MultiCompartmentModel: holds several diffusion compartments, ordered by type It also handles weights of the different compartments. Although there are N weights in memory for N compartments, the parameters returned and set are considered to have one less weight in them, the first one being removed. This comes from the fact that they sum up to 1. More...

#include <animaMultiCompartmentModel.h>

Inheritance diagram for anima::MultiCompartmentModel:

Collaboration diagram for anima::MultiCompartmentModel:

Public Types
typedef BaseCompartment::Pointer	BaseCompartmentPointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef BaseCompartment::ListType	ListType

typedef BaseCompartment::ModelOutputVectorType	ModelOutputVectorType

typedef itk::SmartPointer< Self >	Pointer

typedef MultiCompartmentModel	Self

typedef itk::LightObject	Superclass

typedef BaseCompartment::Vector3DType	Vector3DType

Public Member Functions
void	AddCompartment (double weight, BaseCompartment *compartment)

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

virtual bool	GetCommonConcentrationParameters ()

virtual bool	GetCommonDiffusivityParameters ()

virtual bool	GetCommonExtraAxonalFractionParameters ()

BaseCompartment *	GetCompartment (unsigned int i)

double	GetCompartmentWeight (unsigned int i)

const ListType &	GetCompartmentWeights ()

double	GetDiffusionProfile (Vector3DType &sample)

ModelOutputVectorType &	GetModelVector ()

virtual const char *	GetNameOfClass () const

virtual bool	GetNegativeWeightBounds ()

unsigned int	GetNumberOfCompartments ()

virtual unsigned int	GetNumberOfIsotropicCompartments ()

unsigned int	GetNumberOfOptimizedWeights ()
	Number of weights that are optimized. More...

unsigned int	GetNumberOfParameters ()
	Number of parameters to be optimized. More...

virtual bool	GetOptimizeWeights ()

ListType &	GetParameterLowerBounds ()

ListType &	GetParametersAsVector ()

ListType &	GetParameterUpperBounds ()

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

ListType &	GetSignalJacobian (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient)

unsigned int	GetSize ()
	Number of parameters to have a self-contained description of the MCM. More...

itk::LightObject::Pointer	InternalClone () const ITK_OVERRIDE

void	Reorient (vnl_matrix< double > &orientationMatrix, bool affineTransform)
	Re-orient the MCM using the provided transform, the flag precises if the transform id rigid or affine. More...

void	SetCommonConcentrationParameters (bool val)

void	SetCommonDiffusivityParameters (bool val)

void	SetCommonExtraAxonalFractionParameters (bool val)

void	SetCompartmentWeights (const ListType &weights)

void	SetModelVector (const itk::VariableLengthVector< float > &mcmVec)

void	SetModelVector (const ModelOutputVectorType &mcmVec)

void	SetNegativeWeightBounds (bool val)

void	SetOptimizeWeights (bool val)

void	SetParametersFromVector (ListType &params)

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	MultiCompartmentModel ()

	~MultiCompartmentModel ()

Detailed Description

MultiCompartmentModel: holds several diffusion compartments, ordered by type It also handles weights of the different compartments. Although there are N weights in memory for N compartments, the parameters returned and set are considered to have one less weight in them, the first one being removed. This comes from the fact that they sum up to 1.

Definition at line 19 of file animaMultiCompartmentModel.h.

Member Typedef Documentation

◆ BaseCompartmentPointer

typedef BaseCompartment::Pointer anima::MultiCompartmentModel::BaseCompartmentPointer

Definition at line 33 of file animaMultiCompartmentModel.h.

◆ ConstPointer

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

Definition at line 26 of file animaMultiCompartmentModel.h.

◆ ListType

typedef BaseCompartment::ListType anima::MultiCompartmentModel::ListType

Definition at line 35 of file animaMultiCompartmentModel.h.

◆ ModelOutputVectorType

typedef BaseCompartment::ModelOutputVectorType anima::MultiCompartmentModel::ModelOutputVectorType

Definition at line 36 of file animaMultiCompartmentModel.h.

◆ Pointer

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

Definition at line 25 of file animaMultiCompartmentModel.h.

◆ Self

typedef MultiCompartmentModel anima::MultiCompartmentModel::Self

Definition at line 23 of file animaMultiCompartmentModel.h.

◆ Superclass

typedef itk::LightObject anima::MultiCompartmentModel::Superclass

Definition at line 24 of file animaMultiCompartmentModel.h.

◆ Vector3DType

typedef BaseCompartment::Vector3DType anima::MultiCompartmentModel::Vector3DType

Definition at line 34 of file animaMultiCompartmentModel.h.

Constructor & Destructor Documentation

◆ MultiCompartmentModel()

anima::MultiCompartmentModel::MultiCompartmentModel ( )

protected

Definition at line 7 of file animaMultiCompartmentModel.cxx.

◆ ~MultiCompartmentModel()

anima::MultiCompartmentModel::~MultiCompartmentModel ( )

protected

Definition at line 18 of file animaMultiCompartmentModel.cxx.

Member Function Documentation

◆ AddCompartment()

void anima::MultiCompartmentModel::AddCompartment	(	double	weight,
		BaseCompartment *	compartment
	)

Definition at line 41 of file animaMultiCompartmentModel.cxx.

References anima::FreeWater, anima::BaseCompartment::GetCompartmentType(), anima::IsotropicRestrictedWater, anima::Stanisz, and anima::StationaryWater.

Referenced by InternalClone().

