#include <animaNODDICompartment.h>

Inheritance diagram for anima::NODDICompartment:

Collaboration diagram for anima::NODDICompartment:

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 NODDICompartment	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

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...

virtual ListType &	GetParameterLowerBounds () ITK_OVERRIDE

virtual ListType &	GetParametersAsVector () ITK_OVERRIDE

virtual ListType &	GetParameterUpperBounds () ITK_OVERRIDE

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

bool	GetTensorCompatible () ITK_OVERRIDE

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	SetEstimateAxialDiffusivity (bool arg)

void	SetEstimateExtraAxonalFraction (bool arg)

void	SetEstimateOrientationConcentration (bool arg)

void	SetExtraAxonalFraction (double num) ITK_OVERRIDE

void	SetOrientationConcentration (double num) ITK_OVERRIDE

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...

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	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 double	GetExtraAxonalFraction ()

virtual double	GetOrientationConcentration ()

virtual double	GetOrientationPhi ()

virtual double	GetOrientationTheta ()

virtual double	GetPerpendicularAngle ()

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

virtual double	GetRadialDiffusivity1 ()

virtual double	GetRadialDiffusivity2 ()

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	SetPerpendicularAngle (double num)

virtual void	SetRadialDiffusivity1 (double num)

virtual void	SetRadialDiffusivity2 (double num)

virtual void	SetTissueRadius (double num)

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	NODDICompartment ()

void	UpdateKappaValues ()
	Update quantities that depend on kappa. More...

void	UpdateSignals (double bValue, const Vector3DType &gradient)
	Compute intra- and extra-axonal signals and useful signals for derivatives. More...

virtual	~NODDICompartment ()

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 animaNODDICompartment.h.

Member Typedef Documentation

◆ BasePointer

typedef Superclass::Pointer anima::NODDICompartment::BasePointer

Definition at line 15 of file animaNODDICompartment.h.

◆ ConstPointer

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

Definition at line 17 of file animaNODDICompartment.h.

◆ Matrix3DType

typedef Superclass::Matrix3DType anima::NODDICompartment::Matrix3DType

Definition at line 20 of file animaNODDICompartment.h.

◆ ModelOutputVectorType

typedef Superclass::ModelOutputVectorType anima::NODDICompartment::ModelOutputVectorType

Definition at line 18 of file animaNODDICompartment.h.

◆ Pointer

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

Definition at line 16 of file animaNODDICompartment.h.

◆ Self

typedef NODDICompartment anima::NODDICompartment::Self

Definition at line 13 of file animaNODDICompartment.h.

◆ Superclass

typedef BaseCompartment anima::NODDICompartment::Superclass

Definition at line 14 of file animaNODDICompartment.h.

◆ Vector3DType

typedef Superclass::Vector3DType anima::NODDICompartment::Vector3DType

Definition at line 19 of file animaNODDICompartment.h.

Constructor & Destructor Documentation

◆ NODDICompartment()

anima::NODDICompartment::NODDICompartment ( )

inlineprotected

Definition at line 63 of file animaNODDICompartment.h.

◆ ~NODDICompartment()

virtual anima::NODDICompartment::~NODDICompartment ( )

inlineprotectedvirtual

Definition at line 89 of file animaNODDICompartment.h.

Member Function Documentation

◆ CreateAnother()

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

◆ GetApparentFractionalAnisotropy()

double anima::NODDICompartment::GetApparentFractionalAnisotropy ( )

virtual

Reimplemented from anima::BaseCompartment.

Definition at line 502 of file animaNODDICompartment.cxx.

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

◆ GetCompartmentSize()

unsigned int anima::NODDICompartment::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 406 of file animaNODDICompartment.cxx.

Referenced by GetCompartmentVector(), and SetCompartmentVector().

◆ GetCompartmentType()

DiffusionModelCompartmentType anima::NODDICompartment::GetCompartmentType ( )

inlinevirtual

Utility function to return compartment type without needing dynamic casts.

Implements anima::BaseCompartment.

Definition at line 28 of file animaNODDICompartment.h.

References anima::NODDI.

◆ GetCompartmentVector()

NODDICompartment::ModelOutputVectorType & anima::NODDICompartment::GetCompartmentVector ( )

virtual

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

Implements anima::BaseCompartment.

Definition at line 431 of file animaNODDICompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), GetCompartmentSize(), anima::BaseCompartment::GetExtraAxonalFraction(), anima::BaseCompartment::GetOrientationConcentration(), anima::BaseCompartment::GetOrientationPhi(), anima::BaseCompartment::GetOrientationTheta(), anima::BaseCompartment::m_CompartmentVector, anima::BaseCompartment::m_SpaceDimension, and anima::TransformSphericalToCartesianCoordinates().

◆ GetDiffusionTensor()

const NODDICompartment::Matrix3DType & anima::NODDICompartment::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 459 of file animaNODDICompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), anima::BaseCompartment::GetExtraAxonalFraction(), anima::BaseCompartment::GetOrientationPhi(), anima::BaseCompartment::GetOrientationTheta(), anima::BaseCompartment::m_DiffusionTensor, anima::BaseCompartment::m_SpaceDimension, anima::TransformSphericalToCartesianCoordinates(), and UpdateKappaValues().

◆ GetFourierTransformedDiffusionProfile()

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

virtual

Implements anima::BaseCompartment.

Definition at line 93 of file animaNODDICompartment.cxx.

References anima::GetBValueFromAcquisitionParameters(), anima::BaseCompartment::GetExtraAxonalFraction(), and UpdateSignals().

◆ GetLogDiffusionProfile()

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

virtual

Implements anima::BaseCompartment.

Definition at line 186 of file animaNODDICompartment.cxx.

References anima::ComputeScalarProduct(), anima::BaseCompartment::GetAxialDiffusivity(), anima::BaseCompartment::GetExtraAxonalFraction(), anima::BaseCompartment::GetOrientationPhi(), anima::BaseCompartment::GetOrientationTheta(), anima::TransformSphericalToCartesianCoordinates(), and UpdateKappaValues().

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods)

Reimplemented from anima::BaseCompartment.

◆ GetNumberOfParameters()

unsigned int anima::NODDICompartment::GetNumberOfParameters ( )

virtual

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

Implements anima::BaseCompartment.

Definition at line 411 of file animaNODDICompartment.cxx.

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

◆ GetParameterLowerBounds()

NODDICompartment::ListType & anima::NODDICompartment::GetParameterLowerBounds ( )

virtual

Implements anima::BaseCompartment.

Definition at line 307 of file animaNODDICompartment.cxx.

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

◆ GetParametersAsVector()

NODDICompartment::ListType & anima::NODDICompartment::GetParametersAsVector ( )

virtual

Implements anima::BaseCompartment.

Definition at line 281 of file animaNODDICompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity(), anima::BaseCompartment::GetExtraAxonalFraction(), GetNumberOfParameters(), anima::BaseCompartment::GetOrientationConcentration(), anima::BaseCompartment::GetOrientationPhi(), anima::BaseCompartment::GetOrientationTheta(), and anima::BaseCompartment::m_ParametersVector.

◆ GetParameterUpperBounds()

NODDICompartment::ListType & anima::NODDICompartment::GetParameterUpperBounds ( )

virtual

Implements anima::BaseCompartment.

Definition at line 319 of file animaNODDICompartment.cxx.

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

◆ GetSignalAttenuationJacobian()

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