diff --git a/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt b/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt index e96d8eff85..1ab7395704 100644 --- a/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt +++ b/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt @@ -1,5 +1,6 @@ numpy SimpleITK dipy sklearn https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip +https://github.com/MIC-DKFZ/TractSeg/archive/v1.3.zip diff --git a/Modules/DiffusionImaging/DiffusionCore/files.cmake b/Modules/DiffusionImaging/DiffusionCore/files.cmake index d76b1fbe9c..5a2471e704 100644 --- a/Modules/DiffusionImaging/DiffusionCore/files.cmake +++ b/Modules/DiffusionImaging/DiffusionCore/files.cmake @@ -1,163 +1,163 @@ 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 # Rendering include/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 # Fitting functions include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h include/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 # Properties include/IODataStructures/Properties/mitkBValueMapProperty.h include/IODataStructures/Properties/mitkGradientDirectionsProperty.h include/IODataStructures/Properties/mitkMeasurementFrameProperty.h include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h include/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/itkFiniteDiffOdfMaximaExtractionFilter.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 ) set( TOOL_FILES ) diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp new file mode 100644 index 0000000000..94d27a76b5 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp @@ -0,0 +1,101 @@ +/*=================================================================== + +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 __itkFourDToVectorImageFilter_cpp +#define __itkFourDToVectorImageFilter_cpp + +#include "itkFourDToVectorImageFilter.h" +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include + + +using namespace boost::math; + +namespace itk { + +template< class PixelType > +FourDToVectorImageFilter< PixelType>::FourDToVectorImageFilter() +{ + +} + + +template< class PixelType > +void FourDToVectorImageFilter< PixelType> +::GenerateData() +{ + Vector spacing4 = m_InputImage->GetSpacing(); + Point origin4 = m_InputImage->GetOrigin(); + Matrix direction4 = m_InputImage->GetDirection(); + ImageRegion<4> imageRegion4 = m_InputImage->GetLargestPossibleRegion(); + + Vector spacing3; + Point origin3; + Matrix direction3; + ImageRegion<3> imageRegion3; + + spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2]; + origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2]; + for (int r=0; r<3; r++) + for (int c=0; c<3; c++) + direction3[r][c] = direction4[r][c]; + imageRegion3.SetSize(0, imageRegion4.GetSize()[0]); + imageRegion3.SetSize(1, imageRegion4.GetSize()[1]); + imageRegion3.SetSize(2, imageRegion4.GetSize()[2]); + + m_OutputImage = OutputImageType::New(); + m_OutputImage->SetSpacing( spacing3 ); + m_OutputImage->SetOrigin( origin3 ); + m_OutputImage->SetDirection( direction3 ); + m_OutputImage->SetRegions( imageRegion3 ); + m_OutputImage->SetVectorLength(imageRegion4.GetSize()[3]); + m_OutputImage->Allocate(); + typename OutputImageType::PixelType pix; pix.SetSize(imageRegion4.GetSize()[3]); pix.Fill(0.0); + m_OutputImage->FillBuffer(pix); + ImageRegionIterator< OutputImageType > oit(m_OutputImage, m_OutputImage->GetLargestPossibleRegion() ); + + while( !oit.IsAtEnd() ) + { + auto idx3 = oit.GetIndex(); + + typename OutputImageType::PixelType pix = oit.Get(); + for (unsigned int i=0; iGetPixel(idx4); + } + oit.Set(pix); + + ++oit; + } +} + +} + +#endif // __itkFourDToVectorImageFilter_cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h new file mode 100644 index 0000000000..f4c29d9082 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h @@ -0,0 +1,74 @@ +/*========================================================================= + + Program: Insight Segmentation & Registration Toolkit + Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $ + Language: C++ + Date: $Date: 2006-03-27 17:01:06 $ + Version: $Revision: 1.12 $ + + Copyright (c) Insight Software Consortium. All rights reserved. + See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ +#ifndef __itkFourDToVectorImageFilter_h_ +#define __itkFourDToVectorImageFilter_h_ + +#include "itkImageToImageFilter.h" +#include +#include + +namespace itk{ + +/** +* \brief Flip peaks along specified axes +*/ + +template< class PixelType > +class FourDToVectorImageFilter : public ProcessObject +{ + +public: + + typedef FourDToVectorImageFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ProcessObject Superclass; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** Runtime information support. */ + itkTypeMacro(FourDToVectorImageFilter, ProcessObject) + + typedef Image InputImageType; + typedef VectorImage OutputImageType; + typedef typename OutputImageType::RegionType OutputImageRegionType; + + itkSetMacro(InputImage, typename InputImageType::Pointer) + itkGetMacro(OutputImage, typename