#include <elxMetricBase.h>

Detailed Description

template<typename 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.

UseMultiThreadingForMetrics: Flag that can set to "true" or "false". If "true" the metric may use multi-threading (at least if multi-threading is implemented for the selected metric). If "false", it will run single-threaded. This flag will not affect the output of the metric.
example: (UseMultiThreadingForMetrics "false")
Default is "true".

Definition at line 77 of file elxMetricBase.h.

Inheritance diagram for elastix::MetricBase< TElastix >:

[legend]

Public Types
using	AdvancedMetricType = itk::AdvancedImageToImageMetric<FixedImageType, MovingImageType>
using	CoordinateRepresentationType = typename ITKBaseType::ParametersValueType
using	ElastixType
using	FixedImageType = typename ElastixType::FixedImageType
using	FixedPointSetType
using	FixedPointType = typename FixedImageType::PointType
using	FixedPointValueType = typename FixedPointType::ValueType
using	ImageSamplerBaseType = typename AdvancedMetricType::ImageSamplerType
using	ITKBaseType = itk::SingleValuedCostFunction
using	MeasureType = typename ITKBaseType::MeasureType
using	MovingImageDerivativeScalesType = typename AdvancedMetricType::MovingImageDerivativeScalesType
using	MovingImageType = typename ElastixType::MovingImageType
using	MovingPointSetType
using	MovingPointType = typename MovingImageType::PointType
using	MovingPointValueType = typename MovingPointType::ValueType
using	RegistrationType
using	Self = MetricBase
using	Superclass = BaseComponentSE<TElastix>
Public Types inherited from elastix::BaseComponentSE< TElastix >
using	ElastixType = TElastix
using	RegistrationType = typename ElastixType::RegistrationBaseType
using	Self = BaseComponentSE
using	Superclass = BaseComponent

Public Member Functions
void	AfterEachIterationBase () override
void	BeforeEachResolutionBase () override
void	BeforeRegistrationBase () override
virtual ImageSamplerBaseType *	GetAdvancedMetricImageSampler () const
virtual bool	GetAdvancedMetricUseImageSampler () const
ITKBaseType *	GetAsITKBaseType ()
const ITKBaseType *	GetAsITKBaseType () const
virtual MeasureType	GetCurrentExactMetricValue () const
virtual bool	GetShowExactMetricValue () const
	ITK_DISALLOW_COPY_AND_MOVE (MetricBase)
	itkOverrideGetNameOfClassMacro (MetricBase)
	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
virtual void	SelectNewSamples ()
virtual void	SetAdvancedMetricImageSampler (ImageSamplerBaseType *sampler)
Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
void	AddTargetCellToIterationInfo (const char *const name)
const Configuration *	GetConfiguration () const
ElastixType *	GetElastix () const
auto &	GetIterationInfoAt (const char *const name)
itk::Statistics::MersenneTwisterRandomVariateGenerator &	GetRandomVariateGenerator ()
RegistrationType *	GetRegistration () const
	ITK_DISALLOW_COPY_AND_MOVE (BaseComponentSE)
void	RemoveTargetCellFromIterationInfo (const char *const name)
void	SetConfiguration (const Configuration *_arg)
void	SetElastix (ElastixType *_arg)
Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration ()
virtual void	AfterEachResolution ()
virtual void	AfterEachResolutionBase ()
virtual void	AfterRegistration ()
virtual void	AfterRegistrationBase ()
virtual int	BeforeAll ()
virtual int	BeforeAllBase ()
virtual void	BeforeEachResolution ()
virtual void	BeforeRegistration ()
virtual const char *	elxGetClassName () const
const char *	GetComponentLabel () const
	ITK_DISALLOW_COPY_AND_MOVE (BaseComponent)
	itkVirtualGetNameOfClassMacro (BaseComponent)
void	SetComponentLabel (const char *label, unsigned int idx)

Protected Types
using	ExactMetricImageSamplerPointer = typename ExactMetricImageSamplerType::Pointer
using	ExactMetricImageSamplerType = itk::ImageGridSampler<FixedImageType>
using	ExactMetricSampleGridSpacingType = typename ExactMetricImageSamplerType::SampleGridSpacingType
using	ParametersType = typename ITKBaseType::ParametersType

Protected Member Functions
virtual MeasureType	GetExactValue (const ParametersType &parameters)
	MetricBase ()=default
	~MetricBase () override=default
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 { 0.0 }
unsigned int	m_ExactMetricEachXNumberOfIterations { 1 }
ExactMetricSampleGridSpacingType	m_ExactMetricSampleGridSpacing
ExactMetricImageSamplerPointer	m_ExactMetricSampler { nullptr }
bool	m_ShowExactMetricValue { false }
Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
Configuration::ConstPointer	m_Configuration {}
itk::WeakPointer< TElastix >	m_Elastix {}
RegistrationType *	m_Registration {}

Private Member Functions
	elxDeclarePureVirtualGetSelfMacro (ITKBaseType)

Additional Inherited Members
Static Public Member Functions inherited from elastix::BaseComponent
template<typename TBaseComponent>
static auto	AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())
static void	InitializeElastixExecutable ()
static bool	IsElastixLibrary ()

Member Typedef Documentation

◆ AdvancedMetricType

template<typename TElastix>

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

Definition at line 103 of file elxMetricBase.h.

