#include <itkMutualInformationImageToImageMetric.h>

Inheritance diagram for itk::MutualInformationImageToImageMetric< TFixedImage, TMovingImage >:

Collaboration diagram for itk::MutualInformationImageToImageMetric< TFixedImage, TMovingImage >:

Detailed Description

template<typename TFixedImage, typename TMovingImage>
class itk::MutualInformationImageToImageMetric< TFixedImage, TMovingImage >

Computes the mutual information between two images to be registered.

MutualInformationImageToImageMetric computes the mutual information between a fixed and moving image to be registered.

This class is templated over the FixedImage type and the MovingImage type.

The fixed and moving images are set via methods SetFixedImage() and SetMovingImage(). This metric makes use of user specified Transform and Interpolator. The Transform is used to map points from the fixed image to the moving image domain. The Interpolator is used to evaluate the image intensity at user specified geometric points in the moving image. The Transform and Interpolator are set via methods SetTransform() and SetInterpolator().

Warning: This metric assumes that the moving image has already been connected to the interpolator outside of this class.

The method GetValue() computes of the mutual information while method GetValueAndDerivative() computes both the mutual information and its derivatives with respect to the transform parameters.

The calculations are based on the method of Viola and Wells where the probability density distributions are estimated using Parzen windows.

By default a Gaussian kernel is used in the density estimation. Other option include Cauchy and spline-based. A user can specify the kernel passing in a pointer a KernelFunctionBase using the SetKernelFunction() method.

Mutual information is estimated using two sample sets: one to calculate the singular and joint pdf's and one to calculate the entropy integral. By default 50 samples points are used in each set. Other values can be set via the SetNumberOfSpatialSamples() method.

Quality of the density estimate depends on the choice of the kernel's standard deviation. Optimal choice will depend on the images. It is can be shown that around the optimal variance, the mutual information estimate is relatively insensitive to small changes of the standard deviation. In our experiments, we have found that a standard deviation of 0.4 works well for images normalized to have a mean of zero and standard deviation of 1.0. The variance can be set via methods SetFixedImageStandardDeviation() and SetMovingImageStandardDeviation().

Implementaton of this class is based on: Viola, P. and Wells III, W. (1997). "Alignment by Maximization of Mutual Information" International Journal of Computer Vision, 24(2):137-154

See Also: KernelFunctionBase; GaussianKernelFunction

Wiki Examples:

Examples:: Examples/RegistrationITKv3/ImageRegistration2.cxx, Examples/RegistrationITKv4/ImageRegistration2.cxx, SphinxExamples/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Code.cxx, WikiExamples/Registration/MutualInformation.cxx, and WikiExamples/Registration/MutualInformationAffine.cxx.

Definition at line 94 of file itkMutualInformationImageToImageMetric.h.

Classes
class	SpatialSample

Public Types
using	ConstPointer = SmartPointer< const Self >

using	DerivativeType = typename Superclass::DerivativeType

using	FixedImageConstPointer = typename Superclass::FixedImageConstPointer

using	FixedImageIndexType = typename FixedImageType::IndexType

using	FixedImageIndexValueType = typename FixedImageIndexType::IndexValueType

using	FixedImagePointType = typename TransformType::InputPointType

using	FixedImageType = typename Superclass::FixedImageType

using	InterpolatorType = typename Superclass::InterpolatorType

using	KernelFunctionType = KernelFunctionBase< double >

using	MeasureType = typename Superclass::MeasureType

using	MovingImageCosntPointer = typename Superclass::MovingImageConstPointer

using	MovingImageIndexType = typename MovingImageType::IndexType

using	MovingImagePointType = typename TransformType::OutputPointType

using	MovingImageType = typename Superclass::MovingImageType

using	ParametersType = typename Superclass::ParametersType

using	Pointer = SmartPointer< Self >

using	Self = MutualInformationImageToImageMetric

using	Superclass = ImageToImageMetric< TFixedImage, TMovingImage >

using	TransformJacobianType = typename Superclass::TransformJacobianType

using	TransformPointer = typename Superclass::TransformPointer

using	TransformType = typename Superclass::TransformType

Public Types inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
using	ConstPointer = SmartPointer< const Self >

