#include <animaTensorCompartment.h>

Inheritance diagram for anima::TensorCompartment:

Collaboration diagram for anima::TensorCompartment:

Public Types
typedef Superclass::Pointer	BasePointer

typedef itk::SmartPointer< const Self >	ConstPointer

using	LEcalculatorPointer = LEcalculatorType::Pointer

using	LEcalculatorType = anima::LogEuclideanTensorCalculator< double >

typedef Superclass::Matrix3DType	Matrix3DType

typedef Superclass::ModelOutputVectorType	ModelOutputVectorType

typedef itk::SmartPointer< Self >	Pointer

typedef TensorCompartment	Self

typedef BaseCompartment	Superclass

typedef Superclass::Vector3DType	Vector3DType

Public Types inherited from anima::BaseCompartment
typedef itk::SmartPointer< const Self >	ConstPointer

typedef std::vector< double >	ListType

typedef itk::Matrix< double, 3, 3 >	Matrix3DType

typedef itk::VariableLengthVector< double >	ModelOutputVectorType

typedef itk::SmartPointer< Self >	Pointer

typedef BaseCompartment	Self

typedef itk::LightObject	Superclass

typedef vnl_vector_fixed< double, 3 >	Vector3DType

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const

double	GetApparentFractionalAnisotropy () ITK_OVERRIDE

double	GetApparentMeanDiffusivity () ITK_OVERRIDE

double	GetApparentParallelDiffusivity () ITK_OVERRIDE
	Get approximation to parallel diffusivity of the compartment (may be different from axial diffusivity which is an internal parameter of the model) More...

double	GetApparentPerpendicularDiffusivity () ITK_OVERRIDE
	Get approximation to perpendicular diffusivity of the compartment (may be different from radial diffusivities which are internal parameters of the model) More...

double	GetAxialDiffusivity () ITK_OVERRIDE

unsigned int	GetCompartmentSize () ITK_OVERRIDE
	Number of parameters to describe the model, these parameters will be self-contained, i.e. include fixed parameters for example. More...

DiffusionModelCompartmentType	GetCompartmentType () ITK_OVERRIDE
	Utility function to return compartment type without needing dynamic casts. More...

ModelOutputVectorType &	GetCompartmentVector () ITK_OVERRIDE
	Get compartment overall description vector, mainly for writing, should be self-contained. More...

const Matrix3DType &	GetDiffusionTensor () ITK_OVERRIDE
	Get compartment as a 3D tensor (default behavior: throw exception if not supported by the compartment model) More...

virtual double	GetFourierTransformedDiffusionProfile (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient) ITK_OVERRIDE

virtual double	GetLogDiffusionProfile (const Vector3DType &sample) ITK_OVERRIDE

virtual const char *	GetNameOfClass () const

unsigned int	GetNumberOfParameters () ITK_OVERRIDE
	Number of optimized parameters: smaller than total number of parameters. More...

double	GetOrientationPhi () ITK_OVERRIDE

double	GetOrientationTheta () ITK_OVERRIDE

virtual ListType &	GetParameterLowerBounds () ITK_OVERRIDE

virtual ListType &	GetParametersAsVector () ITK_OVERRIDE

virtual ListType &	GetParameterUpperBounds () ITK_OVERRIDE

double	GetPerpendicularAngle () ITK_OVERRIDE

double	GetRadialDiffusivity1 () ITK_OVERRIDE

double	GetRadialDiffusivity2 () ITK_OVERRIDE

virtual ListType &	GetSignalAttenuationJacobian (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient) ITK_OVERRIDE

void	Reorient (vnl_matrix< double > &orientationMatrix, bool affineTransform) ITK_OVERRIDE
	Reorient the fascicle compartment using a matrix, the flag specifies if the transform is affine or rigid. More...

void	SetAxialDiffusivity (double num) ITK_OVERRIDE

void	SetCompartmentVector (ModelOutputVectorType &compartmentVector) ITK_OVERRIDE
	Set compartment overall description vector, for setting automatically the individual parameters when reading from disk. More...

void	SetEstimateDiffusivities (bool arg)

void	SetOrientationPhi (double num) ITK_OVERRIDE

void	SetOrientationTheta (double num) ITK_OVERRIDE

virtual void	SetParametersFromVector (const ListType &params) ITK_OVERRIDE
	Various methods for optimization parameters setting and getting. More...