◆ CreateAnother()

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

◆ GetCommonConcentrationParameters()

virtual bool anima::MultiCompartmentModel::GetCommonConcentrationParameters ( )

virtual

◆ GetCommonDiffusivityParameters()

virtual bool anima::MultiCompartmentModel::GetCommonDiffusivityParameters ( )

virtual

◆ GetCommonExtraAxonalFractionParameters()

virtual bool anima::MultiCompartmentModel::GetCommonExtraAxonalFractionParameters ( )

virtual

◆ GetCompartment()

BaseCompartment * anima::MultiCompartmentModel::GetCompartment ( unsigned int i )

Definition at line 61 of file animaMultiCompartmentModel.cxx.

References GetNumberOfCompartments().

◆ GetCompartmentWeight()

double anima::MultiCompartmentModel::GetCompartmentWeight ( unsigned int i )

Definition at line 102 of file animaMultiCompartmentModel.cxx.

◆ GetCompartmentWeights()

const ListType& anima::MultiCompartmentModel::GetCompartmentWeights ( )

inline

Definition at line 54 of file animaMultiCompartmentModel.h.

◆ GetDiffusionProfile()

double anima::MultiCompartmentModel::GetDiffusionProfile ( Vector3DType & sample )

Definition at line 278 of file animaMultiCompartmentModel.cxx.

◆ GetModelVector()

MultiCompartmentModel::ModelOutputVectorType & anima::MultiCompartmentModel::GetModelVector ( )

Definition at line 161 of file animaMultiCompartmentModel.cxx.

References GetNumberOfCompartments(), and GetSize().

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods)

◆ GetNegativeWeightBounds()

virtual bool anima::MultiCompartmentModel::GetNegativeWeightBounds ( )

virtual

◆ GetNumberOfCompartments()

unsigned int anima::MultiCompartmentModel::GetNumberOfCompartments ( )

inline

Definition at line 46 of file animaMultiCompartmentModel.h.

Referenced by GetCompartment(), GetModelVector(), SetModelVector(), and SetParametersFromVector().

◆ GetNumberOfIsotropicCompartments()

virtual unsigned int anima::MultiCompartmentModel::GetNumberOfIsotropicCompartments ( )

virtual

◆ GetNumberOfOptimizedWeights()

unsigned int anima::MultiCompartmentModel::GetNumberOfOptimizedWeights ( )

Number of weights that are optimized.

Definition at line 367 of file animaMultiCompartmentModel.cxx.

Referenced by GetNumberOfParameters(), GetParameterLowerBounds(), GetParametersAsVector(), GetParameterUpperBounds(), GetSignalJacobian(), and SetParametersFromVector().

◆ GetNumberOfParameters()

unsigned int anima::MultiCompartmentModel::GetNumberOfParameters ( )

Number of parameters to be optimized.

Definition at line 376 of file animaMultiCompartmentModel.cxx.

References GetNumberOfOptimizedWeights().

Referenced by GetParameterLowerBounds(), GetParametersAsVector(), GetParameterUpperBounds(), and GetSignalJacobian().

◆ GetOptimizeWeights()

virtual bool anima::MultiCompartmentModel::GetOptimizeWeights ( )

virtual

◆ GetParameterLowerBounds()

MultiCompartmentModel::ListType & anima::MultiCompartmentModel::GetParameterLowerBounds ( )

Definition at line 291 of file animaMultiCompartmentModel.cxx.

References GetNumberOfOptimizedWeights(), GetNumberOfParameters(), anima::MCMFractionUpperBound, and anima::MCMZeroLowerBound.

◆ GetParametersAsVector()

MultiCompartmentModel::ListType & anima::MultiCompartmentModel::GetParametersAsVector ( )

Definition at line 69 of file animaMultiCompartmentModel.cxx.

References GetNumberOfOptimizedWeights(), and GetNumberOfParameters().

◆ GetParameterUpperBounds()

MultiCompartmentModel::ListType & anima::MultiCompartmentModel::GetParameterUpperBounds ( )

Definition at line 329 of file animaMultiCompartmentModel.cxx.

References GetNumberOfOptimizedWeights(), GetNumberOfParameters(), anima::MCMCompartmentsFractionUpperBound, and anima::MCMZeroLowerBound.

◆ GetPredictedSignal()

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

Definition at line 232 of file animaMultiCompartmentModel.cxx.

◆ GetSignalJacobian()

MultiCompartmentModel::ListType & anima::MultiCompartmentModel::GetSignalJacobian	(	double	smallDelta,
		double	bigDelta,
		double	gradientStrength,
		const Vector3DType &	gradient
	)

Definition at line 245 of file animaMultiCompartmentModel.cxx.

References GetNumberOfOptimizedWeights(), and GetNumberOfParameters().

◆ GetSize()

unsigned int anima::MultiCompartmentModel::GetSize ( )

Number of parameters to have a self-contained description of the MCM.

Definition at line 388 of file animaMultiCompartmentModel.cxx.

Referenced by GetModelVector().

◆ InternalClone()

itk::LightObject::Pointer anima::MultiCompartmentModel::InternalClone ( ) const

Returns a clone of this MCM in terms of compartment organization, used by Clone method Does not copy parameters of each compartment though, neither weights

Definition at line 22 of file animaMultiCompartmentModel.cxx.

References AddCompartment(), SetCommonConcentrationParameters(), SetCommonDiffusivityParameters(), SetCommonExtraAxonalFractionParameters(), and SetOptimizeWeights().