using	CoordinateRepresentationType = typename Superclass::ParametersValueType

using	DerivativeType = typename Superclass::DerivativeType

using	FixedImageConstPointer = typename FixedImageType::ConstPointer

using	FixedImageIndexContainer = std::vector< FixedImageIndexType >

using	FixedImageIndexType = typename FixedImageType::IndexType

using	FixedImageIndexValueType = typename FixedImageIndexType::IndexValueType

using	FixedImageMaskConstPointer = typename FixedImageMaskType::ConstPointer

using	FixedImageMaskPointer = typename FixedImageMaskType::Pointer

using	FixedImageMaskType = SpatialObject< Self::FixedImageDimension >

using	FixedImagePixelType = typename TFixedImage::PixelType

using	FixedImagePointType = typename TransformType::InputPointType

using	FixedImageRegionType = typename FixedImageType::RegionType

using	FixedImageType = TFixedImage

using	GradientImageFilterPointer = typename GradientImageFilterType::Pointer

using	GradientImageFilterType = GradientRecursiveGaussianImageFilter< MovingImageType, GradientImageType >

using	GradientImagePointer = SmartPointer< GradientImageType >

using	GradientImageType = Image< GradientPixelType, Self::MovingImageDimension >

using	GradientPixelType = CovariantVector< RealType, Self::MovingImageDimension >

using	InputPointType = typename TransformType::InputPointType

using	InterpolatorPointer = typename InterpolatorType::Pointer

using	InterpolatorType = InterpolateImageFunction< MovingImageType, CoordinateRepresentationType >

using	MeasureType = typename Superclass::MeasureType

using	MovingImageConstPointer = typename MovingImageType::ConstPointer

using	MovingImageIndexType = typename MovingImageType::IndexType

using	MovingImageMaskConstPointer = typename MovingImageMaskType::ConstPointer

using	MovingImageMaskPointer = typename MovingImageMaskType::Pointer

using	MovingImageMaskType = SpatialObject< Self::MovingImageDimension >

using	MovingImagePixelType = typename TMovingImage::PixelType

using	MovingImagePointType = typename TransformType::OutputPointType

using	MovingImageType = TMovingImage

using	MultiThreaderType = MultiThreaderBase

using	OutputPointType = typename TransformType::OutputPointType

using	ParametersType = typename Superclass::ParametersType

using	Pointer = SmartPointer< Self >

using	RealType = typename NumericTraits< MovingImagePixelType >::RealType

using	Self = ImageToImageMetric

using	Superclass = SingleValuedCostFunction

using	TransformJacobianType = typename TransformType::JacobianType

using	TransformParametersType = typename TransformType::ParametersType

using	TransformPointer = typename TransformType::Pointer

using	TransformType = Transform< CoordinateRepresentationType, Self::MovingImageDimension, Self::FixedImageDimension >

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

using	DerivativeType = Array< ParametersValueType >

using	MeasureType = double

using	ParametersType = Superclass::ParametersType

using	ParametersValueType = Superclass::ParametersValueType

using	Pointer = SmartPointer< Self >

using	Self = SingleValuedCostFunction

using	Superclass = CostFunction

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

using	ParametersType = OptimizerParameters< TInternalComputationValueType >

using	ParametersValueType = TInternalComputationValueType

using	Pointer = SmartPointer< Self >

using	Self = CostFunctionTemplate

using	Superclass = Object

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

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

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

using	Pointer = SmartPointer< Self >

using	Self = LightObject

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

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

virtual const char *	GetNameOfClass () const

virtual const unsigned int &	GetNumberOfSpatialSamples () const

MeasureType	GetValue (const ParametersType &parameters) const override

void	GetValueAndDerivative (const ParametersType &parameters, MeasureType &Value, DerivativeType &Derivative) const override

void	SetNumberOfSpatialSamples (unsigned int num)


