#include <itkOdfMaximaExtractionFilter.h>

Inheritance diagram for itk::OdfMaximaExtractionFilter< TOdfPixelType >:

Collaboration diagram for itk::OdfMaximaExtractionFilter< TOdfPixelType >:

Public Types
enum	NormalizationMethods { NO_NORM, SINGLE_VEC_NORM, MAX_VEC_NORM }

typedef OdfMaximaExtractionFilter	Self

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef ProcessObject	Superclass

typedef itk::AnalyticalDiffusionQballReconstructionImageFilter< short, short, float, 4, QBALL_ODFSIZE >	QballReconstructionFilterType

typedef QballReconstructionFilterType::CoefficientImageType	CoefficientImageType

typedef CoefficientImageType::PixelType	CoefficientPixelType

typedef itk::VectorImage< short, 3 >	DiffusionImageType

typedef vnl_vector_fixed< double, 3 >	Vector3D

typedef VectorContainer< unsigned int, Vector3D >	DirectionContainerType

typedef VectorContainer< unsigned int, DirectionContainerType::Pointer >	ContainerType

typedef itk::Image< unsigned char, 3 >	ItkUcharImgType

typedef itk::Image< itk::Vector< float, 3 >, 3 >	ItkDirectionImage

typedef itk::VectorContainer< unsigned int, ItkDirectionImage::Pointer >	ItkDirectionImageContainer

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

virtual mitk::FiberBundle::Pointer	GetOutputFiberBundle ()
	vector field (peak sizes rescaled for visualization purposes) More...

virtual ItkUcharImgType::Pointer	GetNumDirectionsImage ()
	number of peaks per voxel More...

virtual ItkDirectionImageContainer::Pointer	GetDirectionImageContainer ()
	container for output peaks More...

virtual void	SetMaskImage (ItkUcharImgType::Pointer _arg)
	only voxels inside the binary mask are processed More...

virtual void	SetNormalizationMethod (NormalizationMethods _arg)
	normalization method of ODF peaks More...

virtual void	SetDiffusionGradients (DirectionContainerType::Pointer _arg)
	input for qball reconstruction More...

virtual void	SetDiffusionImage (DiffusionImageType::Pointer _arg)
	input for qball reconstruction More...

virtual void	SetBvalue (float _arg)
	input for qball reconstruction More...

virtual void	SetShCoeffImage (CoefficientImageType::Pointer _arg)
	conatins spherical harmonic coefficients More...

virtual void	SetMaxNumPeaks (unsigned int _arg)
	if more peaks are found, only the largest are kept More...

virtual void	SetPeakThreshold (double _arg)
	threshold on peak length relative to the largest peak in the current voxel More...

void	GenerateData () override

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	OdfMaximaExtractionFilter ()

	~OdfMaximaExtractionFilter ()

bool	ReconstructQballImage ()

std::vector< double >	SolveCubic (const double &a, const double &b, const double &c, const double &d)

double	ODF_dtheta2 (const double &sn, const double &cs, const double &A, const double &B, const double &C, const double &D, const double &E, const double &F, const double &G, const double &H)

double	ODF_dphi2 (const double &sn, const double &cs, const double &A, const double &B, const double &C, const double &D, const double &E, const double &F, const double &G, const double &H)

double	ODF_dtheta (const double &sn, const double &cs, const double &A, const double &B, const double &C, const double &D, const double &E, const double &F, const double &G, const double &H)

void	FindCandidatePeaks (const CoefficientPixelType &SHcoeff)

std::vector< Vector3D >	ClusterPeaks (const CoefficientPixelType &shCoeff)

void	Cart2Sph (const std::vector< Vector3D > &dir, vnl_matrix< double > &sphCoords)

vnl_matrix< double >	CalcShBasis (vnl_matrix< double > &sphCoords, const int &shOrder)

Protected Attributes
DirectionContainerType::Pointer	m_DiffusionGradients
	input for qball reconstruction More...

DiffusionImageType::Pointer	m_DiffusionImage
	input for qball reconstruction More...

float	m_Bvalue
	input for qball reconstruction More...

