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

#include <itkMRIBiasFieldCorrectionFilter.h>

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

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

[legend]List of all members.

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Detailed Description

template<class TImage, class TImageMask, class 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 48 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 double	ParametersValueType
typedef SmartPointer< Self >	Pointer
typedef unsigned int	SamplingFactorType [SpaceDimension]
typedef MRIBiasEnergyFunction	Self
typedef SingleValuedCostFunction	Superclass
Public Member Functions
virtual LightObject::Pointer	CreateAnother () const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
void	GetDerivative (const ParametersType &, DerivativeType &) const
double	GetEnergy0 (double diff)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
MetaDataDictionary &	GetMetaDataDictionary (void)
virtual unsigned long	GetMTime () const
virtual const char *	GetNameOfClass () const
unsigned int	GetNumberOfParameters (void) const
virtual int	GetReferenceCount () const
MeasureType	GetValue (const ParametersType &parameters) const
This method returns the value and derivative of the cost function corresponding *to the specified parameters *virtual void	GetValueAndDerivative (const ParametersType &parameters, MeasureType &value, DerivativeType &derivative) const
bool	HasObserver (const EventObject &event) const
void	InitializeDistributions (Array< double > classMeans, Array< double > classSigmas)
void	InvokeEvent (const EventObject &) const
void	InvokeEvent (const EventObject &)
	itkStaticConstMacro (SpaceDimension, unsigned int, 3)
virtual void	Modified () const
void	Print (std::ostream &os, Indent indent=0) const
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetBiasField (BiasFieldType *bias)
void	SetDebug (bool debugFlag) const
virtual void	SetImage (ImageType *_arg)
virtual void	SetMask (MaskType *_arg)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	SetRegion (ImageRegionType _arg)
Sets the sampling factors of the energy function in each direction *Default is in each dimension *void	SetSamplingFactors (SamplingFactorType factor)
virtual void	UnRegister () const
Static Public Member Functions
static void	BreakOnError ()
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
This is a global flag that controls whether any warning *or error messages are displayed *static void	SetGlobalWarningDisplay (bool flag)
Public Attributes
Allow people to add remove invoke observers(callbacks) to any ITK *object.This is an implementation of the subject/observer design *pattern.An observer is added by specifying an event to respond to *and an itk unsigned lon	AddObserver )(const EventObject &event, Command *) const
This is a global flag that controls whether any	debug
Protected Member Functions
	MRIBiasEnergyFunction ()
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~MRIBiasEnergyFunction ()
Protected Attributes
int	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock
Methods invoked by virtual Print() to print information about the object *including superclasses.Typically not called by the user(use Print()*instead) but used in the hierarchical print process to combine the *output of several classes.*/virtual void PrintSelf(std voi	PrintHeader )(std::ostream &os, Indent indent) const

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Member Typedef Documentation

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

Bias field type definition. Definition at line 74 of file itkMRIBiasFieldCorrectionFilter.h.

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

Reimplemented from itk::SingleValuedCostFunction. Definition at line 55 of file itkMRIBiasFieldCorrectionFilter.h.

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

Not used, but expected by SingleValuedNonLinearOptimizer class. Reimplemented from itk::SingleValuedCostFunction. Definition at line 81 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 68 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 70 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 66 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 71 of file itkMRIBiasFieldCorrectionFilter.h.

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

Image related type definitions. Definition at line 61 of file itkMRIBiasFieldCorrectionFilter.h.

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

The type of the internal energy function. Definition at line 89 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 69 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 67 of file itkMRIBiasFieldCorrectionFilter.h.

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

Definition at line 65 of file itkMRIBiasFieldCorrectionFilter.h.

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

The cost value type. Reimplemented from itk::SingleValuedCostFunction. Definition at line 84 of file itkMRIBiasFieldCorrectionFilter.h.

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

Parameters type for optimizier (coefficients type for bias field estimate). Reimplemented from itk::SingleValuedCostFunction. Definition at line 78 of file itkMRIBiasFieldCorrectionFilter.h.

typedef double itk::CostFunction::ParametersValueType [inherited]

ParametersType typedef. It defines a position in the optimization search space. Definition at line 46 of file itkCostFunction.h.

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

Reimplemented from itk::SingleValuedCostFunction. Definition at line 54 of file itkMRIBiasFieldCorrectionFilter.h.

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

The type of the sampling factors Definition at line 92 of file itkMRIBiasFieldCorrectionFilter.h.

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

Standard class typedefs. Reimplemented from itk::SingleValuedCostFunction. Definition at line 52 of file itkMRIBiasFieldCorrectionFilter.h.

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

Reimplemented from itk::SingleValuedCostFunction. Definition at line 53 of file itkMRIBiasFieldCorrectionFilter.h.

