elastix::AdvancedAffineTransformElastix< TElastix > Class Template Reference

#include <elxAdvancedAffineTransform.h>

Detailed Description

template<class TElastix>
class elastix::AdvancedAffineTransformElastix< TElastix >

A transform based on the itk::AdvancedMatrixOffsetTransformBase.

This transform is an affine transformation.

The first couple of parameters (4 in 2D and 9 in 3D) define the affine matrix, the last couple (2 in 2D and 3 in 3D) define the translation.

The parameters used in this class are:

Parameters:

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

Scales: the scale factor between the rotations and translations, used in the optimizer.
example: (Scales 200000.0)
example: (Scales 100000.0 60000.0 ... 80000.0)
If only one argument is given, that factor is used for the rotations. If more than one argument is given, then 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. See also the AutomaticScalesEstimation parameter.

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, Origins, GeometryTop}.
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) deprecated! 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 77 of file elxAdvancedAffineTransform.h.

Inheritance diagram for elastix::AdvancedAffineTransformElastix< TElastix >:

Public Types
typedef AffineTransformType::Pointer	AffineTransformPointer
typedef itk::AdvancedMatrixOffsetTransformBase< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension, elx::TransformBase< TElastix >::MovingImageDimension >	AffineTransformType
typedef Superclass2::CombinationTransformType	CombinationTransformType
typedef Superclass2::ConfigurationPointer	ConfigurationPointer
typedef Superclass2::ConfigurationType	ConfigurationType
typedef itk::SmartPointer< const Self >	ConstPointer
typedef Superclass2::CoordRepType	CoordRepType
typedef FixedImageType::DirectionType	DirectionType
typedef Superclass2::ElastixPointer	ElastixPointer
typedef Superclass2::ElastixType	ElastixType
typedef Superclass2::FixedImageType	FixedImageType
typedef FixedImageType::IndexType	IndexType
typedef IndexType::IndexValueType	IndexValueType
typedef Superclass1::InputCovariantVectorType	InputCovariantVectorType
typedef Superclass1::InputPointType	InputPointType
typedef Superclass1::InputVectorType	InputVectorType
typedef Superclass1::InputVnlVectorType	InputVnlVectorType
typedef Superclass2::ITKBaseType	ITKBaseType
typedef Superclass1::JacobianType	JacobianType
typedef Superclass2::MovingImageType	MovingImageType
typedef Superclass1::NumberOfParametersType	NumberOfParametersType
typedef Superclass1::OutputCovariantVectorType	OutputCovariantVectorType
typedef Superclass1::OutputPointType	OutputPointType
typedef Superclass1::OutputVectorType	OutputVectorType
typedef Superclass1::OutputVnlVectorType	OutputVnlVectorType
typedef Superclass2::ParameterMapType	ParameterMapType
typedef Superclass1::ParametersType	ParametersType
typedef itk::SmartPointer< Self >	Pointer
typedef FixedImageType::PointType	PointType
typedef FixedImageType::RegionType	RegionType
typedef Superclass2::RegistrationPointer	RegistrationPointer
typedef Superclass2::RegistrationType	RegistrationType
typedef Superclass1::ScalarType	ScalarType
typedef Superclass2::ScalesType	ScalesType
typedef AdvancedAffineTransformElastix	Self
typedef FixedImageType::SizeType	SizeType
typedef FixedImageType::SpacingType	SpacingType
typedef itk::AdvancedCombinationTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >	Superclass1
typedef elx::TransformBase< TElastix >	Superclass2
typedef TransformInitializerType::Pointer	TransformInitializerPointer
typedef itk::CenteredTransformInitializer2< AffineTransformType, FixedImageType, MovingImageType >	TransformInitializerType
Public Types inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
typedef SmartPointer< const Self >	ConstPointer
typedef CurrentTransformType::ConstPointer	CurrentTransformConstPointer
typedef CurrentTransformType::InverseTransformBasePointer	CurrentTransformInverseTransformBasePointer
