diff --git a/Modules/DiffusionCmdApps/CMakeLists.txt b/Modules/DiffusionCmdApps/CMakeLists.txt index e9a13ae..cde5fab 100644 --- a/Modules/DiffusionCmdApps/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/CMakeLists.txt @@ -1,20 +1,20 @@ MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion # INCLUDE_DIRS Helpers - DEPENDS MitkDiffusionCore MitkDiffusionIO MitkFiberTracking MitkMriSimulation MitkQuantification MitkConnectomics + DEPENDS MitkDiffusionCore MitkDiffusionIO MitkFiberTracking MitkMriSimulation MitkConnectomics PACKAGE_DEPENDS PUBLIC ITK ) if(MODULE_IS_ENABLED) add_subdirectory(Connectomics) add_subdirectory(Fiberfox) add_subdirectory(FiberProcessing) add_subdirectory(Tractography) add_subdirectory(TractographyEvaluation) add_subdirectory(Misc) add_subdirectory(Quantification) if(MITK_USE_Python) add_subdirectory(Python) endif() endif() diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h diff --git a/Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h diff --git a/Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h diff --git a/Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h diff --git a/Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkMultiTensorImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkMultiTensorImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkOrientationDistributionFunction.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkOrientationDistributionFunction.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.h b/Modules/DiffusionCore/Algorithms/Reconstruction/itkPointShell.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkPointShell.h diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx b/Modules/DiffusionCore/Algorithms/Reconstruction/itkPointShell.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx rename to Modules/DiffusionCore/Algorithms/Reconstruction/itkPointShell.txx diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp b/Modules/DiffusionCore/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h b/Modules/DiffusionCore/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h rename to Modules/DiffusionCore/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h diff --git a/Modules/DiffusionCore/src/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp b/Modules/DiffusionCore/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp rename to Modules/DiffusionCore/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h b/Modules/DiffusionCore/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h rename to Modules/DiffusionCore/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h diff --git a/Modules/DiffusionCore/src/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp b/Modules/DiffusionCore/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp rename to Modules/DiffusionCore/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h b/Modules/DiffusionCore/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h rename to Modules/DiffusionCore/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h diff --git a/Modules/DiffusionCore/include/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h b/Modules/DiffusionCore/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h rename to Modules/DiffusionCore/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h diff --git a/Modules/DiffusionCore/src/Algorithms/Registration/mitkRegistrationWrapper.cpp b/Modules/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/Registration/mitkRegistrationWrapper.cpp rename to Modules/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/Registration/mitkRegistrationWrapper.h b/Modules/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/Registration/mitkRegistrationWrapper.h rename to Modules/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkAdcImageFilter.h b/Modules/DiffusionCore/Algorithms/itkAdcImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkAdcImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkAdcImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkAdcImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkAdcImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkAdcImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkAdcImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.h b/Modules/DiffusionCore/Algorithms/itkB0ImageExtractionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkB0ImageExtractionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkB0ImageExtractionImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkB0ImageExtractionImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h b/Modules/DiffusionCore/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.h b/Modules/DiffusionCore/Algorithms/itkBrainMaskExtractionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkBrainMaskExtractionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkBrainMaskExtractionImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkBrainMaskExtractionImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkCartesianToPolarVectorImageFilter.h b/Modules/DiffusionCore/Algorithms/itkCartesianToPolarVectorImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkCartesianToPolarVectorImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkCartesianToPolarVectorImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h b/Modules/DiffusionCore/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx diff --git a/Modules/DiffusionCore/src/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h b/Modules/DiffusionCore/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h b/Modules/DiffusionCore/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkDistanceMapFilter.h b/Modules/DiffusionCore/Algorithms/itkDistanceMapFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDistanceMapFilter.h rename to Modules/DiffusionCore/Algorithms/itkDistanceMapFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDistanceMapFilter.txx b/Modules/DiffusionCore/Algorithms/itkDistanceMapFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDistanceMapFilter.txx rename to Modules/DiffusionCore/Algorithms/itkDistanceMapFilter.txx diff --git a/Modules/DiffusionCore/src/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp b/Modules/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkDwiGradientLengthCorrectionFilter.h b/Modules/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDwiGradientLengthCorrectionFilter.h rename to Modules/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h b/Modules/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h rename to Modules/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx b/Modules/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx rename to Modules/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h b/Modules/DiffusionCore/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h rename to Modules/DiffusionCore/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx b/Modules/DiffusionCore/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx rename to Modules/DiffusionCore/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.h b/Modules/DiffusionCore/Algorithms/itkExtractChannelFromRgbaImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkExtractChannelFromRgbaImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.h b/Modules/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.h rename to Modules/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.txx b/Modules/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.txx rename to Modules/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.cpp b/Modules/DiffusionCore/Algorithms/itkFlipPeaksFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkFlipPeaksFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.h b/Modules/DiffusionCore/Algorithms/itkFlipPeaksFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.h rename to Modules/DiffusionCore/Algorithms/itkFlipPeaksFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkFourDToVectorImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkFourDToVectorImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h b/Modules/DiffusionCore/Algorithms/itkFourDToVectorImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkFourDToVectorImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.h b/Modules/DiffusionCore/Algorithms/itkGaussianInterpolateImageFunction.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.h rename to Modules/DiffusionCore/Algorithms/itkGaussianInterpolateImageFunction.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.txx b/Modules/DiffusionCore/Algorithms/itkGaussianInterpolateImageFunction.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.txx rename to Modules/DiffusionCore/Algorithms/itkGaussianInterpolateImageFunction.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.h b/Modules/DiffusionCore/Algorithms/itkMergeDiffusionImagesFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.h rename to Modules/DiffusionCore/Algorithms/itkMergeDiffusionImagesFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.txx b/Modules/DiffusionCore/Algorithms/itkMergeDiffusionImagesFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.txx rename to Modules/DiffusionCore/Algorithms/itkMergeDiffusionImagesFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.h b/Modules/DiffusionCore/Algorithms/itkNonLocalMeansDenoisingFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.h rename to Modules/DiffusionCore/Algorithms/itkNonLocalMeansDenoisingFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.txx b/Modules/DiffusionCore/Algorithms/itkNonLocalMeansDenoisingFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.txx rename to Modules/DiffusionCore/Algorithms/itkNonLocalMeansDenoisingFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.cpp b/Modules/DiffusionCore/Algorithms/itkOdfMaximaExtractionFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkOdfMaximaExtractionFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.h b/Modules/DiffusionCore/Algorithms/itkOdfMaximaExtractionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.h rename to Modules/DiffusionCore/Algorithms/itkOdfMaximaExtractionFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkOdfToRgbImageFilter.h b/Modules/DiffusionCore/Algorithms/itkOdfToRgbImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkOdfToRgbImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkOdfToRgbImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkPolarToCartesianVectorImageFilter.h b/Modules/DiffusionCore/Algorithms/itkPolarToCartesianVectorImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkPolarToCartesianVectorImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkPolarToCartesianVectorImageFilter.h diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.h b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionFilter.h similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.h rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionFilter.h diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.txx b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionFilter.txx similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.txx rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionFilter.txx diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h diff --git a/Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx b/Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx similarity index 100% rename from Modules/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx rename to Modules/DiffusionCore/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.h b/Modules/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.h rename to Modules/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.txx b/Modules/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.txx rename to Modules/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.h b/Modules/DiffusionCore/Algorithms/itkResampleDwiImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkResampleDwiImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkResampleDwiImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkResampleDwiImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkResidualImageFilter.h b/Modules/DiffusionCore/Algorithms/itkResidualImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkResidualImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkResidualImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkResidualImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkResidualImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkResidualImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkResidualImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.cpp b/Modules/DiffusionCore/Algorithms/itkShCoefficientImageExporter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.cpp rename to Modules/DiffusionCore/Algorithms/itkShCoefficientImageExporter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.h b/Modules/DiffusionCore/Algorithms/itkShCoefficientImageExporter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.h rename to Modules/DiffusionCore/Algorithms/itkShCoefficientImageExporter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.cpp b/Modules/DiffusionCore/Algorithms/itkShCoefficientImageImporter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.cpp rename to Modules/DiffusionCore/Algorithms/itkShCoefficientImageImporter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.h b/Modules/DiffusionCore/Algorithms/itkShCoefficientImageImporter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.h rename to Modules/DiffusionCore/Algorithms/itkShCoefficientImageImporter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkShToOdfImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkShToOdfImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.h b/Modules/DiffusionCore/Algorithms/itkShToOdfImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkShToOdfImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkShToRgbImageFilter.h b/Modules/DiffusionCore/Algorithms/itkShToRgbImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkShToRgbImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkShToRgbImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.h b/Modules/DiffusionCore/Algorithms/itkSplitDWImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkSplitDWImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkSplitDWImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkSplitDWImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkSplitVectorImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkSplitVectorImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h b/Modules/DiffusionCore/Algorithms/itkSplitVectorImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkSplitVectorImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorDerivedMeasurementsFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorDerivedMeasurementsFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.txx b/Modules/DiffusionCore/Algorithms/itkTensorDerivedMeasurementsFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.txx rename to Modules/DiffusionCore/Algorithms/itkTensorDerivedMeasurementsFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorImageToDiffusionImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorImageToDiffusionImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkTensorImageToDiffusionImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkTensorImageToDiffusionImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorImageToOdfImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorImageToOdfImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkTensorImageToOdfImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkTensorImageToOdfImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx b/Modules/DiffusionCore/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx rename to Modules/DiffusionCore/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorToL2NormImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorToL2NormImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkTensorToL2NormImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkTensorToL2NormImageFilter.txx diff --git a/Modules/DiffusionCore/include/Algorithms/itkTensorToRgbImageFilter.h b/Modules/DiffusionCore/Algorithms/itkTensorToRgbImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkTensorToRgbImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkTensorToRgbImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp b/Modules/DiffusionCore/Algorithms/itkVectorImageToFourDImageFilter.cpp similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp rename to Modules/DiffusionCore/Algorithms/itkVectorImageToFourDImageFilter.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h b/Modules/DiffusionCore/Algorithms/itkVectorImageToFourDImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkVectorImageToFourDImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.h b/Modules/DiffusionCore/Algorithms/itkVectorImageToImageFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.h rename to Modules/DiffusionCore/Algorithms/itkVectorImageToImageFilter.h diff --git a/Modules/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.txx b/Modules/DiffusionCore/Algorithms/itkVectorImageToImageFilter.txx similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.txx rename to Modules/DiffusionCore/Algorithms/itkVectorImageToImageFilter.txx diff --git a/Modules/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp b/Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp rename to Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h b/Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h rename to Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h diff --git a/Modules/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp b/Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp similarity index 100% rename from Modules/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp rename to Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp diff --git a/Modules/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h b/Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h similarity index 100% rename from Modules/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h rename to Modules/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h diff --git a/Modules/DiffusionCore/CMakeLists.txt b/Modules/DiffusionCore/CMakeLists.txt index b001ffe..5affec6 100644 --- a/Modules/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionCore/CMakeLists.txt @@ -1,26 +1,26 @@ # With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled if(APPLE) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion - INCLUDE_DIRS include/ include/Algorithms include/Algorithms/Reconstruction include/Algorithms/Registration include/Algorithms/Reconstruction/MultishellProcessing include/Algorithms/Reconstruction/FittingFunctions include/DicomImport include/IODataStructures/DiffusionWeightedImages include/IODataStructures/Properties include/IODataStructures/OdfImages include/IODataStructures/TensorImages include/IODataStructures include/Rendering ${CMAKE_CURRENT_BINARY_DIR} + INCLUDE_DIRS Algorithms Algorithms/Reconstruction Algorithms/Registration Algorithms/Reconstruction/MultishellProcessing Algorithms/Reconstruction/FittingFunctions DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/Properties IODataStructures/OdfImages IODataStructures/TensorImages IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkSceneSerializationBase MitkDICOMReader MitkMatchPointRegistration PACKAGE_DEPENDS PUBLIC ITK|ITKTestKernel+ITKRegistrationCommon+ITKMetricsv4+ITKRegistrationMethodsv4+ITKDistanceMap+ITKLabelVoting+ITKVTK PUBLIC VTK|vtkFiltersProgrammable OpenMP|OpenMP_CXX ) if(MSVC) mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() add_subdirectory(Testing) add_subdirectory(autoload/IO) if(MITK_USE_Python) MITK_INSTALL(FILES PythonRequirements.txt) endif() configure_file(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/mitkDiffusionImagingConfigure.h) diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageHeaderReader.h b/Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageHeaderReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageHeaderReader.h rename to Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageHeaderReader.h diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageReader.cpp similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.h b/Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.h rename to Modules/DiffusionCore/DicomImport/mitkDicomDiffusionImageReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReader.h diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReaderHelper.