#include <animaBaseIsotropicCompartment.h>

Inheritance diagram for anima::BaseIsotropicCompartment:

Collaboration diagram for anima::BaseIsotropicCompartment:

Public Types
typedef Superclass::Pointer	BasePointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef Superclass::Matrix3DType	Matrix3DType

typedef Superclass::ModelOutputVectorType	ModelOutputVectorType

typedef itk::SmartPointer< Self >	Pointer

typedef BaseIsotropicCompartment	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
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...

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...

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...

bool	GetEstimateAxialDiffusivity ()

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...

virtual ListType &	GetParametersAsVector () 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
	Reimplements re-orientation, useless in isotropic water compartment. More...

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

void	SetEstimateAxialDiffusivity (bool arg)

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

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	GetAxialDiffusivity ()

virtual DiffusionModelCompartmentType	GetCompartmentType ()=0
	Utility function to return compartment type without needing dynamic casts. More...

virtual double	GetExtraAxonalFraction ()

virtual double	GetOrientationConcentration ()

virtual double	GetOrientationPhi ()

virtual double	GetOrientationTheta ()

virtual ListType &	GetParameterLowerBounds ()=0

virtual ListType &	GetParameterUpperBounds ()=0

virtual double	GetPerpendicularAngle ()

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

virtual double	GetRadialDiffusivity1 ()

virtual double	GetRadialDiffusivity2 ()

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	SetAxialDiffusivity (double num)

virtual void	SetExtraAxonalFraction (double num)

virtual void	SetOrientationConcentration (double num)

virtual void	SetOrientationPhi (double num)

virtual void	SetOrientationTheta (double num)

virtual void	SetPerpendicularAngle (double num)

virtual void	SetRadialDiffusivity1 (double num)

virtual void	SetRadialDiffusivity2 (double num)

virtual void	SetTissueRadius (double num)

Protected Member Functions
	BaseIsotropicCompartment ()

virtual	~BaseIsotropicCompartment ()

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 9 of file animaBaseIsotropicCompartment.h.

Member Typedef Documentation

◆ BasePointer

typedef Superclass::Pointer anima::BaseIsotropicCompartment::BasePointer

Definition at line 15 of file animaBaseIsotropicCompartment.h.

◆ ConstPointer

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

Definition at line 17 of file animaBaseIsotropicCompartment.h.

◆ Matrix3DType

typedef Superclass::Matrix3DType anima::BaseIsotropicCompartment::Matrix3DType

Definition at line 20 of file animaBaseIsotropicCompartment.h.

◆ ModelOutputVectorType

typedef Superclass::ModelOutputVectorType anima::BaseIsotropicCompartment::ModelOutputVectorType

Definition at line 18 of file animaBaseIsotropicCompartment.h.

◆ Pointer

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

Definition at line 16 of file animaBaseIsotropicCompartment.h.

◆ Self

typedef BaseIsotropicCompartment anima::BaseIsotropicCompartment::Self

Definition at line 13 of file animaBaseIsotropicCompartment.h.

◆ Superclass

typedef BaseCompartment anima::BaseIsotropicCompartment::Superclass

Definition at line 14 of file animaBaseIsotropicCompartment.h.

◆ Vector3DType

typedef Superclass::Vector3DType anima::BaseIsotropicCompartment::Vector3DType

Definition at line 19 of file animaBaseIsotropicCompartment.h.

Constructor & Destructor Documentation

◆ BaseIsotropicCompartment()

anima::BaseIsotropicCompartment::BaseIsotropicCompartment ( )

inlineprotected

Definition at line 52 of file animaBaseIsotropicCompartment.h.

◆ ~BaseIsotropicCompartment()

virtual anima::BaseIsotropicCompartment::~BaseIsotropicCompartment ( )

inlineprotectedvirtual

Definition at line 60 of file animaBaseIsotropicCompartment.h.

Member Function Documentation

◆ GetApparentFractionalAnisotropy()

double anima::BaseIsotropicCompartment::GetApparentFractionalAnisotropy ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 113 of file animaBaseIsotropicCompartment.cxx.

◆ GetApparentMeanDiffusivity()

double anima::BaseIsotropicCompartment::GetApparentMeanDiffusivity ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 118 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity().

◆ GetApparentParallelDiffusivity()

double anima::BaseIsotropicCompartment::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 123 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity().

◆ GetApparentPerpendicularDiffusivity()

double anima::BaseIsotropicCompartment::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 128 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity().

◆ GetCompartmentSize()

unsigned int anima::BaseIsotropicCompartment::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 74 of file animaBaseIsotropicCompartment.cxx.

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

◆ GetCompartmentVector()

BaseIsotropicCompartment::ModelOutputVectorType & anima::BaseIsotropicCompartment::GetCompartmentVector ( )

virtual

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

Implements anima::BaseCompartment.

Definition at line 93 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), GetCompartmentSize(), and anima::BaseCompartment::m_CompartmentVector.

◆ GetDiffusionTensor()

const BaseIsotropicCompartment::Matrix3DType & anima::BaseIsotropicCompartment::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 103 of file animaBaseIsotropicCompartment.cxx.

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

◆ GetEstimateAxialDiffusivity()

bool anima::BaseIsotropicCompartment::GetEstimateAxialDiffusivity ( )

inline

Definition at line 34 of file animaBaseIsotropicCompartment.h.

Referenced by anima::FreeWaterCompartment::GetParameterLowerBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterLowerBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterUpperBounds(), and anima::FreeWaterCompartment::GetParameterUpperBounds().

◆ GetFourierTransformedDiffusionProfile()

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

virtual

Implements anima::BaseCompartment.

Definition at line 9 of file animaBaseIsotropicCompartment.cxx.

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

Referenced by GetSignalAttenuationJacobian().

◆ GetLogDiffusionProfile()

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

virtual

Implements anima::BaseCompartment.

Definition at line 29 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity().

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods)

Reimplemented from anima::BaseCompartment.

Reimplemented in anima::FreeWaterCompartment, anima::IsotropicRestrictedWaterCompartment, and anima::StationaryWaterCompartment.

◆ GetNumberOfParameters()

unsigned int anima::BaseIsotropicCompartment::GetNumberOfParameters ( )

virtual

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

Implements anima::BaseCompartment.

Definition at line 79 of file animaBaseIsotropicCompartment.cxx.

References GetCompartmentSize().

Referenced by anima::FreeWaterCompartment::GetParameterLowerBounds(), anima::StationaryWaterCompartment::GetParameterLowerBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterLowerBounds(), GetParametersAsVector(), anima::StationaryWaterCompartment::GetParameterUpperBounds(), anima::FreeWaterCompartment::GetParameterUpperBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterUpperBounds(), GetSignalAttenuationJacobian(), and SetParametersFromVector().

◆ GetParametersAsVector()

BaseCompartment::ListType & anima::BaseIsotropicCompartment::GetParametersAsVector ( )

virtual

Implements anima::BaseCompartment.

Definition at line 47 of file animaBaseIsotropicCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), GetNumberOfParameters(), and anima::BaseCompartment::m_ParametersVector.

◆ GetSignalAttenuationJacobian()

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