typedef CurrentTransformType::InverseTransformBaseType	CurrentTransformInverseTransformBaseType
typedef CurrentTransformType::Pointer	CurrentTransformPointer
typedef Superclass	CurrentTransformType
typedef Superclass::DerivativeType	DerivativeType
typedef void(Self::*	EvaluateJacobianWithImageGradientProductFunctionPointer) (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const
typedef Superclass::FixedParametersType	FixedParametersType
typedef void(Self::*	GetJacobianOfSpatialHessianFunctionPointer) (const InputPointType &, JacobianOfSpatialHessianType &, NonZeroJacobianIndicesType &) const
typedef void(Self::*	GetJacobianOfSpatialHessianFunctionPointer2) (const InputPointType &, SpatialHessianType &, JacobianOfSpatialHessianType &, NonZeroJacobianIndicesType &) const
typedef void(Self::*	GetJacobianOfSpatialJacobianFunctionPointer) (const InputPointType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const
typedef void(Self::*	GetJacobianOfSpatialJacobianFunctionPointer2) (const InputPointType &, SpatialJacobianType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const
typedef void(Self::*	GetSparseJacobianFunctionPointer) (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const
typedef void(Self::*	GetSpatialHessianFunctionPointer) (const InputPointType &, SpatialHessianType &) const
typedef void(Self::*	GetSpatialJacobianFunctionPointer) (const InputPointType &, SpatialJacobianType &) const
typedef InitialTransformType::ConstPointer	InitialTransformConstPointer
typedef InitialTransformType::InverseTransformBasePointer	InitialTransformInverseTransformBasePointer
typedef InitialTransformType::InverseTransformBaseType	InitialTransformInverseTransformBaseType
typedef InitialTransformType::Pointer	InitialTransformPointer
typedef Superclass	InitialTransformType
typedef Superclass::InputCovariantVectorType	InputCovariantVectorType
typedef Superclass::InputPointType	InputPointType
typedef Superclass::InputVectorType	InputVectorType
typedef Superclass::InputVnlVectorType	InputVnlVectorType
typedef Superclass::InternalMatrixType	InternalMatrixType
typedef Superclass::InverseTransformBasePointer	InverseTransformBasePointer
typedef Superclass::InverseTransformBaseType	InverseTransformBaseType
typedef Superclass::JacobianOfSpatialHessianType	JacobianOfSpatialHessianType
typedef Superclass::JacobianOfSpatialJacobianType	JacobianOfSpatialJacobianType
typedef Superclass::JacobianType	JacobianType
typedef Superclass::MovingImageGradientType	MovingImageGradientType
typedef Superclass::MovingImageGradientValueType	MovingImageGradientValueType
typedef Superclass::NonZeroJacobianIndicesType	NonZeroJacobianIndicesType
typedef Superclass::NumberOfParametersType	NumberOfParametersType
typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType
typedef Superclass::OutputPointType	OutputPointType
typedef Superclass::OutputVectorType	OutputVectorType
typedef Superclass::OutputVnlVectorType	OutputVnlVectorType
typedef Superclass::ParametersType	ParametersType
typedef Superclass::ParametersValueType	ParametersValueType
typedef SmartPointer< Self >	Pointer
typedef Superclass::ScalarType	ScalarType
typedef AdvancedCombinationTransform	Self
typedef Superclass::SpatialHessianType	SpatialHessianType
typedef Superclass::SpatialJacobianType	SpatialJacobianType
typedef AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >	Superclass
typedef Superclass::TransformCategoryEnum	TransformCategoryEnum
typedef OutputPointType(Self::*	TransformPointFunctionPointer) (const InputPointType &) const
typedef Superclass::TransformType	TransformType
typedef TransformType::ConstPointer	TransformTypeConstPointer
typedef TransformType::Pointer	TransformTypePointer
Public Types inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::DerivativeType	DerivativeType
typedef Superclass::FixedParametersType	FixedParametersType
typedef Superclass::InputCovariantVectorType	InputCovariantVectorType
typedef Superclass::InputPointType	InputPointType
typedef Superclass::InputVectorType	InputVectorType
