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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,30 @@ | ||
| if(BUILD_TOOLS AND USE_NLOPT) | ||
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| project(animaTODEstimator) | ||
| project(animaTODEstimator) | ||
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| ## ############################################################################# | ||
| ## List Sources | ||
| ## ############################################################################# | ||
| # ############################################################################ | ||
| # List Sources | ||
| # ############################################################################ | ||
|
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| list_source_files(${PROJECT_NAME} | ||
| ${CMAKE_CURRENT_SOURCE_DIR} | ||
| ) | ||
| list_source_files(${PROJECT_NAME} ${CMAKE_CURRENT_SOURCE_DIR}) | ||
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| # ############################################################################ | ||
| # add executable | ||
| # ############################################################################ | ||
|
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| ## ############################################################################# | ||
| ## add executable | ||
| ## ############################################################################# | ||
| add_executable(${PROJECT_NAME} ${${PROJECT_NAME}_CFILES}) | ||
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| add_executable(${PROJECT_NAME} | ||
| ${${PROJECT_NAME}_CFILES} | ||
| ) | ||
| # ############################################################################ | ||
| # Link | ||
| # ############################################################################ | ||
|
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| ## ############################################################################# | ||
| ## Link | ||
| ## ############################################################################# | ||
| target_link_libraries(${PROJECT_NAME} ${ITKIO_LIBRARIES} AnimaDataIO | ||
| AnimaSHTools) | ||
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| target_link_libraries(${PROJECT_NAME} | ||
| ${VTK_LIBRARIES} | ||
| ${ITKIO_LIBRARIES} | ||
| AnimaSHTools | ||
| AnimaDataIO | ||
| ) | ||
| # ############################################################################ | ||
| # install | ||
| # ############################################################################ | ||
|
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| ## ############################################################################# | ||
| ## install | ||
| ## ############################################################################# | ||
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| set_exe_install_rules(${PROJECT_NAME}) | ||
| set_exe_install_rules(${PROJECT_NAME}) | ||
|
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| endif() |
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176 changes: 75 additions & 101 deletions
176
Anima/diffusion/odf/tod_estimator/animaTODEstimatorImageFilter.h
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,138 +1,112 @@ | ||
| #pragma once | ||
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| #include <iostream> | ||
| #include <itkImageSource.h> | ||
| #include <itkVectorImage.h> | ||
| #include <itkImage.h> | ||
| #include <vector> | ||
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| #include <animaNumberedThreadImageToImageFilter.h> | ||
| #include <animaODFSphericalHarmonicBasis.h> | ||
| #include <animaVectorOperations.h> | ||
| #include <animaReadWriteFunctions.h> | ||
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| #include <vtkPoints.h> | ||
| #include <vtkVector.h> | ||
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| namespace anima | ||
| { | ||
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| //template <typename TOutputPixelType> | ||
| class TODEstimatorImageFilter : | ||
| public anima::NumberedThreadImageToImageFilter < itk::Image<double,3>, itk::VectorImage<double,3> > | ||
| { | ||
| public: | ||
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| typedef TODEstimatorImageFilter Self; | ||
| // typedef itk::Vector<float, 3> pointType; | ||
| typedef itk::Point<float, 3> PointType; | ||
| // typedef PointType DirType; | ||
| typedef itk::Vector<double, 3> DirType; | ||
| typedef std::vector<DirType> DirVectorType; | ||
| typedef std::vector<PointType> FiberType; | ||
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| typedef double MathScalarType; | ||
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| typedef itk::Matrix <MathScalarType,3,3> Matrix3DType; | ||