OutputImageType::Pointer) + + void GenerateData(); + +protected: + FourDToVectorImageFilter(); + ~FourDToVectorImageFilter(){} + + typename InputImageType::Pointer m_InputImage; + typename OutputImageType::Pointer m_OutputImage; + +private: +}; + +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkFourDToVectorImageFilter.cpp" +#endif + +#endif //__itkFourDToVectorImageFilter_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp new file mode 100644 index 0000000000..cad351efe0 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp @@ -0,0 +1,79 @@ +/*=================================================================== + +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 __itkSplitVectorImageFilter_cpp +#define __itkSplitVectorImageFilter_cpp + +#include "itkSplitVectorImageFilter.h" +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include + + +using namespace boost::math; + +namespace itk { + +template< class PixelType > +SplitVectorImageFilter< PixelType>::SplitVectorImageFilter() +{ + +} + + +template< class PixelType > +void SplitVectorImageFilter< PixelType> +::GenerateData() +{ + m_OutputImages.clear(); + for (unsigned int i=0; iGetVectorLength(); ++i) + { + typename OutputImageType::Pointer m_OutputImage = OutputImageType::New(); + m_OutputImage->SetSpacing( m_InputImage->GetSpacing() ); + m_OutputImage->SetOrigin( m_InputImage->GetOrigin() ); + m_OutputImage->SetDirection( m_InputImage->GetDirection() ); + m_OutputImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); + m_OutputImage->Allocate(); + m_OutputImage->FillBuffer(0); + m_OutputImages.push_back(m_OutputImage); + } + + ImageRegionIterator< InputImageType > iit(m_InputImage, m_InputImage->GetLargestPossibleRegion() ); + + while( !iit.IsAtEnd() ) + { + auto idx = iit.GetIndex(); + typename InputImageType::PixelType pix = iit.Get(); + for (unsigned int i=0; iSetPixel(idx, pix[i]); + ++iit; + } +} + +} + +#endif // __itkSplitVectorImageFilter_cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h new file mode 100644 index 0000000000..21599950bb --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h @@ -0,0 +1,73 @@ +/*========================================================================= + + Program: Insight Segmentation & Registration Toolkit + Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $ + Language: C++ + Date: $Date: 2006-03-27 17:01:06 $ + Version: $Revision: 1.12 $ + + Copyright (c) Insight Software Consortium. All rights reserved. + See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ +#ifndef __itkSplitVectorImageFilter_h_ +#define __itkSplitVectorImageFilter_h_ + +#include "itkImageToImageFilter.h" +#include +#include + +namespace itk{ + +/** +* \brief Flip peaks along specified axes +*/ + +template< class PixelType > +class SplitVectorImageFilter : public ProcessObject +{ + +public: + + typedef SplitVectorImageFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ProcessObject Superclass; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** Runtime information support. */ + itkTypeMacro(SplitVectorImageFilter, ProcessObject) + + typedef VectorImage InputImageType; + typedef Image OutputImageType; + typedef typename OutputImageType::RegionType OutputImageRegionType; + + itkSetMacro(InputImage, typename InputImageType::Pointer) + std::vector< typename OutputImageType::Pointer > GetOutputImages(){ return m_OutputImages; } + void GenerateData(); + +protected: + SplitVectorImageFilter(); + ~SplitVectorImageFilter(){} + + typename InputImageType::Pointer m_InputImage; + std::vector< typename OutputImageType::Pointer > m_OutputImages; + +private: +}; + +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkSplitVectorImageFilter.cpp" +#endif + +#endif //__itkSplitVectorImageFilter_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp new file mode 100644 index 0000000000..e03fbe84fb --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp @@ -0,0 +1,101 @@ +/*=================================================================== + +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 __itkVectorImageToFourDImageFilter_cpp +#define __itkVectorImageToFourDImageFilter_cpp + +#include "itkVectorImageToFourDImageFilter.h" +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include + + +using namespace boost::math; + +namespace itk { + +template< class PixelType > +VectorImageToFourDImageFilter< PixelType>::VectorImageToFourDImageFilter() +{ + +} + + +template< class PixelType > +void VectorImageToFourDImageFilter< PixelType> +::GenerateData() +{ + Vector spacing4; + Point origin4; + Matrix direction4; direction4.SetIdentity(); + ImageRegion<4> imageRegion4; + + Vector spacing3 = m_InputImage->GetSpacing(); + Point origin3 = m_InputImage->GetOrigin(); + Matrix direction3 = m_InputImage->GetDirection(); + ImageRegion<3> imageRegion3 = m_InputImage->GetLargestPossibleRegion(); + + spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1; + origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0; + for (int r=0; r<3; r++) + for (int