typedef Superclass::InputVnlVectorType	InputVnlVectorType
typedef SpatialJacobianType::InternalMatrixType	InternalMatrixType
typedef Superclass::InverseTransformBasePointer	InverseTransformBasePointer
typedef Superclass::InverseTransformBaseType	InverseTransformBaseType
typedef std::vector< SpatialHessianType >	JacobianOfSpatialHessianType
typedef std::vector< SpatialJacobianType >	JacobianOfSpatialJacobianType
typedef Superclass::JacobianType	JacobianType
typedef OutputCovariantVectorType	MovingImageGradientType
typedef MovingImageGradientType::ValueType	MovingImageGradientValueType
typedef std::vector< unsigned long >	NonZeroJacobianIndicesType
typedef Superclass::NumberOfParametersType	NumberOfParametersType
typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType
typedef Superclass::OutputPointType	OutputPointType
typedef Superclass::OutputVectorType	OutputVectorType
typedef Superclass::OutputVnlVectorType	OutputVnlVectorType
typedef Superclass::ParametersType	ParametersType
typedef Superclass::ParametersValueType	ParametersValueType
typedef SmartPointer< Self >	Pointer
typedef Superclass::ScalarType	ScalarType
typedef AdvancedTransform	Self
typedef FixedArray< Matrix< ScalarType, InputSpaceDimension, InputSpaceDimension >, OutputSpaceDimension >	SpatialHessianType
typedef Matrix< ScalarType, OutputSpaceDimension, InputSpaceDimension >	SpatialJacobianType
typedef Transform< elx::TransformBase< TElastix >::CoordRepType, NInputDimensions, NOutputDimensions >	Superclass
typedef Transform< elx::TransformBase< TElastix >::CoordRepType, NInputDimensions, NOutputDimensions >	TransformType
typedef TransformType::ConstPointer	TransformTypeConstPointer
typedef TransformType::Pointer	TransformTypePointer
Public Types inherited from elastix::TransformBase< TElastix >
typedef itk::AdvancedCombinationTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension) >	CombinationTransformType
typedef ConfigurationType::CommandLineArgumentMapType	CommandLineArgumentMapType
typedef ConfigurationType::CommandLineEntryType	CommandLineEntryType
typedef ComponentDatabase	ComponentDatabaseType
typedef ComponentDatabaseType::ComponentDescriptionType	ComponentDescriptionType
typedef Configuration::Pointer	ConfigurationPointer
typedef Configuration	ConfigurationType
typedef ElastixType::CoordRepType	CoordRepType
typedef itk::Image< VectorPixelType, FixedImageDimension >	DeformationFieldImageType
typedef itk::WeakPointer< ElastixType >	ElastixPointer
typedef TElastix	ElastixType
typedef ElastixType::FixedImageType	FixedImageType
typedef CombinationTransformType::InitialTransformType	InitialTransformType
typedef ITKBaseType::InputPointType	InputPointType
typedef itk::AdvancedTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension), itkGetStaticConstMacro(MovingImageDimension) >	ITKBaseType
typedef RegistrationType::ITKBaseType	ITKRegistrationType
typedef ElastixType::MovingImageType	MovingImageType
typedef itk::Object	ObjectType
typedef ITKRegistrationType::OptimizerType	OptimizerType
typedef ITKBaseType::OutputPointType	OutputPointType
typedef ElastixType::ParameterMapType	ParameterMapType
typedef ITKBaseType::ParametersType	ParametersType
typedef elx::ProgressCommand	ProgressCommandType
typedef ComponentDatabase::PtrToCreator	PtrToCreator
typedef RegistrationType *	RegistrationPointer
typedef ElastixType::RegistrationBaseType	RegistrationType
typedef OptimizerType::ScalesType	ScalesType
typedef TransformBase	Self
typedef BaseComponentSE< TElastix >	Superclass
typedef ParametersType::ValueType	ValueType
typedef itk::Vector< float, FixedImageDimension >	VectorPixelType
Public Types inherited from elastix::BaseComponentSE< TElastix >
typedef Configuration::Pointer	ConfigurationPointer
typedef Configuration	ConfigurationType
typedef itk::WeakPointer< ElastixType >	ElastixPointer
typedef TElastix	ElastixType
typedef RegistrationType *	RegistrationPointer
typedef ElastixType::RegistrationBaseType	RegistrationType
typedef BaseComponentSE	Self
typedef BaseComponent	Superclass

