAppUI.h ├── GPDM3DTest ├── CMakeLists.txt ├── GPDM3DTest.cpp ├── My3DView.cxx ├── My3DView.fl ├── My3DView.h ├── MySegmentation.cxx ├── MySegmentation.h ├── MyTestAppUI.cxx ├── MyTestAppUI.fl └── MyTestAppUI.h ├── GaussianFilter ├── CMakeLists.txt ├── GaussianFilter.cxx ├── GaussianFilter.h ├── GaussianFilter2D.cxx ├── GaussianFilter2D.h ├── README ├── liFilterConsole.cxx ├── liFilterConsole.h ├── liFilterConsole2D.cxx ├── liFilterConsole2D.h ├── liFilterConsole2DBase.cxx ├── liFilterConsole2DBase.h ├── liFilterConsole2DGUI.fl ├── liFilterConsoleBase.cxx ├── liFilterConsoleBase.h └── liFilterConsoleGUI.fl ├── GaussianMinimumErrorClassifier ├── CMakeLists.txt ├── GaussianMinimumErrorClassifier.cxx ├── OutputEvaluator.h ├── OutputEvaluator.txx └── readme ├── GeodesicActiveContour ├── CMakeLists.txt ├── GeodesicActiveContour.cxx ├── GeodesicActiveContour.h ├── GeodesicActiveContourBase.cxx ├── GeodesicActiveContourBase.h └── GeodesicActiveContourGUI.fl ├── IBSRValidation ├── AtlasSegmentation │ ├── CMakeLists.txt │ ├── Code │ │ ├── ApplicationBase.h │ │ ├── ApplicationBase.txx │ │ ├── AtlasLabeler.h │ │ ├── AtlasLabeler.txx │ │ ├── BrainStripValidationApp.cxx │ │ ├── BrainStripValidationApp.h │ │ ├── BrainStripValidationApp.txx │ │ ├── DemonsPreprocessor.h │ │ ├── DemonsPreprocessor.txx │ │ ├── DemonsRegistrator.h │ │ ├── DemonsRegistrator.txx │ │ ├── SimpleAppOutput.h │ │ ├── SimpleAppOutput.txx │ │ ├── ValidationInputParser.h │ │ ├── ValidationInputParser.txx │ │ ├── ValidationOutput.h │ │ └── ValidationOutput.txx │ ├── Inputs │ │ ├── input_1.txt │ │ ├── input_2.txt │ │ ├── input_3.txt │ │ ├── input_4.txt │ │ ├── input_5.txt │ │ ├── input_6.txt │ │ ├── param_1.txt │ │ ├── param_2.txt │ │ └── param_3.txt │ ├── ReadMe.txt │ └── Results │ │ ├── output_1.txt │ │ ├── output_2.txt │ │ ├── output_3.txt │ │ ├── output_4.txt │ │ ├── output_5.txt │ │ └── output_6.txt ├── CMakeLists.txt ├── Common │ ├── PGMVolumeWriter.h │ ├── PGMVolumeWriter.txx │ ├── RawSliceVolumeReader.h │ ├── RawSliceVolumeReader.txx │ ├── RawVolumeReader.h │ ├── RawVolumeReader.txx │ ├── RawVolumeWriter.h │ └── RawVolumeWriter.txx ├── FEMAtlasSegmentation │ ├── CMakeLists.txt │ ├── Code │ │ ├── FEMAtlasLabeler.h │ │ ├── FEMAtlasLabeler.txx │ │ ├── FEMBrainStripValidationApp.cxx │ │ ├── FEMBrainStripValidationApp.h │ │ ├── FEMBrainStripValidationApp.txx │ │ ├── FEMPreprocessor.h │ │ ├── FEMPreprocessor.txx │ │ ├── FEMRegistrator.h │ │ ├── FEMRegistrator.txx │ │ ├── FEMValidationInputParser.h │ │ └── FEMValidationInputParser.txx │ └── Inputs │ │ ├── FEMregLMparams3D.txt │ │ ├── input.txt │ │ └── input_resample.txt ├── IBSRClassification │ ├── CMakeLists.txt │ ├── Code │ │ ├── ClassifierApplicationBase.h │ │ ├── ClassifierApplicationBase.txx │ │ ├── ClassifierValidationInputParser.h │ │ ├── ClassifierValidationInputParser.txx │ │ ├── ClassifierValidationOutput.h │ │ ├── ClassifierValidationOutput.txx │ │ ├── GaussianClassifierValidationApp.cxx │ │ ├── GaussianClassifierValidationApp.h │ │ ├── GaussianClassifierValidationApp.txx │ │ ├── GaussianImageClassifierApp.h │ │ ├── GaussianImageClassifierApp.txx │ │ ├── KmeansClassifierValidationApp.cxx │ │ ├── KmeansClassifierValidationApp.h │ │ ├── KmeansClassifierValidationApp.txx │ │ ├── KmeansImageClassifierApp.h │ │ ├── KmeansImageClassifierApp.txx │ │ ├── MRFGaussianClassifierValidationApp.cxx │ │ ├── MRFGaussianClassifierValidationApp.h │ │ ├── MRFGaussianClassifierValidationApp.txx │ │ ├── MRFGaussianImageClassifierApp.h │ │ ├── MRFGaussianImageClassifierApp.txx │ │ ├── MRFKMeansClassifierValidationApp.h │ │ ├── MRFKMeansClassifierValidationApp.txx │ │ ├── MRFKMeansImageClassifierApp.h │ │ ├── MRFKMeansImageClassifierApp.txx │ │ └── MRFKmeansClassifierValidationApp.cxx │ ├── Inputs │ │ ├── ReadMe.txt │ │ ├── TestGaussianClassifierInput.txt │ │ ├── TestKmeansClassifierInput.txt │ │ ├── TestMRFGaussianClassifierInput.txt │ │ ├── TestMRFKmeansClassifierInput.txt │ │ ├── param100_23.txt │ │ ├── param110_3.txt │ │ ├── param111_2.txt │ │ ├── param112_2.txt │ │ ├── param11_3.txt │ │ ├── param12_3.txt │ │ ├── param13_3.txt │ │ ├── param15_3.txt │ │ ├── param16_3.txt │ │ ├── param17_3.txt │ │ ├── param191_3.txt │ │ ├── param202_3.txt │ │ ├── param205_3.txt │ │ ├── param2_4.txt │ │ ├── param4_8.txt │ │ ├── param6_10.txt │ │ ├── param7_8.txt │ │ └── param8_4.txt │ ├── ReadMe.txt │ └── Results │ │ ├── GaussianIBSRoutput.txt │ │ ├── KmeansIBSRoutput.txt │ │ ├── MRFGaussianIBSRoutput.txt │ │ └── MRFKMeansIBSRoutput.txt └── ReadMe.txt ├── ITKFilterLib ├── CMakeLists.txt ├── ITKFilterLib.cxx ├── ITKFilterLib.h └── ITKFilterLibTest.cxx ├── ITKRegistrationLib ├── CMakeLists.txt ├── ITKRegistrationLib.cxx ├── ITKRegistrationLib.h └── ITKRegistrationLibTest.cxx ├── ImageCalculator ├── CMakeLists.txt ├── ImageCalculator.cxx ├── ImageCalculatorProcess2D.cxx ├── ImageCalculatorProcess3D.cxx ├── ImageCalculatorTemplates.h ├── ImageCalculatorTests.cxx ├── ImageCalculatorUtils.cxx ├── ImageCalculatorUtils.h ├── ImageGenerate.cxx ├── Imgmath.h ├── TestImages │ ├── AllFifties.png │ ├── AllFiveHundreds.png │ ├── AllHundreds.png │ ├── AllTens.png │ ├── AllTwos.hdr │ ├── AllTwos.img │ ├── AllZeroes.png │ ├── GaussianIOFilteringTest.png │ ├── Hundred.hdr │ ├── Hundred.img │ ├── LowerHalfHundreds.png │ ├── TestCommands │ ├── TwoHundred.hdr │ ├── TwoHundred.img │ └── UpperHalfHundreds.png ├── doc │ ├── ImageCalculator.tex │ ├── InsightArticle.cls │ ├── InsightJournal.bib │ ├── InsightJournal.ist │ ├── InsightJournal.sty │ ├── Makefile │ ├── algorithm.sty │ ├── algorithmic.sty │ ├── amssymb.sty │ ├── fancyhdr.sty │ ├── figs │ │ ├── ImageCalculator.dia │ │ └── ImageCalculator.eps │ ├── floatflt.sty │ ├── fncychap.sty │ └── times.sty └── itkTestMain.h ├── ImageColorViewer ├── CMakeLists.txt ├── ImageColorViewer.cxx ├── ImageColorViewerGUI.fl └── sampleMetaHeader.mhd ├── ImageRegistration ├── CMakeLists.txt ├── ImageRegistration.cxx ├── ImageRegistration.h ├── README ├── liImageRegistrationConsole.cxx ├── liImageRegistrationConsole.h ├── liImageRegistrationConsoleBase.cxx ├── liImageRegistrationConsoleBase.h └── liImageRegistrationConsoleGUI.fl ├── ImageRegistration2D ├── CMakeLists.txt ├── CommandIterationUpdate.h ├── ImageRegistration2D.cxx ├── ImageRegistration2D.h ├── ImageRegistrationConsole.cxx ├── ImageRegistrationConsole.h ├── ImageRegistrationConsoleBase.cxx ├── ImageRegistrationConsoleBase.h └── ImageRegistrationConsoleGUI.fl ├── ImageRegistrationMFC ├── CMakeLists.txt ├── ItkRegMFC.aps ├── ItkRegMFC.cpp ├── ItkRegMFC.h ├── ItkRegMFC.rc ├── ItkRegMFCDoc.cpp ├── ItkRegMFCDoc.h ├── ItkRegMFCView.cpp ├── ItkRegMFCView.h ├── MainFrm.cpp ├── MainFrm.h ├── README_FIRST.txt ├── ReadMe.txt ├── res │ ├── ItkRegMFC.ico │ ├── ItkRegMFC.manifest │ ├── ItkRegMFC.rc2 │ ├── ItkRegMFCDoc.ico │ └── Toolbar.bmp ├── resource.h ├── stdafx.cpp └── stdafx.h ├── ImageViewer ├── CMakeLists.txt ├── ImageViewer.cxx └── ImageViewerGUI.fl ├── IntensityBased2D3DRegistration ├── CMakeLists.txt ├── GenerateProjection.cxx ├── IntensityBased2D3DRegistration.cxx └── README.txt ├── InverseConsistentLandmarkRegistration ├── BaselineResults │ ├── g1_To_g2_xdisp.hdr │ ├── g1_To_g2_ydisp.hdr │ ├── g1_To_g2_zdisp.hdr │ ├── g2_To_g1_xdisp.hdr │ ├── g2_To_g1_ydisp.hdr │ └── g2_To_g1_zdisp.hdr ├── CLReg.cxx ├── CLRegTest.cxx ├── CMakeLists.txt ├── TestInputs │ ├── grids.hdr │ ├── grids.img │ ├── set1.lmk │ └── set2.lmk ├── itkInverseConsistentLandmarkRegistration.h ├── itkInverseConsistentLandmarkRegistration.txx ├── itkInverseConsistentLandmarks.h ├── itkInverseConsistentLandmarks.txx ├── johnson_christensen_tmi02_front_page.pdf └── testScript.in ├── ItkJava ├── CMakeLists.txt ├── itkModule.cxx ├── itkModule.h └── myApp.java ├── ItkMFC ├── CMakeLists.txt ├── ItkMFC.cpp ├── ItkMFC.h ├── ItkMFC.rc ├── ItkMFCDoc.cpp ├── ItkMFCDoc.h ├── ItkMFCView.cpp ├── ItkMFCView.h ├── ItkPipeline.cxx ├── ItkPipeline.h ├── MainFrm.cpp ├── MainFrm.h ├── ReadMe.txt ├── Resource.h ├── StdAfx.cpp ├── StdAfx.h └── res │ ├── ItkMFC.ico │ ├── ItkMFC.rc2 │ ├── ItkMFCDoc.ico │ └── Toolbar.bmp ├── LandmarkInitializedMutualInformationRegistration ├── AffineRegistrator.h ├── AffineRegistrator.txx ├── CMakeLists.txt ├── DeformableRegistrator.h ├── DeformableRegistrator.txx ├── Help │ └── Index.html ├── ImageRegTool_README.txt ├── ImageRegistrationApp.h ├── ImageRegistrationApp.txx ├── LandmarkRegistrator.cxx ├── LandmarkRegistrator.h ├── LandmarkSliceViewer.h ├── LandmarkSliceViewer.txx ├── MomentRegistrator.h ├── MomentRegistrator.txx ├── RigidRegistrator.h ├── RigidRegistrator.txx ├── guiMain.fl ├── guiMainImplementation.cxx ├── guiMainImplementation.h ├── itkLeastSquaredDistanceCostFunction.h ├── itkLeastSquaredDistanceCostFunction.txx └── main.cxx ├── LevelSetSegmentation ├── CMakeLists.txt ├── README.txt ├── itk2DCannySegmentationLevelSetImageFilter.cxx ├── itk2DThresholdSegmentationLevelSetImageFilter.cxx └── vtkViewOutput.tcl ├── LevelSetSurfaceProcessing ├── CMakeLists.txt ├── README.txt ├── itk3DAnisotropicFourthOrderLevelSetImageFilter.cxx ├── itk3DIsotropicFourthOrderLevelSetImageFilter.cxx └── itk3DUnsharpMaskLevelSetImageFilter.cxx ├── LiverTumorSegmentation ├── CMakeLists.txt ├── ClickedPointEvent.h ├── ConfidenceConnectedModule.cxx ├── ConfidenceConnectedModule.h ├── ConnectedThresholdModule.cxx ├── ConnectedThresholdModule.h ├── DicomImageReader.h ├── DicomImageReader.txx ├── DicomImageReaderBase.cxx ├── DicomImageReaderBase.h ├── DicomImageReaderGUI.fl ├── ImageSliceViewer.cxx ├── ImageSliceViewer.h ├── InteractorObserver.cxx ├── InteractorObserver.h ├── LiverTumorSegmentation.cxx ├── LiverTumorSegmentation.h ├── LiverTumorSegmentationBase.cxx ├── LiverTumorSegmentationBase.h ├── LiverTumorSegmentationGUI.fl ├── ResampleVolumes.cxx ├── ThresholdLevelSetSegmentationModule.cxx ├── ThresholdLevelSetSegmentationModule.h ├── how_to_use.html ├── macros.h └── main.cxx ├── MATITK ├── Credits.txt ├── Documentation │ └── MATITK.pdf ├── PrecompiledBinaries │ ├── matitk.dll │ ├── msvcp71.dll │ └── msvcr71.dll └── src │ ├── MATITKTemplatedVariables.h │ ├── ParameterContainer.h │ ├── ParameterContainer.inl │ ├── itkcore.h │ ├── itkcore.inl │ ├── itkfiltercore.h │ ├── itkfiltercore.inl │ ├── itkregistrationcore.h │ ├── itkregistrationcore.inl │ ├── itksegmentationcore.h │ ├── itksegmentationcore.inl │ ├── matitk.cxx │ ├── matitk.h │ ├── mexopts.bat │ ├── seedcontainer.h │ ├── seedcontainer.inl │ └── typedefs.inl ├── MIValidation ├── CMakeLists.txt ├── Code │ ├── MIValidationApp.cxx │ ├── VanderbiltHeaderParser.h │ ├── VanderbiltHeaderParser.txx │ ├── VanderbiltModality.cxx │ ├── VanderbiltModality.h │ ├── VanderbiltValidationApp.h │ ├── VanderbiltValidationApp.txx │ ├── VanderbiltValidationInputParser.h │ ├── VanderbiltValidationInputParser.txx │ ├── VanderbiltValidationOutput.h │ └── VanderbiltValidationOutput.txx ├── Inputs │ ├── input_1.txt │ ├── param_1.txt │ └── param_2.txt ├── ReadMe.txt └── Results │ └── output_1.txt ├── MRIBiasCorrection ├── BiasCorrector.cxx ├── BiasFieldEstimator.cxx ├── BiasImageGenerator.cxx ├── CMakeLists.txt ├── EnergyTablePlotter.cxx ├── ImageCorrector.cxx ├── IntensityHistogram3D.cxx ├── InterSliceIntensityCorrector.cxx ├── OptionList.cxx ├── OptionList.h ├── README ├── SlabIdentifier.cxx ├── imageutils.h └── myutils.h ├── MRIRegistration ├── CMakeLists.txt ├── MIRegistration.cxx ├── MultiCompareAD.tcl ├── OptionList.cxx ├── OptionList.h ├── WindowLevelInterface2.tcl ├── mri1.bat ├── mri1.csh ├── vtk2itk2vtk.h ├── vtkImageStatistics.cxx └── vtkImageStatistics.h ├── MatroxInput ├── CMakeLists.txt ├── MatroxInput.cxx ├── MatroxViewer.cxx ├── MatroxViewer.h ├── MatroxViewerBase.cxx ├── MatroxViewerBase.h ├── MatroxViewerGUI.fl └── main.cxx ├── MetaImageImporter ├── CMakeLists.txt └── MetaImageImporter.cxx ├── MetaImageReadWrite ├── CMakeLists.txt └── MetaImageReadWrite.cxx ├── Morphogenesis ├── Bacteria.cxx ├── Bacteria.h ├── BacterialColony.cxx ├── BacterialColony.h ├── BacterialColonyGUI.fl ├── BilayerOrganism.cxx ├── BilayerOrganism.h ├── CMakeLists.txt ├── Cell.cxx ├── Cell.h ├── CellsViewer.cxx ├── CellsViewer.h ├── CellsViewerBase.cxx ├── CellsViewerBase.h ├── CellsViewerCommand.cxx ├── CellsViewerCommand.h ├── CellsViewerGUI.fl ├── CellularAggregate.cxx ├── CellularAggregate.dat ├── CellularAggregate.h ├── CommandEvents.h ├── Eukariote.cxx ├── Eukariote.h ├── Genome.cxx ├── Genome.h ├── GradientEatingBacteria.cxx ├── GradientEatingBacteria.dat ├── GradientEatingBacteria.h ├── PressureSensitiveBacteria.cxx ├── PressureSensitiveBacteria.h ├── Prokariote.cxx ├── Prokariote.h ├── README.txt └── main.cxx ├── MultiResMIRegistration ├── CMakeLists.txt ├── Common │ ├── MIMApplicationBase.h │ ├── MIMApplicationBase.txx │ ├── MIMPreprocessor.h │ ├── MIMPreprocessor.txx │ ├── MIMRegistrator.h │ ├── MIMRegistrator.txx │ ├── MultiResMIRegistration.cxx │ ├── SimpleApp.h │ ├── SimpleAppInputParser.h │ ├── SimpleAppInputParser.txx │ ├── SimpleAppOutput.h │ └── SimpleAppOutput.txx ├── ReadMe.doc ├── ReadMe.pdf └── SampleInputs │ ├── BrainWebT1toT2a.txt │ ├── BrainWebT1toT2b.txt │ ├── PracCTtoT1.txt │ └── PracPETToPD.txt ├── MultichannelTissueClassificationValidation ├── CMakeLists.txt ├── Code │ ├── GaussianImageMSClassifierApp.h │ ├── GaussianImageMSClassifierApp.txx │ ├── GaussianMSClassifierValidationApp.cxx │ ├── GaussianMSClassifierValidationApp.h │ ├── GaussianMSClassifierValidationApp.txx │ ├── KmeansImageMSClassifierApp.h │ ├── KmeansImageMSClassifierApp.txx │ ├── KmeansMSClassifierValidationApp.cxx │ ├── KmeansMSClassifierValidationApp.h │ ├── KmeansMSClassifierValidationApp.txx │ ├── MRFGaussianImageMSClassifierApp.h │ ├── MRFGaussianImageMSClassifierApp.txx │ ├── MRFGaussianMSClassifierValidationApp.cxx │ ├── MRFGaussianMSClassifierValidationApp.h │ ├── MRFGaussianMSClassifierValidationApp.txx │ ├── MRFKmeansImageMSClassifierApp.h │ ├── MRFKmeansImageMSClassifierApp.txx │ ├── MRFKmeansMSClassifierValidationApp.cxx │ ├── MRFKmeansMSClassifierValidationApp.h │ ├── MRFKmeansMSClassifierValidationApp.txx │ ├── MSClassifierApplicationBase.h │ ├── MSClassifierApplicationBase.txx │ ├── MSClassifierValidationInputParser.h │ ├── MSClassifierValidationInputParser.txx │ ├── MSClassifierValidationOutput.h │ └── MSClassifierValidationOutput.txx ├── Common │ ├── PGMVolumeWriter.h │ ├── PGMVolumeWriter.txx │ ├── RawSliceVolumeReader.h │ ├── RawSliceVolumeReader.txx │ ├── RawVolumeReader.h │ ├── RawVolumeReader.txx │ ├── RawVolumeWriter.h │ ├── RawVolumeWriter.txx │ ├── itkRawImageSequenceReader.h │ └── itkRawImageSequenceReader.txx ├── Inputs │ ├── ReadMe.txt │ ├── TestGaussianClassifierInput.txt │ ├── TestKmeansClassifierInput.txt │ ├── TestMRFGaussianClassifierInput.txt │ ├── TestMRFKmeansClassifierInput.txt │ └── paramphantom.txt ├── ReadMe.txt └── Results │ ├── GaussianMSoutput.txt │ ├── KmeansMSoutput.txt │ ├── MRFGaussianMSoutput.txt │ └── MRFKmeansMSoutput.txt ├── MutualInformationEuler2DRegistration ├── CMakeLists.txt ├── CommandIterationUpdate.h ├── MIAffine2DRegistrator.h ├── MIAffine2DRegistrator.txx ├── MIEuler2DRegistrator.h ├── MIEuler2DRegistrator.txx ├── MIScaleRegistrator.h ├── MIScaleRegistrator.txx ├── MISimilarity2DRegistrator.h ├── MISimilarity2DRegistrator.txx ├── MIThinPlateSplineRegistrator.h ├── MIThinPlateSplineRegistrator.txx ├── OutputGenerator.h ├── OutputGenerator.txx ├── Preprocessor.h ├── Preprocessor.txx ├── RegisterApplication.cxx ├── RegisterApplication.h ├── RegisterWindow.cxx ├── RegisterWindow.h ├── register.cxx ├── register.h └── registerGUI.fl ├── QtITK ├── CMakeLists.txt ├── itkQtAdaptor.h ├── itkQtLightIndicator.h ├── itkQtProgressBar.cxx ├── itkQtProgressBar.h └── qtITK.cxx ├── README.txt ├── RawImageReaderViewer ├── CMakeLists.txt ├── RawImageReaderViewer.cxx ├── itkRawImageReaderViewer.cxx ├── itkRawImageReaderViewer.h └── itkRawImageReaderViewerGUI.fl ├── RegionGrowingSegmentation ├── CMakeLists.txt ├── RegionGrowingSegmentation.cxx ├── RegionGrowingSegmentation.h ├── RegionGrowingSegmentation2D.cxx ├── RegionGrowingSegmentation2D.h ├── RegionGrowingSegmentation2DGUI.fl ├── RegionGrowingSegmentationBase.cxx ├── RegionGrowingSegmentationBase.h ├── RegionGrowingSegmentationBase2D.cxx ├── RegionGrowingSegmentationBase2D.h └── RegionGrowingSegmentationGUI.fl ├── SCIRun ├── Doc │ └── WrappingITKFiltersInSCIRun.pdf ├── Examples │ ├── CodeGenerator │ │ └── SCIRun │ │ │ ├── GenerateSCIRunCode.class │ │ │ ├── GenerateSCIRunCode.java │ │ │ ├── Generator.class │ │ │ ├── Generator.java │ │ │ ├── Parser.class │ │ │ └── Parser.java │ ├── XML │ │ ├── gui_BinaryThresholdImageFilter.xml │ │ ├── gui_CannySegmentationLevelSetImageFilter.xml │ │ ├── gui_DiscreteGuassianImageFilter.xml │ │ ├── gui_GradientAnisotropicDiffusionImageFilter.xml │ │ ├── gui_GradientRecursiveGaussianImageFilter.xml │ │ ├── gui_MeanImageFilter.xml │ │ ├── gui_ReflectImageFilter.xml │ │ ├── gui_ThresholdSegmentationLevelSetImageFilter.xml │ │ ├── gui_WatershedImageFilter.xml │ │ ├── gui_WatershedRelabeler.xml │ │ ├── gui_WatershedSegmentTreeGenerator.xml │ │ ├── gui_WatershedSegmenter.xml │ │ ├── gui_filter.dtd │ │ ├── sci_BinaryThresholdImageFilter.xml │ │ ├── sci_CannySegmentationLevelSetImageFilter.xml │ │ ├── sci_ConfidenceConnectedImageFilter.xml │ │ ├── sci_ConnectedThresholdImageFilter.xml │ │ ├── sci_CurvatureAnisotropicDiffusionImageFilter.xml │ │ ├── sci_CurvatureFlowImageFilter.xml │ │ ├── sci_DiscreteGaussianImageFilter.xml │ │ ├── sci_GradientAnisotropicDiffusionImageFilter.xml │ │ ├── sci_GradientMagnitudeImageFilter.xml │ │ ├── sci_GradientRecursiveGaussianImageFilter.xml │ │ ├── sci_IsolatedConnectedImageFilter.xml │ │ ├── sci_MeanImageFilter.xml │ │ ├── sci_NeighborhoodConnectedImageFilter.xml │ │ ├── sci_ReflectImageFilter.xml │ │ ├── sci_RescaleIntensityImageFilter.xml │ │ ├── sci_ThresholdSegmentationLevelSetImageFilter.xml │ │ ├── sci_UnaryFunctorImageFilter.xml │ │ ├── sci_VectorConfidenceConnectedImageFilter.xml │ │ ├── sci_VectorCurvatureAnisotropicDiffusionImageFilter.xml │ │ ├── sci_VectorGradientAnisotropicDiffusionImageFilter.xml │ │ ├── sci_VectorIndexSelectionCastImageFilter.xml │ │ ├── sci_WatershedImageFilter.xml │ │ ├── sci_WatershedRelabeler.xml │ │ ├── sci_WatershedSegmentTreeGenerator.xml │ │ ├── sci_WatershedSegmenter.xml │ │ └── sci_filter.dtd │ └── XSL │ │ ├── SCIRun_generateCC.xsl │ │ ├── SCIRun_generateTCL.xsl │ │ └── SCIRun_generateXML.xsl ├── ITK │ ├── itk_BinaryThresholdImageFilter.xml │ ├── itk_CannySegmentationLevelSetImageFilter.xml │ ├── itk_ConfidenceConnectedImageFilter.xml │ ├── itk_ConnectedThresholdImageFilter.xml │ ├── itk_CurvatureAnisotropicDiffusionImageFilter.xml │ ├── itk_CurvatureFlowImageFilter.xml │ ├── itk_DiscreteGaussianImageFilter.xml │ ├── itk_GradientAnisotropicDiffusionImageFilter.xml │ ├── itk_GradientMagnitudeImageFilter.xml │ ├── itk_GradientRecursiveGaussianImageFilter.xml │ ├── itk_IsolatedConnectedImageFilter.xml │ ├── itk_MeanImageFilter.xml │ ├── itk_NeighborhoodConnectedImageFilter.xml │ ├── itk_ReflectImageFilter.xml │ ├── itk_RescaleIntensityImageFilter.xml │ ├── itk_ThresholdSegmentationLevelSetImageFilter.xml │ ├── itk_UnaryFunctorImageFilter.xml │ ├── itk_VectorConfidenceConnectedImageFilter.xml │ ├── itk_VectorCurvatureAnisotropicDiffusionImageFilter.xml │ ├── itk_VectorGradientAnisotropicDiffusionImageFilter.xml │ ├── itk_VectorIndexSelectionCastImageFilter.xml │ ├── itk_WatershedImageFilter.xml │ ├── itk_WatershedRelabeler.xml │ ├── itk_WatershedSegmentTreeGenerator.xml │ ├── itk_WatershedSegmenter.xml │ └── itk_filter.dtd ├── Test │ ├── README │ ├── Validate.py │ └── Validate.xsl └── Thirdparty │ ├── xalan.jar │ ├── xalanj-license.txt │ ├── xercesImpl.jar │ └── xml-apis.jar ├── SampleProject ├── CMakeLists.txt └── itkSampleProject.cxx ├── SegmentationEditor ├── CMakeLists.txt ├── Common │ ├── CMakeLists.txt │ ├── itkWatershedFilterAndWriter.h │ ├── itkWatershedFilterAndWriter.txx │ ├── itkWatershedSegmentTreeWriter.h │ ├── itkWatershedSegmentTreeWriter.txx │ ├── vtkBinaryVolume.cxx │ ├── vtkBinaryVolume.h │ ├── vtkBinaryVolumeLogic.cxx │ ├── vtkBinaryVolumeLogic.h │ ├── vtkITKWatershedFilterAndWriter.h │ ├── vtkLookupTableEquivalencyHash.cxx │ ├── vtkLookupTableEquivalencyHash.h │ ├── vtkWSBoundingBox.cxx │ ├── vtkWSBoundingBox.h │ ├── vtkWSBoundingBoxHash.h │ ├── vtkWSBoundingBoxManager.cxx │ ├── vtkWSBoundingBoxManager.h │ ├── vtkWSLookupTableManager.cxx │ └── vtkWSLookupTableManager.h ├── Graphics │ ├── SCI_logo.gif │ ├── geek_head.gif │ ├── instructions.gif │ ├── itkLogoSmallTransparentBackground.gif │ └── uutah.gif ├── README.txt ├── Scripts │ ├── Configure.tcl │ ├── Copyright.txt │ ├── DataHelp.txt │ ├── DataModule.tcl │ ├── EditorHelp.txt │ ├── EditorModule.tcl │ ├── ExitModule.tcl │ ├── Fonts.tcl │ ├── Globals.tcl │ ├── Graphics.tcl │ ├── Help.txt │ ├── HelpModule.tcl │ ├── LicenseModule.tcl │ ├── Main.tcl │ ├── Options.tcl │ ├── PostprocessorModule.tcl │ ├── PreprocessorHelp.txt │ ├── PreprocessorModule.tcl │ ├── SegmenterHelp.txt │ ├── SegmenterModule.tcl │ ├── Utility.tcl │ └── segmenterinteraction │ │ ├── TkSegmentationWindowInteractor.tcl │ │ └── pkgIndex.tcl ├── Tutorial.pdf ├── WST.cmake └── Wrapping │ ├── CMakeLists.txt │ ├── MakePackages.tcl │ └── Tcl │ ├── CMakeLists.txt │ └── tkAppInit.cxx ├── ShapeDetectionLevelSet ├── CMakeLists.txt ├── ShapeDetectionLevelSet.cxx ├── ShapeDetectionLevelSet.h ├── ShapeDetectionLevelSetBase.cxx ├── ShapeDetectionLevelSetBase.h └── ShapeDetectionLevelSetGUI.fl ├── SimpleFuzzyConnectedness ├── CMakeLists.txt ├── FuzzySegGrayRun.cxx ├── FuzzySegGrayRun.h ├── FuzzySegGrayUI.fl └── FuzzySegMain.cpp ├── SimpleLevelSetsExample ├── CMakeLists.txt ├── README.txt ├── View2DOutputInVTK.tcl ├── View2DOutputInVTK4.1.1.tcl ├── View3DOutputInVTK.tcl ├── View3DOutputInVTK4.1.1.tcl ├── itk2DSimpleLevelSetsExample.cxx └── itk3DSimpleLevelSetsExample.cxx ├── StreamedWatershedSegmentation ├── CMakeLists.txt ├── ParameterFileParser │ ├── CMakeLists.txt │ ├── README │ ├── lex.yy.cxx │ ├── param.cxx │ ├── param.h │ ├── param.l │ ├── param.y │ ├── y.tab.cxx │ └── y.tab.h ├── README ├── VolumeChunker │ ├── CMakeLists.txt │ ├── README │ ├── catchunkfile.cxx │ ├── chunker.cxx │ ├── chunks.cxx │ ├── chunks.h │ ├── vhchunker.cxx │ └── vhunchunker.cxx ├── itkEquivalenceRelabelerApp.cxx ├── itkRelabelerApp.cxx ├── itkResolverApp.cxx ├── itkSWSBoundaryDataReader.h ├── itkSWSBoundaryDataReader.txx ├── itkSWSBoundaryDataWriter.h ├── itkSWSBoundaryDataWriter.txx ├── itkSWSEquivalencyTableReader.h ├── itkSWSEquivalencyTableReader.txx ├── itkSWSEquivalencyTableWriter.h ├── itkSWSEquivalencyTableWriter.txx ├── itkSWSRawFileReader.h ├── itkSWSRawFileReader.txx ├── itkSWSRawFileWriter.h ├── itkSWSRawFileWriter.txx ├── itkSWSSegmentTableReader.h ├── itkSWSSegmentTableReader.txx ├── itkSWSSegmentTableWriter.h ├── itkSWSSegmentTableWriter.txx ├── itkSWSSegmentTreeReader.h ├── itkSWSSegmentTreeReader.txx ├── itkSWSSegmentTreeWriter.h ├── itkSWSSegmentTreeWriter.txx ├── itkSegmenterApp.cxx └── itkTreeGeneratorApp.cxx ├── Superbuild ├── CMakeLists.txt ├── External-FLTK.cmake ├── External-ITK.cmake ├── External-VTK.cmake ├── Superbuild.cmake ├── fltk.diff └── patch-FLTK.sh.in ├── SymmetricEllipsoidInteriorExteriorSpatialFunction ├── CMakeLists.txt ├── README.doc ├── README.htm ├── README.pdf ├── README.ps ├── README.tex ├── itkSymmetricEllipsoidInteriorExteriorSpatialFunctionExample.cxx ├── symmetricEllipsoid.eps └── symmetricEllipsoid.jpg ├── ThinPlateSplines ├── CMakeLists.txt ├── ThinPlateSplinesApplication.cxx ├── ThinPlateSplinesApplication.h ├── ThinPlateSplinesApplicationBase.cxx ├── ThinPlateSplinesApplicationBase.h ├── ThinPlateSplinesApplicationGUI.fl └── main.cxx ├── ThresholdSegmentationLevelSet ├── CMakeLists.txt ├── ThresholdSegmentationLevelSet.cxx ├── ThresholdSegmentationLevelSet.h ├── ThresholdSegmentationLevelSetBase.cxx ├── ThresholdSegmentationLevelSetBase.h └── ThresholdSegmentationLevelSetGUI.fl ├── ThresholdSegmentationLevelSetFltkGui ├── CMakeLists.txt ├── ImageViewer.h ├── ImageViewer.txx ├── ImageViewerGUI.fl ├── README ├── Segmenter.cxx ├── Segmenter.h ├── SegmenterConsole.cxx ├── SegmenterConsole.h ├── SegmenterConsoleBase.cxx ├── SegmenterConsoleBase.h └── SegmenterConsoleGUI.fl ├── TumorSegmentationEvaluation ├── CMakeLists.txt ├── README.txt ├── TumorVolumeEvaluationDeveloperManual.pdf ├── TumorVolumeEvaluationUserManual.pdf ├── vtkVVPluginAPI.h ├── vvITKAntiAliasingVoxelCount.cxx ├── vvITKAntiAliasingVoxelCount.h ├── vvITKContourMeanDistance.cxx ├── vvITKFilterModule.h ├── vvITKFilterModuleBase.h ├── vvITKFilterModuleTwoInputs.h ├── vvITKHausdorffDistance.cxx ├── vvITKVolume.cxx └── vvITKVolumeOverlap.cxx ├── Utilities ├── DevelopmentSetupScripts │ ├── SetupGerrit.sh │ ├── SetupGitAliases.sh │ ├── SetupHooks.sh │ ├── SetupTopicStage.sh │ └── SetupUser.sh ├── Hooks │ ├── commit-msg │ ├── pre-commit │ └── prepare-commit-msg └── SetupForDevelopment.sh ├── VolviewPlugIns ├── CMakeLists.txt ├── README.txt ├── vtkVVPluginAPI.h ├── vvITKAntiAlias.cxx ├── vvITKBinaryMedian.cxx ├── vvITKCannyEdgeDetection.cxx ├── vvITKCannySegmentationLevelSetModule.cxx ├── vvITKCannySegmentationLevelSetModule.h ├── vvITKCannySegmentationLevelSetModule.txx ├── vvITKConfidenceConnected.cxx ├── vvITKConnectedThreshold.cxx ├── vvITKCurvatureAnisotropicDiffusion.cxx ├── vvITKCurvatureFlow.cxx ├── vvITKDanielssonDistanceMap.cxx ├── vvITKDeformableModelModule.cxx ├── vvITKDeformableModelModule.h ├── vvITKDeformableModelModule.txx ├── vvITKFastMarching.cxx ├── vvITKFastMarchingModule.cxx ├── vvITKFastMarchingModule.h ├── vvITKFastMarchingModule.txx ├── vvITKFilterModule.h ├── vvITKFilterModuleBase.h ├── vvITKFilterModuleDoubleOutput.h ├── vvITKFilterModuleRGBDoubleOutput.h ├── vvITKFilterModuleTwoInputs.h ├── vvITKFilterModuleWithCasting.h ├── vvITKFilterModuleWithRescaling.h ├── vvITKGeodesicActiveContour.cxx ├── vvITKGeodesicActiveContour.h ├── vvITKGeodesicActiveContourModule.cxx ├── vvITKGeodesicActiveContourModule.h ├── vvITKGeodesicActiveContourModule.txx ├── vvITKGradientAnisotropicDiffusion.cxx ├── vvITKGradientMagnitude.cxx ├── vvITKGradientMagnitudeRecursiveGaussian.cxx ├── vvITKImageRegistration.cxx ├── vvITKIntensityWindowing.cxx ├── vvITKIsolatedConnected.cxx ├── vvITKIsotropicFourthOrderLevelSet.cxx ├── vvITKLandmarkWarping.cxx ├── vvITKMask.cxx ├── vvITKMask.h ├── vvITKMaskNegated.cxx ├── vvITKMaskNegated.h ├── vvITKMedian.cxx ├── vvITKRescaleIntensityTo8Bits.cxx ├── vvITKScalarImageKMeansClassifier.cxx ├── vvITKShapeDetectionModule.cxx ├── vvITKShapeDetectionModule.h ├── vvITKShapeDetectionModule.txx ├── vvITKSigmoid.cxx ├── vvITKSurfaceSpline.cxx ├── vvITKSurfaceSpline.h ├── vvITKSurfaceSpline.txx ├── vvITKThresholdSegmentationLevelSet.cxx ├── vvITKThresholdSegmentationLevelSet.h ├── vvITKVectorConfidenceConnected.cxx ├── vvITKWatershedModule.cxx ├── vvITKWatershedModule.h ├── vvITKWatershedModule.txx ├── vvITKWatershedRGBModule.cxx ├── vvITKWatershedRGBModule.h └── vvITKWatershedRGBModule.txx ├── VoronoiSegmentation ├── CMakeLists.txt ├── VDSegGrayRun.cxx ├── VDSegGrayRun.h ├── VDSegGrayUI.fl └── VDSegMain.cpp └── vtkITK ├── CMakeLists.txt ├── Common ├── CMakeLists.txt ├── vtkITKAntiAliasBinaryImageFilter.h ├── vtkITKArchetypeImageSeriesReader.cxx ├── vtkITKArchetypeImageSeriesReader.h ├── vtkITKBilateralImageFilter.h ├── vtkITKConfidenceConnectedImageFilter.h ├── vtkITKConnectedThresholdImageFilter.h ├── vtkITKCurvatureAnisotropicDiffusionImageFilter.h ├── vtkITKCurvatureAnisotropicDiffusionImageFilterSF.h ├── vtkITKDanielssonDistanceMapImageFilter.h ├── vtkITKDiscreteGaussianImageFilter.h ├── vtkITKGradientAnisotropicDiffusionImageFilter.h ├── vtkITKGradientMagnitudeImageFilter.h ├── vtkITKGradientMagnitudeRecursiveGaussianImageFilterFF.h ├── vtkITKGradientMagnitudeRecursiveGaussianImageFilterSS.h ├── vtkITKGrayscaleFillholeImageFilter.h ├── vtkITKImageToImageFilter.h ├── vtkITKImageToImageFilter2DFF.h ├── vtkITKImageToImageFilterF2F.h ├── vtkITKImageToImageFilterF2F2.h ├── vtkITKImageToImageFilterF3F3.h ├── vtkITKImageToImageFilterFF.h ├── vtkITKImageToImageFilterFUL.h ├── vtkITKImageToImageFilterSF.h ├── vtkITKImageToImageFilterSS.h ├── vtkITKImageToImageFilterSUL.h ├── vtkITKImageToImageFilterULUL.h ├── vtkITKImageToImageFilterUSUL.h ├── vtkITKImageToImageFilterUSUS.h ├── vtkITKIsolateConnectedImageFilter.h ├── vtkITKIsolatedConnectedImageFilter.h ├── vtkITKLaplacianSegmentationLevelSetImageFilter.h ├── vtkITKMutualInformationTransform.cxx ├── vtkITKMutualInformationTransform.h ├── vtkITKNeighborhoodConnectedImageFilter.h ├── vtkITKNormalizeImageFilter.h ├── vtkITKNormalizeImageFilterSF.h ├── vtkITKOtsuThresholdImageFilter.h ├── vtkITKPDEDeformableRegistrationFilter.h ├── vtkITKRelabelComponentImageFilter.h ├── vtkITKSmoothingRecursiveGaussianImageFilter.h ├── vtkITKSmoothingRecursiveGaussianImageFilterSS.h ├── vtkITKStatisticsImageFilterULUL.h ├── vtkITKThresholdSegmentationLevelSetImageFilter.h ├── vtkITKTobogganImageFilter.h ├── vtkITKUtility.h ├── vtkITKWatershedImageFilter.h └── vtkITKWatershedImageFilterSUL.h ├── README.txt ├── Scripts ├── ConnectedThreshold.tcl ├── DemoMutual.tcl ├── TestMutualInformation.tcl └── WindowLevelInterface2.tcl ├── Wrapping ├── CMakeLists.txt └── Tcl │ ├── CMakeLists.txt │ ├── MakePackages.tcl │ └── tkAppInit.cxx ├── vtkITK.cmake └── vtkITKToolkits.h.in /AnisotropicDiffusionImageFilter/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(AnisotropicDiffusionImageFilter) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | ADD_EXECUTABLE(itk2DAnisotropicDiffusionImageFilter itk2DAnisotropicDiffusionImageFilter.cxx) 17 | INSTALL_TARGETS(/bin itk2DAnisotropicDiffusionImageFilter) 18 | 19 | TARGET_LINK_LIBRARIES (itk2DAnisotropicDiffusionImageFilter 20 | ${ITK_LIBRARIES} 21 | ) 22 | 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /AnisotropicDiffusionImageFilter/README.txt: -------------------------------------------------------------------------------- 1 | This example shows how to take in a 2D scalar PNG image and filter 2 | it using Perona-Malik style anisotropic diffusion. 3 | 4 | Use: 5 | 6 | itk2DAnisotropicDiffusionImageFilter input.png output.png number_of_iterations conductance_term 7 | 8 | Note that this example does NOT handle COLOR PNG images. 9 | 10 | See the documentation for itkAnisotropicDiffusionImageFilter for more information. 11 | -------------------------------------------------------------------------------- /AntiAliasBinaryImageFilter/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(AntiAliasBinaryImageFilter) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | 18 | INCLUDE_DIRECTORIES( 19 | ${AntiAliasBinaryImageFilter_SOURCE_DIR} 20 | ${AntiAliasBinaryImageFilter_SOURCE_DIR}/../StreamedWatershedSegmentation/ParameterFileParser 21 | ) 22 | 23 | ADD_EXECUTABLE(itkAntiAliasBinaryImageFilterExample itkAntiAliasBinaryImageFilterExample.cxx) 24 | INSTALL_TARGETS(/bin itkAntiAliasBinaryImageFilterExample) 25 | TARGET_LINK_LIBRARIES (itkAntiAliasBinaryImageFilterExample 26 | param 27 | ${ITK_LIBRARIES}) 28 | 29 | 30 | ADD_EXECUTABLE(itkSampleDataGenerator itkSampleDataGenerator.cxx) 31 | INSTALL_TARGETS(/bin itkSampleDataGenerator) 32 | TARGET_LINK_LIBRARIES (itkSampleDataGenerator 33 | param 34 | ${ITK_LIBRARIES}) 35 | 36 | 37 | -------------------------------------------------------------------------------- /AntiAliasBinaryImageFilter/sample.parameters: -------------------------------------------------------------------------------- 1 | (INPUT_FILENAME "sample_input.64x64x64.mha" ) 2 | (OUTPUT_FILENAME "sample_output.64x64x64.mha" ) 3 | 4 | (IMAGE_SIZE 64 64 64) // The size of the input image 5 | 6 | (MAXIMUM_ERROR 0.03 ) // Maximum error threshold parameter 7 | 8 | (NUMBER_OF_LAYERS 3) // Number of layers to use in the calculations. 9 | // For 3 dimensional volumes, this should be 3. 10 | // For 2d this can be decreased to 2. 11 | 12 | (OUTPUT_TYPE 0) // 0 == level set output, 13 | // 1 == zero crossings, may be interesting to see 14 | 15 | -------------------------------------------------------------------------------- /Auxiliary/.NoDartCoverage: -------------------------------------------------------------------------------- 1 | # do not do coverage in this directory 2 | -------------------------------------------------------------------------------- /Auxiliary/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # Add an option to build or not build the FltkImageViewer Library 2 | IF(FLTK_FOUND) 3 | SUBDIRS(FltkImageViewer ITKFlFileWriter) 4 | IF(VTK_FOUND) 5 | SUBDIRS(VtkFltk) 6 | ENDIF(VTK_FOUND) 7 | ENDIF(FLTK_FOUND) 8 | 9 | # Add an option to build or not build the vtk interface Library 10 | IF(NOT BORLAND) 11 | IF(VTK_FOUND) 12 | SUBDIRS(vtk) 13 | ENDIF(VTK_FOUND) 14 | ENDIF(NOT BORLAND) 15 | -------------------------------------------------------------------------------- /Auxiliary/FltkImageViewer/fltkDrawer.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: fltkDrawer.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #ifndef fltkDRAWERCLASS 19 | #define fltkDRAWERCLASS 20 | 21 | namespace fltk { 22 | 23 | 24 | class Drawer 25 | { 26 | 27 | public: 28 | Drawer() {}; 29 | virtual ~Drawer() {}; 30 | virtual void Draw(void) const =0; 31 | }; 32 | 33 | 34 | } 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /Auxiliary/FltkImageViewer/fltkGlDrawer.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: fltkGlDrawer.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | #ifndef fltkGLDRAWERCLASS 20 | #define fltkGLDRAWERCLASS 21 | 22 | 23 | namespace fltk { 24 | 25 | class ITK_EXPORT GlDrawer 26 | { 27 | 28 | public: 29 | GlDrawer() {}; 30 | virtual ~GlDrawer() {}; 31 | virtual void glDraw(void) const =0; 32 | }; 33 | 34 | typedef GlDrawer * GlDrawerPtr; 35 | 36 | } 37 | 38 | 39 | #endif 40 | -------------------------------------------------------------------------------- /Auxiliary/FltkImageViewer/fltkGlWindowInteractiveFlat.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: fltkGlWindowInteractiveFlat.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | #ifndef fltkGLWINDOWINTERFLATCLASS 20 | #define fltkGLWINDOWINTERFLATCLASS 21 | 22 | #include 23 | 24 | namespace fltk { 25 | 26 | class GlWindowInteractiveFlat: public GlWindowInteractive { 27 | public: 28 | GlWindowInteractiveFlat(int x,int y,int w,int h, const char * label=0); 29 | virtual ~GlWindowInteractiveFlat(); 30 | virtual void SetViewPoint(void); 31 | }; 32 | 33 | 34 | } // end namespace fltk 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /Auxiliary/ITKFlFileWriter/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | ADD_LIBRARY(ITKFlFileWriter 2 | Fl_File_ChooserModified.cxx 3 | Fl_File_ChooserModified2.cxx 4 | vsnprintf.c 5 | ) 6 | INSTALL_TARGETS(/lib ITKFlFileWriter) 7 | 8 | TARGET_LINK_LIBRARIES(ITKFlFileWriter ${FLTK_LIBRARIES}) 9 | 10 | IF(CMAKE_COMPILER_IS_GNUCXX) 11 | SET_SOURCE_FILES_PROPERTIES (Fl_File_ChooserModified.cxx PROPERTIES COMPILE_FLAGS "-Wno-shadow -Wno-cast-qual") 12 | SET_SOURCE_FILES_PROPERTIES (Fl_File_ChooserModified2.cxx PROPERTIES COMPILE_FLAGS "-Wno-shadow -Wno-cast-qual") 13 | ENDIF(CMAKE_COMPILER_IS_GNUCXX) 14 | 15 | 16 | -------------------------------------------------------------------------------- /Auxiliary/QtImageViewer/itkLogoSmall.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/Auxiliary/QtImageViewer/itkLogoSmall.png -------------------------------------------------------------------------------- /Auxiliary/VtkFltk/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # This directory only builds if FLTK and VTK can be found 2 | INCLUDE_DIRECTORIES( 3 | ${ITKApps_SOURCE_DIR}/Auxiliary/VtkFltk 4 | ${ITKApps_SOURCE_DIR}/Auxiliary/vtk 5 | ) 6 | 7 | FLTK_WRAP_UI(ITKVtkFltk fltkVTKImageViewerGUI.fl) 8 | 9 | ITK_DISABLE_FLTK_GENERATED_WARNINGS( 10 | "vtkFlRenderWindowInteractor.cxx;${ITKVtkFltk_FLTK_UI_SRCS}" 11 | ) 12 | 13 | 14 | ADD_LIBRARY(ITKVtkFltk 15 | vtkFlRenderWindowInteractor.cxx 16 | fltkVTKImageViewerBase.cxx 17 | ${ITKVtkFltk_FLTK_UI_SRCS} 18 | ) 19 | INSTALL_TARGETS(/lib ITKVtkFltk) 20 | 21 | TARGET_LINK_LIBRARIES(ITKVtkFltk ${VTK_LIBRARIES} ${FLTK_LIBRARIES} ${OPENGL_glu_LIBRARY} ${OPENGL_gl_LIBRARY}) 22 | 23 | ADD_EXECUTABLE( vtkFltkExample vtkFlRenderWindowInteractorExample.cxx) 24 | TARGET_LINK_LIBRARIES( vtkFltkExample ITKVtkFltk ) 25 | 26 | IF(VTK_USE_VOLUMERENDERING) 27 | TARGET_LINK_LIBRARIES(ITKVtkFltk vtkVolumeRendering) 28 | ENDIF(VTK_USE_VOLUMERENDERING) 29 | -------------------------------------------------------------------------------- /Auxiliary/VtkFltk/fltkVTKImageViewerBase.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: fltkVTKImageViewerBase.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include "fltkVTKImageViewerBase.h" 19 | 20 | 21 | namespace fltk { 22 | 23 | VTKImageViewerBase 24 | ::VTKImageViewerBase() 25 | { 26 | } 27 | 28 | 29 | 30 | VTKImageViewerBase 31 | ::~VTKImageViewerBase() 32 | { 33 | 34 | } 35 | 36 | 37 | 38 | } // end namespace itk 39 | -------------------------------------------------------------------------------- /Auxiliary/VtkFltk/fltkVTKImageViewerGUI.fl: -------------------------------------------------------------------------------- 1 | # data file for the Fltk User Interface Designer (fluid) 2 | version 1.0100 3 | header_name {.h} 4 | code_name {.cxx} 5 | class fltkVTKImageViewerGUI {open : {public fltk::VTKImageViewerBase} 6 | } { 7 | Function {fltkVTKImageViewerGUI()} {open 8 | } { 9 | Fl_Window externalWindow {open 10 | xywh {133 346 435 465} resizable 11 | code0 {\#include "fltkVTKImageViewerBase.h"} visible 12 | } { 13 | Fl_Box fltkRenderWindowInteractor {selected 14 | xywh {5 10 425 445} box DOWN_FRAME resizable 15 | code0 {\#include "vtkFlRenderWindowInteractor.h"} 16 | class vtkFlRenderWindowInteractor 17 | } 18 | } 19 | } 20 | Function {~fltkVTKImageViewerGUI()} {open return_type virtual 21 | } { 22 | code {} {} 23 | } 24 | Function {Show()} {open return_type {virtual void} 25 | } { 26 | code {externalWindow->show(); 27 | fltkRenderWindowInteractor->show();} {} 28 | } 29 | Function {Hide()} {open return_type {virtual void} 30 | } { 31 | code {externalWindow->hide();} {} 32 | } 33 | } 34 | -------------------------------------------------------------------------------- /Auxiliary/vtk/README.txt: -------------------------------------------------------------------------------- 1 | VTK Interface Classes 2 | --------------------- 3 | 4 | These classes are used to interface VTK to and from Insight. 5 | 6 | Make sure that VTK is built with ANSI C++ in order to avoid 7 | conflicts with the iostream library. We use the following 8 | flags when building VTK (in Microsoft C++). 9 | 10 | /D "VTK_USE_ANSI_STDLIB" /GX /Zm1000 11 | 12 | -------------------------------------------------------------------------------- /Auxiliary/vtk/vtkImageInclude.tcl: -------------------------------------------------------------------------------- 1 | # this file replicates definitions in classes for tcl. 2 | 3 | set VTK_VOID 0 4 | set VTK_BIT 1 5 | set VTK_CHAR 2 6 | set VTK_UNSIGNED_CHAR 3 7 | set VTK_SHORT 4 8 | set VTK_UNSIGNED_SHORT 5 9 | set VTK_INT 6 10 | set VTK_UNSIGNED_INT 7 11 | set VTK_LONG 8 12 | set VTK_UNSIGNED_LONG 9 13 | set VTK_FLOAT 10 14 | set VTK_DOUBLE 11 15 | 16 | set VTK_IMAGE_X_AXIS 0 17 | set VTK_IMAGE_Y_AXIS 1 18 | set VTK_IMAGE_Z_AXIS 2 19 | 20 | set VTK_CLAW_NEAREST_NETWORK 0 21 | set VTK_CLAW_NEAREST_MINIMUM 1 22 | set VTK_CLAW_NEAREST_GLOBAL 2 23 | set VTK_CLAW_PIONEER_LOCAL 3 24 | set VTK_CLAW_PIONEER_GLOBAL 4 25 | set VTK_CLAW_WELL_NOISE 6 26 | set VTK_CLAW_WELL_DIRECTED_NOISE 7 27 | set VTK_CLAW_MINIMUM_WELL 8 28 | set VTK_CLAW_INSERT 9 29 | set VTK_CLAW_NARROW_WEL 10 30 | 31 | -------------------------------------------------------------------------------- /CTestConfig.cmake: -------------------------------------------------------------------------------- 1 | set(CTEST_PROJECT_NAME "ITKApps") 2 | set(CTEST_NIGHTLY_START_TIME "21:00:00 EDT") 3 | 4 | set(CTEST_DROP_METHOD "http") 5 | set(CTEST_DROP_SITE "open.cdash.org") 6 | set(CTEST_DROP_LOCATION "/submit.php?project=Insight") 7 | set(CTEST_DROP_SITE_CDASH TRUE) 8 | -------------------------------------------------------------------------------- /CellularSegmentation/ClickedPointEvent.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ClickedPointEvent.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #ifndef __itkClickedPointEvent_h__ 19 | #define __itkClickedPointEvent_h__ 20 | 21 | #include "itkEventObject.h" 22 | 23 | /** 24 | \class ClickedPointEvent 25 | \brief Class for defining ClickedPointEvent 26 | 27 | This defines a ClickedEventEvent class which is derived from the 28 | itk::AnyEvent class. 29 | 30 | */ 31 | 32 | itkEventMacro( ClickedPointEvent, itk::AnyEvent ); 33 | 34 | 35 | #endif 36 | 37 | -------------------------------------------------------------------------------- /CellularSegmentation/InteractorObserver.cxx: -------------------------------------------------------------------------------- 1 | #include "InteractorObserver.h" 2 | 3 | #include 4 | 5 | 6 | 7 | 8 | InteractorObserver 9 | ::InteractorObserver() 10 | { 11 | m_SliceViewer = NULL; 12 | m_Motion = false; 13 | } 14 | 15 | 16 | 17 | 18 | InteractorObserver 19 | ::~InteractorObserver() 20 | { 21 | m_SliceViewer = NULL; 22 | } 23 | 24 | 25 | 26 | void 27 | InteractorObserver 28 | ::SetImageSliceViewer( ImageSliceViewer * viewer ) 29 | { 30 | m_SliceViewer = viewer; 31 | } 32 | 33 | 34 | 35 | void 36 | InteractorObserver 37 | ::Execute(vtkObject * itkNotUsed(caller), unsigned long eventId, void *) 38 | { 39 | if ( eventId == ::vtkCommand::LeftButtonPressEvent ) 40 | { 41 | m_Motion = true; 42 | } 43 | if ( eventId == ::vtkCommand::LeftButtonReleaseEvent ) 44 | { 45 | m_Motion = false; 46 | } 47 | if( m_SliceViewer && m_Motion ) 48 | { 49 | //point selected when mouse button pressed!! 50 | const int x = Fl::event_x(); 51 | const int y = Fl::event_y(); 52 | m_Motion = false; 53 | m_SliceViewer->SelectPoint( x, y ); 54 | } 55 | } 56 | 57 | 58 | 59 | 60 | 61 | 62 | -------------------------------------------------------------------------------- /CellularSegmentation/InteractorObserver.h: -------------------------------------------------------------------------------- 1 | #include "vtkCommand.h" 2 | #include "ImageSliceViewer.h" 3 | 4 | /** 5 | \class InteractorObserver 6 | \brief This class defines observer command for user event 7 | (Keyboard/Mouse)in a ImageSliceViewer window. 8 | */ 9 | 10 | 11 | class InteractorObserver : public vtkCommand 12 | { 13 | public: 14 | 15 | static InteractorObserver *New() 16 | {return new InteractorObserver;}; 17 | 18 | /** The SetImageSliceViewer method inputs pointer of the ImageSliceViewer 19 | serviced. 20 | */ 21 | void SetImageSliceViewer( ImageSliceViewer * viewer ); 22 | 23 | /** The Execute method defines the code to be run when the 24 | command is invoked. 25 | */ 26 | void Execute(vtkObject * caller, unsigned long eventId, void *callData); 27 | 28 | protected: 29 | 30 | InteractorObserver(); 31 | virtual ~InteractorObserver(); 32 | 33 | private: 34 | 35 | ImageSliceViewer * m_SliceViewer; 36 | bool m_Motion; 37 | 38 | }; 39 | 40 | 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /CellularSegmentation/main.cxx: -------------------------------------------------------------------------------- 1 | 2 | 3 | #include "CellularSegmentationApplication.h" 4 | 5 | 6 | int main( int argc, char * argv [] ) 7 | { 8 | 9 | CellularSegmentationApplication app; 10 | 11 | try 12 | { 13 | app.Show(); 14 | 15 | if( argc > 1 ) 16 | { 17 | Fl::check(); 18 | app.Load( argv[1] ); 19 | } 20 | 21 | Fl::run(); 22 | } 23 | catch( std::exception & ex ) 24 | { 25 | std::cerr << ex.what() << std::endl; 26 | } 27 | 28 | return 0; 29 | } 30 | 31 | 32 | -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/ImageCompareTests.cxx: -------------------------------------------------------------------------------- 1 | // this file defines the ImageCompare-Tests for the test driver 2 | // and all it expects is that you have a function called RegisterTests 3 | #if defined(_MSC_VER) 4 | #pragma warning ( disable : 4786 ) 5 | #endif 6 | #include 7 | #include "itkTestMain.h" 8 | 9 | // A dummy method that does nothing. We intend doing a comparison which is done 10 | // by the itkTestMain.h. (It requires a main program, prior to the compare) 11 | int Dummy(int, char *[]) 12 | { 13 | return EXIT_SUCCESS; 14 | } 15 | 16 | void RegisterTests() 17 | { 18 | REGISTER_TEST(Dummy); 19 | } 20 | 21 | -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/Testing/Data/BigEndian.mhd: -------------------------------------------------------------------------------- 1 | ObjectType = Image 2 | NDims = 3 3 | BinaryData = True 4 | BinaryDataByteOrderMSB = False 5 | CompressedData = False 6 | TransformMatrix = 1 0 0 0 0 1 0 -1 0 7 | Offset = 0 0 0 8 | CenterOfRotation = 0 0 0 9 | AnatomicalOrientation = RIP 10 | ElementSpacing = 1 1 1 11 | DimSize = 6 6 8 12 | ElementType = MET_SHORT 13 | ElementDataFile = BigEndian.raw 14 | -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/Testing/Data/BigEndian.raw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ConvertBetweenFileFormats/Testing/Data/BigEndian.raw -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/Testing/Data/image_in.mhd: -------------------------------------------------------------------------------- 1 | ObjectType = Image 2 | NDims = 2 3 | BinaryData = True 4 | BinaryDataByteOrderMSB = False 5 | TransformMatrix = 1 0 0 1 6 | Offset = 0 0 7 | CenterOfRotation = 0 0 8 | ElementSpacing = 1 1 9 | DimSize = 181 217 10 | AnatomicalOrientation = ?? 11 | ElementType = MET_USHORT 12 | ElementDataFile = image_in.raw 13 | -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/Testing/Data/image_in.raw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ConvertBetweenFileFormats/Testing/Data/image_in.raw -------------------------------------------------------------------------------- /ConvertBetweenFileFormats/castconvertConfigure.h.in: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: castconvertConfigure.h.in 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) Insight Software Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #cmakedefine USE_VTK 19 | -------------------------------------------------------------------------------- /Curves2DExtractor/README: -------------------------------------------------------------------------------- 1 | 2 | 3 | 2D Curves Extractor Application 4 | 5 | 6 | WHAT IS THIS ? 7 | 8 | This program is an example of a small 9 | application based on Insight. 10 | It includes image display, GUI, and IO. 11 | 12 | This program detects and extracts curves 13 | from 2D images. The extraction method is 14 | based on the computation of the Hessian 15 | matrix. 16 | 17 | 18 | WHAT DO I NEED TO RUN IT ? 19 | 20 | As GUI and visualization are not part of 21 | Insight, external libraries are required 22 | for this program. The GUI is implemented 23 | using FLTK (the Fast Light Toolkit) that 24 | can be freely downloaded from 25 | http://www.fltk.org. 26 | 27 | 28 | We appreciate your feedback. 