c=0; c<3; c++) + direction4[r][c] = direction3[r][c]; + + imageRegion4.SetSize(0, imageRegion3.GetSize()[0]); + imageRegion4.SetSize(1, imageRegion3.GetSize()[1]); + imageRegion4.SetSize(2, imageRegion3.GetSize()[2]); + imageRegion4.SetSize(3, m_InputImage->GetVectorLength()); + + m_OutputImage = OutputImageType::New(); + m_OutputImage->SetSpacing( spacing4 ); + m_OutputImage->SetOrigin( origin4 ); + m_OutputImage->SetDirection( direction4 ); + m_OutputImage->SetRegions( imageRegion4 ); + m_OutputImage->Allocate(); + m_OutputImage->FillBuffer(0); + ImageRegionIterator< InputImageType > iit(m_InputImage, m_InputImage->GetLargestPossibleRegion() ); + + while( !iit.IsAtEnd() ) + { + auto idx3 = iit.GetIndex(); + + typename InputImageType::PixelType pix = iit.Get(); + + for (unsigned int i=0; iSetPixel(idx4, pix[i]); + } + + ++iit; + } +} + +} + +#endif // __itkVectorImageToFourDImageFilter_cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h new file mode 100644 index 0000000000..88856faf34 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h @@ -0,0 +1,74 @@ +/*========================================================================= + + Program: Insight Segmentation & Registration Toolkit + Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $ + Language: C++ + Date: $Date: 2006-03-27 17:01:06 $ + Version: $Revision: 1.12 $ + + Copyright (c) Insight Software Consortium. All rights reserved. + See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ +#ifndef __itkVectorImageToFourDImageFilter_h_ +#define __itkVectorImageToFourDImageFilter_h_ + +#include "itkImageToImageFilter.h" +#include +#include + +namespace itk{ + +/** +* \brief Flip peaks along specified axes +*/ + +template< class PixelType > +class VectorImageToFourDImageFilter : public ProcessObject +{ + +public: + + typedef VectorImageToFourDImageFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ProcessObject Superclass; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** Runtime information support. */ + itkTypeMacro(VectorImageToFourDImageFilter, ProcessObject) + + typedef VectorImage InputImageType; + typedef Image OutputImageType; + typedef typename OutputImageType::RegionType OutputImageRegionType; + + itkSetMacro(InputImage, typename InputImageType::Pointer) + itkGetMacro(OutputImage, typename OutputImageType::Pointer) + + void GenerateData(); + +protected: + VectorImageToFourDImageFilter(); + ~VectorImageToFourDImageFilter(){} + + typename InputImageType::Pointer m_InputImage; + typename OutputImageType::Pointer m_OutputImage; + +private: +}; + +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkVectorImageToFourDImageFilter.cpp" +#endif + +#endif //__itkVectorImageToFourDImageFilter_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h index a029f28849..a30d5f188e 100644 --- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h +++ b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h @@ -1,66 +1,66 @@ /*=================================================================== 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 __mitkPeakImage__h #define __mitkPeakImage__h #include "mitkImage.h" #include #include #include namespace mitk { /** * \brief this class encapsulates tensor images */ class MITKDIFFUSIONCORE_EXPORT PeakImage : public Image { public: - typedef itk::Image ItkPeakImageType; typedef float PixelType; + typedef itk::Image ItkPeakImageType; mitkClassMacro( PeakImage, Image ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) void ConstructPolydata(); vtkSmartPointer< vtkPolyData > GetPolyData() { if (m_PolyData==nullptr) this->ConstructPolydata(); return m_PolyData; } void SetCustomColor(float r, float g, float b); void ColorByOrientation(); protected: PeakImage(); ~PeakImage() override; mutable vtkSmartPointer< vtkPolyData > m_PolyData; }; } // namespace mitk #endif /* __mitkPeakImage__h */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp index 4951495f93..776da102c1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp @@ -1,52 +1,52 @@ /*=================================================================== 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 "QmitkDwiPreprocessingPerspective.h" #include "berryIViewLayout.h" void QmitkDwiPreprocessingPerspective::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.diffusionpreprocessing"); + left->AddView("org.mitk.views.brainextraction"); left->AddView("org.mitk.views.denoisingview"); left->AddView("org.mitk.views.simpleregistrationview"); left->AddView("org.mitk.views.headmotioncorrectionview"); -// left->AddView("org.mitk.views.brainextraction"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake index 96637f8307..a99ac9995d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake @@ -1,45 +1,49 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkBrainExtractionView.cpp QmitkDipyReconstructionsView.cpp + QmitkTractSegView.cpp ) set(UI_FILES src/internal/QmitkBrainExtractionViewControls.ui src/internal/QmitkDipyReconstructionsViewControls.ui + src/internal/QmitkTractSegViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkBrainExtractionView.h src/internal/QmitkDipyReconstructionsView.h + src/internal/QmitkTractSegView.h ) set(CACHED_RESOURCE_FILES plugin.xml - resources/dwi2.png + resources/tract_seg.png + resources/brain_extraction.png resources/dipy.png ) set(QRC_FILES resources/diffusion_python_resources.