Public Member Functions
void	BeforeRegistration (void) override
void	CreateTransformParametersMap (const ParametersType &param, ParameterMapType *paramsMap) const override
	elxClassNameMacro ("AffineTransform")
virtual const char *	GetClassName () const
virtual void	InitializeTransform (void)
	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
void	ReadFromFile (void) override
virtual void	SetScales (void)
void	WriteToFile (const ParametersType &param) const override
Public Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
void	EvaluateJacobianWithImageGradientProduct (const InputPointType &ipp, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
virtual const char *	GetClassName () const
const FixedParametersType &	GetFixedParameters (void) const override
bool	GetHasNonZeroSpatialHessian (void) const override
virtual bool	GetInverse (Self *inverse) const
void	GetJacobian (const InputPointType &ipp, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialHessian (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
virtual const TransformTypePointer	GetNthTransform (SizeValueType n) const
NumberOfParametersType	GetNumberOfNonZeroJacobianIndices (void) const override
NumberOfParametersType	GetNumberOfParameters (void) const override
virtual SizeValueType	GetNumberOfTransforms (void) const
const ParametersType &	GetParameters (void) const override
void	GetSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh) const override
void	GetSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj) const override
TransformCategoryEnum	GetTransformCategory () const override
virtual bool	GetUseAddition () const
virtual bool	GetUseComposition () const
virtual bool	HasNonZeroJacobianOfSpatialHessian (void) const
bool	IsLinear (void) const override
	itkGetModifiableObjectMacro (CurrentTransform, CurrentTransformType)
	itkGetModifiableObjectMacro (InitialTransform, InitialTransformType)
	itkStaticConstMacro (SpaceDimension, unsigned int, NDimensions)
virtual void	SetCurrentTransform (CurrentTransformType *_arg)
void	SetFixedParameters (const FixedParametersType &fixedParam) override
virtual void	SetInitialTransform (InitialTransformType *_arg)
void	SetParameters (const ParametersType &param) override
void	SetParametersByValue (const ParametersType &param) override
virtual void	SetUseAddition (bool _arg)
virtual 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< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
void	ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const override
virtual void	EvaluateJacobianWithImageGradientProduct (const InputPointType &ipp, 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 &ipp, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0
virtual void	GetJacobianOfSpatialHessian (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0
virtual void	GetJacobianOfSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0
virtual void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0
virtual void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0
virtual NumberOfParametersType	GetNumberOfNonZeroJacobianIndices (void) const
virtual void	GetSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh) const=0
virtual void	GetSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj) const=0
	itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)
	itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)
Public Member Functions inherited from elastix::TransformBase< TElastix >
void	AfterRegistrationBase (void) override
int	BeforeAllBase (void) override
virtual int	BeforeAllTransformix (void)
void	BeforeRegistrationBase (void) override
virtual void	ComputeDeterminantOfSpatialJacobian (void) const
virtual void	ComputeSpatialJacobian (void) const
virtual void	CreateTransformParametersMap (const ParametersType &param, ParameterMapType *paramsMap) const
DeformationFieldImageType::Pointer	GenerateDeformationFieldImage (void) const
virtual CombinationTransformType *	GetAsCombinationTransform (void)
virtual const CombinationTransformType *	GetAsCombinationTransform (void) const
virtual ITKBaseType *	GetAsITKBaseType (void)
virtual const ITKBaseType *	GetAsITKBaseType (void) const
virtual const char *	GetClassName () const
virtual const InitialTransformType *	GetInitialTransform (void) const
virtual const char *	GetTransformParametersFileName () const
	ITK_DISALLOW_COPY_AND_ASSIGN (TransformBase)
	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
virtual void	ReadFromFile (void)
virtual void	ReadInitialTransformFromFile (const char *transformParameterFileName)
virtual void	ReadInitialTransformFromVector (const vcl_size_t index)
virtual void	SetFinalParameters (void)
virtual void	SetInitialTransform (InitialTransformType *_arg)
virtual void	SetReadWriteTransformParameters (const bool _arg)
virtual void	SetTransformParametersFileName (const char *filename)
virtual void	TransformPoints (void) const
virtual void	TransformPointsAllPoints (void) const
virtual void	TransformPointsSomePoints (const std::string filename) const
virtual void	TransformPointsSomePointsVTK (const std::string filename) const
void	WriteDeformationFieldImage (typename DeformationFieldImageType::Pointer) const
virtual void	WriteToFile (const ParametersType &param) const
virtual void	WriteToFile (void) const
Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
ConfigurationType *	GetConfiguration (void) const
ElastixType *	GetElastix (void) const
RegistrationPointer	GetRegistration (void) const
	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponentSE)
void	SetConfiguration (ConfigurationType *_arg)
void	SetElastix (ElastixType *_arg)
Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration (void)
virtual void	AfterEachIterationBase (void)
virtual void	AfterEachResolution (void)
virtual void	AfterEachResolutionBase (void)
virtual void	AfterRegistration (void)
virtual void	AfterRegistrationBase (void)
virtual int	BeforeAll (void)
virtual int	BeforeAllBase (void)
virtual void	BeforeEachResolution (void)
virtual void	BeforeEachResolutionBase (void)
virtual void	BeforeRegistration (void)
virtual void	BeforeRegistrationBase (void)
virtual const char *	elxGetClassName (void) const
const char *	GetComponentLabel (void) const
	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponent)
	itkTypeMacroNoParent (BaseComponent)
void	SetComponentLabel (const char *label, unsigned int idx)