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReaderHelper.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReaderHelper.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionDICOMFileReaderHelper.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderDICOMFileReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h b/Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h rename to Modules/DiffusionCore/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionCore/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h b/Modules/DiffusionCore/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h rename to Modules/DiffusionCore/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkGroupDiffusionHeadersFilter.cpp b/Modules/DiffusionCore/DicomImport/mitkGroupDiffusionHeadersFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkGroupDiffusionHeadersFilter.cpp rename to Modules/DiffusionCore/DicomImport/mitkGroupDiffusionHeadersFilter.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkGroupDiffusionHeadersFilter.h b/Modules/DiffusionCore/DicomImport/mitkGroupDiffusionHeadersFilter.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkGroupDiffusionHeadersFilter.h rename to Modules/DiffusionCore/DicomImport/mitkGroupDiffusionHeadersFilter.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionCore/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h b/Modules/DiffusionCore/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h rename to Modules/DiffusionCore/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionCore/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h b/Modules/DiffusionCore/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h rename to Modules/DiffusionCore/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h diff --git a/Modules/DiffusionCore/src/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionCore/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp similarity index 100% rename from Modules/DiffusionCore/src/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp rename to Modules/DiffusionCore/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp diff --git a/Modules/DiffusionCore/include/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h b/Modules/DiffusionCore/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h similarity index 100% rename from Modules/DiffusionCore/include/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h rename to Modules/DiffusionCore/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h diff --git a/Modules/DiffusionCore/DicomImport/test.txt b/Modules/DiffusionCore/DicomImport/test.txt deleted file mode 100644 index e69de29..0000000 diff --git a/Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h diff --git a/Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h diff --git a/Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h diff --git a/Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx diff --git a/Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h b/Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h rename to Modules/DiffusionCore/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h diff --git a/Modules/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImage.cpp b/Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImage.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImage.cpp rename to Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImage.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImage.h b/Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImage.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImage.h rename to Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImage.h diff --git a/Modules/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImageSource.cpp b/Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImageSource.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImageSource.cpp rename to Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImageSource.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImageSource.h b/Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImageSource.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImageSource.h rename to Modules/DiffusionCore/IODataStructures/OdfImages/mitkOdfImageSource.h diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapProperty.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapProperty.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapProperty.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapProperty.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/Properties/mitkBValueMapProperty.h b/Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapProperty.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/Properties/mitkBValueMapProperty.h rename to Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapProperty.h diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h b/Modules/DiffusionCore/IODataStructures/Properties/mitkDiffusionPropertyHelper.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h rename to Modules/DiffusionCore/IODataStructures/Properties/mitkDiffusionPropertyHelper.h diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/Properties/mitkGradientDirectionsProperty.h b/Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsProperty.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/Properties/mitkGradientDirectionsProperty.h rename to Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsProperty.h diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/Properties/mitkMeasurementFrameProperty.h b/Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFrameProperty.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/Properties/mitkMeasurementFrameProperty.h rename to Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFrameProperty.h diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp diff --git a/Modules/DiffusionCore/src/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp b/Modules/DiffusionCore/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp rename to Modules/DiffusionCore/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/Properties/mitkNodePredicateIsDWI.h b/Modules/DiffusionCore/IODataStructures/Properties/mitkNodePredicateIsDWI.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/Properties/mitkNodePredicateIsDWI.h rename to Modules/DiffusionCore/IODataStructures/Properties/mitkNodePredicateIsDWI.h diff --git a/Modules/DiffusionCore/src/IODataStructures/TensorImages/mitkTensorImage.cpp b/Modules/DiffusionCore/IODataStructures/TensorImages/mitkTensorImage.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/TensorImages/mitkTensorImage.cpp rename to Modules/DiffusionCore/IODataStructures/TensorImages/mitkTensorImage.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/TensorImages/mitkTensorImage.h b/Modules/DiffusionCore/IODataStructures/TensorImages/mitkTensorImage.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/TensorImages/mitkTensorImage.h rename to Modules/DiffusionCore/IODataStructures/TensorImages/mitkTensorImage.h diff --git a/Modules/DiffusionCore/src/IODataStructures/mitkPeakImage.cpp b/Modules/DiffusionCore/IODataStructures/mitkPeakImage.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/mitkPeakImage.cpp rename to Modules/DiffusionCore/IODataStructures/mitkPeakImage.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/mitkPeakImage.h b/Modules/DiffusionCore/IODataStructures/mitkPeakImage.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/mitkPeakImage.h rename to Modules/DiffusionCore/IODataStructures/mitkPeakImage.h diff --git a/Modules/DiffusionCore/src/IODataStructures/mitkRegistrationObject.cpp b/Modules/DiffusionCore/IODataStructures/mitkRegistrationObject.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/mitkRegistrationObject.cpp rename to Modules/DiffusionCore/IODataStructures/mitkRegistrationObject.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/mitkRegistrationObject.h b/Modules/DiffusionCore/IODataStructures/mitkRegistrationObject.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/mitkRegistrationObject.h rename to Modules/DiffusionCore/IODataStructures/mitkRegistrationObject.h diff --git a/Modules/DiffusionCore/src/IODataStructures/mitkShImage.cpp b/Modules/DiffusionCore/IODataStructures/mitkShImage.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/mitkShImage.cpp rename to Modules/DiffusionCore/IODataStructures/mitkShImage.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/mitkShImage.h b/Modules/DiffusionCore/IODataStructures/mitkShImage.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/mitkShImage.h rename to Modules/DiffusionCore/IODataStructures/mitkShImage.h diff --git a/Modules/DiffusionCore/src/IODataStructures/mitkShImageSource.cpp b/Modules/DiffusionCore/IODataStructures/mitkShImageSource.cpp similarity index 100% rename from Modules/DiffusionCore/src/IODataStructures/mitkShImageSource.cpp rename to Modules/DiffusionCore/IODataStructures/mitkShImageSource.cpp diff --git a/Modules/DiffusionCore/include/IODataStructures/mitkShImageSource.h b/Modules/DiffusionCore/IODataStructures/mitkShImageSource.h similarity index 100% rename from Modules/DiffusionCore/include/IODataStructures/mitkShImageSource.h rename to Modules/DiffusionCore/IODataStructures/mitkShImageSource.h diff --git a/Modules/DiffusionCore/src/Rendering/mitkOdfNormalizationMethodProperty.cpp b/Modules/DiffusionCore/Rendering/mitkOdfNormalizationMethodProperty.cpp similarity index 100% rename from Modules/DiffusionCore/src/Rendering/mitkOdfNormalizationMethodProperty.cpp rename to Modules/DiffusionCore/Rendering/mitkOdfNormalizationMethodProperty.cpp diff --git a/Modules/DiffusionCore/include/Rendering/mitkOdfNormalizationMethodProperty.h b/Modules/DiffusionCore/Rendering/mitkOdfNormalizationMethodProperty.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/mitkOdfNormalizationMethodProperty.h rename to Modules/DiffusionCore/Rendering/mitkOdfNormalizationMethodProperty.h diff --git a/Modules/DiffusionCore/src/Rendering/mitkOdfScaleByProperty.cpp b/Modules/DiffusionCore/Rendering/mitkOdfScaleByProperty.cpp similarity index 100% rename from Modules/DiffusionCore/src/Rendering/mitkOdfScaleByProperty.cpp rename to Modules/DiffusionCore/Rendering/mitkOdfScaleByProperty.cpp diff --git a/Modules/DiffusionCore/include/Rendering/mitkOdfScaleByProperty.h b/Modules/DiffusionCore/Rendering/mitkOdfScaleByProperty.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/mitkOdfScaleByProperty.h rename to Modules/DiffusionCore/Rendering/mitkOdfScaleByProperty.h diff --git a/Modules/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.h b/Modules/DiffusionCore/Rendering/mitkOdfVtkMapper2D.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.h rename to Modules/DiffusionCore/Rendering/mitkOdfVtkMapper2D.h diff --git a/Modules/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.txx b/Modules/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx similarity index 100% rename from Modules/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.txx rename to Modules/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx diff --git a/Modules/DiffusionCore/src/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp b/Modules/DiffusionCore/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp similarity index 100% rename from Modules/DiffusionCore/src/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp rename to Modules/DiffusionCore/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp diff --git a/Modules/DiffusionCore/include/Rendering/mitkVectorImageVtkGlyphMapper3D.h b/Modules/DiffusionCore/Rendering/mitkVectorImageVtkGlyphMapper3D.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/mitkVectorImageVtkGlyphMapper3D.h rename to Modules/DiffusionCore/Rendering/mitkVectorImageVtkGlyphMapper3D.h diff --git a/Modules/DiffusionCore/src/Rendering/vtkMaskedProgrammableGlyphFilter.cpp b/Modules/DiffusionCore/Rendering/vtkMaskedProgrammableGlyphFilter.cpp similarity index 100% rename from Modules/DiffusionCore/src/Rendering/vtkMaskedProgrammableGlyphFilter.cpp rename to Modules/DiffusionCore/Rendering/vtkMaskedProgrammableGlyphFilter.cpp diff --git a/Modules/DiffusionCore/include/Rendering/vtkMaskedProgrammableGlyphFilter.h b/Modules/DiffusionCore/Rendering/vtkMaskedProgrammableGlyphFilter.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/vtkMaskedProgrammableGlyphFilter.h rename to Modules/DiffusionCore/Rendering/vtkMaskedProgrammableGlyphFilter.h diff --git a/Modules/DiffusionCore/src/Rendering/vtkOdfSource.cxx b/Modules/DiffusionCore/Rendering/vtkOdfSource.cxx similarity index 100% rename from Modules/DiffusionCore/src/Rendering/vtkOdfSource.cxx rename to Modules/DiffusionCore/Rendering/vtkOdfSource.cxx diff --git a/Modules/DiffusionCore/include/Rendering/vtkOdfSource.h b/Modules/DiffusionCore/Rendering/vtkOdfSource.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/vtkOdfSource.h rename to Modules/DiffusionCore/Rendering/vtkOdfSource.h diff --git a/Modules/DiffusionCore/src/Rendering/vtkThickPlane.cxx b/Modules/DiffusionCore/Rendering/vtkThickPlane.cxx similarity index 100% rename from Modules/DiffusionCore/src/Rendering/vtkThickPlane.cxx rename to Modules/DiffusionCore/Rendering/vtkThickPlane.cxx diff --git a/Modules/DiffusionCore/include/Rendering/vtkThickPlane.h b/Modules/DiffusionCore/Rendering/vtkThickPlane.h similarity index 100% rename from Modules/DiffusionCore/include/Rendering/vtkThickPlane.h rename to Modules/DiffusionCore/Rendering/vtkThickPlane.h diff --git a/Modules/DiffusionCore/files.cmake b/Modules/DiffusionCore/files.cmake index b8972e7..c0278c8 100644 --- a/Modules/DiffusionCore/files.cmake +++ b/Modules/DiffusionCore/files.cmake @@ -1,162 +1,164 @@ set(CPP_FILES # DicomImport # DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp DicomImport/mitkDiffusionDICOMFileReader.cpp DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp # Properties IODataStructures/Properties/mitkBValueMapProperty.cpp IODataStructures/Properties/mitkGradientDirectionsProperty.cpp IODataStructures/Properties/mitkMeasurementFrameProperty.cpp IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp IODataStructures/Properties/mitkNodePredicateIsDWI.cpp # Serializer IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp # DataStructures -> Odf IODataStructures/OdfImages/mitkOdfImageSource.cpp IODataStructures/OdfImages/mitkOdfImage.cpp IODataStructures/mitkShImage.cpp IODataStructures/mitkShImageSource.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImage.cpp # DataStructures -> Peaks IODataStructures/mitkPeakImage.cpp Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp Algorithms/itkDwiGradientLengthCorrectionFilter.cpp # Registration Algorithms & Co. Algorithms/Registration/mitkRegistrationWrapper.cpp Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp # Algorithms/Registration/mitkRegistrationMethodITK4.cpp Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp # MultishellProcessing Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp # Function Collection mitkDiffusionFunctionCollection.cpp ) set(H_FILES # function Collection - include/mitkDiffusionFunctionCollection.h + mitkDiffusionFunctionCollection.h # Rendering - include/Rendering/mitkOdfVtkMapper2D.h + Rendering/mitkOdfVtkMapper2D.h # Reconstruction - include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h - include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h - include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h - include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h - include/Algorithms/Reconstruction/itkPointShell.h - include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h - include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h - include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h - include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h - include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h + Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h + Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h + Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h + Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h + Algorithms/Reconstruction/itkPointShell.h + Algorithms/Reconstruction/itkOrientationDistributionFunction.h + Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h + Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h + Algorithms/Reconstruction/itkBallAndSticksImageFilter.h + Algorithms/Reconstruction/itkMultiTensorImageFilter.h # Fitting functions - include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h - include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h - include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h + Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h + Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h + Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h # MultishellProcessing - include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h - include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h - include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h - include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h - include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h - include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h + Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h + Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h + Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h + Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h + Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h + Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h # Properties - include/IODataStructures/Properties/mitkBValueMapProperty.h - include/IODataStructures/Properties/mitkGradientDirectionsProperty.h - include/IODataStructures/Properties/mitkMeasurementFrameProperty.h - include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h + IODataStructures/Properties/mitkBValueMapProperty.h + IODataStructures/Properties/mitkGradientDirectionsProperty.h + IODataStructures/Properties/mitkMeasurementFrameProperty.h + IODataStructures/Properties/mitkDiffusionPropertyHelper.h - include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h + IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h # Algorithms - include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h - include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h - include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h - include/Algorithms/itkTensorDerivedMeasurementsFilter.h - include/Algorithms/itkBrainMaskExtractionImageFilter.h - include/Algorithms/itkB0ImageExtractionImageFilter.h - include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h - include/Algorithms/itkTensorImageToDiffusionImageFilter.h - include/Algorithms/itkTensorToL2NormImageFilter.h - include/Algorithms/itkGaussianInterpolateImageFunction.h - include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h - include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h - include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h - include/Algorithms/itkCartesianToPolarVectorImageFilter.h - include/Algorithms/itkPolarToCartesianVectorImageFilter.h - include/Algorithms/itkDistanceMapFilter.h - include/Algorithms/itkProjectionFilter.h - include/Algorithms/itkResidualImageFilter.h - include/Algorithms/itkExtractChannelFromRgbaImageFilter.h - include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h - include/Algorithms/itkMergeDiffusionImagesFilter.h - include/Algorithms/itkShCoefficientImageImporter.h - include/Algorithms/itkShCoefficientImageExporter.h - include/Algorithms/itkOdfMaximaExtractionFilter.h - include/Algorithms/itkResampleDwiImageFilter.h - include/Algorithms/itkDwiGradientLengthCorrectionFilter.h - include/Algorithms/itkAdcImageFilter.h - include/Algorithms/itkDwiNormilzationFilter.h - include/Algorithms/itkSplitDWImageFilter.h - include/Algorithms/itkRemoveDwiChannelFilter.h - include/Algorithms/itkExtractDwiChannelFilter.h - include/Algorithms/itkFlipPeaksFilter.h - include/Algorithms/itkShToOdfImageFilter.h - include/Algorithms/itkFourDToVectorImageFilter.h - include/Algorithms/itkVectorImageToFourDImageFilter.h - include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h - include/Algorithms/itkNonLocalMeansDenoisingFilter.h - include/Algorithms/itkVectorImageToImageFilter.h - include/Algorithms/itkSplitVectorImageFilter.h + Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h + Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h + Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h + Algorithms/itkTensorDerivedMeasurementsFilter.h + Algorithms/itkBrainMaskExtractionImageFilter.h + Algorithms/itkB0ImageExtractionImageFilter.h + Algorithms/itkB0ImageExtractionToSeparateImageFilter.h + Algorithms/itkTensorImageToDiffusionImageFilter.h + Algorithms/itkTensorToL2NormImageFilter.h + Algorithms/itkGaussianInterpolateImageFunction.h + Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h + Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h + Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h + Algorithms/itkCartesianToPolarVectorImageFilter.h + Algorithms/itkPolarToCartesianVectorImageFilter.h + Algorithms/itkDistanceMapFilter.h + Algorithms/itkResidualImageFilter.h + Algorithms/itkExtractChannelFromRgbaImageFilter.h + Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h + Algorithms/itkMergeDiffusionImagesFilter.h + Algorithms/itkShCoefficientImageImporter.h + Algorithms/itkShCoefficientImageExporter.h + Algorithms/itkOdfMaximaExtractionFilter.h + Algorithms/itkResampleDwiImageFilter.h + Algorithms/itkDwiGradientLengthCorrectionFilter.h + Algorithms/itkAdcImageFilter.h + Algorithms/itkDwiNormilzationFilter.h + Algorithms/itkSplitDWImageFilter.h + Algorithms/itkRemoveDwiChannelFilter.h + Algorithms/itkExtractDwiChannelFilter.h + Algorithms/itkFlipPeaksFilter.h + Algorithms/itkShToOdfImageFilter.h + Algorithms/itkFourDToVectorImageFilter.h + Algorithms/itkVectorImageToFourDImageFilter.h + Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h + Algorithms/itkNonLocalMeansDenoisingFilter.h + Algorithms/itkVectorImageToImageFilter.h + Algorithms/itkSplitVectorImageFilter.h + Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h + Algorithms/itkRegularizedIVIMReconstructionFilter.h + Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h ) set( TOOL_FILES ) diff --git a/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.h b/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.h deleted file mode 100644 index 20db22d..0000000 --- a/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.h +++ /dev/null @@ -1,159 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef ITKPROJECTIONFILTER_H_ -#define ITKPROJECTIONFILTER_H_ - -#include "itkObject.h" -#include "itkImage.h" -#include "mitkImage.h" -#include "mitkTbssImage.h" - -namespace itk -{ - - -/** - * \brief Projection part of the TBSS pipeline - * - * This class performs the projection step of the TBSS pipeline - * (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 ) - * As input it takes a binary skeleton, a distance map, and a vector image containing the image gradients - * that are typically provided by the itkSkeletonizationFilter and the itkDistanceMapFilter. - * Furthermore it requires a 4d dataset with patient data registered to the same space as the mean FA image. - * This 4D dataset is typically created by the TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index), - * in which case it is often named all_FA.nii.gz - */ - - -class ProjectionFilter : public Object -{ - -public: - - typedef itk::Image RealImageType; - - typedef itk::CovariantVector VectorType; - - typedef itk::Image VectorImageType; - - typedef itk::Image CharImageType; - - typedef itk::Image Float4DImageType; - typedef itk::Image FloatImageType; - - - -public: - - /** */ - typedef ProjectionFilter Self; - - /** Superclass */ - typedef Object Superclass; - - /** Smart Pointer */ - typedef SmartPointer Pointer; - - /** Smart Pointer */ - typedef SmartPointer ConstPointer; - - /** */ - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - - /** \brief Does the actual projection */ - void Project(); - - - /** \brief Set the distance map - * - * Sets the distance map that decodes for every voxel the distance to the nearest point on the skeleton. - */ - itkSetMacro(DistanceMap, RealImageType::Pointer) - - - /** \brief Set the directions - * - * Sets the direction calculated by the TBSS skeletonization algorithm in itkSkeletonizationFilter. - */ - itkSetMacro(Directions, VectorImageType::Pointer) - - - /** \brief Set the binary skeleton - * - * Sets the binary skeleton that defines on which voxels must be projected. - */ - itkSetMacro(Skeleton, CharImageType::Pointer) - - - /** \brief Set the mask defining tubular structures on the skeleton - * - * Sets a binary mask that defines wich part of the white matter skeleton are tubular instead of sheet like. - * This is important because the a different projection method is used for sheet like structues and - * tubular structures. - */ - itkSetMacro(Tube, CharImageType::Pointer) - - - /** \brief Set a 4D image containing the 3D registered FA maps of all study subjects. */ - itkSetMacro(AllFA, Float4DImageType::Pointer) - - - /** \brief Returns a 4D image containing the skeleton projections of all subjects */ - itkGetMacro(Projections, Float4DImageType::Pointer) - - -protected: - - /** Constructor */ - ProjectionFilter(); - - /** Destructor */ - ~ProjectionFilter() override; - - RealImageType::Pointer m_DistanceMap; - - VectorImageType::Pointer m_Directions; - - CharImageType::Pointer m_Skeleton; - - CharImageType::Pointer m_Tube; - - Float4DImageType::Pointer m_Projections; - - Float4DImageType::Pointer m_AllFA; - - int round(float x) - { - if (x>0.0) return ((int) (x+0.5)); - else return ((int) (x-0.5)); - } - -protected: - - - -}; - -} - -#ifndef ITK_MANUAL_INSTANTIATION -#include "itkProjectionFilter.txx" -#endif - -#endif diff --git a/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.txx b/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.txx deleted file mode 100644 index 16d9de6..0000000 --- a/Modules/DiffusionCore/include/Algorithms/itkProjectionFilter.txx +++ /dev/null @@ -1,196 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ -#ifndef _itkProjectionFilter_txx -#define _itkProjectionFilter_txx - -#include "itkProjectionFilter.h" - -#include "mitkProgressBar.h" -//#include - -#define SEARCHSIGMA 10 /* length in linear voxel dimensions */ -#define MAXSEARCHLENGTH (3*SEARCHSIGMA) - - -namespace itk -{ - - - ProjectionFilter::ProjectionFilter() - { - - } - - ProjectionFilter::~ProjectionFilter() - { - - - } - - void ProjectionFilter::Project() - { - // Contains only code for the projection of FA data. The original FSL code contains some extra lines - // For projection of other measurements than FA - - mitk::ProgressBar::GetInstance()->AddStepsToDo( 3 ); - - Float4DImageType::Pointer data_4d_projected = Float4DImageType::New(); - data_4d_projected->SetRegions(m_AllFA->GetRequestedRegion()); - data_4d_projected->SetDirection(m_AllFA->GetDirection()); - data_4d_projected->SetSpacing(m_AllFA->GetSpacing()); - data_4d_projected->SetOrigin(m_AllFA->GetOrigin()); - data_4d_projected->Allocate(); - data_4d_projected->FillBuffer(0.0); - - Float4DImageType::SizeType size = m_AllFA->GetRequestedRegion().GetSize(); - long s0 = size[0], s1 = size[1], s2 = size[2], s3 = size[3]; - - for(int t=0; tGetPixel(ix) != 0) - { - VectorImageType::PixelType dir = m_Directions->GetPixel(ix); - - Float4DImageType::IndexType ix4d; - ix4d[0]=x; ix4d[1]=y; ix4d[2]=z; ix4d[3]=t; - float maxval = m_AllFA->GetPixel(ix4d); - float maxval_weighted = maxval; - float exponentfactor = -0.5 * (dir[0]*dir[0]+dir[1]*dir[1]+dir[2]*dir[2]) / (float)(SEARCHSIGMA*SEARCHSIGMA); - - - // No tubular structure here - if(m_Tube->GetPixel(ix) == 0) - { - for(int iters=0;iters<2;iters++) - { - float distance=0; - - for(int d=1;d=s0 && dy<=s1 && dz<=s2)) - { - d=MAXSEARCHLENGTH; - } - else if(m_DistanceMap->GetPixel(ix3d)>=distance) - { - float distanceweight = exp(d * d * exponentfactor); - distance = m_DistanceMap->GetPixel(ix3d); - - ix4d[0]=x+dir[0]*D; ix4d[1]=y+dir[1]*D; ix4d[2]=z+dir[2]*D; ix4d[3]=t; - - if(distanceweight*m_AllFA->GetPixel(ix4d)>maxval_weighted) - { - maxval = m_AllFA->GetPixel(ix4d); - maxval_weighted = maxval*distanceweight; - } - } - else{ - d=MAXSEARCHLENGTH; - } - - - - } - - } - } - - // Tubular structure - else - { - for(int dy=-MAXSEARCHLENGTH; dy<=MAXSEARCHLENGTH;dy++) { - for(int dx=-MAXSEARCHLENGTH; dx<=MAXSEARCHLENGTH; dx++) { - - float distanceweight = exp(-0.5 * (dx*dx+dy*dy) / (float)(SEARCHSIGMA*SEARCHSIGMA) ); - float r=sqrt((float)(dx*dx+dy*dy)); - - if (r>0) - { - int allok=1; - - for(float rr=1; rr<=r+0.1; rr++) /* search outwards from centre to current voxel - test that distancemap always increasing */ - { - - int dx1=round(rr*dx/r); - int dy1=round(rr*dy/r); - int dx2=round((rr+1)*dx/r); - int dy2=round((rr+1)*dy/r); - - RealImageType::IndexType ix1, ix2; - ix1[0]=x+dx1; ix1[1]=y+dy1; ix1[2]=z; - ix2[0]=x+dx2; ix2[1]=y+dy2; ix2[2]=z; - if(m_DistanceMap->GetPixel(ix1) > m_DistanceMap->GetPixel(ix2) ) - { - allok=0; - } - - } - - ix4d[0]=x+dx; ix4d[1]=y+dy, ix4d[2]=z; ix4d[3]=t; - if( allok && (distanceweight * m_AllFA->GetPixel(ix4d) > maxval_weighted) ) - { - maxval = m_AllFA->GetPixel(ix4d); - maxval_weighted = maxval * distanceweight; - } - - - } - - } - } - } - - ix4d[0]=x; ix4d[1]=y; ix4d[2]=z; ix4d[3]=t; - - data_4d_projected->SetPixel(ix4d, maxval); - - } - } - } - } - } - - m_Projections = data_4d_projected; - - - - } - - - - - -} -#endif // _itkProjectionFilter_txx diff --git a/Modules/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp b/Modules/DiffusionCore/mitkDiffusionFunctionCollection.cpp similarity index 100% rename from Modules/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp rename to Modules/DiffusionCore/mitkDiffusionFunctionCollection.cpp diff --git a/Modules/DiffusionCore/include/mitkDiffusionFunctionCollection.h b/Modules/DiffusionCore/mitkDiffusionFunctionCollection.h similarity index 100% rename from Modules/DiffusionCore/include/mitkDiffusionFunctionCollection.h rename to Modules/DiffusionCore/mitkDiffusionFunctionCollection.h diff --git a/Modules/DiffusionIO/CMakeLists.txt b/Modules/DiffusionIO/CMakeLists.txt index 5723bab..f38cfad 100644 --- a/Modules/DiffusionIO/CMakeLists.txt +++ b/Modules/DiffusionIO/CMakeLists.txt @@ -1,8 +1,8 @@ MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS MitkConnectomics MitkQuantification MitkFiberTracking + DEPENDS MitkConnectomics MitkFiberTracking AUTOLOAD_WITH MitkCore PACKAGE_DEPENDS PUBLIC DCMTK ) diff --git a/Modules/DiffusionIO/files.cmake b/Modules/DiffusionIO/files.cmake index 7af682f..a68e3cd 100644 --- a/Modules/DiffusionIO/files.cmake +++ b/Modules/DiffusionIO/files.cmake @@ -1,42 +1,35 @@ set(CPP_FILES mitkDiffusionModuleActivator.cpp - mitkNrrdTbssImageWriterFactory.cpp - #mitkFiberBundleIOFactory.cpp mitkConnectomicsNetworkReader.cpp mitkConnectomicsNetworkWriter.cpp mitkConnectomicsNetworkCSVWriter.cpp mitkConnectomicsNetworkMatrixWriter.cpp mitkConnectomicsNetworkSerializer.cpp mitkConnectomicsNetworkDefinitions.cpp - mitkNrrdTbssRoiImageIOFactory.cpp - #mitkFiberBundleWriterFactory.cpp - mitkNrrdTbssRoiImageWriterFactory.cpp mitkFiberTrackingObjectFactory.cpp mitkConnectomicsObjectFactory.cpp - mitkQuantificationObjectFactory.cpp - mitkNrrdTbssImageIOFactory.cpp mitkDiffusionIOMimeTypes.cpp mitkFiberBundleDicomReader.cpp mitkFiberBundleDicomWriter.cpp mitkFiberBundleTckReader.cpp mitkFiberBundleTrackVisReader.cpp mitkFiberBundleTrackVisWriter.cpp mitkFiberBundleVtkReader.cpp mitkFiberBundleVtkWriter.cpp mitkFiberBundleSerializer.cpp mitkFiberBundleMapper2D.cpp mitkFiberBundleMapper3D.cpp mitkPeakImageMapper2D.cpp mitkPeakImageMapper3D.cpp mitkTractographyForestReader.cpp mitkTractographyForestWriter.cpp mitkTractographyForestSerializer.cpp mitkPlanarFigureCompositeWriter.cpp mitkPlanarFigureCompositeReader.cpp mitkPlanarFigureCompositeSerializer.cpp ) diff --git a/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp b/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp deleted file mode 100644 index f54b946..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "mitkNrrdTbssImageIOFactory.h" -#include "mitkIOAdapter.h" -#include "mitkNrrdTbssImageReader.h" - -#include "itkVersion.h" - - -namespace mitk -{ - -NrrdTbssImageIOFactory::NrrdTbssImageIOFactory() -{ - typedef NrrdTbssImageReader NrrdTbssVolReaderType; - this->RegisterOverride("mitkIOAdapter", - "mitkNrrdTbssImageReader", - "mitk Tbss Image IO", - true, - itk::CreateObjectFunction >::New()); -} - -NrrdTbssImageIOFactory::~NrrdTbssImageIOFactory() -{ -} - -const char* NrrdTbssImageIOFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* NrrdTbssImageIOFactory::GetDescription() const -{ - return "NrrdTbssImage IO Factory, allows the loading of NRRD Tbss data"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.h b/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.h deleted file mode 100644 index 8808d92..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssImageIOFactory.h +++ /dev/null @@ -1,63 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ -#ifndef __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__ -#define __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__ - -#ifdef _MSC_VER -#pragma warning ( disable : 4786 ) -#endif - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -namespace mitk -{ -//##Documentation -//## @brief Create instances of NrrdDiffusionImageReader objects using an object factory. -//## -class NrrdTbssImageIOFactory : public itk::ObjectFactoryBase -{ -public: - /** Standard class typedefs. */ - typedef NrrdTbssImageIOFactory Self; - typedef itk::ObjectFactoryBase Superclass; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - /** Class methods used to interface with the registered factories. */ - const char* GetITKSourceVersion(void) const override; - const char* GetDescription(void) const override; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self); - static NrrdTbssImageIOFactory* FactoryNew() { return new NrrdTbssImageIOFactory;} - /** Run-time type information (and related methods). */ - itkTypeMacro(NrrdTbssImageIOFactory, ObjectFactoryBase); - -protected: - NrrdTbssImageIOFactory(); - ~NrrdTbssImageIOFactory() override; - -private: - NrrdTbssImageIOFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - - -} // end namespace mitk - -#endif // __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__ diff --git a/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp b/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp deleted file mode 100644 index 50515ff..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp +++ /dev/null @@ -1,50 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "mitkNrrdTbssImageWriterFactory.h" - -#include "itkCreateObjectFunction.h" -#include "itkVersion.h" - -#include - -namespace mitk -{ - -NrrdTbssImageWriterFactory::NrrdTbssImageWriterFactory() -{ - this->RegisterOverride("IOWriter", - "NrrdTbssImageWriter", - "NrrdTbssImage Writer", - true, - itk::CreateObjectFunction< mitk::NrrdTbssImageWriter >::New()); -} - -NrrdTbssImageWriterFactory::~NrrdTbssImageWriterFactory() -{ -} - -const char* NrrdTbssImageWriterFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* NrrdTbssImageWriterFactory::GetDescription() const -{ - return "NrrdTbssImageWriterFactory"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.h b/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.h deleted file mode 100644 index a9189dd..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssImageWriterFactory.h +++ /dev/null @@ -1,54 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED -#define NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -namespace mitk -{ - -class NrrdTbssImageWriterFactory : public itk::ObjectFactoryBase -{ -public: - - mitkClassMacroItkParent( mitk::NrrdTbssImageWriterFactory, itk::ObjectFactoryBase ) - - /** Class methods used to interface with the registered factories. */ - const char* GetITKSourceVersion(void) const override; - const char* GetDescription(void) const override; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self); - -protected: - NrrdTbssImageWriterFactory(); - ~NrrdTbssImageWriterFactory() override; - -private: - NrrdTbssImageWriterFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - -} // end namespace mitk - -#endif // NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED - - - diff --git a/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp b/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp deleted file mode 100644 index 7d81733..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "mitkNrrdTbssRoiImageIOFactory.h" -#include "mitkIOAdapter.h" -#include "mitkNrrdTbssRoiImageReader.h" - -#include "itkVersion.h" - - -namespace mitk -{ - -NrrdTbssRoiImageIOFactory::NrrdTbssRoiImageIOFactory() -{ - typedef NrrdTbssRoiImageReader NrrdTbssRoiVolReaderType; - this->RegisterOverride("mitkIOAdapter", - "mitkNrrdTbssRoiImageReader", - "mitk Tbss Image IO", - true, - itk::CreateObjectFunction >::New()); -} - -NrrdTbssRoiImageIOFactory::~NrrdTbssRoiImageIOFactory() -{ -} - -const char* NrrdTbssRoiImageIOFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* NrrdTbssRoiImageIOFactory::GetDescription() const -{ - return "NrrdTbssImage IO Factory, allows the loading of NRRD Tbss data"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h b/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h deleted file mode 100644 index 07bcdf3..