#include <animaBaseCompartment.h>

Inheritance diagram for anima::BaseCompartment:

Collaboration diagram for anima::BaseCompartment:

Public Types
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 void	CopyFromOther (Self *rhs)
	Copy internal parameters from another compartment, faster than a set/get compartment vector. More...

virtual double	GetApparentFractionalAnisotropy ()

virtual double	GetApparentMeanDiffusivity ()

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

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

virtual double	GetAxialDiffusivity ()

virtual unsigned int	GetCompartmentSize ()=0
	Number of parameters to describe the model, these parameters will be self-contained, i.e. include fixed parameters for example. More...

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

virtual ModelOutputVectorType &	GetCompartmentVector ()=0
	Get compartment overall description vector, mainly for writing, should be self-contained. More...

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

virtual double	GetExtraAxonalFraction ()

virtual double	GetFourierTransformedDiffusionProfile (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient)=0

virtual double	GetLogDiffusionProfile (const Vector3DType &sample)=0

virtual const char *	GetNameOfClass () const

virtual unsigned int	GetNumberOfParameters ()=0
	Number of optimized parameters: smaller than total number of parameters. More...

virtual double	GetOrientationConcentration ()

virtual double	GetOrientationPhi ()

virtual double	GetOrientationTheta ()

virtual ListType &	GetParameterLowerBounds ()=0

virtual ListType &	GetParametersAsVector ()=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 ListType &	GetSignalAttenuationJacobian (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient)=0

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

virtual void	SetAxialDiffusivity (double num)

virtual void	SetCompartmentVector (ModelOutputVectorType &compartmentVector)=0
	Set compartment overall description vector, for setting automatically the individual parameters when reading from disk. More...

virtual void	SetExtraAxonalFraction (double num)

virtual void	SetOrientationConcentration (double num)

virtual void	SetOrientationPhi (double num)

virtual void	SetOrientationTheta (double num)

virtual void	SetParametersFromVector (const ListType &params)=0
	Various methods for optimization parameters setting and getting. More...

virtual void	SetPerpendicularAngle (double num)

virtual void	SetRadialDiffusivity1 (double num)

virtual void	SetRadialDiffusivity2 (double num)

virtual void	SetTissueRadius (double num)

Protected Member Functions
	BaseCompartment ()

virtual	~BaseCompartment ()

Protected Attributes
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
static const unsigned int	m_SpaceDimension = 3

Detailed Description

Definition at line 30 of file animaBaseCompartment.h.

Member Typedef Documentation

◆ ConstPointer

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

Definition at line 37 of file animaBaseCompartment.h.

◆ ListType

typedef std::vector<double> anima::BaseCompartment::ListType

Definition at line 47 of file animaBaseCompartment.h.

◆ Matrix3DType

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

Definition at line 38 of file animaBaseCompartment.h.

◆ ModelOutputVectorType

typedef itk::VariableLengthVector<double> anima::BaseCompartment::ModelOutputVectorType

Definition at line 48 of file animaBaseCompartment.h.

◆ Pointer

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

Definition at line 36 of file animaBaseCompartment.h.

◆ Self

typedef BaseCompartment anima::BaseCompartment::Self

Definition at line 34 of file animaBaseCompartment.h.

◆ Superclass

typedef itk::LightObject anima::BaseCompartment::Superclass

Definition at line 35 of file animaBaseCompartment.h.

◆ Vector3DType

typedef vnl_vector_fixed<double,3> anima::BaseCompartment::Vector3DType

Definition at line 46 of file animaBaseCompartment.h.

Constructor & Destructor Documentation

◆ BaseCompartment()

anima::BaseCompartment::BaseCompartment ( )

inlineprotected

Definition at line 120 of file animaBaseCompartment.h.

References anima::MCMAzimuthAngleUpperBound.

◆ ~BaseCompartment()

virtual anima::BaseCompartment::~BaseCompartment ( )

inlineprotectedvirtual

Definition at line 135 of file animaBaseCompartment.h.

Member Function Documentation

◆ CopyFromOther()

void anima::BaseCompartment::CopyFromOther ( Self * rhs )

virtual

Copy internal parameters from another compartment, faster than a set/get compartment vector.

Definition at line 86 of file animaBaseCompartment.cxx.