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Constructor & Destructor Documentation

template<class TImage, class TImageMask, class TBiasField> itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::MRIBiasEnergyFunction (   )  [protected]

Constructor:

template<class TImage, class TImageMask, class TBiasField> virtual itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::~MRIBiasEnergyFunction (   )  [protected, virtual]

Destructor:

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Member Function Documentation

static void itk::LightObject::BreakOnError (   )  [static, inherited]

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

virtual LightObject::Pointer itk::Object::CreateAnother (   )  const [virtual, inherited]

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::LightObject.

virtual void itk::Object::DebugOff (   )  const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn (   )  const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete (   )  [virtual, inherited]

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

Command* itk::Object::GetCommand (  unsigned long  tag  )  [inherited]

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

bool itk::Object::GetDebug (   )  const [inherited]

Get the value of the debug flag.

template<class TImage, class TImageMask, class TBiasField> void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::GetDerivative (  const ParametersType &  , DerivativeType &  )  const [inline, virtual]

Dummy implementation to confirm to the SingleValuedCostFunction interfaces. It is pure virtual in the superclass Implements itk::SingleValuedCostFunction. Definition at line 131 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TImage, class TImageMask, class 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 120 of file itkMRIBiasFieldCorrectionFilter.h.

static bool itk::Object::GetGlobalWarningDisplay (   )  [static, inherited]

const MetaDataDictionary& itk::Object::GetMetaDataDictionary (  void   )  const [inherited]

Returns: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary (  void   )  [inherited]

Returns: A reference to this objects MetaDataDictionary. Warning: This reference may be changed.

virtual unsigned long itk::Object::GetMTime (   )  const [virtual, inherited]

Return this objects modified time. Reimplemented in itk::ImageRegistrationMethod< TFixedImage, TMovingImage >, itk::DeformationFieldSource< TOutputImage >, itk::InverseDeformationFieldImageFilter< TInputImage, TOutputImage >, itk::ResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >, itk::VectorResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >, itk::BoundingBox< TPointIdentifier, VPointDimension, TCoordRep, TPointsContainer >, itk::SceneSpatialObject< SpaceDimension >, and itk::SceneSpatialObject< NDimensions >.

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

Run-time type information (and related methods). Reimplemented from itk::SingleValuedCostFunction.

template<class TImage, class TImageMask, class TBiasField> 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::CostFunction.

virtual int itk::LightObject::GetReferenceCount (   )  const [inline, virtual, inherited]

Gets the reference count on this object. Definition at line 98 of file itkLightObject.h.

template<class TImage, class TImageMask, class TBiasField> 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.

This method returns the value and derivative of the cost function corresponding* to the specified parameters* virtual void itk::SingleValuedCostFunction::GetValueAndDerivative (  const ParametersType &  parameters, MeasureType &  value, DerivativeType &  derivative )  const [inline, virtual, inherited]

Reimplemented in itk::ImageToSpatialObjectMetric< TFixedImage, TMovingSpatialObject >, itk::MattesMutualInformationImageToImageMetric< TFixedImage, TMovingImage >, and itk::MutualInformationImageToImageMetric< TFixedImage, TMovingImage >. Definition at line 71 of file itkSingleValuedCostFunction.h.

static void itk::Object::GlobalWarningDisplayOff (   )  [inline, static, inherited]

Definition at line 100 of file itkObject.h. References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn (   )  [inline, static, inherited]

Definition at line 98 of file itkObject.h. References itk::Object::SetGlobalWarningDisplay().

bool itk::Object::HasObserver (  const EventObject &  event  )  const [inherited]

Return true if an observer is registered for this event.

template<class TImage, class TImageMask, class 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 attemp to evaluate the Function because it instantiate the internal energy function

void itk::Object::InvokeEvent (  const EventObject &   )  const [inherited]

Call Execute on all the Commands observing this event id. The actions triggered by this call doesn't modify this object.

void itk::Object::InvokeEvent (  const EventObject &   )  [inherited]

Call Execute on all the Commands observing this event id.

template<class TImage, class TImageMask, class TBiasField> itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::itkStaticConstMacro (  SpaceDimension  , unsigned  int, 3  )

virtual void itk::Object::Modified (   )  const [virtual, inherited]

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data. Referenced by itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::HistogramAlgorithmBase< TInputHistogram >::SetInputHistogram(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::CollidingFrontsImageFilter< TInputImage, TOutputImage >::SetSeedPoints1(), itk::CollidingFrontsImageFilter< TInputImage, TOutputImage >::SetSeedPoints2(), itk::NonUniformBSpline< TDimension >::SetSplineOrder(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< typename ComponentType::HistogramType >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

template<class TImage, class TImageMask, class TBiasField> static Pointer itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::New (   )  [static]

Method for creation through the object factory. Reimplemented from itk::Object.

void itk::LightObject::Print (  std::ostream &  os, Indent  indent = 0 )  const [inherited]

Cause the object to print itself out.

bool itk::Object::PrintObservers (  std::ostream &  os, Indent  indent )  const [protected, inherited]

void itk::CostFunction::PrintSelf (  std::ostream &  os, Indent  indent )  const [protected, virtual, inherited]

