itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField > Class Template Reference

#include <itkMRIBiasFieldCorrectionFilter.h>

Inheritance diagram for itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >:

Collaboration diagram for itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >:

Public Types
using	BiasFieldType = TBiasField
using	ConstPointer = SmartPointer< const Self >
using	DerivativeType = Superclass::DerivativeType
using	ImageElementType = typename ImageType::PixelType
using	ImageIndexType = typename ImageType::IndexType
using	ImagePointer = typename ImageType::Pointer
using	ImageRegionType = typename ImageType::RegionType
using	ImageType = TImage
using	InternalEnergyFunction = CompositeValleyFunction
using	MaskElementType = typename MaskType::PixelType
using	MaskPointer = typename MaskType::Pointer
using	MaskType = TImageMask
using	MeasureType = Superclass::MeasureType
using	ParametersType = typename Superclass::ParametersType
using	Pointer = SmartPointer< Self >
using	SamplingFactorType = unsigned int[SpaceDimension]
using	Self = MRIBiasEnergyFunction
using	Superclass = SingleValuedCostFunction
Public Types inherited from itk::SingleValuedCostFunction
using	ConstPointer = SmartPointer< const Self >
using	DerivativeType = Array< ParametersValueType >
using	MeasureType = double
using	ParametersType = Superclass::ParametersType
using	ParametersValueType = Superclass::ParametersValueType
using	Pointer = SmartPointer< Self >
using	Self = SingleValuedCostFunction
using	Superclass = CostFunction
Public Types inherited from itk::CostFunctionTemplate< TInternalComputationValueType >
using	ConstPointer = SmartPointer< const Self >
using	ParametersType = OptimizerParameters< TInternalComputationValueType >
using	ParametersValueType = TInternalComputationValueType
using	Pointer = SmartPointer< Self >
using	Self = CostFunctionTemplate
using	Superclass = Object
Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >
using	Pointer = SmartPointer< Self >
using	Self = Object
using	Superclass = LightObject
Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >
using	Pointer = SmartPointer< Self >
using	Self = LightObject

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother () const
virtual const char *	GetNameOfClass () const
void	SetBiasField (BiasFieldType *bias)
virtual void	SetImage (ImageType *_arg)
virtual void	SetMask (MaskType *_arg)
virtual void	SetRegion (ImageRegionType _arg)
Public Member Functions inherited from itk::SingleValuedCostFunction
virtual void	GetValueAndDerivative (const ParametersType &parameters, MeasureType &value, DerivativeType &derivative) const
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
virtual void	DebugOff () const
virtual void	DebugOn () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary ()
const MetaDataDictionary &	GetMetaDataDictionary () const
virtual ModifiedTimeType	GetMTime () const
virtual const TimeStamp &	GetTimeStamp () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
void	Register () const override
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetReferenceCount (int) override
void	UnRegister () const noexcept override
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)
virtual void	SetObjectName (std::string _arg)
virtual const std::string &	GetObjectName () const
Public Member Functions inherited from itk::LightObject
Pointer	Clone () const
virtual void	Delete ()
virtual int	GetReferenceCount () const
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool val)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
static Pointer	New ()

Static Public Attributes
static constexpr unsigned int	SpaceDimension = 3
BiasFieldType *	m_BiasField
ImagePointer	m_Image
MaskPointer	m_Mask
ImageRegionType	m_Region
InternalEnergyFunction *	m_InternalEnergyFunction
SamplingFactorType	m_SamplingFactor
void	SetSamplingFactors (const SamplingFactorType factor)
double	GetEnergy0 (double diff)
MeasureType	GetValue (const ParametersType &parameters) const override
void	GetDerivative (const ParametersType &, DerivativeType &) const override
void	InitializeDistributions (Array< double > classMeans, Array< double > classSigmas)
unsigned int	GetNumberOfParameters () const override
	MRIBiasEnergyFunction ()
	~MRIBiasEnergyFunction () override

Additional Inherited Members
Protected Member Functions inherited from itk::SingleValuedCostFunction
	SingleValuedCostFunction ()=default
	~SingleValuedCostFunction () override
Protected Member Functions inherited from itk::CostFunctionTemplate< TInternalComputationValueType >
	CostFunctionTemplate ()=default
void	PrintSelf (std::ostream &os, Indent indent) const override
	~CostFunctionTemplate () override=default
Protected Member Functions inherited from itk::Object
	Object ()
	~Object () override
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &timeStamp)
Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const
	LightObject ()
virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~LightObject ()
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

Detailed Description

template<typename TImage, typename TImageMask, typename TBiasField>
class itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >

Represents a cost function for MRI bias field correction optimization.