29 | Please send your comments to the Insight 30 | mailing list. 31 | 32 | 33 | -------------------------------------------------------------------------------- /DICOMApp/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(DICOMApp) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATION ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATION ) 15 | 16 | 17 | ADD_EXECUTABLE(DICOMApp main.cxx) 18 | INSTALL_TARGETS(/bin DICOMApp) 19 | TARGET_LINK_LIBRARIES(DICOMApp ${ITK_LIBRARIES}) 20 | -------------------------------------------------------------------------------- /DartConfig.cmake: -------------------------------------------------------------------------------- 1 | set(CTEST_PROJECT_NAME "Insight") 2 | set(CTEST_NIGHTLY_START_TIME "21:00:00 EDT") 3 | 4 | set(CTEST_DROP_METHOD "http") 5 | set(CTEST_DROP_SITE "www.cdash.org") 6 | set(CTEST_DROP_LOCATION "/CDash/submit.php?project=Insight") 7 | set(CTEST_DROP_SITE_CDASH TRUE) 8 | -------------------------------------------------------------------------------- /DeformableModelSimplexMesh/ClickedPointEvent.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ClickedPointEvent.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #ifndef __itkClickedPointEvent_h__ 19 | #define __itkClickedPointEvent_h__ 20 | 21 | #include "itkEventObject.h" 22 | 23 | /** 24 | \class ClickedPointEvent 25 | \brief Class for defining ClickedPointEvent 26 | 27 | This defines a ClickedEventEvent class which is derived from the 28 | itk::AnyEvent class. 29 | 30 | */ 31 | 32 | itkEventMacro( ClickedPointEvent, itk::AnyEvent ); 33 | 34 | 35 | #endif 36 | 37 | -------------------------------------------------------------------------------- /DeformableModelSimplexMesh/InteractorObserver.cxx: -------------------------------------------------------------------------------- 1 | #include "InteractorObserver.h" 2 | 3 | #include 4 | 5 | 6 | 7 | 8 | InteractorObserver 9 | ::InteractorObserver() 10 | { 11 | m_SliceViewer = NULL; 12 | m_Motion = false; 13 | } 14 | 15 | 16 | 17 | 18 | InteractorObserver 19 | ::~InteractorObserver() 20 | { 21 | m_SliceViewer = NULL; 22 | } 23 | 24 | 25 | 26 | void 27 | InteractorObserver 28 | ::SetImageSliceViewer( ImageSliceViewer * viewer ) 29 | { 30 | m_SliceViewer = viewer; 31 | } 32 | 33 | 34 | 35 | void 36 | InteractorObserver 37 | ::Execute(vtkObject * caller, unsigned long eventId, void *callData) 38 | { 39 | if ( eventId == ::vtkCommand::LeftButtonPressEvent ) 40 | { 41 | m_Motion = true; 42 | } 43 | if ( eventId == ::vtkCommand::LeftButtonReleaseEvent ) 44 | { 45 | m_Motion = false; 46 | } 47 | if( m_SliceViewer && m_Motion ) 48 | { 49 | //point selected when mouse button pressed!! 50 | const int x = Fl::event_x(); 51 | const int y = Fl::event_y(); 52 | m_SliceViewer->SelectPoint( x, y ); 53 | } 54 | } 55 | 56 | 57 | 58 | 59 | 60 | 61 | -------------------------------------------------------------------------------- /DeformableModelSimplexMesh/InteractorObserver.h: -------------------------------------------------------------------------------- 1 | #include "vtkCommand.h" 2 | #include "ImageSliceViewer.h" 3 | 4 | /** 5 | \class InteractorObserver 6 | \brief This class defines observer command for user event 7 | (Keyboard/Mouse)in a ImageSliceViewer window. 8 | */ 9 | 10 | 11 | class InteractorObserver : public vtkCommand 12 | { 13 | public: 14 | 15 | static InteractorObserver *New() 16 | {return new InteractorObserver;}; 17 | 18 | /** The SetImageSliceViewer method inputs pointer of the ImageSliceViewer 19 | serviced. 20 | */ 21 | void SetImageSliceViewer( ImageSliceViewer * viewer ); 22 | 23 | /** The Execute method defines the code to be run when the 24 | command is invoked. 25 | */ 26 | void Execute(vtkObject * caller, unsigned long eventId, void *callData); 27 | 28 | protected: 29 | 30 | InteractorObserver(); 31 | virtual ~InteractorObserver(); 32 | 33 | private: 34 | 35 | ImageSliceViewer * m_SliceViewer; 36 | bool m_Motion; 37 | 38 | }; 39 | 40 | 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /DeformableModelSimplexMesh/main.cxx: -------------------------------------------------------------------------------- 1 | 2 | 3 | #include "DeformableModelApplication.h" 4 | 5 | 6 | int main( int argc, char *[] ) 7 | { 8 | 9 | DeformableModelApplication app; 10 | 11 | try 12 | { 13 | app.Show(); 14 | Fl::run(); 15 | } 16 | catch( std::exception & ex ) 17 | { 18 | std::cerr << ex.what() << std::endl; 19 | } 20 | 21 | return 0; 22 | } 23 | 24 | 25 | -------------------------------------------------------------------------------- /DeformableModelSimplexMesh/vtkPolyDataToitkMesh.h: -------------------------------------------------------------------------------- 1 | #ifndef __vtkPolyDataToitkMesh_h__ 2 | #define __vtkPolyDataToitkMesh_h__ 3 | 4 | #include "vtkPoints.h" 5 | #include "vtkCellArray.h" 6 | #include "vtkPolyData.h" 7 | #include "itkDefaultDynamicMeshTraits.h" 8 | #include "itkMesh.h" 9 | #include "itkTriangleCell.h" 10 | 11 | 12 | /** 13 | \class vtkPolyDataToitkMesh 14 | \brief 15 | \warning 16 | \sa 17 | */ 18 | 19 | class vtkPolyDataToitkMesh 20 | { 21 | 22 | public: 23 | 24 | vtkPolyDataToitkMesh( void ); 25 | virtual ~vtkPolyDataToitkMesh( void ); 26 | 27 | typedef itk::DefaultDynamicMeshTraits TriangleMeshTraits; 28 | typedef itk::Mesh TriangleMeshType; 29 | 30 | /** 31 | The SetInput method provides pointer to the vtkPolyData 32 | */ 33 | void SetInput( vtkPolyData * polydata); 34 | TriangleMeshType * GetOutput(); 35 | void ConvertvtkToitk(); 36 | 37 | TriangleMeshType::Pointer m_itkMesh; 38 | 39 | vtkPolyData * m_PolyData; 40 | 41 | 42 | }; 43 | 44 | #endif 45 | -------------------------------------------------------------------------------- /DeformableRegistration3DTimeSeries/DicomImageReaderBase.cxx: -------------------------------------------------------------------------------- 1 | 2 | #include "DicomImageReaderBase.h" 3 | 4 | #include 5 | 6 | 7 | namespace ISIS 8 | { 9 | 10 | 11 | DicomImageReaderBase 12 | ::DicomImageReaderBase() 13 | { 14 | m_FilenamesGenerator = SeriesFileNamesType::New(); 15 | } 16 | 17 | 18 | 19 | DicomImageReaderBase 20 | ::~DicomImageReaderBase() 21 | { 22 | } 23 | 24 | 25 | void 26 | DicomImageReaderBase 27 | ::SetDirectory( const char * directory ) 28 | { 29 | std::string directoryName = directory; 30 | m_FilenamesGenerator->SetDirectory( directoryName ); 31 | } 32 | 33 | const std::vector & DicomImageReaderBase::GetSeriesUIDs(){ 34 | return m_FilenamesGenerator->GetSeriesUIDs(); 35 | 36 | } 37 | 38 | } // end namespace ISIS 39 | 40 | 41 | -------------------------------------------------------------------------------- /DeformableRegistration3DTimeSeries/caimr.bmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/DeformableRegistration3DTimeSeries/caimr.bmp -------------------------------------------------------------------------------- /DicomImageViewer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(DicomImageViewer) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | 14 | FIND_PACKAGE(FLTK) 15 | IF(FLTK_FOUND) 16 | INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR}) 17 | ENDIF(FLTK_FOUND) 18 | 19 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 20 | 21 | 22 | 23 | INCLUDE_DIRECTORIES ( 24 | ${ITKApps_SOURCE_DIR}/Auxiliary/FltkImageViewer 25 | ${ITKApps_BINARY_DIR}/Auxiliary/FltkImageViewer 26 | ) 27 | 28 | 29 | ITK_DISABLE_FLTK_GENERATED_WARNINGS("DicomImageViewer.cxx") 30 | 31 | ADD_GUI_EXECUTABLE( DicomImageViewer DicomImageViewer.cxx ) 32 | TARGET_LINK_LIBRARIES (DicomImageViewer 33 | ${ITK_LIBRARIES} 34 | ITKFltkImageViewer 35 | ) 36 | 37 | 38 | -------------------------------------------------------------------------------- /DigitalArchive/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | SUBDIRS(FlDicomQueryChooser ThumbnailGenerator) 2 | -------------------------------------------------------------------------------- /DigitalArchive/FlDicomQueryChooser/ImageViewerGUI.fl: -------------------------------------------------------------------------------- 1 | # data file for the Fltk User Interface Designer (fluid) 2 | version 1.0011 3 | header_name {.h} 4 | code_name {.cpp} 5 | Function {make_window()} {open 6 | } { 7 | Fl_Window tkMain { 8 | label SimpleImageViewer open selected 9 | xywh {435 32 520 520} resizable visible 10 | } { 11 | Fl_Box tkWin { 12 | label label 13 | xywh {5 5 512 512} box ENGRAVED_FRAME resizable 14 | code0 {\#include } 15 | class {GLSliceView} 16 | } 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /DigitalArchive/FlDicomQueryChooser/fldqcNet.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: fldqcNet.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) Insight Software Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | #ifndef NET_H 18 | #define NET_H 19 | 20 | #include "fldqcDatatypes.h" 21 | #include "fldqcRemoteNetworkQuery.h" 22 | 23 | OFBool ChangeAssociation(Config *conf); 24 | OFBool AttachAssociation(Config *conf); 25 | OFBool DetatchAssociation(Config *conf, OFBool abortFlag); 26 | 27 | #endif 28 | -------------------------------------------------------------------------------- /DigitalArchive/ThumbnailGenerator/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | FIND_PACKAGE(ITK) 2 | 3 | IF(ITK_FOUND) 4 | INCLUDE(${ITK_USE_FILE}) 5 | ELSE(ITK_FOUND) 6 | MESSAGE(FATAL_ERROR 7 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 8 | ENDIF(ITK_FOUND) 9 | 10 | ADD_EXECUTABLE(ITKThumbnailGenerator GenerateThumbnail.cxx) 11 | INSTALL_TARGETS(/bin ITKThumbnailGenerator) 12 | TARGET_LINK_LIBRARIES(ITKThumbnailGenerator ${ITK_LIBRARIES}) 13 | 14 | ADD_EXECUTABLE(DicomThumbnailGenerator DicomGenerateThumbnail.cxx) 15 | INSTALL_TARGETS(/bin DicomThumbnailGenerator) 16 | TARGET_LINK_LIBRARIES(DicomThumbnailGenerator ${ITK_LIBRARIES}) 17 | 18 | -------------------------------------------------------------------------------- /DistanceMapFilter/DistanceMapFilter.cxx: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | #include "DistanceMapFilter.h" 5 | #include 6 | #include "FL/fl_ask.H" 7 | 8 | 9 | DistanceMapFilter:: 10 | DistanceMapFilter() 11 | { 12 | } 13 | 14 | 15 | DistanceMapFilter:: 16 | ~DistanceMapFilter() 17 | { 18 | } 19 | 20 | 21 | void 22 | DistanceMapFilter:: 23 | ComputeDistance(void) 24 | { 25 | 26 | if( ! this->ImageHasBeenLoaded() ) 27 | { 28 | fl_alert("Please load an image first"); 29 | return; 30 | } 31 | 32 | progressWindow->show(); 33 | Fl::check(); 34 | DistanceMapFilterBase::ComputeDistance(); 35 | progressWindow->hide(); 36 | } 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /DistanceMapFilter/main.cxx: -------------------------------------------------------------------------------- 1 | 2 | #include "DistanceMapFilter.h" 3 | #include "itkMacro.h" 4 | 5 | int main() 6 | { 7 | 8 | DistanceMapFilter::Pointer example = 9 | DistanceMapFilter::New(); 10 | 11 | example->Show(); 12 | example->ShowDisplay(); 13 | 14 | try 15 | { 16 | Fl::run(); 17 | } 18 | catch( itk::ExceptionObject & exception ) 19 | { 20 | std::cout << "Exception caught !" << std::endl; 21 | std::cout << "Description : " << exception.GetDescription() << std::endl; 22 | std::cout << "Location : " << exception.GetLocation() << std::endl; 23 | } 24 | 25 | return 0; 26 | 27 | } 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /DuctExtractor/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(DuctExtractor) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | FIND_PACKAGE(FLTK) 15 | IF(FLTK_FOUND) 16 | INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR}) 17 | ENDIF(FLTK_FOUND) 18 | 19 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 20 | 21 | 22 | 23 | INCLUDE_DIRECTORIES( 24 | ${ITKApps_SOURCE_DIR}/Auxiliary/FltkImageViewer 25 | ${ITKApps_BINARY_DIR}/Auxiliary/FltkImageViewer 26 | ${ITKApps_SOURCE_DIR}/DuctExtractor 27 | ${ITKApps_BINARY_DIR}/DuctExtractor 28 | ) 29 | 30 | FLTK_WRAP_UI(DuctExtractor DuctExtractorConsoleGUI.fl) 31 | ITK_DISABLE_FLTK_GENERATED_WARNINGS(DuctExtractorConsoleGUI.fl) 32 | 33 | SET(DuctExtractor_SRCS 34 | DuctExtractorConsole.cxx 35 | DuctExtractorConsoleBase.cxx 36 | DuctExtractor.cxx 37 | ${DuctExtractor_FLTK_UI_SRCS} 38 | ) 39 | 40 | ADD_GUI_EXECUTABLE(DuctExtractor "${DuctExtractor_SRCS}") 41 | TARGET_LINK_LIBRARIES(DuctExtractor ITKFltkImageViewer ${ITK_LIBRARIES}) 42 | 43 | 44 | -------------------------------------------------------------------------------- /DuctExtractor/DuctExtractor.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: DuctExtractor.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include 19 | 20 | int main() 21 | { 22 | 23 | 24 | DuctExtractorConsole * console = new DuctExtractorConsole(); 25 | 26 | console->Show(); 27 | 28 | Fl::run(); 29 | 30 | delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /DuctExtractor/DuctExtractor.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: DuctExtractor.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | 20 | #include 21 | 22 | 23 | -------------------------------------------------------------------------------- /DuctExtractor/DuctExtractorConsoleGUI.txt: -------------------------------------------------------------------------------- 1 | # generated by Fast Light User Interface Designer (fluid) version 1.0106 2 | -------------------------------------------------------------------------------- /EdgeDetection/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(EdgeDetection) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | 18 | INCLUDE_DIRECTORIES(${ITKApps_SOURCE_DIR}/EdgeDetection) 19 | 20 | #ADD_EXECUTABLE(itk2DEdgeDetectionSample itk2DEdgeDetectionSample.cxx) 21 | ADD_EXECUTABLE(itk3DEdgeDetectionSample itk3DEdgeDetectionSample.cxx) 22 | INSTALL_TARGETS(/bin itk3DEdgeDetectionSample) 23 | TARGET_LINK_LIBRARIES(itk3DEdgeDetectionSample ${ITK_LIBRARIES}) 24 | -------------------------------------------------------------------------------- /EdgeDetection/README: -------------------------------------------------------------------------------- 1 | 2 | README 3 | 4 | You need to make change in CMakeLists.txt file to select one of the following 5 | example. 6 | 7 | 1. itk3DEdgeDetectionSample.txx : 8 | 9 | This is an example for edge detection for 3D images. 10 | 11 | Important: You need to define the macros in the Makefile to indicate which edge detector you want to use: zero-crossing edge detector, sobel detector, canny edge detector. 12 | 13 | ZEROCORSSING ---zerocrossing based edge detector 14 | SOBEL --- use sobel detector 15 | CANNY --- use canny edge detector 16 | 17 | This example reads a VTK format raw image file, and writes output to VTK format image. 18 | 19 | 20 | 2. itk2DEdgeDetectionSample.txx 21 | 22 | This is an example for edge detection for 2D images. 23 | 24 | Important: You need to define the macros in the Makefile to indicate which edge detector you want to use: zero-crossing based edge detector, sobel detector, canny edge detector. 25 | 26 | ZEROCORSSING ---zerocrossing based edge detector 27 | SOBEL --- use sobel detector 28 | CANNY --- use canny edge detector 29 | 30 | This example reads a PGM ascii format raw image file, and writes output to ascii raw image format. 31 | -------------------------------------------------------------------------------- /EllipsoidInteriorExteriorSpatialFunction/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(EllipsoidInteriorExteriorSpatialFunction) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | 17 | INCLUDE_DIRECTORIES( 18 | ${EllipsoidInteriorExteriorSpatialFunction_SOURCE_DIR} 19 | ) 20 | 21 | SET(ELLIPSOID_SPATIAL_FUNCTION_SRCS 22 | itkEllipsoidInteriorExteriorSpatialFunctionExample.cxx 23 | ) 24 | 25 | ADD_EXECUTABLE(itkEllipsoidInteriorExteriorSpatialFunctionExample ${ELLIPSOID_SPATIAL_FUNCTION_SRCS}) 26 | INSTALL_TARGETS(/bin itkEllipsoidInteriorExteriorSpatialFunctionExample) 27 | 28 | TARGET_LINK_LIBRARIES (itkEllipsoidInteriorExteriorSpatialFunctionExample 29 | ${ITK_LIBRARIES} 30 | ) 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /EllipsoidInteriorExteriorSpatialFunction/README.doc: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /FindFltkImageViewer.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # Find the FltkImageViewer includes and library 3 | # 4 | # The following settings are defined 5 | # FltkImageViewer_INCLUDE_DIR = Where to find include files 6 | # FltkImageViewer_LIBRARY = The full path to ITKFltkImageViewer.lib 7 | # FltkImageViewer_FOUND = Don't use if false. 8 | 9 | # The following settings should not be used in general. 10 | 11 | 12 | FIND_PATH(FltkImageViewer_INCLUDE_DIR fltkImageViewer.h) 13 | 14 | FIND_LIBRARY(FltkImageViewer_LIBRARY NAMES ITKFltkImageViewer) 15 | 16 | SET(FltkImageViewer_FOUND 1) 17 | FOREACH(var FltkImageViewer_INCLUDE_DIR 18 | FltkImageViewer_LIBRARY) 19 | IF(NOT ${var}) 20 | SET(FltkImageViewer_FOUND 0) 21 | ENDIF(NOT ${var}) 22 | ENDFOREACH(var) 23 | 24 | -------------------------------------------------------------------------------- /FloodFilledSpatialFunction/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(FloodFilledSpatialFunction) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | INCLUDE_DIRECTORIES( 17 | ${FloodFilledSpatialFunction_SOURCE_DIR} 18 | ) 19 | 20 | 21 | ADD_EXECUTABLE(itkFloodFilledSpatialFunctionExample itkFloodFilledSpatialFunctionExample.cxx) 22 | INSTALL_TARGETS(/bin itkFloodFilledSpatialFunctionExample) 23 | TARGET_LINK_LIBRARIES(itkFloodFilledSpatialFunctionExample ${ITK_LIBRARIES}) 24 | -------------------------------------------------------------------------------- /FuzzyConnectedness/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(FuzzyConnectedness) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | 18 | INCLUDE_DIRECTORIES(${ITKApps_SOURCE_DIR}/FuzzyConnectedness 19 | ${ITKApps_SOURCE_DIR}/IBSRValidation/Common) 20 | 21 | ADD_EXECUTABLE(FuzzyConnectedness FuzzyConnectApp.cxx FuzzyConnectedness.cxx) 22 | INSTALL_TARGETS(/bin FuzzyConnectedness) 23 | 24 | TARGET_LINK_LIBRARIES(FuzzyConnectedness ${ITK_LIBRARIES}) 25 | -------------------------------------------------------------------------------- /FuzzyConnectedness/ReadMe.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/FuzzyConnectedness/ReadMe.doc -------------------------------------------------------------------------------- /FuzzyConnectedness/ReadMe.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/FuzzyConnectedness/ReadMe.pdf -------------------------------------------------------------------------------- /GPDM2DTest/GPDM2DTest.cpp: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: GPDM2DTest.cpp 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include "MyTestAppUI.h" 19 | 20 | int main() 21 | { 22 | 23 | 24 | MyTestAppInterface * mywin = new MyTestAppInterface; 25 | 26 | mywin->Show(); 27 | 28 | Fl::run(); 29 | 30 | // delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | -------------------------------------------------------------------------------- /GPDM3DTest/GPDM3DTest.cpp: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: GPDM3DTest.cpp 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include "MyTestAppUI.h" 19 | 20 | int main() 21 | { 22 | 23 | 24 | MyTestAppInterface * mywin = new MyTestAppInterface; 25 | 26 | mywin->Show(); 27 | 28 | Fl::run(); 29 | 30 | // delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | -------------------------------------------------------------------------------- /GaussianFilter/GaussianFilter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: GaussianFilter.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include 19 | 20 | int main() 21 | { 22 | 23 | 24 | liFilterConsole * console = new liFilterConsole(); 25 | 26 | console->Show(); 27 | 28 | Fl::run(); 29 | 30 | delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /GaussianFilter/GaussianFilter.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: GaussianFilter.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | /************************************************************ 20 | * 21 | * Project: Gaussian Filter 22 | * 23 | * This is an example of a full application 24 | * written using the Insight toolkit. 25 | * 26 | * It includes: 27 | * 28 | * - GUI using FLTK from http://www.fltk.org 29 | * - Input/Output using any file format registered with factories 30 | * 31 | **********************************************************/ 32 | 33 | #include 34 | 35 | 36 | -------------------------------------------------------------------------------- /GaussianFilter/GaussianFilter2D.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: GaussianFilter2D.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include 19 | 20 | int main() 21 | { 22 | 23 | 24 | liFilterConsole2D * console = new liFilterConsole2D(); 25 | 26 | console->Show(); 27 | 28 | Fl::run(); 29 | 30 | delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /GaussianFilter/README: -------------------------------------------------------------------------------- 1 | 2 | 3 | Gaussian Filter Application 4 | 5 | 6 | WHAT IS THIS ? 7 | 8 | This program is an example of a small 9 | application based on Insight. 10 | It includes image display, GUI, and IO. 11 | 12 | The program allows the user to load an 13 | image from a file, apply gaussian filters 14 | to it, visualize the results and save 15 | them on files. 16 | 17 | 18 | WHAT DO I NEED TO RUN IT ? 19 | 20 | As GUI and visualization are not part of 21 | Insight, external libraries are required 22 | for this program. The GUI is implemented 23 | using FLTK (the Fast Light Toolkit) that 24 | can be freely downloaded from 25 | http://www.fltk.org. 26 | 27 | FLTK is multiplatform and will run without 28 | trouble on Linux, IRIX and Windows 95/NT 29 | and SunOS. 30 | 31 | 32 | 33 | We appreciate your feedback. 34 | Please send your comments to the Insight 35 | mailing list, 36 | 37 | 38 | -------------------------------------------------------------------------------- /GaussianMinimumErrorClassifier/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | IF (NOT ITK_USE_REVIEW_STATISTICS) 2 | 3 | PROJECT(GaussianMinimumErrorClassifier) 4 | 5 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 6 | 7 | FIND_PACKAGE(ITK) 8 | IF(ITK_FOUND) 9 | INCLUDE(${ITK_USE_FILE}) 10 | ELSE(ITK_FOUND) 11 | MESSAGE(FATAL_ERROR 12 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 13 | ENDIF(ITK_FOUND) 14 | 15 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 16 | 17 | 18 | INCLUDE_DIRECTORIES( 19 | ${GaussianMinimumErrorClassifier_SOURCE_DIR} 20 | ${GaussianMinimumErrorClassifier_SOURCE_DIR}/../MRIBiasCorrection 21 | ) 22 | 23 | SET (GaussianMinimumErrorClassifier_SRCS 24 | ${GaussianMinimumErrorClassifier_SOURCE_DIR}/../MRIBiasCorrection/OptionList.cxx 25 | GaussianMinimumErrorClassifier.cxx 26 | ) 27 | 28 | ADD_EXECUTABLE(GaussianMinimumErrorClassifier ${GaussianMinimumErrorClassifier_SRCS}) 29 | INSTALL_TARGETS(/bin GaussianMinimumErrorClassifier) 30 | TARGET_LINK_LIBRARIES (GaussianMinimumErrorClassifier 31 | ${ITK_LIBRARIES} 32 | ) 33 | 34 | ENDIF (NOT ITK_USE_REVIEW_STATISTICS) 35 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( AtlasSegmentation ) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | INCLUDE_DIRECTORIES( 17 | ${AtlasSegmentation_SOURCE_DIR}/../Common 18 | ${AtlasSegmentation_SOURCE_DIR} 19 | ) 20 | 21 | ADD_EXECUTABLE(BrainStripValidationApp Code/BrainStripValidationApp.cxx) 22 | INSTALL_TARGETS(/bin BrainStripValidationApp) 23 | TARGET_LINK_LIBRARIES(BrainStripValidationApp ${ITK_LIBRARIES}) 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_1.