References GetAxialDiffusivity(), GetExtraAxonalFraction(), GetOrientationConcentration(), GetOrientationPhi(), GetOrientationTheta(), GetPerpendicularAngle(), GetRadialDiffusivity1(), GetRadialDiffusivity2(), GetTissueRadius(), SetAxialDiffusivity(), SetExtraAxonalFraction(), SetOrientationConcentration(), SetOrientationPhi(), SetOrientationTheta(), SetPerpendicularAngle(), SetRadialDiffusivity1(), SetRadialDiffusivity2(), and SetTissueRadius().

◆ GetApparentFractionalAnisotropy()

double anima::BaseCompartment::GetApparentFractionalAnisotropy ( )

virtual

Reimplemented in anima::TensorCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Definition at line 125 of file animaBaseCompartment.cxx.

Referenced by anima::MCMScalarMapsImageFilter< TPixelType >::DynamicThreadedGenerateData().

◆ GetApparentMeanDiffusivity()

double anima::BaseCompartment::GetApparentMeanDiffusivity ( )

virtual

Reimplemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Definition at line 130 of file animaBaseCompartment.cxx.

Referenced by anima::MCMScalarMapsImageFilter< TPixelType >::DynamicThreadedGenerateData().

◆ GetApparentParallelDiffusivity()

double anima::BaseCompartment::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 in anima::TensorCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Definition at line 135 of file animaBaseCompartment.cxx.

Referenced by anima::MCMScalarMapsImageFilter< TPixelType >::DynamicThreadedGenerateData().

◆ GetApparentPerpendicularDiffusivity()

double anima::BaseCompartment::GetApparentPerpendicularDiffusivity ( )

virtual

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

Reimplemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Definition at line 140 of file animaBaseCompartment.cxx.

Referenced by anima::MCMScalarMapsImageFilter< TPixelType >::DynamicThreadedGenerateData().

◆ GetAxialDiffusivity()

virtual double anima::BaseCompartment::GetAxialDiffusivity ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 85 of file animaBaseCompartment.h.

◆ GetCompartmentSize()

virtual unsigned int anima::BaseCompartment::GetCompartmentSize ( )

pure virtual

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

Implemented in anima::TensorCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetCompartmentType()

virtual DiffusionModelCompartmentType anima::BaseCompartment::GetCompartmentType ( )

pure virtual

Utility function to return compartment type without needing dynamic casts.

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, anima::FreeWaterCompartment, anima::IsotropicRestrictedWaterCompartment, and anima::StationaryWaterCompartment.

Referenced by anima::MultiCompartmentModel::AddCompartment(), and anima::MCMScalarMapsImageFilter< TPixelType >::DynamicThreadedGenerateData().

◆ GetCompartmentVector()

virtual ModelOutputVectorType& anima::BaseCompartment::GetCompartmentVector ( )

pure virtual

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

Implemented in anima::TensorCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetDiffusionTensor()

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

virtual

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

Reimplemented in anima::TensorCompartment, anima::NODDICompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Definition at line 120 of file animaBaseCompartment.cxx.

Referenced by IsEqual().

◆ GetExtraAxonalFraction()

virtual double anima::BaseCompartment::GetExtraAxonalFraction ( )

inlinevirtual

Definition at line 89 of file animaBaseCompartment.h.

◆ GetFourierTransformedDiffusionProfile()

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

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Referenced by GetPredictedSignal().

◆ GetLogDiffusionProfile()

virtual double anima::BaseCompartment::GetLogDiffusionProfile ( const Vector3DType & sample )

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods)

Reimplemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, anima::FreeWaterCompartment, anima::IsotropicRestrictedWaterCompartment, anima::StationaryWaterCompartment, and anima::BaseIsotropicCompartment.

◆ GetNumberOfParameters()

virtual unsigned int anima::BaseCompartment::GetNumberOfParameters ( )

pure virtual

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

Implemented in anima::TensorCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetOrientationConcentration()

virtual double anima::BaseCompartment::GetOrientationConcentration ( )

inlinevirtual

Definition at line 88 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::NODDICompartment::GetCompartmentVector(), anima::NODDICompartment::GetParametersAsVector(), IsEqual(), anima::NODDICompartment::SetOrientationConcentration(), and anima::NODDICompartment::UpdateKappaValues().