virtual void	SetMovingImageStandardDeviation (double _arg)

virtual const double &	GetMovingImageStandardDeviation () const


virtual void	SetFixedImageStandardDeviation (double _arg)

virtual double	GetFixedImageStandardDeviation () const


virtual void	SetKernelFunction (KernelFunctionType *_arg)

virtual KernelFunctionType *	GetModifiableKernelFunction ()

virtual const KernelFunctionType *	GetKernelFunction () const

Public Member Functions inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
virtual void	ComputeGradient ()

virtual const FixedImageRegionType &	GetFixedImageRegion () const

virtual const FixedImagePixelType &	GetFixedImageSamplesIntensityThreshold () const

virtual const GradientImageType *	GetGradientImage () const

virtual const InterpolatorType *	GetInterpolator () const

virtual GradientImageType *	GetModifiableGradientImage ()

virtual InterpolatorType *	GetModifiableInterpolator ()

virtual TransformType *	GetModifiableTransform ()

SizeValueType	GetNumberOfMovingImageSamples ()

unsigned int	GetNumberOfParameters () const override

virtual const SizeValueType &	GetNumberOfPixelsCounted () const

SizeValueType	GetNumberOfSpatialSamples ()

virtual const TransformType *	GetTransform () const

virtual const bool &	GetUseAllPixels () const

virtual const bool &	GetUseFixedImageIndexes () const

virtual const bool &	GetUseFixedImageSamplesIntensityThreshold () const

virtual const bool &	GetUseSequentialSampling () const

virtual void	Initialize ()

virtual void	MultiThreadingInitialize ()

void	SetFixedImageIndexes (const FixedImageIndexContainer &indexes)

virtual void	SetFixedImageRegion (const FixedImageRegionType reg)

void	SetFixedImageSamplesIntensityThreshold (const FixedImagePixelType &thresh)

virtual void	SetInterpolator (InterpolatorType *_arg)

void	SetNumberOfSpatialSamples (SizeValueType num)

virtual void	SetTransform (TransformType *_arg)

void	SetTransformParameters (const ParametersType &parameters) const

void	SetUseAllPixels (bool useAllPixels)

void	SetUseFixedImageIndexes (bool useIndex)

void	SetUseFixedImageSamplesIntensityThreshold (bool useThresh)

void	SetUseSequentialSampling (bool sequentialSampling)

void	UseAllPixelsOff ()

void	UseAllPixelsOn ()

virtual void	SetFixedImage (const FixedImageType *_arg)

virtual const FixedImageType *	GetFixedImage () const

virtual void	SetMovingImage (const MovingImageType *_arg)

virtual const MovingImageType *	GetMovingImage () const

virtual void	SetMovingImageMask (MovingImageMaskType *_arg)

virtual void	SetMovingImageMask (const MovingImageMaskType *_arg)

virtual const MovingImageMaskType *	GetMovingImageMask () const

virtual void	SetFixedImageMask (FixedImageMaskType *_arg)

virtual void	SetFixedImageMask (const FixedImageMaskType *_arg)

virtual const FixedImageMaskType *	GetFixedImageMask () const

void	SetNumberOfWorkUnits (ThreadIdType numberOfThreads)

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

virtual void	SetComputeGradient (bool _arg)

virtual const bool &	GetComputeGradient () const

virtual void	ComputeGradientOn ()

virtual void	ComputeGradientOff ()

virtual void	SetNumberOfFixedImageSamples (SizeValueType numSamples)

virtual const SizeValueType &	GetNumberOfFixedImageSamples () const

void	ReinitializeSeed ()

void	ReinitializeSeed (int seed)

virtual void	SetUseCachingOfBSplineWeights (bool _arg)

virtual const bool &	GetUseCachingOfBSplineWeights () const

virtual void	UseCachingOfBSplineWeightsOn ()

virtual void	UseCachingOfBSplineWeightsOff ()

virtual MultiThreaderType *	GetModifiableThreader ()

virtual const MultiThreaderType *	GetThreader () const

const TransformPointer *	GetThreaderTransform ()

