anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType > Class Template Reference

#include <animaBaseProbabilisticTractographyImageFilter.h>

Inheritance diagram for anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >:

Collaboration diagram for anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >:

Classes
struct	FiberWorkType
struct	pair_comparator
struct	trackerArguments

Public Types
enum	ColinearityDirectionType {   Center = 0,   Outward,   Top,   Bottom,   Left,   Right,   Front,   Back }
	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 {   Colinear = 0,   Weight }
	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 TInputModelImageType	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
void	createVTKOutput (FiberProcessVectorType &filteredFibers, ListType &filteredWeights)
virtual InitialDirectionModeType	GetInitialDirectionMode ()
InputModelImageType *	GetInputModelImage ()
virtual double	GetKappaOfPriorDistribution ()
virtual unsigned int	GetModelDimension ()
virtual InterpolatorType *	GetModelInterpolator ()
virtual const char *	GetNameOfClass () const
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

Protected Member Functions
	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 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 ()

Static Protected Member Functions
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreadTracker (void *arg)
	Multithread util function. More...

Detailed Description

template<class TInputModelImageType>
class anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >

Definition at line 20 of file animaBaseProbabilisticTractographyImageFilter.h.

Member Typedef Documentation

ConstPointer

template<class TInputModelImageType>

typedef itk::SmartPointer<const Self> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ConstPointer

Definition at line 28 of file animaBaseProbabilisticTractographyImageFilter.h.

ContinuousIndexType

template<class TInputModelImageType>

typedef InterpolatorType::ContinuousIndexType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ContinuousIndexType

Definition at line 61 of file animaBaseProbabilisticTractographyImageFilter.h.

DirectionVectorType

template<class TInputModelImageType>

typedef std::vector<Vector3DType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::DirectionVectorType

Definition at line 56 of file animaBaseProbabilisticTractographyImageFilter.h.

FiberProcessVectorType

template<class TInputModelImageType>

typedef std::vector<FiberType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::FiberProcessVectorType

Definition at line 65 of file animaBaseProbabilisticTractographyImageFilter.h.

FiberType

template<class TInputModelImageType>

typedef std::vector<PointType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::FiberType

Definition at line 64 of file animaBaseProbabilisticTractographyImageFilter.h.

IndexType

template<class TInputModelImageType>

typedef MaskImageType::IndexType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::IndexType

Definition at line 49 of file animaBaseProbabilisticTractographyImageFilter.h.

InputModelImagePointer

template<class TInputModelImageType>

typedef InputModelImageType::Pointer anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InputModelImagePointer

Definition at line 37 of file animaBaseProbabilisticTractographyImageFilter.h.

InputModelImageType

template<class TInputModelImageType>

typedef TInputModelImageType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InputModelImageType

Definition at line 36 of file animaBaseProbabilisticTractographyImageFilter.h.

InterpolatorPointer

template<class TInputModelImageType>

typedef InterpolatorType::Pointer anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InterpolatorPointer

Definition at line 60 of file animaBaseProbabilisticTractographyImageFilter.h.

InterpolatorType

template<class TInputModelImageType>

typedef itk::InterpolateImageFunction<InputModelImageType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InterpolatorType

Definition at line 59 of file animaBaseProbabilisticTractographyImageFilter.h.

ListType

template<class TInputModelImageType>

typedef std::vector<ScalarType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ListType

Definition at line 55 of file animaBaseProbabilisticTractographyImageFilter.h.

MaskImagePointer

template<class TInputModelImageType>

typedef MaskImageType::Pointer anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::MaskImagePointer

Definition at line 47 of file animaBaseProbabilisticTractographyImageFilter.h.

MaskImageType

template<class TInputModelImageType>

typedef itk::Image<unsigned short, 3> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::MaskImageType

Definition at line 46 of file animaBaseProbabilisticTractographyImageFilter.h.

Matrix3DType

template<class TInputModelImageType>

typedef itk::Matrix<ScalarType,3,3> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Matrix3DType

Definition at line 52 of file animaBaseProbabilisticTractographyImageFilter.h.

MembershipType

template<class TInputModelImageType>

typedef std::vector<unsigned int> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::MembershipType

Definition at line 66 of file animaBaseProbabilisticTractographyImageFilter.h.