void	SetPerpendicularAngle (double num) ITK_OVERRIDE

void	SetRadialDiffusivity1 (double num) ITK_OVERRIDE

void	SetRadialDiffusivity2 (double num) ITK_OVERRIDE

void	UpdateParametersFromTensor ()

Public Member Functions inherited from anima::BaseCompartment
virtual void	CopyFromOther (Self *rhs)
	Copy internal parameters from another compartment, faster than a set/get compartment vector. More...

virtual double	GetExtraAxonalFraction ()

virtual double	GetOrientationConcentration ()

double	GetPredictedSignal (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient)

virtual bool	GetTensorCompatible ()

virtual double	GetTissueRadius ()

virtual bool	IsEqual (Self *rhs, double tolerance=1.0e-2, double absoluteTolerance=1.0e-8)
	Tests equality to another compartment up to a constant (relative and absolute tolerances) More...

virtual void	SetExtraAxonalFraction (double num)

virtual void	SetOrientationConcentration (double num)

virtual void	SetTissueRadius (double num)

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	TensorCompartment ()

void	UpdateAngleConfiguration ()
	Update angles' sine and cosine values from parameters. More...

void	UpdateDiffusionTensor ()
	Update diffusion tensor value from parameters. More...

void	UpdateInverseDiffusionTensor ()
	Update inverse diffusion tensor value from parameters. More...

virtual	~TensorCompartment ()

Protected Member Functions inherited from anima::BaseCompartment
	BaseCompartment ()

virtual	~BaseCompartment ()

Additional Inherited Members
Protected Attributes inherited from anima::BaseCompartment
ModelOutputVectorType	m_CompartmentVector
	Vector to hold working value of compartment vector. More...

Matrix3DType	m_DiffusionTensor
	Matrix to hold working value of diffusion tensor approximation to the model. More...

ListType	m_JacobianVector
	Vector holding current jacobian value. More...

ListType	m_ParametersLowerBoundsVector
	Vector holding current parameters lower bounds. More...

ListType	m_ParametersUpperBoundsVector
	Vector holding current parameters upper bounds. More...

ListType	m_ParametersVector
	Vector holding current parameters vector. More...

Static Protected Attributes inherited from anima::BaseCompartment
static const unsigned int	m_SpaceDimension = 3

Detailed Description

Definition at line 11 of file animaTensorCompartment.h.

Member Typedef Documentation

◆ BasePointer

typedef Superclass::Pointer anima::TensorCompartment::BasePointer

Definition at line 17 of file animaTensorCompartment.h.

◆ ConstPointer

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

Definition at line 19 of file animaTensorCompartment.h.

◆ LEcalculatorPointer

using anima::TensorCompartment::LEcalculatorPointer = LEcalculatorType::Pointer

Definition at line 24 of file animaTensorCompartment.h.

◆ LEcalculatorType

using anima::TensorCompartment::LEcalculatorType = anima::LogEuclideanTensorCalculator <double>

Definition at line 23 of file animaTensorCompartment.h.

◆ Matrix3DType

typedef Superclass::Matrix3DType anima::TensorCompartment::Matrix3DType

Definition at line 22 of file animaTensorCompartment.h.

◆ ModelOutputVectorType

typedef Superclass::ModelOutputVectorType anima::TensorCompartment::ModelOutputVectorType

Definition at line 20 of file animaTensorCompartment.h.

◆ Pointer

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

Definition at line 18 of file animaTensorCompartment.h.

◆ Self

typedef TensorCompartment anima::TensorCompartment::Self

Definition at line 15 of file animaTensorCompartment.h.

◆ Superclass

typedef BaseCompartment anima::TensorCompartment::Superclass

Definition at line 16 of file animaTensorCompartment.h.

◆ Vector3DType

typedef Superclass::Vector3DType anima::TensorCompartment::Vector3DType

Definition at line 21 of file animaTensorCompartment.h.

Constructor & Destructor Documentation

◆ TensorCompartment()

anima::TensorCompartment::TensorCompartment ( )

inlineprotected

Definition at line 77 of file animaTensorCompartment.h.

◆ ~TensorCompartment()

virtual anima::TensorCompartment::~TensorCompartment ( )

inlineprotectedvirtual

Definition at line 91 of file animaTensorCompartment.h.

