#include <itkMRIBiasFieldCorrectionFilter.h>

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 51 of file 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	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< double >
using	ConstPointer = SmartPointer< const Self >

using	ParametersType = OptimizerParameters< double >

using	ParametersValueType = double

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
void	GetDerivative (const ParametersType &, DerivativeType &) const override

double	GetEnergy0 (double diff)

const char *	GetNameOfClass () const override

unsigned int	GetNumberOfParameters () const override

MeasureType	GetValue (const ParametersType &parameters) const override

void	InitializeDistributions (Array< double > classMeans, Array< double > classSigmas)

void	SetBiasField (BiasFieldType *bias)

virtual void	SetImage (ImageType *_arg)

virtual void	SetMask (MaskType *_arg)

virtual void	SetRegion (ImageRegionType _arg)


void	SetSamplingFactors (const SamplingFactorType factor)

Public Member Functions inherited from itk::SingleValuedCostFunction
virtual void	GetDerivative (const ParametersType &parameters, DerivativeType &derivative) const =0

const char *	GetNameOfClass () const override

virtual MeasureType	GetValue (const ParametersType &parameters) const =0

virtual void	GetValueAndDerivative (const ParametersType &parameters, MeasureType &value, DerivativeType &derivative) const

Public Member Functions inherited from itk::CostFunctionTemplate< double >
const char *	GetNameOfClass () const override

virtual unsigned int	GetNumberOfParameters () const=0

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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

const char *	GetNameOfClass () const override

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) const

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 Pointer	CreateAnother () const

virtual void	Delete ()

virtual const char *	GetNameOfClass () const

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

virtual void	Register () const

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const noexcept

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

Protected Member Functions
	MRIBiasEnergyFunction ()

	~MRIBiasEnergyFunction () override=default

Protected Member Functions inherited from itk::SingleValuedCostFunction
	SingleValuedCostFunction ()=default

	~SingleValuedCostFunction () override

Protected Member Functions inherited from itk::CostFunctionTemplate< double >
	CostFunctionTemplate ()=default

void	PrintSelf (std::ostream &os, Indent indent) const override

	~CostFunctionTemplate () override=default

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

void	PrintSelf (std::ostream &os, Indent indent) const override

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~Object () override

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

virtual void	PrintSelf (std::ostream &os, Indent indent) const

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Private Attributes
BiasFieldType *	m_BiasField {}

ImagePointer	m_Image {}

std::unique_ptr< InternalEnergyFunction >	m_InternalEnergyFunction

MaskPointer	m_Mask {}

ImageRegionType	m_Region {}

SamplingFactorType	m_SamplingFactor {}

Additional Inherited Members
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

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 79 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 60 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 86 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 71 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 72 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 70 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 73 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 69 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 94 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 76 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 75 of file itkMRIBiasFieldCorrectionFilter.h.

◆ MaskType

template<typename TImage , typename TImageMask , typename TBiasField >

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

Definition at line 74 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 89 of file itkMRIBiasFieldCorrectionFilter.h.

◆ Pointer

template<typename TImage , typename TImageMask , typename TBiasField >

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

Definition at line 59 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 97 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 57 of file itkMRIBiasFieldCorrectionFilter.h.

◆ Superclass

template<typename TImage , typename TImageMask , typename TBiasField >

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

Definition at line 58 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 ( )

overrideprotecteddefault

Destructor.

Member Function Documentation

◆ 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 143 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 130 of file itkMRIBiasFieldCorrectionFilter.h.

◆ GetNameOfClass()

template<typename TImage , typename TImageMask , typename TBiasField >

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

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::SingleValuedCostFunction.

◆ GetNumberOfParameters()

template<typename TImage , typename TImageMask , typename TBiasField >

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

overridevirtual

Return the number of parameters required to compute this cost function. This method MUST be overloaded by derived classes.

Implements itk::CostFunctionTemplate< double >.

◆ 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 110 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 118 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 165 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 168 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_InternalEnergyFunction

template<typename TImage , typename TImageMask , typename TBiasField >

std::unique_ptr<InternalEnergyFunction> itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_InternalEnergyFunction

private

Internal energy function object pointer.

Definition at line 177 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 171 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 174 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 180 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 91 of file itkMRIBiasFieldCorrectionFilter.h.

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

itkMRIBiasFieldCorrectionFilter.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BiasFieldType

◆ ConstPointer

◆ DerivativeType

◆ ImageElementType

◆ ImageIndexType

◆ ImagePointer

◆ ImageRegionType

◆ ImageType

◆ InternalEnergyFunction

◆ MaskElementType

◆ MaskPointer

◆ MaskType

◆ MeasureType

◆ Pointer

◆ SamplingFactorType

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ MRIBiasEnergyFunction()

◆ ~MRIBiasEnergyFunction()

Member Function Documentation

◆ GetDerivative()

◆ GetEnergy0()

◆ GetNameOfClass()

◆ GetNumberOfParameters()

◆ GetValue()

◆ InitializeDistributions()

◆ New()

◆ SetBiasField()

◆ SetImage()

◆ SetMask()

◆ SetRegion()

◆ SetSamplingFactors()

Member Data Documentation

◆ m_BiasField

◆ m_Image

◆ m_InternalEnergyFunction

◆ m_Mask

◆ m_Region

◆ m_SamplingFactor

◆ SpaceDimension