elastix::SimilarityTransformElastix< TElastix > Class Template Reference

#include <elxSimilarityTransform.h>

Detailed Description

template<class TElastix>
class elastix::SimilarityTransformElastix< TElastix >

A transform based on the itk SimilarityTransforms.

This transform is a rigid body transformation, with an isotropic scaling. In 2D, the order of parameters is:
[scale, rotation angle, translationx, translationy]
In 3D, the order of parameters is:
[versor1 versor2 versor3 translationx translationy translationz scale]
Make sure, when specifying the Scales manually that you keep in mind this order!

The parameters used in this class are:

Parameters:

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

Scales: the scale factor between the rotations, translations, and the isotropic scaling, used in the optimizer.
example: (Scales 100000.0 60000.0 ... 80000.0)
With this transform, the number of arguments should be equal to the number of parameters: for each parameter its scale factor. If this parameter option is not used, by default the rotations are scaled by a factor of 100000.0 and the scale by a factor 10000.0. These are rather arbitrary values. See also the AutomaticScalesEstimation parameter. See also the comment in the documentation of SimilarityTransformElastix about the order of the parameters in 2D and 3D.

AutomaticScalesEstimation: if this parameter is set to "true" the Scales parameter is ignored and the scales are determined automatically.
example: ( AutomaticScalesEstimation "true" )
Default: "false" (for backwards compatibility). Recommended: "true".

CenterOfRotation: an index around which the image is rotated.
example: (CenterOfRotation 128 128 90)
By default the CenterOfRotation is set to the geometric center of the image.

AutomaticTransformInitialization: whether or not the initial translation between images should be estimated as the distance between their centers.
example: (AutomaticTransformInitialization "true")
By default "false" is assumed. So, no initial translation.

AutomaticTransformInitializationMethod: how to initialize this transform. Should be one of {GeometricalCenter, CenterOfGravity}.
example: (AutomaticTransformInitializationMethod "CenterOfGravity")
By default "GeometricalCenter" is assumed.

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

Transform Parameters:

CenterOfRotation: stores the center of rotation as an index.
example: (CenterOfRotation 128 128 90)
depecrated! From elastix version 3.402 this is changed to CenterOfRotationPoint!

CenterOfRotationPoint: stores the center of rotation, expressed in world coordinates.
example: (CenterOfRotationPoint 10.555 6.666 12.345)

Definition at line 79 of file elxSimilarityTransform.h.

Inheritance diagram for elastix::SimilarityTransformElastix< TElastix >:

Public Types
using	CombinationTransformType = typename Superclass2::CombinationTransformType
using	ConstPointer = itk::SmartPointer< const Self >
using	CoordRepType = ElastixBase::CoordRepType
using	DirectionType = typename FixedImageType::DirectionType
using	FixedImageType = typename TElastix::FixedImageType
using	IndexType = typename FixedImageType::IndexType
using	IndexValueType = typename IndexType::IndexValueType
using	ITKBaseType = typename Superclass2::ITKBaseType
using	MovingImageType = typename TElastix::MovingImageType
using	OffsetType = typename SimilarityTransformType::OffsetType
using	ParameterMapType = typename TElastix::ParameterMapType
using	Pointer = itk::SmartPointer< Self >
using	PointType = typename FixedImageType::PointType
using	RegionType = typename FixedImageType::RegionType
using	ScalesType = typename OptimizerType::ScalesType
using	Self = SimilarityTransformElastix
using	SimilarityTransformPointer = typename SimilarityTransformType::Pointer
using	SimilarityTransformType = itk::SimilarityTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
using	SizeType = typename FixedImageType::SizeType
using	SpacingType = typename FixedImageType::SpacingType
using	Superclass1 = itk::AdvancedCombinationTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
using	Superclass2 = elx::TransformBase< TElastix >
using	TransformInitializerPointer = typename TransformInitializerType::Pointer
using	TransformInitializerType = itk::CenteredTransformInitializer< SimilarityTransformType, FixedImageType, MovingImageType >
Public Types inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
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	InverseTransformBaseType = typename Superclass::InverseTransformBaseType
using	Pointer = SmartPointer< Self >
using	Self = AdvancedCombinationTransform
using	Superclass = AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
using	TransformType = typename Superclass::TransformType
using	TransformTypeConstPointer = typename TransformType::ConstPointer
using	TransformTypePointer = typename TransformType::Pointer
Public Types inherited from itk::AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
using	ConstPointer = SmartPointer< const Self >
using	InternalMatrixType = typename SpatialJacobianType::InternalMatrixType
using	InverseTransformBaseType = typename Superclass::InverseTransformBaseType
using	JacobianOfSpatialHessianType = std::vector< SpatialHessianType >
using	JacobianOfSpatialJacobianType = std::vector< SpatialJacobianType >
using	MovingImageGradientType = OutputCovariantVectorType
using	MovingImageGradientValueType = typename MovingImageGradientType::ValueType
using	NonZeroJacobianIndicesType = std::vector< unsigned long >
using	Pointer = SmartPointer< Self >
using	Self = AdvancedTransform
using	SpatialHessianType = FixedArray< Matrix< ScalarType, InputSpaceDimension, InputSpaceDimension >, OutputSpaceDimension >
using	SpatialJacobianType = Matrix< ScalarType, OutputSpaceDimension, InputSpaceDimension >
using	Superclass = Transform< TScalarType, NInputDimensions, NOutputDimensions >
using	TransformType = Transform< TScalarType, NInputDimensions, NOutputDimensions >
using	TransformTypeConstPointer = typename TransformType::ConstPointer
using	TransformTypePointer = typename TransformType::Pointer
Public Types inherited from elastix::TransformBase< TElastix >
using	CombinationTransformType = itk::AdvancedCombinationTransform< CoordRepType, Self::FixedImageDimension >
using	CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType
using	CommandLineEntryType = Configuration ::CommandLineEntryType
using	ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
using	CoordRepType = ElastixBase::CoordRepType
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	ProgressCommandType = elx::ProgressCommand
using	PtrToCreator = ComponentDatabase::PtrToCreator
using	RegistrationType = typename ElastixType::RegistrationBaseType
using	ScalesType = typename OptimizerType::ScalesType
using	Self = TransformBase
using	SpatialJacobianDeterminantImageType = itk::Image< float, FixedImageDimension >
using	SpatialJacobianMatrixImageType = itk::Image< itk::Matrix< float, MovingImageDimension, FixedImageDimension >, FixedImageDimension >
using	Superclass = BaseComponentSE< TElastix >
using	ValueType = double
using	VectorPixelType = itk::Vector< float, FixedImageDimension >
Public Types inherited from elastix::BaseComponentSE< TElastix >
using	ConfigurationPointer = Configuration::Pointer
using	ElastixType = TElastix
using	RegistrationType = typename ElastixType::RegistrationBaseType
using	Self = BaseComponentSE
using	Superclass = BaseComponent

Public Member Functions
void	BeforeRegistration () override
	elxClassNameMacro ("SimilarityTransform")
virtual const char *	GetClassName () const
	ITK_DISALLOW_COPY_AND_MOVE (SimilarityTransformElastix)
	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
void	ReadFromFile () override
virtual void	SetScales ()
Public Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
void	EvaluateJacobianWithImageGradientProduct (const InputPointType &inputPoint, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
virtual const char *	GetClassName () const
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)
	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, NInputDimensions, NOutputDimensions >
void	ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const override
virtual void	EvaluateJacobianWithImageGradientProduct (const InputPointType &inputPoint, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
virtual const char *	GetClassName () const
virtual bool	GetHasNonZeroJacobianOfSpatialHessian () const
virtual bool	GetHasNonZeroSpatialHessian () const
virtual void	GetJacobian (const InputPointType &inputPoint, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
virtual void	GetJacobianOfSpatialHessian (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
virtual void	GetJacobianOfSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
virtual void	GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
virtual void	GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
virtual NumberOfParametersType	GetNumberOfNonZeroJacobianIndices () const
virtual void	GetSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh) const =0
virtual void	GetSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj) const =0
	ITK_DISALLOW_COPY_AND_MOVE (AdvancedTransform)
	itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)
	itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)
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	CreateTransformParametersMap (const ParametersType &param, ParameterMapType &parameterMap, const bool includeDerivedTransformParameters=true) const
ITKBaseType *	GetAsITKBaseType ()
const ITKBaseType *	GetAsITKBaseType () const
virtual const char *	GetClassName () const
	ITK_DISALLOW_COPY_AND_MOVE (TransformBase)
	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
virtual void	ReadFromFile ()
void	ReadInitialTransformFromFile (const char *transformParameterFileName)
void	SetFinalParameters ()
void	SetInitialTransform (InitialTransformType *_arg)
void	SetReadWriteTransformParameters (const bool _arg)
void	SetTransformParametersFileName (const char *filename)
template<typename TMesh >
TMesh::Pointer	TransformMesh (const TMesh &mesh) const
void	TransformPoints () const
void	WriteToFile (xl::xoutsimple &transformationParameterInfo, const ParametersType &param) const
Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
void	AddTargetCellToIterationInfo (const char *const name)
Configuration *	GetConfiguration () const
ElastixType *	GetElastix () const
xl::xoutbase &	GetIterationInfoAt (const char *const name)
RegistrationType *	GetRegistration () const
	ITK_DISALLOW_COPY_AND_MOVE (BaseComponentSE)
int	RemoveTargetCellFromIterationInfo (const char *const name)
void	SetConfiguration (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 void	AfterRegistrationBase ()
virtual int	BeforeAll ()
virtual int	BeforeAllBase ()
virtual void	BeforeEachResolution ()
virtual void	BeforeEachResolutionBase ()
virtual void	BeforeRegistration ()
virtual void	BeforeRegistrationBase ()
virtual const char *	elxGetClassName () const
const char *	GetComponentLabel () const
	ITK_DISALLOW_COPY_AND_MOVE (BaseComponent)
	itkTypeMacroNoParent (BaseComponent)
void	SetComponentLabel (const char *label, unsigned int idx)