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes. Reimplemented from itk::Object. Reimplemented in itk::CompareHistogramImageToImageMetric< TFixedImage, TMovingImage >, itk::EuclideanDistancePointMetric< TFixedPointSet, TMovingPointSet, TDistanceMap >, itk::GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >, itk::HistogramImageToImageMetric< TFixedImage, TMovingImage >, itk::ImageToImageMetric< TFixedImage, TMovingImage >, itk::ImageToSpatialObjectMetric< TFixedImage, TMovingSpatialObject >, itk::KappaStatisticImageToImageMetric< TFixedImage, TMovingImage >, itk::KullbackLeiblerCompareHistogramImageToImageMetric< TFixedImage, TMovingImage >, itk::MatchCardinalityImageToImageMetric< TFixedImage, TMovingImage >, itk::MattesMutualInformationImageToImageMetric< TFixedImage, TMovingImage >, itk::MeanReciprocalSquareDifferenceImageToImageMetric< TFixedImage, TMovingImage >, itk::MeanReciprocalSquareDifferencePointSetToImageMetric< TFixedPointSet, TMovingImage >, itk::MutualInformationImageToImageMetric< TFixedImage, TMovingImage >, itk::NormalizedCorrelationImageToImageMetric< TFixedImage, TMovingImage >, itk::NormalizedCorrelationPointSetToImageMetric< TFixedPointSet, TMovingImage >, itk::PointSetToImageMetric< TFixedPointSet, TMovingImage >, itk::PointSetToPointSetMetric< TFixedPointSet, TMovingPointSet >, itk::ShapePriorMAPCostFunction< TFeatureImage, TOutputPixel >, itk::ShapePriorMAPCostFunctionBase< TFeatureImage, TOutputPixel >, itk::CumulativeGaussianCostFunction, and itk::Statistics::GoodnessOfFitMixtureModelCostFunction< TInputSample >.

virtual void itk::LightObject::PrintTrailer (  std::ostream &  os, Indent  indent )  const [protected, virtual, inherited]

virtual void itk::Object::Register (   )  const [virtual, inherited]

Increase the reference count (mark as used by another object). Reimplemented from itk::LightObject.

void itk::Object::RemoveAllObservers (   )  [inherited]

Remove all observers .

void itk::Object::RemoveObserver (  unsigned long  tag  )  [inherited]

Remove the observer with this tag value.

template<class TImage, class TImageMask, class TBiasField> void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetBiasField (  BiasFieldType *  bias  )  [inline]

Sets the BiasField object. Definition at line 104 of file itkMRIBiasFieldCorrectionFilter.h.

void itk::Object::SetDebug (  bool  debugFlag  )  const [inherited]

Set the value of the debug flag. A non-zero value turns debugging on.

This is a global flag that controls whether any warning* or error messages are displayed* static void itk::Object::SetGlobalWarningDisplay (  bool  flag  )  [static, inherited]

Referenced by itk::Object::GlobalWarningDisplayOff(), and itk::Object::GlobalWarningDisplayOn().

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

Specify the input image.

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

Specify the input mask image.

void itk::Object::SetMetaDataDictionary (  const MetaDataDictionary &  rhs  )  [inherited]

Returns: Set the MetaDataDictionary

virtual void itk::Object::SetReferenceCount (  int   )  [virtual, inherited]

Sets the reference count (use with care) Reimplemented from itk::LightObject.

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

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

template<class TImage, class TImageMask, class TBiasField> Sets the sampling factors of the energy function in each direction* Default is in each dimension* void itk::MRIBiasEnergyFunction< TImage, TImageMask, TBiasField >::SetSamplingFactors (  SamplingFactorType  factor  )  [inline]

Definition at line 109 of file itkMRIBiasFieldCorrectionFilter.h.

virtual void itk::Object::UnRegister (   )  const [virtual, inherited]

Decrease the reference count (release by another object). Reimplemented from itk::LightObject.

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Member Data Documentation

Allow people to add remove invoke observers (callbacks) to any ITK * object. This is an implementation of the subject/observer design * pattern. An observer is added by specifying an event to respond to * and an itk unsigned lon itk::Object::AddObserver)(const EventObject &event, Command *) const [inherited]

This is a global flag that controls whether any itk::Object::debug [inherited]

Definition at line 94 of file itkObject.h.

int itk::LightObject::m_ReferenceCount [mutable, protected, inherited]

Number of uses of this object by other objects. Definition at line 119 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock [mutable, protected, inherited]

Mutex lock to protect modification to the reference count Definition at line 122 of file itkLightObject.h.

Methods invoked by virtual Print () to print information about the object * including superclasses. Typically not called by the user (use Print() * instead) but used in the hierarchical print process to combine the * output of several classes. */ virtual void PrintSelf(std voi itk::LightObject::PrintHeader)(std::ostream &os, Indent indent) const [protected, inherited]

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

• itkMRIBiasFieldCorrectionFilter.h

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