◆ GetOrientationPhi()

virtual double anima::BaseCompartment::GetOrientationPhi ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 83 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::StickCompartment::GetCompartmentVector(), anima::ZeppelinCompartment::GetCompartmentVector(), anima::NODDICompartment::GetCompartmentVector(), anima::StickCompartment::GetDiffusionTensor(), anima::ZeppelinCompartment::GetDiffusionTensor(), anima::NODDICompartment::GetDiffusionTensor(), anima::StickCompartment::GetFourierTransformedDiffusionProfile(), anima::ZeppelinCompartment::GetFourierTransformedDiffusionProfile(), anima::StickCompartment::GetLogDiffusionProfile(), anima::NODDICompartment::GetLogDiffusionProfile(), anima::ZeppelinCompartment::GetLogDiffusionProfile(), anima::TensorCompartment::GetOrientationPhi(), anima::NODDICompartment::GetParametersAsVector(), anima::StickCompartment::GetParametersAsVector(), anima::ZeppelinCompartment::GetParametersAsVector(), anima::StickCompartment::GetSignalAttenuationJacobian(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::ZeppelinCompartment::GetSignalAttenuationJacobian(), IsEqual(), Reorient(), anima::NODDICompartment::SetOrientationPhi(), and anima::NODDICompartment::UpdateSignals().

◆ GetOrientationTheta()

virtual double anima::BaseCompartment::GetOrientationTheta ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 82 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::StickCompartment::GetCompartmentVector(), anima::ZeppelinCompartment::GetCompartmentVector(), anima::NODDICompartment::GetCompartmentVector(), anima::StickCompartment::GetDiffusionTensor(), anima::ZeppelinCompartment::GetDiffusionTensor(), anima::NODDICompartment::GetDiffusionTensor(), anima::StickCompartment::GetFourierTransformedDiffusionProfile(), anima::ZeppelinCompartment::GetFourierTransformedDiffusionProfile(), anima::StickCompartment::GetLogDiffusionProfile(), anima::NODDICompartment::GetLogDiffusionProfile(), anima::ZeppelinCompartment::GetLogDiffusionProfile(), anima::TensorCompartment::GetOrientationTheta(), anima::NODDICompartment::GetParametersAsVector(), anima::StickCompartment::GetParametersAsVector(), anima::ZeppelinCompartment::GetParametersAsVector(), anima::StickCompartment::GetSignalAttenuationJacobian(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::ZeppelinCompartment::GetSignalAttenuationJacobian(), IsEqual(), Reorient(), anima::NODDICompartment::SetOrientationTheta(), and anima::NODDICompartment::UpdateSignals().

◆ GetParameterLowerBounds()

virtual ListType& anima::BaseCompartment::GetParameterLowerBounds ( )

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, anima::FreeWaterCompartment, anima::IsotropicRestrictedWaterCompartment, and anima::StationaryWaterCompartment.

◆ GetParametersAsVector()

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

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetParameterUpperBounds()

virtual ListType& anima::BaseCompartment::GetParameterUpperBounds ( )

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, anima::FreeWaterCompartment, anima::IsotropicRestrictedWaterCompartment, and anima::StationaryWaterCompartment.

◆ GetPerpendicularAngle()

virtual double anima::BaseCompartment::GetPerpendicularAngle ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 84 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::TensorCompartment::GetPerpendicularAngle(), and IsEqual().

◆ GetPredictedSignal()

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

Definition at line 9 of file animaBaseCompartment.cxx.

References GetFourierTransformedDiffusionProfile().

◆ GetRadialDiffusivity1()

virtual double anima::BaseCompartment::GetRadialDiffusivity1 ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 86 of file animaBaseCompartment.h.

◆ GetRadialDiffusivity2()

virtual double anima::BaseCompartment::GetRadialDiffusivity2 ( )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 87 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::TensorCompartment::GetRadialDiffusivity2(), and IsEqual().

◆ GetSignalAttenuationJacobian()

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

pure virtual

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ GetTensorCompatible()

virtual bool anima::BaseCompartment::GetTensorCompatible ( )

inlinevirtual

Reimplemented in anima::NODDICompartment, and anima::StaniszCompartment.

Definition at line 105 of file animaBaseCompartment.h.

Referenced by IsEqual().

