#include <elxMetricBase.h>

Detailed Description

template<class TElastix>
class elastix::MetricBase< TElastix >

This class is the elastix base class for all Metrics.

This class contains the common functionality for all Metrics.

The parameters used in this class are:

ShowExactMetricValue: Flag that can set to "true" or "false". If "true" the metric computes the exact metric value (computed on all voxels rather than on the set of spatial samples) and shows it each iteration. Must be given for each resolution.
example: (ShowExactMetricValue "true" "true" "false")
Default is "false" for all resolutions.

ExactMetricSampleGridSpacing: Set an integer downsampling rate for computing the "exact" metric. Only meaningful if set in combination with the ShowExactMetricValue set to "true". In some cases, it might be an overkill to really compute the exact metric with the ShowExactMetricValue. The metric computed on a downsampled image might already be accurate enough to draw conclusions about the rate of convergence for example. The downsampling rate must be given for each resolution, for each dimension.
example: (ExactMetricSampleGridSpacing 1 1 2 2 )
This example for a 2D registration of 2 resolutions sets the downsampling rate to 1 in the first resolution (so: use really all pixels), and to 2 in the second resolution. Default: 1 in each resolution and each dimension.

CheckNumberOfSamples: Whether the metric checks if at least a certain fraction (default 1/4) of the samples map inside the moving image. Can be given for each resolution or for all resolutions at once.
example: (CheckNumberOfSamples "false" "true" "false")
The default is true. In general it is wise to set this to true, since it detects if the registration is going really bad.

RequiredRatioOfValidSamples: Defines the fraction needed in CheckNumberOfSamples.
example: (RequiredRatioOfValidSamples 0.1)
The default is 0.25.

Definition at line 72 of file elxMetricBase.h.

Inheritance diagram for elastix::MetricBase< TElastix >:

Public Types
typedef itk::AdvancedImageToImageMetric< FixedImageType, MovingImageType >	AdvancedMetricType

typedef Superclass::ConfigurationPointer	ConfigurationPointer

typedef Superclass::ConfigurationType	ConfigurationType

typedef ITKBaseType::ParametersValueType	CoordinateRepresentationType

typedef Superclass::ElastixPointer	ElastixPointer

typedef Superclass::ElastixType	ElastixType

typedef ElastixType::FixedImageType	FixedImageType

typedef itk::PointSet< CoordinateRepresentationType, FixedImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, FixedImageDimension, FixedImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > >	FixedPointSetType

typedef FixedImageType::PointType	FixedPointType

typedef FixedPointType::ValueType	FixedPointValueType

typedef AdvancedMetricType::ImageSamplerType	ImageSamplerBaseType

typedef itk::SingleValuedCostFunction	ITKBaseType

typedef ITKBaseType::MeasureType	MeasureType

typedef AdvancedMetricType::MovingImageDerivativeScalesType	MovingImageDerivativeScalesType

typedef ElastixType::MovingImageType	MovingImageType

typedef itk::PointSet< CoordinateRepresentationType, MovingImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, MovingImageDimension, MovingImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > >	MovingPointSetType

typedef MovingImageType::PointType	MovingPointType

typedef MovingPointType::ValueType	MovingPointValueType

typedef Superclass::RegistrationPointer	RegistrationPointer

typedef Superclass::RegistrationType	RegistrationType

typedef MetricBase	Self

typedef BaseComponentSE< TElastix >	Superclass

Public Types inherited from elastix::BaseComponentSE< TElastix >
typedef Configuration::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef itk::WeakPointer< ElastixType >	ElastixPointer

typedef TElastix	ElastixType

typedef RegistrationType *	RegistrationPointer

typedef ElastixType::RegistrationBaseType	RegistrationType

typedef BaseComponentSE	Self

typedef BaseComponent	Superclass

Public Member Functions
void	AfterEachIterationBase (void) override

void	BeforeEachResolutionBase (void) override

virtual ImageSamplerBaseType *	GetAdvancedMetricImageSampler (void) const

virtual bool	GetAdvancedMetricUseImageSampler (void) const

virtual ITKBaseType *	GetAsITKBaseType (void)

virtual const ITKBaseType *	GetAsITKBaseType (void) const

virtual const char *	GetClassName () const

virtual MeasureType	GetCurrentExactMetricValue (void) const

virtual bool	GetShowExactMetricValue (void) const

	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)

