mitk::RawShModel< ScalarType > Class Template Reference

The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal. More...

#include <mitkRawShModel.h>

Inheritance diagram for mitk::RawShModel< ScalarType >:

Collaboration diagram for mitk::RawShModel< ScalarType >:

Public Types
typedef itk::Image< double, 3 >	ItkDoubleImageType
typedef itk::Image< unsigned char, 3 >	ItkUcharImageType
typedef itk::Image< itk::DiffusionTensor3D< double >, 3 >	TensorImageType
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter< short, short, float, 2, QBALL_ODFSIZE >	QballFilterType
typedef DiffusionSignalModel< ScalarType >::PixelType	PixelType
typedef DiffusionSignalModel< ScalarType >::GradientType	GradientType
typedef DiffusionSignalModel< ScalarType >::GradientListType	GradientListType
typedef itk::Matrix< double, 3, 3 >	MatrixType
Public Types inherited from mitk::DiffusionSignalModel< ScalarType >
typedef itk::Image< double, 3 >	ItkDoubleImgType
typedef itk::VariableLengthVector< ScalarType >	PixelType
typedef itk::Vector< double, 3 >	GradientType
typedef std::vector< GradientType >	GradientListType
typedef itk::Statistics::MersenneTwisterRandomVariateGenerator	ItkRandGenType

Public Member Functions
	RawShModel ()
template<class OtherType >
	RawShModel (RawShModel< OtherType > *model)
	~RawShModel ()
PixelType	SimulateMeasurement ()
ScalarType	SimulateMeasurement (unsigned int dir)
bool	SetShCoefficients (vnl_vector< double > shCoefficients, double b0)
void	SetFiberDirection (GradientType fiberDirection)
void	SetGradientList (GradientListType gradientList)
void	SetFaRange (double min, double max)
void	SetAdcRange (double min, double max)
void	SetMaxNumKernels (unsigned int max)
unsigned int	GetNumberOfKernels ()
std::pair< double, double >	GetFaRange ()
std::pair< double, double >	GetAdcRange ()
unsigned int	GetMaxNumKernels ()
void	Clear ()
std::vector< vnl_vector< double > >	GetShCoefficients ()
std::vector< double >	GetB0Signals ()
vnl_matrix< double >	GetSphericalCoordinates ()
unsigned int	GetShOrder ()
int	GetModelIndex ()
double	GetBaselineSignal (int index)
vnl_vector< double >	GetCoefficients (int listIndex)
bool	SampleKernels (Image::Pointer diffImg, ItkUcharImageType::Pointer maskImage, TensorImageType::Pointer tensorImage=NULL, QballFilterType::CoefficientImageType::Pointer coeffImage=NULL, ItkDoubleImageType::Pointer adcImage=NULL)
Public Member Functions inherited from mitk::DiffusionSignalModel< ScalarType >
	DiffusionSignalModel ()
	~DiffusionSignalModel ()
GradientType	GetFiberDirection ()
GradientListType	GetGradientList ()
GradientType	GetGradientDirection (int i)
void	SetT2 (double T2)
double	GetT2 ()
void	SetT1 (double T1)
double	GetT1 ()
void	SetVolumeFractionImage (ItkDoubleImgType::Pointer img)
ItkDoubleImgType::Pointer	GetVolumeFractionImage ()
void	SetRandomGenerator (ItkRandGenType::Pointer randgen)
ItkRandGenType::Pointer	GetRandomGenerator ()
void	SetSeed (int s)

Protected Member Functions
void	Cart2Sph (GradientListType gradients)
void	RandomModel ()

