ANIMA  4.0
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | List of all members
anima::StickCompartment Class Reference

#include <animaStickCompartment.h>

+ Inheritance diagram for anima::StickCompartment:
+ Collaboration diagram for anima::StickCompartment:

Public Types

typedef Superclass::Pointer BasePointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef Superclass::Matrix3DType Matrix3DType
 
typedef Superclass::ModelOutputVectorType ModelOutputVectorType
 
typedef itk::SmartPointer< SelfPointer
 
typedef StickCompartment Self
 
typedef BaseCompartment Superclass
 
typedef Superclass::Vector3DType Vector3DType
 
- Public Types inherited from anima::BaseCompartment
typedef itk::SmartPointer< const SelfConstPointer
 
typedef std::vector< double > ListType
 
typedef itk::Matrix< double, 3, 3 > Matrix3DType
 
typedef itk::VariableLengthVector< double > ModelOutputVectorType
 
typedef itk::SmartPointer< SelfPointer
 
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...
 
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...
 
ModelOutputVectorTypeGetCompartmentVector () ITK_OVERRIDE
 Get compartment overall description vector, mainly for writing, should be self-contained. More...
 
const Matrix3DTypeGetDiffusionTensor () 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 ListTypeGetParameterLowerBounds () ITK_OVERRIDE
 
virtual ListTypeGetParametersAsVector () ITK_OVERRIDE
 
virtual ListTypeGetParameterUpperBounds () ITK_OVERRIDE
 
virtual ListTypeGetSignalAttenuationJacobian (double smallDelta, double bigDelta, double gradientStrength, const Vector3DType &gradient) 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)
 
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 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 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 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)
 

Static Public Member Functions

static Pointer New ()
 

Protected Member Functions

 StickCompartment ()
 
virtual ~StickCompartment ()
 
- 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 animaStickCompartment.h.

Member Typedef Documentation

◆ BasePointer

Definition at line 15 of file animaStickCompartment.h.

◆ ConstPointer

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

Definition at line 17 of file animaStickCompartment.h.

◆ Matrix3DType

Definition at line 20 of file animaStickCompartment.h.

◆ ModelOutputVectorType

Definition at line 18 of file animaStickCompartment.h.

◆ Pointer

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

Definition at line 16 of file animaStickCompartment.h.

◆ Self

Definition at line 13 of file animaStickCompartment.h.

◆ Superclass

Definition at line 14 of file animaStickCompartment.h.

◆ Vector3DType

Definition at line 19 of file animaStickCompartment.h.

Constructor & Destructor Documentation

◆ StickCompartment()

anima::StickCompartment::StickCompartment ( )
inlineprotected

Definition at line 55 of file animaStickCompartment.h.

◆ ~StickCompartment()

virtual anima::StickCompartment::~StickCompartment ( )
inlineprotectedvirtual

Definition at line 62 of file animaStickCompartment.h.

Member Function Documentation

◆ CreateAnother()

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

◆ GetApparentFractionalAnisotropy()

double anima::StickCompartment::GetApparentFractionalAnisotropy ( )
virtual

◆ GetApparentMeanDiffusivity()

double anima::StickCompartment::GetApparentMeanDiffusivity ( )
virtual

◆ GetApparentParallelDiffusivity()

double anima::StickCompartment::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 246 of file animaStickCompartment.cxx.

References anima::BaseCompartment::GetAxialDiffusivity().

◆ GetApparentPerpendicularDiffusivity()

double anima::StickCompartment::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 251 of file animaStickCompartment.cxx.

References anima::BaseCompartment::GetRadialDiffusivity1().

◆ GetCompartmentSize()

unsigned int anima::StickCompartment::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 158 of file animaStickCompartment.cxx.

Referenced by GetCompartmentVector(), and SetCompartmentVector().

◆ GetCompartmentType()

DiffusionModelCompartmentType anima::StickCompartment::GetCompartmentType ( )
inlinevirtual

Utility function to return compartment type without needing dynamic casts.

Implements anima::BaseCompartment.

Definition at line 28 of file animaStickCompartment.h.

References anima::Stick.

◆ GetCompartmentVector()

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

◆ GetDiffusionTensor()

const StickCompartment::Matrix3DType & anima::StickCompartment::GetDiffusionTensor ( )
virtual

◆ GetFourierTransformedDiffusionProfile()

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

◆ GetLogDiffusionProfile()

double anima::StickCompartment::GetLogDiffusionProfile ( const Vector3DType sample)
virtual

◆ GetNameOfClass()

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

Run-time type information (and related methods)

Reimplemented from anima::BaseCompartment.

◆ GetNumberOfParameters()

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

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

Implements anima::BaseCompartment.

Definition at line 163 of file animaStickCompartment.cxx.

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

◆ GetParameterLowerBounds()

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

◆ GetParametersAsVector()

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

◆ GetParameterUpperBounds()

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

◆ GetSignalAttenuationJacobian()

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

◆ New()

static Pointer anima::StickCompartment::New ( )
static

◆ SetCompartmentVector()

void anima::StickCompartment::SetCompartmentVector ( ModelOutputVectorType compartmentVector)
virtual

◆ SetEstimateAxialDiffusivity()

void anima::StickCompartment::SetEstimateAxialDiffusivity ( bool  arg)

Definition at line 111 of file animaStickCompartment.cxx.

◆ SetParametersFromVector()

void anima::StickCompartment::SetParametersFromVector ( const ListType params)
virtual

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