	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)

virtual void	SelectNewSamples (void)

virtual void	SetAdvancedMetricImageSampler (ImageSamplerBaseType *sampler)

Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
ConfigurationType *	GetConfiguration (void) const

ElastixType *	GetElastix (void) const

RegistrationPointer	GetRegistration (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponentSE)

void	SetConfiguration (ConfigurationType *_arg)

void	SetElastix (ElastixType *_arg)

Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration (void)

virtual void	AfterEachIterationBase (void)

virtual void	AfterEachResolution (void)

virtual void	AfterEachResolutionBase (void)

virtual void	AfterRegistration (void)

virtual void	AfterRegistrationBase (void)

virtual int	BeforeAll (void)

virtual int	BeforeAllBase (void)

virtual void	BeforeEachResolution (void)

virtual void	BeforeEachResolutionBase (void)

virtual void	BeforeRegistration (void)

virtual void	BeforeRegistrationBase (void)

virtual const char *	elxGetClassName (void) const

const char *	GetComponentLabel (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponent)

	itkTypeMacroNoParent (BaseComponent)

void	SetComponentLabel (const char *label, unsigned int idx)

Protected Types
typedef ExactMetricImageSamplerType::Pointer	ExactMetricImageSamplerPointer

typedef itk::ImageGridSampler< FixedImageType >	ExactMetricImageSamplerType

typedef ExactMetricImageSamplerType::SampleGridSpacingType	ExactMetricSampleGridSpacingType

typedef ITKBaseType::ParametersType	ParametersType

Protected Member Functions
virtual MeasureType	GetExactValue (const ParametersType &parameters)

	MetricBase ()

	~MetricBase () override

Protected Member Functions inherited from elastix::BaseComponentSE< TElastix >
	BaseComponentSE ()=default

	~BaseComponentSE () override=default

Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default

virtual	~BaseComponent ()=default

Protected Attributes
MeasureType	m_CurrentExactMetricValue

unsigned int	m_ExactMetricEachXNumberOfIterations

ExactMetricSampleGridSpacingType	m_ExactMetricSampleGridSpacing

ExactMetricImageSamplerPointer	m_ExactMetricSampler

bool	m_ShowExactMetricValue

Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
ConfigurationPointer	m_Configuration {}

ElastixPointer	m_Elastix {}

RegistrationPointer	m_Registration {}

Private Member Functions
	MetricBase (const Self &)

void	operator= (const Self &)

Additional Inherited Members
Static Public Member Functions inherited from elastix::BaseComponent
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Member Typedef Documentation

◆ AdvancedMetricType

template<class TElastix >

typedef itk::AdvancedImageToImageMetric< FixedImageType, MovingImageType > elastix::MetricBase< TElastix >::AdvancedMetricType

Definition at line 102 of file elxMetricBase.h.

◆ ConfigurationPointer

template<class TElastix >

typedef Superclass::ConfigurationPointer elastix::MetricBase< TElastix >::ConfigurationPointer

Definition at line 87 of file elxMetricBase.h.

◆ ConfigurationType

template<class TElastix >

typedef Superclass::ConfigurationType elastix::MetricBase< TElastix >::ConfigurationType

Definition at line 86 of file elxMetricBase.h.

◆ CoordinateRepresentationType

template<class TElastix >

typedef ITKBaseType::ParametersValueType elastix::MetricBase< TElastix >::CoordinateRepresentationType

Typedefs for point sets.

Definition at line 111 of file elxMetricBase.h.

◆ ElastixPointer

template<class TElastix >

typedef Superclass::ElastixPointer elastix::MetricBase< TElastix >::ElastixPointer

Definition at line 85 of file elxMetricBase.h.

◆ ElastixType

template<class TElastix >

typedef Superclass::ElastixType elastix::MetricBase< TElastix >::ElastixType

Typedef's inherited from Elastix.

Definition at line 84 of file elxMetricBase.h.

◆ ExactMetricImageSamplerPointer

template<class TElastix >

typedef ExactMetricImageSamplerType::Pointer elastix::MetricBase< TElastix >::ExactMetricImageSamplerPointer

protected

Definition at line 195 of file elxMetricBase.h.

