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DMRITool
v0.1.1-139-g860d86b4
Diffusion MRI Tool
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Namespaces | |
| Concept | |
| Detail | |
| Functor | |
Typedefs | |
| typedef LUTExpType::Pointer | LUTExpPointer |
| typedef UnaryFunctorLookUpTable< utl::Functor::Exp< double > > | LUTExpType |
Enumerations | |
| enum | PeakType { XYZV =0, XYZ, NXYZV, NXYZ } |
Functions | |
| template<class ImageWithInfoType , class ImageType > | |
| void | CopyImageInformation (const SmartPointer< ImageWithInfoType > &imageFrom, SmartPointer< ImageType > &imageTo) |
| template<unsigned dimIn, unsigned dimOut> | |
| void | CopyImageRegion (const ImageRegion< dimIn > ®ionIn, ImageRegion< dimOut > ®ionOut, const int numberOfComponens=-1) |
| void | CopyTrackvisHeader (const TrackVisHeaderType &hFrom, TrackVisHeaderType &hTo) |
| template<class ImageType , class ImageOutType , class MaskImageType = Image<double,4>> | |
| void | FunctorFromStringOPImage (const std::vector< itk::SmartPointer< ImageType > > &images, itk::SmartPointer< ImageOutType > &outImage, const std::string &funcStr, const itk::SmartPointer< MaskImageType > &mask=nullptr, int numberOfThreads=-1) |
| template<class ImageType > | |
| ImageType::Pointer | GenerateImage (const typename ImageType::SizeType &size, const int vectorLength=1) |
| template<class ImageType > | |
| ImageType::Pointer | GenerateImageFromSingleVoxel (const typename ImageType::PixelType &pixel) |
| int | GetDimensionOfProperties (const TrackVisHeaderType &header) |
| int | GetDimensionOfScalars (const TrackVisHeaderType &header) |
| int | GetImageType (const std::string &filename) |
| template<class ImageType > | |
| int | GetImageType (const SmartPointer< ImageType > &image) |
| template<class T , unsigned int VImageDimension> | |
| void | GetITKImageFromMXArray (const mxArray *pr, SmartPointer< Image< T, VImageDimension > > &image) |
| template<class T > | |
| void | GetITKVectorImageFromMXArray (const mxArray *pr, SmartPointer< VectorImage< T, 3 > > &image) |
| template<class T , unsigned int VImageDimension> | |
| void | GetMXArrayFromITKImage (const SmartPointer< Image< T, VImageDimension > > &image, mxArray *&pr) |
| template<class T , unsigned int VImageDimension> | |
| void | GetMXArrayFromITKVectorImage (const SmartPointer< VectorImage< T, VImageDimension > > &image, mxArray *&pr) |
| std::vector< std::string > | GetPropertyNames (const TrackVisHeaderType &header) |
| std::vector< std::string > | GetScalarNames (const TrackVisHeaderType &header) |
| template<class ImageType > | |
| std::vector< int > | GetVectorImage3DVolumeSize (const SmartPointer< ImageType > &image) |
| template<class ImageType > | |
| std::vector< int > | GetVectorImageFullSize (const SmartPointer< ImageType > &image) |
| template<class ImageType > | |
| int | GetVectorImageVectorSize (const SmartPointer< ImageType > &image, const int axis=-1) |
| bool | HasPropertyName (const TrackVisHeaderType &header, const std::string &name) |
| bool | HasScalarName (const TrackVisHeaderType &header, const std::string &name) |
| template<class Image1Type , class Image2Type > | |
| void | ImageToImage (const SmartPointer< Image1Type > &image1, SmartPointer< Image2Type > &image2) |
| template<class Image1Type , class Image2Type > | |
| SmartPointer< Image2Type > | ImageToImage (const SmartPointer< Image1Type > &image1) |
| void | InitializeLUTExp () |
| void | InitializeSHRotation (const int rank, const int tess) |
| bool | Is3DImage (const std::string &filename) |
| template<class ImageType > | |
| bool | IsImageEmpty (const SmartPointer< ImageType > &image) |
| bool | IsSameStructure (const TrackVisHeaderType &h1, const TrackVisHeaderType &h2) |