Pointer

template<class TInputModelImageType>

typedef itk::SmartPointer<Self> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Pointer

Definition at line 27 of file animaBaseProbabilisticTractographyImageFilter.h.

PointType

template<class TInputModelImageType>

typedef MaskImageType::PointType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::PointType

Definition at line 48 of file animaBaseProbabilisticTractographyImageFilter.h.

ScalarImagePointer

template<class TInputModelImageType>

typedef ScalarImageType::Pointer anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ScalarImagePointer

Definition at line 41 of file animaBaseProbabilisticTractographyImageFilter.h.

ScalarImageType

template<class TInputModelImageType>

typedef itk::Image<ScalarType, 3> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ScalarImageType

Definition at line 40 of file animaBaseProbabilisticTractographyImageFilter.h.

ScalarInterpolatorPointer

template<class TInputModelImageType>

typedef ScalarInterpolatorType::Pointer anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ScalarInterpolatorPointer

Definition at line 43 of file animaBaseProbabilisticTractographyImageFilter.h.

ScalarInterpolatorType

template<class TInputModelImageType>

typedef itk::LinearInterpolateImageFunction<ScalarImageType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ScalarInterpolatorType

Definition at line 42 of file animaBaseProbabilisticTractographyImageFilter.h.

ScalarType

template<class TInputModelImageType>

typedef double anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ScalarType

Definition at line 33 of file animaBaseProbabilisticTractographyImageFilter.h.

Self

template<class TInputModelImageType>

typedef BaseProbabilisticTractographyImageFilter anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Self

SmartPointer typedef support

Definition at line 24 of file animaBaseProbabilisticTractographyImageFilter.h.

Superclass

template<class TInputModelImageType>

typedef itk::ProcessObject anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Superclass

Definition at line 25 of file animaBaseProbabilisticTractographyImageFilter.h.

Vector3DType

template<class TInputModelImageType>

typedef itk::Vector<ScalarType,3> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Vector3DType

Definition at line 53 of file animaBaseProbabilisticTractographyImageFilter.h.

VectorType

template<class TInputModelImageType>

typedef itk::VariableLengthVector<ScalarType> anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::VectorType

Definition at line 54 of file animaBaseProbabilisticTractographyImageFilter.h.

Member Enumeration Documentation

ColinearityDirectionType

template<class TInputModelImageType>

enum anima::BaseProbabilisticTractographyImageFilter::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) ...

Enumerator
Center
Outward
Top
Bottom
Left
Right
Front
Back

Definition at line 88 of file animaBaseProbabilisticTractographyImageFilter.h.

InitialDirectionModeType

template<class TInputModelImageType>

enum anima::BaseProbabilisticTractographyImageFilter::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.

Enumerator
Colinear
Weight

Definition at line 105 of file animaBaseProbabilisticTractographyImageFilter.h.

Constructor & Destructor Documentation

BaseProbabilisticTractographyImageFilter()

template<class TInputModelImageType >

anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::BaseProbabilisticTractographyImageFilter ( )

protected

Definition at line 29 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

~BaseProbabilisticTractographyImageFilter()

template<class TInputModelImageType >

anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::~BaseProbabilisticTractographyImageFilter ( )

protectedvirtual

Definition at line 65 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

Member Function Documentation

CheckModelProperties()

template<class TInputModelImageType>

virtual bool anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::CheckModelProperties ( double  estimatedB0Value, double  estimatedNoiseValue, VectorType &  modelValue, unsigned int  threadId  )

protectedpure virtual

Check stopping criterions to stop a particle (model dependent, not implemented here)

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

ComputeAdditionalScalarMaps()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ComputeAdditionalScalarMaps ( )

inlineprotectedvirtual

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

Reimplemented in anima::DTIProbabilisticTractographyImageFilter.

Definition at line 222 of file animaBaseProbabilisticTractographyImageFilter.h.

ComputeFiber()

template<class TInputModelImageType >

BaseProbabilisticTractographyImageFilter< TInputModelImageType >::FiberProcessVectorType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ComputeFiber ( FiberType &  fiber, InterpolatorPointer &  modelInterpolator, unsigned int  numThread, ListType &  resultWeights  )

protected

This little guy is the one handling probabilistic tracking.