◆ ExactMetricImageSamplerType

template<class TElastix >

typedef itk::ImageGridSampler< FixedImageType > elastix::MetricBase< TElastix >::ExactMetricImageSamplerType

protected

The full sampler used by the GetExactValue method.

Definition at line 194 of file elxMetricBase.h.

◆ ExactMetricSampleGridSpacingType

template<class TElastix >

typedef ExactMetricImageSamplerType::SampleGridSpacingType elastix::MetricBase< TElastix >::ExactMetricSampleGridSpacingType

protected

Definition at line 196 of file elxMetricBase.h.

◆ FixedImageType

template<class TElastix >

typedef ElastixType::FixedImageType elastix::MetricBase< TElastix >::FixedImageType

Other typedef's.

Definition at line 92 of file elxMetricBase.h.

◆ FixedPointSetType

template<class TElastix >

typedef itk::PointSet< CoordinateRepresentationType, FixedImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, FixedImageDimension, FixedImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > > elastix::MetricBase< TElastix >::FixedPointSetType

Definition at line 118 of file elxMetricBase.h.

◆ FixedPointType

template<class TElastix >

typedef FixedImageType::PointType elastix::MetricBase< TElastix >::FixedPointType

Definition at line 93 of file elxMetricBase.h.

◆ FixedPointValueType

template<class TElastix >

typedef FixedPointType::ValueType elastix::MetricBase< TElastix >::FixedPointValueType

Definition at line 94 of file elxMetricBase.h.

◆ ImageSamplerBaseType

template<class TElastix >

typedef AdvancedMetricType::ImageSamplerType elastix::MetricBase< TElastix >::ImageSamplerBaseType

Typedefs for sampler support.

Definition at line 128 of file elxMetricBase.h.

◆ ITKBaseType

template<class TElastix >

typedef itk::SingleValuedCostFunction elastix::MetricBase< TElastix >::ITKBaseType

ITKBaseType.

Definition at line 100 of file elxMetricBase.h.

◆ MeasureType

template<class TElastix >

typedef ITKBaseType::MeasureType elastix::MetricBase< TElastix >::MeasureType

Return type of GetValue

Definition at line 131 of file elxMetricBase.h.

◆ MovingImageDerivativeScalesType

template<class TElastix >

typedef AdvancedMetricType::MovingImageDerivativeScalesType elastix::MetricBase< TElastix >::MovingImageDerivativeScalesType

Definition at line 103 of file elxMetricBase.h.

◆ MovingImageType

template<class TElastix >

typedef ElastixType::MovingImageType elastix::MetricBase< TElastix >::MovingImageType

Definition at line 95 of file elxMetricBase.h.

◆ MovingPointSetType

template<class TElastix >

typedef itk::PointSet< CoordinateRepresentationType, MovingImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, MovingImageDimension, MovingImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > > elastix::MetricBase< TElastix >::MovingPointSetType

Definition at line 125 of file elxMetricBase.h.

◆ MovingPointType

template<class TElastix >

typedef MovingImageType::PointType elastix::MetricBase< TElastix >::MovingPointType

Definition at line 96 of file elxMetricBase.h.

◆ MovingPointValueType

template<class TElastix >

typedef MovingPointType::ValueType elastix::MetricBase< TElastix >::MovingPointValueType

Definition at line 97 of file elxMetricBase.h.

◆ ParametersType

template<class TElastix >

typedef ITKBaseType::ParametersType elastix::MetricBase< TElastix >::ParametersType

protected

The parameters type.

Definition at line 191 of file elxMetricBase.h.

◆ RegistrationPointer

template<class TElastix >

typedef Superclass::RegistrationPointer elastix::MetricBase< TElastix >::RegistrationPointer

Definition at line 89 of file elxMetricBase.h.

◆ RegistrationType

template<class TElastix >

typedef Superclass::RegistrationType elastix::MetricBase< TElastix >::RegistrationType

Definition at line 88 of file elxMetricBase.h.

◆ Self

template<class TElastix >

typedef MetricBase elastix::MetricBase< TElastix >::Self

Standard ITK stuff.

Definition at line 77 of file elxMetricBase.h.