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_1.txt 4 | 100_23 1 63 5 | 1_24 -1 65 param_1.txt 6 | 11_3 1 63 param_1.txt 7 | 110_3 0 64 param_1.txt 8 | 111_2 0 64 param_1.txt 9 | 112_2 1 63 param_1.txt 10 | 12_3 1 63 param_1.txt 11 | 13_3 1 63 param_1.txt 12 | 15_3 1 60 param_1.txt 13 | 16_3 1 60 param_1.txt 14 | 17_3 1 63 param_1.txt 15 | 191_3 1 63 param_1.txt 16 | 2_4 1 65 param_1.txt 17 | 202_3 1 63 param_1.txt 18 | 205_3 1 63 param_1.txt 19 | 4_8 7 61 param_1.txt 20 | 5_8 1 60 param_1.txt 21 | 6_10 1 63 param_1.txt 22 | 7_8 1 60 param_1.txt 23 | 8_4 1 63 param_1.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_2.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_2.txt 4 | 100_23 1 63 5 | 1_24 -1 65 param_2.txt 6 | 11_3 1 63 param_2.txt 7 | 110_3 0 64 param_2.txt 8 | 111_2 0 64 param_2.txt 9 | 112_2 1 63 param_2.txt 10 | 12_3 1 63 param_2.txt 11 | 13_3 1 63 param_2.txt 12 | 15_3 1 60 param_2.txt 13 | 16_3 1 60 param_2.txt 14 | 17_3 1 63 param_2.txt 15 | 191_3 1 63 param_2.txt 16 | 2_4 1 65 param_2.txt 17 | 202_3 1 63 param_2.txt 18 | 205_3 1 63 param_2.txt 19 | 4_8 7 61 param_2.txt 20 | 5_8 1 60 param_2.txt 21 | 6_10 1 63 param_2.txt 22 | 7_8 1 60 param_2.txt 23 | 8_4 1 63 param_2.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_3.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_3.txt 4 | 100_23 1 63 5 | 1_24 -1 65 param_3.txt 6 | 11_3 1 63 param_3.txt 7 | 110_3 0 64 param_3.txt 8 | 111_2 0 64 param_3.txt 9 | 112_2 1 63 param_3.txt 10 | 12_3 1 63 param_3.txt 11 | 13_3 1 63 param_3.txt 12 | 15_3 1 60 param_3.txt 13 | 16_3 1 60 param_3.txt 14 | 17_3 1 63 param_3.txt 15 | 191_3 1 63 param_3.txt 16 | 2_4 1 65 param_3.txt 17 | 202_3 1 63 param_3.txt 18 | 205_3 1 63 param_3.txt 19 | 4_8 7 61 param_3.txt 20 | 5_8 1 60 param_3.txt 21 | 6_10 1 63 param_3.txt 22 | 7_8 1 60 param_3.txt 23 | 8_4 1 63 param_3.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_4.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_4.txt 4 | 13_3 1 63 5 | 1_24 -1 65 param_1.txt 6 | 100_23 1 63 param_1.txt 7 | 11_3 1 63 param_1.txt 8 | 110_3 0 64 param_1.txt 9 | 111_2 0 64 param_1.txt 10 | 112_2 1 63 param_1.txt 11 | 12_3 1 63 param_1.txt 12 | 15_3 1 60 param_1.txt 13 | 16_3 1 60 param_1.txt 14 | 17_3 1 63 param_1.txt 15 | 191_3 1 63 param_1.txt 16 | 2_4 1 65 param_1.txt 17 | 202_3 1 63 param_1.txt 18 | 205_3 1 63 param_1.txt 19 | 4_8 7 61 param_1.txt 20 | 5_8 1 60 param_1.txt 21 | 6_10 1 63 param_1.txt 22 | 7_8 1 60 param_1.txt 23 | 8_4 1 63 param_1.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_5.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_5.txt 4 | 13_3 1 63 5 | 1_24 -1 65 param_2.txt 6 | 100_23 1 63 param_2.txt 7 | 11_3 1 63 param_2.txt 8 | 110_3 0 64 param_2.txt 9 | 111_2 0 64 param_2.txt 10 | 112_2 1 63 param_2.txt 11 | 12_3 1 63 param_2.txt 12 | 15_3 1 60 param_2.txt 13 | 16_3 1 60 param_2.txt 14 | 17_3 1 63 param_2.txt 15 | 191_3 1 63 param_2.txt 16 | 2_4 1 65 param_2.txt 17 | 202_3 1 63 param_2.txt 18 | 205_3 1 63 param_2.txt 19 | 4_8 7 61 param_2.txt 20 | 5_8 1 60 param_2.txt 21 | 6_10 1 63 param_2.txt 22 | 7_8 1 60 param_2.txt 23 | 8_4 1 63 param_2.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/input_6.txt: -------------------------------------------------------------------------------- 1 | I:/IBSR/20Normals_T1 2 | I:/IBSR/20Normals_T1_brain 3 | output_6.txt 4 | 13_3 1 63 5 | 1_24 -1 65 param_3.txt 6 | 100_23 1 63 param_3.txt 7 | 11_3 1 63 param_3.txt 8 | 110_3 0 64 param_3.txt 9 | 111_2 0 64 param_3.txt 10 | 112_2 1 63 param_3.txt 11 | 12_3 1 63 param_3.txt 12 | 15_3 1 60 param_3.txt 13 | 16_3 1 60 param_3.txt 14 | 17_3 1 63 param_3.txt 15 | 191_3 1 63 param_3.txt 16 | 2_4 1 65 param_3.txt 17 | 202_3 1 63 param_3.txt 18 | 205_3 1 63 param_3.txt 19 | 4_8 7 61 param_3.txt 20 | 5_8 1 60 param_3.txt 21 | 6_10 1 63 param_3.txt 22 | 7_8 1 60 param_3.txt 23 | 8_4 1 63 param_3.txt -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/param_1.txt: -------------------------------------------------------------------------------- 1 | 512 2 | 1 3 | 4 4 | 256 64 32 8 5 | 8 8 1 6 | 8 8 1 7 | 8 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/param_2.txt: -------------------------------------------------------------------------------- 1 | 1024 2 | 7 3 | 4 4 | 256 64 32 8 5 | 8 8 1 6 | 8 8 1 7 | 8 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Inputs/param_3.txt: -------------------------------------------------------------------------------- 1 | 2048 2 | 14 3 | 4 4 | 256 64 32 8 5 | 8 8 1 6 | 8 8 1 7 | 8 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/ReadMe.txt: -------------------------------------------------------------------------------- 1 | 2 | AtlasSegmentation: 3 | ================== 4 | 5 | This directory contains source code, input parameter files and ouput files 6 | for atlas-based segmentation validation study. 7 | 8 | The study evaluates the effectivenessof the ITK implementation of the 9 | "demons" based deformable registration algorithm for the application 10 | of atlas-based segmentation of the whole brain volume from MR images. 11 | 12 | The accompanying validation report can be found at 13 | InsightDocuments/Validation/AtlasSegmentation/AtlasSegmentationStudy.pdf 14 | 15 | Code: 16 | ===== 17 | 18 | This sub-directory contains the source code to build the 19 | BrainStripValidationApp application used for the study described 20 | in the report above. 21 | 22 | 23 | Inputs: 24 | ======= 25 | 26 | This sub-directory contains the input parameters files used to 27 | produce the results described in the report above. 28 | 29 | 30 | Results: 31 | ======== 32 | 33 | This sub-directory contains the output files produced as part 34 | of the validation study described in the report above. 35 | 36 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_1.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.96088 5.916 319123 307754 2 | 11_3 0.96931 5.099 561736 550042 3 | 110_3 0.95755 11.225 462308 436254 4 | 111_2 0.96220 5.831 469604 454508 5 | 112_2 0.95747 10.247 407340 381965 6 | 12_3 0.95351 7.000 537377 505911 7 | 13_3 0.95840 6.403 527830 503408 8 | 15_3 0.94407 9.487 318876 342290 9 | 16_3 0.95892 6.000 285764 293896 10 | 17_3 0.95206 12.570 313802 312181 11 | 191_3 0.96771 6.000 384699 377303 12 | 2_4 0.93759 8.602 302434 310908 13 | 202_3 0.95984 7.211 441775 428414 14 | 205_3 0.96564 5.385 431825 424755 15 | 4_8 0.92512 10.817 265283 291695 16 | 5_8 0.91328 10.050 343192 320335 17 | 6_10 0.88929 24.269 412854 356557 18 | 7_8 0.96026 6.708 331952 323103 19 | 8_4 0.95866 7.616 340615 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_2.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.96102 5.916 313196 307754 2 | 11_3 0.96951 5.385 553803 550042 3 | 110_3 0.96294 7.000 453066 436254 4 | 111_2 0.96171 5.099 462415 454508 5 | 112_2 0.96573 5.000 397745 381965 6 | 12_3 0.95685 6.083 529522 505911 7 | 13_3 0.96024 7.874 520123 503408 8 | 15_3 0.94234 7.874 317742 342290 9 | 16_3 0.95762 6.083 285426 293896 10 | 17_3 0.95538 11.225 312153 312181 11 | 191_3 0.96731 7.000 383214 377303 12 | 2_4 0.93837 8.544 297353 310908 13 | 202_3 0.96277 7.000 438896 428414 14 | 205_3 0.96548 5.385 432895 424755 15 | 4_8 0.92155 11.576 264022 291695 16 | 5_8 0.92349 10.050 335545 320335 17 | 6_10 0.92130 21.471 379347 356557 18 | 7_8 0.96499 6.481 325320 323103 19 | 8_4 0.96010 6.000 333269 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_3.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.96060 6.083 312792 307754 2 | 11_3 0.96941 5.385 553414 550042 3 | 110_3 0.96309 7.000 452859 436254 4 | 111_2 0.96155 5.099 462020 454508 5 | 112_2 0.96559 5.000 397975 381965 6 | 12_3 0.95695 6.083 528901 505911 7 | 13_3 0.96015 7.874 518968 503408 8 | 15_3 0.94273 7.348 318164 342290 9 | 16_3 0.95748 6.000 285404 293896 10 | 17_3 0.95559 11.225 312580 312181 11 | 191_3 0.96718 7.000 383558 377303 12 | 2_4 0.93812 9.220 296634 310908 13 | 202_3 0.96299 6.164 438568 428414 14 | 205_3 0.96549 5.385 432716 424755 15 | 4_8 0.92064 10.817 262799 291695 16 | 5_8 0.93509 10.050 326850 320335 17 | 6_10 0.92863 20.543 372927 356557 18 | 7_8 0.96513 6.481 325484 323103 19 | 8_4 0.95991 6.000 332884 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_4.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.95745 7.000 301851 307754 2 | 100_23 0.95097 8.544 418701 442195 3 | 11_3 0.96420 6.403 539245 550042 4 | 110_3 0.96486 6.403 444108 436254 5 | 111_2 0.96297 7.280 453849 454508 6 | 112_2 0.96631 6.083 391927 381965 7 | 12_3 0.95712 6.000 514901 505911 8 | 15_3 0.91442 9.487 301001 342290 9 | 16_3 0.93947 6.481 270624 293896 10 | 17_3 0.95587 9.000 307626 312181 11 | 191_3 0.95993 7.616 372973 377303 12 | 2_4 0.92537 12.042 291407 310908 13 | 202_3 0.96247 7.874 429514 428414 14 | 205_3 0.96342 8.000 419408 424755 15 | 4_8 0.91908 10.817 261680 291695 16 | 5_8 0.91184 10.050 316225 320335 17 | 6_10 0.89166 42.732 384652 356557 18 | 7_8 0.95852 9.434 320216 323103 19 | 8_4 0.95596 6.928 328028 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_5.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.95819 9.000 304818 307754 2 | 100_23 0.96110 6.708 429531 442195 3 | 11_3 0.96578 5.745 540393 550042 4 | 110_3 0.96489 6.403 443699 436254 5 | 111_2 0.96355 7.280 452761 454508 6 | 112_2 0.96638 6.164 390969 381965 7 | 12_3 0.95764 6.164 518001 505911 8 | 15_3 0.92268 9.055 305765 342290 9 | 16_3 0.94850 6.481 277244 293896 10 | 17_3 0.95723 18.547 312526 312181 11 | 191_3 0.96251 8.000 379592 377303 12 | 2_4 0.92825 13.000 292712 310908 13 | 202_3 0.96230 8.062 435481 428414 14 | 205_3 0.96733 8.246 429149 424755 15 | 4_8 0.92826 10.000 268866 291695 16 | 5_8 0.91152 10.050 323860 320335 17 | 6_10 0.88928 47.550 390843 356557 18 | 7_8 0.95851 17.029 321238 323103 19 | 8_4 0.95490 6.000 326160 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/AtlasSegmentation/Results/output_6.txt: -------------------------------------------------------------------------------- 1 | 1_24 0.95814 9.000 304959 307754 2 | 100_23 0.96140 6.403 430199 442195 3 | 11_3 0.96572 5.831 540608 550042 4 | 110_3 0.96490 6.708 444047 436254 5 | 111_2 0.96369 7.280 452937 454508 6 | 112_2 0.96630 6.164 391761 381965 7 | 12_3 0.95764 6.164 518806 505911 8 | 15_3 0.92278 10.000 305859 342290 9 | 16_3 0.94882 6.481 277728 293896 10 | 17_3 0.95720 19.339 312551 312181 11 | 191_3 0.96291 8.246 379978 377303 12 | 2_4 0.92770 13.000 292140 310908 13 | 202_3 0.96273 8.062 436017 428414 14 | 205_3 0.96723 8.775 429315 424755 15 | 4_8 0.92839 10.000 268711 291695 16 | 5_8 0.91628 10.050 320768 320335 17 | 6_10 0.89236 46.583 388144 356557 18 | 7_8 0.95839 18.028 321382 323103 19 | 8_4 0.95486 6.000 326165 335016 20 | -------------------------------------------------------------------------------- /IBSRValidation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | # Build application for altas-based segmentation of brain volume 3 | SUBDIRS( AtlasSegmentation ) 4 | 5 | if (ITK_VERSION_MAJOR STRLESS 4) 6 | # Build FEM application for altas-based segmentation of brain volume 7 | SUBDIRS( FEMAtlasSegmentation ) 8 | endif() 9 | 10 | # Build application for gray, white matter classification of brain volume 11 | SUBDIRS( IBSRClassification ) 12 | -------------------------------------------------------------------------------- /IBSRValidation/FEMAtlasSegmentation/Inputs/input.txt: -------------------------------------------------------------------------------- 1 | .\temp\IBSR\20Normals_T1_8bit\ 2 | .\temp\IBSR\20Normals_T1_8bit\ 3 | .\temp\output.txt 4 | 10 128 128 0 91 200 11 5 | 18 128 128 0 91 .\temp\FEMregLMparams3D.txt 6 | 11 128 128 0 91 .\temp\FEMregLMparams3D.txt 7 | 27 128 128 0 91 .\temp\FEMregLMparams3D.txt 8 | 22 128 128 0 91 .\temp\FEMregLMparams3D.txt 9 | 21 128 128 0 91 .\temp\FEMregLMparams3D.txt 10 | 14 128 128 0 91 .\temp\FEMregLMparams3D.txt 11 | 13 128 128 0 91 .\temp\FEMregLMparams3D.txt 12 | 15 128 128 0 91 .\temp\FEMregLMparams3D.txt 13 | 16 128 128 0 91 .\temp\FEMregLMparams3D.txt 14 | 17 128 128 0 91 .\temp\FEMregLMparams3D.txt 15 | 19 128 128 0 91 .\temp\FEMregLMparams3D.txt 16 | 20 128 128 0 91 .\temp\FEMregLMparams3D.txt 17 | 23 128 128 0 91 .\temp\FEMregLMparams3D.txt 18 | 24 128 128 0 91 .\temp\FEMregLMparams3D.txt 19 | 25 128 128 0 91 .\temp\FEMregLMparams3D.txt 20 | 26 128 128 0 91 .\temp\FEMregLMparams3D.txt 21 | 12 128 128 0 91 .\temp\FEMregLMparams3D.txt 22 | 28 128 128 0 91 .\temp\FEMregLMparams3D.txt 23 | 29 128 128 0 91 .\temp\FEMregLMparams3D.txt 24 | 25 | 26 | -------------------------------------------------------------------------------- /IBSRValidation/FEMAtlasSegmentation/Inputs/input_resample.txt: -------------------------------------------------------------------------------- 1 | .\temp\IBSR\OriginalNormals\20Normals_T1_8bit 2 | .\temp\IBSR\OriginalNormals\20Normals_T1_brain 3 | .\temp\output_ncc.txt 4 | 10 128 128 0 91 200 11 -1 5 | 11 128 128 0 91 .\temp\FEMregLMparams3D.txt 6 | 18 128 128 0 91 .\temp\FEMregLMparams3D.txt 7 | 25 128 128 0 91 .\temp\FEMregLMparams3D.txt 8 | 26 128 128 0 91 .\temp\FEMregLMparams3D.txt 9 | 27 128 128 0 91 .\temp\FEMregLMparams3D.txt 10 | 28 128 128 0 91 .\temp\FEMregLMparams3D.txt 11 | 29 128 128 0 91 .\temp\FEMregLMparams3D.txt 12 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/ReadMe.txt: -------------------------------------------------------------------------------- 1 | This file shows the systax followed in the parameter files. 2 | The parameter files are needed for the Gaussian Classifier based applications and are generated 3 | apriori manually. 4 | 5 | #NumberOfClasses (number of tissue type + 1 for background) 6 | 0 1173 1255 1323 (each #corresponds to the mean of background, tissue type 1,2 and 3) 7 | 0 2156 1120 581 (each #corresponds to the variance of background, tissue type 1,2 and 3) 8 | 0 254 6979 3974 (each #corresponds to the number of samples of background, tissue type 1,2 and 3 in the model) 9 | 10 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/TestKmeansClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1 2 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1_brain 3 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1_seg 4 | E:\Insight-clean\Insight\Applications\IBSRValidation\IBSRClassification\Results\KmeansIBSRoutput.txt 5 | 1 6 | 11_3 1 63 1 58 NoParamFile.txt 7 | 100_23 1 63 0 53 NoParamFile.txt 8 | 110_3 0 63 2 55 NoParamFile.txt 9 | 111_2 0 63 3 58 NoParamFile.txt 10 | 112_2 1 63 1 55 NoParamFile.txt 11 | 12_3 1 63 0 59 NoParamFile.txt 12 | 13_3 1 63 0 57 NoParamFile.txt 13 | 15_3 1 60 0 55 NoParamFile.txt 14 | 16_3 1 60 0 51 NoParamFile.txt 15 | 17_3 1 63 3 57 NoParamFile.txt 16 | 191_3 1 63 3 56 NoParamFile.txt 17 | 2_4 1 65 6 56 NoParamFile.txt 18 | 202_3 1 63 3 58 NoParamFile.txt 19 | 205_3 1 63 2 58 NoParamFile.txt 20 | 6_10 1 63 0 61 NoParamFile.txt 21 | 7_8 1 60 0 56 NoParamFile.txt 22 | 8_4 1 63 2 55 NoParamFile.txt 23 | 4_8 7 61 2 55 NoParamFile.txt 24 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/TestMRFKmeansClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1 2 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1_brain 3 | E:\Insight-clean\WorkDirData\IBSRClassification\20Normals_T1_seg 4 | E:\Insight-clean\Insight\Applications\IBSRValidation\IBSRClassification\Results\MRFKMeansIBSRoutput.txt 5 | 1 6 | 11_3 1 63 1 58 NoParamFile.txt 7 | 100_23 1 63 0 53 NoParamFile.txt 8 | 110_3 0 63 2 55 NoParamFile.txt 9 | 111_2 0 63 3 58 NoParamFile.txt 10 | 112_2 1 63 1 55 NoParamFile.txt 11 | 12_3 1 63 0 59 NoParamFile.txt 12 | 13_3 1 63 0 57 NoParamFile.txt 13 | 15_3 1 60 0 55 NoParamFile.txt 14 | 16_3 1 60 0 51 NoParamFile.txt 15 | 17_3 1 63 3 57 NoParamFile.txt 16 | 191_3 1 63 3 56 NoParamFile.txt 17 | 2_4 1 65 6 56 NoParamFile.txt 18 | 202_3 1 63 3 58 NoParamFile.txt 19 | 205_3 1 63 2 58 NoParamFile.txt 20 | 6_10 1 63 0 61 NoParamFile.txt 21 | 7_8 1 60 0 56 NoParamFile.txt 22 | 8_4 1 63 2 55 NoParamFile.txt 23 | 4_8 7 61 2 55 NoParamFile.txt 24 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param100_23.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1173 1255 1323 3 | 0 2156 1120 581 4 | 0 254 6979 3974 5 | 6 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param110_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1290 1383 1464 3 | 0 4739 2230 1354 4 | 0 3372 174228 91814 5 | 6 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param111_2.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1228 1348 1419 3 | 0 2900 1791 1202 4 | 0 156 6280 4818 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param112_2.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1341 1461 1564 3 | 0 8478 3150 1307 4 | 0 150 5759 3471 5 | 6 | [1,] 1340.847 7 | [2,] 8478.386 8 | 9 | $models[[3]]: 10 | [,1] 11 | [1,] 1461.314 12 | [2,] 3150.156 13 | 14 | $models[[4]]: 15 | [,1] 16 | [1,] 1564.004 17 | [2,] 1307.984 18 | 19 | 20 | $nsamples: 21 | [,1] [,2] [,3] [,4] 22 | [1,] 0 150 5759 3471 23 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param11_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1254 1395 1482 3 | 0 550 2998 901 4 | 0 348 9099 4380 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param12_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1232 1385 1471 3 | 0 4716 1827 1149 4 | 0 286 6709 4561 5 | 6 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param13_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1393 1514 1636 3 | 0 10886 3271 1475 4 | 0 186 7501 4750 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param15_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 38 68 86 3 | 0 242 214 131 4 | 0 5106 135779 78499 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param16_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 38 70 91 3 | 0 197 144 97 4 | 0 167 4367 2637 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param17_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 102 164 196 3 | 0 2334 843 398 4 | 0 124 4609 2981 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param191_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1335 1448 1548 3 | 0 5630 6168 2545 4 | 0 106 6232 3746 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param202_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1237 1453 1548 3 | 0 1000 4401 2118 4 | 0 357 5745 4772 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param205_3.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 1248 1482 1579 3 | 0 4127 4409 2560 4 | 0 241 6060 4787 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param2_4.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 100 137 168 3 | 0 658 1080 596 4 | 0 38 4617 3633 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param4_8.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 84 142 176 3 | 0 967 1190 757 4 | 0 221 4271 3923 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param6_10.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 50 72 89 3 | 0 102 201 175 4 | 0 180 4899 3012 -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param7_8.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 453 617 771 3 | 0 1000 3000 5744 4 | 0 135 4818 2663 5 | -------------------------------------------------------------------------------- /IBSRValidation/IBSRClassification/Inputs/param8_4.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 0 241 366 442 3 | 0 1000 3000 1145 4 | 0 187 5001 3122 -------------------------------------------------------------------------------- /IBSRValidation/ReadMe.txt: -------------------------------------------------------------------------------- 1 | 2 | IBSRValidation: 3 | =============== 4 | 5 | This directory contains source code, parameter files and output files for various 6 | validation studies using data from IBSR (Internet Brain Segmentation Repository) 7 | http://neuro-www.mgh.harvard.edu/cma/ibsr 8 | 9 | 10 | Common: 11 | ======= 12 | 13 | This sub-directory contains source code that common to several validation studies. 14 | 15 | 16 | AtlasSegmentation: 17 | ================== 18 | 19 | This sub-directory contains source code, input parameter files and ouput files 20 | for atlas-based segmentation validation study. 21 | 22 | The study evaluates the effectiveness of the ITK implementation of the 23 | "demons" based deformable registration algorithm for the application 24 | of atlas-based segmentation of the whole brain volume from MR images. 25 | 26 | The accompanying validation report can be found at 27 | InsightDocuments/Validation/AtlasSegmentation/AtlasSegmentationStudy.pdf 28 | 29 | See also AtlasSegmentation/ReadMe.txt 30 | 31 | 32 | -------------------------------------------------------------------------------- /ITKFilterLib/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(Example_ITKFilterLib) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | ADD_LIBRARY(Example_ITKFilterLib ITKFilterLib.cxx ) 17 | INSTALL_TARGETS(/lib Example_ITKFilterLib) 18 | TARGET_LINK_LIBRARIES(Example_ITKFilterLib ${ITK_LIBRARIES}) 19 | 20 | ADD_EXECUTABLE(Example_ITKFilterLibTest ITKFilterLibTest.cxx ) 21 | INSTALL_TARGETS(/bin Example_ITKFilterLibTest) 22 | TARGET_LINK_LIBRARIES(Example_ITKFilterLibTest Example_ITKFilterLib) 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /ITKRegistrationLib/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(ITKRegistrationLib) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | #INCLUDE_REGULAR_EXPRESSION(".*") 17 | 18 | INCLUDE_DIRECTORIES( 19 | ${ITKRegistrationLib_SOURCE_DIR}/../MultiResMIRegistration/Common 20 | ${ITKRegistrationLib_SOURCE_DIR}/../IBSRValidation/Common 21 | ) 22 | 23 | 24 | ADD_LIBRARY(Example_ITKRegistrationLib ITKRegistrationLib.cxx ) 25 | INSTALL_TARGETS(/lib Example_ITKRegistrationLib) 26 | TARGET_LINK_LIBRARIES(Example_ITKRegistrationLib ${ITK_LIBRARIES}) 27 | 28 | ADD_EXECUTABLE(Example_ITKRegistrationLibTest ITKRegistrationLibTest.cxx) 29 | INSTALL_TARGETS(/bin Example_ITKRegistrationLibTest) 30 | TARGET_LINK_LIBRARIES(Example_ITKRegistrationLibTest Example_ITKRegistrationLib) 31 | 32 | IF(CMAKE_COMPILER_IS_GNUCXX) 33 | SET_SOURCE_FILES_PROPERTIES (ITKRegistrationLib.cxx PROPERTIES COMPILE_FLAGS -w) 34 | ENDIF(CMAKE_COMPILER_IS_GNUCXX) 35 | -------------------------------------------------------------------------------- /ImageCalculator/ImageCalculator.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageCalculator.cxx 5 | Language: C++ 6 | 7 | Copyright (c) Insight Software Consortium. All rights reserved. 8 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 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 above copyright notices for more information. 13 | 14 | =========================================================================*/ 15 | 16 | #include "ImageCalculatorUtils.h" 17 | #ifdef ITKV3_COMPATIBILITY 18 | #include "itkAnalyzeImageIOFactory.h" 19 | #endif 20 | int main(int argc, char *argv[]) 21 | { 22 | #ifdef ITKV3_COMPATIBILITY 23 | itk::ObjectFactoryBase::RegisterFactory( itk::AnalyzeImageIOFactory::New() ); 24 | #endif 25 | return PrimaryImageCalculatorRoutine(argc, argv); 26 | } 27 | 28 | 29 | 30 | 31 | // End of main() 32 | -------------------------------------------------------------------------------- /ImageCalculator/ImageCalculatorProcess2D.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageCalculatorProcess2D.cxx 5 | Language: C++ 6 | 7 | Copyright (c) Insight Software Consortium. All rights reserved. 