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 >:

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 (void) const
void	GetDerivative (const ParametersType &, DerivativeType &) const ITK_OVERRIDE
double	GetEnergy0 (double diff)
virtual const char *	GetNameOfClass () const
virtual unsigned int	GetNumberOfParameters (void) const ITK_OVERRIDE
virtual MeasureType	GetValue (const ParametersType &parameters) const ITK_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 (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) 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 ITK_OVERRIDE
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int) ITK_OVERRIDE
virtual void	UnRegister () const ITK_OVERRIDE
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 ITK_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 Types inherited from itk::LightObject
typedef int	InternalReferenceCountType
Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock

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 ( void  ) 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

inlinevirtual

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

virtual

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

virtual

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().

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

• itkMRIBiasFieldCorrectionFilter.h