◆ Superclass

template<class TElastix >

typedef BaseComponentSE< TElastix > elastix::MetricBase< TElastix >::Superclass

Definition at line 78 of file elxMetricBase.h.

Constructor & Destructor Documentation

◆ MetricBase() [1/2]

template<class TElastix >

elastix::MetricBase< TElastix >::MetricBase ( )

protected

The constructor.

◆ ~MetricBase()

template<class TElastix >

elastix::MetricBase< TElastix >::~MetricBase ( )

inlineoverrideprotected

The destructor.

Definition at line 201 of file elxMetricBase.h.

◆ MetricBase() [2/2]

template<class TElastix >

elastix::MetricBase< TElastix >::MetricBase ( const Self & )

private

The private constructor.

Member Function Documentation

◆ AfterEachIterationBase()

template<class TElastix >

void elastix::MetricBase< TElastix >::AfterEachIterationBase ( void )

overridevirtual

Execute stuff after each iteration:

Optionally compute the exact metric value and plot it to screen.

Reimplemented from elastix::BaseComponent.

◆ BeforeEachResolutionBase()

template<class TElastix >

void elastix::MetricBase< TElastix >::BeforeEachResolutionBase ( void )

overridevirtual

Execute stuff before each resolution:

Check if the exact metric value should be computed (to monitor the progress of the registration).

Reimplemented from elastix::BaseComponent.

◆ GetAdvancedMetricImageSampler()

template<class TElastix >

virtual ImageSamplerBaseType * elastix::MetricBase< TElastix >::GetAdvancedMetricImageSampler ( void ) const

virtual

Methods to get the image sampler. The image sampler is only used when the metric is of type AdvancedMetricType, and has UseImageSampler set to true. In other cases, the function returns 0.

◆ GetAdvancedMetricUseImageSampler()

template<class TElastix >

virtual bool elastix::MetricBase< TElastix >::GetAdvancedMetricUseImageSampler ( void ) const

virtual

Returns whether the metric uses a sampler. When the metric is not of AdvancedMetricType, the function returns false immediately.

◆ GetAsITKBaseType() [1/2]

template<class TElastix >

virtual ITKBaseType * elastix::MetricBase< TElastix >::GetAsITKBaseType ( void )

inlinevirtual

Cast to ITKBaseType.

Definition at line 134 of file elxMetricBase.h.

◆ GetAsITKBaseType() [2/2]

template<class TElastix >

virtual const ITKBaseType * elastix::MetricBase< TElastix >::GetAsITKBaseType ( void ) const

inlinevirtual

Cast to ITKBaseType, to use in const functions.

Definition at line 141 of file elxMetricBase.h.

◆ GetClassName()

template<class TElastix >

virtual const char * elastix::MetricBase< TElastix >::GetClassName ( ) const

virtual

Run-time type information (and related methods).

◆ GetCurrentExactMetricValue()

template<class TElastix >

virtual MeasureType elastix::MetricBase< TElastix >::GetCurrentExactMetricValue ( void ) const

inlinevirtual

Get the last computed exact metric value

Definition at line 185 of file elxMetricBase.h.

◆ GetExactValue()

template<class TElastix >

virtual MeasureType elastix::MetricBase< TElastix >::GetExactValue ( const ParametersType & parameters )

protectedvirtual

Get the exact value. Mutual information computed over all points. It is meant in situations when you optimize using just a subset of pixels, but are interested in the exact value of the metric.

This method only works when the itkYourMetric inherits from the AdvancedMetricType. In other cases it returns 0. You may re-implement this method in the elxYourMetric, if you like.

◆ GetShowExactMetricValue()

template<class TElastix >

virtual bool elastix::MetricBase< TElastix >::GetShowExactMetricValue ( void ) const

inlinevirtual

Get if the exact metric value is computed

Definition at line 181 of file elxMetricBase.h.

◆ itkStaticConstMacro() [1/2]

template<class TElastix >

elastix::MetricBase< TElastix >::itkStaticConstMacro	(	FixedImageDimension	,
		unsigned int	,
		FixedImageType::ImageDimension
	)

Get the dimension of the fixed image.

◆ itkStaticConstMacro() [2/2]

template<class TElastix >

elastix::MetricBase< TElastix >::itkStaticConstMacro	(	MovingImageDimension	,
		unsigned int	,
		MovingImageType::ImageDimension
	)

Get the dimension of the moving image.