8 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 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 above copyright notices for more information. 13 | 14 | =========================================================================*/ 15 | 16 | #include "ImageCalculatorTemplates.h" 17 | 18 | //This program calls the 2d function to process the algorithm. 19 | void ImageCalculatorProcess2D(const std::string & InType,MetaCommand &command) 20 | { 21 | ImageCalculatorProcessND<2>(InType,command); 22 | } 23 | -------------------------------------------------------------------------------- /ImageCalculator/ImageCalculatorProcess3D.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageCalculatorProcess3D.cxx 5 | Language: C++ 6 | 7 | Copyright (c) Insight Software Consortium. All rights reserved. 8 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 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 above copyright notices for more information. 13 | 14 | =========================================================================*/ 15 | 16 | #include "ImageCalculatorTemplates.h" 17 | 18 | //This program calls the 3d function to process the algorithm. 19 | void ImageCalculatorProcess3D(const std::string & InType,MetaCommand &command) 20 | { 21 | ImageCalculatorProcessND<3>(InType,command); 22 | } 23 | 24 | -------------------------------------------------------------------------------- /ImageCalculator/ImageCalculatorTests.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageCalculatorTests.cxx 5 | Language: C++ 6 | 7 | Copyright (c) Insight Software Consortium. All rights reserved. 8 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 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 above copyright notices for more information. 13 | 14 | =========================================================================*/ 15 | 16 | // this file defines the ImageCalculator-Tests for the test driver 17 | // and all it expects is that you have a function called RegisterTests 18 | 19 | #if defined(_MSC_VER) 20 | #pragma warning ( disable : 4786 ) 21 | #endif 22 | #include 23 | #include "itkTestMain.h" 24 | 25 | void RegisterTests() 26 | { 27 | REGISTER_TEST(ImageCalculatorTest); 28 | } 29 | #undef main 30 | #define main ImageCalculatorTest 31 | #include "ImageCalculator.cxx" 32 | 33 | 34 | -------------------------------------------------------------------------------- /ImageCalculator/TestImages/AllFifties.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageCalculator/TestImages/AllFifties.png 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/ImageCalculator/doc/ImageCalculator.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageCalculator/doc/ImageCalculator.tex -------------------------------------------------------------------------------- /ImageCalculator/doc/InsightJournal.ist: -------------------------------------------------------------------------------- 1 | line_max 100 2 | headings_flag 1 3 | heading_prefix " \\bigletter " 4 | 5 | preamble "\\begin{theindex} 6 | \\def\\bigletter#1{{\\Large\\sffamily#1}\\nopagebreak\\vspace{1mm}} 7 | 8 | " 9 | 10 | symhead_positive "{Symbols}" 11 | numhead_positive "{Numbers}" 12 | -------------------------------------------------------------------------------- /ImageCalculator/doc/Makefile: -------------------------------------------------------------------------------- 1 | 2 | 3 | NAME = ImageCalculator 4 | 5 | BIBTEXDATABSENAME = InsightJournal 6 | 7 | 8 | all: ps pdf dvi 9 | 10 | 11 | ps: ${NAME}.ps 12 | 13 | 14 | pdf: ${NAME}.pdf 15 | 16 | 17 | dvi: ${NAME}.dvi 18 | 19 | 20 | bbl: ${NAME}.bbl 21 | 22 | 23 | 24 | ${NAME}.ps: ${NAME}.dvi 25 | dvips -o ${NAME}.ps ${NAME}.dvi 26 | 27 | 28 | ${NAME}.pdf: ${NAME}.ps 29 | ps2pdf ${NAME}.ps 30 | 31 | 32 | ${NAME}.dvi: ${NAME}.tex ${BIBTEXDATABSENAME}.bib 33 | latex ${NAME}.tex 34 | latex ${NAME}.tex 35 | latex ${NAME}.tex 36 | latex ${NAME}.tex 37 | 38 | 39 | ${NAME}.aux: ${NAME}.tex ${BIBTEXDATABSENAME}.bib 40 | latex ${NAME}.tex 41 | 42 | 43 | clean: 44 | rm ${NAME}.dvi ${NAME}.ps ${NAME}.pdf ${NAME}.aux ${NAME}.log ${NAME}.bbl ${NAME}.blg ${NAME}.toc ${NAME}.out ${NAME}.brf 45 | 46 | -------------------------------------------------------------------------------- /ImageCalculator/doc/figs/ImageCalculator.dia: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageCalculator/doc/figs/ImageCalculator.dia -------------------------------------------------------------------------------- /ImageCalculator/doc/times.sty: -------------------------------------------------------------------------------- 1 | %% 2 | %% This is file `times.sty', 3 | %% generated with the docstrip utility. 4 | %% 5 | %% The original source files were: 6 | %% 7 | %% psfonts.dtx (with options: `times') 8 | %% 9 | %% IMPORTANT NOTICE: 10 | %% 11 | %% For the copyright see the source file. 12 | %% 13 | %% Any modified versions of this file must be renamed 14 | %% with new filenames distinct from times.sty. 15 | %% 16 | %% For distribution of the original source see the terms 17 | %% for copying and modification in the file psfonts.dtx. 18 | %% 19 | %% This generated file may be distributed as long as the 20 | %% original source files, as listed above, are part of the 21 | %% same distribution. (The sources need not necessarily be 22 | %% in the same archive or directory.) 23 | \ProvidesPackage{times} 24 | [2002/09/08 PSNFSS-v9.0a 25 | (SPQR) 26 | ] 27 | \renewcommand{\sfdefault}{phv} 28 | \renewcommand{\rmdefault}{ptm} 29 | \renewcommand{\ttdefault}{pcr} 30 | \endinput 31 | %% 32 | %% End of file `times.sty'. 33 | -------------------------------------------------------------------------------- /ImageColorViewer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(ImageColorViewer) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | FIND_PACKAGE(FLTK) 15 | IF(FLTK_FOUND) 16 | INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR}) 17 | ENDIF(FLTK_FOUND) 18 | 19 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 20 | 21 | INCLUDE_DIRECTORIES ( 22 | ${ITKApps_SOURCE_DIR}/Auxiliary/FltkImageViewer 23 | ) 24 | 25 | SET(ImageColorViewer_GUI_SRCS 26 | ImageColorViewerGUI.fl 27 | ) 28 | 29 | FLTK_WRAP_UI( ImageColorViewer ${ImageColorViewer_GUI_SRCS} ) 30 | ITK_DISABLE_FLTK_GENERATED_WARNINGS("${ImageColorViewer_GUI_SRCS}") 31 | 32 | SET ( ImageColorViewer_SRCS 33 | ImageColorViewer.cxx 34 | ${ImageColorViewer_FLTK_UI_SRCS} 35 | ) 36 | 37 | ADD_GUI_EXECUTABLE( ImageColorViewer "${ImageColorViewer_SRCS}" ) 38 | 39 | TARGET_LINK_LIBRARIES (ImageColorViewer 40 | ${ITK_LIBRARIES} 41 | ITKFltkImageViewer 42 | ) 43 | -------------------------------------------------------------------------------- /ImageColorViewer/ImageColorViewerGUI.fl: -------------------------------------------------------------------------------- 1 | # data file for the Fltk User Interface Designer (fluid) 2 | version 1.0011 3 | header_name {.h} 4 | code_name {.cpp} 5 | Function {make_window()} {open 6 | } { 7 | Fl_Window tkMain { 8 | label SimpleImageViewer open selected 9 | xywh {435 32 520 520} resizable visible 10 | } { 11 | Fl_Box tkWin { 12 | label label 13 | xywh {5 5 512 512} box ENGRAVED_FRAME resizable 14 | code0 {\#include } 15 | class {itk::GLColorSliceView} 16 | } 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /ImageColorViewer/sampleMetaHeader.mhd: -------------------------------------------------------------------------------- 1 | NDims = 3 2 | Comment = Load four slices of RGB data: slice00[1-4].raw 3 | DimSize = 256 256 4 4 | ElementByteOrderMSB = False 5 | ElementNumberOfChannels = 3 6 | ElementType = MET_UCHAR 7 | ElementDataFile = slice%03d.raw 1 4 1 8 | -------------------------------------------------------------------------------- /ImageRegistration/ImageRegistration.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageRegistration.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | /************************************************************ 20 | * 21 | * Project: ImageRegistration 22 | * 23 | * This is an example of a full application 24 | * written using the Insight toolkit. 25 | * 26 | * It includes: 27 | * 28 | * - GUI using FLTK from http://www.fltk.org 29 | * - Input/Output using the MetaImage file format 30 | * 31 | **********************************************************/ 32 | 33 | #include 34 | 35 | 36 | -------------------------------------------------------------------------------- /ImageRegistration/README: -------------------------------------------------------------------------------- 1 | 2 | 3 | Image Registration Application 4 | 5 | 6 | WHAT IS THIS ? 7 | 8 | This program is an example of a small 9 | application based on Insight. 10 | It includes image display, GUI, and IO. 11 | 12 | The program allows the user to load an 13 | image from a file, apply a known space 14 | transformation to it, and then register 15 | the result with the original image. 16 | 17 | 18 | WHAT DO I NEED TO RUN IT ? 19 | 20 | As GUI and visualization are not part of 21 | Insight, external libraries are required 22 | for this program. The GUI is implemented 23 | using FLTK (the Fast Light Toolkit) that 24 | can be freely downloaded from 25 | http://www.fltk.org. 26 | 27 | 28 | We appreciate your feedback. 29 | Please send your comments to the Insight 30 | mailing list. 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /ImageRegistration2D/ImageRegistration2D.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ImageRegistration2D.h 5 | Language: C++ 6 | 7 | Copyright (c) 2002 Insight Consortium. All rights reserved. 8 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 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 above copyright notices for more information. 13 | 14 | =========================================================================*/ 15 | 16 | 17 | /************************************************************ 18 | * 19 | * Project: ImageRegistration 20 | * 21 | * This is an example of a full application 22 | * written using the Insight toolkit. 23 | * 24 | * It includes: 25 | * 26 | * - GUI using FLTK from http://www.fltk.org 27 | * - Input/Output using the MetaImage file format 28 | * 29 | **********************************************************/ 30 | 31 | #include 32 | 33 | 34 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | PROJECT( ItkRegMFC ) 3 | 4 | #ADD_DEFINITIONS(-D_AFXDLL) 5 | 6 | SET(CMAKE_MFC_FLAG 2) 7 | 8 | 9 | SET(ItkRegMFC_SRCS 10 | stdAfx.cpp 11 | stdAfx.h 12 | ItkRegMFC.cpp 13 | ItkRegMFC.h 14 | ItkRegMFC.rc 15 | ItkRegMFCDoc.cpp 16 | ItkRegMFCDoc.h 17 | MainFrm.cpp 18 | MainFrm.h 19 | ItkRegMFCView.cpp 20 | ItkRegMFCView.h 21 | ) 22 | 23 | IF(WIN32) 24 | LINK_LIBRARIES( 25 | wsock32 26 | ) 27 | ENDIF(WIN32) 28 | 29 | 30 | FIND_PACKAGE(ITK) 31 | IF(ITK_FOUND) 32 | INCLUDE(${ITK_USE_FILE}) 33 | ELSE(ITK_FOUND) 34 | MESSAGE(FATAL_ERROR 35 | "Cannot build without ITK. Please set ITK_DIR.") 36 | ENDIF(ITK_FOUND) 37 | 38 | 39 | ADD_EXECUTABLE(ItkRegMFC WIN32 ${ItkRegMFC_SRCS}) 40 | INSTALL_TARGETS(/bin ItkRegMFC) 41 | TARGET_LINK_LIBRARIES(ItkRegMFC ${ITK_LIBRARIES} ) 42 | 43 | 44 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/ItkRegMFC.aps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageRegistrationMFC/ItkRegMFC.aps -------------------------------------------------------------------------------- /ImageRegistrationMFC/ItkRegMFC.h: -------------------------------------------------------------------------------- 1 | // ItkRegMFC.h : main header file for the ItkRegMFC application 2 | // 3 | #pragma once 4 | 5 | #ifndef __AFXWIN_H__ 6 | #error include 'stdafx.h' before including this file for PCH 7 | #endif 8 | 9 | #include "resource.h" // main symbols 10 | 11 | // CItkRegMFCApp: 12 | // See ItkRegMFC.cpp for the implementation of this class 13 | // 14 | 15 | class CItkRegMFCApp : public CWinApp 16 | { 17 | public: 18 | CItkRegMFCApp(); 19 | 20 | 21 | // Overrides 22 | public: 23 | virtual BOOL InitInstance(); 24 | 25 | // Implementation 26 | afx_msg void OnAppAbout(); 27 | DECLARE_MESSAGE_MAP() 28 | }; 29 | 30 | extern CItkRegMFCApp theApp; 31 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/ItkRegMFCDoc.h: -------------------------------------------------------------------------------- 1 | // ItkRegMFCDoc.h : interface of the CItkRegMFCDoc class 2 | // 3 | 4 | 5 | #pragma once 6 | 7 | class CItkRegMFCDoc : public CDocument 8 | { 9 | protected: // create from serialization only 10 | CItkRegMFCDoc(); 11 | DECLARE_DYNCREATE(CItkRegMFCDoc) 12 | 13 | // Attributes 14 | public: 15 | 16 | // Operations 17 | public: 18 | 19 | // Overrides 20 | public: 21 | virtual BOOL OnNewDocument(); 22 | virtual void Serialize(CArchive& ar); 23 | 24 | // Implementation 25 | public: 26 | virtual ~CItkRegMFCDoc(); 27 | #ifdef _DEBUG 28 | virtual void AssertValid() const; 29 | virtual void Dump(CDumpContext& dc) const; 30 | #endif 31 | 32 | protected: 33 | 34 | // Generated message map functions 35 | protected: 36 | DECLARE_MESSAGE_MAP() 37 | }; 38 | 39 | 40 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/MainFrm.h: -------------------------------------------------------------------------------- 1 | // MainFrm.h : interface of the CMainFrame class 2 | // 3 | 4 | 5 | #pragma once 6 | class CMainFrame : public CFrameWnd 7 | { 8 | 9 | protected: // create from serialization only 10 | CMainFrame(); 11 | DECLARE_DYNCREATE(CMainFrame) 12 | 13 | // Attributes 14 | public: 15 | 16 | // Operations 17 | public: 18 | 19 | // Overrides 20 | public: 21 | virtual BOOL PreCreateWindow(CREATESTRUCT& cs); 22 | 23 | // Implementation 24 | public: 25 | virtual ~CMainFrame(); 26 | #ifdef _DEBUG 27 | virtual void AssertValid() const; 28 | virtual void Dump(CDumpContext& dc) const; 29 | #endif 30 | 31 | protected: // control bar embedded members 32 | CStatusBar m_wndStatusBar; 33 | CToolBar m_wndToolBar; 34 | public: 35 | // Instance of CDialogBar 36 | // Set it as public instance, it will be accessed by CView class 37 | CDialogBar m_wndDialogBar; 38 | // Generated message map functions 39 | protected: 40 | afx_msg int OnCreate(LPCREATESTRUCT lpCreateStruct); 41 | DECLARE_MESSAGE_MAP() 42 | }; 43 | 44 | 45 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/README_FIRST.txt: -------------------------------------------------------------------------------- 1 | 2 | The code in this directory was contributed by 3 | 4 | Yong Su 5 | Sidney, Australia 6 | 7 | as a paper to the Insight Journal: 8 | 9 | "How to use ITK and MFC" 10 | 11 | 12 | The full paper and the code can be found at: 13 | 14 | http://www.insight-journal.org/InsightJournalManager/view_reviews.php?back=publications.php%3Fjournalid%3D7%26order%3Drating%26revision_display%3Dcombined&pubid=141 15 | 16 | The permanent handle to the paper can be found at: 17 | 18 | http://insight-journal.org/dspace/handle/1926/479 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/res/ItkRegMFC.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageRegistrationMFC/res/ItkRegMFC.ico -------------------------------------------------------------------------------- /ImageRegistrationMFC/res/ItkRegMFC.manifest: -------------------------------------------------------------------------------- 1 | 2 | 3 | 9 | Your app description here 10 | 11 | 12 | 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/res/ItkRegMFC.rc2: -------------------------------------------------------------------------------- 1 | // 2 | // ItkRegMFC.RC2 - resources Microsoft Visual C++ does not edit directly 3 | // 4 | 5 | #ifdef APSTUDIO_INVOKED 6 | #error this file is not editable by Microsoft Visual C++ 7 | #endif //APSTUDIO_INVOKED 8 | 9 | 10 | ///////////////////////////////////////////////////////////////////////////// 11 | // Add manually edited resources here... 12 | 13 | ///////////////////////////////////////////////////////////////////////////// 14 | -------------------------------------------------------------------------------- /ImageRegistrationMFC/res/ItkRegMFCDoc.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageRegistrationMFC/res/ItkRegMFCDoc.ico -------------------------------------------------------------------------------- /ImageRegistrationMFC/res/Toolbar.bmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ImageRegistrationMFC/res/Toolbar.bmp -------------------------------------------------------------------------------- /ImageRegistrationMFC/stdafx.cpp: -------------------------------------------------------------------------------- 1 | // stdafx.cpp : source file that includes just the standard includes 2 | // ItkRegMFC.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 | -------------------------------------------------------------------------------- /ImageViewer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(ImageViewer) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | FIND_PACKAGE(FLTK) 14 | IF(FLTK_FOUND) 15 | INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR}) 16 | ENDIF(FLTK_FOUND) 17 | 18 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 19 | 20 | INCLUDE_DIRECTORIES ( 21 | ${ITKApps_SOURCE_DIR}/Auxiliary/FltkImageViewer 22 | ) 23 | 24 | SET(ImageViewer_GUI_SRCS 25 | ImageViewerGUI.fl 26 | ) 27 | 28 | FLTK_WRAP_UI( ImageViewer ${ImageViewer_GUI_SRCS} ) 29 | 30 | SET ( ImageViewer_SRCS 31 | ImageViewer.cxx 32 | ${ImageViewer_FLTK_UI_SRCS} 33 | ) 34 | ITK_DISABLE_FLTK_GENERATED_WARNINGS("${ImageViewer_SRCS}") 35 | 36 | ADD_GUI_EXECUTABLE( ImageViewer "${ImageViewer_SRCS}" ) 37 | TARGET_LINK_LIBRARIES (ImageViewer ${ITK_LIBRARIES} ITKFltkImageViewer) 38 | -------------------------------------------------------------------------------- /ImageViewer/ImageViewerGUI.fl: -------------------------------------------------------------------------------- 1 | # data file for the Fltk User Interface Designer (fluid) 2 | version 1.0011 3 | header_name {.h} 4 | code_name {.cpp} 5 | Function {make_window()} {open 6 | } { 7 | Fl_Window tkMain { 8 | label SimpleImageViewer open selected 9 | xywh {435 32 520 520} resizable visible 10 | } { 11 | Fl_Box tkWin { 12 | label label 13 | xywh {5 5 512 512} box ENGRAVED_FRAME resizable 14 | code0 {\#include } 15 | class {itk::GLSliceView} 16 | } 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /IntensityBased2D3DRegistration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(IntensityBased2D3DRegistration) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | #ADD_DEFINITIONS(-Wno-non-template-friend -g) 16 | #SET(CMAKE_VERBOSE_MAKEFILE ON) 17 | 18 | ADD_EXECUTABLE(IntensityBased2D3DRegistration IntensityBased2D3DRegistration.cxx) 19 | INSTALL_TARGETS(/bin IntensityBased2D3DRegistration) 20 | TARGET_LINK_LIBRARIES( IntensityBased2D3DRegistration ${ITK_LIBRARIES}) 21 | 22 | ADD_EXECUTABLE(GenerateProjection GenerateProjection.cxx) 23 | INSTALL_TARGETS(/bin GenerateProjection) 24 | TARGET_LINK_LIBRARIES( GenerateProjection ${ITK_LIBRARIES}) 25 | -------------------------------------------------------------------------------- /IntensityBased2D3DRegistration/README.txt: -------------------------------------------------------------------------------- 1 | Examples of usage: 2 | 3 | A) GenerateProjection 4 | 5 | 6 | A.1) Translate the image by (-100,-100,-100) then project. 7 | 8 | ./GenerateProjection -t -100 -100 -100 /data/BrainWeb/brainweb165a10f17.mha projection.mhd 9 | 10 | A.2) Translate the image by (-100,-100,-100), 11 | rotate 10 degrees around x, then project. 12 | 13 | ./GenerateProjection -t -100 -100 -100 -rx 10 /data/BrainWeb/brainweb165a10f17.mha projection.mhd 14 | 15 | 16 | B) IntensityBased2D3DRegistration 17 | 18 | 19 | B.1) Register the image that was generated. 20 | 21 | ./IntensityBased2D3DRegistration -t -100 -100 -100 projection.mhd /data/BrainWeb/brainweb165a10f17.mha 22 | 23 | 24 | B.2) Register the image that was generated with rotation. 25 | 26 | 27 | ./IntensityBased2D3DRegistration -t -100 -100 -100 -rx 10 projection.mhd /data/BrainWeb/brainweb165a10f17.mha 28 | -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_xdisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_xdisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_ydisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_ydisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_zdisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g1_To_g2_zdisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_xdisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_xdisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_ydisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_ydisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_zdisp.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/BaselineResults/g2_To_g1_zdisp.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(CLReg) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | LINK_LIBRARIES( ${ITK_LIBRARIES}) 17 | CONFIGURE_FILE(${CLReg_SOURCE_DIR}/testScript.in 18 | ${CLReg_BINARY_DIR}/testScript IMMEDIATE ) 19 | ADD_EXECUTABLE(CLReg CLReg.cxx) 20 | INSTALL_TARGETS(/bin CLReg) 21 | ADD_EXECUTABLE(CLRegTest CLRegTest.cxx) 22 | INSTALL_TARGETS(/bin CLRegTest) 23 | 24 | -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/TestInputs/grids.hdr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/TestInputs/grids.hdr -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/TestInputs/grids.img: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/TestInputs/grids.img -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/TestInputs/set1.lmk: -------------------------------------------------------------------------------- 1 | #GECLANDMARKS-v1.0 2 | #IMAGEDIMS 32 32 32 1 3 | pt1 12 12 12 0 1 4 | pt2 20 20 12 0 1 5 | pt3 12 20 12 0 1 6 | pt4 20 12 12 0 1 7 | pt5 12 12 20 0 1 8 | pt6 20 20 20 0 1 9 | pt7 12 20 20 0 1 10 | pt8 20 12 20 0 1 11 | -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/TestInputs/set2.lmk: -------------------------------------------------------------------------------- 1 | #GECLANDMARKS-v1.0 2 | #IMAGEDIMS 32 32 32 1 3 | pt1 8 8 8 0 1 4 | pt2 24 24 8 0 1 5 | pt3 8 24 8 0 1 6 | pt4 24 8 8 0 1 7 | pt5 8 8 24 0 1 8 | pt6 24 24 24 0 1 9 | pt7 8 24 24 0 1 10 | pt8 24 8 24 0 1 11 | -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/johnson_christensen_tmi02_front_page.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/InverseConsistentLandmarkRegistration/johnson_christensen_tmi02_front_page.pdf -------------------------------------------------------------------------------- /InverseConsistentLandmarkRegistration/testScript.in: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # Program: Insight Segmentation & Registration Toolkit 3 | # Module: testScript.in 4 | # Language: C++ 5 | # Date: $Date$ 6 | # Version: $Revision$ 7 | # 8 | # Copyright (c) 2002 Insight Consortium. All rights reserved. 9 | # See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | # 11 | # This software is distributed WITHOUT ANY WARRANTY; without even 12 | # the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | # PURPOSE. See the above copyright notices for more information. 14 | # 15 | # This script assumes that it's running in the binary directory for 16 | # InverseConsistentRegistration, if not, you need to edit in the proper 17 | # path 18 | 19 | @CLReg_BINARY_DIR@/CLReg \ 20 | @CLReg_SOURCE_DIR@/TestInputs/grids.hdr \ 21 | @CLReg_SOURCE_DIR@/TestInputs/grids.hdr \ 22 | @CLReg_SOURCE_DIR@/TestInputs/set1.lmk \ 23 | @CLReg_SOURCE_DIR@/TestInputs/set2.lmk 24 | 25 | @CLReg_BINARY_DIR@/CLRegTest @CLReg_SOURCE_DIR@/BaselineResults . 