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h +++ /dev/null @@ -1,63 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ -#ifndef __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_H_HEADER__ -#define __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_H_HEADER__ - -#ifdef _MSC_VER -#pragma warning ( disable : 4786 ) -#endif - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -namespace mitk -{ -//##Documentation -//## @brief Create instances of NrrdDiffusionImageReader objects using an object factory. -//## -class NrrdTbssRoiImageIOFactory : public itk::ObjectFactoryBase -{ -public: - /** Standard class typedefs. */ - typedef NrrdTbssRoiImageIOFactory Self; - typedef itk::ObjectFactoryBase Superclass; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - /** Class methods used to interface with the registered factories. */ - const char* GetITKSourceVersion(void) const override; - const char* GetDescription(void) const override; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self); - static NrrdTbssRoiImageIOFactory* FactoryNew() { return new NrrdTbssRoiImageIOFactory;} - /** Run-time type information (and related methods). */ - itkTypeMacro(NrrdTbssRoiImageIOFactory, ObjectFactoryBase); - -protected: - NrrdTbssRoiImageIOFactory(); - ~NrrdTbssRoiImageIOFactory() override; - -private: - NrrdTbssRoiImageIOFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - - -} // end namespace mitk - -#endif // __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__ diff --git a/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp b/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp deleted file mode 100644 index 348267d..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp +++ /dev/null @@ -1,50 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "mitkNrrdTbssRoiImageWriterFactory.h" - -#include "itkCreateObjectFunction.h" -#include "itkVersion.h" - -#include - -namespace mitk -{ - -NrrdTbssRoiImageWriterFactory::NrrdTbssRoiImageWriterFactory() -{ - this->RegisterOverride("IOWriter", - "NrrdTbssRoiImageWriter", - "NrrdTbssRoiImage ROI Writer", - true, - itk::CreateObjectFunction< mitk::NrrdTbssRoiImageWriter >::New()); -} - -NrrdTbssRoiImageWriterFactory::~NrrdTbssRoiImageWriterFactory() -{ -} - -const char* NrrdTbssRoiImageWriterFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* NrrdTbssRoiImageWriterFactory::GetDescription() const -{ - return "NrrdTbssRoiImageWriterFactory"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h b/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h deleted file mode 100644 index 665b034..0000000 --- a/Modules/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h +++ /dev/null @@ -1,54 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef NRRDTBSSROIIMAGE_WRITERFACTORY_H_HEADER_INCLUDED -#define NRRDTBSSROIIMAGE_WRITERFACTORY_H_HEADER_INCLUDED - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -namespace mitk -{ - -class NrrdTbssRoiImageWriterFactory : public itk::ObjectFactoryBase -{ -public: - - mitkClassMacroItkParent( mitk::NrrdTbssRoiImageWriterFactory, itk::ObjectFactoryBase ) - - /** Class methods used to interface with the registered factories. */ - const char* GetITKSourceVersion(void) const override; - const char* GetDescription(void) const override; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self) - -protected: - NrrdTbssRoiImageWriterFactory(); - ~NrrdTbssRoiImageWriterFactory() override; - -private: - NrrdTbssRoiImageWriterFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - -} // end namespace mitk - -#endif // NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED - - - diff --git a/Modules/DiffusionIO/mitkQuantificationObjectFactory.cpp b/Modules/DiffusionIO/mitkQuantificationObjectFactory.cpp deleted file mode 100644 index e1679ec..0000000 --- a/Modules/DiffusionIO/mitkQuantificationObjectFactory.cpp +++ /dev/null @@ -1,172 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "mitkQuantificationObjectFactory.h" - -#include "mitkTbssImageMapper.h" - -#include "mitkNrrdTbssImageIOFactory.h" -#include "mitkNrrdTbssImageWriterFactory.h" -#include "mitkNrrdTbssImageWriter.h" - -#include "mitkNrrdTbssRoiImageIOFactory.h" -#include "mitkNrrdTbssRoiImageWriterFactory.h" -#include "mitkNrrdTbssRoiImageWriter.h" - -#include "mitkGPUVolumeMapper3D.h" - -typedef char TbssRoiPixelType; -typedef float TbssPixelType; -typedef int TbssGradientPixelType; - -mitk::QuantificationObjectFactory::QuantificationObjectFactory() - : CoreObjectFactoryBase() - , m_NrrdTbssImageIOFactory(mitk::NrrdTbssImageIOFactory::New().GetPointer()) - , m_NrrdTbssRoiImageIOFactory(mitk::NrrdTbssRoiImageIOFactory::New().GetPointer()) - , m_NrrdTbssImageWriterFactory(mitk::NrrdTbssImageWriterFactory::New().GetPointer()) - , m_NrrdTbssRoiImageWriterFactory(mitk::NrrdTbssRoiImageWriterFactory::New().GetPointer()) -{ - - static bool alreadyDone = false; - if (!alreadyDone) - { - MITK_DEBUG << "QuantificationObjectFactory c'tor" << std::endl; - - itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssImageIOFactory); - itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageIOFactory); - - itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssImageWriterFactory); - itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageWriterFactory); - - m_FileWriters.push_back( NrrdTbssImageWriter::New().GetPointer() ); - m_FileWriters.push_back( NrrdTbssRoiImageWriter::New().GetPointer() ); - - CreateFileExtensionsMap(); - - alreadyDone = true; - } - -} - -mitk::QuantificationObjectFactory::~QuantificationObjectFactory() -{ - itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssImageIOFactory); - itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageIOFactory); - - itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssImageWriterFactory); - itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssRoiImageWriterFactory); -} - -mitk::Mapper::Pointer mitk::QuantificationObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) -{ - mitk::Mapper::Pointer newMapper=nullptr; - - if ( id == mitk::BaseRenderer::Standard2D ) - { - std::string classname = "TbssRoiImage"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - newMapper = mitk::ImageVtkMapper2D::New(); - newMapper->SetDataNode(node); - } - - classname = "TbssImage"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - newMapper = mitk::TbssImageMapper::New(); - newMapper->SetDataNode(node); - } - - } - else if ( id == mitk::BaseRenderer::Standard3D ) - { - std::string classname = "TbssImage"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - newMapper = mitk::TbssImageMapper::New(); - newMapper->SetDataNode(node); - } - - } - - return newMapper; -} - -void mitk::QuantificationObjectFactory::SetDefaultProperties(mitk::DataNode* node) -{ - std::string classname = "TbssRoiImage"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - mitk::ImageVtkMapper2D::SetDefaultProperties(node); - } - - classname = "TbssImage"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - mitk::TbssImageMapper::SetDefaultProperties(node); - mitk::GPUVolumeMapper3D::SetDefaultProperties(node); - } -} - -const char* mitk::QuantificationObjectFactory::GetFileExtensions() -{ - std::string fileExtension; - this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); - return fileExtension.c_str(); -}; - -mitk::CoreObjectFactoryBase::MultimapType mitk::QuantificationObjectFactory::GetFileExtensionsMap() -{ - return m_FileExtensionsMap; -} - -const char* mitk::QuantificationObjectFactory::GetSaveFileExtensions() -{ - std::string fileExtension; - this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); - return fileExtension.c_str(); -}; - -mitk::CoreObjectFactoryBase::MultimapType mitk::QuantificationObjectFactory::GetSaveFileExtensionsMap() -{ - return m_SaveFileExtensionsMap; -} - -void mitk::QuantificationObjectFactory::CreateFileExtensionsMap() -{ - m_FileExtensionsMap.insert(std::pair("*.tbss", "TBSS data")); - m_FileExtensionsMap.insert(std::pair("*.roi", "TBSS ROI data")); - - m_SaveFileExtensionsMap.insert(std::pair("*.tbss", "TBSS data")); - m_SaveFileExtensionsMap.insert(std::pair("*.roi", "TBSS ROI data")); -} - -struct RegisterQuantificationObjectFactory{ - RegisterQuantificationObjectFactory() - : m_Factory( mitk::QuantificationObjectFactory::New() ) - { - mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory ); - } - - ~RegisterQuantificationObjectFactory() - { - mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory ); - } - - mitk::QuantificationObjectFactory::Pointer m_Factory; -}; - -static RegisterQuantificationObjectFactory registerQuantificationObjectFactory; diff --git a/Modules/DiffusionIO/mitkQuantificationObjectFactory.h b/Modules/DiffusionIO/mitkQuantificationObjectFactory.h deleted file mode 100644 index 382adf4..0000000 --- a/Modules/DiffusionIO/mitkQuantificationObjectFactory.h +++ /dev/null @@ -1,49 +0,0 @@ -#ifndef MITKQUANTIFICATIONOBJECTFACTORY_H -#define MITKQUANTIFICATIONOBJECTFACTORY_H - - -#include "mitkCoreObjectFactory.h" - -namespace mitk { - -class QuantificationObjectFactory : public CoreObjectFactoryBase -{ - public: - mitkClassMacro(QuantificationObjectFactory,CoreObjectFactoryBase) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - ~QuantificationObjectFactory() override; - - Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId) override; - - void SetDefaultProperties(mitk::DataNode* node) override; - - const char* GetFileExtensions() override; - - mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override; - - const char* GetSaveFileExtensions() override; - - mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override; - -protected: - QuantificationObjectFactory(); - private: - void CreateFileExtensionsMap(); - std::string m_ExternalFileExtensions; - std::string m_InternalFileExtensions; - std::string m_SaveFileExtensions; - MultimapType m_FileExtensionsMap; - MultimapType m_SaveFileExtensionsMap; - - itk::ObjectFactoryBase::Pointer m_NrrdTbssImageIOFactory; - itk::ObjectFactoryBase::Pointer m_NrrdTbssRoiImageIOFactory; - - itk::ObjectFactoryBase::Pointer m_NrrdTbssImageWriterFactory; - itk::ObjectFactoryBase::Pointer m_NrrdTbssRoiImageWriterFactory; -}; - -} - -#endif // MITKQUANTIFICATIONOBJECTFACTORY_H diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake index 67b692a..ac97051 100644 --- a/Modules/ModuleList.cmake +++ b/Modules/ModuleList.cmake @@ -1,9 +1,8 @@ set(MITK_MODULES DiffusionCore FiberTracking Connectomics - Quantification MriSimulation DiffusionIO DiffusionCmdApps ) diff --git a/Modules/Quantification/Algorithms/itkSkeletonizationFilter.h b/Modules/Quantification/Algorithms/itkSkeletonizationFilter.h deleted file mode 100644 index 5b479f9..0000000 --- a/Modules/Quantification/Algorithms/itkSkeletonizationFilter.h +++ /dev/null @@ -1,119 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef ITKSKELETONIZATIONFILTER_H_ -#define ITKSKELETONIZATIONFILTER_H_ - -#include "itkImageToImageFilter.h" -#include "itkImage.h" -#include "mitkImage.h" -#include - -namespace itk -{ - -/** - * \brief Skeletonization part of the TBSS pipeline - * - * This class takes a 3D image which is typically the mean FA image that is calculated after registration by the FSL TBSS pipeline (see - * http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index for the user manual) and performs the non-maximum-suppression to create a white matter skeleton. - * - * - * The skeletonization algorithm is described in Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 ) - */ - - -template < class TInputImage, class TOutputImage > -class SkeletonizationFilter : public ImageToImageFilter -{ - - -public: - - /** Typedef for input ImageType. */ - typedef TInputImage InputImageType; - - typedef itk::CovariantVector VectorType; - - typedef itk::Image VectorImageType; - - - /** Typedef for output ImageType. */ - typedef TOutputImage OutputImageType; - - typedef itk::VectorImage GradientImageType; - - - /** */ - typedef SkeletonizationFilter Self; - - /** Superclass */ - typedef ImageToImageFilter Superclass; - - typedef SmartPointer Pointer; - - typedef SmartPointer ConstPointer; - - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - /** \brief Performs the work */ - void GenerateData() override; - - - /** \brief Output the gradient image as itkVectorImage - * - * Output the gradient image by first converting it to an itk vector image - */ - GradientImageType::Pointer GetGradientImage(); - - /** \brief Output the gradient image as an itkImage containing vector */ - VectorImageType::Pointer GetVectorImage() - { - return m_DirectionImage; - } - - - - -protected: - - SkeletonizationFilter(); - - ~SkeletonizationFilter() override; - - VectorImageType::Pointer m_DirectionImage; - - int round(float x) - { - if (x>0.0) return ((int) (x+0.5)); - else return ((int) (x-0.5)); - } - - -protected: - - - -}; - -} - -#ifndef ITK_MANUAL_INSTANTIATION -#include "itkSkeletonizationFilter.txx" -#endif - -#endif diff --git a/Modules/Quantification/Algorithms/itkSkeletonizationFilter.txx b/Modules/Quantification/Algorithms/itkSkeletonizationFilter.txx deleted file mode 100644 index 1933a12..0000000 --- a/Modules/Quantification/Algorithms/itkSkeletonizationFilter.txx +++ /dev/null @@ -1,306 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ -#ifndef _itkSkeletonizationFilter_txx -#define _itkSkeletonizationFilter_txx - -#include "itkSkeletonizationFilter.h" -#include "mitkProgressBar.h" -#include -#include - -namespace itk -{ - - template< class TInputImage, class TOutputImage > - SkeletonizationFilter::SkeletonizationFilter() - { - m_DirectionImage = VectorImageType::New(); - } - - template< class TInputImage, class TOutputImage > - SkeletonizationFilter::~SkeletonizationFilter() - { - - } - - - - - template< class TInputImage, class TOutputImage > - void SkeletonizationFilter::GenerateData() - { - //----------------------------------------------------------------------// - // Progress bar // - //----------------------------------------------------------------------// - mitk::ProgressBar::GetInstance()->AddStepsToDo( 3 ); - - std::cout << "Skeletonize" << std::endl; - - - const InputImageType* faImage = this->GetInput(); - typename InputImageType::SizeType size = faImage->GetRequestedRegion().GetSize(); - - //typename RealImageType::SizeType size = m_FaImage->GetRequestedRegion().GetSize(); - - m_DirectionImage->SetRegions(faImage->GetRequestedRegion()); - m_DirectionImage->SetDirection(faImage->GetDirection()); - m_DirectionImage->SetSpacing(faImage->GetSpacing()); - m_DirectionImage->SetOrigin(faImage->GetOrigin()); - m_DirectionImage->Allocate(); - m_DirectionImage->FillBuffer(0.0); - - - for(unsigned int z=1; zGetPixel(ix); - - if(theval != 0) - { - - /* Calculate point of gravity. We will consider each 3x3x3 neighbourhood as a unit cube. The center - * point of each voxel will be a multiplicative of 1/6. The center of the unit cube is 3/6 = 1/2/ - */ - - float cogX = 0.0; float cogY = 0.0; float cogZ = 0.0; float sum = 0.0; float l; - int vecX = 0; int vecY = 0; int vecZ = 0; - - for(int dz=-1; dz<=1; dz++) for(int dy=-1; dy<=1; dy++) for(int dx=-1; dx<=1;dx++) - { - typename InputImageType::IndexType p; - p[0] = x+dx; p[1] = y+dy; p[2] = z+dz; - float mass = faImage->GetPixel(p); - - sum += mass; - cogX += (float)dx*mass; cogY += (float)dy*mass; cogZ += (float)dz*mass; - } - - cogX /= sum; cogY /= sum; cogZ /= sum; - l = sqrt(cogX*cogX + cogY*cogY + cogZ*cogZ); - - if (l > 0.1) /* is CofG far enough away from centre voxel? */ - { - vecX = std::max(std::min(round(cogX/l),1),-1); - vecY = std::max(std::min(round(cogY/l),1),-1); - vecZ = std::max(std::min(round(cogZ/l),1),-1); - } - else - // Find direction of max curvature - { - - float maxcost=0, centreval=2*theval; - for(int zz=0; zz<=1; zz++) // note - starts at zero as we're only searching half the voxels - { - for(int yy=-1; yy<=1; yy++) - { - for(int xx=-1; xx<=1; xx++) - { - if ( (zz==1) || (yy==1) || ((yy==0)&&(xx==1)) ) - { - float weighting = pow( (float)(xx*xx+yy*yy+zz*zz) , (float)-0.7 ); // power is arbitrary: maybe test other functions here - - - typename InputImageType::IndexType i,j; - i[0] = x+xx; i[1] = y+yy; i[2] = z+zz; - j[0] = x-xx; j[1] = y-yy; j[2] = z-zz; - float cost = weighting * ( centreval - - (float)faImage->GetPixel(i) - - (float)faImage->GetPixel(j)); - - if (cost>maxcost) - { - maxcost=cost; - vecX=xx; - vecY=yy; - vecZ=zz; - } - } - } - } - } - } - - VectorType vec; - vec[0] = vecX; vec[1] = vecY; vec[2]=vecZ; - m_DirectionImage->SetPixel(ix, vec); - - } - } - - mitk::ProgressBar::GetInstance()->Progress(); - - - // Smooth m_DirectionImage and store in directionSmoothed by finding the - // mode in a 3*3 neighbourhoud - VectorImageType::Pointer directionSmoothed = VectorImageType::New(); - directionSmoothed->SetRegions(faImage->GetRequestedRegion()); - directionSmoothed->SetDirection(faImage->GetDirection()); - directionSmoothed->SetSpacing(faImage->GetSpacing()); - directionSmoothed->SetOrigin(faImage->GetOrigin()); - directionSmoothed->Allocate(); - - VectorImageType::PixelType p; - p[0]=0; p[1]=0; p[2]=0; - directionSmoothed->FillBuffer(p); - - - - for(unsigned int z=1; zGetPixel(i); - xxx = v[0]; - yyy = v[1]; - zzz = v[2]; - - localsum[(1+zzz)*9+(1+yyy)*3+1+xxx]++; - localsum[(1-zzz)*9+(1-yyy)*3+1-xxx]++; - } - - for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++) - { - if (localsum[(1+zz)*9+(1+yy)*3+1+xx]>localmax) - { - localmax=localsum[(1+zz)*9+(1+yy)*3+1+xx]; - VectorType v; - v[0] = xx; v[1] = yy; v[2] = zz; - directionSmoothed->SetPixel(ix, v); - } - } - - delete[] localsum; - - } - - m_DirectionImage = directionSmoothed; - - mitk::ProgressBar::GetInstance()->Progress(); - - // Do non-max-suppression in the direction of perp and set as output of the filter - typename OutputImageType::Pointer outputImg = OutputImageType::New(); - outputImg->SetRegions(faImage->GetRequestedRegion()); - outputImg->SetDirection(faImage->GetDirection()); - outputImg->SetSpacing(faImage->GetSpacing()); - outputImg->SetOrigin(faImage->GetOrigin()); - outputImg->Allocate(); - outputImg->FillBuffer(0.0); - - for(unsigned int z=1; zGetPixel(ix); - VectorType v = directionSmoothed->GetPixel(ix); - - typename VectorImageType::IndexType i; - - i[0] = x-v[0]; i[1] = y-v[1]; i[2] = z-v[2]; - float min = faImage->GetPixel(i); - - i[0] = x+v[0]; i[1] = y+v[1]; i[2] = z+v[2]; - float plus = faImage->GetPixel(i); - - i[0] = x-2*v[0]; i[1] = y-2*v[1]; i[2] = z-2*v[2]; - float minmin = faImage->GetPixel(i); - - i[0] = x+2*v[0]; i[1] = y+2*v[1]; i[2] = z+2*v[2]; - float plusplus = faImage->GetPixel(i); - - if( ((v[0]!=0) || (v[1]!=0) || (v[2]!