DTI tractography image filter. Simple step by step tratpography, using advection-diffusion tricks from Weinstein et al. 1999. Tensorlines: Advection-Diffusion based Propagation through Diffusion Tensor Fields. More...

#include <animaDTITractographyImageFilter.h>

Inheritance diagram for anima::dtiTractographyImageFilter:

Collaboration diagram for anima::dtiTractographyImageFilter:

Public Types
typedef itk::SmartPointer< const Self >	ConstPointer

typedef DTIInterpolatorType::Pointer	DTIInterpolatorPointer

typedef itk::LinearInterpolateImageFunction< ModelImageType >	DTIInterpolatorType

typedef Superclass::ModelImageType	ModelImageType

typedef itk::SmartPointer< Self >	Pointer

typedef Superclass::PointType	PointType

typedef dtiTractographyImageFilter	Self

typedef anima::BaseTractographyImageFilter	Superclass

typedef Superclass::VectorType	VectorType

Public Types inherited from anima::BaseTractographyImageFilter
typedef itk::SmartPointer< const Self >	ConstPointer

typedef itk::ContinuousIndex< double, 3 >	ContinuousIndexType

typedef std::vector< std::pair< FiberProgressType, FiberType > >	FiberProcessVectorType

enum	FiberProgressType { Forward, Backward, Both }

typedef std::vector< PointType >	FiberType

typedef MaskImageType::IndexType	IndexType

typedef MaskImageType::Pointer	MaskImagePointer

typedef itk::Image< unsigned short, 3 >	MaskImageType

typedef ModelImageType::Pointer	ModelImagePointer

typedef itk::VectorImage< double, 3 >	ModelImageType

typedef itk::SmartPointer< Self >	Pointer

typedef MaskImageType::PointType	PointType

typedef ModelImageType::RegionType	RegionType

typedef BaseTractographyImageFilter	Self

typedef itk::ProcessObject	Superclass

typedef ModelImageType::PixelType	VectorType

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual const char *	GetNameOfClass () const

virtual double	GetPunctureWeight ()

virtual void	SetInputImage (ModelImageType *input) ITK_OVERRIDE

virtual void	SetPunctureWeight (double _arg)

void	SetStopADCThreshold (double num)

void	SetStopFAThreshold (double num)

Public Member Functions inherited from anima::BaseTractographyImageFilter
void	createVTKOutput (std::vector< std::vector< PointType > > &filteredFibers)

ModelImageType *	GetInputImage ()

vtkPolyData *	GetOutput ()

void	SetComputeLocalColors (bool flag)

void	SetCutMask (MaskImageType *mask)

void	SetFilteringMask (MaskImageType *mask)

void	SetForbiddenMask (MaskImageType *mask)

void	SetMaxFiberAngle (double num)

void	SetMaxLengthFiber (double num)

void	SetMinLengthFiber (double num)

void	SetNumberOfFibersPerPixel (unsigned int num)

void	SetSeedingMask (MaskImageType *mask)

void	SetStepProgression (double num)

void	Update () ITK_OVERRIDE

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
virtual bool	CheckIndexInImageBounds (ContinuousIndexType &index) ITK_OVERRIDE

virtual bool	CheckModelCompatibility (VectorType &modelValue, itk::ThreadIdType threadId) ITK_OVERRIDE

virtual void	ComputeAdditionalScalarMaps () ITK_OVERRIDE

	dtiTractographyImageFilter ()

virtual PointType	GetModelPrincipalDirection (VectorType &modelValue, bool is2d, itk::ThreadIdType threadId) ITK_OVERRIDE

virtual void	GetModelValue (ContinuousIndexType &index, VectorType &modelValue) ITK_OVERRIDE
	Computes value of model from data. May use SNR and previous model value to perform smart interpolation. Replaces SNR and modelValue by the outputs. More...

virtual PointType	GetNextDirection (PointType &previousDirection, VectorType &modelValue, bool is2d, itk::ThreadIdType threadId) ITK_OVERRIDE

virtual	~dtiTractographyImageFilter ()

Protected Member Functions inherited from anima::BaseTractographyImageFilter
	BaseTractographyImageFilter ()

bool	CheckIndexInImageBounds (IndexType &index, ImageBaseType *testImage)

FiberProcessVectorType	ComputeFiber (FiberType &fiber, FiberProgressType ways, itk::ThreadIdType threadId)

std::vector< FiberType >	FilterOutputFibers (std::vector< FiberType > &fibers)

bool	isZero (VectorType &value)

virtual void	PrepareTractography ()

void	ThreadedTrackComputer (unsigned int numThread, std::vector< FiberType > &resultFibers, unsigned int startSeedIndex, unsigned int endSeedIndex)

void	ThreadTrack (unsigned int numThread, std::vector< FiberType > &resultFibers)

virtual	~BaseTractographyImageFilter ()

Additional Inherited Members
Protected Types inherited from anima::BaseTractographyImageFilter
typedef itk::ImageBase< ModelImageType::ImageDimension >	ImageBaseType

Static Protected Member Functions inherited from anima::BaseTractographyImageFilter
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreadTracker (void *arg)

Detailed Description

DTI tractography image filter. Simple step by step tratpography, using advection-diffusion tricks from Weinstein et al. 1999. Tensorlines: Advection-Diffusion based Propagation through Diffusion Tensor Fields.