26 | -------------------------------------------------------------------------------- /ItkMFC/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | PROJECT( ItkMFC ) 3 | 4 | ADD_DEFINITIONS(-D_AFXDLL) 5 | 6 | SET(CMAKE_MFC_FLAG 1) 7 | 8 | 9 | SET(ItkMFC_SRCS 10 | StdAfx.cpp 11 | ItkMFC.cpp 12 | ItkMFC.rc 13 | ItkMFCDoc.cpp 14 | MainFrm.cpp 15 | ItkMFCView.cpp 16 | ItkPipeline.cxx 17 | ) 18 | 19 | IF(WIN32) 20 | LINK_LIBRARIES( 21 | wsock32 22 | ) 23 | ENDIF(WIN32) 24 | 25 | 26 | FIND_PACKAGE(ITK) 27 | IF(ITK_FOUND) 28 | INCLUDE(${ITK_USE_FILE}) 29 | ELSE(ITK_FOUND) 30 | MESSAGE(FATAL_ERROR 31 | "Cannot build without ITK. Please set ITK_DIR.") 32 | ENDIF(ITK_FOUND) 33 | 34 | 35 | ADD_EXECUTABLE(ItkMFC WIN32 ${ItkMFC_SRCS}) 36 | INSTALL_TARGETS(/bin ItkMFC) 37 | TARGET_LINK_LIBRARIES(ItkMFC ${ITK_LIBRARIES} ) 38 | 39 | 40 | -------------------------------------------------------------------------------- /ItkMFC/ItkPipeline.cxx: -------------------------------------------------------------------------------- 1 | #include "ItkPipeline.h" 2 | 3 | 4 | ItkPipeline 5 | ::ItkPipeline() 6 | { 7 | m_ImageReader = ReaderType::New(); 8 | m_ImageWriter = WriterType::New(); 9 | } 10 | 11 | 12 | 13 | ItkPipeline 14 | ::~ItkPipeline() 15 | { 16 | 17 | } 18 | 19 | 20 | void 21 | ItkPipeline 22 | ::SetInputFileName( const char * filename ) 23 | { 24 | m_ImageReader->SetFileName( filename ); 25 | } 26 | 27 | 28 | 29 | void 30 | ItkPipeline 31 | ::SetOutputFileName( const char * filename ) 32 | { 33 | m_ImageWriter->SetFileName( filename ); 34 | } 35 | 36 | 37 | void 38 | ItkPipeline 39 | ::LoadInputFile() 40 | { 41 | m_ImageReader->Update(); 42 | } 43 | 44 | 45 | 46 | void 47 | ItkPipeline 48 | ::SaveOutputFile() 49 | { 50 | m_ImageWriter->Update(); 51 | } 52 | 53 | -------------------------------------------------------------------------------- /ItkMFC/ItkPipeline.h: -------------------------------------------------------------------------------- 1 | #ifndef _ITK_PIPELINE_h 2 | #define _ITK_PIPELINE_h 3 | 4 | #include "itkImage.h" 5 | #include "itkImageFileReader.h" 6 | #include "itkImageFileWriter.h" 7 | 8 | 9 | class ItkPipeline 10 | { 11 | 12 | public: 13 | 14 | typedef unsigned char PixelType; 15 | typedef itk::Image< PixelType, 2 > ImageType; 16 | typedef itk::ImageFileReader< ImageType > ReaderType; 17 | typedef itk::ImageFileWriter< ImageType > WriterType; 18 | 19 | public: 20 | 21 | ItkPipeline(); 22 | ~ItkPipeline(); 23 | 24 | void SetInputFileName( const char * filename ); 25 | void SetOutputFileName( const char * filename ); 26 | void LoadInputFile(); 27 | void SaveOutputFile(); 28 | 29 | private: 30 | 31 | ReaderType::Pointer m_ImageReader; 32 | WriterType::Pointer m_ImageWriter; 33 | 34 | }; 35 | 36 | 37 | #endif 38 | 39 | 40 | -------------------------------------------------------------------------------- /ItkMFC/Resource.h: -------------------------------------------------------------------------------- 1 | //{{NO_DEPENDENCIES}} 2 | // Microsoft Visual C++ generated include file. 3 | // Used by ITKMFC.RC 4 | // 5 | #define IDD_ABOUTBOX 100 6 | #define IDP_SOCKETS_INIT_FAILED 104 7 | #define IDR_MAINFRAME 128 8 | #define IDR_ITKMFCTYPE 129 9 | 10 | // Next default values for new objects 11 | // 12 | #ifdef APSTUDIO_INVOKED 13 | #ifndef APSTUDIO_READONLY_SYMBOLS 14 | #define _APS_3D_CONTROLS 1 15 | #define _APS_NEXT_RESOURCE_VALUE 130 16 | #define _APS_NEXT_CONTROL_VALUE 1000 17 | #define _APS_NEXT_SYMED_VALUE 101 18 | #define _APS_NEXT_COMMAND_VALUE 32771 19 | #endif 20 | #endif 21 | -------------------------------------------------------------------------------- /ItkMFC/StdAfx.cpp: -------------------------------------------------------------------------------- 1 | // stdafx.cpp : source file that includes just the standard includes 2 | // ItkMFC.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 | -------------------------------------------------------------------------------- /ItkMFC/StdAfx.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__3CD712F6_052C_459A_B7A5_84019C6372AE__INCLUDED_) 7 | #define AFX_STDAFX_H__3CD712F6_052C_459A_B7A5_84019C6372AE__INCLUDED_ 8 | 9 | #if _MSC_VER > 1000 10 | #pragma once 11 | #endif // _MSC_VER > 1000 12 | 13 | #define VC_EXTRALEAN // Exclude rarely-used stuff from Windows headers 14 | 15 | #include // MFC core and standard components 16 | #include // MFC extensions 17 | #include // MFC Automation classes 18 | #include // MFC support for Internet Explorer 4 Common Controls 19 | #ifndef _AFX_NO_AFXCMN_SUPPORT 20 | #include // MFC support for Windows Common Controls 21 | #endif // _AFX_NO_AFXCMN_SUPPORT 22 | 23 | #include // MFC socket extensions 24 | 25 | //{{AFX_INSERT_LOCATION}} 26 | // Microsoft Visual C++ will insert additional declarations immediately before the previous line. 27 | 28 | #endif // !defined(AFX_STDAFX_H__3CD712F6_052C_459A_B7A5_84019C6372AE__INCLUDED_) 29 | -------------------------------------------------------------------------------- /ItkMFC/res/ItkMFC.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ItkMFC/res/ItkMFC.ico -------------------------------------------------------------------------------- /ItkMFC/res/ItkMFC.rc2: -------------------------------------------------------------------------------- 1 | // 2 | // ITKMFC.RC2 - resources Microsoft Visual C++ does not edit directly 3 | // 4 | 5 | #ifdef APSTUDIO_INVOKED 6 | #error this file is not editable by Microsoft Visual C++ 7 | #endif //APSTUDIO_INVOKED 8 | 9 | 10 | ///////////////////////////////////////////////////////////////////////////// 11 | // Add manually edited resources here... 12 | 13 | ///////////////////////////////////////////////////////////////////////////// 14 | -------------------------------------------------------------------------------- /ItkMFC/res/ItkMFCDoc.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ItkMFC/res/ItkMFCDoc.ico -------------------------------------------------------------------------------- /ItkMFC/res/Toolbar.bmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/ItkMFC/res/Toolbar.bmp -------------------------------------------------------------------------------- /LevelSetSegmentation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(LevelSetSegmentation) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | ADD_EXECUTABLE(itk2DThresholdSegmentationLevelSetImageFilter itk2DThresholdSegmentationLevelSetImageFilter.cxx) 18 | INSTALL_TARGETS(/bin itk2DThresholdSegmentationLevelSetImageFilter) 19 | TARGET_LINK_LIBRARIES (itk2DThresholdSegmentationLevelSetImageFilter 20 | ${ITK_LIBRARIES}) 21 | 22 | 23 | ADD_EXECUTABLE(itk2DCannySegmentationLevelSetImageFilter itk2DCannySegmentationLevelSetImageFilter.cxx) 24 | INSTALL_TARGETS(/bin itk2DCannySegmentationLevelSetImageFilter) 25 | TARGET_LINK_LIBRARIES (itk2DCannySegmentationLevelSetImageFilter 26 | ${ITK_LIBRARIES} 27 | ) 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /LevelSetSurfaceProcessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(LevelSetSurfaceProcessing) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | 18 | ADD_EXECUTABLE(itk3DIsotropicFourthOrderLevelSetImageFilter itk3DIsotropicFourthOrderLevelSetImageFilter.cxx) 19 | INSTALL_TARGETS(/bin itk3DIsotropicFourthOrderLevelSetImageFilter) 20 | ADD_EXECUTABLE(itk3DAnisotropicFourthOrderLevelSetImageFilter itk3DAnisotropicFourthOrderLevelSetImageFilter.cxx) 21 | INSTALL_TARGETS(/bin itk3DAnisotropicFourthOrderLevelSetImageFilter) 22 | ADD_EXECUTABLE(itk3DUnsharpMaskLevelSetImageFilter itk3DUnsharpMaskLevelSetImageFilter.cxx) 23 | INSTALL_TARGETS(/bin itk3DUnsharpMaskLevelSetImageFilter) 24 | 25 | TARGET_LINK_LIBRARIES (itk3DIsotropicFourthOrderLevelSetImageFilter ${ITK_LIBRARIES}) 26 | TARGET_LINK_LIBRARIES (itk3DAnisotropicFourthOrderLevelSetImageFilter ${ITK_LIBRARIES}) 27 | TARGET_LINK_LIBRARIES (itk3DUnsharpMaskLevelSetImageFilter ${ITK_LIBRARIES}) 28 | -------------------------------------------------------------------------------- /LiverTumorSegmentation/ClickedPointEvent.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ClickedPointEvent.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #ifndef __ISIS_itkClickedPointEvent_h__ 19 | #define __ISIS_itkClickedPointEvent_h__ 20 | 21 | #include "itkEventObject.h" 22 | 23 | /** 24 | \class ClickedPointEvent 25 | \brief Class for defining ClickedPointEvent 26 | 27 | This defines a ClickedEventEvent class which is derived from the 28 | itk::AnyEvent class. 29 | 30 | */ 31 | namespace ISIS 32 | { 33 | 34 | itkEventMacro( ClickedPointEvent, itk::AnyEvent ); 35 | 36 | } // end namespace ISIS 37 | 38 | #endif 39 | 40 | -------------------------------------------------------------------------------- /LiverTumorSegmentation/DicomImageReaderBase.cxx: -------------------------------------------------------------------------------- 1 | 2 | #include "DicomImageReaderBase.h" 3 | 4 | #include 5 | 6 | 7 | namespace ISIS 8 | { 9 | 10 | 11 | DicomImageReaderBase 12 | ::DicomImageReaderBase() 13 | { 14 | m_FilenamesGenerator = SeriesFileNamesType::New(); 15 | } 16 | 17 | 18 | 19 | DicomImageReaderBase 20 | ::~DicomImageReaderBase() 21 | { 22 | } 23 | 24 | 25 | void 26 | DicomImageReaderBase 27 | ::SetDirectory( const char * directory ) 28 | { 29 | std::string directoryName = directory; 30 | m_FilenamesGenerator->SetDirectory( directoryName ); 31 | } 32 | 33 | const std::vector & DicomImageReaderBase::GetSeriesUIDs(){ 34 | return m_FilenamesGenerator->GetSeriesUIDs(); 35 | 36 | } 37 | 38 | } // end namespace ISIS 39 | 40 | 41 | -------------------------------------------------------------------------------- /LiverTumorSegmentation/InteractorObserver.cxx: -------------------------------------------------------------------------------- 1 | #include "InteractorObserver.h" 2 | 3 | #include 4 | 5 | namespace ISIS 6 | { 7 | 8 | 9 | InteractorObserver 10 | ::InteractorObserver() 11 | { 12 | m_SliceViewer = NULL; 13 | m_Motion = false; 14 | } 15 | 16 | 17 | 18 | 19 | InteractorObserver 20 | ::~InteractorObserver() 21 | { 22 | m_SliceViewer = NULL; 23 | } 24 | 25 | 26 | 27 | void 28 | InteractorObserver 29 | ::SetImageSliceViewer( ImageSliceViewer * viewer ) 30 | { 31 | m_SliceViewer = viewer; 32 | } 33 | 34 | 35 | 36 | void 37 | InteractorObserver 38 | ::Execute(vtkObject * , unsigned long eventId, void *) 39 | { 40 | if ( eventId == ::vtkCommand::LeftButtonPressEvent ) 41 | { 42 | m_Motion = true; 43 | } 44 | if ( eventId == ::vtkCommand::LeftButtonReleaseEvent ) 45 | { 46 | m_Motion = false; 47 | } 48 | if( m_SliceViewer && m_Motion ) 49 | { 50 | const int x = Fl::event_x(); 51 | const int y = Fl::event_y(); 52 | m_SliceViewer->SelectPoint( x, y ); 53 | } 54 | } 55 | 56 | 57 | 58 | } 59 | 60 | 61 | 62 | -------------------------------------------------------------------------------- /LiverTumorSegmentation/InteractorObserver.h: -------------------------------------------------------------------------------- 1 | #include "vtkCommand.h" 2 | #include "ImageSliceViewer.h" 3 | 4 | /** 5 | \class InteractorObserver 6 | \brief This class defines observer command for user event 7 | (Keyboard/Mouse)in a ImageSliceViewer window. 8 | */ 9 | 10 | namespace ISIS 11 | { 12 | 13 | class InteractorObserver : public vtkCommand 14 | { 15 | public: 16 | 17 | static InteractorObserver *New() 18 | {return new InteractorObserver;}; 19 | 20 | /** The SetImageSliceViewer method inputs pointer of the ImageSliceViewer 21 | serviced. 22 | */ 23 | void SetImageSliceViewer( ImageSliceViewer * viewer ); 24 | 25 | /** The Execute method defines the code to be run when the 26 | command is invoked. 27 | */ 28 | void Execute(vtkObject * caller, unsigned long eventId, void *callData); 29 | 30 | protected: 31 | 32 | InteractorObserver(); 33 | virtual ~InteractorObserver(); 34 | 35 | private: 36 | 37 | ImageSliceViewer * m_SliceViewer; 38 | bool m_Motion; 39 | 40 | }; 41 | 42 | 43 | 44 | 45 | 46 | 47 | } 48 | 49 | 50 | 51 | -------------------------------------------------------------------------------- /LiverTumorSegmentation/how_to_use.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/LiverTumorSegmentation/how_to_use.html -------------------------------------------------------------------------------- /LiverTumorSegmentation/main.cxx: -------------------------------------------------------------------------------- 1 | 2 | 3 | #include "LiverTumorSegmentation.h" 4 | 5 | 6 | int main( int , char * [] ) 7 | { 8 | 9 | LiverTumorSegmentation app; 10 | 11 | try 12 | { 13 | app.Show(); 14 | Fl::run(); 15 | } 16 | catch( std::exception & ex ) 17 | { 18 | std::cerr << ex.what() << std::endl; 19 | } 20 | 21 | return 0; 22 | } 23 | 24 | 25 | -------------------------------------------------------------------------------- /MATITK/Credits.txt: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: Credits.txt 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | This application was developed by 17 | 18 | Vincent Chu and Dr. Ghassan Hamarneh, 19 | Medical Image Analysis Lab, 20 | Simon Fraser University, Canada. 21 | 22 | http://mial.fas.sfu.ca/researchProject.php?s=308 23 | 24 | -------------------------------------------------------------------------------- /MATITK/Documentation/MATITK.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MATITK/Documentation/MATITK.pdf -------------------------------------------------------------------------------- /MATITK/PrecompiledBinaries/matitk.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MATITK/PrecompiledBinaries/matitk.dll -------------------------------------------------------------------------------- /MATITK/PrecompiledBinaries/msvcp71.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MATITK/PrecompiledBinaries/msvcp71.dll -------------------------------------------------------------------------------- /MATITK/PrecompiledBinaries/msvcr71.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MATITK/PrecompiledBinaries/msvcr71.dll -------------------------------------------------------------------------------- /MATITK/src/MATITKTemplatedVariables.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: MATITKTemplatedVariables.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | #ifndef MATITKTEMPLATEDVARIABLES_H 16 | #define MATITKTEMPLATEDVARIABLES_H 17 | #include "seedcontainer.h" 18 | template 19 | class MATITKTemplatedVariables{ 20 | #include "typedefs.inl" 21 | public: 22 | std::vector< ITKPIXELTYPEArray > pixelContainers; 23 | typename ImageType::PixelContainerPointer pixelContainer; 24 | MATPARAMTYPE* pParameters; 25 | typename ImportFilterType::Pointer importFilter[2]; 26 | SeedContainer seedsIndex; 27 | }; 28 | #endif 29 | -------------------------------------------------------------------------------- /MATITK/src/ParameterContainer.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: ParameterContainer.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | #ifndef PARAMETERCONTAINER_H 17 | #define PARAMETERCONTAINER_H 18 | #include "mex.h" 19 | #include "string.h" 20 | 21 | 22 | 23 | 24 | #include "ParameterContainer.inl" 25 | 26 | #endif 27 | -------------------------------------------------------------------------------- /MATITK/src/itkcore.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: itkcore.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | #ifndef ITKCORE_H 17 | #define ITKCORE_H 18 | #include "matitk.h" 19 | #include "ParameterContainer.h" 20 | #include "seedcontainer.h" 21 | #define CONTACT "Vincent Chu , Ghassan Hamarneh " 22 | #define OPCOMMAND "matitk(operationName,[parameters],[inputArray1],[inputArray2],[seed(s)Array],[Image(s)Spacing])\n" 23 | //#define CONTACT "HIDDEN TO PRESERVE ANONYMITY" 24 | 25 | #include "itkcore.inl" 26 | #endif 27 | -------------------------------------------------------------------------------- /MATITK/src/itkfiltercore.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: itkfiltercore.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | #ifndef ITKFILTERCORE_H 17 | #define ITKFILTERCORE_H 18 | #include "matitk.h" 19 | #include "ParameterContainer.h" 20 | #include "MATITKTemplatedVariables.h" 21 | #include "itkfiltercore.inl" 22 | #endif 23 | -------------------------------------------------------------------------------- /MATITK/src/itkregistrationcore.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: itkregistrationcore.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | #ifndef ITKREGISTRATIONCORE_H 17 | #define ITKREGISTRATIONCORE_H 18 | #include "matitk.h" 19 | #include "itkcore.h" 20 | #include "seedcontainer.h" 21 | #include "ParameterContainer.h" 22 | #include "MATITKTemplatedVariables.h" 23 | #include "itkregistrationcore.inl" 24 | #endif 25 | -------------------------------------------------------------------------------- /MATITK/src/itksegmentationcore.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: itksegmentationcore.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | #ifndef ITKSEGMENTATIONCORE_H 16 | #define ITKSEGMENTATIONCORE_H 17 | #include "matitk.h" 18 | #include "seedcontainer.h" 19 | #include "ParameterContainer.h" 20 | #include "MATITKTemplatedVariables.h" 21 | 22 | #include "itksegmentationcore.inl" 23 | #endif 24 | -------------------------------------------------------------------------------- /MATITK/src/seedcontainer.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: seedcontainer.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | #ifndef SEEDCONTAINER_H 17 | #define SEEDCONTAINER_H 18 | #include "matitk.h" 19 | 20 | #include "seedcontainer.inl" 21 | #endif 22 | -------------------------------------------------------------------------------- /MATITK/src/typedefs.inl: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: typedefs.inl 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | Copyright (c) 2003 Insight Consortium. All rights reserved. 9 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 10 | 11 | This software is distributed WITHOUT ANY WARRANTY; without even 12 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 13 | PURPOSE. See the above copyright notices for more information. 14 | =========================================================================*/ 15 | 16 | typedef itk::Image< ITKPIXELTYPE, DIMENSION > ImageType; 17 | typedef ImageType InternalImageType; 18 | //the following two lines are here out of laziness - save time during conversion since example code often use In/OutputImageType 19 | typedef ImageType InputImageType; 20 | typedef ImageType OutputImageType; 21 | typedef itk::ImportImageFilter< ITKPIXELTYPE, DIMENSION > ImportFilterType; 22 | typedef void (*pt2Function)(); 23 | -------------------------------------------------------------------------------- /MIValidation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( MIValidation ) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | INCLUDE_REGULAR_EXPRESSION(".*") 16 | 17 | INCLUDE_DIRECTORIES( 18 | ${MIValidation_SOURCE_DIR}/../MultiResMIRegistration/Common 19 | ${MIValidation_SOURCE_DIR}/../IBSRValidation/Common 20 | ) 21 | 22 | SET( MIValidation_SRCS 23 | Code/MIValidationApp.cxx 24 | Code/VanderbiltModality.cxx ) 25 | 26 | ADD_EXECUTABLE(MIValidationApp ${MIValidation_SRCS} ) 27 | INSTALL_TARGETS(/bin MIValidationApp) 28 | TARGET_LINK_LIBRARIES(MIValidationApp ${ITK_LIBRARIES}) 29 | 30 | -------------------------------------------------------------------------------- /MIValidation/Inputs/param_1.txt: -------------------------------------------------------------------------------- 1 | 4 2 | 2500 2500 2500 2500 3 | 5e-4 1e-4 5e-5 1e-5 4 | -------------------------------------------------------------------------------- /MIValidation/Inputs/param_2.txt: -------------------------------------------------------------------------------- 1 | 3 2 | 3500 3500 3500 3 | 5e-5 1e-5 1e-6 4 | -------------------------------------------------------------------------------- /MRIBiasCorrection/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(MRIBiasCorrection) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | INCLUDE_DIRECTORIES(MRIBiasCorrection_SOURCE_DIR) 18 | 19 | FOREACH(exe BiasFieldEstimator BiasImageGenerator IntensityHistogram3D 20 | InterSliceIntensityCorrector SlabIdentifier EnergyTablePlotter 21 | ImageCorrector BiasCorrector) 22 | ADD_EXECUTABLE(${exe} ${exe}.cxx OptionList.cxx) 23 | INSTALL_TARGETS(/bin ${exe}) 24 | INSTALL_TARGETS(/bin ${exe}) 25 | TARGET_LINK_LIBRARIES(${exe} ${ITK_LIBRARIES}) 26 | ENDFOREACH(exe) 27 | -------------------------------------------------------------------------------- /MRIBiasCorrection/myutils.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: myutils.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | #ifndef __MYUTILS_H 18 | #define __MYUTILS_H 19 | 20 | #include 21 | #include 22 | 23 | void print_line(std::string msg) 24 | { 25 | std::cout << msg << std::endl ; 26 | } 27 | 28 | void dump(vnl_vector vect) 29 | { 30 | std::cout << "vector dump" << std::endl ; 31 | for (unsigned int i = 0 ; i < vect.size() ; i++) 32 | { 33 | std::cout << i << ": " << vect[i] << std::endl ; 34 | } 35 | } 36 | #endif 37 | -------------------------------------------------------------------------------- /MRIRegistration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(MIRegistration) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | FIND_PACKAGE(VTK) 14 | IF (VTK_FOUND) 15 | INCLUDE (${VTK_USE_FILE}) 16 | ENDIF (VTK_FOUND) 17 | 18 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 19 | 20 | 21 | SET(MIRegistration_SRCS 22 | OptionList 23 | MIRegistration 24 | ) 25 | 26 | ADD_EXECUTABLE(MIRegistration ${MIRegistration_SRCS}) 27 | INSTALL_TARGETS(/bin MIRegistration) 28 | 29 | TARGET_LINK_LIBRARIES(MIRegistration 30 | vtkRendering 31 | vtkGraphics 32 | vtkImaging 33 | vtkIO 34 | vtkFiltering 35 | vtkCommon 36 | ${ITK_LIBRARIES}) 37 | 38 | -------------------------------------------------------------------------------- /MatroxInput/MatroxViewer.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef ISISMatroxViewer_h 3 | #define ISISMatroxViewer_h 4 | 5 | 6 | 7 | #include "MatroxViewerGUI.h" 8 | 9 | // VTK Includes 10 | #include "vtkActor.h" 11 | #include "vtkCamera.h" 12 | #include "vtkProperty.h" 13 | #include "vtkRenderer.h" 14 | #include "vtkRenderWindow.h" 15 | #include "vtkImageActor.h" 16 | #include "vtkVideoSource.h" 17 | #include "vtkImageMapper.h" 18 | 19 | 20 | 21 | namespace ISIS 22 | { 23 | 24 | class MatroxViewer : public MatroxViewerGUI 25 | { 26 | 27 | public: 28 | MatroxViewer(); 29 | ~MatroxViewer(); 30 | void Show(); 31 | void Hide(); 32 | void Grab(); 33 | void Stop(); 34 | void Quit(); 35 | void LoadImageFromFile(); 36 | 37 | 38 | private: 39 | 40 | vtkRenderWindow * m_RenderWindow; 41 | vtkRenderer * m_Renderer; 42 | vtkVideoSource * m_VideoSource; 43 | vtkImageMapper * m_ImageMapper; 44 | vtkImageActor * m_ImageActor; 45 | 46 | }; 47 | 48 | 49 | 50 | } 51 | 52 | 53 | 54 | #endif 55 | -------------------------------------------------------------------------------- /MatroxInput/MatroxViewerBase.cxx: -------------------------------------------------------------------------------- 1 | 2 | #include "MatroxViewerBase.h" 3 | 4 | 5 | 6 | namespace ISIS 7 | { 8 | 9 | MatroxViewerBase 10 | ::MatroxViewerBase() 11 | { 12 | m_Reader = vtkPNGReader::New(); 13 | m_ImageCast = vtkImageCast::New(); 14 | m_ImageCast->SetInput( m_Reader->GetOutput() ); 15 | m_ImageCast->SetOutputScalarTypeToUnsignedChar(); 16 | m_ImageIsLoaded = false; 17 | } 18 | 19 | 20 | 21 | MatroxViewerBase 22 | ::~MatroxViewerBase() 23 | { 24 | m_ImageCast->Delete(); 25 | m_Reader->Delete(); 26 | } 27 | 28 | 29 | 30 | void 31 | MatroxViewerBase 32 | ::Show() 33 | { 34 | } 35 | 36 | 37 | void 38 | MatroxViewerBase 39 | ::Hide() 40 | { 41 | 42 | } 43 | 44 | 45 | void 46 | MatroxViewerBase 47 | ::Grab() 48 | { 49 | 50 | } 51 | 52 | 53 | void 54 | MatroxViewerBase 55 | ::Stop() 56 | { 57 | } 58 | 59 | 60 | void 61 | MatroxViewerBase 62 | ::Quit() 63 | { 64 | } 65 | 66 | 67 | 68 | void 69 | MatroxViewerBase 70 | ::LoadImageFromFile() 71 | { 72 | } 73 | 74 | 75 | 76 | void 77 | MatroxViewerBase 78 | ::LoadImageFromFile(const char * filename) 79 | { 80 | m_Reader->SetFileName( filename ); 81 | m_Reader->Update(); 82 | m_ImageIsLoaded = true; 83 | } 84 | 85 | 86 | 87 | } 88 | 89 | -------------------------------------------------------------------------------- /MatroxInput/MatroxViewerBase.