ItkUcharImgType::Pointer	m_MaskImage
	only voxels inside the binary mask are processed More...

NormalizationMethods	m_NormalizationMethod
	normalization for peaks More...

double	m_PeakThreshold
	threshold on peak length relative to the largest peak in the current voxel More...

unsigned int	m_MaxNumPeaks
	if more peaks are found, only the largest are kept More...

CoefficientImageType::Pointer	m_ShCoeffImage
	conatins spherical harmonic coefficients More...

std::vector< vnl_vector_fixed< double, 2 > >	m_CandidatePeaks
	container for candidate peaks (all extrema, also minima) More...

mitk::FiberBundle::Pointer	m_OutputFiberBundle
	vector field (peak sizes rescaled for visualization purposes) More...

ItkUcharImgType::Pointer	m_NumDirectionsImage
	number of peaks per voxel More...

ItkDirectionImageContainer::Pointer	m_DirectionImageContainer
	output peaks More...

Detailed Description

template<class TOdfPixelType>
class itk::OdfMaximaExtractionFilter< TOdfPixelType >

Class that estimates the maxima of the 4th order SH representation of an ODF using analytic calculations (according to Aganj et al, MICCAI, 2010)

Definition at line 33 of file itkOdfMaximaExtractionFilter.h.

Member Typedef Documentation

template<class TOdfPixelType >

typedef QballReconstructionFilterType::CoefficientImageType itk::OdfMaximaExtractionFilter< TOdfPixelType >::CoefficientImageType

Definition at line 57 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef CoefficientImageType::PixelType itk::OdfMaximaExtractionFilter< TOdfPixelType >::CoefficientPixelType

Definition at line 58 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef SmartPointer<const Self> itk::OdfMaximaExtractionFilter< TOdfPixelType >::ConstPointer

Definition at line 46 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef VectorContainer< unsigned int, DirectionContainerType::Pointer > itk::OdfMaximaExtractionFilter< TOdfPixelType >::ContainerType

Definition at line 62 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef itk::VectorImage< short, 3 > itk::OdfMaximaExtractionFilter< TOdfPixelType >::DiffusionImageType

Definition at line 59 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef VectorContainer< unsigned int, Vector3D > itk::OdfMaximaExtractionFilter< TOdfPixelType >::DirectionContainerType

Definition at line 61 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef itk::Image< itk::Vector< float, 3 >, 3> itk::OdfMaximaExtractionFilter< TOdfPixelType >::ItkDirectionImage

Definition at line 64 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef itk::VectorContainer< unsigned int, ItkDirectionImage::Pointer > itk::OdfMaximaExtractionFilter< TOdfPixelType >::ItkDirectionImageContainer

Definition at line 65 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef itk::Image<unsigned char, 3> itk::OdfMaximaExtractionFilter< TOdfPixelType >::ItkUcharImgType

Definition at line 63 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef SmartPointer<Self> itk::OdfMaximaExtractionFilter< TOdfPixelType >::Pointer

Definition at line 45 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> itk::OdfMaximaExtractionFilter< TOdfPixelType >::QballReconstructionFilterType

Definition at line 56 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef OdfMaximaExtractionFilter itk::OdfMaximaExtractionFilter< TOdfPixelType >::Self

Definition at line 44 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef ProcessObject itk::OdfMaximaExtractionFilter< TOdfPixelType >::Superclass

Definition at line 47 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

typedef vnl_vector_fixed< double, 3 > itk::OdfMaximaExtractionFilter< TOdfPixelType >::Vector3D

Definition at line 60 of file itkOdfMaximaExtractionFilter.h.

Member Enumeration Documentation

template<class TOdfPixelType >

enum itk::OdfMaximaExtractionFilter::NormalizationMethods

Enumerator
NO_NORM	don't normalize peaks
SINGLE_VEC_NORM	normalize peaks to length 1
MAX_VEC_NORM	largest peak is normalized to length 1, other peaks relative to it

Definition at line 38 of file itkOdfMaximaExtractionFilter.h.