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
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
virtual bool	ReadCenterOfRotationIndex (InputPointType &rotationPoint) const
virtual bool	ReadCenterOfRotationPoint (InputPointType &rotationPoint) const
	SimilarityTransformElastix ()
	~SimilarityTransformElastix () override=default
Protected Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
	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, NInputDimensions, NOutputDimensions >
	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 Member Functions
ParameterMapType	CreateDerivedTransformParametersMap () const override
void	InitializeTransform ()

Private Attributes
	elxOverrideGetSelfMacro
const SimilarityTransformPointer	m_SimilarityTransform { SimilarityTransformType::New() }

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

Member Typedef Documentation

CombinationTransformType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::CombinationTransformType = typename Superclass2::CombinationTransformType

Definition at line 144 of file elxSimilarityTransform.h.

ConstPointer

template<class TElastix >

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

Definition at line 93 of file elxSimilarityTransform.h.

CoordRepType

template<class TElastix >

using elastix::TransformBase< TElastix >::CoordRepType = ElastixBase::CoordRepType

Elastix typedef's.

Definition at line 153 of file elxTransformBase.h.

DirectionType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::DirectionType = typename FixedImageType::DirectionType

Definition at line 153 of file elxSimilarityTransform.h.

FixedImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::FixedImageType = typename TElastix::FixedImageType

Definition at line 154 of file elxTransformBase.h.

IndexType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::IndexType = typename FixedImageType::IndexType

Other typedef's.

Definition at line 147 of file elxSimilarityTransform.h.

IndexValueType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::IndexValueType = typename IndexType::IndexValueType

Definition at line 148 of file elxSimilarityTransform.h.

ITKBaseType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::ITKBaseType = typename Superclass2::ITKBaseType

Definition at line 143 of file elxSimilarityTransform.h.

MovingImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::MovingImageType = typename TElastix::MovingImageType

Definition at line 155 of file elxTransformBase.h.

OffsetType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::OffsetType = typename SimilarityTransformType::OffsetType

Definition at line 134 of file elxSimilarityTransform.h.

ParameterMapType

template<class TElastix >

using elastix::TransformBase< TElastix >::ParameterMapType = typename TElastix::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 199 of file elxTransformBase.h.

Pointer

template<class TElastix >

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

Definition at line 92 of file elxSimilarityTransform.h.

PointType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::PointType = typename FixedImageType::PointType

Definition at line 150 of file elxSimilarityTransform.h.

RegionType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::RegionType = typename FixedImageType::RegionType

Definition at line 152 of file elxSimilarityTransform.h.

ScalesType

template<class TElastix >

using elastix::TransformBase< TElastix >::ScalesType = typename OptimizerType::ScalesType

Definition at line 190 of file elxTransformBase.h.

Self

template<class TElastix >

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

Standard ITK-stuff.

Definition at line 88 of file elxSimilarityTransform.h.

SimilarityTransformPointer

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::SimilarityTransformPointer = typename SimilarityTransformType::Pointer

NOTE: use this one only in 3D (otherwise it's just an int).

Definition at line 133 of file elxSimilarityTransform.h.

SimilarityTransformType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::SimilarityTransformType = itk::SimilarityTransform<typename elx::TransformBase<TElastix>::CoordRepType, elx::TransformBase<TElastix>::FixedImageDimension>

The ITK-class that provides most of the functionality, and that is set as the "CurrentTransform" in the CombinationTransform

Definition at line 97 of file elxSimilarityTransform.h.

SizeType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::SizeType = typename FixedImageType::SizeType

Definition at line 149 of file elxSimilarityTransform.h.

SpacingType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::SpacingType = typename FixedImageType::SpacingType

Definition at line 151 of file elxSimilarityTransform.h.

Superclass1

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::Superclass1 = itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType, elx::TransformBase<TElastix>::FixedImageDimension>

Definition at line 89 of file elxSimilarityTransform.h.

Superclass2

template<class TElastix >

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

Definition at line 91 of file elxSimilarityTransform.h.

