#include <itkMRIBiasFieldCorrectionFilter.h>

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

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

Detailed Description

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

a cost function for 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 47 of file itkMRIBiasFieldCorrectionFilter.h.

Public Types
typedef TBiasField	BiasFieldType

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DerivativeType	DerivativeType

typedef ImageType::PixelType	ImageElementType

typedef ImageType::IndexType	ImageIndexType

typedef ImageType::Pointer	ImagePointer

typedef ImageType::RegionType	ImageRegionType

typedef TImage	ImageType

typedef CompositeValleyFunction	InternalEnergyFunction

typedef MaskType::PixelType	MaskElementType

typedef MaskType::Pointer	MaskPointer

typedef TImageMask	MaskType

typedef Superclass::MeasureType	MeasureType

typedef Superclass::ParametersType	ParametersType

typedef SmartPointer< Self >	Pointer

typedef unsigned int	SamplingFactorType [SpaceDimension]

typedef MRIBiasEnergyFunction	Self

typedef SingleValuedCostFunction	Superclass

Public Types inherited from itk::SingleValuedCostFunction
typedef SmartPointer< const Self >	ConstPointer

typedef Array < ParametersValueType >	DerivativeType

typedef double	MeasureType

typedef Superclass::ParametersType	ParametersType

typedef Superclass::ParametersValueType	ParametersValueType

typedef SmartPointer< Self >	Pointer

typedef SingleValuedCostFunction	Self

typedef CostFunction	Superclass

Public Types inherited from itk::CostFunctionTemplate< TInternalComputationValueType >
typedef SmartPointer< const Self >	ConstPointer

typedef OptimizerParameters < TInternalComputationValueType >	ParametersType

typedef TInternalComputationValueType	ParametersValueType

typedef SmartPointer< Self >	Pointer

typedef CostFunctionTemplate	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother () const

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

double	GetEnergy0 (double diff)

virtual const char *	GetNameOfClass () const

virtual unsigned int	GetNumberOfParameters (void) const override

virtual 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 (SamplingFactorType factor)

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

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

virtual void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
virtual void	Delete ()

virtual int	GetReferenceCount () const

	itkCloneMacro (Self)

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 flag)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Static Public Attributes
static const unsigned int	SpaceDimension = 3

Protected Member Functions
	MRIBiasEnergyFunction ()

virtual	~MRIBiasEnergyFunction ()

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

virtual	~SingleValuedCostFunction ()

Protected Member Functions inherited from itk::CostFunctionTemplate< TInternalComputationValueType >
	CostFunctionTemplate ()

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

virtual	~CostFunctionTemplate ()

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

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

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

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 ()

Private Member Functions
	MRIBiasEnergyFunction (const Self &)

void	operator= (const Self &)

Private Attributes
BiasFieldType *	m_BiasField

ImagePointer	m_Image

InternalEnergyFunction *	m_InternalEnergyFunction

MaskPointer	m_Mask

ImageRegionType	m_Region

SamplingFactorType	m_SamplingFactor

Additional Inherited Members
Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

template<typename TImage , typename TImageMask , typename TBiasField >

typedef TBiasField itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::BiasFieldType

Bias field type definition.

Definition at line 73 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

Definition at line 54 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef Superclass::DerivativeType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::DerivativeType

Not used, but expected by SingleValuedNonLinearOptimizer class.

Definition at line 80 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef ImageType::PixelType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageElementType

Definition at line 65 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef ImageType::IndexType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageIndexType

Definition at line 66 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef ImageType::Pointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImagePointer

Definition at line 64 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef ImageType::RegionType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageRegionType

Definition at line 67 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef TImage itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ImageType

Image related type definitions.

Definition at line 60 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef CompositeValleyFunction itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::InternalEnergyFunction

The type of the internal energy function.

Definition at line 88 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef MaskType::PixelType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskElementType

Definition at line 70 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef MaskType::Pointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskPointer

Definition at line 69 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef TImageMask itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MaskType

Definition at line 68 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef Superclass::MeasureType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MeasureType

The cost value type.

Definition at line 83 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef Superclass::ParametersType itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::ParametersType

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

Definition at line 77 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

Definition at line 53 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

The type of the sampling factors

Definition at line 91 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef MRIBiasEnergyFunction itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::Self

Standard class typedefs.

Definition at line 51 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

typedef SingleValuedCostFunction itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::Superclass

Definition at line 52 of file itkMRIBiasFieldCorrectionFilter.h.

Constructor & Destructor Documentation

template<typename TImage , typename TImageMask , typename TBiasField >

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

protected

Constructor:

template<typename TImage , typename TImageMask , typename TBiasField >

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

protectedvirtual

Destructor:

template<typename TImage , typename TImageMask , typename TBiasField >

itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MRIBiasEnergyFunction ( const Self & )

private

Member Function Documentation

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.

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 130 of file itkMRIBiasFieldCorrectionFilter.h.

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 119 of file itkMRIBiasFieldCorrectionFilter.h.

References itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_InternalEnergyFunction.

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.

template<typename TImage , typename TImageMask , typename TBiasField >

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

overridevirtual

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

Implements itk::CostFunctionTemplate< TInternalComputationValueType >.

template<typename TImage , typename TImageMask , typename TBiasField >

virtual 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.

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

template<typename TImage , typename TImageMask , typename TBiasField >

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

static

Method for creation through the object factory.

template<typename TImage , typename TImageMask , typename TBiasField >

void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::operator= ( const Self & )

private

template<typename TImage , typename TImageMask , typename TBiasField >

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

inline

Sets the BiasField object.

Definition at line 103 of file itkMRIBiasFieldCorrectionFilter.h.

References itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_BiasField.

template<typename TImage , typename TImageMask , typename TBiasField >

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

virtual

Specify the input image.

template<typename TImage , typename TImageMask , typename TBiasField >

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

virtual

Specify the input mask image.

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.

template<typename TImage , typename TImageMask , typename TBiasField >

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

inline

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

Definition at line 108 of file itkMRIBiasFieldCorrectionFilter.h.

References itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::m_SamplingFactor, and itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SpaceDimension.

Member Data Documentation

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Bias field object pointer.

Definition at line 153 of file itkMRIBiasFieldCorrectionFilter.h.

Referenced by itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetBiasField().

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Input image smart pointer.

Definition at line 156 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Internal energy function object pointer.

Definition at line 165 of file itkMRIBiasFieldCorrectionFilter.h.

Referenced by itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetEnergy0().

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Input mask image smart pointer.

Definition at line 159 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Region of interest.

Definition at line 162 of file itkMRIBiasFieldCorrectionFilter.h.

template<typename TImage , typename TImageMask , typename TBiasField >

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

private

Sampling factors

Definition at line 168 of file itkMRIBiasFieldCorrectionFilter.h.

Referenced by itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetSamplingFactors().

template<typename TImage , typename TImageMask , typename TBiasField >

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

static

Definition at line 85 of file itkMRIBiasFieldCorrectionFilter.h.

Referenced by itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetSamplingFactors().

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

itkMRIBiasFieldCorrectionFilter.h

Detailed Description

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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