Definition at line 15 of file animaDTITractographyImageFilter.h.

Member Typedef Documentation

◆ ConstPointer

typedef itk::SmartPointer<const Self> anima::dtiTractographyImageFilter::ConstPointer

Definition at line 23 of file animaDTITractographyImageFilter.h.

◆ DTIInterpolatorPointer

typedef DTIInterpolatorType::Pointer anima::dtiTractographyImageFilter::DTIInterpolatorPointer

Definition at line 33 of file animaDTITractographyImageFilter.h.

◆ DTIInterpolatorType

typedef itk::LinearInterpolateImageFunction<ModelImageType> anima::dtiTractographyImageFilter::DTIInterpolatorType

Definition at line 32 of file animaDTITractographyImageFilter.h.

◆ ModelImageType

typedef Superclass::ModelImageType anima::dtiTractographyImageFilter::ModelImageType

Definition at line 29 of file animaDTITractographyImageFilter.h.

◆ Pointer

typedef itk::SmartPointer<Self> anima::dtiTractographyImageFilter::Pointer

Definition at line 22 of file animaDTITractographyImageFilter.h.

◆ PointType

typedef Superclass::PointType anima::dtiTractographyImageFilter::PointType

Definition at line 31 of file animaDTITractographyImageFilter.h.

◆ Self

typedef dtiTractographyImageFilter anima::dtiTractographyImageFilter::Self

SmartPointer typedef support

Definition at line 19 of file animaDTITractographyImageFilter.h.

◆ Superclass

typedef anima::BaseTractographyImageFilter anima::dtiTractographyImageFilter::Superclass

Definition at line 20 of file animaDTITractographyImageFilter.h.

◆ VectorType

typedef Superclass::VectorType anima::dtiTractographyImageFilter::VectorType

Definition at line 30 of file animaDTITractographyImageFilter.h.

Constructor & Destructor Documentation

◆ dtiTractographyImageFilter()

anima::dtiTractographyImageFilter::dtiTractographyImageFilter ( )

protected

Definition at line 12 of file animaDTITractographyImageFilter.cxx.

◆ ~dtiTractographyImageFilter()

anima::dtiTractographyImageFilter::~dtiTractographyImageFilter ( )

protectedvirtual

Definition at line 18 of file animaDTITractographyImageFilter.cxx.

Member Function Documentation

◆ CheckIndexInImageBounds()

bool anima::dtiTractographyImageFilter::CheckIndexInImageBounds ( ContinuousIndexType & index )

protectedvirtual

Implements anima::BaseTractographyImageFilter.

Definition at line 70 of file animaDTITractographyImageFilter.cxx.

◆ CheckModelCompatibility()

bool anima::dtiTractographyImageFilter::CheckModelCompatibility	(	VectorType &	modelValue,
		itk::ThreadIdType	threadId
	)

protectedvirtual

Implements anima::BaseTractographyImageFilter.

Definition at line 30 of file animaDTITractographyImageFilter.cxx.

References anima::GetTensorFromVectorRepresentation().

◆ ComputeAdditionalScalarMaps()

void anima::dtiTractographyImageFilter::ComputeAdditionalScalarMaps ( )

protectedvirtual

Reimplemented from anima::BaseTractographyImageFilter.

Definition at line 169 of file animaDTITractographyImageFilter.cxx.

References anima::BaseTractographyImageFilter::GetInputImage(), GetModelValue(), anima::BaseTractographyImageFilter::GetOutput(), anima::LogEuclideanTensorCalculator< TScalarType >::GetTensorExponential(), and anima::GetTensorFromVectorRepresentation().

◆ CreateAnother()

virtual::itk::LightObject::Pointer anima::dtiTractographyImageFilter::CreateAnother ( void ) const

◆ GetModelPrincipalDirection()

dtiTractographyImageFilter::PointType anima::dtiTractographyImageFilter::GetModelPrincipalDirection	(	VectorType &	modelValue,
		bool	is2d,
		itk::ThreadIdType	threadId
	)

protectedvirtual

Implements anima::BaseTractographyImageFilter.

Definition at line 82 of file animaDTITractographyImageFilter.cxx.

References anima::GetTensorFromVectorRepresentation().

Referenced by GetNextDirection().

◆ GetModelValue()

void anima::dtiTractographyImageFilter::GetModelValue	(	ContinuousIndexType &	index,
		VectorType &	modelValue
	)

protectedvirtual

Computes value of model from data. May use SNR and previous model value to perform smart interpolation. Replaces SNR and modelValue by the outputs.

Implements anima::BaseTractographyImageFilter.

Definition at line 76 of file animaDTITractographyImageFilter.cxx.

Referenced by ComputeAdditionalScalarMaps().

◆ GetNameOfClass()

virtual const char* anima::dtiTractographyImageFilter::GetNameOfClass ( ) const

virtual

Reimplemented from anima::BaseTractographyImageFilter.

◆ GetNextDirection()

dtiTractographyImageFilter::PointType anima::dtiTractographyImageFilter::GetNextDirection	(	PointType &	previousDirection,
		VectorType &	modelValue,
		bool	is2d,
		itk::ThreadIdType	threadId
	)