elastix::ExternalTransform< TElastix > Class Template Reference

#include <elxExternalTransform.h>

Detailed Description

template<typename TElastix>
class elastix::ExternalTransform< TElastix >

An external transform.

This transform warps an external transform. This transform is NOT meant to be used for optimization. Just use it as an initial transform, or with transformix.

The parameters used in this class are:

Parameters

Transform: Select this transform as follows:
(Transform "ExternalTransform")

The transform parameters necessary for transformix, additionally defined by this class, are:

Transform Parameters

TransformAddress: specifies the memory address of the external transform.
example: (TransformAddress "000002A3CB9AACC0")

Definition at line 48 of file elxExternalTransform.h.

Inheritance diagram for elastix::ExternalTransform< TElastix >:

Public Types
using	ConstPointer = itk::SmartPointer<const Self>
using	CoordinateType
using	ParameterMapType
using	Pointer = itk::SmartPointer<Self>
using	Self = ExternalTransform
using	Superclass1
using	Superclass2 = elx::TransformBase<TElastix>
Public Types inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
using	ConstPointer = SmartPointer<const Self>
using	CurrentTransformConstPointer = typename CurrentTransformType::ConstPointer
using	CurrentTransformInverseTransformBasePointer = typename CurrentTransformType::InverseTransformBasePointer
using	CurrentTransformInverseTransformBaseType = typename CurrentTransformType::InverseTransformBaseType
using	CurrentTransformPointer = typename CurrentTransformType::Pointer
using	CurrentTransformType = Superclass
using	InitialTransformConstPointer = typename InitialTransformType::ConstPointer
using	InitialTransformInverseTransformBasePointer = typename InitialTransformType::InverseTransformBasePointer
using	InitialTransformInverseTransformBaseType = typename InitialTransformType::InverseTransformBaseType
using	InitialTransformPointer = typename InitialTransformType::Pointer
using	InitialTransformType = Superclass
using	InternalMatrixType
using	InverseTransformBaseType = typename Superclass::InverseTransformBaseType
using	JacobianOfSpatialHessianType
using	JacobianOfSpatialJacobianType
using	MovingImageGradientType
using	MovingImageGradientValueType
using	NonZeroJacobianIndicesType
using	Pointer = SmartPointer<Self>
using	Self = AdvancedCombinationTransform
using	SpatialHessianType
using	SpatialJacobianType
using	Superclass = AdvancedTransform<TScalarType, NDimensions, NDimensions>
using	TransformType = typename Superclass::TransformType
using	TransformTypeConstPointer = typename TransformType::ConstPointer
using	TransformTypePointer = typename TransformType::Pointer
Public Types inherited from itk::AdvancedTransform< TScalarType, 3, 3 >
using	ConstPointer
using	InternalMatrixType
using	InverseTransformBaseType
using	JacobianOfSpatialHessianType
using	JacobianOfSpatialJacobianType
using	MovingImageGradientType
using	MovingImageGradientValueType
using	NonZeroJacobianIndicesType
using	Pointer
using	Self
using	SpatialHessianType
using	SpatialJacobianType
using	Superclass
using	TransformType
using	TransformTypeConstPointer
using	TransformTypePointer
Public Types inherited from elastix::TransformBase< TElastix >
using	CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, Self::FixedImageDimension>
using	CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType
using	CommandLineEntryType = Configuration ::CommandLineEntryType
using	ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
using	CoordinateType = ElastixBase::CoordinateType
using	DeformationFieldImageType = itk::Image<VectorPixelType, FixedImageDimension>
using	FixedImageType = typename TElastix::FixedImageType
using	InitialTransformType = typename CombinationTransformType::InitialTransformType
using	InputPointType = typename ITKBaseType::InputPointType
using	ITKBaseType = CombinationTransformType
using	ITKRegistrationType = typename RegistrationType::ITKBaseType
using	MovingImageType = typename TElastix::MovingImageType
using	OptimizerType = typename ITKRegistrationType::OptimizerType
using	OutputPointType = typename ITKBaseType::OutputPointType
using	ParameterMapType = typename TElastix::ParameterMapType
using	ParametersType = itk::OptimizerParameters<ValueType>
using	PtrToCreator = ComponentDatabase::PtrToCreator
using	RegistrationType
using	ScalesType = itk::Optimizer::ScalesType
using	Self = TransformBase
using	SpatialJacobianDeterminantImageType = itk::Image<float, FixedImageDimension>
using	SpatialJacobianMatrixImageType
using	Superclass = BaseComponentSE<TElastix>
using	ValueType = double
using	VectorPixelType = itk::Vector<float, FixedImageDimension>
Public Types inherited from elastix::BaseComponentSE< TElastix >
using	ElastixType = TElastix
using	RegistrationType = typename ElastixType::RegistrationBaseType
using	Self = BaseComponentSE
using	Superclass = BaseComponent