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
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)
static void	InitializeElastixExecutable ()
static bool	IsElastixLibrary ()

Protected Member Functions
	AdvancedAffineTransformElastix ()
virtual bool	ReadCenterOfRotationPoint (InputPointType &rotationPoint) const
	~AdvancedAffineTransformElastix () override
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 &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoCurrentTransform (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
virtual void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &ipp, 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 &ipp, SpatialHessianType &sh) const
void	GetSpatialHessianNoInitialTransform (const InputPointType &ipp, SpatialHessianType &sh) const
void	GetSpatialHessianUseAddition (const InputPointType &ipp, SpatialHessianType &sh) const
void	GetSpatialHessianUseComposition (const InputPointType &ipp, SpatialHessianType &sh) const
void	GetSpatialJacobianNoCurrentTransform (const InputPointType &ipp, SpatialJacobianType &sj) const
void	GetSpatialJacobianNoInitialTransform (const InputPointType &ipp, SpatialJacobianType &sj) const
void	GetSpatialJacobianUseAddition (const InputPointType &ipp, SpatialJacobianType &sj) const
void	GetSpatialJacobianUseComposition (const InputPointType &ipp, SpatialJacobianType &sj) const
virtual void	NoCurrentTransformSet (void) 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
virtual void	UpdateCombinationMethod (void)
	~AdvancedCombinationTransform () override
Protected Member Functions inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
	AdvancedTransform ()
	AdvancedTransform (NumberOfParametersType numberOfParameters)
	~AdvancedTransform () override
Protected Member Functions inherited from elastix::TransformBase< TElastix >
void	AutomaticScalesEstimation (ScalesType &scales) const
void	AutomaticScalesEstimationStackTransform (const unsigned int &numSubTransforms, ScalesType &scales) 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
	AdvancedAffineTransformElastix (const Self &)
void	operator= (const Self &)

Private Attributes
AffineTransformPointer	m_AffineTransform

Additional Inherited Members
Protected Attributes inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
CurrentTransformPointer	m_CurrentTransform
InitialTransformPointer	m_InitialTransform
EvaluateJacobianWithImageGradientProductFunctionPointer	m_SelectedEvaluateJacobianWithImageGradientProductFunction
GetJacobianOfSpatialHessianFunctionPointer	m_SelectedGetJacobianOfSpatialHessianFunction
GetJacobianOfSpatialHessianFunctionPointer2	m_SelectedGetJacobianOfSpatialHessianFunction2
GetJacobianOfSpatialJacobianFunctionPointer	m_SelectedGetJacobianOfSpatialJacobianFunction
GetJacobianOfSpatialJacobianFunctionPointer2	m_SelectedGetJacobianOfSpatialJacobianFunction2
GetSparseJacobianFunctionPointer	m_SelectedGetSparseJacobianFunction
GetSpatialHessianFunctionPointer	m_SelectedGetSpatialHessianFunction
GetSpatialJacobianFunctionPointer	m_SelectedGetSpatialJacobianFunction
TransformPointFunctionPointer	m_SelectedTransformPointFunction
bool	m_UseAddition
bool	m_UseComposition
Protected Attributes inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
bool	m_HasNonZeroJacobianOfSpatialHessian
bool	m_HasNonZeroSpatialHessian
Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
ConfigurationPointer	m_Configuration {}
ElastixPointer	m_Elastix {}
RegistrationPointer	m_Registration {}

Member Typedef Documentation

AffineTransformPointer

template<class TElastix >

typedef AffineTransformType::Pointer elastix::AdvancedAffineTransformElastix< TElastix >::AffineTransformPointer

Definition at line 157 of file elxAdvancedAffineTransform.h.

