#include <animaDTIProbabilisticTractographyImageFilter.h>

Inheritance diagram for anima::DTIProbabilisticTractographyImageFilter:

Collaboration diagram for anima::DTIProbabilisticTractographyImageFilter:

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

typedef itk::SmartPointer< Self >	Pointer

typedef DTIProbabilisticTractographyImageFilter	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	SetFAThreshold (double _arg)

void	SetKappaPolynomialCoefficients (std::vector< double > &coefs)

virtual void	SetThresholdForProlateTensor (double _arg)

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

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

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

	DTIProbabilisticTractographyImageFilter ()

void	GetDTIMinorDirection (VectorType &modelValue, Vector3DType &resVec)

void	GetDTIPrincipalDirection (const VectorType &modelValue, Vector3DType &resVec, bool is2d)

void	GetEigenValueCombinations (VectorType &modelValue, double &meanLambda, double &perpLambda)

double	GetFractionalAnisotropy (VectorType &modelValue)

double	GetKappaFromFA (double FA)

double	GetLinearCoefficient (VectorType &modelValue)

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

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	~DTIProbabilisticTractographyImageFilter ()

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...

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 void	PrepareTractography ()
	Generate seed points (can be re-implemented but this one has to be called) 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 13 of file animaDTIProbabilisticTractographyImageFilter.h.

Member Typedef Documentation

◆ ConstPointer

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

Definition at line 21 of file animaDTIProbabilisticTractographyImageFilter.h.

◆ Pointer

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

Definition at line 20 of file animaDTIProbabilisticTractographyImageFilter.h.

◆ Self

typedef DTIProbabilisticTractographyImageFilter anima::DTIProbabilisticTractographyImageFilter::Self

SmartPointer typedef support

Definition at line 17 of file animaDTIProbabilisticTractographyImageFilter.h.

◆ Superclass

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

Definition at line 18 of file animaDTIProbabilisticTractographyImageFilter.h.

Constructor & Destructor Documentation

◆ DTIProbabilisticTractographyImageFilter()

anima::DTIProbabilisticTractographyImageFilter::DTIProbabilisticTractographyImageFilter ( )

protected

Definition at line 19 of file animaDTIProbabilisticTractographyImageFilter.cxx.

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

◆ ~DTIProbabilisticTractographyImageFilter()

anima::DTIProbabilisticTractographyImageFilter::~DTIProbabilisticTractographyImageFilter ( )

protectedvirtual

Definition at line 28 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Member Function Documentation

◆ CheckModelProperties()

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

protectedvirtual

Definition at line 164 of file animaDTIProbabilisticTractographyImageFilter.cxx.

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

◆ ComputeAdditionalScalarMaps()

void anima::DTIProbabilisticTractographyImageFilter::ComputeAdditionalScalarMaps ( )

protectedvirtual

Computes additional scalar maps that are model dependent to add to the output.

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

Definition at line 408 of file animaDTIProbabilisticTractographyImageFilter.cxx.

References ComputeModelValue(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetModelInterpolator(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput(), and anima::GetTensorFromVectorRepresentation().

◆ ComputeLogWeightUpdate()

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

protectedvirtual

Definition at line 189 of file animaDTIProbabilisticTractographyImageFilter.cxx.

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

◆ ComputeModelValue()

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

protectedvirtual

Definition at line 291 of file animaDTIProbabilisticTractographyImageFilter.cxx.

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

Referenced by ComputeAdditionalScalarMaps().

◆ CreateAnother()

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

◆ GetDTIMinorDirection()

void anima::DTIProbabilisticTractographyImageFilter::GetDTIMinorDirection	(	VectorType &	modelValue,
		Vector3DType &	resVec
	)

protected

Definition at line 267 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Referenced by ComputeLogWeightUpdate().

◆ GetDTIPrincipalDirection()

void anima::DTIProbabilisticTractographyImageFilter::GetDTIPrincipalDirection	(	const VectorType &	modelValue,
		Vector3DType &	resVec,
		bool	is2d
	)

protected

Definition at line 237 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Referenced by ComputeLogWeightUpdate(), and ProposeNewDirection().

◆ GetEigenValueCombinations()

void anima::DTIProbabilisticTractographyImageFilter::GetEigenValueCombinations	(	VectorType &	modelValue,
		double &	meanLambda,
		double &	perpLambda
	)

protected

Definition at line 376 of file animaDTIProbabilisticTractographyImageFilter.cxx.

◆ GetFractionalAnisotropy()

double anima::DTIProbabilisticTractographyImageFilter::GetFractionalAnisotropy ( VectorType & modelValue )

protected

Definition at line 338 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Referenced by CheckModelProperties(), and ProposeNewDirection().

◆ GetKappaFromFA()

double anima::DTIProbabilisticTractographyImageFilter::GetKappaFromFA ( double FA )

protected

Definition at line 228 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Referenced by ProposeNewDirection().

◆ GetLinearCoefficient()

double anima::DTIProbabilisticTractographyImageFilter::GetLinearCoefficient ( VectorType & modelValue )

protected

Definition at line 311 of file animaDTIProbabilisticTractographyImageFilter.cxx.

Referenced by ComputeLogWeightUpdate(), and ProposeNewDirection().

◆ GetNameOfClass()

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

virtual

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

◆ InitializeFirstIterationFromModel()

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

protectedvirtual

Definition at line 92 of file animaDTIProbabilisticTractographyImageFilter.cxx.

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

Referenced by ProposeNewDirection().

◆ New()

static Pointer anima::DTIProbabilisticTractographyImageFilter::New ( )

static

◆ ProposeNewDirection()

DTIProbabilisticTractographyImageFilter::Vector3DType anima::DTIProbabilisticTractographyImageFilter::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 33 of file animaDTIProbabilisticTractographyImageFilter.cxx.

References anima::ComputeScalarProduct(), anima::EvaluateWatsonPDF(), GetDTIPrincipalDirection(), GetFractionalAnisotropy(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage(), GetKappaFromFA(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetKappaOfPriorDistribution(), GetLinearCoefficient(), InitializeFirstIterationFromModel(), anima::safe_log(), and anima::SampleFromWatsonDistribution().

◆ SetFAThreshold()

virtual void anima::DTIProbabilisticTractographyImageFilter::SetFAThreshold ( double _arg )

virtual

◆ SetKappaPolynomialCoefficients()

void anima::DTIProbabilisticTractographyImageFilter::SetKappaPolynomialCoefficients ( std::vector< double > & coefs )

Definition at line 221 of file animaDTIProbabilisticTractographyImageFilter.cxx.

◆ SetThresholdForProlateTensor()

virtual void anima::DTIProbabilisticTractographyImageFilter::SetThresholdForProlateTensor ( double _arg )

virtual

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

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

◆ DTIProbabilisticTractographyImageFilter()

◆ ~DTIProbabilisticTractographyImageFilter()

Member Function Documentation

◆ CheckModelProperties()

◆ ComputeAdditionalScalarMaps()

◆ ComputeLogWeightUpdate()

◆ ComputeModelValue()

◆ CreateAnother()

◆ GetDTIMinorDirection()

◆ GetDTIPrincipalDirection()

◆ GetEigenValueCombinations()

◆ GetFractionalAnisotropy()

◆ GetKappaFromFA()

◆ GetLinearCoefficient()

◆ GetNameOfClass()

◆ InitializeFirstIterationFromModel()

◆ New()

◆ ProposeNewDirection()

◆ SetFAThreshold()

◆ SetKappaPolynomialCoefficients()

◆ SetThresholdForProlateTensor()