◆ CoordinateRepresentationType

template<typename TElastix>

using elastix::MetricBase< TElastix >::CoordinateRepresentationType = typename ITKBaseType::ParametersValueType

Typedefs for point sets.

Definition at line 112 of file elxMetricBase.h.

◆ ElastixType

template<typename TElastix>

using elastix::BaseComponentSE< TElastix >::ElastixType

Elastix typedef.

Definition at line 58 of file elxBaseComponentSE.h.

◆ ExactMetricImageSamplerPointer

template<typename TElastix>

using elastix::MetricBase< TElastix >::ExactMetricImageSamplerPointer = typename ExactMetricImageSamplerType::Pointer

protected

Definition at line 214 of file elxMetricBase.h.

◆ ExactMetricImageSamplerType

template<typename TElastix>

using elastix::MetricBase< TElastix >::ExactMetricImageSamplerType = itk::ImageGridSampler<FixedImageType>

protected

The full sampler used by the GetExactValue method.

Definition at line 213 of file elxMetricBase.h.

◆ ExactMetricSampleGridSpacingType

template<typename TElastix>

using elastix::MetricBase< TElastix >::ExactMetricSampleGridSpacingType = typename ExactMetricImageSamplerType::SampleGridSpacingType

protected

Definition at line 215 of file elxMetricBase.h.

◆ FixedImageType

template<typename TElastix>

using elastix::MetricBase< TElastix >::FixedImageType = typename ElastixType::FixedImageType

Other typedef's.

Definition at line 94 of file elxMetricBase.h.

◆ FixedPointSetType

template<typename TElastix>

using elastix::MetricBase< TElastix >::FixedPointSetType

Initial value:

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

Definition at line 113 of file elxMetricBase.h.

◆ FixedPointType

template<typename TElastix>

using elastix::MetricBase< TElastix >::FixedPointType = typename FixedImageType::PointType

Definition at line 95 of file elxMetricBase.h.

◆ FixedPointValueType

template<typename TElastix>

using elastix::MetricBase< TElastix >::FixedPointValueType = typename FixedPointType::ValueType

Definition at line 96 of file elxMetricBase.h.

◆ ImageSamplerBaseType

template<typename TElastix>

using elastix::MetricBase< TElastix >::ImageSamplerBaseType = typename AdvancedMetricType::ImageSamplerType

Typedefs for sampler support.

Definition at line 131 of file elxMetricBase.h.

◆ ITKBaseType

template<typename TElastix>

using elastix::MetricBase< TElastix >::ITKBaseType = itk::SingleValuedCostFunction

ITKBaseType.

Definition at line 102 of file elxMetricBase.h.

◆ MeasureType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MeasureType = typename ITKBaseType::MeasureType

Return type of GetValue

Definition at line 134 of file elxMetricBase.h.

◆ MovingImageDerivativeScalesType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MovingImageDerivativeScalesType = typename AdvancedMetricType::MovingImageDerivativeScalesType

Definition at line 104 of file elxMetricBase.h.

◆ MovingImageType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MovingImageType = typename ElastixType::MovingImageType

Definition at line 97 of file elxMetricBase.h.

◆ MovingPointSetType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MovingPointSetType

Initial value:

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

Definition at line 121 of file elxMetricBase.h.

◆ MovingPointType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MovingPointType = typename MovingImageType::PointType

Definition at line 98 of file elxMetricBase.h.

◆ MovingPointValueType

template<typename TElastix>

using elastix::MetricBase< TElastix >::MovingPointValueType = typename MovingPointType::ValueType

Definition at line 99 of file elxMetricBase.h.

◆ ParametersType

template<typename TElastix>

using elastix::MetricBase< TElastix >::ParametersType = typename ITKBaseType::ParametersType

protected

The parameters type.

Definition at line 210 of file elxMetricBase.h.

◆ RegistrationType

template<typename TElastix>

using elastix::BaseComponentSE< TElastix >::RegistrationType

RegistrationType; NB: this is the elx::RegistrationBase not an itk::Object or something like that.

Definition at line 63 of file elxBaseComponentSE.h.

◆ Self

template<typename TElastix>

using elastix::MetricBase< TElastix >::Self = MetricBase

Standard ITK stuff.

Definition at line 83 of file elxMetricBase.h.

◆ Superclass

template<typename TElastix>

using elastix::MetricBase< TElastix >::Superclass = BaseComponentSE<TElastix>

Definition at line 84 of file elxMetricBase.h.

Constructor & Destructor Documentation

◆ MetricBase()

template<typename TElastix>

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

protecteddefault

The constructor.

◆ ~MetricBase()

template<typename TElastix>

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

overrideprotecteddefault

The destructor.