This is a wrapping class which provides interfaces between images, the bias field, the internal energy function (CompositeValleyFunction), and the Optimizer.

This class is templated over the type of the input image (TImage), the image mask (which tells which pixels in the input image should be included for energy value calculation), and the bias field (TBiasField).

Definition at line 48 of file itkMRIBiasFieldCorrectionFilter.h.

Member Typedef Documentation

BiasFieldType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::BiasFieldType = TBiasField

Bias field type definition.

Definition at line 76 of file itkMRIBiasFieldCorrectionFilter.h.

ConstPointer

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ConstPointer = SmartPointer<const Self>

Definition at line 57 of file itkMRIBiasFieldCorrectionFilter.h.

DerivativeType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::DerivativeType = Superclass::DerivativeType

Not used, but expected by SingleValuedNonLinearOptimizer class.

Definition at line 83 of file itkMRIBiasFieldCorrectionFilter.h.

ImageElementType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageElementType = typename ImageType::PixelType

Definition at line 68 of file itkMRIBiasFieldCorrectionFilter.h.

ImageIndexType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageIndexType = typename ImageType::IndexType

Definition at line 69 of file itkMRIBiasFieldCorrectionFilter.h.

ImagePointer

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImagePointer = typename ImageType::Pointer

Definition at line 67 of file itkMRIBiasFieldCorrectionFilter.h.

ImageRegionType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageRegionType = typename ImageType::RegionType

Definition at line 70 of file itkMRIBiasFieldCorrectionFilter.h.

ImageType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageType = TImage

Image related type definitions.

Definition at line 66 of file itkMRIBiasFieldCorrectionFilter.h.

InternalEnergyFunction

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::InternalEnergyFunction = CompositeValleyFunction

The type of the internal energy function.

Definition at line 91 of file itkMRIBiasFieldCorrectionFilter.h.

MaskElementType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskElementType = typename MaskType::PixelType

Definition at line 73 of file itkMRIBiasFieldCorrectionFilter.h.

MaskPointer

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskPointer = typename MaskType::Pointer

Definition at line 72 of file itkMRIBiasFieldCorrectionFilter.h.

MaskType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskType = TImageMask

Definition at line 71 of file itkMRIBiasFieldCorrectionFilter.h.

MeasureType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MeasureType = Superclass::MeasureType

The cost value type.

Definition at line 86 of file itkMRIBiasFieldCorrectionFilter.h.

ParametersType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ParametersType = typename Superclass::ParametersType

Parameters type for optimizer (coefficients type for bias field estimate).

Definition at line 80 of file itkMRIBiasFieldCorrectionFilter.h.

Pointer

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::Pointer = SmartPointer<Self>

Definition at line 56 of file itkMRIBiasFieldCorrectionFilter.h.

SamplingFactorType

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SamplingFactorType = unsigned int[SpaceDimension]

The type of the sampling factors.

Definition at line 94 of file itkMRIBiasFieldCorrectionFilter.h.

Self

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::Self = MRIBiasEnergyFunction

Standard class type aliases.

Definition at line 54 of file itkMRIBiasFieldCorrectionFilter.h.

Superclass

template<typename TImage , typename TImageMask , typename TBiasField >

using itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::Superclass = SingleValuedCostFunction

Definition at line 55 of file itkMRIBiasFieldCorrectionFilter.h.

Constructor & Destructor Documentation

MRIBiasEnergyFunction()

template<typename TImage , typename TImageMask , typename TBiasField >

itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MRIBiasEnergyFunction ( )

protected

Constructor.

~MRIBiasEnergyFunction()

template<typename TImage , typename TImageMask , typename TBiasField >

itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::~MRIBiasEnergyFunction ( )

overrideprotected

Destructor.

Member Function Documentation

CreateAnother()

template<typename TImage , typename TImageMask , typename TBiasField >

virtual::itk::LightObject::Pointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::CreateAnother ( ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

GetDerivative()

template<typename TImage , typename TImageMask , typename TBiasField >

void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetDerivative ( const ParametersType &  , DerivativeType &    ) const

inlineoverridevirtual

Dummy implementation to confirm to the SingleValuedCostFunction interfaces. It is pure virtual in the superclass.