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

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 constexpr unsigned int	MovingImageDimension = MovingImageType::ImageDimension

Static Public Attributes inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
static constexpr unsigned int	FixedImageDimension = TFixedImage::ImageDimension

static constexpr unsigned int	MovingImageDimension = TMovingImage::ImageDimension

Protected Member Functions
	MutualInformationImageToImageMetric ()

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

	~MutualInformationImageToImageMetric () override=default

Protected Member Functions inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
virtual void	ComputeImageDerivatives (const MovingImagePointType &mappedPoint, ImageDerivativesType &gradient, ThreadIdType threadId) const

void	GetValueAndDerivativeMultiThreadedInitiate () const

void	GetValueAndDerivativeMultiThreadedPostProcessInitiate () const

virtual void	GetValueAndDerivativeThread (ThreadIdType threadId) const

virtual void	GetValueAndDerivativeThreadPostProcess (ThreadIdType, bool) const

virtual void	GetValueAndDerivativeThreadPreProcess (ThreadIdType, bool) const

virtual bool	GetValueAndDerivativeThreadProcessSample (ThreadIdType, SizeValueType, const MovingImagePointType &, double, const ImageDerivativesType &) const

void	GetValueMultiThreadedInitiate () const

void	GetValueMultiThreadedPostProcessInitiate () const

virtual void	GetValueThread (ThreadIdType threadId) const

virtual void	GetValueThreadPostProcess (ThreadIdType, bool) const

virtual void	GetValueThreadPreProcess (ThreadIdType, bool) const

virtual bool	GetValueThreadProcessSample (ThreadIdType, SizeValueType, const MovingImagePointType &, double) const

	ImageToImageMetric ()

virtual void	PreComputeTransformValues ()

virtual void	SampleFixedImageIndexes (FixedImageSampleContainer &samples) const

virtual void	SampleFixedImageRegion (FixedImageSampleContainer &samples) const

virtual void	SampleFullFixedImageRegion (FixedImageSampleContainer &samples) const

virtual void	SynchronizeTransforms () const

virtual void	TransformPoint (unsigned int sampleNumber, MovingImagePointType &mappedPoint, bool &sampleWithinSupportRegion, double &movingImageValue, ThreadIdType threadId) const

virtual void	TransformPointWithDerivatives (unsigned int sampleNumber, MovingImagePointType &mappedPoint, bool &sampleWithinSupportRegion, double &movingImageValue, ImageDerivativesType &gradient, ThreadIdType threadId) const

	~ImageToImageMetric () override

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

	~SingleValuedCostFunction () override

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

	~CostFunctionTemplate () override=default

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

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

virtual void	SetTimeStamp (const TimeStamp &time)

	~Object () override

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 Types
using	CoordinateRepresentationType = typename Superclass::CoordinateRepresentationType

using	DerivativeFunctionType = CentralDifferenceImageFunction< MovingImageType, CoordinateRepresentationType >

using	SpatialSampleContainer = std::vector< SpatialSample >

Private Member Functions
void	CalculateDerivatives (const FixedImagePointType &, DerivativeType &, TransformJacobianType &) const

virtual void	SampleFixedImageDomain (SpatialSampleContainer &samples) const

Private Attributes
DerivativeFunctionType::Pointer	m_DerivativeCalculator

double	m_FixedImageStandardDeviation

KernelFunctionType::Pointer	m_KernelFunction

double	m_MinProbability

double	m_MovingImageStandardDeviation

unsigned int	m_NumberOfSpatialSamples

SpatialSampleContainer	m_SampleA

SpatialSampleContainer	m_SampleB

Additional Inherited Members
Protected Types inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
using	BooleanArrayType = std::vector< bool >

using	BSplineInterpolatorType = BSplineInterpolateImageFunction< MovingImageType, CoordinateRepresentationType >

using	BSplineParametersOffsetType = FixedArray< SizeValueType, FixedImageType::ImageDimension >