Protected Attributes
std::vector< vnl_vector< double > >	m_ShCoefficients
std::vector< double >	m_B0Signal
std::vector< GradientType >	m_PrototypeMaxDirection
vnl_matrix< double >	m_SphCoords
std::pair< double, double >	m_AdcRange
std::pair< double, double >	m_FaRange
unsigned int	m_ShOrder
int	m_ModelIndex
unsigned int	m_MaxNumKernels
Protected Attributes inherited from mitk::DiffusionSignalModel< ScalarType >
GradientType	m_FiberDirection
	Needed to generate anisotropc signal to determin direction of anisotropy. More...
GradientListType	m_GradientList
	Diffusion gradient direction container. More...
double	m_T2
	Tissue specific transversal relaxation time. More...
double	m_T1
	Tissue specific longitudinal relaxation time. More...
ItkDoubleImgType::Pointer	m_VolumeFractionImage
	Tissue specific volume fraction for each voxel (only relevant for non fiber compartments) More...
ItkRandGenType::Pointer	m_RandGen
	Random number generator. More...

Additional Inherited Members
Public Attributes inherited from mitk::DiffusionSignalModel< ScalarType >
unsigned int	m_CompartmentId
	GUI flag. Which compartment is this model assigned to? More...

Detailed Description

template<class ScalarType = double>
class mitk::RawShModel< ScalarType >

The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal.

Definition at line 32 of file mitkRawShModel.h.

Member Typedef Documentation

template<class ScalarType = double>

typedef DiffusionSignalModel< ScalarType >::GradientListType mitk::RawShModel< ScalarType >::GradientListType

Definition at line 63 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef DiffusionSignalModel< ScalarType >::GradientType mitk::RawShModel< ScalarType >::GradientType

Definition at line 62 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef itk::Image< double, 3 > mitk::RawShModel< ScalarType >::ItkDoubleImageType

Definition at line 57 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef itk::Image< unsigned char, 3 > mitk::RawShModel< ScalarType >::ItkUcharImageType

Definition at line 58 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef itk::Matrix< double, 3, 3 > mitk::RawShModel< ScalarType >::MatrixType

Definition at line 64 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef DiffusionSignalModel< ScalarType >::PixelType mitk::RawShModel< ScalarType >::PixelType

Definition at line 61 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,2,QBALL_ODFSIZE> mitk::RawShModel< ScalarType >::QballFilterType

Definition at line 60 of file mitkRawShModel.h.

template<class ScalarType = double>

typedef itk::Image< itk::DiffusionTensor3D< double >, 3 > mitk::RawShModel< ScalarType >::TensorImageType

Definition at line 59 of file mitkRawShModel.h.

Constructor & Destructor Documentation

template<class ScalarType >

RawShModel::RawShModel

(

)

Definition at line 33 of file mitkRawShModel.cpp.

References mitk::RawShModel< ScalarType >::m_AdcRange, mitk::RawShModel< ScalarType >::m_FaRange, mitk::DiffusionSignalModel< ScalarType >::m_RandGen, and mitk::New().

template<class ScalarType = double>

template<class OtherType >

mitk::RawShModel< ScalarType >::RawShModel ( RawShModel< OtherType > *  model )

inline

Definition at line 37 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::GetAdcRange(), mitk::RawShModel< ScalarType >::GetB0Signals(), mitk::RawShModel< ScalarType >::GetFaRange(), mitk::DiffusionSignalModel< ScalarType >::GetFiberDirection(), mitk::DiffusionSignalModel< ScalarType >::GetGradientList(), mitk::RawShModel< ScalarType >::GetMaxNumKernels(), mitk::RawShModel< ScalarType >::GetModelIndex(), mitk::DiffusionSignalModel< ScalarType >::GetRandomGenerator(), mitk::RawShModel< ScalarType >::GetShCoefficients(), mitk::RawShModel< ScalarType >::GetShOrder(), mitk::RawShModel< ScalarType >::GetSphericalCoordinates(), mitk::DiffusionSignalModel< ScalarType >::GetT2(), mitk::DiffusionSignalModel< ScalarType >::GetVolumeFractionImage(), mitk::RawShModel< ScalarType >::m_AdcRange, mitk::RawShModel< ScalarType >::m_B0Signal, mitk::DiffusionSignalModel< ScalarType >::m_CompartmentId, mitk::RawShModel< ScalarType >::m_FaRange, mitk::DiffusionSignalModel< ScalarType >::m_FiberDirection, mitk::DiffusionSignalModel< ScalarType >::m_GradientList, mitk::RawShModel< ScalarType >::m_MaxNumKernels, mitk::RawShModel< ScalarType >::m_ModelIndex, mitk::DiffusionSignalModel< ScalarType >::m_RandGen, mitk::RawShModel< ScalarType >::m_ShCoefficients, mitk::RawShModel< ScalarType >::m_ShOrder, mitk::RawShModel< ScalarType >::m_SphCoords, mitk::DiffusionSignalModel< ScalarType >::m_T2, and mitk::DiffusionSignalModel< ScalarType >::m_VolumeFractionImage.

