#include <animaODFProbabilisticTractographyImageFilter.h>

Inheritance diagram for anima::ODFProbabilisticTractographyImageFilter:

Collaboration diagram for anima::ODFProbabilisticTractographyImageFilter:

Classes
struct	XYZ

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

typedef itk::SmartPointer< Self >	Pointer

typedef ODFProbabilisticTractographyImageFilter	Self

typedef BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >	Superclass

Public Types inherited from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >
enum	ColinearityDirectionType
	Which direction should the very first direction point to? (used in conjunction with InitialDirectionMode) Center: towards gravity center Outward: outward from gravity center Top: Image top (z axis) Bottom: Image bottom (reverse z axis) ... More...

typedef itk::SmartPointer< const Self >	ConstPointer

typedef InterpolatorType::ContinuousIndexType	ContinuousIndexType

typedef std::vector< Vector3DType >	DirectionVectorType

typedef std::vector< FiberType >	FiberProcessVectorType

typedef std::vector< PointType >	FiberType

typedef MaskImageType::IndexType	IndexType

enum	InitialDirectionModeType
	Tells how to choose the very first direction of each particle Colinear: Most colinear to colinear direction specified (ColinearityDirectionType) Weight: Model direction with the highest weight. More...

typedef InputModelImageType::Pointer	InputModelImagePointer

typedef itk::VectorImage< double, 3 >	InputModelImageType

typedef InterpolatorType::Pointer	InterpolatorPointer

typedef itk::InterpolateImageFunction< InputModelImageType >	InterpolatorType

typedef std::vector< ScalarType >	ListType

typedef MaskImageType::Pointer	MaskImagePointer

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

typedef itk::Matrix< ScalarType, 3, 3 >	Matrix3DType

typedef std::vector< unsigned int >	MembershipType

typedef itk::SmartPointer< Self >	Pointer

typedef MaskImageType::PointType	PointType

typedef ScalarImageType::Pointer	ScalarImagePointer

typedef itk::Image< ScalarType, 3 >	ScalarImageType

typedef ScalarInterpolatorType::Pointer	ScalarInterpolatorPointer

typedef itk::LinearInterpolateImageFunction< ScalarImageType >	ScalarInterpolatorType

typedef double	ScalarType

typedef BaseProbabilisticTractographyImageFilter	Self

typedef itk::ProcessObject	Superclass

typedef itk::Vector< ScalarType, 3 >	Vector3DType

typedef itk::VariableLengthVector< ScalarType >	VectorType

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

virtual const char *	GetNameOfClass () const

virtual void	SetCurvatureScale (double _arg)

virtual void	SetGFAThreshold (double _arg)

virtual void	SetMinimalDiffusionProbability (double _arg)

void	SetODFSHOrder (unsigned int num)

Public Member Functions inherited from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >
void	createVTKOutput (FiberProcessVectorType &filteredFibers, ListType &filteredWeights)

virtual InitialDirectionModeType	GetInitialDirectionMode ()

InputModelImageType *	GetInputModelImage ()

virtual double	GetKappaOfPriorDistribution ()

virtual unsigned int	GetModelDimension ()

virtual InterpolatorType *	GetModelInterpolator ()

vtkPolyData *	GetOutput ()

virtual void	SetB0Image (ScalarImageType *_arg)

virtual void	SetClusterDistance (unsigned int _arg)

virtual void	SetComputeLocalColors (bool _arg)

virtual void	SetCutMask (MaskImageType *_arg)

virtual void	SetFiberTrashThreshold (double _arg)

virtual void	SetFilterMask (MaskImageType *_arg)

virtual void	SetForbiddenMask (MaskImageType *_arg)

void	SetInitialColinearityDirection (const ColinearityDirectionType &colDir)

void	SetInitialDirectionMode (const InitialDirectionModeType &dir)

virtual void	SetInputModelImage (InputModelImageType *inImage)

virtual void	SetKappaOfPriorDistribution (double _arg)

virtual void	SetKappaSplitThreshold (double _arg)

virtual void	SetMAPMergeFibers (bool _arg)