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef ISISMatroxViewerBase_h 3 | #define ISISMatroxViewerBase_h 4 | 5 | #include "vtkPNGReader.h" 6 | #include "vtkImageCast.h" 7 | 8 | namespace ISIS 9 | { 10 | 11 | class MatroxViewerBase 12 | { 13 | 14 | public: 15 | MatroxViewerBase(); 16 | virtual ~MatroxViewerBase(); 17 | 18 | /** Display the FLTK GUI interface */ 19 | virtual void Show(); 20 | 21 | /** Hide the FLTK GUI interface */ 22 | virtual void Hide(); 23 | 24 | /** Acquire images from the video grabber */ 25 | virtual void Grab(); 26 | 27 | /** Stop image acquisition from the grabber */ 28 | virtual void Stop(); 29 | 30 | /** Quit the application */ 31 | virtual void Quit(); 32 | 33 | /** Load image from a file */ 34 | virtual void LoadImageFromFile(); 35 | virtual void LoadImageFromFile(const char *); 36 | 37 | protected: 38 | 39 | vtkPNGReader * m_Reader; 40 | vtkImageCast * m_ImageCast; 41 | bool m_ImageIsLoaded; 42 | }; 43 | 44 | 45 | 46 | } 47 | 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /MatroxInput/main.cxx: -------------------------------------------------------------------------------- 1 | #include "MatroxViewer.h" 2 | #include "itkExceptionObject.h" 3 | 4 | 5 | int main() 6 | { 7 | ISIS::MatroxViewer application; 8 | 9 | application.Show(); 10 | 11 | try 12 | { 13 | Fl::run(); 14 | } 15 | catch( itk::ExceptionObject & exp ) 16 | { 17 | std::cerr << "ITK Exception thrown !" << std::endl; 18 | std::cerr << exp << std::endl; 19 | } 20 | catch( std::exception & exp ) 21 | { 22 | std::cerr << "STL Exception thrown !" << std::endl; 23 | std::cerr << exp.what() << std::endl; 24 | } 25 | catch( ... ) 26 | { 27 | std::cerr << "Unknown Exception thrown !" << std::endl; 28 | } 29 | 30 | return 0; 31 | } 32 | 33 | 34 | -------------------------------------------------------------------------------- /MetaImageImporter/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(MetaImageImporter) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | ADD_EXECUTABLE(MetaImageImporter MetaImageImporter.cxx ) 17 | INSTALL_TARGETS(/bin MetaImageImporter) 18 | -------------------------------------------------------------------------------- /MetaImageReadWrite/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(MetaImageReadWrite) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | ADD_EXECUTABLE(MetaImageReadWrite MetaImageReadWrite.cxx ) 18 | INSTALL_TARGETS(/bin MetaImageReadWrite) 19 | TARGET_LINK_LIBRARIES (MetaImageReadWrite ${ITK_LIBRARIES}) 20 | -------------------------------------------------------------------------------- /Morphogenesis/CellularAggregate.dat: -------------------------------------------------------------------------------- 1 | 10 10 0 2 | -------------------------------------------------------------------------------- /Morphogenesis/CommandEvents.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: CommandEvents.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | #ifndef bio_Command_Events_h 18 | #define bio_Command_Events_h 19 | 20 | #include "itkCommand.h" 21 | #include "itkEventObject.h" 22 | 23 | namespace bio { 24 | 25 | /** List of the events expected in this domain. */ 26 | itkEventMacro( TimeStepEvent, itk::UserEvent ); 27 | 28 | } // end namespace bio 29 | 30 | 31 | #endif 32 | -------------------------------------------------------------------------------- /Morphogenesis/GradientEatingBacteria.dat: -------------------------------------------------------------------------------- 1 | 1.00 2 | 0.01 3 | 2.00 4 | 200 5 | 210 6 | -------------------------------------------------------------------------------- /Morphogenesis/README.txt: -------------------------------------------------------------------------------- 1 | 2 | This is an example of Morphogenesis simulation. 3 | 4 | Morphogenesis is the process responsible for generating shapes in living 5 | organisms. The understanding of Morphogenesis is important in medical image 6 | processing because it set up the basis for creating shape models of organs. 7 | 8 | Morphogenesis is acomplished by the most part during the first stages of 9 | formation of an embryo, and continues at a slower pace until the death of the 10 | organism. 11 | 12 | This program simulates some of the aspects involved in morphogenesis. For that 13 | itkMeshes are used to represent living cells interacting via adhesion and 14 | mechanical resistance, exchanging information via biochemical compounds, 15 | dividing by mitosis and eventually disapearing by programmed cell death. 16 | 17 | 18 | To build this program you will need the FLTK associated library, in the 19 | Auxiliary/FltkImageViewer directory. 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /MultiResMIRegistration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( MultiResMIRegistration ) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | FIND_PACKAGE(FLTK) 15 | IF(FLTK_FOUND) 16 | INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR}) 17 | ENDIF(FLTK_FOUND) 18 | 19 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 20 | 21 | 22 | 23 | INCLUDE_REGULAR_EXPRESSION(".*") 24 | 25 | INCLUDE_DIRECTORIES( 26 | ${MultiResMIRegistration_SOURCE_DIR}/Common 27 | ${MultiResMIRegistration_SOURCE_DIR}/../IBSRValidation/Common 28 | ) 29 | 30 | ADD_GUI_EXECUTABLE(MultiResMIRegistration Common/MultiResMIRegistration.cxx ) 31 | TARGET_LINK_LIBRARIES(MultiResMIRegistration ${ITK_LIBRARIES}) 32 | -------------------------------------------------------------------------------- /MultiResMIRegistration/ReadMe.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MultiResMIRegistration/ReadMe.doc -------------------------------------------------------------------------------- /MultiResMIRegistration/ReadMe.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MultiResMIRegistration/ReadMe.pdf -------------------------------------------------------------------------------- /MultiResMIRegistration/SampleInputs/BrainWebT1toT2a.txt: -------------------------------------------------------------------------------- 1 | brainweb165a10f17.mhd 2 | brainweb1e5a10f17.mhd 3 | 0 1 2 4 | 0 0 0 5 | 5 6 | 4 4 1 7 | 8 8 1 8 | 2500 2500 2500 2500 2500 9 | 1e-4 1e-5 5e-6 1e-6 5e-7 10 | 320 11 | t1tot2.mhd 12 | 13 | 14 | -------------------------------------------------------------------------------- /MultiResMIRegistration/SampleInputs/BrainWebT1toT2b.txt: -------------------------------------------------------------------------------- 1 | brainweb165a10f17.mhd 2 | brainweb1e5a10f17Rot10Tx15.mhd 3 | 0 1 2 4 | 0 0 0 5 | 5 6 | 4 4 1 7 | 8 8 1 8 | 2500 2500 2500 2500 2500 9 | 1e-4 1e-5 5e-6 1e-6 5e-7 10 | 320 11 | t1tot2.mhd 12 | 13 | 14 | -------------------------------------------------------------------------------- /MultiResMIRegistration/SampleInputs/PracCTtoT1.txt: -------------------------------------------------------------------------------- 1 | N:/Vanderbilt/registration/meta_headers/practice_mr_T1.mhd 2 | N:/Vanderbilt/registration/meta_headers/practice_ct.mhd 3 | 0 1 2 4 | 0 0 0 5 | 5 6 | 4 4 1 7 | 8 8 1 8 | 2500 2500 2500 2500 2500 9 | 1e-4 1e-5 5e-6 1e-6 5e-7 10 | 320 11 | cttot1.mhd 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /MultiResMIRegistration/SampleInputs/PracPETToPD.txt: -------------------------------------------------------------------------------- 1 | N:/Vanderbilt/registration/meta_headers/practice_mr_PD.mhd 2 | N:/Vanderbilt/registration/meta_headers/practice_pet.mhd 3 | 0 1 2 4 | 0 0 0 5 | 4 6 | 2 2 1 7 | 4 4 1 8 | 5000 2500 2500 2500 9 | 1e-4 1e-5 5e-6 1e-6 10 | 320 11 | pettopd.mhd 12 | 13 | 14 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/ReadMe.txt: -------------------------------------------------------------------------------- 1 | This file shows the systax followed in the parameter files. 2 | The parameter files are needed for the Gaussian Classifier based applications involving 2 channels and are generated 3 | apriori manually. 4 | 5 | #NumberOfClasses (number of tissue type + 1 for background) 6 | #0 #0 #1 #1 #2 #2 #3 #3 #4 #4 (each #corresponds to the mean of channel 1 & 2, for tissue type 1-4 & #0 for background) 7 | #0 #0 #0 #0 #1 #1 #1 #1 #2 #2 #2 #2 #3 #3 #3 #3 #4 #4 #4 #4 (each group of 4 numbers corresponds to the covariances in two channel data, tissue type 1-4 & #0 for background) 8 | 9 | #0 #1 #2 #3 #4 (each #corresponds to the number of samples of background, tissue type 1-4 in the model) 10 | 11 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/TestGaussianClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:/Insight-clean/WorkDirData/MultichannelTissueClassificationValidation 2 | _FLw.raw 3 | _T2w.raw 4 | E:/Insight-clean/Insight/Applications/MultichannelTissueClassificationValidation/Results/GaussianMSoutput.txt 5 | 2 6 | phantom 11 E:/Insight-clean/Insight/Applications/MultichannelTissueClassificationValidation/Inputs/paramphantom.txt 7 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/TestKmeansClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:/Insight-clean/WorkDirData/MultichannelTissueClassificationValidation 2 | _FLw.raw 3 | _T2w.raw 4 | E:/Insight-clean/Insight/Applications/MultichannelTissueClassificationValidation/Results/KmeansMSoutput.txt 5 | 2 6 | phantom 11 NoParamFile.txt 7 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/TestMRFGaussianClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:/Insight-clean/WorkDirData/MultichannelTissueClassificationValidation 2 | _FLw.raw 3 | _T2w.raw 4 | E:/Insight-clean/WorkDir/MultichannelTissueClassificationValidation/Results/MRFGaussianMSoutput.txt 5 | 2 6 | phantom 11 E:/Insight-clean/WorkDir/MultichannelTissueClassificationValidation/Inputs/paramphantom.txt -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/TestMRFKmeansClassifierInput.txt: -------------------------------------------------------------------------------- 1 | E:/Insight-clean/WorkDirData/MultichannelTissueClassificationValidation 2 | _FLw.raw 3 | _T2w.raw 4 | E:/Insight-clean/WorkDir/MultichannelTissueClassificationValidation/Results/MRFKmeansMSoutput.txt 5 | 2 6 | phantom 11 NoParamFile.txt -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Inputs/paramphantom.txt: -------------------------------------------------------------------------------- 1 | 5 2 | 0 0 24 23 667 767 361 1851 925 950 3 | 0 0 0 0 136 0 0 123 1218 1050 1050 1796 771 -339 -339 1473 1497 1102 1102 1544 4 | 0 1329 989 274 887 5 | 6 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Results/GaussianMSoutput.txt: -------------------------------------------------------------------------------- 1 | 2 | phantom 4 29.65 3 | phantom 4 29.65 4 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Results/KmeansMSoutput.txt: -------------------------------------------------------------------------------- 1 | 2 | phantom 4 34.67 3 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Results/MRFGaussianMSoutput.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /MultichannelTissueClassificationValidation/Results/MRFKmeansMSoutput.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/MultichannelTissueClassificationValidation/Results/MRFKmeansMSoutput.txt -------------------------------------------------------------------------------- /MutualInformationEuler2DRegistration/register.cxx: -------------------------------------------------------------------------------- 1 | #include "RegisterWindow.h" 2 | 3 | int main(int, char*[]) 4 | { 5 | 6 | try 7 | { 8 | RegisterWindow* win = new RegisterWindow(); 9 | win->Show(); 10 | Fl::run(); 11 | delete win ; 12 | } 13 | catch(...) 14 | { 15 | std::cerr << "Exception caught in main" << std::endl; 16 | } 17 | 18 | return 0 ; 19 | } 20 | 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /MutualInformationEuler2DRegistration/register.h: -------------------------------------------------------------------------------- 1 | #include "itkFixedArray.h" 2 | #include "itkArray.h" 3 | 4 | template< class TSource, class TTarget > 5 | void ConvertVectorToFixedArray(TSource &vec, TTarget& array) 6 | { 7 | typename TSource::iterator v_iter = vec.begin() ; 8 | typename TTarget::Iterator a_iter = array.Begin() ; 9 | while (v_iter != vec.end()) 10 | { 11 | *a_iter = (typename TTarget::ValueType) *v_iter ; 12 | std::cout << " " <<*a_iter << std::endl ; 13 | ++v_iter ; 14 | ++a_iter ; 15 | } 16 | } 17 | 18 | template< class TSource, class TTarget > 19 | void ConvertVectorToArray(TSource &vec, TTarget& array) 20 | { 21 | typename TSource::iterator v_iter = vec.begin() ; 22 | typename TTarget::iterator a_iter = array.begin() ; 23 | while (v_iter != vec.end()) 24 | { 25 | *a_iter = (typename TTarget::ValueType) *v_iter ; 26 | std::cout << " " <<*a_iter << std::endl ; 27 | ++v_iter ; 28 | ++a_iter ; 29 | } 30 | } 31 | -------------------------------------------------------------------------------- /QtITK/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | CMAKE_MINIMUM_REQUIRED(VERSION 2.4) 2 | IF(COMMAND CMAKE_POLICY) 3 | CMAKE_POLICY(SET CMP0003 NEW) 4 | ENDIF(COMMAND CMAKE_POLICY) 5 | 6 | PROJECT(QtITKExample) 7 | 8 | SET( BUILD_OUTSIDE_INSIGHT_APPLICATIONS TRUE ) 9 | 10 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 11 | 12 | FIND_PACKAGE(ITK) 13 | IF(ITK_FOUND) 14 | INCLUDE(${ITK_USE_FILE}) 15 | ELSE(ITK_FOUND) 16 | MESSAGE(FATAL_ERROR 17 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 18 | ENDIF(ITK_FOUND) 19 | 20 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 21 | 22 | # 23 | # Find QT 24 | # 25 | FIND_PACKAGE(Qt4 REQUIRED) 26 | INCLUDE( ${QT_USE_FILE} ) 27 | 28 | 29 | SET(QtITK_SRCS itkQtProgressBar.cxx qtITK.cxx ) 30 | 31 | QT4_WRAP_CPP(QT_MOC_SRCS itkQtAdaptor.h itkQtLightIndicator.h) 32 | 33 | ADD_EXECUTABLE(QtITK ${QtITK_SRCS} ${QT_MOC_SRCS}) 34 | TARGET_LINK_LIBRARIES(QtITK ${ITK_LIBRARIES} ${QT_LIBRARIES}) 35 | 36 | INSTALL_TARGETS(/bin QtITK) 37 | 38 | -------------------------------------------------------------------------------- /QtITK/itkQtLightIndicator.h: -------------------------------------------------------------------------------- 1 | 2 | #include 3 | #include "itkCommand.h" 4 | 5 | namespace itk { 6 | 7 | class QtLightIndicator : public QPushButton 8 | { 9 | 10 | Q_OBJECT 11 | 12 | public: 13 | 14 | /** Constructor */ 15 | QtLightIndicator( QWidget *parent ):QPushButton( parent ) {} 16 | 17 | public slots: 18 | 19 | void Start() 20 | { 21 | QColor yellow(255,255,0); 22 | QPalette pal = this->palette( ); 23 | pal.setColor(QPalette::Window, yellow); 24 | } 25 | 26 | void Modified() 27 | { 28 | QColor red(255,0,0); 29 | QPalette pal = this->palette( ); 30 | pal.setColor(QPalette::Window, red); 31 | } 32 | 33 | void End() 34 | { 35 | QColor green(0,255,0); 36 | QPalette pal = this->palette( ); 37 | pal.setColor(QPalette::Window, green); 38 | } 39 | 40 | }; 41 | 42 | 43 | } // end of namespace 44 | -------------------------------------------------------------------------------- /QtITK/itkQtProgressBar.h: -------------------------------------------------------------------------------- 1 | #include 2 | #include "itkCommand.h" 3 | 4 | namespace itk { 5 | 6 | 7 | class QtProgressBar : public ::QProgressBar 8 | { 9 | 10 | public: 11 | 12 | /** Command Class invoked for button redraw */ 13 | typedef itk::MemberCommand< QtProgressBar > RedrawCommandType; 14 | 15 | /** Constructor */ 16 | QtProgressBar( QWidget *parent ); 17 | 18 | /** Get Command */ 19 | RedrawCommandType * GetRedrawCommand( void ) const; 20 | 21 | 22 | /** Manage a Progress event */ 23 | void ProcessEvent(itk::Object * caller, const itk::EventObject & event ); 24 | void ConstProcessEvent(const itk::Object * caller, const itk::EventObject & event ); 25 | 26 | 27 | /** Manage a Progress event */ 28 | void Observe( itk::Object *caller ); 29 | 30 | private: 31 | 32 | RedrawCommandType::Pointer m_RedrawCommand; 33 | 34 | 35 | 36 | }; 37 | 38 | 39 | } // end of namespace 40 | -------------------------------------------------------------------------------- /RawImageReaderViewer/RawImageReaderViewer.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: RawImageReaderViewer.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include "itkRawImageReaderViewerGUI.h" 19 | 20 | int main() 21 | { 22 | 23 | 24 | RawImageReaderViewerGUI * console = new RawImageReaderViewerGUI; 25 | 26 | console->Show(); 27 | 28 | Fl::run(); 29 | 30 | delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /SCIRun/Doc/WrappingITKFiltersInSCIRun.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Doc/WrappingITKFiltersInSCIRun.pdf -------------------------------------------------------------------------------- /SCIRun/Examples/CodeGenerator/SCIRun/GenerateSCIRunCode.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Examples/CodeGenerator/SCIRun/GenerateSCIRunCode.class -------------------------------------------------------------------------------- /SCIRun/Examples/CodeGenerator/SCIRun/Generator.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Examples/CodeGenerator/SCIRun/Generator.class -------------------------------------------------------------------------------- /SCIRun/Examples/CodeGenerator/SCIRun/Parser.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Examples/CodeGenerator/SCIRun/Parser.class -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_DiscreteGuassianImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 10 26 | 27 | 28 | 29 | 30 | 31 | 0.001 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_GradientRecursiveGaussianImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 0 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_MeanImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 1 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_ReflectImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_WatershedRelabeler.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 0.25 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_WatershedSegmentTreeGenerator.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 0.25 26 | 27 | 28 | 29 | 30 | 0 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/gui_WatershedSegmenter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | 0.25 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_CurvatureAnisotropicDiffusionImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | Insight 25 | Filters 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_MeanImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | Insight 26 | Filters 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_ReflectImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | Insight 26 | Filters 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_UnaryFunctorImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | Insight 25 | Filters 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_VectorConfidenceConnectedImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | 25 | Insight 26 | 27 | Filters 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_VectorCurvatureAnisotropicDiffusionImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | Insight 25 | Filters 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_VectorGradientAnisotropicDiffusionImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | Insight 25 | Filters 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /SCIRun/Examples/XML/sci_VectorIndexSelectionCastImageFilter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 20 | 21 | 22 | 23 | 24 | Insight 25 | Filters 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /SCIRun/Thirdparty/xalan.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Thirdparty/xalan.jar -------------------------------------------------------------------------------- /SCIRun/Thirdparty/xercesImpl.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Thirdparty/xercesImpl.jar -------------------------------------------------------------------------------- /SCIRun/Thirdparty/xml-apis.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SCIRun/Thirdparty/xml-apis.jar -------------------------------------------------------------------------------- /SampleProject/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(SampleProject) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | # Add the executable with our source file. 16 | ADD_EXECUTABLE(itkSampleProject itkSampleProject.cxx) 17 | INSTALL_TARGETS(/bin itkSampleProject) 18 | 19 | # We only need ITK's Common components. Link to the common library. 20 | TARGET_LINK_LIBRARIES(itkSampleProject ITKCommon) 21 | -------------------------------------------------------------------------------- /SegmentationEditor/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( SegmentationEditor ) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | FIND_PACKAGE(VTK) 14 | IF (VTK_FOUND) 15 | INCLUDE (${VTK_USE_FILE}) 16 | ENDIF (VTK_FOUND) 17 | 18 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 19 | 20 | 21 | INCLUDE_REGULAR_EXPRESSION("^.*$") 22 | 23 | # Link in with ITK 24 | INCLUDE_DIRECTORIES ( ${SegmentationEditor_SOURCE_DIR}/../vtkITK/Common ) 25 | INCLUDE_DIRECTORIES ( ${SegmentationEditor_SOURCE_DIR}/Common ) 26 | INCLUDE_DIRECTORIES ( ${TCL_INCLUDE_PATH} ) 27 | 28 | LINK_DIRECTORIES ( ${SegmentationEditor_BINARY_DIR}/../vtkITK/Common ) 29 | LINK_DIRECTORIES ( ${SegmentationEditor_BINARY_DIR}/Common ) 30 | 31 | 32 | # Add the common directory 33 | SUBDIRS ( Common ) 34 | SUBDIRS ( Wrapping ) 35 | -------------------------------------------------------------------------------- /SegmentationEditor/Common/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | SET(WSTCommon_SRCS 2 | vtkBinaryVolume.cxx 3 | vtkBinaryVolumeLogic.cxx 4 | vtkWSBoundingBox.cxx 5 | vtkITKWatershedFilterAndWriter.h 6 | vtkLookupTableEquivalencyHash.cxx 7 | vtkWSBoundingBoxManager.cxx 8 | vtkWSLookupTableManager.cxx 9 | ) 10 | 11 | SET_SOURCE_FILES_PROPERTIES(vtkLookupTableEquivalencyHash.cxx vtkITKWatershedFilterAndWriter.h WRAP_EXCLUDE) 12 | 13 | ADD_LIBRARY(vtkWSTCommon ${WSTCommon_SRCS}) 14 | INSTALL_TARGETS(/lib vtkWSTCommon) 15 | TARGET_LINK_LIBRARIES(vtkWSTCommon vtkVTKITKCommon) 16 | 17 | # Configure Tcl wrappers. 18 | VTK_WRAP_TCL2(vtkWSTCommonTCL WSTCommonTCL_SRCS ${WSTCommon_SRCS}) 19 | ADD_LIBRARY(vtkWSTCommonTCL ${WSTCommonTCL_SRCS}) 20 | INSTALL_TARGETS(/lib vtkWSTCommonTCL) 21 | 22 | TARGET_LINK_LIBRARIES(vtkWSTCommonTCL vtkWSTCommon vtkFilteringTCL 23 | vtkCommonTCL) 24 | 25 | IF(BORLAND) 26 | SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w-8004") 27 | ENDIF(BORLAND) 28 | 29 | -------------------------------------------------------------------------------- /SegmentationEditor/Common/vtkWSBoundingBoxHash.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: vtkWSBoundingBoxHash.