template<class ScalarType >

RawShModel::~RawShModel

(

)

Definition at line 47 of file mitkRawShModel.cpp.

Member Function Documentation

template<class ScalarType >

void RawShModel::Cart2Sph ( GradientListType  gradients )

protected

Definition at line 201 of file mitkRawShModel.cpp.

template<class ScalarType >

void RawShModel::Clear

(

)

Definition at line 53 of file mitkRawShModel.cpp.

template<class ScalarType = double>

std::pair< double, double > mitk::RawShModel< ScalarType >::GetAdcRange ( )

inline

Definition at line 78 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_AdcRange.

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

std::vector< double > mitk::RawShModel< ScalarType >::GetB0Signals ( )

inline

Definition at line 83 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_B0Signal.

Referenced by mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

double mitk::RawShModel< ScalarType >::GetBaselineSignal ( int  index )

inline

Definition at line 88 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_B0Signal.

Referenced by mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

vnl_vector< double > mitk::RawShModel< ScalarType >::GetCoefficients ( int  listIndex )

inline

Definition at line 89 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_ShCoefficients.

Referenced by mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

std::pair< double, double > mitk::RawShModel< ScalarType >::GetFaRange ( )

inline

Definition at line 77 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_FaRange.

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

unsigned int mitk::RawShModel< ScalarType >::GetMaxNumKernels ( )

inline

Definition at line 79 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_MaxNumKernels.

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

int mitk::RawShModel< ScalarType >::GetModelIndex ( )

inline

Definition at line 86 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_ModelIndex.

Referenced by mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType >

unsigned int RawShModel::GetNumberOfKernels

(

)

Definition at line 67 of file mitkRawShModel.cpp.

Referenced by mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

std::vector< vnl_vector< double > > mitk::RawShModel< ScalarType >::GetShCoefficients ( )

inline

Definition at line 82 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_ShCoefficients.

Referenced by mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

unsigned int mitk::RawShModel< ScalarType >::GetShOrder ( )

inline

Definition at line 85 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_ShOrder.

Referenced by mitk::RawShModel< ScalarType >::RawShModel(), and mitk::FiberfoxParameters< ScalarType >::SaveParameters().

template<class ScalarType = double>

vnl_matrix<double> mitk::RawShModel< ScalarType >::GetSphericalCoordinates ( )

inline

Definition at line 84 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_SphCoords.

Referenced by mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType >

void RawShModel::RandomModel ( )

protected

Definition at line 61 of file mitkRawShModel.cpp.

template<class ScalarType >

bool RawShModel::SampleKernels	(	Image::Pointer	diffImg,
		ItkUcharImageType::Pointer	maskImage,
		TensorImageType::Pointer	tensorImage = NULL,
		QballFilterType::CoefficientImageType::Pointer	coeffImage = NULL,
		ItkDoubleImageType::Pointer	adcImage = NULL
	)

Definition at line 73 of file mitkRawShModel.cpp.

References mitk::CastToItkImage(), mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, max(), MITK_INFO, mitk::New(), itk::AdcImageFilter< TInPixelType, TOutPixelType >::New(), mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME, and mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.

template<class ScalarType = double>

void mitk::RawShModel< ScalarType >::SetAdcRange ( double  min, double  max  )

inline

Definition at line 74 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_AdcRange, max(), and min().