| typedef itk::Vector <MathScalarType,3> Vector3DType; | ||
| typedef itk::VariableLengthVector <MathScalarType> VectorType; | ||
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| typedef anima::ODFSphericalHarmonicBasis baseSH; | ||
| typedef std::complex <double> complexType; | ||
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| typedef itk::VectorImage<double, 3> TOutputImage; | ||
| typedef itk::Image<int, 3> TRefImage; | ||
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| typedef anima::NumberedThreadImageToImageFilter <InputImageType, OutputImageType> Superclass; | ||
| typedef itk::SmartPointer<Self> Pointer; | ||
| typedef itk::SmartPointer<const Self> ConstPointer; | ||
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| itkNewMacro(Self) | ||
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| itkTypeMacro(TODEstimatorImageFilter, anima::NumberedThreadImageToImageFilter); | ||
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| typedef typename TOutputImage::Pointer OutputImagePointer; | ||
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| typedef typename Superclass::InputImageRegionType InputImageRegionType; | ||
| typedef typename Superclass::OutputImageRegionType OutputImageRegionType; | ||
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| itkSetMacro(InputFileName,std::string); | ||
| itkSetMacro(RefFileName,std::string); | ||
| itkSetMacro(LOrder,unsigned int); | ||
| itkSetMacro(Normalize, bool); | ||
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| protected: | ||
| TODEstimatorImageFilter() | ||
| : Superclass() | ||
| template <typename ScalarType> | ||
| class TODEstimatorImageFilter : public anima::NumberedThreadImageToImageFilter<itk::Image<ScalarType, 3>, itk::VectorImage<ScalarType, 3>> | ||
| { | ||
| } | ||
| public: | ||
| /** Standard class typedefs. */ | ||
| using Self = TODEstimatorImageFilter; | ||
| using InputImageType = itk::Image<ScalarType, 3>; | ||
| using OutputImageType = itk::VectorImage<ScalarType, 3>; | ||
| using ReferenceImageType = itk::Image<unsigned int, 3>; | ||
| using Superclass = anima::NumberedThreadImageToImageFilter<InputImageType, OutputImageType>; | ||
| using Pointer = itk::SmartPointer<Self>; | ||
| using ConstPointer = itk::SmartPointer<const Self>; | ||
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| virtual ~TODEstimatorImageFilter() | ||
| { | ||
| /** Method for creation through the object factory. */ | ||
| itkNewMacro(Self); | ||
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| /** Run-time type information (and related methods) */ | ||
| itkTypeMacro(TODEstimatorImageFilter, anima::NumberedThreadImageToImageFilter); | ||
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| } | ||
| /** Superclass typedefs. */ | ||
| using InputImageRegionType = typename Superclass::InputImageRegionType; | ||
| using OutputImageRegionType = typename Superclass::OutputImageRegionType; | ||
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| // void GenerateData() ITK_OVERRIDE; | ||
| using InputImagePointerType = typename InputImageType::Pointer; | ||
| using OutputImagePointerType = typename OutputImageType::Pointer; | ||
| using ReferenceImagePointerType = typename ReferenceImageType::Pointer; | ||
| using InputImagePixelType = typename InputImageType::PixelType; | ||
| using OutputImagePixelType = typename OutputImageType::PixelType; | ||
| using ReferenceImagePixelType = ReferenceImageType::PixelType; | ||
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| void BeforeThreadedGenerateData() ITK_OVERRIDE; | ||
| void DynamicThreadedGenerateData(const OutputImageRegionType &outputRegionForThread) ITK_OVERRIDE; | ||
| void AfterThreadedGenerateData() ITK_OVERRIDE; | ||
| using PointType = itk::Point<ScalarType, 3>; | ||
| using DirType = itk::Vector<double, 3>; | ||
| using DirVectorType = std::vector<DirType>; | ||
| using FiberType = std::vector<PointType>; | ||
| using Matrix3DType = itk::Matrix<double, 3, 3>; | ||
| using Vector3DType = itk::Vector<double, 3>; | ||
| using MatrixType = vnl_matrix<double>; | ||
| using BasisType = anima::ODFSphericalHarmonicBasis; | ||
| using ComplexType = std::complex<double>; | ||
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| itkSetMacro(InputFileName, std::string); | ||
| itkSetMacro(ReferenceFileName, std::string); | ||
| itkSetMacro(LOrder, unsigned int); | ||
| itkSetMacro(UseNormalization, bool); | ||
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| FiberType readFiber(vtkIdType numberOfPoints, const vtkIdType *indices, vtkPoints *points); | ||
| PointType getCenterVoxel(int index, FiberType &fiber); | ||
| DirType getFiberDirection(int index, FiberType &fiber); | ||