AffineTransformType

template<class TElastix >

typedef itk::AdvancedMatrixOffsetTransformBase< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension, elx::TransformBase< TElastix >::MovingImageDimension > elastix::AdvancedAffineTransformElastix< TElastix >::AffineTransformType

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

Definition at line 99 of file elxAdvancedAffineTransform.h.

CombinationTransformType

template<class TElastix >

typedef Superclass2::CombinationTransformType elastix::AdvancedAffineTransformElastix< TElastix >::CombinationTransformType

Definition at line 142 of file elxAdvancedAffineTransform.h.

ConfigurationPointer

template<class TElastix >

typedef Superclass2::ConfigurationPointer elastix::AdvancedAffineTransformElastix< TElastix >::ConfigurationPointer

Definition at line 135 of file elxAdvancedAffineTransform.h.

ConfigurationType

template<class TElastix >

typedef Superclass2::ConfigurationType elastix::AdvancedAffineTransformElastix< TElastix >::ConfigurationType

Definition at line 134 of file elxAdvancedAffineTransform.h.

ConstPointer

template<class TElastix >

typedef itk::SmartPointer< const Self > elastix::AdvancedAffineTransformElastix< TElastix >::ConstPointer

Definition at line 92 of file elxAdvancedAffineTransform.h.

CoordRepType

template<class TElastix >

typedef Superclass2::CoordRepType elastix::AdvancedAffineTransformElastix< TElastix >::CoordRepType

Definition at line 138 of file elxAdvancedAffineTransform.h.

DirectionType

template<class TElastix >

typedef FixedImageType::DirectionType elastix::AdvancedAffineTransformElastix< TElastix >::DirectionType

Definition at line 151 of file elxAdvancedAffineTransform.h.

ElastixPointer

template<class TElastix >

typedef Superclass2::ElastixPointer elastix::AdvancedAffineTransformElastix< TElastix >::ElastixPointer

Definition at line 132 of file elxAdvancedAffineTransform.h.

ElastixType

template<class TElastix >

typedef Superclass2::ElastixType elastix::AdvancedAffineTransformElastix< TElastix >::ElastixType

Typedef's from the TransformBase class.

Definition at line 131 of file elxAdvancedAffineTransform.h.

FixedImageType

template<class TElastix >

typedef Superclass2::FixedImageType elastix::AdvancedAffineTransformElastix< TElastix >::FixedImageType

Definition at line 139 of file elxAdvancedAffineTransform.h.

IndexType

template<class TElastix >

typedef FixedImageType::IndexType elastix::AdvancedAffineTransformElastix< TElastix >::IndexType

Other typedef's.

Definition at line 145 of file elxAdvancedAffineTransform.h.

IndexValueType

template<class TElastix >

typedef IndexType::IndexValueType elastix::AdvancedAffineTransformElastix< TElastix >::IndexValueType

Definition at line 146 of file elxAdvancedAffineTransform.h.

InputCovariantVectorType

template<class TElastix >

typedef Superclass1::InputCovariantVectorType elastix::AdvancedAffineTransformElastix< TElastix >::InputCovariantVectorType

Definition at line 123 of file elxAdvancedAffineTransform.h.

InputPointType

template<class TElastix >

typedef Superclass1::InputPointType elastix::AdvancedAffineTransformElastix< TElastix >::InputPointType

Definition at line 127 of file elxAdvancedAffineTransform.h.

InputVectorType

template<class TElastix >

typedef Superclass1::InputVectorType elastix::AdvancedAffineTransformElastix< TElastix >::InputVectorType

Definition at line 121 of file elxAdvancedAffineTransform.h.

InputVnlVectorType

template<class TElastix >

typedef Superclass1::InputVnlVectorType elastix::AdvancedAffineTransformElastix< TElastix >::InputVnlVectorType

Definition at line 125 of file elxAdvancedAffineTransform.h.