Member Function Documentation

◆ CreateAnother()

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

◆ GetApparentFractionalAnisotropy()

double anima::TensorCompartment::GetApparentFractionalAnisotropy ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 475 of file animaTensorCompartment.cxx.

References GetAxialDiffusivity(), GetRadialDiffusivity1(), and GetRadialDiffusivity2().

◆ GetApparentMeanDiffusivity()

double anima::TensorCompartment::GetApparentMeanDiffusivity ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 491 of file animaTensorCompartment.cxx.

References GetAxialDiffusivity(), GetRadialDiffusivity1(), and GetRadialDiffusivity2().

◆ GetApparentParallelDiffusivity()

double anima::TensorCompartment::GetApparentParallelDiffusivity ( )

virtual

Get approximation to parallel diffusivity of the compartment (may be different from axial diffusivity which is an internal parameter of the model)

Reimplemented from anima::BaseCompartment.

Definition at line 500 of file animaTensorCompartment.cxx.

References GetAxialDiffusivity().

◆ GetApparentPerpendicularDiffusivity()

double anima::TensorCompartment::GetApparentPerpendicularDiffusivity ( )

virtual

Get approximation to perpendicular diffusivity of the compartment (may be different from radial diffusivities which are internal parameters of the model)

Reimplemented from anima::BaseCompartment.

Definition at line 505 of file animaTensorCompartment.cxx.

References GetRadialDiffusivity1(), and GetRadialDiffusivity2().

◆ GetAxialDiffusivity()

double anima::TensorCompartment::GetAxialDiffusivity ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 149 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), and UpdateParametersFromTensor().

Referenced by GetApparentFractionalAnisotropy(), GetApparentMeanDiffusivity(), GetApparentParallelDiffusivity(), GetParametersAsVector(), GetSignalAttenuationJacobian(), SetAxialDiffusivity(), and UpdateDiffusionTensor().

◆ GetCompartmentSize()

unsigned int anima::TensorCompartment::GetCompartmentSize ( )

virtual

Number of parameters to describe the model, these parameters will be self-contained, i.e. include fixed parameters for example.

Implements anima::BaseCompartment.

Definition at line 334 of file animaTensorCompartment.cxx.

Referenced by GetCompartmentVector(), GetNumberOfParameters(), Reorient(), and SetCompartmentVector().

◆ GetCompartmentType()

DiffusionModelCompartmentType anima::TensorCompartment::GetCompartmentType ( )

inlinevirtual

Utility function to return compartment type without needing dynamic casts.

Implements anima::BaseCompartment.

Definition at line 32 of file animaTensorCompartment.h.

References anima::Tensor.

◆ GetCompartmentVector()

TensorCompartment::ModelOutputVectorType & anima::TensorCompartment::GetCompartmentVector ( )

virtual

Get compartment overall description vector, mainly for writing, should be self-contained.

Implements anima::BaseCompartment.

Definition at line 353 of file animaTensorCompartment.cxx.

References GetCompartmentSize(), anima::GetVectorRepresentation(), anima::BaseCompartment::m_CompartmentVector, and UpdateDiffusionTensor().

◆ GetDiffusionTensor()

const TensorCompartment::Matrix3DType & anima::TensorCompartment::GetDiffusionTensor ( )

virtual

Get compartment as a 3D tensor (default behavior: throw exception if not supported by the compartment model)

Reimplemented from anima::BaseCompartment.

Definition at line 393 of file animaTensorCompartment.cxx.

References UpdateDiffusionTensor().

◆ GetFourierTransformedDiffusionProfile()

double anima::TensorCompartment::GetFourierTransformedDiffusionProfile	(	double	smallDelta,
		double	bigDelta,
		double	gradientStrength,
		const Vector3DType &	gradient
	)

virtual

Implements anima::BaseCompartment.

Definition at line 9 of file animaTensorCompartment.cxx.

References anima::GetBValueFromAcquisitionParameters(), anima::BaseCompartment::m_SpaceDimension, and UpdateDiffusionTensor().

Referenced by GetSignalAttenuationJacobian().

◆ GetLogDiffusionProfile()

double anima::TensorCompartment::GetLogDiffusionProfile ( const Vector3DType & sample )

virtual

Implements anima::BaseCompartment.