TransformInitializerPointer

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::TransformInitializerPointer = typename TransformInitializerType::Pointer

Definition at line 157 of file elxSimilarityTransform.h.

TransformInitializerType

template<class TElastix >

using elastix::SimilarityTransformElastix< TElastix >::TransformInitializerType = itk::CenteredTransformInitializer<SimilarityTransformType, FixedImageType, MovingImageType>

Definition at line 155 of file elxSimilarityTransform.h.

Constructor & Destructor Documentation

SimilarityTransformElastix()

template<class TElastix >

elastix::SimilarityTransformElastix< TElastix >::SimilarityTransformElastix ( )

protected

The constructor.

~SimilarityTransformElastix()

template<class TElastix >

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

overrideprotecteddefault

The destructor.

Member Function Documentation

BeforeRegistration()

template<class TElastix >

void elastix::SimilarityTransformElastix< TElastix >::BeforeRegistration ( )

overridevirtual

Execute stuff before the actual registration:

• Call InitializeTransform
• Set the scales.

Reimplemented from elastix::BaseComponent.

CreateDerivedTransformParametersMap()

template<class TElastix >

ParameterMapType elastix::SimilarityTransformElastix< TElastix >::CreateDerivedTransformParametersMap ( ) const

overrideprivatevirtual

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

Implements elastix::TransformBase< TElastix >.

elxClassNameMacro()

template<class TElastix >

elastix::SimilarityTransformElastix< TElastix >::elxClassNameMacro

(

"SimilarityTransform"

)

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

GetClassName()

template<class TElastix >

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

virtual

Run-time type information (and related methods).

Reimplemented from elastix::TransformBase< TElastix >.

InitializeTransform()

template<class TElastix >

void elastix::SimilarityTransformElastix< TElastix >::InitializeTransform ( )

private

Initialize Transform.

• Set all parameters to zero.
• Set center of rotation: automatically initialized to the geometric center of the image, or assigned a user entered voxel index, given by the parameter (CenterOfRotation <index-x> <index-y> ...); If an initial transform is present and HowToCombineTransforms is set to "Compose", the initial transform is taken into account while setting the center of rotation.
• Set initial translation: the initial translation between fixed and moving image is guessed, if the user has set (AutomaticTransformInitialization "true").

It is not yet possible to enter an initial rotation angle.

ITK_DISALLOW_COPY_AND_MOVE()

template<class TElastix >

elastix::SimilarityTransformElastix< TElastix >::ITK_DISALLOW_COPY_AND_MOVE

(

SimilarityTransformElastix< TElastix >

)

itkStaticConstMacro()

template<class TElastix >

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

Dimension of the fixed image.

New()

template<class TElastix >

static Pointer elastix::SimilarityTransformElastix< TElastix >::New ( )

static

Method for creation through the object factory.

ReadCenterOfRotationIndex()

template<class TElastix >

virtual bool elastix::SimilarityTransformElastix< TElastix >::ReadCenterOfRotationIndex ( InputPointType &  rotationPoint ) const

protectedvirtual

Try to read the CenterOfRotation from the transform parameter file This is an index value, and, thus, converted to world coordinates. Transform parameter files generated by elastix version < 3.402 saved the center of rotation in this way.

ReadCenterOfRotationPoint()

template<class TElastix >

virtual bool elastix::SimilarityTransformElastix< TElastix >::ReadCenterOfRotationPoint ( InputPointType &  rotationPoint ) const

protectedvirtual

Try to read the CenterOfRotationPoint from the transform parameter file The CenterOfRotationPoint is already in world coordinates. Transform parameter files generated by elastix version > 3.402 save the center of rotation in this way.

ReadFromFile()

template<class TElastix >

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

overridevirtual

Function to read transform-parameters from a file.

It reads the center of rotation and calls the superclass' implementation.

Reimplemented from elastix::TransformBase< TElastix >.

SetScales()

template<class TElastix >

virtual void elastix::SimilarityTransformElastix< TElastix >::SetScales ( )

virtual

Set the scales

• If AutomaticScalesEstimation is "true" estimate scales
• If scales are provided by the user use those,
• Otherwise use some default value This function is called by BeforeRegistration, after the InitializeTransform function is called

Field Documentation

elxOverrideGetSelfMacro

template<class TElastix >

elastix::SimilarityTransformElastix< TElastix >::elxOverrideGetSelfMacro

private

Definition at line 209 of file elxSimilarityTransform.h.

m_SimilarityTransform

template<class TElastix >

const SimilarityTransformPointer elastix::SimilarityTransformElastix< TElastix >::m_SimilarityTransform { SimilarityTransformType::New() }

private

Definition at line 233 of file elxSimilarityTransform.h.