ITKBaseType

template<class TElastix >

typedef Superclass2::ITKBaseType elastix::AdvancedAffineTransformElastix< TElastix >::ITKBaseType

Definition at line 141 of file elxAdvancedAffineTransform.h.

JacobianType

template<class TElastix >

typedef Superclass1::JacobianType elastix::AdvancedAffineTransformElastix< TElastix >::JacobianType

Definition at line 120 of file elxAdvancedAffineTransform.h.

MovingImageType

template<class TElastix >

typedef Superclass2::MovingImageType elastix::AdvancedAffineTransformElastix< TElastix >::MovingImageType

Definition at line 140 of file elxAdvancedAffineTransform.h.

NumberOfParametersType

template<class TElastix >

typedef Superclass1::NumberOfParametersType elastix::AdvancedAffineTransformElastix< TElastix >::NumberOfParametersType

Definition at line 119 of file elxAdvancedAffineTransform.h.

OutputCovariantVectorType

template<class TElastix >

typedef Superclass1::OutputCovariantVectorType elastix::AdvancedAffineTransformElastix< TElastix >::OutputCovariantVectorType

Definition at line 124 of file elxAdvancedAffineTransform.h.

OutputPointType

template<class TElastix >

typedef Superclass1::OutputPointType elastix::AdvancedAffineTransformElastix< TElastix >::OutputPointType

Definition at line 128 of file elxAdvancedAffineTransform.h.

OutputVectorType

template<class TElastix >

typedef Superclass1::OutputVectorType elastix::AdvancedAffineTransformElastix< TElastix >::OutputVectorType

Definition at line 122 of file elxAdvancedAffineTransform.h.

OutputVnlVectorType

template<class TElastix >

typedef Superclass1::OutputVnlVectorType elastix::AdvancedAffineTransformElastix< TElastix >::OutputVnlVectorType

Definition at line 126 of file elxAdvancedAffineTransform.h.

ParameterMapType

template<class TElastix >

typedef Superclass2::ParameterMapType elastix::AdvancedAffineTransformElastix< TElastix >::ParameterMapType

Definition at line 133 of file elxAdvancedAffineTransform.h.

ParametersType

template<class TElastix >

typedef Superclass1::ParametersType elastix::AdvancedAffineTransformElastix< TElastix >::ParametersType

Definition at line 118 of file elxAdvancedAffineTransform.h.

Pointer

template<class TElastix >

typedef itk::SmartPointer< Self > elastix::AdvancedAffineTransformElastix< TElastix >::Pointer

Definition at line 91 of file elxAdvancedAffineTransform.h.

PointType

template<class TElastix >

typedef FixedImageType::PointType elastix::AdvancedAffineTransformElastix< TElastix >::PointType

Definition at line 148 of file elxAdvancedAffineTransform.h.

RegionType

template<class TElastix >

typedef FixedImageType::RegionType elastix::AdvancedAffineTransformElastix< TElastix >::RegionType

Definition at line 150 of file elxAdvancedAffineTransform.h.

RegistrationPointer

template<class TElastix >

typedef Superclass2::RegistrationPointer elastix::AdvancedAffineTransformElastix< TElastix >::RegistrationPointer

Definition at line 137 of file elxAdvancedAffineTransform.h.

RegistrationType

template<class TElastix >

typedef Superclass2::RegistrationType elastix::AdvancedAffineTransformElastix< TElastix >::RegistrationType

Definition at line 136 of file elxAdvancedAffineTransform.h.

ScalarType

template<class TElastix >

typedef Superclass1::ScalarType elastix::AdvancedAffineTransformElastix< TElastix >::ScalarType

Typedefs inherited from the superclass.

Definition at line 117 of file elxAdvancedAffineTransform.h.

ScalesType

template<class TElastix >

typedef Superclass2::ScalesType elastix::AdvancedAffineTransformElastix< TElastix >::ScalesType

For scales setting in the optimizer

Definition at line 160 of file elxAdvancedAffineTransform.h.

Self

template<class TElastix >

typedef AdvancedAffineTransformElastix elastix::AdvancedAffineTransformElastix< TElastix >::Self

Standard ITK-stuff.