| bool | IsSparseImage (const std::string &filename) |
| bool | IsVectorImage (const std::string &filename) |
| double | lutExpValue (const double x) |
| template<class ImageType , class ImageOutType , class OpFunctor , class MaskImageType = Image<double,4>> | |
| void | MultiVariableVectorOPImage (const std::vector< itk::SmartPointer< ImageType > > &images, itk::SmartPointer< ImageOutType > &outImage, const OpFunctor &func, const itk::SmartPointer< MaskImageType > &mask=nullptr, int numberOfThreads=-1, int vectorAxis=3) |
| template<class ScalarType , unsigned Dim> | |
| void | MultiVolumeToVectorImage (const SmartPointer< Image< ScalarType, Dim+1 > > &image1, SmartPointer< VectorImage< ScalarType, Dim > > &image2) |
| template<class PointsContainer , class VnlValueType > | |
| void | PointsContainerToVnlMatrix (const PointsContainer &points, vnl_matrix< VnlValueType > &matrix) |
| template<class TPixelType , unsigned int VImageDimension> | |
| void | PrintImage (const SmartPointer< Image< TPixelType, VImageDimension > > image, const std::string &mse="", std::ostream &os=std::cout, bool isPrintHeader=false) |
| template<class TPixelType , unsigned int VImageDimension> | |
| void | PrintImage3D (const SmartPointer< Image< TPixelType, VImageDimension > > &image, const std::string &mse="", std::ostream &os=std::cout, bool isPrintHeader=false) |
| template<class TPixelType , unsigned int VImageDimension> | |
| void | PrintImage4D (const SmartPointer< Image< TPixelType, VImageDimension > > &image, const std::string &mse="", std::ostream &os=std::cout, bool isPrintHeader=false) |
| void | PrintTractVisHeader (const TrackVisHeaderType &header, std::ostream &os=std::cout) |
| template<class T > | |
| void | PrintVariableLengthVector (const VariableLengthVector< T >vec, const std::string &str="", const char *separate=" ", std::ostream &os=std::cout) |
| template<class TPixelType , unsigned int VImageDimension> | |
| void | PrintVectorImage (const SmartPointer< VectorImage< TPixelType, VImageDimension > > &image, const std::string &mse="", std::ostream &os=std::cout, bool isPrintHeader=false) |
| bool | ReadFibers (const std::string &filename, SmartPointer< FiberTracts< double > > &fibers, const std::string &printInfo="Reading fibers:") |
| template<class ImageType > | |
| bool | ReadImage (const std::string &filename, SmartPointer< ImageType > &image, const std::string &printInfo="Reading Image:") |
| template<class ImageType , class ReaderType > | |
| bool | ReadImage (const std::string &filename, SmartPointer< ImageType > &image, const std::string &printInfo="Reading Image:") |
| template<class ImageType > | |
| bool | ReadImageInformation (const std::string &filename, SmartPointer< ImageType > &image) |
| void | ReadTrackVisHeader (const std::string &filename, TrackVisHeaderType &header) |
| template<class PixelType > | |
| void | ReadVectorImage (const std::string &filename, SmartPointer< VectorImage< PixelType, 3 > > &image, const std::string &printInfo="Reading Image:") |
| void | RemovePropertyName (TrackVisHeaderType &header, const std::string &name) |
| void | RemoveScalarName (TrackVisHeaderType &header, const std::string &name) |
| bool | SaveFibers (const SmartPointer< FiberTracts< double > > &fibers, const std::string &filename, const std::string &printInfo="Writing fibers:") |
| template<class ImageType > | |
| bool | SaveImage (const SmartPointer< ImageType > &image, const std::string &filename, const std::string &printInfo="Writing Image:") |
| template<class ImageType , class WriterType > | |
| bool | SaveImage (const SmartPointer< ImageType > &image, const std::string &filename, const std::string &printInfo="Writing Image:") |