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml index ae4e4cfdaa..de706ba265 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml @@ -1,25 +1,33 @@ + icon="resources/brain_extraction.png"> + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png new file mode 100644 index 0000000000..23b5bc8322 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/diffusion_python_resources.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/diffusion_python_resources.qrc index 863ac9b7a0..ab90055058 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/diffusion_python_resources.qrc +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/diffusion_python_resources.qrc @@ -1,5 +1,6 @@ dipy_reconstructions.py + tractseg.py diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py index 7008312528..922c449441 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py @@ -1,390 +1,391 @@ error_string = None del error_string try: import dipy.direction.peaks as dpp from dipy.reconst.shore import ShoreModel from dipy.reconst.shm import CsaOdfModel, OpdtModel, SphHarmModel import dipy.reconst.sfm as sfm from dipy.reconst.csdeconv import auto_response, ConstrainedSphericalDeconvModel from dipy.core import sphere import numpy as np from dipy.core.gradients import gradient_table import SimpleITK as sitk def get_mitk_sphere(): """ Return MITK compliant dipy Sphere object. MITK stores ODFs as 252 values spherically sampled from the continuous ODF. The sampling directions are generate by a 5-fold subdivisions of an icosahedron. """ xyz = np.array([ 0.9756767549555488, 0.9977154378498742, 0.9738192119472443, 0.8915721200771204, 0.7646073555341725, 0.6231965669156312, 0.9817040172417226, 0.9870396762453547, 0.9325589150767597, 0.8173592116492303, 0.6708930871960926, 0.9399233672993689, 0.9144882783890762, 0.8267930935417315, 0.6931818659696647, 0.8407280774774689, 0.782394344826989, 0.6762337155773353, 0.7005607434301688, 0.6228579759074076, 0.5505632701289798, 0.4375940376503738, 0.3153040621970065, 0.1569517536476641, -0.01984099037382634, -0.1857690950088067, -0.3200730131503601, 0.5232435944036425, 0.3889403678268736, 0.2135250052622625, 0.02420694871807206, -0.1448539951504302, 0.5971534158422009, 0.4482053228282282, 0.2597018771197477, 0.06677517278138323, 0.6404616222418184, 0.4782876117785159, 0.2868761951248767, 0.6459894362878276, 0.4789651252338281, 0.3200724178002418, 0.4973180497018747, 0.6793811951363423, 0.8323587928990375, 0.9308933612987835, 0.4036036036586492, 0.5984781165037405, 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0.5992589358516202, 0.4261046359672609, 0.2252066549797059, 0.6250522113657903, 0.4317325950511361, 0.6101482870567641, 0.9096403689902206, 0.9275522217134882, 0.8909112253661301, 0.796262827475376, 0.6691520068054228, 0.8241233338640371, 0.810859375773786, 0.7430057321681839, 0.6332085061147845, 0.6854064426268304, 0.6413714065577412, 0.5581299045184589, 0.5164832226272315, 0.4563611494403301, 0.3496833143594963, -0.3951892821849063, -0.6114960336943951, -0.787988199289983, -0.4544844137443082, -0.657492739431111, -0.484187939006181, 0.4936478319326018, 0.2653148405479006, 0.01970714938077021, -0.1989850169013517, 0.4302075642722875, 0.1852629793843341, -0.0559739158243807, 0.3387563694841473, 0.09867487876932232, 0.2393267951217032, -0.999553621201999, -0.9653354239158236, -0.8682642090770526, -0.9597077173597477, -0.8918540989344099, -0.8573751662344773, -0.2980738893651726, -0.3916343988495664, -0.4596955428592778, -0.4950341577852201, -0.1432117197792371, -0.2267418620329016, -0.2909964852939082, 0.02097514873862574, -0.05800679989935065, 0.1653145532988453, -0.3786231842883476, -0.1464197032303796, 0.09531724619007391, -0.1924163631703616, 0.05252803743712917, 0.006318730357784829, -0.3534800054422614, -0.1720548071373146, 0.02057294660420643, 0.190134278339324, -0.1169519894866824, 0.07636807502743861, 0.2529338262925594, 0.1271908635410245, 0.3046134343217798, 0.3366066958443542, 0.6094980941008995, 0.7135382519498201, 0.7711196978950583, 0.7870198804193677, 0.8705500304441893, 0.9132984713369965, 0.403998910419839, 0.62060207699311, 0.7967976318501995, 0.4726965405256068, 0.6757048258462731, 0.5106167801856609]) n = int(xyz.shape[0] / 3) x = xyz[:n] y = xyz[n:2 * n] z = xyz[2 * n:] for i in range(n): v = np.array([x[i], y[i], z[i]]) norm = np.linalg.norm(v) if norm > 0: v /= norm x[i] = v[0] y[i] = v[1] z[i] = v[2] s = sphere.Sphere(x=x, y=y, z=z) return s def fit_data(data, bvals, bvecs, model_type='3D-SHORE', calculate_peak_image=False): """ Fits the defined model to the input dMRI and returns an MITK compliant ODF image. """ # create dipy Sphere sphere = get_mitk_sphere() odf = None model = None gtab = gradient_table(bvals, bvecs) # fit selected model if model_type == '3D-SHORE': print('Fitting 3D-SHORE') print("radial_order: ", radial_order) print("zeta: ", zeta) print("lambdaN: ", lambdaN) print("lambdaL: ", lambdaL) model = ShoreModel(gtab, radial_order=radial_order, zeta=zeta, lambdaN=lambdaN, lambdaL=lambdaL) asmfit = model.fit(data) odf = asmfit.odf(sphere) elif model_type == 'CSA-QBALL': print('Fitting CSA-QBALL') print("sh_order: ", sh_order) print("smooth: ", smooth) model = CsaOdfModel(gtab=gtab, sh_order=sh_order, smooth=smooth) odf = model.fit(data).odf(sphere) odf = np.clip(odf, 0, np.max(odf, -1)[..., None]) elif model_type == 'SFM': print('Fitting SFM') print("fa_thr: ", fa_thr) response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=fa_thr) model = sfm.SparseFascicleModel(gtab, sphere=sphere, l1_ratio=0.5, alpha=0.001, response=response[0]) odf = model.fit(data).odf(sphere) elif model_type == 'CSD': print('Fitting CSD') print("sh_order: ", sh_order) print("fa_thr: ", fa_thr) response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=fa_thr) model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=sh_order) odf = model.fit(data).odf(sphere) elif model_type == 'Opdt': print('Orientation Probability Density Transform') print("sh_order: ", sh_order) print("smooth: ", smooth) model = OpdtModel(gtab=gtab, sh_order=sh_order, smooth=smooth) odf = model.fit(data).odf(sphere) else: raise ValueError('Model type not supported. Available models: 3D-SHORE, CSA-QBALL, SFM, CSD, Opdt') print('Preparing ODF image') odf_image = sitk.Image([data.shape[2], data.shape[1], data.shape[0]], sitk.sitkVectorFloat32, len(sphere.vertices)) for x in range(data.shape[2]): for y in range(data.shape[1]): for z in range(data.shape[0]): odf_image.SetPixel(x, y, z, odf[z, y, x, :]) # if not calculate_peak_image: return odf_image, None # # calculate peak image # sf_peaks = dpp.peaks_from_model(model, # data, # sphere, # relative_peak_threshold=.4, # min_separation_angle=15, # return_sh=False, npeaks=5, parallel=True) # # # reshape to be MITK/MRtrix compliant # s = sf_peaks.peak_dirs.shape # peaks = sf_peaks.peak_dirs.reshape((s[0], s[1], s[2], s[3] * s[4]), order='C') # # # scale peaks # for x in range(s[0]): # for y in range(s[1]): # for z in range(s[2]): # for i in range(3): # peaks[x, y, z, i * 3] *= sf_peaks.peak_values[x, y, z, i] # peaks[x, y, z, i * 3 + 1] *= sf_peaks.peak_values[x, y, z, i] # peaks[x, y, z, i * 3 + 2] *= sf_peaks.peak_values[x, y, z, i] # # peaks = peaks.astype('float32') # return odf_image, peaks print('DIPY Reconstructions') data = sitk.GetArrayFromImage(in_image) bvals = np.array(bvals) bvecs = np.array(bvecs) odf_image, peaks = fit_data(data=data, bvals=bvals, bvecs=bvecs, model_type=model_type, calculate_peak_image=calculate_peak_image) odf_image.SetOrigin(in_image.GetOrigin()) odf_image.SetSpacing(in_image.GetSpacing()) odf_image.SetDirection(in_image.GetDirection()) + except Exception as e: error_string = str(e) print(error_string) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dwi2.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dwi2.png deleted file mode 100644 index c2087367ce..0000000000 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dwi2.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png new file mode 100755 index 0000000000..4462301d22 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py new file mode 100644 index 0000000000..c25cc15987 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py @@ -0,0 +1,54 @@ +error_string = None +del error_string +try: + import SimpleITK as sitk + import nibabel as nib + import numpy as np + from tractseg.TractSeg import run_tractseg + + data = sitk.GetArrayFromImage(in_image) + data = np.nan_to_num(data) + swapaxes = False + if data.shape != (sx, sy, sz): + data = np.swapaxes(data, 0, 2) + swapaxes = True + + seg = run_tractseg(data=data, output_type=output_type, input_type="peaks", verbose=verbose, get_probs=get_probs) + + if swapaxes: + seg = np.swapaxes(seg, 0, 2) + + if not output_type == "TOM": + + if not get_probs: + if collapse: + temp = np.zeros((seg.shape[0], seg.shape[1], seg.shape[2])) + for l in range(seg.shape[3]): + temp[np.where(seg[:, :, :, l]>0)] = l + 1 + seg = temp + segmentation = sitk.GetImageFromArray(seg.astype(np.uint8)) + else: + segmentation = sitk.GetImageFromArray(seg) + + segmentation.SetOrigin(in_image.GetOrigin()) + segmentation.SetSpacing(in_image.GetSpacing()) + segmentation.SetDirection(in_image.GetDirection()) + else: + if not collapse: + for x in range(0, 20): + tom = sitk.GetImageFromArray(seg[:, :, :, x * 3:x * 3 + 3]) + tom.SetOrigin(in_image.GetOrigin()) + tom.SetSpacing(in_image.GetSpacing()) + tom.SetDirection(in_image.GetDirection()) + globals()['tom%s' % x] = tom + else: + tom0 = sitk.GetImageFromArray(seg) + tom0.SetOrigin(in_image.GetOrigin()) + tom0.SetSpacing(in_image.GetSpacing()) + tom0.SetDirection(in_image.GetDirection()) + + + +except Exception as e: + error_string = str(e) + print(error_string) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h index a60a588042..9630c8d601 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h @@ -1,79 +1,77 @@ /*=================================================================== 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 "ui_QmitkBrainExtractionViewControls.h" #include -#include -#include #include /*! -\brief View for diffusion image registration / head motion correction +\brief */ class QmitkBrainExtractionView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef mitk::GradientDirectionsProperty GradProp; QmitkBrainExtractionView(); virtual ~QmitkBrainExtractionView(); virtual void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; protected slots: void StartBrainExtraction(); void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection std::string GetPythonFile(std::string filename); protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkBrainExtractionViewControls* m_Controls; mitk::Image::Pointer m_DiffusionImage; std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes; private: void UpdateRegistrationStatus(); ///< update textual status display of the Registration process // the Qt parent of our GUI (NOT of this object) QWidget* m_Parent; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h index 3bdb00f673..f305993b4e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h @@ -1,74 +1,72 @@ /*=================================================================== 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 "ui_QmitkDipyReconstructionsViewControls.h" #include -#include -#include #include /*! -\brief View for diffusion image registration / head motion correction +\brief */ class QmitkDipyReconstructionsView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef mitk::GradientDirectionsProperty GradProp; QmitkDipyReconstructionsView(); virtual ~QmitkDipyReconstructionsView(); virtual void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; protected slots: void StartFit(); void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkDipyReconstructionsViewControls* m_Controls; private: void UpdateRegistrationStatus(); ///< update textual status display of the Registration process // the Qt parent of our GUI (NOT of this object) QWidget* m_Parent; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp new file mode 100644 index 0000000000..c2839bbf80 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp @@ -0,0 +1,278 @@ +/*=================================================================== + +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. + +===================================================================*/ + + +// Blueberry +#include +#include + +// Qmitk +#include "QmitkTractSegView.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +const std::string QmitkTractSegView::VIEW_ID = "org.mitk.views.tractseg"; + +QmitkTractSegView::QmitkTractSegView() + : QmitkAbstractView() + , m_Controls( 0 ) +{ + +} + +// Destructor +QmitkTractSegView::~QmitkTractSegView() +{ +} + +void QmitkTractSegView::CreateQtPartControl( QWidget *parent ) +{ + // build up qt view, unless already done + if ( !m_Controls ) + { + // create GUI widgets from the Qt Designer's .ui file + m_Controls = new Ui::QmitkTractSegViewControls; + m_Controls->setupUi( parent ); + connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) ); + connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(Start()) ); + connect( m_Controls->m_OutputTypeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) ); + this->m_Parent = parent; + + m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); + mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("PeakImage"); + m_Controls->m_ImageBox->SetPredicate( isDwi ); + + UpdateGUI(); + } +} + +void QmitkTractSegView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) +{ +} + +void QmitkTractSegView::UpdateGUI() +{ + if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull()) + m_Controls->m_StartButton->setEnabled(true); + else + m_Controls->m_StartButton->setEnabled(false); +} + +void QmitkTractSegView::SetFocus() +{ + UpdateGUI(); + m_Controls->m_StartButton->setFocus(); +} + +void QmitkTractSegView::Start() +{ + mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); + mitk::Image::Pointer input_image = dynamic_cast(node->GetData()); + + // get python script as string + QString data; + QString fileName(":/QmitkDiffusionImaging/tractseg.py"); + QFile file(fileName); + if(!file.open(QIODevice::ReadOnly)) { + qDebug()<<"filenot opened"< m_PythonServiceRef = context->GetServiceReference(); + mitk::IPythonService* m_PythonService = dynamic_cast ( context->GetService(m_PythonServiceRef) ); + mitk::IPythonService::ForceLoadModule(); + + typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(input_image); + caster->Update(); + mitk::PeakImage::ItkPeakImageType::Pointer itk_peaks = caster->GetOutput(); + if (itk_peaks->GetLargestPossibleRegion().GetSize()[3]!