Definition at line 72 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::m_SpaceDimension, and UpdateInverseDiffusionTensor().

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods)

Reimplemented from anima::BaseCompartment.

◆ GetNumberOfParameters()

unsigned int anima::TensorCompartment::GetNumberOfParameters ( )

virtual

Number of optimized parameters: smaller than total number of parameters.

Implements anima::BaseCompartment.

Definition at line 339 of file animaTensorCompartment.cxx.

References GetCompartmentSize().

Referenced by GetParameterLowerBounds(), GetParametersAsVector(), GetParameterUpperBounds(), GetSignalAttenuationJacobian(), and SetParametersFromVector().

◆ GetOrientationPhi()

double anima::TensorCompartment::GetOrientationPhi ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 118 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetOrientationPhi(), and UpdateParametersFromTensor().

Referenced by GetParametersAsVector(), SetOrientationPhi(), and UpdateAngleConfiguration().

◆ GetOrientationTheta()

double anima::TensorCompartment::GetOrientationTheta ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 102 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetOrientationTheta(), and UpdateParametersFromTensor().

Referenced by GetParametersAsVector(), SetOrientationTheta(), and UpdateAngleConfiguration().

◆ GetParameterLowerBounds()

TensorCompartment::ListType & anima::TensorCompartment::GetParameterLowerBounds ( )

virtual

Implements anima::BaseCompartment.

Definition at line 220 of file animaTensorCompartment.cxx.

References GetNumberOfParameters(), anima::BaseCompartment::m_ParametersLowerBoundsVector, anima::MCMAxialDiffusivityAddonLowerBound, anima::MCMDiffusivityLowerBound, and anima::MCMZeroLowerBound.

◆ GetParametersAsVector()

TensorCompartment::ListType & anima::TensorCompartment::GetParametersAsVector ( )

virtual

Implements anima::BaseCompartment.

Definition at line 202 of file animaTensorCompartment.cxx.

References GetAxialDiffusivity(), GetNumberOfParameters(), GetOrientationPhi(), GetOrientationTheta(), GetPerpendicularAngle(), GetRadialDiffusivity1(), GetRadialDiffusivity2(), and anima::BaseCompartment::m_ParametersVector.

◆ GetParameterUpperBounds()

TensorCompartment::ListType & anima::TensorCompartment::GetParameterUpperBounds ( )

virtual

Implements anima::BaseCompartment.

Definition at line 234 of file animaTensorCompartment.cxx.

References GetNumberOfParameters(), anima::BaseCompartment::m_ParametersUpperBoundsVector, anima::MCMAzimuthAngleUpperBound, anima::MCMDiffusivityUpperBound, anima::MCMPolarAngleUpperBound, and anima::MCMRadialDiffusivityUpperBound.

◆ GetPerpendicularAngle()

double anima::TensorCompartment::GetPerpendicularAngle ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 134 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetPerpendicularAngle(), and UpdateParametersFromTensor().

Referenced by GetParametersAsVector(), SetPerpendicularAngle(), and UpdateAngleConfiguration().

◆ GetRadialDiffusivity1()

double anima::TensorCompartment::GetRadialDiffusivity1 ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 164 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetRadialDiffusivity1(), and UpdateParametersFromTensor().

Referenced by GetApparentFractionalAnisotropy(), GetApparentMeanDiffusivity(), GetApparentPerpendicularDiffusivity(), GetParametersAsVector(), GetSignalAttenuationJacobian(), SetRadialDiffusivity1(), and UpdateDiffusionTensor().

◆ GetRadialDiffusivity2()

double anima::TensorCompartment::GetRadialDiffusivity2 ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 179 of file animaTensorCompartment.cxx.

References anima::BaseCompartment::GetRadialDiffusivity2(), and UpdateParametersFromTensor().

Referenced by GetApparentFractionalAnisotropy(), GetApparentMeanDiffusivity(), GetApparentPerpendicularDiffusivity(), GetParametersAsVector(), GetSignalAttenuationJacobian(), SetRadialDiffusivity2(), and UpdateDiffusionTensor().

◆ GetSignalAttenuationJacobian()

TensorCompartment::ListType & anima::TensorCompartment::GetSignalAttenuationJacobian	(	double	smallDelta,
		double	bigDelta,
		double	gradientStrength,
		const Vector3DType &	gradient
	)