| template<class ImageType > | |
| void | SetVectorImage3DVolumeSize (SmartPointer< ImageType > &image, const std::vector< int > &size) |
| template<class ImageType > | |
| void | SetVectorImageFullSize (SmartPointer< ImageType > &image, const std::vector< int > &size) |
| template<class ImageType > | |
| void | SetVectorImageVectorSize (const SmartPointer< ImageType > &image, const int vecsize) |
| template<class ImageType , class ImageOutType , class OpFunctor , class MaskImageType = Image<double,4>> | |
| void | UnaryVectorOPImage (const itk::SmartPointer< ImageType > &image, itk::SmartPointer< ImageOutType > &outImage, const OpFunctor &func, const itk::SmartPointer< MaskImageType > &mask=nullptr, int numberOfThreads=-1, int vectorAxis=3) |
| template<class T > | |
| vnl_vector< T > | VariableLengthVectorToVnlVector (const VariableLengthVector< T > &vec) |
| template<class ScalarType , unsigned Dim> | |
| void | VectorToMultiVolumeImage (const SmartPointer< VectorImage< ScalarType, Dim > > &image1, SmartPointer< Image< ScalarType, Dim+1 > > &image2) |
| template<class Image1Type , class Image2Type > | |
| bool | VerifyImageInformation (const SmartPointer< Image1Type > &image1, const SmartPointer< Image2Type > &image2, const bool isMinimalDimension=false) |
| template<class Image1Type > | |
| bool | VerifyImageInformation (const SmartPointer< Image1Type > &image1, const std::string &file2, const bool isMinimalDimension=false) |
| bool | VerifyImageInformation (const std::string &file1, const std::string &file2, const bool isMinimalDimension=false) |
| template<class Image1Type , class Image2Type > | |
| bool | VerifyImageSize (const SmartPointer< Image1Type > &image1, const SmartPointer< Image2Type > &image2, const bool isMinimalDimension=false) |
| template<class Image1Type > | |
| bool | VerifyImageSize (const SmartPointer< Image1Type > &image1, const std::string &file2, const bool isMinimalDimension=false) |
| bool | VerifyImageSize (const std::string &file1, const std::string &file2, const bool isMinimalDimension=false) |
| template<class VnlValueType , class PointsContainer > | |
| void | VnlMatrixToPointsContainer (const vnl_matrix< VnlValueType > &matrix, PointsContainer &points) |
| template<class T > | |
| VariableLengthVector< T > | VnlVectorToVariableLengthVector (const vnl_vector< T > &vec) |
| void | WriteTrackVisHeader (const TrackVisHeaderType &header, FILE *file) |
Variables | |
| static LUTExpPointer | lutExp = LUTExpType::New() |
Definition at line 32 of file utlDMRIStoredTables.h.
| typedef UnaryFunctorLookUpTable<utl::Functor::Exp<double> > itk::LUTExpType |
Definition at line 31 of file utlDMRIStoredTables.h.
| enum itk::PeakType |
Definition at line 28 of file itkPeakContainerHelper.h.
| void itk::CopyTrackvisHeader | ( | const TrackVisHeaderType & | hFrom, |
| TrackVisHeaderType & | hTo | ||
| ) |
Definition at line 57 of file itkTrackvisHeader.h.
Referenced by itk::FiberTracts< TValue >::DeepClone(), itk::FiberTracts< TValue >::SelectByBallROI(), and itk::FiberTracts< TValue >::SelectByIndicesOfTracts().
Here is the caller graph for this function:| void itk::FunctorFromStringOPImage | ( | const std::vector< itk::SmartPointer< ImageType > > & | images, |
| itk::SmartPointer< ImageOutType > & | outImage, | ||
| const std::string & | funcStr, | ||
| const itk::SmartPointer< MaskImageType > & | mask = nullptr, |
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| int | numberOfThreads = -1 |
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| ) |
By defining a functor which maps multiple vectors to another vector, this function perform the functor on a set of images (VectorImage or NDImage).