Definition at line 468 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

ComputeLogWeightUpdate()

template<class TInputModelImageType>

virtual double anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ComputeLogWeightUpdate ( double  b0Value, double  noiseValue, Vector3DType &  newDirection, VectorType &  modelValue, double &  log_prior, double &  log_proposal, unsigned int  threadId  )

protectedpure virtual

Update particle weight based on an underlying model and the chosen direction (model dependent, not implemented here)

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

ComputeModelValue()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ComputeModelValue ( InterpolatorPointer &  modelInterpolator, ContinuousIndexType &  index, VectorType &  modelValue  )

protectedpure virtual

Estimate model from raw diffusion data (model dependent, not implemented here)

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

createVTKOutput()

template<class TInputModelImageType >

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::createVTKOutput	(	FiberProcessVectorType &	filteredFibers,
		ListType &	filteredWeights
	)

Definition at line 431 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage().

FilterOutputFibers()

template<class TInputModelImageType >

BaseProbabilisticTractographyImageFilter< TInputModelImageType >::FiberProcessVectorType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::FilterOutputFibers ( FiberProcessVectorType &  fibers, ListType &  weights  )

protected

Filter output fibers by ROIs and compute local colors.

Definition at line 355 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

GetInitialDirectionMode()

template<class TInputModelImageType>

virtual InitialDirectionModeType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetInitialDirectionMode ( )

virtual

GetInputModelImage()

template<class TInputModelImageType>

InputModelImageType* anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetInputModelImage ( )

inline

Definition at line 127 of file animaBaseProbabilisticTractographyImageFilter.h.

GetKappaOfPriorDistribution()

template<class TInputModelImageType>

virtual double anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetKappaOfPriorDistribution ( )

virtual

GetModelDimension()

template<class TInputModelImageType>

virtual unsigned int anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetModelDimension ( )

virtual

GetModelInterpolator()

template<class TInputModelImageType >

BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InterpolatorType * anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetModelInterpolator ( )

virtual

Definition at line 255 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage().

GetNameOfClass()

template<class TInputModelImageType>

virtual const char* anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetNameOfClass ( ) const

virtual

Reimplemented in anima::DTIProbabilisticTractographyImageFilter, and anima::ODFProbabilisticTractographyImageFilter.

GetOutput()

template<class TInputModelImageType>

vtkPolyData* anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::GetOutput ( )

inline

Definition at line 168 of file animaBaseProbabilisticTractographyImageFilter.h.

InitializeFirstIterationFromModel()

template<class TInputModelImageType>

virtual Vector3DType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::InitializeFirstIterationFromModel ( Vector3DType &  colinearDir, VectorType &  modelValue, unsigned int  threadId  )

protectedpure virtual

Initialize first direction from user input (model dependent, not implemented here)

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

MergeParticleClassFibers()

template<class TInputModelImageType >

bool anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::MergeParticleClassFibers ( FiberWorkType &  fiberData, FiberProcessVectorType &  outputMerged, unsigned int  classNumber  )

protected

This guy takes the result of computefiber and merges the classes, each one becomes one fiber.

Definition at line 1214 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

PrepareTractography()

template<class TInputModelImageType >

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::PrepareTractography ( )

protectedvirtual

Generate seed points (can be re-implemented but this one has to be called)

Reimplemented in anima::ODFProbabilisticTractographyImageFilter.

Definition at line 123 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput(), and anima::ODFProbabilisticTractographyImageFilter::PrepareTractography().