◆ GetTissueRadius()

virtual double anima::BaseCompartment::GetTissueRadius ( )

inlinevirtual

Definition at line 90 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::StaniszCompartment::GetCompartmentVector(), anima::StaniszCompartment::GetFourierTransformedDiffusionProfile(), anima::StaniszCompartment::GetLogDiffusionProfile(), anima::StaniszCompartment::GetParametersAsVector(), anima::StaniszCompartment::GetSignalAttenuationJacobian(), IsEqual(), anima::StaniszCompartment::SetTissueRadius(), and anima::StaniszCompartment::UpdateSignals().

◆ IsEqual()

bool anima::BaseCompartment::IsEqual	(	Self *	rhs,
		double	tolerance = `1.0e-2`,
		double	absoluteTolerance = `1.0e-8`
	)

virtual

Tests equality to another compartment up to a constant (relative and absolute tolerances)

Definition at line 16 of file animaBaseCompartment.cxx.

References anima::ComputeScalarProduct(), GetAxialDiffusivity(), GetDiffusionTensor(), GetExtraAxonalFraction(), GetOrientationConcentration(), GetOrientationPhi(), GetOrientationTheta(), GetPerpendicularAngle(), GetRadialDiffusivity1(), GetRadialDiffusivity2(), GetTensorCompatible(), GetTissueRadius(), and anima::TransformSphericalToCartesianCoordinates().

◆ Reorient()

void anima::BaseCompartment::Reorient	(	vnl_matrix< double > &	orientationMatrix,
		bool	affineTransform
	)

virtual

Reorient the fascicle compartment using a matrix, the flag specifies if the transform is affine or rigid.

Reimplemented in anima::TensorCompartment, and anima::BaseIsotropicCompartment.

Definition at line 99 of file animaBaseCompartment.cxx.

References GetOrientationPhi(), GetOrientationTheta(), SetOrientationPhi(), SetOrientationTheta(), anima::TransformCartesianToSphericalCoordinates(), and anima::TransformSphericalToCartesianCoordinates().

◆ SetAxialDiffusivity()

virtual void anima::BaseCompartment::SetAxialDiffusivity ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment, anima::NODDICompartment, and anima::StaniszCompartment.

Definition at line 96 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::StaniszCompartment::SetAxialDiffusivity(), anima::NODDICompartment::SetAxialDiffusivity(), anima::TensorCompartment::SetAxialDiffusivity(), anima::BaseIsotropicCompartment::SetCompartmentVector(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetCompartmentVector(), anima::BaseIsotropicCompartment::SetParametersFromVector(), anima::StickCompartment::SetParametersFromVector(), and anima::ZeppelinCompartment::SetParametersFromVector().

◆ SetCompartmentVector()

virtual void anima::BaseCompartment::SetCompartmentVector ( ModelOutputVectorType & compartmentVector )

pure virtual

Set compartment overall description vector, for setting automatically the individual parameters when reading from disk.

Implemented in anima::TensorCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::ZeppelinCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

Referenced by anima::MCMWeightedAverager::ComputeOutputTensorCompatibleModel().

◆ SetExtraAxonalFraction()

virtual void anima::BaseCompartment::SetExtraAxonalFraction ( double num )

inlinevirtual

Reimplemented in anima::NODDICompartment.

Definition at line 100 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), and anima::NODDICompartment::SetExtraAxonalFraction().

◆ SetOrientationConcentration()

virtual void anima::BaseCompartment::SetOrientationConcentration ( double num )

inlinevirtual

Reimplemented in anima::NODDICompartment.

Definition at line 99 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), and anima::NODDICompartment::SetOrientationConcentration().

◆ SetOrientationPhi()

virtual void anima::BaseCompartment::SetOrientationPhi ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment, and anima::NODDICompartment.

Definition at line 94 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), Reorient(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetCompartmentVector(), anima::NODDICompartment::SetOrientationPhi(), anima::TensorCompartment::SetOrientationPhi(), anima::StickCompartment::SetParametersFromVector(), anima::ZeppelinCompartment::SetParametersFromVector(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks().

◆ SetOrientationTheta()

virtual void anima::BaseCompartment::SetOrientationTheta ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment, and anima::NODDICompartment.