using	BSplineTransformIndexArrayType = typename BSplineTransformType::ParameterIndexArrayType

using	BSplineTransformIndicesArrayType = Array2D< IndexValueType >

using	BSplineTransformType = BSplineBaseTransform< CoordinateRepresentationType, FixedImageType::ImageDimension, Self::DeformationSplineOrder >

using	BSplineTransformWeightsArrayType = Array2D< WeightsValueType >

using	BSplineTransformWeightsType = typename BSplineTransformType::WeightsType

using	DerivativeFunctionType = CentralDifferenceImageFunction< MovingImageType, CoordinateRepresentationType >

using	FixedImageSampleContainer = std::vector< FixedImageSamplePoint >

using	ImageDerivativesType = CovariantVector< double, Self::MovingImageDimension >

using	IndexValueType = typename BSplineTransformIndexArrayType::ValueType

using	MovingImagePointArrayType = std::vector< MovingImagePointType >

using	WeightsValueType = typename BSplineTransformWeightsType::ValueType

Static Protected Member Functions inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	GetValueAndDerivativeMultiThreaded (void *arg)

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	GetValueAndDerivativeMultiThreadedPostProcess (void *arg)

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	GetValueMultiThreaded (void *arg)

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	GetValueMultiThreadedPostProcess (void *arg)

Protected Attributes inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
BSplineInterpolatorType::Pointer	m_BSplineInterpolator

BSplineParametersOffsetType	m_BSplineParametersOffset

MovingImagePointArrayType	m_BSplinePreTransformPointsArray

BSplineTransformType::Pointer	m_BSplineTransform

BSplineTransformIndexArrayType	m_BSplineTransformIndices

BSplineTransformIndicesArrayType	m_BSplineTransformIndicesArray

BSplineTransformWeightsType	m_BSplineTransformWeights

BSplineTransformWeightsArrayType	m_BSplineTransformWeightsArray

bool	m_ComputeGradient {true}

ConstantPointerWrapper *	m_ConstSelfWrapper

DerivativeFunctionType::Pointer	m_DerivativeCalculator

FixedImageConstPointer	m_FixedImage

FixedImageIndexContainer	m_FixedImageIndexes

FixedImageMaskConstPointer	m_FixedImageMask

FixedImageSampleContainer	m_FixedImageSamples

FixedImagePixelType	m_FixedImageSamplesIntensityThreshold

GradientImagePointer	m_GradientImage

InterpolatorPointer	m_Interpolator

bool	m_InterpolatorIsBSpline {false}

MovingImageConstPointer	m_MovingImage

MovingImageMaskConstPointer	m_MovingImageMask

SizeValueType	m_NumberOfFixedImageSamples {50000}

SizeValueType	m_NumberOfParameters {0}

SizeValueType	m_NumberOfPixelsCounted {0}

ThreadIdType	m_NumberOfWorkUnits {1}

SizeValueType	m_NumBSplineWeights {0}

int	m_RandomSeed

bool	m_ReseedIterator {false}

MultiThreaderType::Pointer	m_Threader

BSplineTransformIndexArrayType *	m_ThreaderBSplineTransformIndices

BSplineTransformWeightsType *	m_ThreaderBSplineTransformWeights

unsigned int *	m_ThreaderNumberOfMovingImageSamples {nullptr}

TransformPointer *	m_ThreaderTransform

TransformPointer	m_Transform

bool	m_TransformIsBSpline {false}

bool	m_UseAllPixels {false}

bool	m_UseCachingOfBSplineWeights {true}

bool	m_UseFixedImageIndexes {false}

bool	m_UseFixedImageSamplesIntensityThreshold {false}

bool	m_UseSequentialSampling {false}

BooleanArrayType	m_WithinBSplineSupportRegionArray

bool	m_WithinThreadPostProcess {false}

bool	m_WithinThreadPreProcess {false}

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

Static Protected Attributes inherited from itk::ImageToImageMetric< TFixedImage, TMovingImage >
static constexpr unsigned int	DeformationSplineOrder = 3