Definition at line 109 of file itkFunctorFromStringImageFilter.h.
References IsImageEmpty(), utl::IsLogDebug(), and utl::LogLevel.
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Get total dimension of properties
Definition at line 141 of file itkTrackvisHeader.h.
References utl::GetScalarsDimentionByName(), itk::TrackVisHeaderType::n_properties, and itk::TrackVisHeaderType::property_name.
Referenced by itk::Fiber< TValue >::PrintSelf(), PrintTractVisHeader(), ReadTrackVisHeader(), itk::FiberTractsReader::ReadTractsTRK(), and itk::FiberTractsWriter::WriteTractsTRK().
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Get total dimension of scalars
Definition at line 125 of file itkTrackvisHeader.h.
References utl::GetScalarsDimentionByName(), itk::TrackVisHeaderType::n_scalars, and itk::TrackVisHeaderType::scalar_name.
Referenced by PrintTractVisHeader(), ReadTrackVisHeader(), itk::FiberTractsReader::ReadTractsTRK(), and itk::FiberTractsWriter::WriteTractsTRK().
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Definition at line 55 of file mexITK.h.
References utlException.
Referenced by callFunction().
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Definition at line 128 of file mexITK.h.
References utl::min(), and utlException.
Referenced by callFunction().
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Definition at line 32 of file mexITK.h.
References utlException.
Referenced by callFunction().
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Definition at line 96 of file mexITK.h.
References utlException.
Referenced by callFunction().
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Definition at line 96 of file itkTrackvisHeader.h.
References utl::CovertChar2DArrayToStringArray(), and itk::TrackVisHeaderType::property_name.
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Definition at line 90 of file itkTrackvisHeader.h.
References utl::CovertChar2DArrayToStringArray(), and itk::TrackVisHeaderType::scalar_name.
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Definition at line 102 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::n_properties, and itk::TrackVisHeaderType::property_name.
Referenced by itk::FiberTracts< TValue >::HasPropertyName().
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Definition at line 113 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::n_scalars, and itk::TrackVisHeaderType::scalar_name.
Referenced by itk::FiberTracts< TValue >::HasScalarName().
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Definition at line 37 of file utlDMRIStoredTables.h.
References itk::UnaryFunctorLookUpTable< TFunctor >::New().
Referenced by main().
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Definition at line 176 of file itkSHCoefficientsRotation.h.
| bool itk::IsSameStructure | ( | const TrackVisHeaderType & | h1, |
| const TrackVisHeaderType & | h2 | ||
| ) |
test if two fibers can be merged
Definition at line 64 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::dim, itk::TrackVisHeaderType::n_properties, itk::TrackVisHeaderType::n_scalars, itk::TrackVisHeaderType::property_name, itk::TrackVisHeaderType::scalar_name, and itk::TrackVisHeaderType::voxel_size.
Referenced by itk::FiberTracts< TValue >::AppendFibers().
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Definition at line 50 of file utlDMRIStoredTables.h.
References utl::SH3IntegralTable().
Referenced by utl::ComputeDWISHCoefficientsForGPDCylinder(), utl::GetExpProductLegendreCoef(), utl::GetSymmetricTensorSHCoef(), and utl::GetSymmetricTensorSHCoefDerivative().
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Here is the caller graph for this function:| void itk::MultiVariableVectorOPImage | ( | const std::vector< itk::SmartPointer< ImageType > > & | images, |
| itk::SmartPointer< ImageOutType > & | outImage, | ||
| const OpFunctor & | func, | ||
| const itk::SmartPointer< MaskImageType > & | mask = nullptr, |
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| int | numberOfThreads = -1, |
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| int | vectorAxis = 3 |
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| ) |
By defining a functor which maps multiple vectors to another vector, this function perform the functor on a set of images (VectorImage or NDImage, along axis).
Definition at line 103 of file itkMultiVariableFunctorVectorImageFilter.h.
References IsImageEmpty(), utl::IsLogDebug(), and utl::LogLevel.