virtual void	SetMaxLengthFiber (double _arg)

virtual void	SetMinimalNumberOfParticlesPerClass (unsigned int _arg)

virtual void	SetMinLengthFiber (double _arg)

virtual void	SetModelDimension (unsigned int _arg)

virtual void	SetNoiseImage (ScalarImageType *_arg)

virtual void	SetNumberOfFibersPerPixel (unsigned int _arg)

virtual void	SetNumberOfParticles (unsigned int _arg)

virtual void	SetPositionDistanceFuseThreshold (double _arg)

virtual void	SetResamplingThreshold (double _arg)

virtual void	SetSeedMask (MaskImageType *_arg)

virtual void	SetStepProgression (double _arg)

void	Update () ITK_OVERRIDE

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
virtual bool	CheckModelProperties (double estimatedB0Value, double estimatedNoiseValue, VectorType &modelValue, unsigned int threadId) ITK_OVERRIDE

virtual double	ComputeLogWeightUpdate (double b0Value, double noiseValue, Vector3DType &newDirection, VectorType &modelValue, double &log_prior, double &log_proposal, unsigned int threadId) ITK_OVERRIDE

virtual void	ComputeModelValue (InterpolatorPointer &modelInterpolator, ContinuousIndexType &index, VectorType &modelValue) ITK_OVERRIDE

unsigned int	FindODFMaxima (const VectorType &modelValue, DirectionVectorType &maxima, double minVal, bool is2d)
	Returns ODF maxima ordered by probability of diffusion, only those with probability superior to minVal are given. More...

double	GetGeneralizedFractionalAnisotropy (VectorType &modelValue)

virtual Vector3DType	InitializeFirstIterationFromModel (Vector3DType &colinearDir, VectorType &modelValue, unsigned int threadId) ITK_OVERRIDE

	ODFProbabilisticTractographyImageFilter ()

void	PrepareTractography () ITK_OVERRIDE
	Generate seed points. More...

virtual Vector3DType	ProposeNewDirection (Vector3DType &oldDirection, VectorType &modelValue, Vector3DType &sampling_direction, double &log_prior, double &log_proposal, std::mt19937 &random_generator, unsigned int threadId) ITK_OVERRIDE

virtual	~ODFProbabilisticTractographyImageFilter ()

Protected Member Functions inherited from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >
	BaseProbabilisticTractographyImageFilter ()

virtual bool	CheckModelProperties (double estimatedB0Value, double estimatedNoiseValue, VectorType &modelValue, unsigned int threadId)=0
	Check stopping criterions to stop a particle (model dependent, not implemented here) More...

virtual void	ComputeAdditionalScalarMaps ()
	Computes additional scalar maps that are model dependent to add to the output. More...

FiberProcessVectorType	ComputeFiber (FiberType &fiber, InterpolatorPointer &modelInterpolator, unsigned int numThread, ListType &resultWeights)
	This little guy is the one handling probabilistic tracking. More...

virtual double	ComputeLogWeightUpdate (double b0Value, double noiseValue, Vector3DType &newDirection, VectorType &modelValue, double &log_prior, double &log_proposal, unsigned int threadId)=0
	Update particle weight based on an underlying model and the chosen direction (model dependent, not implemented here) More...

virtual void	ComputeModelValue (InterpolatorPointer &modelInterpolator, ContinuousIndexType &index, VectorType &modelValue)=0
	Estimate model from raw diffusion data (model dependent, not implemented here) More...

FiberProcessVectorType	FilterOutputFibers (FiberProcessVectorType &fibers, ListType &weights)
	Filter output fibers by ROIs and compute local colors. More...

virtual Vector3DType	InitializeFirstIterationFromModel (Vector3DType &colinearDir, VectorType &modelValue, unsigned int threadId)=0
	Initialize first direction from user input (model dependent, not implemented here) More...

bool	MergeParticleClassFibers (FiberWorkType &fiberData, FiberProcessVectorType &outputMerged, unsigned int classNumber)
	This guy takes the result of computefiber and merges the classes, each one becomes one fiber. More...