Public Member Functions
	elxClassNameMacro ("ExternalTransform")
	ITK_DISALLOW_COPY_AND_MOVE (ExternalTransform)
	itkOverrideGetNameOfClassMacro (ExternalTransform)
	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
void	ReadFromFile () override
Public Member Functions inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
void	EvaluateJacobianWithImageGradientProduct (const InputPointType &inputPoint, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
const FixedParametersType &	GetFixedParameters () const override
bool	GetHasNonZeroSpatialHessian () const override
bool	GetInverse (Self *inverse) const
void	GetJacobian (const InputPointType &inputPoint, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialHessian (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
const TransformTypePointer	GetNthTransform (SizeValueType n) const
NumberOfParametersType	GetNumberOfNonZeroJacobianIndices () const override
NumberOfParametersType	GetNumberOfParameters () const override
SizeValueType	GetNumberOfTransforms () const
const ParametersType &	GetParameters () const override
void	GetSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh) const override
void	GetSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj) const override
TransformCategoryEnum	GetTransformCategory () const override
virtual bool	GetUseAddition () const
virtual bool	GetUseComposition () const
bool	HasNonZeroJacobianOfSpatialHessian () const
bool	IsLinear () const override
	ITK_DISALLOW_COPY_AND_MOVE (AdvancedCombinationTransform)
	itkGetModifiableObjectMacro (CurrentTransform, CurrentTransformType)
	itkGetModifiableObjectMacro (InitialTransform, InitialTransformType)
	itkOverrideGetNameOfClassMacro (AdvancedCombinationTransform)
	itkStaticConstMacro (SpaceDimension, unsigned int, NDimensions)
void	SetCurrentTransform (CurrentTransformType *_arg)
void	SetFixedParameters (const FixedParametersType &fixedParam) override
void	SetInitialTransform (InitialTransformType *_arg)
void	SetParameters (const ParametersType &param) override
void	SetParametersByValue (const ParametersType &param) override
void	SetUseAddition (bool _arg)
void	SetUseComposition (bool _arg)
OutputCovariantVectorType	TransformCovariantVector (const InputCovariantVectorType &) const override
OutputPointType	TransformPoint (const InputPointType &point) const override
OutputVectorType	TransformVector (const InputVectorType &) const override
OutputVnlVectorType	TransformVector (const InputVnlVectorType &) const override
Public Member Functions inherited from itk::AdvancedTransform< TScalarType, 3, 3 >
void	ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const override
virtual bool	GetHasNonZeroJacobianOfSpatialHessian () const
	ITK_DISALLOW_COPY_AND_MOVE (AdvancedTransform)
	itkOverrideGetNameOfClassMacro (AdvancedTransform)
	itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)
Public Member Functions inherited from elastix::TransformBase< TElastix >
int	BeforeAllTransformix ()
void	ComputeAndWriteSpatialJacobianDeterminantImage () const
void	ComputeAndWriteSpatialJacobianMatrixImage () const
SpatialJacobianDeterminantImageType::Pointer	ComputeSpatialJacobianDeterminantImage () const
SpatialJacobianMatrixImageType::Pointer	ComputeSpatialJacobianMatrixImage () const
void	CreateTransformParameterMap (const ParametersType &param, ParameterMapType &parameterMap, const bool includeDerivedTransformParameters=true) const
ITKBaseType *	GetAsITKBaseType ()
const ITKBaseType *	GetAsITKBaseType () const
	ITK_DISALLOW_COPY_AND_MOVE (TransformBase)
	itkOverrideGetNameOfClassMacro (TransformBase)
	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
void	ReadInitialTransformFromFile (const std::string &transformParameterFileName)
void	SetFinalParameters ()
void	SetInitialTransform (InitialTransformType *_arg)
void	SetReadWriteTransformParameters (const bool _arg)
void	SetTransformParameterFileName (const std::string &filename)
template<typename TMesh>
TMesh::Pointer	TransformMesh (const TMesh &mesh) const
void	TransformPoints () const
void	WriteToFile (std::ostream &transformationParameterInfo, const ParametersType &param) const
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	AfterEachIterationBase ()
virtual void	AfterEachResolution ()
virtual void	AfterEachResolutionBase ()
virtual void	AfterRegistration ()
virtual int	BeforeAll ()
virtual void	BeforeEachResolution ()
virtual void	BeforeEachResolutionBase ()
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)