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters().

template<class ScalarType = double>

void mitk::RawShModel< ScalarType >::SetFaRange ( double  min, double  max  )

inline

Definition at line 73 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_FaRange, max(), and min().

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters().

template<class ScalarType >

void RawShModel::SetFiberDirection ( GradientType  fiberDirection )

virtual

Implements mitk::DiffusionSignalModel< ScalarType >.

Definition at line 219 of file mitkRawShModel.cpp.

References rotation.

template<class ScalarType = double>

void mitk::RawShModel< ScalarType >::SetGradientList ( GradientListType  gradientList )

inlinevirtual

Implements mitk::DiffusionSignalModel< ScalarType >.

Definition at line 72 of file mitkRawShModel.h.

References mitk::DiffusionSignalModel< ScalarType >::m_GradientList.

template<class ScalarType = double>

void mitk::RawShModel< ScalarType >::SetMaxNumKernels ( unsigned int  max )

inline

Definition at line 75 of file mitkRawShModel.h.

References mitk::RawShModel< ScalarType >::m_MaxNumKernels, and max().

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters().

template<class ScalarType >

bool RawShModel::SetShCoefficients	(	vnl_vector< double >	shCoefficients,
		double	b0
	)

Definition at line 249 of file mitkRawShModel.cpp.

Referenced by mitk::FiberfoxParameters< ScalarType >::LoadParameters().

template<class ScalarType >

RawShModel< ScalarType >::PixelType RawShModel::SimulateMeasurement ( )

virtual

Actual signal generation

Implements mitk::DiffusionSignalModel< ScalarType >.

Definition at line 341 of file mitkRawShModel.cpp.

References M_PI.

template<class ScalarType >

ScalarType RawShModel::SimulateMeasurement ( unsigned int  dir )

virtual

Implements mitk::DiffusionSignalModel< ScalarType >.

Definition at line 299 of file mitkRawShModel.cpp.

References M_PI.

Member Data Documentation

template<class ScalarType = double>

std::pair< double, double > mitk::RawShModel< ScalarType >::m_AdcRange

protected

Definition at line 102 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetAdcRange(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::RawShModel< ScalarType >::SetAdcRange().

template<class ScalarType = double>

std::vector< double > mitk::RawShModel< ScalarType >::m_B0Signal

protected

Definition at line 99 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetB0Signals(), mitk::RawShModel< ScalarType >::GetBaselineSignal(), and mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

std::pair< double, double > mitk::RawShModel< ScalarType >::m_FaRange

protected

Definition at line 103 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetFaRange(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::RawShModel< ScalarType >::SetFaRange().

template<class ScalarType = double>

unsigned int mitk::RawShModel< ScalarType >::m_MaxNumKernels

protected

Definition at line 106 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetMaxNumKernels(), mitk::RawShModel< ScalarType >::RawShModel(), and mitk::RawShModel< ScalarType >::SetMaxNumKernels().

template<class ScalarType = double>

int mitk::RawShModel< ScalarType >::m_ModelIndex

protected

Definition at line 105 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetModelIndex(), and mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

std::vector< GradientType > mitk::RawShModel< ScalarType >::m_PrototypeMaxDirection

protected

Definition at line 100 of file mitkRawShModel.h.

template<class ScalarType = double>

std::vector< vnl_vector< double > > mitk::RawShModel< ScalarType >::m_ShCoefficients

protected

Definition at line 98 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetCoefficients(), mitk::RawShModel< ScalarType >::GetShCoefficients(), and mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

unsigned int mitk::RawShModel< ScalarType >::m_ShOrder

protected

Definition at line 104 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetShOrder(), and mitk::RawShModel< ScalarType >::RawShModel().

template<class ScalarType = double>

vnl_matrix<double> mitk::RawShModel< ScalarType >::m_SphCoords

protected

Definition at line 101 of file mitkRawShModel.h.

Referenced by mitk::RawShModel< ScalarType >::GetSphericalCoordinates(), and mitk::RawShModel< ScalarType >::RawShModel().

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

• mitkRawShModel.h
• mitkRawShModel.cpp