Definition at line 93 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), Reorient(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetCompartmentVector(), anima::NODDICompartment::SetOrientationTheta(), anima::TensorCompartment::SetOrientationTheta(), anima::StickCompartment::SetParametersFromVector(), anima::ZeppelinCompartment::SetParametersFromVector(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks().

◆ SetParametersFromVector()

virtual void anima::BaseCompartment::SetParametersFromVector ( const ListType & params )

pure virtual

Various methods for optimization parameters setting and getting.

Implemented in anima::TensorCompartment, anima::ZeppelinCompartment, anima::NODDICompartment, anima::StaniszCompartment, anima::StickCompartment, and anima::BaseIsotropicCompartment.

◆ SetPerpendicularAngle()

virtual void anima::BaseCompartment::SetPerpendicularAngle ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 95 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), and anima::TensorCompartment::SetPerpendicularAngle().

◆ SetRadialDiffusivity1()

virtual void anima::BaseCompartment::SetRadialDiffusivity1 ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment, and anima::ZeppelinCompartment.

Definition at line 97 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetRadialDiffusivity1(), and anima::TensorCompartment::SetRadialDiffusivity1().

◆ SetRadialDiffusivity2()

virtual void anima::BaseCompartment::SetRadialDiffusivity2 ( double num )

inlinevirtual

Reimplemented in anima::TensorCompartment.

Definition at line 98 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), anima::ZeppelinCompartment::SetRadialDiffusivity1(), and anima::TensorCompartment::SetRadialDiffusivity2().

◆ SetTissueRadius()

virtual void anima::BaseCompartment::SetTissueRadius ( double num )

inlinevirtual

Reimplemented in anima::StaniszCompartment.

Definition at line 101 of file animaBaseCompartment.h.

Referenced by CopyFromOther(), and anima::StaniszCompartment::SetTissueRadius().

Member Data Documentation

◆ m_CompartmentVector

ModelOutputVectorType anima::BaseCompartment::m_CompartmentVector

protected

Vector to hold working value of compartment vector.

Definition at line 155 of file animaBaseCompartment.h.

Referenced by anima::BaseIsotropicCompartment::GetCompartmentVector(), anima::StickCompartment::GetCompartmentVector(), anima::ZeppelinCompartment::GetCompartmentVector(), anima::StaniszCompartment::GetCompartmentVector(), anima::NODDICompartment::GetCompartmentVector(), and anima::TensorCompartment::GetCompartmentVector().

◆ m_DiffusionTensor

Matrix3DType anima::BaseCompartment::m_DiffusionTensor

protected

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

Definition at line 140 of file animaBaseCompartment.h.

Referenced by anima::StickCompartment::GetDiffusionTensor(), anima::ZeppelinCompartment::GetDiffusionTensor(), and anima::NODDICompartment::GetDiffusionTensor().

◆ m_JacobianVector

ListType anima::BaseCompartment::m_JacobianVector

protected

Vector holding current jacobian value.

Definition at line 143 of file animaBaseCompartment.h.

Referenced by anima::BaseIsotropicCompartment::GetSignalAttenuationJacobian(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::StickCompartment::GetSignalAttenuationJacobian(), anima::StaniszCompartment::GetSignalAttenuationJacobian(), anima::ZeppelinCompartment::GetSignalAttenuationJacobian(), and anima::TensorCompartment::GetSignalAttenuationJacobian().

◆ m_ParametersLowerBoundsVector

ListType anima::BaseCompartment::m_ParametersLowerBoundsVector

protected

Vector holding current parameters lower bounds.

Definition at line 149 of file animaBaseCompartment.h.

Referenced by anima::FreeWaterCompartment::GetParameterLowerBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterLowerBounds(), anima::StationaryWaterCompartment::GetParameterLowerBounds(), anima::StickCompartment::GetParameterLowerBounds(), anima::StaniszCompartment::GetParameterLowerBounds(), anima::NODDICompartment::GetParameterLowerBounds(), anima::ZeppelinCompartment::GetParameterLowerBounds(), and anima::TensorCompartment::GetParameterLowerBounds().

◆ m_ParametersUpperBoundsVector

ListType anima::BaseCompartment::m_ParametersUpperBoundsVector

protected

Vector holding current parameters upper bounds.

Definition at line 152 of file animaBaseCompartment.h.