Definition at line 86 of file elxAdvancedAffineTransform.h.

SizeType

template<class TElastix >

typedef FixedImageType::SizeType elastix::AdvancedAffineTransformElastix< TElastix >::SizeType

Definition at line 147 of file elxAdvancedAffineTransform.h.

SpacingType

template<class TElastix >

typedef FixedImageType::SpacingType elastix::AdvancedAffineTransformElastix< TElastix >::SpacingType

Definition at line 149 of file elxAdvancedAffineTransform.h.

Superclass1

template<class TElastix >

typedef itk::AdvancedCombinationTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > elastix::AdvancedAffineTransformElastix< TElastix >::Superclass1

Definition at line 89 of file elxAdvancedAffineTransform.h.

Superclass2

template<class TElastix >

typedef elx::TransformBase< TElastix > elastix::AdvancedAffineTransformElastix< TElastix >::Superclass2

Definition at line 90 of file elxAdvancedAffineTransform.h.

TransformInitializerPointer

template<class TElastix >

typedef TransformInitializerType::Pointer elastix::AdvancedAffineTransformElastix< TElastix >::TransformInitializerPointer

Definition at line 156 of file elxAdvancedAffineTransform.h.

TransformInitializerType

template<class TElastix >

typedef itk::CenteredTransformInitializer2< AffineTransformType, FixedImageType, MovingImageType > elastix::AdvancedAffineTransformElastix< TElastix >::TransformInitializerType

Definition at line 155 of file elxAdvancedAffineTransform.h.

Constructor & Destructor Documentation

AdvancedAffineTransformElastix() [1/2]

template<class TElastix >

elastix::AdvancedAffineTransformElastix< TElastix >::AdvancedAffineTransformElastix ( )

protected

The constructor.

~AdvancedAffineTransformElastix()

template<class TElastix >

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

inlineoverrideprotected

The destructor.

Definition at line 216 of file elxAdvancedAffineTransform.h.

AdvancedAffineTransformElastix() [2/2]

template<class TElastix >

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

private

The private constructor.

Member Function Documentation

BeforeRegistration()

template<class TElastix >

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

overridevirtual

Execute stuff before the actual registration:

• Call InitializeTransform
• Set the scales.

Reimplemented from elastix::BaseComponent.

CreateTransformParametersMap()

template<class TElastix >

void elastix::AdvancedAffineTransformElastix< TElastix >::CreateTransformParametersMap ( const ParametersType &  param, ParameterMapType *  paramsMap  ) const

overridevirtual

Function to create transform-parameters map. Creates the TransformParametersmap

Reimplemented from elastix::TransformBase< TElastix >.

elxClassNameMacro()

template<class TElastix >

elastix::AdvancedAffineTransformElastix< TElastix >::elxClassNameMacro

(

"AffineTransform"

)

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

GetClassName()

template<class TElastix >

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

virtual

Run-time type information (and related methods).

Reimplemented from elastix::TransformBase< TElastix >.

InitializeTransform()

template<class TElastix >

virtual void elastix::AdvancedAffineTransformElastix< TElastix >::InitializeTransform ( void  )

virtual

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 or scaling.

itkStaticConstMacro()

template<class TElastix >

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

Dimension of the domain space.

New()

template<class TElastix >

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

static

Method for creation through the object factory.

operator=()

template<class TElastix >

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

private

The private copy constructor.

ReadCenterOfRotationPoint()

template<class TElastix >

virtual bool elastix::AdvancedAffineTransformElastix< 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::AdvancedAffineTransformElastix< TElastix >::ReadFromFile ( void  )

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::AdvancedAffineTransformElastix< TElastix >::SetScales ( void  )

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

WriteToFile()

template<class TElastix >

void elastix::AdvancedAffineTransformElastix< TElastix >::WriteToFile ( const ParametersType &  param ) const

overridevirtual

Function to write transform-parameters to a file. It writes the center of rotation to file and calls the superclass' implementation.

Reimplemented from elastix::TransformBase< TElastix >.

Field Documentation

m_AffineTransform

template<class TElastix >

AffineTransformPointer elastix::AdvancedAffineTransformElastix< TElastix >::m_AffineTransform

private

Definition at line 232 of file elxAdvancedAffineTransform.h.