=9) + { + QMessageBox::warning(nullptr, "Error", "TractSeg only works with 3-peak images!", QMessageBox::Ok); + return; + } + + itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New(); + flipper->SetInput(itk_peaks); + flipper->SetFlipX(false); + flipper->SetFlipY(true); + flipper->SetFlipZ(false); + flipper->Update(); + + itk::FourDToVectorImageFilter< float >::Pointer converter = itk::FourDToVectorImageFilter< float >::New(); + converter->SetInputImage(flipper->GetOutput()); + converter->GenerateData(); + mitk::Image::Pointer mitk_vec_img = mitk::GrabItkImageMemory( converter->GetOutputImage().GetPointer() ); + + m_PythonService->Execute("import SimpleITK as sitk"); + m_PythonService->Execute("import SimpleITK._SimpleITK as _SimpleITK"); + m_PythonService->Execute("import numpy"); + m_PythonService->CopyToPythonAsSimpleItkImage( mitk_vec_img, "in_image"); + + m_PythonService->Execute("sx=" + boost::lexical_cast(itk_peaks->GetLargestPossibleRegion().GetSize()[0])); + m_PythonService->Execute("sy=" + boost::lexical_cast(itk_peaks->GetLargestPossibleRegion().GetSize()[1])); + m_PythonService->Execute("sz=" + boost::lexical_cast(itk_peaks->GetLargestPossibleRegion().GetSize()[2])); + + if (m_PythonService->DoesVariableExist("segmentation")) + m_PythonService->Execute("del segmentation"); + + switch(m_Controls->m_OutputTypeBox->currentIndex()) + { + case 0: + { + m_PythonService->Execute("output_type=\"tract_segmentation\""); + break; + } + case 1: + { + m_PythonService->Execute("output_type=\"endings_segmentation\""); + break; + } + case 2: + { + m_PythonService->Execute("output_type=\"TOM\""); + break; + } + } + + if (m_Controls->m_CollapseBox->isChecked()) + m_PythonService->Execute("collapse=True"); + else + m_PythonService->Execute("collapse=False"); + m_PythonService->Execute("get_probs=False"); + m_PythonService->Execute("verbose=False"); + m_PythonService->Execute(data.toStdString(), mitk::IPythonService::MULTI_LINE_COMMAND); + + // clean up after running script (better way than deleting individual variables?) + if(m_PythonService->DoesVariableExist("in_image")) + m_PythonService->Execute("del in_image"); + if(m_PythonService->DoesVariableExist("collapse")) + m_PythonService->Execute("del collapse"); + + // check for errors + if(!m_PythonService->GetVariable("error_string").empty()) + { + QMessageBox::warning(nullptr, "Error", QString(m_PythonService->GetVariable("error_string").c_str()), QMessageBox::Ok); + return; + } + + std::vector small_name_list = {"AF_left", "AF_right", "CA", "CST_left", "CST_right", "CG_left", "CG_right", + "ICP_left", "ICP_right", "MCP", "SCP_left", "SCP_right", "ILF_left", "ILF_right", + "IFO_left", "IFO_right", "OR_left", "OR_right", "UF_left", "UF_right"}; + + std::vector large_name_list = {"AF_left", "AF_right", "ATR_left", "ATR_right", "CA", "CC_1", "CC_2", "CC_3", "CC_4", "CC_5", + "CC_6", "CC_7","CG_left","CG_right","CST_left","CST_right" ,"MLF_left","MLF_right","FPT_left" + ,"FPT_right","FX_left","FX_right","ICP_left","ICP_right","IFO_left","IFO_right" + ,"ILF_left" ,"ILF_right","MCP","OR_left","OR_right","POPT_left","POPT_right" + ,"SCP_left","SCP_right","SLF_I_left","SLF_I_right","SLF_II_left","SLF_II_right" + ,"SLF_III_left","SLF_III_right","STR_left","STR_right","UF_left","UF_right" + ,"CC","T_PREF_left","T_PREF_right","T_PREM_left","T_PREM_right","T_PREC_left" + ,"T_PREC_right","T_POSTC_left","T_POSTC_right","T_PAR_left","T_PAR_right","T_OCC_left" + ,"T_OCC_right","ST_FO_left","ST_FO_right","ST_PREF_left","ST_PREF_right","ST_PREM_left" + ,"ST_PREM_right","ST_PREC_left","ST_PREC_right","ST_POSTC_left","ST_POSTC_right" + ,"ST_PAR_left","ST_PAR_right","ST_OCC_left","ST_OCC_right"}; + + if (m_PythonService->DoesVariableExist("segmentation")) + { + mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("segmentation"); + + if (!m_Controls->m_CollapseBox->isChecked()) + { + itk::VectorImage::Pointer vectorImage = itk::VectorImage::New(); + mitk::CastToItkImage(out_image, vectorImage); + itk::SplitVectorImageFilter::Pointer splitter = itk::SplitVectorImageFilter::New(); + splitter->SetInputImage(vectorImage); + splitter->GenerateData(); + int c = 0; + for (auto itk_seg : splitter->GetOutputImages()) + { + mitk::DataNode::Pointer seg = mitk::DataNode::New(); + seg->SetData( mitk::GrabItkImageMemory(itk_seg) ); + seg->SetBoolProperty("binary", true); + if (m_Controls->m_OutputTypeBox->currentIndex()==0) + seg->SetName(large_name_list.at(c)); + else if (c%2==0) + seg->SetName(small_name_list.at(c/2) + "_Start"); + else if (c%2==1) + seg->SetName(small_name_list.at((c-1)/2) + "_End"); + GetDataStorage()->Add(seg, node); + ++c; + } + } + else + { + mitk::DataNode::Pointer seg = mitk::DataNode::New(); + seg->SetData(out_image); + + if (m_Controls->m_OutputTypeBox->currentIndex()==0) + seg->SetName("TractLabels"); + else if (m_Controls->m_OutputTypeBox->currentIndex()==1) + seg->SetName("TractEndpointRegionLabels"); + GetDataStorage()->Add(seg, node); + } + + m_PythonService->Execute("del segmentation"); + } + else + { + for (int i=0; i<20; ++i) + if (m_PythonService->DoesVariableExist("tom" + boost::lexical_cast(i))) + { + mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("tom" + boost::lexical_cast(i)); + itk::VectorImage::Pointer vectorImage = itk::VectorImage::New(); + mitk::CastToItkImage(out_image, vectorImage); + + itk::VectorImageToFourDImageFilter< float >::Pointer converter = itk::VectorImageToFourDImageFilter< float >::New(); + converter->SetInputImage(vectorImage); + converter->GenerateData(); + mitk::PeakImage::ItkPeakImageType::Pointer itk_peaks = converter->GetOutputImage(); + + mitk::Image::Pointer mitk_peaks = dynamic_cast(mitk::PeakImage::New().GetPointer()); + mitk::CastToMitkImage(itk_peaks, mitk_peaks); + mitk_peaks->SetVolume(itk_peaks->GetBufferPointer()); + + mitk::DataNode::Pointer seg = mitk::DataNode::New(); + seg->SetData( mitk_peaks ); + if (!m_Controls->m_CollapseBox->isChecked()) + seg->SetName(small_name_list.at(i) + "_TOM"); + else + seg->SetName("Collapsed_TOM"); + GetDataStorage()->Add(seg, node); + m_PythonService->Execute("del tom" + boost::lexical_cast(i)); + } + } +} diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h similarity index 72% copy from Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h copy to Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h index 3bdb00f673..3a8888d970 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h @@ -1,74 +1,65 @@ /*=================================================================== 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 "ui_QmitkDipyReconstructionsViewControls.h" -#include -#include -#include - -#include - +#include "ui_QmitkTractSegViewControls.h" /*! -\brief View for diffusion image registration / head motion correction +\brief */ -class QmitkDipyReconstructionsView : public QmitkAbstractView +class QmitkTractSegView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; - typedef itk::VectorImage< short, 3 > ItkDwiType; - typedef mitk::GradientDirectionsProperty GradProp; - - QmitkDipyReconstructionsView(); - virtual ~QmitkDipyReconstructionsView(); + QmitkTractSegView(); + virtual ~QmitkTractSegView(); virtual void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; protected slots: - void StartFit(); + void Start(); void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; - Ui::QmitkDipyReconstructionsViewControls* m_Controls; + Ui::QmitkTractSegViewControls* m_Controls; private: void UpdateRegistrationStatus(); ///< update textual status display of the Registration process // the Qt parent of our GUI (NOT of this object) QWidget* m_Parent; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui new file mode 100644 index 0000000000..c20a546ac3 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui @@ -0,0 +1,136 @@ + + + QmitkTractSegViewControls + + + + 0 + 0 + 435 + 803 + + + + Form + + + QCommandLinkButton:disabled { + border: none; +} + +QGroupBox { + background-color: transparent; +} + + + + 25 + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + false + + + + + + Start TractSeg + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + + Input Peaks: + + + + + + + Output: + + + + + + + + Tract Segmentations + + + + + Tract Endpoint Regions + + + + + Tract Orientation Maps + + + + + + + + + + + + + + Collapse tracts into single 3D volume + + + + + + + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+ + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp index c1f97d25fa..6d4bd857d3 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp @@ -1,44 +1,46 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include "src/internal/QmitkBrainExtractionView.h" #include "src/internal/QmitkDipyReconstructionsView.h" +#include "src/internal/QmitkTractSegView.h" #include ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; US_INITIALIZE_MODULE ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkBrainExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDipyReconstructionsView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkTractSegView, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp index c32959dc7a..e64a4bb757 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp @@ -1,50 +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 "QmitkReconstructionPerspective.h" #include "berryIViewLayout.h" void QmitkReconstructionPerspective::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.tensorreconstruction"); left->AddView("org.mitk.views.qballreconstruction"); left->AddView("org.mitk.views.odfmaximaextraction"); + left->AddView("org.mitk.views.dipyreconstruction"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp index d2b5bc791f..5c9020b266 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp @@ -1,49 +1,50 @@ /*=================================================================== 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 "QmitkSegmentationPerspective.h" #include "berryIViewLayout.h" void QmitkSegmentationPerspective::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.tractseg"); left->AddView("org.mitk.views.segmentation"); left->AddView("org.mitk.views.segmentationutilities"); }