#include <itkStochasticTractographyFilter.h>

Inheritance diagram for itk::StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >:

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Collaboration diagram for itk::StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >:

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Classes
struct	StochasticTractGenerationCallbackStruct

Public Types
typedef StochasticTractographyFilter	Self

typedef ImageToImageFilter< TInputDWIImage, TOutputConnectivityImage >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef TInputDWIImage	InputDWIImageType

typedef TOutputConnectivityImage	OutputConnectivityImageType

typedef TInputWhiteMatterProbabilityImage	InputWhiteMatterProbabilityImageType

typedef SlowPolyLineParametricPath< 3 >	TractType

typedef VectorContainer< unsigned int, typename TractType::Pointer >	TractContainerType

typedef Image< DiffusionTensor3D< double >, 3 >	OutputTensorImageType

typedef VectorContainer< unsigned int, vnl_vector_fixed< double, 3 > >	GradientDirectionContainerType

typedef double	bValueType

typedef VectorContainer< unsigned int, bValueType >	bValueContainerType

typedef vnl_matrix_fixed< double, 3, 3 >	MeasurementFrameType

typedef VectorContainer< unsigned int, vnl_vector_fixed< double, 3 > >	TractOrientationContainerType

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

virtual void	SetTotalTracts (unsigned int _arg)

virtual unsigned int	GetTotalTracts ()

virtual void	SetMaxTractLength (unsigned int _arg)

virtual unsigned int	GetMaxTractLength ()

virtual void	SetbValues (const bValueContainerType *_arg)

virtual const bValueContainerType *	GetbValues ()

virtual void	SetGradients (const GradientDirectionContainerType *_arg)

virtual const GradientDirectionContainerType *	GetGradients ()

	itkSetInputMacro (WhiteMatterProbabilityImage, InputWhiteMatterProbabilityImageType) itkGetInputMacro(WhiteMatterProbabilityImage

InputWhiteMatterProbabilityImageType void	SetPrimaryInput (DataObject *input)

virtual void	SetSeedIndex (typename InputDWIImageType::IndexType _arg)

virtual InputDWIImageType::IndexType	GetSeedIndex ()

virtual void	SetSampleDirections (const TractOrientationContainerType *_arg)

virtual const TractOrientationContainerType *	GetSampleDirections ()

virtual void	SetMeasurementFrame (MeasurementFrameType _arg)

virtual MeasurementFrameType	GetMeasurementFrame ()

virtual void	SetMaxLikelihoodCacheSize (unsigned int _arg)

virtual unsigned int	GetMaxLikelihoodCacheSize ()

virtual TractContainerType *	GetOutputTractContainer ()

virtual OutputTensorImageType *	GetOutputTensorImage ()

void	GenerateData ()

void	GenerateTractContainerOutput (void)

void	GenerateTensorImageOutput (void)

Static Public Member Functions
static Pointer	New ()

Protected Types
typedef vnl_vector_fixed< double, 7 >	TensorModelParamType

typedef vnl_vector_fixed< double, 6 >	ConstrainedModelParamType

typedef Image< VariableLengthVector< double >, 3 >	DWIVectorImageType

typedef Image< Array< double >, 3 >	ProbabilityDistributionImageType

typedef Image< SimpleFastMutexLock, 3 >	LikelihoodCacheMutexImageType

Protected Member Functions
	StochasticTractographyFilter ()

virtual	~StochasticTractographyFilter ()

void	LoadDefaultSampleDirections (void)

void	ProbabilisticallyInterpolate (vnl_random &randomgenerator, const TractType::ContinuousIndexType &cindex, typename InputDWIImageType::IndexType &index)

void	UpdateGradientDirections (void)

void	UpdateTensorModelFittingMatrices (void)

void	CalculateTensorModelParameters (const DWIVectorImageType::PixelType &dwivalues, vnl_diag_matrix< double > &W, TensorModelParamType &tensormodelparams)

void	CalculateConstrainedModelParameters (const TensorModelParamType &tensormodelparams, ConstrainedModelParamType &constrainedmodelparams)

void	CalculateNoiseFreeDWIFromConstrainedModel (const ConstrainedModelParamType &constrainedmodelparams, DWIVectorImageType::PixelType &noisefreedwi)

void	CalculateResidualVariance (const DWIVectorImageType::PixelType &noisydwi, const DWIVectorImageType::PixelType &noisefreedwi, const vnl_diag_matrix< double > &W, const unsigned int numberofparameters, double &residualvariance)

void	CalculateLikelihood (const DWIVectorImageType::PixelType &dwipixel, TractOrientationContainerType::ConstPointer orientations, ProbabilityDistributionImageType::PixelType &likelihood)

void	CalculatePrior (TractOrientationContainerType::Element v_prev, TractOrientationContainerType::ConstPointer orientations, ProbabilityDistributionImageType::PixelType &prior)

void	CalculatePosterior (const ProbabilityDistributionImageType::PixelType &likelihood, const ProbabilityDistributionImageType::PixelType &prior, ProbabilityDistributionImageType::PixelType &posterior)

void	SampleTractOrientation (vnl_random &randomgenerator, const ProbabilityDistributionImageType::PixelType &posterior, TractOrientationContainerType::ConstPointer orientations, TractOrientationContainerType::Element &choosendirection)

void	StochasticTractGeneration (typename InputDWIImageType::ConstPointer dwiimagePtr, typename InputWhiteMatterProbabilityImageType::ConstPointer maskimagePtr, typename InputDWIImageType::IndexType seedindex, unsigned long randomseed, TractType::Pointer tract)

ProbabilityDistributionImageType::PixelType &	AccessLikelihoodCache (typename InputDWIImageType::IndexType index)

bool	DelegateTract (unsigned long &randomseed)

void	TractContainerToConnectivityMap (TractContainerType::Pointer tractcontainer)

void	StoreTract (TractType::Pointer tract)

bool	FiberExistenceTest (vnl_random &randomgenerator, typename InputWhiteMatterProbabilityImageType::ConstPointer wmpimage, typename InputWhiteMatterProbabilityImageType::IndexType index)

Static Protected Member Functions
static ITK_THREAD_RETURN_TYPE	StochasticTractGenerationCallback (void *arg)

Protected Attributes
MeasurementFrameType	m_MeasurementFrame

LikelihoodCacheMutexImageType::Pointer	m_LikelihoodCacheMutexImagePtr

unsigned int	m_TotalTracts

unsigned int	m_MaxTractLength

GradientDirectionContainerType::ConstPointer	m_Gradients

GradientDirectionContainerType::Pointer	m_TransformedGradients

bValueContainerType::ConstPointer	m_bValues

InputDWIImageType::IndexType	m_SeedIndex

TractOrientationContainerType::ConstPointer	m_SampleDirections

vnl_matrix< double > *	m_A

vnl_qr< double > *	m_Aqr

ProbabilityDistributionImageType::Pointer	m_LikelihoodCachePtr

unsigned long	m_MaxLikelihoodCacheSize

unsigned long	m_MaxLikelihoodCacheElements

unsigned long	m_CurrentLikelihoodCacheElements

SimpleFastMutexLock	m_LikelihoodCacheMutex

RealTimeClock::Pointer	m_ClockPtr

unsigned int	m_TotalDelegatedTracts

SimpleFastMutexLock	m_TotalDelegatedTractsMutex

SimpleFastMutexLock	m_OutputImageMutex

TractContainerType::Pointer	m_OutputTractContainer

SimpleFastMutexLock	m_OutputTractContainerMutex

OutputTensorImageType::Pointer	m_OutputTensorImage

vnl_random	m_RandomGenerator