Here is the call graph for this function:| void itk::MultiVolumeToVectorImage | ( | const SmartPointer< Image< ScalarType, Dim+1 > > & | image1, |
| SmartPointer< VectorImage< ScalarType, Dim > > & | image2 | ||
| ) |
Definition at line 88 of file itkMultiVolumeImageToVectorImageFilter.hxx.
Referenced by ConvertImage< NDImageType, VectorImageType >().
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print trackvis header
Definition at line 247 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::dim, GetDimensionOfProperties(), GetDimensionOfScalars(), itk::TrackVisHeaderType::id_string, itk::TrackVisHeaderType::image_orientation_patient, itk::TrackVisHeaderType::n_count, itk::TrackVisHeaderType::n_properties, itk::TrackVisHeaderType::n_scalars, itk::TrackVisHeaderType::origin, itk::TrackVisHeaderType::property_name, itk::TrackVisHeaderType::scalar_name, itk::TrackVisHeaderType::version, itk::TrackVisHeaderType::vox_to_ras, itk::TrackVisHeaderType::voxel_order, and itk::TrackVisHeaderType::voxel_size.
Referenced by itk::FiberTracts< TValue >::PrintFibersHeader().
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Definition at line 83 of file itkFiberTractsReader.h.
References utl::IsLogNormal(), and itk::FiberTractsReader::New().
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read trackvis header
Definition at line 194 of file itkTrackvisHeader.h.
References GetDimensionOfProperties(), GetDimensionOfScalars(), itk::TrackVisHeaderType::id_string, itk::TrackVisHeaderType::n_count, utlGlobalException, and utlSAGlobalWarning.
Referenced by itk::FiberTractsReader::ReadTractsTRK().
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if it is a VectorImage, directly read it. If it is a 4D image, read it as Image, then convert it to a VectorImage
Definition at line 66 of file utl.h.
References utl::IsFileExist(), IsVectorImage(), and utlGlobalException.
Referenced by main().
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remove properties by its name
Definition at line 175 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::n_properties, and itk::TrackVisHeaderType::property_name.
Referenced by itk::FiberTracts< TValue >::RemovePropertiesByName().
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remove scalars by its name
Definition at line 157 of file itkTrackvisHeader.h.
References itk::TrackVisHeaderType::n_scalars, and itk::TrackVisHeaderType::scalar_name.
Referenced by itk::FiberTracts< TValue >::RemoveScalarsByName().
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Definition at line 79 of file itkFiberTractsWriter.h.
References utl::IsLogNormal(), and itk::FiberTractsWriter::New().
Here is the call graph for this function:| void itk::UnaryVectorOPImage | ( | const itk::SmartPointer< ImageType > & | image, |
| itk::SmartPointer< ImageOutType > & | outImage, | ||
| const OpFunctor & | func, | ||
| const itk::SmartPointer< MaskImageType > & | mask = nullptr, |
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| int | numberOfThreads = -1, |
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| int | vectorAxis = 3 |
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| ) |
By defining a functor which maps a vector to another vector, this function perform the functor on an image (VectorImage or NDImage, along axis).
Definition at line 116 of file itkUnaryFunctorVectorImageFilter.h.
References IsImageEmpty(), utl::IsLogDebug(), and utl::LogLevel.
Here is the call graph for this function:| void itk::VectorToMultiVolumeImage | ( | const SmartPointer< VectorImage< ScalarType, Dim > > & | image1, |
| SmartPointer< Image< ScalarType, Dim+1 > > & | image2 | ||
| ) |
Definition at line 97 of file itkVectorImageToMultiVolumeImageFilter.hxx.
Referenced by ConvertImage< VectorImageType, NDImageType >().
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write trackvis header
Definition at line 236 of file itkTrackvisHeader.h.
References utlGlobalException.
Referenced by itk::FiberTractsWriter::WriteTractsTRK().
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use lookup table to approximate exp(-x)
Definition at line 34 of file utlDMRIStoredTables.h.
1.8.11