Constructor & Destructor Documentation

template<class TOdfPixelType >

itk::OdfMaximaExtractionFilter< TOdfPixelType >::OdfMaximaExtractionFilter ( )

protected

Definition at line 41 of file itkOdfMaximaExtractionFilter.cpp.

template<class TOdfPixelType >

itk::OdfMaximaExtractionFilter< TOdfPixelType >::~OdfMaximaExtractionFilter ( )

inlineprotected

Definition at line 86 of file itkOdfMaximaExtractionFilter.h.

Member Function Documentation

template<class TOdfPixelType >

vnl_matrix< double > itk::OdfMaximaExtractionFilter< TOdfPixelType >::CalcShBasis	(	vnl_matrix< double > &	sphCoords,
		const int &	shOrder
	)

protected

Definition at line 431 of file itkOdfMaximaExtractionFilter.cpp.

References M_PI.

template<class TOdfPixelType >

void itk::OdfMaximaExtractionFilter< TOdfPixelType >::Cart2Sph	(	const std::vector< Vector3D > &	dir,
		vnl_matrix< double > &	sphCoords
	)

protected

Definition at line 407 of file itkOdfMaximaExtractionFilter.cpp.

References mitk::eps, and M_PI.

template<class TOdfPixelType >

Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::Clone ( ) const

template<class TOdfPixelType >

std::vector< vnl_vector_fixed< double, 3 > > itk::OdfMaximaExtractionFilter< TOdfPixelType >::ClusterPeaks ( const CoefficientPixelType & shCoeff )

protected

cluster the peaks detected by FindCandidatePeaks and retain maximum m_MaxNumPeaks

Definition at line 290 of file itkOdfMaximaExtractionFilter.cpp.

References max(), and min().

template<class TOdfPixelType >

void itk::OdfMaximaExtractionFilter< TOdfPixelType >::FindCandidatePeaks ( const CoefficientPixelType & SHcoeff )

protected

calculate all directions fullfilling the maximum consitions

Definition at line 174 of file itkOdfMaximaExtractionFilter.cpp.

References M_PI.

template<class TOdfPixelType >

void itk::OdfMaximaExtractionFilter< TOdfPixelType >::GenerateData ( )

override

Definition at line 462 of file itkOdfMaximaExtractionFilter.cpp.

References max(), and mitk::New().

template<class TOdfPixelType >

virtual const char* itk::OdfMaximaExtractionFilter< TOdfPixelType >::GetClassName ( ) const

virtual

Runtime information support.

template<class TOdfPixelType >

virtual ItkDirectionImageContainer::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::GetDirectionImageContainer ( )

virtual

container for output peaks

template<class TOdfPixelType >

virtual ItkUcharImgType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::GetNumDirectionsImage ( )

virtual

number of peaks per voxel

template<class TOdfPixelType >

virtual mitk::FiberBundle::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::GetOutputFiberBundle ( )

virtual

vector field (peak sizes rescaled for visualization purposes)

template<class TOdfPixelType >

static Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::New ( )

static

Method for creation through the object factory.

template<class TOdfPixelType >

double itk::OdfMaximaExtractionFilter< TOdfPixelType >::ODF_dphi2	(	const double &	sn,
		const double &	cs,
		const double &	A,
		const double &	B,
		const double &	C,
		const double &	D,
		const double &	E,
		const double &	F,
		const double &	G,
		const double &	H
	)

protected

derivatives of SH representation of the ODF

Definition at line 166 of file itkOdfMaximaExtractionFilter.cpp.

template<class TOdfPixelType >

double itk::OdfMaximaExtractionFilter< TOdfPixelType >::ODF_dtheta	(	const double &	sn,
		const double &	cs,
		const double &	A,
		const double &	B,
		const double &	C,
		const double &	D,
		const double &	E,
		const double &	F,
		const double &	G,
		const double &	H
	)

protected

derivatives of SH representation of the ODF

Definition at line 150 of file itkOdfMaximaExtractionFilter.cpp.