ProposeNewDirection()

template<class TInputModelImageType>

virtual Vector3DType anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ProposeNewDirection ( Vector3DType &  oldDirection, VectorType &  modelValue, Vector3DType &  sampling_direction, double &  log_prior, double &  log_proposal, std::mt19937 &  random_generator, unsigned int  threadId  )

protectedpure virtual

Propose new direction for a particle, given the old direction, and a model (model dependent, not implemented here)

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

SetB0Image()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetB0Image ( ScalarImageType *  _arg )

virtual

SetClusterDistance()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetClusterDistance ( unsigned int  _arg )

virtual

SetComputeLocalColors()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetComputeLocalColors ( bool  _arg )

virtual

SetCutMask()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetCutMask ( MaskImageType *  _arg )

virtual

SetFiberTrashThreshold()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetFiberTrashThreshold ( double  _arg )

virtual

SetFilterMask()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetFilterMask ( MaskImageType *  _arg )

virtual

SetForbiddenMask()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetForbiddenMask ( MaskImageType *  _arg )

virtual

SetInitialColinearityDirection()

template<class TInputModelImageType>

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetInitialColinearityDirection ( const ColinearityDirectionType &  colDir )

inline

Definition at line 122 of file animaBaseProbabilisticTractographyImageFilter.h.

SetInitialDirectionMode()

template<class TInputModelImageType>

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetInitialDirectionMode ( const InitialDirectionModeType &  dir )

inline

Definition at line 123 of file animaBaseProbabilisticTractographyImageFilter.h.

SetInputModelImage()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetInputModelImage ( InputModelImageType *  inImage )

inlinevirtual

Definition at line 126 of file animaBaseProbabilisticTractographyImageFilter.h.

SetKappaOfPriorDistribution()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetKappaOfPriorDistribution ( double  _arg )

virtual

SetKappaSplitThreshold()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetKappaSplitThreshold ( double  _arg )

virtual

SetMAPMergeFibers()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetMAPMergeFibers ( bool  _arg )

virtual

SetMaxLengthFiber()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetMaxLengthFiber ( double  _arg )

virtual

SetMinimalNumberOfParticlesPerClass()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetMinimalNumberOfParticlesPerClass ( unsigned int  _arg )

virtual

SetMinLengthFiber()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetMinLengthFiber ( double  _arg )

virtual

SetModelDimension()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetModelDimension ( unsigned int  _arg )

virtual

SetNoiseImage()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetNoiseImage ( ScalarImageType *  _arg )

virtual

SetNumberOfFibersPerPixel()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetNumberOfFibersPerPixel ( unsigned int  _arg )

virtual

SetNumberOfParticles()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetNumberOfParticles ( unsigned int  _arg )

virtual

SetPositionDistanceFuseThreshold()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetPositionDistanceFuseThreshold ( double  _arg )

virtual

SetResamplingThreshold()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetResamplingThreshold ( double  _arg )

virtual

SetSeedMask()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetSeedMask ( MaskImageType *  _arg )

virtual

SetStepProgression()

template<class TInputModelImageType>

virtual void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::SetStepProgression ( double  _arg )

virtual

ThreadedTrackComputer()

template<class TInputModelImageType >

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ThreadedTrackComputer ( unsigned int  numThread, FiberProcessVectorType &  resultFibers, ListType &  resultWeights, unsigned int  startSeedIndex, unsigned int  endSeedIndex  )

protected

Doing the real tracking by calling ComputeFiber and merging its results.

Definition at line 324 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

ThreadTrack()

template<class TInputModelImageType >

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ThreadTrack ( unsigned int  numThread, FiberProcessVectorType &  resultFibers, ListType &  resultWeights  )

protected

Doing the thread work dispatch.

Definition at line 283 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::ThreadTracker().

ThreadTracker()

template<class TInputModelImageType >

ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::ThreadTracker ( void *  arg )

staticprotected

Multithread util function.

Definition at line 269 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

Update()

template<class TInputModelImageType >

void anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::Update

(

)

Definition at line 74 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetInputModelImage().

UpdateClassesMemberships()

template<class TInputModelImageType >

unsigned int anima::BaseProbabilisticTractographyImageFilter< TInputModelImageType >::UpdateClassesMemberships ( FiberWorkType &  fiberData, DirectionVectorType &  directions, std::mt19937 &  random_generator  )

protected

This ugly guy is the heart of multi-modal probabilistic tractography, making decisions on split and merges of particles.

Definition at line 845 of file animaBaseProbabilisticTractographyImageFilter.hxx.

Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::GetOutput().

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

• animaBaseProbabilisticTractographyImageFilter.h
• animaBaseProbabilisticTractographyImageFilter.hxx