Member Function Documentation

◆ AfterEachIterationBase()

template<typename TElastix>

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

overridevirtual

Execute stuff after each iteration:

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

Reimplemented from elastix::BaseComponent.

◆ BeforeEachResolutionBase()

template<typename TElastix>

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

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.

◆ BeforeRegistrationBase()

template<typename TElastix>

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

overridevirtual

Reimplemented from elastix::BaseComponent.

◆ elxDeclarePureVirtualGetSelfMacro()

template<typename TElastix>

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

private

◆ GetAdvancedMetricImageSampler()

template<typename TElastix>

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

virtual bool elastix::MetricBase< TElastix >::GetAdvancedMetricUseImageSampler ( ) 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<typename TElastix>

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

inline

Retrieves this object as ITKBaseType.

Definition at line 138 of file elxMetricBase.h.

◆ GetAsITKBaseType() [2/2]

template<typename TElastix>

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

inline

Retrieves this object as ITKBaseType, to use in const functions.

Definition at line 146 of file elxMetricBase.h.

◆ GetCurrentExactMetricValue()

template<typename TElastix>

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

inlinevirtual

Get the last computed exact metric value

Definition at line 203 of file elxMetricBase.h.

◆ GetExactValue()

template<typename 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<typename TElastix>

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

inlinevirtual

Get if the exact metric value is computed

Definition at line 196 of file elxMetricBase.h.

◆ ITK_DISALLOW_COPY_AND_MOVE()

template<typename TElastix>

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

◆ itkOverrideGetNameOfClassMacro()

template<typename TElastix>

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

Run-time type information (and related methods).

◆ itkStaticConstMacro() [1/2]

template<typename TElastix>

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

Get the dimension of the fixed image.

◆ itkStaticConstMacro() [2/2]

template<typename TElastix>

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

Get the dimension of the moving image.

◆ SelectNewSamples()

template<typename TElastix>

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

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::StatisticalShapePenalty< TElastix >, and elastix::TransformRigidityPenalty< TElastix >.

◆ SetAdvancedMetricImageSampler()

template<typename 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.

Member Data Documentation

◆ m_CurrentExactMetricValue

template<typename TElastix>

MeasureType elastix::MetricBase< TElastix >::m_CurrentExactMetricValue { 0.0 }

protected

Definition at line 238 of file elxMetricBase.h.

◆ m_ExactMetricEachXNumberOfIterations

template<typename TElastix>

unsigned int elastix::MetricBase< TElastix >::m_ExactMetricEachXNumberOfIterations { 1 }

protected

Definition at line 241 of file elxMetricBase.h.

◆ m_ExactMetricSampleGridSpacing

template<typename TElastix>

ExactMetricSampleGridSpacingType elastix::MetricBase< TElastix >::m_ExactMetricSampleGridSpacing

protected

Initial value:

{ itk::MakeFilled<ExactMetricSampleGridSpacingType>(

1) }

Definition at line 239 of file elxMetricBase.h.

◆ m_ExactMetricSampler

template<typename TElastix>

ExactMetricImageSamplerPointer elastix::MetricBase< TElastix >::m_ExactMetricSampler { nullptr }

protected

Definition at line 237 of file elxMetricBase.h.

◆ m_ShowExactMetricValue

template<typename TElastix>

bool elastix::MetricBase< TElastix >::m_ShowExactMetricValue { false }

protected

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

Definition at line 236 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

◆ CoordinateRepresentationType

◆ ElastixType

◆ ExactMetricImageSamplerPointer

◆ ExactMetricImageSamplerType

◆ ExactMetricSampleGridSpacingType

◆ FixedImageType

◆ FixedPointSetType

◆ FixedPointType

◆ FixedPointValueType

◆ ImageSamplerBaseType

◆ ITKBaseType

◆ MeasureType

◆ MovingImageDerivativeScalesType

◆ MovingImageType

◆ MovingPointSetType

◆ MovingPointType

◆ MovingPointValueType

◆ ParametersType

◆ RegistrationType

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ MetricBase()

◆ ~MetricBase()

Member Function Documentation

◆ AfterEachIterationBase()

◆ BeforeEachResolutionBase()

◆ BeforeRegistrationBase()

◆ elxDeclarePureVirtualGetSelfMacro()

◆ GetAdvancedMetricImageSampler()

◆ GetAdvancedMetricUseImageSampler()

◆ GetAsITKBaseType() [1/2]

◆ GetAsITKBaseType() [2/2]

◆ GetCurrentExactMetricValue()

◆ GetExactValue()

◆ GetShowExactMetricValue()

◆ ITK_DISALLOW_COPY_AND_MOVE()

◆ itkOverrideGetNameOfClassMacro()

◆ itkStaticConstMacro() [1/2]

◆ itkStaticConstMacro() [2/2]

◆ SelectNewSamples()

◆ SetAdvancedMetricImageSampler()

Member Data Documentation

◆ m_CurrentExactMetricValue

◆ m_ExactMetricEachXNumberOfIterations

◆ m_ExactMetricSampleGridSpacing

◆ m_ExactMetricSampler

◆ m_ShowExactMetricValue