=0)) && - theval >= plus && theval > min && theval >= plusplus && theval > minmin ) - { - outputImg->SetPixel(ix, theval); - } - - } - - - - Superclass::SetNthOutput( 0, outputImg ); - mitk::ProgressBar::GetInstance()->Progress(); - - } - - - - // Can provide a vector image to visualize the gradient image used in the search for local maxima. - template< class TInputImage, class TOutputImage > - itk::VectorImage::Pointer SkeletonizationFilter::GetGradientImage() - { - GradientImageType::Pointer gradImg = GradientImageType::New(); - - if(m_DirectionImage.IsNotNull()) - { - gradImg->SetSpacing(m_DirectionImage->GetSpacing()); - gradImg->SetOrigin(m_DirectionImage->GetOrigin()); - gradImg->SetDirection(m_DirectionImage->GetDirection()); - gradImg->SetRegions(m_DirectionImage->GetLargestPossibleRegion().GetSize()); - gradImg->SetVectorLength(3); - gradImg->Allocate(); - - - VectorImageType::SizeType size = m_DirectionImage->GetLargestPossibleRegion().GetSize(); - - for(std::size_t i=0; i ix; - ix[0] = i; - ix[1] = j; - ix[2] = k; - - VectorType vec = m_DirectionImage->GetPixel(ix); - - itk::VariableLengthVector pixel; - pixel.SetSize(3); - pixel.SetElement(0, vec.GetElement(0)); - pixel.SetElement(1, vec.GetElement(1)); - pixel.SetElement(2, vec.GetElement(2)); - - gradImg->SetPixel(ix, pixel); - - } - } - } - - } - - - - - return gradImg; - } - -} -#endif // _itkSkeletonizationFilter_txx diff --git a/Modules/Quantification/Algorithms/mitkTractAnalyzer.cpp b/Modules/Quantification/Algorithms/mitkTractAnalyzer.cpp deleted file mode 100644 index 7d0b7b9..0000000 --- a/Modules/Quantification/Algorithms/mitkTractAnalyzer.cpp +++ /dev/null @@ -1,216 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkTractAnalyzer_cpp -#define __mitkTractAnalyzer_cpp - - -#include -#include -#include - -#include - - -#include -#include - -#include -#include - -namespace mitk { - - TractAnalyzer::TractAnalyzer() { } - - - void TractAnalyzer::MakeRoi() - { - - m_CostSum = 0.0; - - int n = 0; - if(m_PointSetNode.IsNotNull()) - { - n = m_PointSetNode->GetSize(); - if(n==0) - { - mitkThrow() << "No points have been set yet."; - } - } - else{ - mitkThrow() << "No points have been set yet."; - } - - std::string pathDescription = ""; - std::vector< itk::Index<3> > totalPath; - - if(n>0) - { - for(int i=0; iProgress(); - - mitk::Point3D p = m_PointSetNode->GetPoint(i); - mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1); - - - itk::Index<3> startPoint; - itk::Index<3> endPoint; - - m_InputImage->GetGeometry()->WorldToIndex(p,startPoint); - m_InputImage->GetGeometry()->WorldToIndex(p2,endPoint); - - MITK_INFO << "create roi"; - - std::vector< itk::Index<3> > path = CreateSegment(startPoint, endPoint); - - for(auto it = path.begin(); - it != path.end(); it++) - { - itk::Index<3> ix = *it; - - if (!(ix==endPoint)) - { - mitk::ProgressBar::GetInstance()->Progress(); - - totalPath.push_back(ix); - std::stringstream ss; - ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n"; - pathDescription += ss.str(); - } - else - { - // Only when dealing with the last segment the last point should be added. This one will not occur - // as the first point of the next roi segment. - if(i == (n-2)) - { - totalPath.push_back(endPoint); - std::stringstream ss; - ss << endPoint[0] << " " << endPoint[1] << " " << endPoint[2] << "\n"; - pathDescription += ss.str(); - } - - } - - } - - } - - - // save pathDescription to m_PathDescription - m_PathDescription = pathDescription; - - FloatImageType::Pointer itkImg = FloatImageType::New(); - mitk::CastToItkImage(m_InputImage, itkImg); - - CharImageType::Pointer roiImg = CharImageType::New(); - roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize()); - roiImg->SetOrigin(itkImg->GetOrigin()); - roiImg->SetSpacing(itkImg->GetSpacing()); - roiImg->SetDirection(itkImg->GetDirection()); - roiImg->Allocate(); - roiImg->FillBuffer(0); - - - std::vector< itk::Index<3> > roi; - - std::vector< itk::Index<3> >::iterator it; - for(it = totalPath.begin(); - it != totalPath.end(); - it++) - { - itk::Index<3> ix = *it; - roiImg->SetPixel(ix, 1); - roi.push_back(ix); - } - - - m_TbssRoi = mitk::TbssRoiImage::New(); - - m_TbssRoi->SetRoi(roi); - - m_TbssRoi->SetImage(roiImg); - - m_TbssRoi->InitializeFromImage(); - - - - } - - - - } - - - - std::vector< itk::Index<3> > TractAnalyzer::CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint) - { - - typedef itk::ShortestPathImageFilter ShortestPathFilterType; - typedef itk::ShortestPathCostFunctionTbss CostFunctionType; - - - FloatImageType::Pointer meanSkeleton; - - mitk::CastToItkImage(m_InputImage, meanSkeleton); - - // Only use the mitk image - - - - if(meanSkeleton) - { - CostFunctionType::Pointer costFunction = CostFunctionType::New(); - costFunction->SetImage(meanSkeleton); - costFunction->SetStartIndex(startPoint); - costFunction->SetEndIndex(endPoint); - costFunction->SetThreshold(m_Threshold); - - ShortestPathFilterType::Pointer pathFinder = ShortestPathFilterType::New(); - pathFinder->SetCostFunction(costFunction); - pathFinder->SetFullNeighborsMode(true); - pathFinder->SetGraph_fullNeighbors(true); - //pathFinder->SetCalcMode(ShortestPathFilterType::A_STAR); - pathFinder->SetInput(meanSkeleton); - pathFinder->SetStartIndex(startPoint); - pathFinder->SetEndIndex(endPoint); - pathFinder->Update(); - - double segmentCost = 0.0; - std::vector< itk::Index<3> > path = pathFinder->GetVectorPath(); - - for(unsigned int i=0; i ix1 = path[i]; - itk::Index<3> ix2 = path[i+1]; - - segmentCost += costFunction->GetCost(ix1, ix2); - } - - m_CostSum += segmentCost; - - - return pathFinder->GetVectorPath(); - - - } - return std::vector< itk::Index<3> >(); - } - - -} -#endif diff --git a/Modules/Quantification/Algorithms/mitkTractAnalyzer.h b/Modules/Quantification/Algorithms/mitkTractAnalyzer.h deleted file mode 100644 index 6abdbea..0000000 --- a/Modules/Quantification/Algorithms/mitkTractAnalyzer.h +++ /dev/null @@ -1,155 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef __mitkTractAnalyzer_h_ -#define __mitkTractAnalyzer_h_ - -#include "MitkQuantificationExports.h" -#include -#include "mitkImage.h" -#include "mitkImageCast.h" - -#include -#include - - -namespace mitk{ -/** - * \brief Creates a region of interest for tract-specific analysis of existing TBSS data - * - * This class needs a 3D image, which is the mean FA skeleton as produced by the standard TBSS pipeline of FSL. - * How this dataset can be obtained can be found in the TBSS user manual: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index - * Furthermore, this class requires a user-defined point set defining the points through which the region of interest should pass. - * The output is a TBSS roi image, which is a binary images defining the roi and metadata containing indices - * that can be used for plotting graphs using the QmitkTbssRoiAnalysisWidget - */ - - -class MITKQUANTIFICATION_EXPORT TractAnalyzer -{ - -public: - - - TractAnalyzer(); - ~TractAnalyzer() {} - - - /** Image type definitions */ - typedef itk::Image CharImageType; - typedef itk::Image FloatImageType; - - - /** \brief Main method for region of interest calculation - * - * A region of interest is calculated adding the segments between the points on the ROI - * that was specified by the user. - */ - void MakeRoi(); - - - - /** \brief Returns the TbssRoiImage **/ - mitk::TbssRoiImage::Pointer GetRoiImage() - { - return m_TbssRoi; - } - - - /** \brief Sets the input image - * - * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated - * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS). - */ - void SetInputImage(mitk::Image::Pointer inputImage) - { - m_InputImage = inputImage; - } - - - /** \brief Sets the user-defined point set - * - * Set the user-defined point sets. The region of interest must pass through these points. - */ - void SetPointSet(mitk::PointSet::Pointer pointSet) - { - m_PointSetNode = pointSet; - } - - - /** \brief Sets a lower bound for the threshold. - * - * Low fractional anisotropy values can indicate partial volume of non white matter tissue. - * This thresholds limits the search for a region of interest to voxels with a minimum value. - */ - void SetThreshold(double threshold) - { - m_Threshold = threshold; - } - - - - /** \brief Returns a string with the indices of points on the region of interest - * - * The region of interest calculated by the TractAnalyzer contains a list of ITK indices. - * This method returns a string containing these indices for display in the GUI - */ - std::string GetPathDescription() - { - return m_PathDescription; - } - - itkGetMacro(CostSum, double) - -protected: - - - - /** \brief Calculates a segment of the region of interest - * - * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated - * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS). - */ - std::vector< itk::Index<3> > CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint); - - - /** \brief Output TbssRoiImage */ - mitk::TbssRoiImage::Pointer m_TbssRoi; - - /** \brief Inputimage */ - mitk::Image::Pointer m_InputImage; - - /** \brief Threshold for ROI search */ - double m_Threshold; - - /** \brief User defined point set */ - mitk::PointSet::Pointer m_PointSetNode; - - /** \brief Path description in as string for display in GUI */ - std::string m_PathDescription; - - /** \brief Total cost of the path */ - double m_CostSum; - - -private: - -}; - -} - -#endif //__itkTractAnalyzer_h_ diff --git a/Modules/Quantification/CMakeLists.txt b/Modules/Quantification/CMakeLists.txt deleted file mode 100644 index 67367c3..0000000 --- a/Modules/Quantification/CMakeLists.txt +++ /dev/null @@ -1,14 +0,0 @@ -# With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled -if(APPLE) - mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) -endif() - -#DiffusionImaging/Quantification -MITK_CREATE_MODULE( - SUBPROJECTS MITK-Diffusion - INCLUDE_DIRS Algorithms IODataStructures IODataStructures/TbssImages Rendering ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS MitkDiffusionCore MitkFiberTracking MitkGraphAlgorithms - PACKAGE_DEPENDS ITK|ITKThresholding -) - -add_subdirectory(Testing) diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp deleted file mode 100644 index e276c48..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp +++ /dev/null @@ -1,295 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssImageReader_cpp -#define __mitkNrrdTbssImageReader_cpp - -#include "mitkNrrdTbssImageReader.h" - -#include "itkImageFileReader.h" -#include "itkMetaDataObject.h" -#include "itkNrrdImageIO.h" -#include "itkNiftiImageIO.h" - -#include - -#include -#include - -#include "itksys/SystemTools.hxx" - - -namespace mitk -{ - void NrrdTbssImageReader - ::GenerateData() - { - - // Since everything is completely read in GenerateOutputInformation() it is stored - // in a cache variable. A timestamp is associated. - // If the timestamp of the cache variable is newer than the MTime, we only need to - // assign the cache variable to the DataObject. - // Otherwise, the tree must be read again from the file and OuputInformation must - // be updated! - if ( ( ! m_OutputCache ) || ( this->GetMTime( ) > m_CacheTime.GetMTime( ) ) ) - { - this->GenerateOutputInformation(); - itkWarningMacro("Cache regenerated!"); - } - - if (!m_OutputCache) - { - itkWarningMacro("Tree cache is empty!") - } - - - static_cast(this->GetPrimaryOutput()) - ->SetImage(m_OutputCache->GetImage()); - static_cast(this->GetPrimaryOutput()) - ->SetGroupInfo(m_OutputCache->GetGroupInfo()); - - static_cast(this->GetPrimaryOutput()) - ->InitializeFromVectorImage(); - - } - - void NrrdTbssImageReader - ::GenerateOutputInformation() - { - OutputType::Pointer outputForCache = OutputType::New(); - - if ( m_FileName == "") - { - throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!"); - } - else - { - try - { - const std::string& locale = "C"; - const std::string& currLocale = setlocale( LC_ALL, nullptr ); - - if ( locale.compare(currLocale)!=0 ) - { - try - { - MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, nullptr) << " to '" << locale << "'"; - setlocale(LC_ALL, locale.c_str()); - } - catch(...) - { - MITK_INFO << "Could not set locale " << locale; - } - } - - - MITK_INFO << "NrrdTbssImageReader READING IMAGE INFORMATION"; - ImageType::Pointer img; - - std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); - ext = itksys::SystemTools::LowerCase(ext); - if (ext == ".tbss") - { - typedef itk::ImageFileReader FileReaderType; - FileReaderType::Pointer reader = FileReaderType::New(); - reader->SetFileName(this->m_FileName); - itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); - reader->SetImageIO(io); - - reader->Update(); - img = reader->GetOutput(); - - - MITK_INFO << "NrrdTbssImageReader READING HEADER INFORMATION"; - - - itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary(); - std::vector imgMetaKeys = imgMetaDictionary.GetKeys(); - std::vector::const_iterator itKey = imgMetaKeys.begin(); - std::string metaString; - - - - std::string measurementInfo; - - - std::vector< std::pair > groups; - - for (; itKey != imgMetaKeys.end(); itKey ++) - { - itk::ExposeMetaData (imgMetaDictionary, *itKey, metaString); - - MITK_INFO << *itKey << " ---> " << metaString; - - if (itKey->find("Group_index") != std::string::npos) - { - - std::vector tokens; - this->Tokenize(metaString, tokens, " "); - - - std::pair< std::string, int > p; - - p.first=""; - for (unsigned int i=0; ifind("Measurement info") != std::string::npos) - { - measurementInfo = metaString; - } - - - - - } - - - outputForCache->SetGroupInfo(groups); - outputForCache->SetMeasurementInfo(measurementInfo); - - - } - - - - // This call updates the output information of the associated VesselTreeData - outputForCache->SetImage(img); - - - // Since we have already read the tree, we can store it in a cache variable - // so that it can be assigned to the DataObject in GenerateData(); - m_OutputCache = outputForCache; - m_CacheTime.Modified(); - - try - { - MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, nullptr) << " to '" << currLocale << "'"; - setlocale(LC_ALL, currLocale.c_str()); - } - catch(...) - { - MITK_INFO << "Could not reset locale " << currLocale; - } - } - catch(std::exception& e) - { - MITK_INFO << "Std::Exception while reading file!!"; - MITK_INFO << e.what(); - throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what()); - } - catch(...) - { - MITK_INFO << "Exception while reading file!!"; - throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!"); - } - } - } - - - - const char* NrrdTbssImageReader - ::GetFileName() const - { - return m_FileName.c_str(); - } - - void NrrdTbssImageReader - ::SetFileName(const char* aFileName) - { - m_FileName = aFileName; - } - - const char* NrrdTbssImageReader - ::GetFilePrefix() const - { - return m_FilePrefix.c_str(); - } - - void NrrdTbssImageReader - ::SetFilePrefix(const char* aFilePrefix) - { - m_FilePrefix = aFilePrefix; - } - - const char* NrrdTbssImageReader - ::GetFilePattern() const - { - return m_FilePattern.c_str(); - } - - void NrrdTbssImageReader - ::SetFilePattern(const char* aFilePattern) - { - m_FilePattern = aFilePattern; - } - - bool NrrdTbssImageReader - ::CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern) - { - - // First check the extension - if( filename == "" ) - return false; - - // check if image is serie - if( filePattern != "" && filePrefix != "" ) - return false; - - - std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); - ext = itksys::SystemTools::LowerCase(ext); - - if (ext == ".tbss") - { - itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); - - typedef itk::ImageFileReader FileReaderType; - FileReaderType::Pointer reader = FileReaderType::New(); - reader->SetImageIO(io); - reader->SetFileName(filename); - - try - { - reader->Update(); - } - catch(itk::ExceptionObject e) - { - MITK_INFO << e.GetDescription(); - return false; - } - - - return true; - } - return false; - } - -} //namespace MITK - -#endif diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h deleted file mode 100644 index 8198306..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h +++ /dev/null @@ -1,103 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssImageReader_h -#define __mitkNrrdTbssImageReader_h - -#include "mitkCommon.h" -#include "mitkFileReader.h" -#include "mitkTbssImageSource.h" -#include "itkImage.h" -#include "itkVectorImage.h" -#include "mitkTbssImage.h" - -namespace mitk -{ - - /** \brief - */ - - - class MITKQUANTIFICATION_EXPORT NrrdTbssImageReader : public mitk::TbssImageSource, public FileReader - { - public: - - typedef mitk::TbssImage OutputType; - typedef itk::VectorImage ImageType; - typedef TbssImageSource TbssVolSourceType; - - - - mitkClassMacro( NrrdTbssImageReader, TbssVolSourceType ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - const char* GetFileName() const override; - void SetFileName(const char* aFileName) override; - const char* GetFilePrefix() const override; - void SetFilePrefix(const char* aFilePrefix) override; - const char* GetFilePattern() const override; - void SetFilePattern(const char* aFilePattern) override; - - static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern); - - protected: - - /** Does the real work. */ - void GenerateData() override; - void GenerateOutputInformation() override; - - - std::string m_FileName; - std::string m_FilePrefix; - std::string m_FilePattern; - - std::vector< std::pair > m_GroupInfo; - - OutputType::Pointer m_OutputCache; - itk::TimeStamp m_CacheTime; - - - void Tokenize(const std::string& str, - std::vector& tokens, - const std::string& delimiters = " ") - { - // Skip delimiters at beginning. - std::string::size_type lastPos = str.find_first_not_of(delimiters, 0); - // Find first "non-delimiter". - std::string::size_type pos = str.find_first_of(delimiters, lastPos); - - while (std::string::npos != pos || std::string::npos != lastPos) - { - // Found a token, add it to the vector. - tokens.push_back(str.substr(lastPos, pos - lastPos)); - // Skip delimiters. Note the "not_of" - lastPos = str.find_first_not_of(delimiters, pos); - // Find next "non-delimiter" - pos = str.find_first_of(delimiters, lastPos); - } - } - - - - private: - void operator=(const Self&); //purposely not implemented - }; - -} //namespace MITK - - -#endif // __mitkNrrdTbssImageReader_h diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp deleted file mode 100644 index 0396e6a..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp +++ /dev/null @@ -1,165 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssImageWriter__cpp -#define __mitkNrrdTbssImageWriter__cpp - -#include "mitkNrrdTbssImageWriter.h" -#include "itkMetaDataDictionary.h" -#include "itkMetaDataObject.h" -#include "itkNrrdImageIO.h" -//#include "itkNiftiImageIO.h" -#include "itkImageFileWriter.h" -#include "itksys/SystemTools.hxx" -#include "mitkLexicalCast.h" - -#include -#include - - -mitk::NrrdTbssImageWriter::NrrdTbssImageWriter() - : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) -{ - this->SetNumberOfRequiredInputs( 1 ); -} - -mitk::NrrdTbssImageWriter::~NrrdTbssImageWriter() -{} - - -void mitk::NrrdTbssImageWriter::GenerateData() -{ - m_Success = false; - InputType* input = this->GetInput(); - if (input == nullptr) - { - itkWarningMacro(<<"Sorry, input to NrrdTbssImageWriter is nullptr!"); - return; - } - if ( m_FileName == "" ) - { - itkWarningMacro( << "Sorry, filename has not been set!" ); - return ; - } - - - - itk::VectorImage::Pointer img = input->GetImage(); - - - - - std::string key; - std::string val; - - - /* For the case of a tbss image containing data of the patients: - Save info about the groups and the type of measurement */ - - - - - std::vector< std::pair > groups = input->GetGroupInfo(); - auto it = groups.begin(); - - int i=0; - while(it != groups.end()) - { - std::pair p = *it; - - key = "Group_index_" + boost::lexical_cast(i); - val = " " + p.first + " " + boost::lexical_cast(p.second); - //sprintf( keybuffer, "Group_index_%04d", std::string(i) ); - // sprintf( valbuffer, "%1d %1d", p.first, p.second); - - //std::cout << valbuffer << std::endl; - - //itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer)); - itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),key,val); - it++; - ++i; - } - - key = "Measurement info"; - val = input->GetMeasurementInfo(); - itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),key,val); - - - - - - typedef itk::VectorImage ImageType; - - itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); - io->SetFileType( itk::ImageIOBase::Binary ); - io->UseCompressionOn(); - - - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer nrrdWriter = WriterType::New(); - nrrdWriter->UseInputMetaDataDictionaryOn(); - nrrdWriter->SetInput( img ); - nrrdWriter->SetImageIO(io); - nrrdWriter->SetFileName(m_FileName); - nrrdWriter->UseCompressionOn(); - nrrdWriter->SetImageIO(io); - try - { - nrrdWriter->Update(); - } - catch (const itk::ExceptionObject& e) - { - std::cout << e.GetDescription() << std::endl; - } - - m_Success = true; -} - - - - -void mitk::NrrdTbssImageWriter::SetInput( InputType* tbssVol ) -{ - this->ProcessObject::SetNthInput( 0, tbssVol ); -} - - -mitk::TbssImage* mitk::NrrdTbssImageWriter::GetInput() -{ - if ( this->GetNumberOfInputs() < 1 ) - { - return nullptr; - } - else - { - return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); - } -} - - -std::vector mitk::NrrdTbssImageWriter::GetPossibleFileExtensions() -{ - std::vector possibleFileExtensions; - possibleFileExtensions.push_back(".tbss"); - return possibleFileExtensions; -} - -std::string mitk::NrrdTbssImageWriter::GetSupportedBaseData() const -{ - return TbssImage::GetStaticNameOfClass(); -} - -#endif //__mitkNrrdTbssImageWriter__cpp diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h deleted file mode 100644 index fb5e950..