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
static Pointer	New ()
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 ()

Protected Member Functions
	ExternalTransform ()
	~ExternalTransform () override=default
Protected Member Functions inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
	AdvancedCombinationTransform ()
void	EvaluateJacobianWithImageGradientProductNoCurrentTransform (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const
void	EvaluateJacobianWithImageGradientProductNoInitialTransform (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const
void	EvaluateJacobianWithImageGradientProductUseAddition (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const
void	EvaluateJacobianWithImageGradientProductUseComposition (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const
void	GetJacobianNoCurrentTransform (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const
void	GetJacobianNoInitialTransform (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const
void	GetJacobianOfSpatialHessianNoCurrentTransform (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoCurrentTransform (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianUseAddition (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const
void	GetJacobianUseComposition (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const
void	GetSpatialHessianNoCurrentTransform (const InputPointType &inputPoint, SpatialHessianType &sh) const
void	GetSpatialHessianNoInitialTransform (const InputPointType &inputPoint, SpatialHessianType &sh) const
void	GetSpatialHessianUseAddition (const InputPointType &inputPoint, SpatialHessianType &sh) const
void	GetSpatialHessianUseComposition (const InputPointType &inputPoint, SpatialHessianType &sh) const
void	GetSpatialJacobianNoCurrentTransform (const InputPointType &inputPoint, SpatialJacobianType &sj) const
void	GetSpatialJacobianNoInitialTransform (const InputPointType &inputPoint, SpatialJacobianType &sj) const
void	GetSpatialJacobianUseAddition (const InputPointType &inputPoint, SpatialJacobianType &sj) const
void	GetSpatialJacobianUseComposition (const InputPointType &inputPoint, SpatialJacobianType &sj) const
OutputPointType	TransformPointNoCurrentTransform (const InputPointType &point) const
OutputPointType	TransformPointNoInitialTransform (const InputPointType &point) const
OutputPointType	TransformPointUseAddition (const InputPointType &point) const
OutputPointType	TransformPointUseComposition (const InputPointType &point) const
void	UpdateCombinationMethod ()
	~AdvancedCombinationTransform () override=default
Protected Member Functions inherited from itk::AdvancedTransform< TScalarType, 3, 3 >
	AdvancedTransform ()=default
	~AdvancedTransform () override=default
Protected Member Functions inherited from elastix::TransformBase< TElastix >
void	AutomaticScalesEstimation (ScalesType &scales) const
void	AutomaticScalesEstimationStackTransform (const unsigned int numSubTransforms, ScalesType &scales) const
bool	HasITKTransformParameters () const
	TransformBase ()=default
	~TransformBase () 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

Private Types
using	AdvancedTransformAdapterType = AdvancedTransformAdapter<CoordinateType, Superclass2::FixedImageDimension>

Private Member Functions
ParameterMapType	CreateDerivedTransformParameterMap () const override

Private Attributes
	elxOverrideGetSelfMacro
const itk::SmartPointer< AdvancedTransformAdapterType >	m_AdvancedTransformAdapter

Additional Inherited Members
Protected Attributes inherited from itk::AdvancedTransform< TScalarType, 3, 3 >
bool	m_HasNonZeroJacobianOfSpatialHessian
bool	m_HasNonZeroSpatialHessian
Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
Configuration::ConstPointer	m_Configuration {}
itk::WeakPointer< TElastix >	m_Elastix {}
RegistrationType *	m_Registration {}

Member Typedef Documentation

AdvancedTransformAdapterType

template<typename TElastix>

using elastix::ExternalTransform< TElastix >::AdvancedTransformAdapterType = AdvancedTransformAdapter<CoordinateType, Superclass2::FixedImageDimension>

private

Definition at line 105 of file elxExternalTransform.h.