| void getSHCoefs(DirType dir, VectorType &resSH, baseSH &basis); | ||
| void ComputeCoefs(); | ||
| void processFiber(FiberType &fiber, baseSH &basis); | ||
| protected: | ||
| TODEstimatorImageFilter() {} | ||
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| void getMainDirections(DirVectorType inDirs, DirVectorType &mainDirs); | ||
| double getEuclideanDistance(DirType dir1, DirType dir2); | ||
| DirType getNewClusterAverage(int numCluster, DirVectorType &dirs, std::vector<int> &cluster); | ||
| virtual ~TODEstimatorImageFilter() {} | ||
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| void getSHCoef(DirType dir, VectorType &coefs); | ||
| void BeforeThreadedGenerateData() ITK_OVERRIDE; | ||
| void DynamicThreadedGenerateData(const OutputImageRegionType &outputRegionForThread) ITK_OVERRIDE; | ||
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| void precomputeSH(); | ||
| void discretizeODF(VectorType ODFCoefs, std::vector<double> &ODFDiscret); | ||
| VectorType getSquareRootODF(std::vector<double> ODFDiscret); | ||
| VectorType getSquareODF(std::vector<double> ODFDiscret); | ||
| void getAverageCoefs(std::vector<VectorType> &vecCoefs, VectorType &avgCoef); | ||
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| void averageODFs(std::vector<VectorType> &vecCoefs, VectorType &resOdf); | ||
| FiberType ReadFiber(vtkIdType numberOfPoints, const vtkIdType *indices, vtkPoints *points); | ||
| PointType GetCenterVoxel(int index, FiberType &fiber); | ||
| DirType GetFiberDirection(int index, FiberType &fiber); | ||
| void GetSHCoefs(DirType dir, OutputImagePixelType &resSH, BasisType &basis); | ||
| void ComputeCoefs(); | ||
| void ProcessFiber(FiberType &fiber, BasisType &basis); | ||
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| vnl_matrix <double> GetRotationMatrix(DirType dir1, DirType dir2); | ||
| void GetMainDirections(DirVectorType inDirs, DirVectorType &mainDirs); | ||
| double GetEuclideanDistance(DirType dir1, DirType dir2); | ||
| DirType GetNewClusterAverage(int numCluster, DirVectorType &dirs, std::vector<int> &cluster); | ||
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| // void GenerateOutputInformation() ITK_OVERRIDE; | ||
| void GetSHCoef(DirType dir, OutputImagePixelType &coefs); | ||
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| private: | ||
| ITK_DISALLOW_COPY_AND_ASSIGN(TODEstimatorImageFilter); | ||
| void PrecomputeSH(); | ||
| void DiscretizeODF(OutputImagePixelType ODFCoefs, std::vector<double> &ODFDiscret); | ||
| OutputImagePixelType GetSquareRootODF(std::vector<double> ODFDiscret); | ||
| OutputImagePixelType GetSquareODF(std::vector<double> ODFDiscret); | ||
| void GetAverageCoefs(std::vector<OutputImagePixelType> &vecCoefs, OutputImagePixelType &avgCoef); | ||
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| std::string m_InputFileName; | ||
| std::string m_RefFileName; | ||
| void AverageODFs(std::vector<OutputImagePixelType> &vecCoefs, OutputImagePixelType &resOdf); | ||
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| DirType m_CstDir; | ||
| MatrixType GetRotationMatrix(DirType dir1, DirType dir2); | ||
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| unsigned int m_LOrder; | ||
| int m_VectorLength; | ||
| private: | ||
| ITK_DISALLOW_COPY_AND_ASSIGN(TODEstimatorImageFilter); | ||
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| double m_NbSample; | ||
| std::string m_InputFileName; | ||
| std::string m_ReferenceFileName; | ||
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| bool m_Normalize; | ||
| DirType m_CstDir; | ||
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| unsigned int m_LOrder; | ||
| int m_VectorLength; | ||
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| VectorType m_GaussCoefs; | ||
| double m_NbSample; | ||
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| std::vector<std::vector<double>> m_SphereSampl; | ||
| vnl_matrix<double> m_SpherHarm; | ||
| bool m_UseNormalization; | ||
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| anima::ODFSphericalHarmonicBasis *m_ODFSHBasis; | ||
| std::vector<std::vector<DirType>> m_ImgDir; | ||
| OutputImagePixelType m_GaussCoefs; | ||
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| itk::Image<int, 3>::Pointer test; | ||
| std::vector<std::vector<double>> m_SphereSampl; | ||
| MatrixType m_SpherHarm; | ||
|
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| }; | ||
| anima::ODFSphericalHarmonicBasis *m_ODFSHBasis; | ||
| std::vector<DirVectorType> m_ImgDir; | ||
| }; | ||
| } // end namespace anima | ||
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| #include "animaTODEstimatorImageFilter.hxx" |
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