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h +++ /dev/null @@ -1,143 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef _MITK_NRRDTBSSVOL_WRITER__H_ -#define _MITK_NRRDTBSSVOL_WRITER__H_ - -#include -#include -#include -#include "MitkQuantificationExports.h" - -namespace mitk -{ - -/** - * Writes diffusion volumes to a file - * @ingroup Process - */ - -class MITKQUANTIFICATION_EXPORT NrrdTbssImageWriter : public mitk::FileWriterWithInformation -{ -public: - - mitkClassMacro( NrrdTbssImageWriter, mitk::FileWriterWithInformation ) - - mitkWriterMacro - - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - typedef mitk::TbssImage InputType; - - /** - * Sets the filename of the file to write. - * @param FileName the nameInputType of the file to write. - */ - itkSetStringMacro( FileName ) - - /** - * @returns the name of the file to be written to disk. - */ - itkGetStringMacro( FileName ) - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePrefix ) - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePrefix ) - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePattern ) - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePattern ) - - /**image - * Sets the input object for the filter. - * @param input the diffusion volumes to write to file. - */ - using ProcessObject::SetInput; - void SetInput( InputType* input ); - /**itk::VectorImage - * @returns the 0'th input object of the filter. - */ - InputType* GetInput(); - - /** - * Returns false if an error happened during writing - */ - itkGetMacro( Success, bool ) - - /** - * @return possible file extensions for the data type associated with the writer - */ - std::vector GetPossibleFileExtensions() override; - - std::string GetSupportedBaseData() const override; - - // FileWriterWithInformation methods - const char * GetDefaultFilename() override { return "TbssImage.tbss"; } - const char * GetFileDialogPattern() override { return "Tbss Images (*.tbss)"; } - const char * GetDefaultExtension() override { return ".tbss"; } - bool CanWriteBaseDataType(BaseData::Pointer data) override - { - return (dynamic_cast(data.GetPointer()) != nullptr); - } - - - void DoWrite(BaseData::Pointer data) override { - if (CanWriteBaseDataType(data)) { - this->SetInput(dynamic_cast(data.GetPointer())); - this->Update(); - } - } - -protected: - - NrrdTbssImageWriter(); - - ~NrrdTbssImageWriter() override; - - void GenerateData() override; - - std::string m_FileName; - - std::string m_FilePrefix; - - std::string m_FilePattern; - - bool m_Success; - - - - -}; - - -} // end of namespace mitk - - - -#endif diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp deleted file mode 100644 index f3ee7f3..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp +++ /dev/null @@ -1,356 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssRoiReader_cpp -#define __mitkNrrdTbssRoiReader_cpp - -#include "mitkNrrdTbssRoiImageReader.h" - -#include "itkImageFileReader.h" -#include "itkMetaDataObject.h" -#include "itkNrrdImageIO.h" -#include "itkNiftiImageIO.h" - -#include - -#include -#include - -#include "itksys/SystemTools.hxx" - -namespace mitk -{ - - - void NrrdTbssRoiImageReader - ::GenerateData() - { - - try - { - - // Change locale if needed - const std::string& locale = "C"; - const std::string& currLocale = setlocale( LC_ALL, nullptr ); - - if ( locale.compare(currLocale)!=0 ) - { - try - { - MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, nullptr) << " to '" << locale << "'"; - setlocale(LC_ALL, locale.c_str()); - } - catch(...) - { - MITK_INFO << "Could not set locale " << locale; - } - } - - - - // READ IMAGE INFORMATION - const unsigned int MINDIM = 3; - const unsigned int MAXDIM = 4; - - MITK_INFO << "loading " << m_FileName << " via mitk::NrrdTbssImageReader... " << std::endl; - - // Check to see if we can read the file given the name or prefix - if ( m_FileName == "" ) - { - itkWarningMacro( << "Filename is empty!" ) - return; - } - - itk::NrrdImageIO::Pointer imageIO = itk::NrrdImageIO::New(); - imageIO->SetFileName( m_FileName.c_str() ); - imageIO->ReadImageInformation(); - - unsigned int ndim = imageIO->GetNumberOfDimensions(); - - if ( ndim < MINDIM || ndim > MAXDIM ) - { - itkWarningMacro( << "Sorry, only dimensions 3 is supported. The given file has " << ndim << " dimensions!" ) - return; - } - - - itk::ImageIORegion ioRegion( ndim ); - itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize(); - itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex(); - - unsigned int dimensions[ MAXDIM ]; - dimensions[ 0 ] = 0; - dimensions[ 1 ] = 0; - dimensions[ 2 ] = 0; - dimensions[ 3 ] = 0; - - ScalarType spacing[ MAXDIM ]; - spacing[ 0 ] = 1.0f; - spacing[ 1 ] = 1.0f; - spacing[ 2 ] = 1.0f; - spacing[ 3 ] = 1.0f; - - - Point3D origin; - origin.Fill(0); - - unsigned int i; - for ( i = 0; i < ndim ; ++i ) - { - ioStart[ i ] = 0; - ioSize[ i ] = imageIO->GetDimensions( i ); - if(iGetDimensions( i ); - spacing[ i ] = imageIO->GetSpacing( i ); - if(spacing[ i ] <= 0) - spacing[ i ] = 1.0f; - } - if(i<3) - { - origin[ i ] = imageIO->GetOrigin( i ); - } - } - - ioRegion.SetSize( ioSize ); - ioRegion.SetIndex( ioStart ); - - MITK_INFO << "ioRegion: " << ioRegion << std::endl; - imageIO->SetIORegion( ioRegion ); - void* buffer = new unsigned char[imageIO->GetImageSizeInBytes()]; - imageIO->Read( buffer ); - //mitk::Image::Pointer static_cast(this->GetOutput())image = mitk::Image::New(); - if((ndim==4) && (dimensions[3]<=1)) - ndim = 3; - if((ndim==3) && (dimensions[2]<=1)) - ndim = 2; - - static_cast(this->GetPrimaryOutput())->Initialize( MakePixelType(imageIO), ndim, dimensions ); - static_cast(this->GetPrimaryOutput())->SetImportChannel( buffer, 0, Image::ManageMemory ); - - // access direction of itk::Image and include spacing - mitk::Matrix3D matrix; - matrix.SetIdentity(); - unsigned int j, itkDimMax3 = (ndim >= 3? 3 : ndim); - for ( i=0; i < itkDimMax3; ++i) - for( j=0; j < itkDimMax3; ++j ) - matrix[i][j] = imageIO->GetDirection(j)[i]; - - // re-initialize PlaneGeometry with origin and direction - PlaneGeometry* planeGeometry = static_cast - (static_cast - (this->GetPrimaryOutput())->GetSlicedGeometry(0)->GetPlaneGeometry(0)); - planeGeometry->SetOrigin(origin); - planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix); - - // re-initialize SlicedGeometry3D - SlicedGeometry3D* slicedGeometry = static_cast(this->GetPrimaryOutput())->GetSlicedGeometry(0); - slicedGeometry->InitializeEvenlySpaced(planeGeometry, static_cast(this->GetPrimaryOutput())->GetDimension(2)); - slicedGeometry->SetSpacing(spacing); - - // re-initialize TimeGeometry - dynamic_cast(static_cast(this->GetPrimaryOutput())->GetTimeGeometry())->Initialize(slicedGeometry, static_cast(this->GetOutput(0))->GetDimension(3)); - - buffer = nullptr; - MITK_INFO << "number of image components: "<< static_cast(this->GetPrimaryOutput())->GetPixelType().GetNumberOfComponents() << std::endl; - - - - // READ TBSS HEADER INFORMATION - ImageType::Pointer img; - - std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); - ext = itksys::SystemTools::LowerCase(ext); - if (ext == ".roi") - { - typedef itk::ImageFileReader FileReaderType; - FileReaderType::Pointer reader = FileReaderType::New(); - reader->SetFileName(this->m_FileName); - - reader->SetImageIO(imageIO); - reader->Update(); - - img = reader->GetOutput(); - - static_cast(this->GetPrimaryOutput())->SetImage(img); - - itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary(); - ReadRoiInfo(imgMetaDictionary); - - - - } - - - // RESET LOCALE - try - { - MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, nullptr) << " to '" << currLocale << "'"; - setlocale(LC_ALL, currLocale.c_str()); - } - catch(...) - { - MITK_INFO << "Could not reset locale " << currLocale; - } - - MITK_INFO << "...finished!" << std::endl; - - } - catch(std::exception& e) - { - MITK_INFO << "Std::Exception while reading file!!"; - MITK_INFO << e.what(); - throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what()); - } - catch(...) - { - MITK_INFO << "Exception while reading file!!"; - throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!"); - } - - - } - - - - void NrrdTbssRoiImageReader - ::ReadRoiInfo(itk::MetaDataDictionary dict) - { - std::vector imgMetaKeys = dict.GetKeys(); - std::vector::const_iterator itKey = imgMetaKeys.begin(); - std::string metaString; - std::vector< itk::Index<3> > roi; - - for (; itKey != imgMetaKeys.end(); itKey ++) - { - double x,y,z; - itk::Index<3> ix; - itk::ExposeMetaData (dict, *itKey, metaString); - - if (itKey->find("ROI_index") != std::string::npos) - { - MITK_INFO << *itKey << " ---> " << metaString; - sscanf(metaString.c_str(), "%lf %lf %lf\n", &x, &y, &z); - ix[0] = x; ix[1] = y; ix[2] = z; - roi.push_back(ix); - } - else if(itKey->find("preprocessed FA") != std::string::npos) - { - MITK_INFO << *itKey << " ---> " << metaString; - static_cast(this->GetPrimaryOutput())->SetPreprocessedFA(true); - static_cast(this->GetPrimaryOutput())->SetPreprocessedFAFile(metaString); - } - - // Name of structure - if (itKey->find("structure") != std::string::npos) - { - MITK_INFO << *itKey << " ---> " << metaString; - static_cast(this->GetPrimaryOutput())->SetStructure(metaString); - } - } - static_cast(this->GetPrimaryOutput())->SetRoi(roi); - - } - - - const char* NrrdTbssRoiImageReader - ::GetFileName() const - { - return m_FileName.c_str(); - } - - - void NrrdTbssRoiImageReader - ::SetFileName(const char* aFileName) - { - m_FileName = aFileName; - } - - - const char* NrrdTbssRoiImageReader - ::GetFilePrefix() const - { - return m_FilePrefix.c_str(); - } - - - void NrrdTbssRoiImageReader - ::SetFilePrefix(const char* aFilePrefix) - { - m_FilePrefix = aFilePrefix; - } - - - const char* NrrdTbssRoiImageReader - ::GetFilePattern() const - { - return m_FilePattern.c_str(); - } - - - void NrrdTbssRoiImageReader - ::SetFilePattern(const char* aFilePattern) - { - m_FilePattern = aFilePattern; - } - - - bool NrrdTbssRoiImageReader - ::CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern) - { - - // First check the extension - if( filename == "" ) - return false; - - // check if image is serie - if( filePattern != "" && filePrefix != "" ) - return false; - - - std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); - ext = itksys::SystemTools::LowerCase(ext); - - if (ext == ".roi") - { - itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); - - typedef itk::ImageFileReader FileReaderType; - FileReaderType::Pointer reader = FileReaderType::New(); - reader->SetImageIO(io); - reader->SetFileName(filename); - - try - { - reader->Update(); - } - catch(itk::ExceptionObject e) - { - MITK_INFO << e.GetDescription(); - return false; - } - - return true; - - - } - - return false; - } - -} //namespace MITK - -#endif diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h deleted file mode 100644 index d2705dd..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h +++ /dev/null @@ -1,80 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssRoiImageReader_h -#define __mitkNrrdTbssRoiImageReader_h - -#include "mitkCommon.h" -#include "mitkFileReader.h" -#include "mitkTbssRoiImageSource.h" -#include "itkImage.h" -#include "mitkTbssRoiImage.h" - -namespace mitk -{ - - /** \brief - */ - - - class MITKQUANTIFICATION_EXPORT NrrdTbssRoiImageReader : public mitk::TbssRoiImageSource, public FileReader - { - public: - - typedef mitk::TbssRoiImage OutputType; - typedef itk::Image ImageType; - typedef TbssRoiImageSource TbssVolSourceType; - - - - mitkClassMacro( NrrdTbssRoiImageReader, TbssVolSourceType ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - const char* GetFileName() const override; - void SetFileName(const char* aFileName) override; - const char* GetFilePrefix() const override; - void SetFilePrefix(const char* aFilePrefix) override; - const char* GetFilePattern() const override; - void SetFilePattern(const char* aFilePattern) override; - - static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern); - - protected: - - /** Does the real work. */ - void GenerateData() override; - - void ReadRoiInfo(itk::MetaDataDictionary dict); - - std::string m_FileName; - std::string m_FilePrefix; - std::string m_FilePattern; - - OutputType::Pointer m_OutputCache; - itk::TimeStamp m_CacheTime; - - - - private: - void operator=(const Self&); //purposely not implemented - }; - -} //namespace MITK - -//#include "mitkNrrdTbssRoiImageReader.cpp" - -#endif // __mitkNrrdTbssImageReader_h diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp deleted file mode 100644 index 51ca992..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp +++ /dev/null @@ -1,147 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkNrrdTbssRoiImageWriter__cpp -#define __mitkNrrdTbssRoiImageWriter__cpp - -#include "mitkNrrdTbssRoiImageWriter.h" -#include "itkMetaDataDictionary.h" -#include "itkMetaDataObject.h" -#include "itkNrrdImageIO.h" -//#include "itkNiftiImageIO.h" -#include "itkImageFileWriter.h" -#include "itksys/SystemTools.hxx" - -#include -#include - - -mitk::NrrdTbssRoiImageWriter::NrrdTbssRoiImageWriter() - : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) -{ - this->SetNumberOfRequiredInputs( 1 ); -} - - -mitk::NrrdTbssRoiImageWriter::~NrrdTbssRoiImageWriter() -{} - -void mitk::NrrdTbssRoiImageWriter::GenerateData() -{ - m_Success = false; - InputType* input = this->GetInput(); - - if (input == nullptr) - { - itkWarningMacro(<<"Sorry, input to NrrdTbssImageWriter is nullptr!") - return; - } - if ( m_FileName == "" ) - { - itkWarningMacro( << "Sorry, filename has not been set!" ) - return ; - } - - - char keybuffer[512]; - std::stringstream valbuffer; - - std::vector< itk::Index<3> > roi = input->GetRoi(); - - auto it = roi.begin(); - - int i=0; - while(it != roi.end()) - { - itk::Index<3> ix = *it; - - sprintf( keybuffer, "ROI_index_%04d", i ); - valbuffer << ix[0] << " " << ix[1] << " " << ix[2]; - - std::cout << valbuffer.str() << std::endl; - - //input->GetImage()->GetMetaDataDictionary(); - - itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(), std::string(keybuffer), valbuffer.str()); - - it++; - ++i; - } - - std::string structure = input->GetStructure(); - itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(), "structure", structure); - - typedef itk::Image ImageType; - ImageType::Pointer img = input->GetImage(); - - itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); - io->SetFileType( itk::ImageIOBase::Binary ); - io->UseCompressionOn(); - - - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer nrrdWriter = WriterType::New(); - nrrdWriter->UseInputMetaDataDictionaryOn(); - nrrdWriter->SetInput( img ); - nrrdWriter->SetImageIO(io); - nrrdWriter->SetFileName(m_FileName); - // nrrdWriter->UseCompressionOn(); - nrrdWriter->SetImageIO(io); - try - { - nrrdWriter->Update(); - } - catch (const itk::ExceptionObject& e) - { - std::cout << e.GetDescription() << std::endl; - } - - m_Success = true; -} - - -void mitk::NrrdTbssRoiImageWriter::SetInput( InputType* tbssVol ) -{ - this->ProcessObject::SetNthInput( 0, tbssVol ); -} - - -mitk::TbssRoiImage* mitk::NrrdTbssRoiImageWriter::GetInput() -{ - if ( this->GetNumberOfInputs() < 1 ) - { - return nullptr; - } - else - { - return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); - } -} - - -std::vector mitk::NrrdTbssRoiImageWriter::GetPossibleFileExtensions() -{ - std::vector possibleFileExtensions; - possibleFileExtensions.push_back(".roi"); - return possibleFileExtensions; -} - -std::string mitk::NrrdTbssRoiImageWriter::GetSupportedBaseData() const -{ - return TbssRoiImage::GetStaticNameOfClass(); -} - -#endif //__mitkNrrdTbssRoiImageWriter__cpp diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h b/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h deleted file mode 100644 index f879e00..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h +++ /dev/null @@ -1,141 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef _MITK_NRRDTBSSROIVOL_WRITER__H_ -#define _MITK_NRRDTBSSROIVOL_WRITER__H_ - -#include -#include -#include -#include "MitkQuantificationExports.h" - -namespace mitk -{ - -/** - * Writes diffusion volumes to a file - * @ingroup Process - */ - -class MITKQUANTIFICATION_EXPORT NrrdTbssRoiImageWriter : public mitk::FileWriterWithInformation -{ -public: - - typedef itk::Image ImageType; - - mitkClassMacro( NrrdTbssRoiImageWriter, mitk::FileWriterWithInformation ) - - mitkWriterMacro - - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - typedef mitk::TbssRoiImage InputType; - - /** - * Sets the filename of the file to write. - * @param FileName the nameInputType of the file to write. - */ - itkSetStringMacro( FileName ); - - /** - * @returns the name of the file to be written to disk. - */ - itkGetStringMacro( FileName ); - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePrefix ); - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePrefix ); - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePattern ); - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePattern ); - - /**image - * Sets the input object for the filter. - * @param input the diffusion volumes to write to file. - */ - using ProcessObject::SetInput; - void SetInput( InputType* input ); - - /** - * @returns the 0'th input object of the filter. - */ - InputType* GetInput(); - - /** - * Returns false if an error happened during writing - */ - itkGetMacro( Success, bool ); - - /** - * @return possible file extensions for the data type associated with the writer - */ - std::vector GetPossibleFileExtensions() override; - - std::string GetSupportedBaseData() const override; - - // FileWriterWithInformation methods - const char * GetDefaultFilename() override { return "TbssRoiImage.roi"; } - const char * GetFileDialogPattern() override { return "Tbss Roi Images (*.roi)"; } - const char * GetDefaultExtension() override { return ".roi"; } - bool CanWriteBaseDataType(BaseData::Pointer data) override - { - return (dynamic_cast(data.GetPointer()) != nullptr); - } - - - void DoWrite(BaseData::Pointer data) override { - if (CanWriteBaseDataType(data)) { - this->SetInput(dynamic_cast(data.GetPointer())); - this->Update(); - } - } - -protected: - - NrrdTbssRoiImageWriter(); - - ~NrrdTbssRoiImageWriter() override; - - void GenerateData() override; - - std::string m_FileName; - - std::string m_FilePrefix; - - std::string m_FilePattern; - - bool m_Success; - -}; - - -} // end of namespace mitk - -#endif diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp deleted file mode 100644 index 30a2d31..