template<class TOdfPixelType >

double itk::OdfMaximaExtractionFilter< TOdfPixelType >::ODF_dtheta2	(	const double &	sn,
		const double &	cs,
		const double &	A,
		const double &	B,
		const double &	C,
		const double &	D,
		const double &	E,
		const double &	F,
		const double &	G,
		const double &	H
	)

protected

derivatives of SH representation of the ODF

Definition at line 158 of file itkOdfMaximaExtractionFilter.cpp.

template<class TOdfPixelType >

bool itk::OdfMaximaExtractionFilter< TOdfPixelType >::ReconstructQballImage ( )

protected

CSA Qball reconstruction (SH order 4)

Definition at line 55 of file itkOdfMaximaExtractionFilter.cpp.

References mitk::New().

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetBvalue ( float _arg )

virtual

input for qball reconstruction

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetDiffusionGradients ( DirectionContainerType::Pointer _arg )

virtual

input for qball reconstruction

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetDiffusionImage ( DiffusionImageType::Pointer _arg )

virtual

input for qball reconstruction

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetMaskImage ( ItkUcharImgType::Pointer _arg )

virtual

only voxels inside the binary mask are processed

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetMaxNumPeaks ( unsigned int _arg )

virtual

if more peaks are found, only the largest are kept

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetNormalizationMethod ( NormalizationMethods _arg )

virtual

normalization method of ODF peaks

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetPeakThreshold ( double _arg )

virtual

threshold on peak length relative to the largest peak in the current voxel

template<class TOdfPixelType >

virtual void itk::OdfMaximaExtractionFilter< TOdfPixelType >::SetShCoeffImage ( CoefficientImageType::Pointer _arg )

virtual

conatins spherical harmonic coefficients

template<class TOdfPixelType >

std::vector< double > itk::OdfMaximaExtractionFilter< TOdfPixelType >::SolveCubic	(	const double &	a,
		const double &	b,
		const double &	c,
		const double &	d
	)

protected

calculate roots of cubic equation ax³ + bx² + cx + d = 0 using cardanos method

Definition at line 85 of file itkOdfMaximaExtractionFilter.cpp.

References offset, and tmp2.

Member Data Documentation

template<class TOdfPixelType >

float itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_Bvalue

protected

input for qball reconstruction

Definition at line 115 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

std::vector< vnl_vector_fixed< double, 2 > > itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_CandidatePeaks

protected

container for candidate peaks (all extrema, also minima)

Definition at line 127 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

DirectionContainerType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_DiffusionGradients

protected

input for qball reconstruction

Definition at line 113 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

DiffusionImageType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_DiffusionImage

protected

input for qball reconstruction

Definition at line 114 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

ItkDirectionImageContainer::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_DirectionImageContainer

protected

output peaks

Definition at line 132 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

ItkUcharImgType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_MaskImage

protected

only voxels inside the binary mask are processed

Definition at line 118 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

unsigned int itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_MaxNumPeaks

protected

if more peaks are found, only the largest are kept

Definition at line 123 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

NormalizationMethods itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_NormalizationMethod

protected

normalization for peaks

Definition at line 121 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

ItkUcharImgType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_NumDirectionsImage

protected

number of peaks per voxel

Definition at line 131 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

mitk::FiberBundle::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_OutputFiberBundle

protected

vector field (peak sizes rescaled for visualization purposes)

Definition at line 130 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

double itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_PeakThreshold

protected

threshold on peak length relative to the largest peak in the current voxel

Definition at line 122 of file itkOdfMaximaExtractionFilter.h.

template<class TOdfPixelType >

CoefficientImageType::Pointer itk::OdfMaximaExtractionFilter< TOdfPixelType >::m_ShCoeffImage

protected

conatins spherical harmonic coefficients

Definition at line 126 of file itkOdfMaximaExtractionFilter.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<class TOdfPixelType> class itk::OdfMaximaExtractionFilter< TOdfPixelType >

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class TOdfPixelType>
class itk::OdfMaximaExtractionFilter< TOdfPixelType >