ConstPointer

template<typename TElastix>

using elastix::ExternalTransform< TElastix >::ConstPointer = itk::SmartPointer<const Self>

Definition at line 66 of file elxExternalTransform.h.

CoordinateType

template<typename TElastix>

using elastix::TransformBase< TElastix >::CoordinateType

Elastix typedef's.

Definition at line 163 of file elxTransformBase.h.

ParameterMapType

template<typename TElastix>

using elastix::TransformBase< TElastix >::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 206 of file elxTransformBase.h.

Pointer

template<typename TElastix>

using elastix::ExternalTransform< TElastix >::Pointer = itk::SmartPointer<Self>

Definition at line 65 of file elxExternalTransform.h.

Self

template<typename TElastix>

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

Standard ITK-stuff.

Definition at line 57 of file elxExternalTransform.h.

Superclass1

template<typename TElastix>

using elastix::ExternalTransform< TElastix >::Superclass1

Initial value:

itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordinateType,
                                                       elx::TransformBase<TElastix>::FixedImageDimension>

The ITK-class that provides most of the functionality

Definition at line 60 of file elxExternalTransform.h.

Superclass2

template<typename TElastix>

using elastix::ExternalTransform< TElastix >::Superclass2 = elx::TransformBase<TElastix>

Definition at line 63 of file elxExternalTransform.h.

Constructor & Destructor Documentation

ExternalTransform()

template<typename TElastix>

elastix::ExternalTransform< TElastix >::ExternalTransform ( )

protected

Default-constructor.

~ExternalTransform()

template<typename TElastix>

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

overrideprotecteddefault

Destructor.

Member Function Documentation

CreateDerivedTransformParameterMap()

template<typename TElastix>

ParameterMapType elastix::ExternalTransform< TElastix >::CreateDerivedTransformParameterMap ( ) const

overrideprivatevirtual

Creates a map of the parameters specific for this (derived) transform type.

Implements elastix::TransformBase< TElastix >.

elxClassNameMacro()

template<typename TElastix>

elastix::ExternalTransform< TElastix >::elxClassNameMacro

(

"ExternalTransform< TElastix >"

)

Name of this class. Use this name in the parameter file to select this specific transform.
example: (Transform "ExternalTransform")

ITK_DISALLOW_COPY_AND_MOVE()

template<typename TElastix>

elastix::ExternalTransform< TElastix >::ITK_DISALLOW_COPY_AND_MOVE

(

ExternalTransform< TElastix >

)

itkOverrideGetNameOfClassMacro()

template<typename TElastix>

elastix::ExternalTransform< TElastix >::itkOverrideGetNameOfClassMacro

(

ExternalTransform< TElastix >

)

Run-time type information (and related methods).

itkStaticConstMacro()

template<typename TElastix>

elastix::ExternalTransform< TElastix >::itkStaticConstMacro	(	SpaceDimension	,
		unsigned int	,
		Superclass2::FixedImageDimension	)

Dimension of the domain space.

New()

template<typename TElastix>

Pointer elastix::ExternalTransform< TElastix >::New ( )

static

Method for creation through the object factory.

ReadFromFile()

template<typename TElastix>

void elastix::ExternalTransform< TElastix >::ReadFromFile ( )

overridevirtual

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

Member Data Documentation

elxOverrideGetSelfMacro

template<typename TElastix>

elastix::ExternalTransform< TElastix >::elxOverrideGetSelfMacro

private

Definition at line 99 of file elxExternalTransform.h.

m_AdvancedTransformAdapter

template<typename TElastix>

const itk::SmartPointer<AdvancedTransformAdapterType> elastix::ExternalTransform< TElastix >::m_AdvancedTransformAdapter

private

Initial value:

{
    AdvancedTransformAdapterType::New()
  }

The transform that is set as current transform in the CombinationTransform

Definition at line 108 of file elxExternalTransform.h.