virtual Vector3DType	ProposeNewDirection (Vector3DType &oldDirection, VectorType &modelValue, Vector3DType &sampling_direction, double &log_prior, double &log_proposal, std::mt19937 &random_generator, unsigned int threadId)=0
	Propose new direction for a particle, given the old direction, and a model (model dependent, not implemented here) More...

void	ThreadedTrackComputer (unsigned int numThread, FiberProcessVectorType &resultFibers, ListType &resultWeights, unsigned int startSeedIndex, unsigned int endSeedIndex)
	Doing the real tracking by calling ComputeFiber and merging its results. More...

void	ThreadTrack (unsigned int numThread, FiberProcessVectorType &resultFibers, ListType &resultWeights)
	Doing the thread work dispatch. More...

unsigned int	UpdateClassesMemberships (FiberWorkType &fiberData, DirectionVectorType &directions, std::mt19937 &random_generator)
	This ugly guy is the heart of multi-modal probabilistic tractography, making decisions on split and merges of particles. More...

virtual	~BaseProbabilisticTractographyImageFilter ()

Additional Inherited Members
Static Protected Member Functions inherited from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreadTracker (void *arg)
	Multithread util function. More...

Detailed Description

Definition at line 12 of file animaODFProbabilisticTractographyImageFilter.h.

Member Typedef Documentation

◆ ConstPointer

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

Definition at line 20 of file animaODFProbabilisticTractographyImageFilter.h.

◆ Pointer

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

Definition at line 19 of file animaODFProbabilisticTractographyImageFilter.h.

◆ Self

typedef ODFProbabilisticTractographyImageFilter anima::ODFProbabilisticTractographyImageFilter::Self

SmartPointer typedef support

Definition at line 16 of file animaODFProbabilisticTractographyImageFilter.h.

◆ Superclass

typedef BaseProbabilisticTractographyImageFilter< itk::VectorImage <double, 3> > anima::ODFProbabilisticTractographyImageFilter::Superclass

Definition at line 17 of file animaODFProbabilisticTractographyImageFilter.h.

Constructor & Destructor Documentation

◆ ODFProbabilisticTractographyImageFilter()

anima::ODFProbabilisticTractographyImageFilter::ODFProbabilisticTractographyImageFilter ( )

protected

Definition at line 17 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::SetModelDimension().

◆ ~ODFProbabilisticTractographyImageFilter()

anima::ODFProbabilisticTractographyImageFilter::~ODFProbabilisticTractographyImageFilter ( )

protectedvirtual

Definition at line 31 of file animaODFProbabilisticTractographyImageFilter.cxx.

Member Function Documentation

◆ CheckModelProperties()

bool anima::ODFProbabilisticTractographyImageFilter::CheckModelProperties	(	double	estimatedB0Value,
		double	estimatedNoiseValue,
		VectorType &	modelValue,
		unsigned int	threadId
	)

protectedvirtual

Definition at line 199 of file animaODFProbabilisticTractographyImageFilter.cxx.

References GetGeneralizedFractionalAnisotropy(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetModelDimension().

◆ ComputeLogWeightUpdate()

double anima::ODFProbabilisticTractographyImageFilter::ComputeLogWeightUpdate	(	double	b0Value,
		double	noiseValue,
		Vector3DType &	newDirection,
		VectorType &	modelValue,
		double &	log_prior,
		double &	log_proposal,
		unsigned int	threadId
	)

protectedvirtual

Definition at line 224 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::EvaluateWatsonPDF(), FindODFMaxima(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage().

◆ ComputeModelValue()

void anima::ODFProbabilisticTractographyImageFilter::ComputeModelValue	(	InterpolatorPointer &	modelInterpolator,
		ContinuousIndexType &	index,
		VectorType &	modelValue
	)

protectedvirtual

Definition at line 400 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetModelDimension().

◆ CreateAnother()

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

◆ FindODFMaxima()

unsigned int anima::ODFProbabilisticTractographyImageFilter::FindODFMaxima	(	const VectorType &	modelValue,
		DirectionVectorType &	maxima,
		double	minVal,
		bool	is2d
	)

protected

Returns ODF maxima ordered by probability of diffusion, only those with probability superior to minVal are given.