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp +++ /dev/null @@ -1,114 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkTbssImage__cpp -#define __mitkTbssImage__cpp - - -#include "mitkTbssImage.h" -#include "itkImageRegionIterator.h" -#include "itkImageRegionConstIterator.h" -#include "mitkImageCast.h" - - - - -mitk::TbssImage::TbssImage() -{ - -} - - -void mitk::TbssImage::InitializeFromVectorImage() -{ - if(!m_Image) - { - MITK_INFO << "TBSS Image could not be initialized. Set all members first!" << std::endl; - return; - } - - - typedef itk::Image ImgType; - ImgType::Pointer img = ImgType::New(); - img->SetSpacing( m_Image->GetSpacing() ); // Set the image spacing - img->SetOrigin( m_Image->GetOrigin() ); // Set the image origin - img->SetDirection( m_Image->GetDirection() ); // Set the image direction - img->SetLargestPossibleRegion( m_Image->GetLargestPossibleRegion()); - img->SetBufferedRegion( m_Image->GetLargestPossibleRegion() ); - img->Allocate(); - - int vecLength = m_Image->GetVectorLength(); - InitializeByItk( img.GetPointer(), 1, vecLength ); - - //for(int i=0; i itw (img, img->GetLargestPossibleRegion() ); - itw.GoToBegin(); - - itk::ImageRegionConstIterator itr (m_Image, m_Image->GetLargestPossibleRegion() ); - itr.GoToBegin(); - - while(!itr.IsAtEnd()) - { - itw.Set(itr.Get().GetElement(0)); - ++itr; - ++itw; - } - - // init - SetImportVolume(img->GetBufferPointer());//, 0, 0, CopyMemory); - //SetVolume( img->GetBufferPointer(), i ); - //}:: - - m_DisplayIndex = 0; - MITK_INFO << "Tbss-Image successfully initialized."; - -} - -void mitk::TbssImage::SetDisplayIndexForRendering(int displayIndex) -{ - MITK_INFO << "displayindex: " << displayIndex; - int index = displayIndex; - int vecLength = m_Image->GetVectorLength(); - index = index > vecLength-1 ? vecLength-1 : index; - if( m_DisplayIndex != index ) - { - typedef itk::Image ImgType; - ImgType::Pointer img = ImgType::New(); - CastToItkImage(this, img); - - itk::ImageRegionIterator itw (img, img->GetLargestPossibleRegion() ); - itw.GoToBegin(); - - itk::ImageRegionConstIterator itr (m_Image, m_Image->GetLargestPossibleRegion() ); - itr.GoToBegin(); - - while(!itr.IsAtEnd()) - { - itw.Set(itr.Get().GetElement(index)); - ++itr; - ++itw; - } - } - - m_DisplayIndex = index; -} - - - -#endif /* __mitkTbssImage__cpp */ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.h b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.h deleted file mode 100644 index 571f8e8..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImage.h +++ /dev/null @@ -1,117 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef __mitkTbssImage__h -#define __mitkTbssImage__h - -#include "mitkImage.h" -#include "itkVectorImage.h" -#include "mitkImageCast.h" -#include "MitkQuantificationExports.h" - -namespace mitk -{ - - /** - * \brief this class encapsulates diffusion volumes (vectorimages not - * yet supported by mitkImage) - */ - - class MITKQUANTIFICATION_EXPORT TbssImage : public Image - { - - public: - - typedef itk::VectorImage ImageType; - - - typedef itk::Index<3> IndexType; - //typedef typename std::vector > RoiType; - - mitkClassMacro( TbssImage, Image ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - - ImageType::Pointer GetImage() - { - return m_Image; - } - void SetImage(ImageType::Pointer image ) - { - this->m_Image = image; - } - - - void InitializeFromImage() - { - MITK_INFO << "make an mitk image that can be shown by mitk"; - this->InitializeByItk(m_Image.GetPointer(),1,1); - } - - void SetGroupInfo( std::vector< std::pair > info) - { - m_GroupInfo = info; - } - - std::vector< std::pair > GetGroupInfo() - { - return m_GroupInfo; - } - - - void SetMeasurementInfo(std::string s) - { - m_MeasurementInfo = s; - } - - std::string GetMeasurementInfo() - { - return m_MeasurementInfo; - } - - void InitializeFromVectorImage(); - - void SetDisplayIndexForRendering(int displayIndex); - - - - - - protected: - - TbssImage(); - - ~TbssImage() override{} - - ImageType::Pointer m_Image; - - - std::vector< std::pair > m_GroupInfo; - - int m_DisplayIndex; - - std::string m_MeasurementInfo; - - - - }; - - -} // namespace mitk -//#include "mitkTbssImage.cpp" -#endif /* __mitkTbssImage__h */ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp deleted file mode 100644 index c428943..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp +++ /dev/null @@ -1,61 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__ -#define __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__ - -#include "mitkTbssImageSource.h" -#include "mitkTbssImage.h" - - -mitk::TbssImageSource::TbssImageSource() -{ - // Create the output. We use static_cast<> here because we know the default - // output must be of type DiffusionImage - mitk::TbssImage::Pointer output - = static_cast(this->MakeOutput(0).GetPointer()); - - Superclass::SetNumberOfRequiredOutputs(1); - Superclass::SetNthOutput(0, output.GetPointer()); -} - -itk::DataObject::Pointer mitk::TbssImageSource::MakeOutput ( DataObjectPointerArraySizeType /*idx*/ ) -{ - return OutputType::New().GetPointer(); -} - - -itk::DataObject::Pointer mitk::TbssImageSource::MakeOutput( const DataObjectIdentifierType & name ) -{ - itkDebugMacro("MakeOutput(" << name << ")"); - if( this->IsIndexedOutputName(name) ) - { - return this->MakeOutput( this->MakeIndexFromOutputName(name) ); - } - return static_cast(OutputType::New().GetPointer()); -} - - - -mitk::TbssImageSource::OutputType* mitk::TbssImageSource::GetOutput(unsigned int idx) -{ - return static_cast - (this->ProcessObject::GetOutput(idx)); -} - - - -#endif //__MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h deleted file mode 100644 index d07f8d2..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h +++ /dev/null @@ -1,94 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef _MITK_TBSS_IMAGE_DATA_SOURCE_H_HEADER_ -#define _MITK_TBSS_IMAGE_DATA_SOURCE_H_HEADER_ - - -// Should be changed in a new type for TBSS -#include "mitkImageSource.h" -#include "MitkQuantificationExports.h" - - -namespace mitk { - - - - class TbssImage; - - -//##Documentation -//## @brief Superclass of all classes generating diffusion volumes (instances -//## of class DiffusionImage) as output. -//## -//## @ingroup Process - -class MITKQUANTIFICATION_EXPORT TbssImageSource : public ImageSource -{ -public: - mitkClassMacro(TbssImageSource, BaseDataSource) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - typedef TbssImage OutputType; - typedef itk::DataObject::Pointer DataObjectPointer; - - /** - * Allocates a new output object and returns it. Currently the - * index idx is not evaluated. - * @param idx the index of the output for which an object should be created - * @returns the new object - */ - itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override; - - /** - * This is a default implementation to make sure we have something. - * Once all the subclasses of ProcessObject provide an appopriate - * MakeOutput(), then ProcessObject::MakeOutput() can be made pure - * virtual. - */ - itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override; - - OutputType* GetOutput() - { - return itkDynamicCastInDebugMode( this->GetPrimaryOutput() ); - } - - //OutputType * GetOutput(unsigned int idx); - - //void SetOutput(OutputType* output); - - //{return Superclass::GetOutput();} - - OutputType* GetOutput(unsigned int idx); - - //virtual void GraftOutput(OutputType* graft); - - //virtual void GraftNthOutput(unsigned int idx, OutputType *graft); - -protected: - TbssImageSource(); - - ~TbssImageSource() override{} -}; - -} // namespace mitk - -//#include "mitkTbssImageSource.cpp" - - -#endif /* _MITK_DIFFUSION_IMAGE_DATA_SOURCE_H_HEADER_ */ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp deleted file mode 100644 index 7fb007e..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp +++ /dev/null @@ -1,137 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkTbssImporter_cpp -#define __mitkTbssImporter_cpp - -#include "mitkTbssImporter.h" -#include -#include "mitkImagePixelReadAccessor.h" - -namespace mitk -{ - -TbssImage::Pointer TbssImporter::Import() -{ - mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New(); - mitkPixelTypeMultiplex1( Import, m_InputVolume->GetPixelType(), tbssImg); - return tbssImg; -} - -template -void TbssImporter::Import(const mitk::PixelType , mitk::TbssImage::Pointer tbssImg) -{ - // read all images with all_*.nii.gz - MITK_INFO << "called import ..."; - m_Data = DataImageType::New(); - - mitk::BaseGeometry* geo = m_InputVolume->GetGeometry(); - mitk::Vector3D spacing = geo->GetSpacing(); - mitk::Point3D origin = geo->GetOrigin(); - - //Size size - DataImageType::SizeType dataSize; - dataSize[0] = m_InputVolume->GetDimension(0); - dataSize[1] = m_InputVolume->GetDimension(1); - dataSize[2] = m_InputVolume->GetDimension(2); - - m_Data->SetRegions(dataSize); - - // Set spacing - DataImageType::SpacingType dataSpacing; - dataSpacing[0] = spacing[0]; - dataSpacing[1] = spacing[1]; - dataSpacing[2] = spacing[2]; - m_Data->SetSpacing(dataSpacing); - - DataImageType::PointType dataOrigin; - dataOrigin[0] = origin[0]; - dataOrigin[1] = origin[1]; - dataOrigin[2] = origin[2]; - m_Data->SetOrigin(dataOrigin); - - //Direction must be set - DataImageType::DirectionType dir; - const itk::Transform* transform3D = geo->GetIndexToWorldTransform(); - itk::Transform::ParametersType p = transform3D->GetParameters(); - int t=0; - for(int i=0; i<3; i++) - { - for(int j=0; j<3; j++) - { - dir[i][j] = p[t]; // row-major order (where the column index varies the fastest) - t++; - } - } - - m_Data->SetDirection(dir); - - // Set the length to one because otherwise allocate fails. Should be changed when groups/measurements are added - m_Data->SetVectorLength(m_InputVolume->GetDimension(3)); - m_Data->Allocate(); - - // Determine vector size of m_Data - - int vecSize = m_Data->GetVectorLength(); - - MITK_INFO << "vecsize " < readTbss( m_InputVolume ); - - for(unsigned int i=0; i pixel; - itk::Index<3> id; - itk::Index<4> ix; - - ix[0] = id[0] = i; - ix[1] = id[1] = j; - ix[2] = id[2] = k; - - pixel = m_Data->GetPixel(id); - - for(int z=0; zSetPixel(id, pixel); - } - } - } - } - catch ( mitk::Exception& e ) - { - MITK_ERROR << "TbssImporter::Import: No read access to tbss image: " << e.what() ; - } - - tbssImg->SetGroupInfo(m_Groups); - tbssImg->SetMeasurementInfo(m_MeasurementInfo); - tbssImg->SetImage(m_Data); - - tbssImg->InitializeFromVectorImage(); - -} - - -} -#endif // __mitkTbssImporter_cpp diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h deleted file mode 100644 index 1e183db..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h +++ /dev/null @@ -1,91 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkTbssImporter_h -#define __mitkTbssImporter_h - -#include "mitkCommon.h" -#include "mitkFileReader.h" - -#include "itkImage.h" -#include "itkVectorImage.h" - -#include "mitkTbssImage.h" -#include "MitkQuantificationExports.h" - - -namespace mitk -{ - -/** - * \brief Converts FSL TBSS data (4D skeleton projection images) to a NRRD image with meta data. - * - * The TBSS pipeline of FSL produces a 4D image containing the 3D skeleton projections of all individuals. - * This class converts the FSL Nifty image to NRRD and adds information about the type of measurement and the study groups. - */ - - class MITKQUANTIFICATION_EXPORT TbssImporter : public itk::Object { - - public: - - // type of the 3d vector image containing the skeletonized images - typedef itk::VectorImage DataImageType; - - mitkClassMacroItkParent( TbssImporter, itk::Object ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - /** \brief Converts the FSL Nifty to NRRD and adds the meta data */ - mitk::TbssImage::Pointer Import(); - - template - void Import(const mitk::PixelType pixelType, mitk::TbssImage::Pointer tbssImg); - - /** \brief Group info is set by providing a vector with pairs of group name and number*/ - void SetGroupInfo(std::vector< std::pair > groups) - { - m_Groups = groups; - } - - /** \brief Used to indicate the type of measurement */ - void SetMeasurementInfo(std::string s) - { - m_MeasurementInfo = s; - } - - /** \brief Sets the FSL import volume */ - void SetImportVolume(mitk::Image::Pointer inputVolume) - { - m_InputVolume = inputVolume; - } - - protected: - - TbssImporter(){} - - ~TbssImporter() override{} - - DataImageType::Pointer m_Data; - - std::vector< std::pair > m_Groups; - - std::string m_MeasurementInfo; - - mitk::Image::Pointer m_InputVolume; - - }; -} -#endif // __mitkTbssImporter_h diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp deleted file mode 100644 index 1e42061..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __mitkTbssRoiImage__cpp -#define __mitkTbssRoiImage__cpp - - -#include "mitkTbssRoiImage.h" -#include "itkImageRegionIterator.h" -#include "itkImageRegionConstIterator.h" -#include "mitkImageCast.h" - - - - -mitk::TbssRoiImage::TbssRoiImage() -{ - m_PreprocessedFA = false; -} - - -/* - -mitk::TbssRoiImage::~TbssImage() -{ - -} - - - -void mitk::TbssRoiImage::InitializeFromImage() -{ - -} - -*/ - -#endif /* __mitkTbssImage__cpp */ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h deleted file mode 100644 index 32617cf..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h +++ /dev/null @@ -1,133 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef __mitkTbssRoiImage__h -#define __mitkTbssRoiImage__h - -#include "mitkImage.h" -#include "itkImage.h" -#include "mitkImageCast.h" -#include "MitkQuantificationExports.h" - -namespace mitk -{ - - /** - * \brief this class encapsulates diffusion volumes (vectorimages not - * yet supported by mitkImage) - */ - - class MITKQUANTIFICATION_EXPORT TbssRoiImage : public Image - { - - public: - - typedef itk::Image ImageType; - typedef itk::Index<3> IndexType; - //typedef typename std::vector > RoiType; - - mitkClassMacro( TbssRoiImage, Image ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - - //void SetRequestedRegionToLargestPossibleRegion(); - //bool RequestedRegionIsOutsideOfTheBufferedRegion(); - //virtual bool VerifyRequestedRegion(); - //void SetRequestedRegion( const itk::DataObject *data); - - ImageType::Pointer GetImage() - { - return m_Image; - } - void SetImage(ImageType::Pointer image ) - { - this->m_Image = image; - } - - itkGetMacro(PreprocessedFA, bool) - itkSetMacro(PreprocessedFA, bool) - itkGetMacro(PreprocessedFAFile, std::string) - itkSetMacro(PreprocessedFAFile, std::string) - itkGetMacro(Structure, std::string) - itkSetMacro(Structure, std::string) - - void SetRoi(std::vector< itk::Index<3> > roi) - { - m_Roi = roi; - } - - - // depricated - std::vector< itk::Index<3> > GetRoi() - { - return m_Roi; - } - - - void InitializeFromImage() - { - MITK_INFO << "make an mitk image that can be shown by mitk"; - this->InitializeByItk(m_Image.GetPointer()); - - this->SetChannel(m_Image->GetBufferPointer()); - } - - - - - protected: - - TbssRoiImage(); - - ~TbssRoiImage() override{} - - ImageType::Pointer m_Image; - - std::vector< itk::Index<3> > m_Roi; - - bool m_PreprocessedFA; - std::string m_PreprocessedFAFile; - - std::string m_Structure; - - - }; - - - // Does the same es the normal CastToMitkImage, but needed to reimplemented due to the templatet pixeltype - /* - template - void CastToTbssImage(const ItkOutputImageType* itkimage, itk::SmartPointer< mitk::TbssRoiImage >& tbssoutputimage) - { - if(tbssoutputimage.IsNull()) - { - tbssoutputimage = mitk::TbssRoiImage::New(); - } - tbssoutputimage->InitializeByItk(itkimage); - tbssoutputimage->SetChannel(itkimage->GetBufferPointer()); - } -*/ - - - - - -} // namespace mitk - -//#include "mitkTbssRoiImage.cpp" -#endif /* __mitkTbssRoiImage__h */ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp deleted file mode 100644 index 1b16532..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp +++ /dev/null @@ -1,60 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_CPP__ -#define __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_CPP__ - -#include "mitkTbssRoiImageSource.h" -#include "mitkTbssRoiImage.h" - - -mitk::TbssRoiImageSource::TbssRoiImageSource() -{ - // Create the output. We use static_cast<> here because we know the default - // output must be of type DiffusionImage - mitk::TbssRoiImage::Pointer output - = static_cast(this->MakeOutput(0).GetPointer()); - - Superclass::SetNumberOfRequiredOutputs(1); - Superclass::SetNthOutput(0, output.GetPointer()); -} - - -itk::DataObject::Pointer mitk::TbssRoiImageSource::MakeOutput ( DataObjectPointerArraySizeType /*idx*/ ) -{ - return OutputType::New().GetPointer(); -} - - -itk::DataObject::Pointer mitk::TbssRoiImageSource::MakeOutput( const DataObjectIdentifierType & name ) -{ - itkDebugMacro("MakeOutput(" << name << ")"); - if( this->IsIndexedOutputName(name) ) - { - return this->MakeOutput( this->MakeIndexFromOutputName(name) ); - } - return static_cast(OutputType::New().GetPointer()); -} - - - -mitk::TbssRoiImageSource::OutputType* mitk::TbssRoiImageSource::GetOutput(unsigned int idx) -{ - return static_cast - (this->ProcessObject::GetOutput(idx)); -} - -#endif //__MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__ diff --git a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h b/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h deleted file mode 100644 index 913073c..0000000 --- a/Modules/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h +++ /dev/null @@ -1,77 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef _MITK_TBSS_ROI_IMAGE_DATA_SOURCE_H_HEADER_ -#define _MITK_TBSS_ROI_IMAGE_DATA_SOURCE_H_HEADER_ - - -// Should be changed in a new type for TBSS -#include "mitkImageSource.h" -#include "MitkQuantificationExports.h" - - -namespace mitk { - - - - class TbssRoiImage; - - -//##Documentation -//## @brief Superclass of all classes generating diffusion volumes (instances -//## of class DiffusionImage) as output. -//## -//## @ingroup Process - -class MITKQUANTIFICATION_EXPORT TbssRoiImageSource : public ImageSource -{ -public: - mitkClassMacro(TbssRoiImageSource, BaseDataSource) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - typedef TbssRoiImage OutputType; - typedef itk::DataObject::Pointer DataObjectPointer; - - /** - * Allocates a new output object and returns it. Currently the - * index idx is not evaluated. - * @param idx the index of the output for which an object should be created - * @returns the new object - */ - itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override; - - /** - * This is a default implementation to make sure we have something. - * Once all the subclasses of ProcessObject provide an appopriate - * MakeOutput(), then ProcessObject::MakeOutput() can be made pure - * virtual. - */ - itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override; - - OutputType* GetOutput(unsigned int idx); - -protected: - TbssRoiImageSource(); - - ~TbssRoiImageSource() override{} -}; - -} // namespace mitk - - -#endif /* _MITK_DIFFUSION_IMAGE_DATA_SOURCE_H_HEADER_ */ diff --git a/Modules/Quantification/Rendering/mitkTbssImageMapper.cpp b/Modules/Quantification/Rendering/mitkTbssImageMapper.cpp deleted file mode 100644 index 4e2bef9..0000000 --- a/Modules/Quantification/Rendering/mitkTbssImageMapper.cpp +++ /dev/null @@ -1,65 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef TbssImageMapper__cpp -#define TbssImageMapper__cpp - -#include "mitkTbssImageMapper.h" - -#include "mitkProperties.h" -#include "mitkTbssImage.h" - - - -mitk::TbssImageMapper::TbssImageMapper() -{ -} - - -mitk::TbssImageMapper::~TbssImageMapper() -{ -} - - -void mitk::TbssImageMapper::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) -{ - int displayIndex(0); - - - this->GetDataNode()->GetIntProperty( "DisplayChannel", displayIndex, renderer ); - mitk::Image *input = const_cast< mitk::Image* >( - this->GetInput() - ); - mitk::TbssImage *input2 = dynamic_cast< mitk::TbssImage* >( - input - ); - - MITK_INFO << "displayindex: " << displayIndex; - - - input2->SetDisplayIndexForRendering(displayIndex); - Superclass::GenerateDataForRenderer(renderer); -} - - -void mitk::TbssImageMapper::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) -{ - node->AddProperty( "DisplayChannel", mitk::IntProperty::New( 0 ), renderer, overwrite ); - Superclass::SetDefaultProperties(node, renderer, overwrite); -} - -#endif diff --git a/Modules/Quantification/Rendering/mitkTbssImageMapper.h b/Modules/Quantification/Rendering/mitkTbssImageMapper.h deleted file mode 100644 index dd319e8..0000000 --- a/Modules/Quantification/Rendering/mitkTbssImageMapper.h +++ /dev/null @@ -1,55 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - - -#ifndef TbssImageMapper_H_HEADER_INCLUDED -#define TbssImageMapper_H_HEADER_INCLUDED - -#include "mitkImageVtkMapper2D.h" -#include "MitkQuantificationExports.h" - -namespace mitk { - - //##Documentation - //## @brief Mapper for raw diffusion weighted images - //## @ingroup Mapper - - class MITKQUANTIFICATION_EXPORT TbssImageMapper : public ImageVtkMapper2D - { - public: - - mitkClassMacro(TbssImageMapper,ImageVtkMapper2D); - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - void GenerateDataForRenderer( mitk::BaseRenderer *renderer ) override; - - static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false ); - - protected: - - TbssImageMapper(); - ~TbssImageMapper() override; - - }; - -} // namespace mitk - -//#include "mitkTbssImageMapper.cpp" - - -#endif /* TbssImageMapper_H_HEADER_INCLUDED */ - diff --git a/Modules/Quantification/Testing/CMakeLists.txt b/Modules/Quantification/Testing/CMakeLists.txt deleted file mode 100644 index a8460a2..0000000 --- a/Modules/Quantification/Testing/CMakeLists.txt +++ /dev/null @@ -1,15 +0,0 @@ -MITK_CREATE_MODULE_TESTS() - -mitkAddCustomModuleTest(mitkTbssNrrdImageReaderTest mitkTbssNrrdImageReaderTest ${MITK_DATA_DIR}/DiffusionImaging/tbss.tbss) -#mitkAddCustomModuleTest(mitkTbssRoiNrrdImageReaderTest mitkTbssRoiNrrdImageReaderTest ${MITK_DATA_DIR}/DiffusionImaging/bodyfornix.roi) -mitkAddCustomModuleTest(mitkTbssNrrdImageWriterTest mitkTbssNrrdImageWriterTest ${MITK_DATA_DIR}/DiffusionImaging/tbss.tbss ${MITK_DATA_DIR}/DiffusionImaging/tbss2.tbss) -mitkAddCustomModuleTest(mitkTbssSkeletonizationTest mitkTbssSkeletonizationTest ${MITK_DATA_DIR}/DiffusionImaging/mean_FA.nii.gz - ${MITK_DATA_DIR}/DiffusionImaging/mean_FA_skeleton.nii.gz - ${MITK_DATA_DIR}/DiffusionImaging/LowerCingulum_1mm.nii.gz - ${MITK_DATA_DIR}/DiffusionImaging/single_subject4d.nhdr - ${MITK_DATA_DIR}/DiffusionImaging/single_subject_projected.nrrd) - - -mitkAddCustomModuleTest(mitkTractAnalyzerTest mitkTractAnalyzerTest ${MITK_DATA_DIR}/DiffusionImaging/mean_FA_skeleton.nii.gz - ${MITK_DATA_DIR}/DiffusionImaging/tbssRoiPointset.mps - ${MITK_DATA_DIR}/DiffusionImaging/roi_cc.roi) diff --git a/Modules/Quantification/Testing/files.cmake b/Modules/Quantification/Testing/files.cmake deleted file mode 100644 index 18fe4ba..0000000 --- a/Modules/Quantification/Testing/files.cmake +++ /dev/null @@ -1,8 +0,0 @@ -SET(MODULE_CUSTOM_TESTS - mitkTbssNrrdImageReaderTest.cpp - #mitkTbssRoiNrrdImageReaderTest.cpp - mitkTbssNrrdImageWriterTest.cpp - mitkTbssSkeletonizationTest.cpp - mitkTractAnalyzerTest.cpp -) - diff --git a/Modules/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp b/Modules/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp deleted file mode 100644 index 9aa78a8..0000000 --- a/Modules/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp +++ /dev/null @@ -1,60 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include "mitkCoreObjectFactory.h" - - -/**Documentation - * test for the class "mitkNrrdTbssImageReader". - */ -int mitkTbssNrrdImageReaderTest(int , char* argv[]) -{ - MITK_TEST_BEGIN("TbssNrrdImageReaderTest"); - - mitk::NrrdTbssImageReader::Pointer tbssNrrdReader = mitk::NrrdTbssImageReader::New(); - - MITK_TEST_CONDITION_REQUIRED(tbssNrrdReader.GetPointer(), "Testing initialization of test object!"); - - tbssNrrdReader->SetFileName(argv[1]); - MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!"); - tbssNrrdReader->Update(); - - mitk::TbssImage* tbssImg = tbssNrrdReader->GetOutput(); - - MITK_TEST_CONDITION_REQUIRED(tbssImg != nullptr, "Testing that tbssImg is not null"); - - mitk::TbssImage::SizeType size = tbssImg->GetLargestPossibleRegion().GetSize(); - - MITK_TEST_CONDITION_REQUIRED(size[0]==2 && size[1]==2 && size[2]==2, "Test size of tbss image"); - - // Test groups - std::vector< std::pair > groups = tbssImg->GetGroupInfo(); - - std::pair group1 = groups.at(0); - std::pair group2 = groups.at(1); - - - - MITK_TEST_CONDITION_REQUIRED(group1.first.compare("group1") && group1.second==1, "Test group 1 info"); - - MITK_TEST_CONDITION_REQUIRED(group2.first.compare("group2") && group2.second==1, "Test group 2 info"); - - - - MITK_TEST_END(); -} diff --git a/Modules/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp b/Modules/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp deleted file mode 100644 index 92b4d05..0000000 --- a/Modules/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp +++ /dev/null @@ -1,76 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include -#include "mitkCoreObjectFactory.h" - - -/**Documentation - * test for the class "mitkNrrdTbssImageWriter". - */ -int mitkTbssNrrdImageWriterTest(int, char* argv[]) -{ - MITK_TEST_BEGIN("TbssNrrdImageWriterTest"); - - mitk::NrrdTbssImageReader::Pointer tbssNrrdReader = mitk::NrrdTbssImageReader::New(); - - MITK_TEST_CONDITION_REQUIRED(tbssNrrdReader.GetPointer(), "Testing initialization of test object!"); - - tbssNrrdReader->SetFileName(argv[1]); - MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!"); - tbssNrrdReader->Update(); - - mitk::TbssImage* tbssImg = tbssNrrdReader->GetOutput(); - - MITK_TEST_CONDITION_REQUIRED(tbssImg != nullptr, "Testing that tbssImg is not null"); - - mitk::NrrdTbssImageWriter::Pointer tbssNrrdWriter = mitk::NrrdTbssImageWriter::New(); - - - try{ - tbssNrrdWriter->SetFileName(argv[2]); - tbssNrrdWriter->SetInput(tbssImg); - tbssNrrdWriter->Update(); - } - catch(...) { - std::cout << "Writing failed" << std::endl; - return EXIT_FAILURE; - } - - mitk::NrrdTbssImageReader::Pointer tbssNrrdReader2 = mitk::NrrdTbssImageReader::New(); - tbssNrrdReader2->SetFileName(argv[1]); - MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader2->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with previously saved file!"); - - tbssNrrdReader2->Update(); - mitk::TbssImage* tbssImg2 = tbssNrrdReader2->GetOutput(); - - - std::vector< std::pair > groups = tbssImg->GetGroupInfo(); - std::vector< std::pair > groups2 = tbssImg2->GetGroupInfo(); - - MITK_TEST_CONDITION(groups == groups2, "Check that group information is identical"); - - - mitk::TbssImage::SizeType size = tbssImg->GetLargestPossibleRegion().GetSize(); - mitk::TbssImage::SizeType size2 = tbssImg2->GetLargestPossibleRegion().GetSize(); - - MITK_TEST_CONDITION(size == size2, "Check that sizes are equal"); - - - MITK_TEST_END(); -} diff --git a/Modules/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp b/Modules/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp deleted file mode 100644 index 55057f9..0000000 --- a/Modules/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp +++ /dev/null @@ -1,69 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include - -#include -#include "mitkDiffusionImagingObjectFactory.h" -#include "mitkCoreObjectFactory.h" - - -/**Documentation - * test for the class "mitkNrrdTbssImageReader". - */ -int mitkTbssRoiNrrdImageReaderTest(int, char* argv[]) -{ - MITK_TEST_BEGIN("NrrdTbssRoiImageReaderTest"); - - - mitk::NrrdTbssRoiImageReader::Pointer roiReader = mitk::NrrdTbssRoiImageReader::New(); - - MITK_TEST_CONDITION_REQUIRED(roiReader.GetPointer(), "Testing initialization of test object!"); - - RegisterDiffusionImagingObjectFactory(); - - - roiReader->SetFileName(argv[1]); - MITK_TEST_CONDITION_REQUIRED( roiReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!"); - roiReader->Update(); - - mitk::TbssRoiImage* roiImg = roiReader->GetOutput(); - - MITK_TEST_CONDITION_REQUIRED(roiImg != nullptr, "Testing that roiImg is not null"); - - mitk::TbssRoiImage::SizeType size = roiImg->GetLargestPossibleRegion().GetSize(); - - MITK_TEST_CONDITION_REQUIRED(size[0]==182 && size[1]==218 && size[2]==182, "Test size of ROI image"); - - - // Test indices of the roi - std::vector< itk::Index<3> > indices = roiImg->GetRoi(); - - MITK_TEST_CONDITION(indices.size() == 24, "Test the number of indices belonging to the Roi"); - - itk::Index<3> ix = indices.at(0); - - MITK_TEST_CONDITION(ix[0]==90 && ix[1]==132 && ix[2]==74, "Test whether first index is correct"); - - ix = indices.at(23); - - MITK_TEST_CONDITION(ix[0]==90 && ix[1]==117 && ix[2]==88, "Test whether last index is correct"); - - - - - MITK_TEST_END(); -} diff --git a/Modules/Quantification/Testing/mitkTbssSkeletonizationTest.cpp b/Modules/Quantification/Testing/mitkTbssSkeletonizationTest.cpp deleted file mode 100644 index 51610a7..0000000 --- a/Modules/Quantification/Testing/mitkTbssSkeletonizationTest.cpp +++ /dev/null @@ -1,167 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include -#include -#include -#include -#include - -/**Documentation - * test for the class "itkSkeletonizationFilter". - */ -int mitkTbssSkeletonizationTest(int, char* argv[]) -{ - - MITK_TEST_BEGIN("TbssSkeletonizationTest"); - - - // Load images - typedef itk::Image FloatImageType; - typedef itk::ImageFileReader ImageReaderType; - - ImageReaderType::Pointer reader = ImageReaderType::New(); - reader->SetFileName(argv[1]); - - // Initialize skeletonization filter and feed it with the mean_FA.nii.gz - - typedef itk::SkeletonizationFilter SkeletonisationFilterType; - SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New(); - skeletonizer->SetInput(reader->GetOutput()); - skeletonizer->Update(); - - - // Create a new image so the skeletonizaton won't be performed every time the skeleton is needed. - FloatImageType::Pointer skeleton = skeletonizer->GetOutput(); - - // Check whether the skeleton is correct - reader->SetFileName(argv[2]); - reader->Update(); - - FloatImageType::Pointer controlSkeleton = reader->GetOutput(); - - - // Convert itk images to mitk images and use the mitk::Equal method to compare the result with the reference skeleton. - - mitk::Image::Pointer mitkSkeleton = mitk::Image::New(); - mitkSkeleton->InitializeByItk(skeleton.GetPointer()); - - mitk::Image::Pointer mitkRefSkeleton = mitk::Image::New(); - mitkRefSkeleton->InitializeByItk(controlSkeleton.GetPointer()); - - - MITK_TEST_CONDITION(mitk::Equal(*mitkSkeleton, *mitkRefSkeleton, 0.001, true), "Check correctness of the skeleton"); - - - // Test the projection filter - - typedef itk::CovariantVector VectorType; - typedef itk::Image DirectionImageType; - - // Retrieve direction image needed later by the projection filter - DirectionImageType::Pointer directionImg = skeletonizer->GetVectorImage(); - - // Define a distance map filter that creates a distance map to limit the projection search - typedef itk::DistanceMapFilter DistanceMapFilterType; - - DistanceMapFilterType::Pointer distanceMapFilter = DistanceMapFilterType::New(); - distanceMapFilter->SetInput(controlSkeleton); //use controlSkeleton to prevent updating the skeletonfilter, which is time consuming - distanceMapFilter->Update(); - - FloatImageType::Pointer distanceMap = distanceMapFilter->GetOutput(); - - - - - // Threshold the skeleton on FA=0.2 to create a binary skeleton mask - typedef itk::Image CharImageType; - typedef itk::BinaryThresholdImageFilter ThresholdFilterType; - ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New(); - thresholder->SetInput(controlSkeleton); //use controlSkeleton to prevent updating the skeletonfilter, which is time consuming - thresholder->SetLowerThreshold(0.2); - thresholder->SetUpperThreshold(std::numeric_limits::max()); - thresholder->SetOutsideValue(0); - thresholder->SetInsideValue(1); - thresholder->Update(); - - - CharImageType::Pointer thresholdedImg = thresholder->GetOutput(); - - - // Load the cingulum mask that defines the region where a tubular structure must be searched for - typedef itk::ImageFileReader< CharImageType > CharReaderType; - CharReaderType::Pointer charReader = CharReaderType::New(); - charReader->SetFileName(argv[3]); - charReader->Update(); - CharImageType::Pointer cingulum = charReader->GetOutput(); - - - - // Define projection filter - typedef itk::ProjectionFilter ProjectionFilterType; - - // Read the 4d test image containing the registered FA data of one subject - typedef itk::Image Float4DImageType; - typedef itk::ImageFileReader ImageReader4DType; - - - - ImageReader4DType::Pointer reader4d = ImageReader4DType::New(); - reader4d->SetFileName(argv[4]); - reader4d->Update(); - - - - ProjectionFilterType::Pointer projectionFilter = ProjectionFilterType::New(); - projectionFilter->SetDistanceMap(distanceMap); - projectionFilter->SetDirections(directionImg); - projectionFilter->SetAllFA(reader4d->GetOutput()); - projectionFilter->SetTube(cingulum); - projectionFilter->SetSkeleton(thresholdedImg); - projectionFilter->Project(); - - - - Float4DImageType::Pointer projected = projectionFilter->GetProjections(); - - - - // Open control projection image - reader4d->SetFileName(argv[5]); - reader4d->Update(); - Float4DImageType::Pointer controlProjection = reader4d->GetOutput(); - - // control dimensions - Float4DImageType::SizeType pSize = projected->GetLargestPossibleRegion().GetSize(); - Float4DImageType::SizeType pControlSize = controlProjection->GetLargestPossibleRegion().GetSize(); - - typedef itk::Testing::ComparisonImageFilter ComparisonFilterType; - ComparisonFilterType::Pointer comparisonFilter = ComparisonFilterType::New(); - comparisonFilter->SetTestInput(projected); - comparisonFilter->SetValidInput(controlProjection); - comparisonFilter->Update(); - float diff = comparisonFilter->GetTotalDifference(); - - - MITK_TEST_CONDITION(pSize == pControlSize, "Size of projection image and control projection image are the same"); - - MITK_TEST_CONDITION(diff < 0.001, "Check correctness of the projections"); - - - MITK_TEST_END(); -} diff --git a/Modules/Quantification/Testing/mitkTractAnalyzerTest.cpp b/Modules/Quantification/Testing/mitkTractAnalyzerTest.cpp deleted file mode 100644 index e913d84..0000000 --- a/Modules/Quantification/Testing/mitkTractAnalyzerTest.cpp +++ /dev/null @@ -1,82 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include -#include -#include - -/**Documentation - * test for the class "mitkTractAnalyzer". - */ -int mitkTractAnalyzerTest(int, char* argv[]) -{ - - MITK_TEST_BEGIN("TractAnalyzer"); - - // Load image - typedef itk::Image FloatImageType; - typedef itk::ImageFileReader ImageReaderType; - - ImageReaderType::Pointer reader = ImageReaderType::New(); - - reader->SetFileName(argv[1]); - reader->Update(); - FloatImageType::Pointer itkImage = reader->GetOutput(); - mitk::Image::Pointer mitkImage = mitk::Image::New(); - - mitk::CastToMitkImage(itkImage, mitkImage); - - // load point set - mitk::PointSet::Pointer pointSet = mitk::IOUtil::Load(argv[2]); - - mitk::TractAnalyzer analyzer; - - analyzer.SetInputImage(mitkImage); - analyzer.SetThreshold(0.2); - analyzer.SetPointSet(pointSet); - analyzer.MakeRoi(); - - mitk::TbssRoiImage::Pointer tbssRoi = analyzer.GetRoiImage(); - - std::vector< itk::Index<3> > roi = tbssRoi->GetRoi(); - - - - // Output roi for debug purposes - std::cout << "ROI\n"; - for(unsigned int t=0; t ix = roi.at(t); - std::cout << ix[0] << ", " << ix[1] << ", " << ix[2] << "\n"; - } - - - std::cout << std::endl; - - // check the cost of the roi - double cost = analyzer.GetCostSum(); - - std::cout << "Cost: " << cost << std::endl; - - bool equal = mitk::Equal(cost, 5162.854, 0.001); - - MITK_TEST_CONDITION(equal, "Checking cost of found ROI"); - - - MITK_TEST_END(); -} diff --git a/Modules/Quantification/files.cmake b/Modules/Quantification/files.cmake deleted file mode 100644 index 9477511..0000000 --- a/Modules/Quantification/files.cmake +++ /dev/null @@ -1,31 +0,0 @@ -set(CPP_FILES - - # DataStructures -> Tbss - IODataStructures/TbssImages/mitkTbssImageSource.cpp - IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp - IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp - IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp - IODataStructures/TbssImages/mitkTbssImage.cpp - IODataStructures/TbssImages/mitkTbssRoiImage.cpp - IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp - IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp - IODataStructures/TbssImages/mitkTbssImporter.cpp - - # Rendering - Rendering/mitkTbssImageMapper.cpp - - #Algorithms - Algorithms/mitkTractAnalyzer.cpp -) - -set(H_FILES - # DataStructures - IODataStructures/TbssImages/mitkTbssImporter.h - - # Rendering - Rendering/mitkTbssImageMapper.h - - Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h - Algorithms/itkRegularizedIVIMReconstructionFilter.h - Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h -) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt index e64c95d..03cd599 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt @@ -1,10 +1,10 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_diffusionimaging_ivim) mitk_create_plugin( SUBPROJECTS MITK-Diffusion EXPORT_DIRECTIVE DIFFUSIONIMAGING_IVIM_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkQtWidgetsExt MitkQuantification + MODULE_DEPENDS MitkQtWidgetsExt MitkDiffusionCore ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt index b4491df..600104b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt @@ -1,10 +1,10 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_diffusionimaging_reconstruction) mitk_create_plugin( SUBPROJECTS MITK-Diffusion EXPORT_DIRECTIVE DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkQtWidgetsExt MitkQuantification + MODULE_DEPENDS MitkQtWidgetsExt MitkDiffusionCore ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp index f99d4ca..26929f0 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp @@ -1,51 +1,51 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkQuantificationPerspective.h" #include "berryIViewLayout.h" void QmitkQuantificationPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// left->AddView("org.mitk.views.diffusionquantification"); - left->AddView("org.mitk.views.imagestatisticsReloaded"); + left->AddView("org.mitk.views.imagestatistics"); left->AddView("org.mitk.views.segmentation"); left->AddView("org.mitk.views.odfdetails"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt index f3e90a3..47a92cd 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt @@ -1,10 +1,10 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_diffusionimaging_tbss) mitk_create_plugin( SUBPROJECTS MITK-Diffusion EXPORT_DIRECTIVE DIFFUSIONIMAGING_TBSS_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkQtWidgetsExt MitkFiberTracking MitkQuantification + MODULE_DEPENDS MitkQtWidgetsExt MitkFiberTracking ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt index 4cab76a..7694d4e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt @@ -1,8 +1,8 @@ project(org_mitk_gui_qt_diffusionimaging) mitk_create_plugin( SUBPROJECTS MITK-Diffusion EXPORT_DIRECTIVE DIFFUSIONIMAGING_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkDiffusionCore MitkQuantification MitkConnectomics + MODULE_DEPENDS MitkDiffusionCore MitkConnectomics )