Implements itk::SingleValuedCostFunction.

Definition at line 140 of file itkMRIBiasFieldCorrectionFilter.h.

GetEnergy0()

template<typename TImage , typename TImageMask , typename TBiasField >

double itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetEnergy0 ( double  diff )

inline

Get an energy value for the intensity difference between a pixel and its corresponding bias.

Definition at line 127 of file itkMRIBiasFieldCorrectionFilter.h.

GetNameOfClass()

template<typename TImage , typename TImageMask , typename TBiasField >

virtual const char* itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::SingleValuedCostFunction.

GetNumberOfParameters()

template<typename TImage , typename TImageMask , typename TBiasField >

unsigned int itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetNumberOfParameters ( ) const

overridevirtual

Bias field object pointer.

Implements itk::CostFunctionTemplate< TInternalComputationValueType >.

GetValue()

template<typename TImage , typename TImageMask , typename TBiasField >

MeasureType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetValue ( const ParametersType &  parameters ) const

overridevirtual

Gets the total energy value of an image or a slice using the given parameters.

Implements itk::SingleValuedCostFunction.

InitializeDistributions()

template<typename TImage , typename TImageMask , typename TBiasField >

void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::InitializeDistributions	(	Array< double >	classMeans,
		Array< double >	classSigmas
	)

Set Mean and Sigma for the normal distributions

Warning

This method MUST be called before any attempt to evaluate the Function because it instantiate the internal energy function.

New()

template<typename TImage , typename TImageMask , typename TBiasField >

static Pointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::New ( )

static

Method for creation through the object factory.

SetBiasField()

template<typename TImage , typename TImageMask , typename TBiasField >

void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetBiasField ( BiasFieldType *  bias )

inline

Sets the BiasField object.

Definition at line 107 of file itkMRIBiasFieldCorrectionFilter.h.

SetImage()

template<typename TImage , typename TImageMask , typename TBiasField >

virtual void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetImage ( ImageType *  _arg )

virtual

Specify the input image.

SetMask()

template<typename TImage , typename TImageMask , typename TBiasField >

virtual void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetMask ( MaskType *  _arg )

virtual

Specify the input mask image.

SetRegion()

template<typename TImage , typename TImageMask , typename TBiasField >

virtual void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetRegion ( ImageRegionType  _arg )

virtual

Set the image region which will be included for energy calculation.

SetSamplingFactors()

template<typename TImage , typename TImageMask , typename TBiasField >

void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetSamplingFactors ( const SamplingFactorType  factor )

inline

Sets the sampling factors of the energy function in each direction. Default is 1 in each dimension

Definition at line 115 of file itkMRIBiasFieldCorrectionFilter.h.

Member Data Documentation

m_BiasField

template<typename TImage , typename TImageMask , typename TBiasField >

BiasFieldType* itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_BiasField

private

Bias field object pointer.

Definition at line 162 of file itkMRIBiasFieldCorrectionFilter.h.

m_Image

template<typename TImage , typename TImageMask , typename TBiasField >

ImagePointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_Image

private

Input image smart pointer.

Definition at line 165 of file itkMRIBiasFieldCorrectionFilter.h.

m_InternalEnergyFunction

template<typename TImage , typename TImageMask , typename TBiasField >

InternalEnergyFunction* itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_InternalEnergyFunction

private

Internal energy function object pointer.

Definition at line 174 of file itkMRIBiasFieldCorrectionFilter.h.

m_Mask

template<typename TImage , typename TImageMask , typename TBiasField >

MaskPointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_Mask

private

Input mask image smart pointer.

Definition at line 168 of file itkMRIBiasFieldCorrectionFilter.h.

m_Region

template<typename TImage , typename TImageMask , typename TBiasField >

ImageRegionType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_Region

private

Region of interest.

Definition at line 171 of file itkMRIBiasFieldCorrectionFilter.h.

m_SamplingFactor

template<typename TImage , typename TImageMask , typename TBiasField >

SamplingFactorType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_SamplingFactor

private

Sampling factors

Definition at line 177 of file itkMRIBiasFieldCorrectionFilter.h.

SpaceDimension

template<typename TImage , typename TImageMask , typename TBiasField >

constexpr unsigned int itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SpaceDimension = 3

staticconstexpr

Definition at line 88 of file itkMRIBiasFieldCorrectionFilter.h.

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

• itkMRIBiasFieldCorrectionFilter.h