◆ operator=()

template<class TElastix >

void elastix::MetricBase< TElastix >::operator= ( const Self & )

private

The private copy constructor.

◆ SelectNewSamples()

template<class TElastix >

virtual void elastix::MetricBase< TElastix >::SelectNewSamples ( void )

virtual

Force the metric to base its computation on a new subset of image samples. Not every metric may have implemented this.

Reimplemented in elastix::CorrespondingPointsEuclideanDistanceMetric< TElastix >, elastix::MissingStructurePenalty< TElastix >, elastix::PolydataDummyPenalty< TElastix >, elastix::TransformRigidityPenalty< TElastix >, and elastix::StatisticalShapePenalty< TElastix >.

◆ SetAdvancedMetricImageSampler()

template<class TElastix >

virtual void elastix::MetricBase< TElastix >::SetAdvancedMetricImageSampler ( ImageSamplerBaseType * sampler )

virtual

Method to set the image sampler. The image sampler is only used when the metric is of type AdvancedMetricType, and has UseImageSampler set to true. In other cases, the function does nothing.

Field Documentation

◆ m_CurrentExactMetricValue

template<class TElastix >

MeasureType elastix::MetricBase< TElastix >::m_CurrentExactMetricValue

protected

Definition at line 218 of file elxMetricBase.h.

◆ m_ExactMetricEachXNumberOfIterations

template<class TElastix >

unsigned int elastix::MetricBase< TElastix >::m_ExactMetricEachXNumberOfIterations

protected

Definition at line 220 of file elxMetricBase.h.

◆ m_ExactMetricSampleGridSpacing

template<class TElastix >

ExactMetricSampleGridSpacingType elastix::MetricBase< TElastix >::m_ExactMetricSampleGridSpacing

protected

Definition at line 219 of file elxMetricBase.h.

◆ m_ExactMetricSampler

template<class TElastix >

ExactMetricImageSamplerPointer elastix::MetricBase< TElastix >::m_ExactMetricSampler

protected

Definition at line 217 of file elxMetricBase.h.

◆ m_ShowExactMetricValue

template<class TElastix >

bool elastix::MetricBase< TElastix >::m_ShowExactMetricValue

protected

Todo:: the method GetExactDerivative could as well be added here.

Definition at line 216 of file elxMetricBase.h.

Detailed Description

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Member Typedef Documentation

◆ AdvancedMetricType

◆ ConfigurationPointer

◆ ConfigurationType

◆ CoordinateRepresentationType

◆ ElastixPointer

◆ ElastixType

◆ ExactMetricImageSamplerPointer

◆ ExactMetricImageSamplerType

◆ ExactMetricSampleGridSpacingType

◆ FixedImageType

◆ FixedPointSetType

◆ FixedPointType

◆ FixedPointValueType

◆ ImageSamplerBaseType

◆ ITKBaseType

◆ MeasureType

◆ MovingImageDerivativeScalesType

◆ MovingImageType

◆ MovingPointSetType

◆ MovingPointType

◆ MovingPointValueType

◆ ParametersType

◆ RegistrationPointer

◆ RegistrationType

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ MetricBase() [1/2]

◆ ~MetricBase()

◆ MetricBase() [2/2]

Member Function Documentation

◆ AfterEachIterationBase()

◆ BeforeEachResolutionBase()

◆ GetAdvancedMetricImageSampler()

◆ GetAdvancedMetricUseImageSampler()

◆ GetAsITKBaseType() [1/2]

◆ GetAsITKBaseType() [2/2]

◆ GetClassName()

◆ GetCurrentExactMetricValue()

◆ GetExactValue()

◆ GetShowExactMetricValue()

◆ itkStaticConstMacro() [1/2]

◆ itkStaticConstMacro() [2/2]

◆ operator=()

◆ SelectNewSamples()

◆ SetAdvancedMetricImageSampler()

Field Documentation

◆ m_CurrentExactMetricValue

◆ m_ExactMetricEachXNumberOfIterations

◆ m_ExactMetricSampleGridSpacing

◆ m_ExactMetricSampler

◆ m_ShowExactMetricValue