Referenced by anima::FreeWaterCompartment::GetParameterUpperBounds(), anima::IsotropicRestrictedWaterCompartment::GetParameterUpperBounds(), anima::StationaryWaterCompartment::GetParameterUpperBounds(), anima::StickCompartment::GetParameterUpperBounds(), anima::StaniszCompartment::GetParameterUpperBounds(), anima::NODDICompartment::GetParameterUpperBounds(), anima::ZeppelinCompartment::GetParameterUpperBounds(), and anima::TensorCompartment::GetParameterUpperBounds().

◆ m_ParametersVector

ListType anima::BaseCompartment::m_ParametersVector

protected

Vector holding current parameters vector.

Definition at line 146 of file animaBaseCompartment.h.

Referenced by anima::BaseIsotropicCompartment::GetParametersAsVector(), anima::NODDICompartment::GetParametersAsVector(), anima::StickCompartment::GetParametersAsVector(), anima::StaniszCompartment::GetParametersAsVector(), anima::ZeppelinCompartment::GetParametersAsVector(), and anima::TensorCompartment::GetParametersAsVector().

◆ m_SpaceDimension

const unsigned int anima::BaseCompartment::m_SpaceDimension = 3

staticprotected

Definition at line 137 of file animaBaseCompartment.h.

Referenced by anima::StickCompartment::GetCompartmentVector(), anima::ZeppelinCompartment::GetCompartmentVector(), anima::NODDICompartment::GetCompartmentVector(), anima::BaseIsotropicCompartment::GetDiffusionTensor(), anima::StickCompartment::GetDiffusionTensor(), anima::ZeppelinCompartment::GetDiffusionTensor(), anima::NODDICompartment::GetDiffusionTensor(), anima::TensorCompartment::GetFourierTransformedDiffusionProfile(), anima::TensorCompartment::GetLogDiffusionProfile(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetCompartmentVector(), anima::NODDICompartment::SetCompartmentVector(), anima::TensorCompartment::SetCompartmentVector(), anima::TensorCompartment::UpdateDiffusionTensor(), anima::TensorCompartment::UpdateInverseDiffusionTensor(), and anima::TensorCompartment::UpdateParametersFromTensor().

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ConstPointer

◆ ListType

◆ Matrix3DType

◆ ModelOutputVectorType

◆ Pointer

◆ Self

◆ Superclass

◆ Vector3DType

Constructor & Destructor Documentation

◆ BaseCompartment()

◆ ~BaseCompartment()

Member Function Documentation

◆ CopyFromOther()

◆ GetApparentFractionalAnisotropy()

◆ GetApparentMeanDiffusivity()

◆ GetApparentParallelDiffusivity()

◆ GetApparentPerpendicularDiffusivity()

◆ GetAxialDiffusivity()

◆ GetCompartmentSize()

◆ GetCompartmentType()

◆ GetCompartmentVector()

◆ GetDiffusionTensor()

◆ GetExtraAxonalFraction()

◆ GetFourierTransformedDiffusionProfile()

◆ GetLogDiffusionProfile()

◆ GetNameOfClass()

◆ GetNumberOfParameters()

◆ GetOrientationConcentration()

◆ GetOrientationPhi()

◆ GetOrientationTheta()

◆ GetParameterLowerBounds()

◆ GetParametersAsVector()

◆ GetParameterUpperBounds()

◆ GetPerpendicularAngle()

◆ GetPredictedSignal()

◆ GetRadialDiffusivity1()

◆ GetRadialDiffusivity2()

◆ GetSignalAttenuationJacobian()

◆ GetTensorCompatible()

◆ GetTissueRadius()

◆ IsEqual()

◆ Reorient()

◆ SetAxialDiffusivity()

◆ SetCompartmentVector()

◆ SetExtraAxonalFraction()

◆ SetOrientationConcentration()

◆ SetOrientationPhi()

◆ SetOrientationTheta()

◆ SetParametersFromVector()

◆ SetPerpendicularAngle()

◆ SetRadialDiffusivity1()

◆ SetRadialDiffusivity2()

◆ SetTissueRadius()

Member Data Documentation

◆ m_CompartmentVector

◆ m_DiffusionTensor

◆ m_JacobianVector

◆ m_ParametersLowerBoundsVector

◆ m_ParametersUpperBoundsVector

◆ m_ParametersVector

◆ m_SpaceDimension