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #ifndef __vtkWSBoundingBoxHash_h_ 19 | #define __vtkWSBoundingBoxHash_h_ 20 | 21 | #include "itksys/hash_map.hxx" 22 | 23 | struct bounding_box_t 24 | { 25 | int x0; 26 | int x1; 27 | int y0; 28 | int y1; 29 | int z0; 30 | int z1; 31 | }; 32 | 33 | typedef itksys::hash_map > 34 | vtkWSBoundingBoxHash; 35 | 36 | 37 | #endif 38 | -------------------------------------------------------------------------------- /SegmentationEditor/Graphics/SCI_logo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Graphics/SCI_logo.gif -------------------------------------------------------------------------------- /SegmentationEditor/Graphics/geek_head.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Graphics/geek_head.gif -------------------------------------------------------------------------------- /SegmentationEditor/Graphics/instructions.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Graphics/instructions.gif -------------------------------------------------------------------------------- /SegmentationEditor/Graphics/itkLogoSmallTransparentBackground.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Graphics/itkLogoSmallTransparentBackground.gif -------------------------------------------------------------------------------- /SegmentationEditor/Graphics/uutah.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Graphics/uutah.gif -------------------------------------------------------------------------------- /SegmentationEditor/Scripts/Globals.tcl: -------------------------------------------------------------------------------- 1 | #/*========================================================================= 2 | # 3 | # Program: Insight Segmentation & Registration Toolkit 4 | # Module: Globals.tcl 5 | # Language: C++ 6 | # Date: $Date$ 7 | # Version: $Revision$ 8 | # 9 | # Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | # See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | # 12 | # This software is distributed WITHOUT ANY WARRANTY; without even 13 | # the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | # PURPOSE. See the above copyright notices for more information. 15 | # 16 | #=========================================================================*/ 17 | 18 | set Globals(default_window) "Help" 19 | set Globals(module_names) "Exit Data Preprocessor Segmenter Editor Postprocessor License Help" 20 | set Globals(functional_module_names) "Data Preprocessor Segmenter Editor Postprocessor" 21 | set Globals(options_module_names) "License Help Exit" 22 | -------------------------------------------------------------------------------- /SegmentationEditor/Scripts/Graphics.tcl: -------------------------------------------------------------------------------- 1 | # This file defines the graphics that will be used by 2 | # the various modules of the program. 3 | 4 | image create photo "WST_ItkLogo" -format "GIF" \ 5 | -file "../Graphics/itkLogoSmallTransparentBackground.gif" 6 | image create photo "WST_UtahLogo" -format "GIF" -file "../Graphics/uutah.gif" 7 | image create photo "WST_SCILogo" -format "GIF" -file "../Graphics/SCI_logo.gif" 8 | image create photo "WST_SomeGeek" -format "GIF" -file "../Graphics/geek_head.gif" 9 | image create photo "WST_EditorHelp" -format "GIF" -file "../Graphics/instructions.gif" 10 | -------------------------------------------------------------------------------- /SegmentationEditor/Scripts/segmenterinteraction/pkgIndex.tcl: -------------------------------------------------------------------------------- 1 | # Tcl package index file, version 1.1 2 | # This file is generated by the "pkg_mkIndex" command 3 | # and sourced either when an application starts up or 4 | # by a "package unknown" script. It invokes the 5 | # "package ifneeded" command to set up package-related 6 | # information so that packages will be loaded automatically 7 | # in response to "package require" commands. When this 8 | # script is sourced, the variable $dir must contain the 9 | # full path name of this file's directory. 10 | 11 | package ifneeded segmenterinteraction 4.0 [list source [file join $dir TkSegmentationWindowInteractor.tcl]] 12 | -------------------------------------------------------------------------------- /SegmentationEditor/Tutorial.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SegmentationEditor/Tutorial.pdf -------------------------------------------------------------------------------- /SegmentationEditor/WST.cmake: -------------------------------------------------------------------------------- 1 | Temporary empty file to let makefile dependencies update. 2 | -------------------------------------------------------------------------------- /SegmentationEditor/Wrapping/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | SUBDIRS ( Tcl ) 2 | -------------------------------------------------------------------------------- /SegmentationEditor/Wrapping/MakePackages.tcl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env tclsh 2 | 3 | # Packages 4 | 5 | pkg_mkIndex -direct -verbose vtkitk 6 | pkg_mkIndex -direct -verbose vtkitkbase 7 | 8 | # Add-ons (scripts) 9 | 10 | exit 11 | -------------------------------------------------------------------------------- /SegmentationEditor/Wrapping/Tcl/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # create the WSTITK executable 2 | ADD_EXECUTABLE(WSTITK tkAppInit.cxx) 3 | INSTALL_TARGETS(/bin WSTITK) 4 | 5 | TARGET_LINK_LIBRARIES (WSTITK 6 | vtkImagingTCL 7 | vtkGraphicsTCL 8 | vtkIOTCL 9 | vtkFilteringTCL 10 | vtkCommonTCL 11 | ${TCL_LIBRARY} ${TK_LIBRARY} 12 | ) 13 | 14 | IF (VTK_USE_RENDERING) 15 | TARGET_LINK_LIBRARIES(WSTITK vtkRenderingTCL) 16 | ENDIF (VTK_USE_RENDERING) 17 | 18 | IF (VTK_USE_PATENTED) 19 | TARGET_LINK_LIBRARIES(WSTITK vtkPatentedTCL) 20 | ENDIF (VTK_USE_PATENTED) 21 | 22 | IF (VTK_USE_HYBRID) 23 | TARGET_LINK_LIBRARIES(WSTITK vtkHybridTCL) 24 | ENDIF (VTK_USE_HYBRID) 25 | 26 | IF (VTK_USE_PARALLEL) 27 | TARGET_LINK_LIBRARIES(WSTITK vtkParallelTCL) 28 | ENDIF (VTK_USE_PARALLEL) 29 | 30 | TARGET_LINK_LIBRARIES(WSTITK vtkWSTCommonTCL vtkWSTCommon vtkVTKITKCommonTCL vtkVTKITKCommon ${ITK_LIBRARIES}) 31 | 32 | INSTALL_TARGETS(/bin WSTITK) 33 | -------------------------------------------------------------------------------- /SimpleFuzzyConnectedness/FuzzySegMain.cpp: -------------------------------------------------------------------------------- 1 | #include "FuzzySegGrayUI.h" 2 | 3 | int main(){ 4 | FuzzySegGrayUI * console=new FuzzySegGrayUI; 5 | console->Show(); 6 | 7 | Fl::run(); 8 | 9 | return 1; 10 | } 11 | -------------------------------------------------------------------------------- /SimpleLevelSetsExample/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(SimpleLevelSetsExample) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 15 | 16 | 17 | ADD_EXECUTABLE(itk2DSimpleLevelSetsExample itk2DSimpleLevelSetsExample.cxx) 18 | INSTALL_TARGETS(/bin itk2DSimpleLevelSetsExample) 19 | TARGET_LINK_LIBRARIES (itk2DSimpleLevelSetsExample ${ITK_LIBRARIES}) 20 | 21 | ADD_EXECUTABLE(itk3DSimpleLevelSetsExample itk3DSimpleLevelSetsExample.cxx) 22 | INSTALL_TARGETS(/bin itk3DSimpleLevelSetsExample) 23 | TARGET_LINK_LIBRARIES (itk3DSimpleLevelSetsExample ${ITK_LIBRARIES}) 24 | 25 | 26 | -------------------------------------------------------------------------------- /StreamedWatershedSegmentation/ParameterFileParser/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # Sources of non-templated classes. 2 | SET(param_SRCS 3 | lex.yy.cxx 4 | y.tab.cxx 5 | param.cxx 6 | ) 7 | 8 | 9 | ADD_LIBRARY(param ${param_SRCS}) 10 | INSTALL_TARGETS(/lib param) 11 | TARGET_LINK_LIBRARIES(param ${ITK_LIBRARIES}) 12 | -------------------------------------------------------------------------------- /StreamedWatershedSegmentation/ParameterFileParser/y.tab.h: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: y.tab.h 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | typedef union 18 | { 19 | long int integer; 20 | float decimal; 21 | std::string *string; 22 | Parameter* Parameter_ptr; 23 | File* File_ptr; 24 | GenericValue * GenericValue_ptr; 25 | std::vector * ValueArray_ptr; 26 | } YYSTYPE; 27 | 28 | #define NUM 257 29 | #define DEC_NUM 258 30 | #define IDENT 259 31 | #define STRING 260 32 | #define EQUALS 261 33 | #define LPAREN 262 34 | #define RPAREN 263 35 | #define NEWLINE 264 36 | 37 | extern YYSTYPE yylval; 38 | -------------------------------------------------------------------------------- /StreamedWatershedSegmentation/VolumeChunker/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # Sources of non-templated classes. 2 | SOURCE_FILES(chunk_SRCS 3 | chunks.cxx 4 | ) 5 | 6 | ADD_LIBRARY(chunks chunk_SRCS) 7 | INSTALL_TARGETS(/lib chunks) 8 | 9 | INCLUDE_DIRECTORIES( 10 | ${StreamedWatershedSegmentation_SOURCE_DIR}/ParameterFileParser 11 | ${StreamedWatershedSegmentation_SOURCE_DIR}/VolumeChunker 12 | ) 13 | 14 | LINK_DIRECTORIES( 15 | ${StreamedWatershedSegmentation_SOURCE_DIR}/ParameterFileParser 16 | ${StreamedWatershedSegmentation_SOURCE_DIR}/VolumeChunker 17 | ) 18 | 19 | LINK_LIBRARIES ( 20 | chunks 21 | param 22 | ) 23 | 24 | ADD_EXECUTABLE(catchunkfile catchunkfile) 25 | INSTALL_TARGETS(/bin catchunkfile) 26 | ADD_EXECUTABLE(chunker chunker) 27 | INSTALL_TARGETS(/bin chunker) 28 | ADD_EXECUTABLE(vhchunker vhchunker) 29 | INSTALL_TARGETS(/bin vhchunker) 30 | ADD_EXECUTABLE(vhunchunker vhunchunker) 31 | INSTALL_TARGETS(/bin vhunchunker) 32 | -------------------------------------------------------------------------------- /Superbuild/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | CMAKE_MINIMUM_REQUIRED(VERSION 2.8) 2 | IF(COMMAND CMAKE_POLICY) 3 | CMAKE_POLICY(SET CMP0003 NEW) 4 | ENDIF(COMMAND CMAKE_POLICY) 5 | 6 | PROJECT(ITKApps) 7 | include( ${CMAKE_SOURCE_DIR}/Superbuild.cmake ) 8 | -------------------------------------------------------------------------------- /Superbuild/External-ITK.cmake: -------------------------------------------------------------------------------- 1 | #--------------------------------------------------------------------------- 2 | # Get and build itk 3 | 4 | set (itk_depends) 5 | 6 | if (VTK_EXTERNAL_PROJECT) 7 | set( itk_depends VTK ) # because of ITKVtkGlue 8 | endif() 9 | 10 | set( ITK_TAG "v4.8.0" ) 11 | ExternalProject_Add( ITK 12 | GIT_REPOSITORY "${git_protocol}://itk.org/ITK.git" 13 | GIT_TAG "${ITK_TAG}" 14 | SOURCE_DIR ITK 15 | BINARY_DIR ITK-build 16 | CMAKE_GENERATOR ${gen} 17 | CMAKE_ARGS 18 | ${ep_common_args} 19 | -DBUILD_SHARED_LIBS:BOOL=ON 20 | -DBUILD_EXAMPLES:BOOL=OFF 21 | -DBUILD_TESTING:BOOL=OFF 22 | -DITK_BUILD_DEFAULT_MODULES:BOOL=ON 23 | -DITK_LEGACY_REMOVE:BOOL=OFF 24 | -DITKV3_COMPATIBILITY:BOOL=ON 25 | -DVTK_DIR:PATH=${VTK_DIR} 26 | -DModule_ITKVtkGlue:BOOL=ON 27 | INSTALL_COMMAND "" 28 | DEPENDS ${itk_depends} 29 | ) 30 | 31 | set(ITK_DIR ${CMAKE_BINARY_DIR}/ITK-build) 32 | set(ITK_EXTERNAL_PROJECT "TRUE") 33 | -------------------------------------------------------------------------------- /Superbuild/External-VTK.cmake: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------- 2 | # Get and build VTK 3 | # 4 | #----------------------------------------------------------------------------- 5 | 6 | set( VTK_TAG "v6.2.0" ) 7 | 8 | ExternalProject_Add(VTK 9 | GIT_REPOSITORY "${git_protocol}://vtk.org/VTK.git" 10 | GIT_TAG "${VTK_TAG}" 11 | SOURCE_DIR VTK 12 | BINARY_DIR VTK-build 13 | CMAKE_GENERATOR ${gen} 14 | CMAKE_ARGS 15 | ${ep_common_args} 16 | -DBUILD_SHARED_LIBS:BOOL=TRUE 17 | -DVTK_DEBUG_LEAKS:BOOL=TRUE 18 | -DVTK_WRAP_TCL:BOOL=${ENABLE_TCL_WRAPPED_APPS} 19 | -DBUILD_EXAMPLES:BOOL=OFF 20 | -DBUILD_TESTING:BOOL=OFF 21 | INSTALL_COMMAND "" 22 | ) 23 | 24 | set(VTK_DIR ${CMAKE_BINARY_DIR}/VTK-build) 25 | set(VTK_EXTERNAL_PROJECT "TRUE") 26 | -------------------------------------------------------------------------------- /Superbuild/patch-FLTK.sh.in: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | echo "Patching FLTK" 3 | cd @CMAKE_BINARY_DIR@/FLTK 4 | patch -p0 -i @CMAKE_SOURCE_DIR@/fltk.diff 5 | -------------------------------------------------------------------------------- /SymmetricEllipsoidInteriorExteriorSpatialFunction/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( SymmetricEllipsoidInteriorExteriorSpatialFunctionExample ) 2 | 3 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 4 | 5 | FIND_PACKAGE(ITK) 6 | IF(ITK_FOUND) 7 | INCLUDE(${ITK_USE_FILE}) 8 | ELSE(ITK_FOUND) 9 | MESSAGE(FATAL_ERROR 10 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 11 | ENDIF(ITK_FOUND) 12 | 13 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 14 | 15 | 16 | ADD_EXECUTABLE(SymmetricEllipsoidInteriorExteriorSpatialFunctionExample 17 | itkSymmetricEllipsoidInteriorExteriorSpatialFunctionExample.cxx) 18 | 19 | TARGET_LINK_LIBRARIES(SymmetricEllipsoidInteriorExteriorSpatialFunctionExample 20 | ${ITK_LIBRARIES}) 21 | 22 | INSTALL_TARGETS(/bin SymmetricEllipsoidInteriorExteriorSpatialFunctionExample) 23 | 24 | -------------------------------------------------------------------------------- /SymmetricEllipsoidInteriorExteriorSpatialFunction/README.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SymmetricEllipsoidInteriorExteriorSpatialFunction/README.doc -------------------------------------------------------------------------------- /SymmetricEllipsoidInteriorExteriorSpatialFunction/README.htm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SymmetricEllipsoidInteriorExteriorSpatialFunction/README.htm -------------------------------------------------------------------------------- /SymmetricEllipsoidInteriorExteriorSpatialFunction/README.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SymmetricEllipsoidInteriorExteriorSpatialFunction/README.pdf -------------------------------------------------------------------------------- /SymmetricEllipsoidInteriorExteriorSpatialFunction/symmetricEllipsoid.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/SymmetricEllipsoidInteriorExteriorSpatialFunction/symmetricEllipsoid.jpg -------------------------------------------------------------------------------- /ThinPlateSplines/main.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: main.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | 19 | /** 20 | 21 | This program illustrate how to make use of the ThinPlateSpline classes 22 | 23 | 24 | */ 25 | 26 | 27 | #include "ThinPlateSplinesApplication.h" 28 | 29 | 30 | 31 | int main(int, char**) 32 | { 33 | 34 | ThinPlateSplinesApplication application; 35 | 36 | application.Show(); 37 | 38 | Fl::run(); 39 | 40 | return 0; 41 | 42 | 43 | } 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /ThresholdSegmentationLevelSetFltkGui/README: -------------------------------------------------------------------------------- 1 | ThresholdSegmentationLevelSet 2 | 3 | This application used ITK and FLTK to 4 | do segmentation. 5 | -------------------------------------------------------------------------------- /ThresholdSegmentationLevelSetFltkGui/Segmenter.cxx: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: Segmenter.cxx 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include 19 | 20 | int main() 21 | { 22 | 23 | 24 | SegmenterConsole * console = new SegmenterConsole(); 25 | 26 | console->Show(); 27 | 28 | Fl::run(); 29 | 30 | delete console; 31 | 32 | return 0; 33 | } 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /TumorSegmentationEvaluation/README.txt: -------------------------------------------------------------------------------- 1 | Tumor Segmentation Evaluation 2 | ----------------------------- 3 | 4 | The directory contains the Volview Plugins for Tumor Mesurement and Comparison 5 | 6 | INSTALL NOTES 7 | 8 | 1.Donwload CMake from www.cmake.org and ITK(Insight ToolKit) from www.itk.org 9 | 10 | 2.Install ITK(see www.itk.org for installation notes) 11 | 12 | 3.Run CMake and select the directory where the plugins are located and the directory where ITK binaries is located 13 | 14 | 4.Run your c++ compiler with the project generated by CMake and compile the project. 15 | 16 | 5.If is not specified in the CMake configuration where should be the plugins compiled then manually copy the compiled plugins to Volview Plugins directory 17 | 18 | 6.Open Volview application and locate them in Filters tab or select from menu View/Filters 19 | 20 | That's it 21 | 22 | -------------------------------------------------------------------------------- /TumorSegmentationEvaluation/TumorVolumeEvaluationDeveloperManual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/TumorSegmentationEvaluation/TumorVolumeEvaluationDeveloperManual.pdf -------------------------------------------------------------------------------- /TumorSegmentationEvaluation/TumorVolumeEvaluationUserManual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKApps/2754058c006ec168868d5232df1a0f113470d182/TumorSegmentationEvaluation/TumorVolumeEvaluationUserManual.pdf -------------------------------------------------------------------------------- /Utilities/Hooks/pre-commit: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | #========================================================================== 3 | # 4 | # Copyright Insight Software Consortium 5 | # 6 | # Licensed under the Apache License, Version 2.0 (the "License"); 7 | # you may not use this file except in compliance with the License. 8 | # You may obtain a copy of the License at 9 | # 10 | # http://www.apache.org/licenses/LICENSE-2.0.txt 11 | # 12 | # Unless required by applicable law or agreed to in writing, software 13 | # distributed under the License is distributed on an "AS IS" BASIS, 14 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | # See the License for the specific language governing permissions and 16 | # limitations under the License. 17 | # 18 | #==========================================================================*/ 19 | 20 | die() { 21 | echo 'pre-commit hook failure' 1>&2 22 | echo '-----------------------' 1>&2 23 | echo '' 1>&2 24 | echo "$@" 1>&2 25 | exit 1 26 | } 27 | 28 | # This is a placeholder for future pre-commit checks. 29 | exit 0 30 | -------------------------------------------------------------------------------- /VolviewPlugIns/README.txt: -------------------------------------------------------------------------------- 1 | 2 | ITK plug-ins for VolView 3 | ------------------------ 4 | 5 | This directory contains code for generating run-time plug-ins for the 6 | visualization application VolView. 7 | 8 | Detailed information about Volview is available at: 9 | 10 | http://www.kitware.com/products/volview.html 11 | 12 | A lite version of VolView will be publicly available this year (2003). 13 | 14 | This plug-ins make part of an ongoing effort for integrating ITK in 15 | academic and commercial applications in order to extend the benefits 16 | of the toolkit to the final users involved in medical image processing 17 | applications. 18 | 19 | -------------------------------------------------------------------------------- /VoronoiSegmentation/VDSegMain.cpp: -------------------------------------------------------------------------------- 1 | /*========================================================================= 2 | 3 | Program: Insight Segmentation & Registration Toolkit 4 | Module: VDSegMain.cpp 5 | Language: C++ 6 | Date: $Date$ 7 | Version: $Revision$ 8 | 9 | Copyright (c) 2002 Insight Consortium. All rights reserved. 10 | See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 11 | 12 | This software is distributed WITHOUT ANY WARRANTY; without even 13 | the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 14 | PURPOSE. See the above copyright notices for more information. 15 | 16 | =========================================================================*/ 17 | 18 | #include "VDSegGrayUI.h" 19 | 20 | int main(){ 21 | VDSegGrayUI * console=new VDSegGrayUI; 22 | console->Show(); 23 | 24 | Fl::run(); 25 | 26 | return 1; 27 | } 28 | 29 | -------------------------------------------------------------------------------- /vtkITK/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT( vtkITK ) 2 | 3 | 4 | IF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 5 | 6 | FIND_PACKAGE(ITK) 7 | IF(ITK_FOUND) 8 | INCLUDE(${ITK_USE_FILE}) 9 | ELSE(ITK_FOUND) 10 | MESSAGE(FATAL_ERROR 11 | "Cannot build ITKApps without ITK. Please set ITK_DIR.") 12 | ENDIF(ITK_FOUND) 13 | 14 | FIND_PACKAGE(VTK) 15 | IF (VTK_FOUND) 16 | INCLUDE (${VTK_USE_FILE}) 17 | ENDIF (VTK_FOUND) 18 | 19 | ENDIF( BUILD_OUTSIDE_INSIGHT_APPLICATIONS ) 20 | 21 | 22 | INCLUDE_REGULAR_EXPRESSION("^.*$") 23 | 24 | INCLUDE_DIRECTORIES ( ${vtkITK_SOURCE_DIR}/Common) 25 | 26 | IF (VTK_WRAP_TCL) 27 | INCLUDE_DIRECTORIES ( ${TCL_INCLUDE_PATH}) 28 | ENDIF() 29 | 30 | IF (VTK_WRAP_PYTHON) 31 | FIND_PACKAGE(PythonLibs) 32 | INCLUDE_DIRECTORIES ( ${PYTHON_INCLUDE_PATH}) 33 | ENDIF() 34 | 35 | # Add the common directory 36 | SUBDIRS ( Common ) 37 | SUBDIRS ( Wrapping ) 38 | -------------------------------------------------------------------------------- /vtkITK/README.txt: -------------------------------------------------------------------------------- 1 | This is a works in progress. Please do not change it. Use at your own risk... 2 | -------------------------------------------------------------------------------- /vtkITK/Wrapping/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | SUBDIRS ( Tcl ) 2 | -------------------------------------------------------------------------------- /vtkITK/Wrapping/Tcl/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # create the vtkITK executable 2 | ADD_EXECUTABLE(vtkITK tkAppInit) 3 | INSTALL_TARGETS(/bin vtkITK) 4 | 5 | TARGET_LINK_LIBRARIES(vtkITK 6 | vtkImagingTCL 7 | vtkGraphicsTCL 8 | vtkIOTCL 9 | vtkFilteringTCL 10 | vtkCommonTCL 11 | ${TCL_LIBRARY} ${TK_LIBRARY} 12 | ) 13 | 14 | IF (VTK_USE_RENDERING) 15 | TARGET_LINK_LIBRARIES(vtkITK vtkRenderingTCL) 16 | ENDIF (VTK_USE_RENDERING) 17 | 18 | IF (VTK_USE_PATENTED) 19 | TARGET_LINK_LIBRARIES(vtkITK vtkPatentedTCL) 20 | ENDIF (VTK_USE_PATENTED) 21 | 22 | IF (VTK_USE_HYBRID) 23 | TARGET_LINK_LIBRARIES(vtkITK vtkHybridTCL) 24 | ENDIF (VTK_USE_HYBRID) 25 | 26 | IF (VTK_USE_PARALLEL) 27 | TARGET_LINK_LIBRARIES(vtkITK vtkParallelTCL) 28 | ENDIF (VTK_USE_PARALLEL) 29 | 30 | TARGET_LINK_LIBRARIES(vtkITK vtkVTKITKCommonTCL vtkVTKITKCommon ${ITK_LIBRARIES}) 31 | 32 | LINK_DIRECTORIES ( ${vtkITK_BINARY_DIR}/Common ) 33 | 34 | INSTALL_TARGETS(/bin vtkITK) 35 | 36 | IF(CMAKE_COMPILER_IS_GNUCXX) 37 | SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-cast-qual -Wno-unused") 38 | ENDIF(CMAKE_COMPILER_IS_GNUCXX) 39 | -------------------------------------------------------------------------------- /vtkITK/Wrapping/Tcl/MakePackages.tcl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env tclsh 2 | 3 | # Packages 4 | 5 | pkg_mkIndex -direct -verbose vtkitk 6 | pkg_mkIndex -direct -verbose vtkitkbase 7 | 8 | # Add-ons (scripts) 9 | 10 | exit 11 | -------------------------------------------------------------------------------- /vtkITK/vtkITK.cmake: -------------------------------------------------------------------------------- 1 | Temporary empty file to let makefile dependencies update. 2 | -------------------------------------------------------------------------------- /vtkITK/vtkITKToolkits.h.in: -------------------------------------------------------------------------------- 1 | 2 | /* what toolkits was VTKITK built with */ 3 | #cmakedefine VTKITK_USE_COMMON 4 | --------------------------------------------------------------------------------