Definition at line 248 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::ComputeOrientationAngle(), anima::TransformCartesianToSphericalCoordinates(), anima::TransformSphericalToCartesianCoordinates(), anima::ODFProbabilisticTractographyImageFilter::XYZ::x, anima::ODFProbabilisticTractographyImageFilter::XYZ::y, and anima::ODFProbabilisticTractographyImageFilter::XYZ::z.

Referenced by ComputeLogWeightUpdate(), InitializeFirstIterationFromModel(), and ProposeNewDirection().

◆ GetGeneralizedFractionalAnisotropy()

double anima::ODFProbabilisticTractographyImageFilter::GetGeneralizedFractionalAnisotropy ( VectorType & modelValue )

protected

Definition at line 410 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetModelDimension().

Referenced by CheckModelProperties().

◆ GetNameOfClass()

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

virtual

Reimplemented from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >.

◆ InitializeFirstIterationFromModel()

ODFProbabilisticTractographyImageFilter::Vector3DType anima::ODFProbabilisticTractographyImageFilter::InitializeFirstIterationFromModel	(	Vector3DType &	colinearDir,
		VectorType &	modelValue,
		unsigned int	threadId
	)

protectedvirtual

Definition at line 141 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::Colinear, anima::ComputeScalarProduct(), FindODFMaxima(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInitialDirectionMode(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::Weight.

◆ New()

static Pointer anima::ODFProbabilisticTractographyImageFilter::New ( )

static

◆ PrepareTractography()

void anima::ODFProbabilisticTractographyImageFilter::PrepareTractography ( )

protectedvirtual

Generate seed points.

Reimplemented from anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >.

Definition at line 37 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage(), anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::PrepareTractography(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::SetModelDimension().

◆ ProposeNewDirection()

ODFProbabilisticTractographyImageFilter::Vector3DType anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection	(	Vector3DType &	oldDirection,
		VectorType &	modelValue,
		Vector3DType &	sampling_direction,
		double &	log_prior,
		double &	log_proposal,
		std::mt19937 &	random_generator,
		unsigned int	threadId
	)

protectedvirtual

Definition at line 53 of file animaODFProbabilisticTractographyImageFilter.cxx.

References anima::ComputeScalarProduct(), anima::EvaluateWatsonPDF(), FindODFMaxima(), anima::ODFSphericalHarmonicBasis::getCurvatureAtPosition(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetKappaOfPriorDistribution(), anima::ODFSphericalHarmonicBasis::getValueAtPosition(), anima::safe_log(), anima::SampleFromWatsonDistribution(), and anima::TransformCartesianToSphericalCoordinates().

◆ SetCurvatureScale()

virtual void anima::ODFProbabilisticTractographyImageFilter::SetCurvatureScale ( double _arg )

virtual

◆ SetGFAThreshold()

virtual void anima::ODFProbabilisticTractographyImageFilter::SetGFAThreshold ( double _arg )

virtual

◆ SetMinimalDiffusionProbability()

virtual void anima::ODFProbabilisticTractographyImageFilter::SetMinimalDiffusionProbability ( double _arg )

virtual

◆ SetODFSHOrder()

void anima::ODFProbabilisticTractographyImageFilter::SetODFSHOrder ( unsigned int num )

The documentation for this class was generated from the following files:

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstPointer

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ ODFProbabilisticTractographyImageFilter()

◆ ~ODFProbabilisticTractographyImageFilter()

Member Function Documentation

◆ CheckModelProperties()

◆ ComputeLogWeightUpdate()

◆ ComputeModelValue()

◆ CreateAnother()

◆ FindODFMaxima()

◆ GetGeneralizedFractionalAnisotropy()

◆ GetNameOfClass()

◆ InitializeFirstIterationFromModel()

◆ New()

◆ PrepareTractography()

◆ ProposeNewDirection()

◆ SetCurvatureScale()

◆ SetGFAThreshold()

◆ SetMinimalDiffusionProbability()

◆ SetODFSHOrder()