elastix::SplineKernelTransform< TElastix > Class Template Reference

#include <elxSplineKernelTransform.h>

Detailed Description

template<class TElastix>
class elastix::SplineKernelTransform< TElastix >

A transform based on the itk::KernelTransform2.

This transform is a nonrigid transformation, based on thin-plate-spline-like kernels.

The ITK code for this class is largely based on code by Rupert Brooks. For elastix a few modifications were made (making the transform thread safe, and make it support the AdvancedTransform framework).

This nonrigid transformation model allows the user to place control points at application-specific positions, unlike the BSplineTransform, which always uses a regular grid of control points.

NB: in order to use this class for registration, the -fp command line argument is mandatory! It is used to place the fixed image landmarks.

The parameters used in this class are:

Parameters:

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

SplineKernelType: Select the deformation model, which must be one of { ThinPlateSpline, ThinPlateR2LogRSpline, VolumeSpline, ElasticBodySpline, ElasticBodyReciprocalSpline). In 2D this option is ignored and a ThinPlateSpline will always be used.
example: (SplineKernelType "ElasticBodySpline")
Default: ThinPlateSpline. You cannot specify this parameter for each resolution differently.

SplineRelaxationFactor: make the spline interpolating or approximating. A value of 0.0 gives an interpolating transform. Higher values result in approximating splines.
example: (SplineRelaxationFactor 0.01 )
Default: 0.0. You cannot specify this parameter for each resolution differently.

SplinePoissonRatio: Set the poisson ratio for the ElasticBodySpline and the ElastixBodyReciprocalSpline. For other SplineKernelTypes this parameters is ignored.
example: (SplinePoissonRatio 0.3 )
Default: 0.3. You cannot specify this parameter for each resolution differently.
Valid values are withing -1.0 and 0.5. 0.5 means incompressible. Negative values are a bit odd, but possible. See Wikipedia on PoissonRatio.

Command line arguments:

-fp: a file specifying a set of points that will serve as fixed image landmarks.
example: -fp fixedImagePoints.txt
The fixedImagePoints.txt file should be structured: first line should be "index" or "point", depending if the user supplies voxel indices or real world coordinates. The second line should be the number of points that should be transformed. The third and following lines give the indices or points. The same structure thus as used for transformix.

-mp: an optional file specifying a set of points that will serve as moving image landmarks, used to initialize the transformation.
example: -mp movingImagePoints.txt
The movingImagePoints.txt should be structured like the fixedImagePoints.txt. The moving landmarks should be corresponding to the fixed landmarks. If no file is provided, the transformation is initialized to be the identity, i.e. the moving landmarks are chosen identical to the fixed landmarks.

Transform Parameters:

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

SplineKernelType: Select the deformation model, which must be one of { ThinPlateSpline, ThinPlateR2LogRSpline, VolumeSpline, ElasticBodySpline, ElasticBodyReciprocalSpline). In 2D this option is ignored and a ThinPlateSpline will always be used.
example: (SplineKernelType "ElasticBodySpline")
*

SplineRelaxationFactor: make the spline interpolating or approximating. A value of 0.0 gives an interpolating transform. Higher values result in approximating splines.
example: (SplineRelaxationFactor 0.01 )
*

SplinePoissonRatio: Set the Poisson ratio for the ElasticBodySpline and the ElastixBodyReciprocalSpline. For other SplineKernelTypes this parameters is ignored.
example: (SplinePoissonRatio 0.3 )
Valid values are withing -1.0 and 0.5. 0.5 means incompressible. Negative values are a bit odd, but possible. See Wikipedia on PoissonRatio.

FixedImageLandmarks: The landmark positions in the fixed image, in world coordinates. Positions written as x1 y1 [z1] x2 y2 [z2] etc.
example: (FixedImageLandmarks 10.0 11.0 12.0 4.0 4.0 4.0 6.0 6.0 6.0 )

Definition at line 115 of file elxSplineKernelTransform.h.

Inheritance diagram for elastix::SplineKernelTransform< TElastix >:

Public Types
typedef Superclass2::CombinationTransformType	CombinationTransformType
typedef Superclass2::ConfigurationPointer	ConfigurationPointer
typedef Superclass2::ConfigurationType	ConfigurationType
typedef itk::SmartPointer< const Self >	ConstPointer
typedef Superclass2::CoordRepType	CoordRepType
typedef Superclass2::ElastixPointer	ElastixPointer
typedef Superclass2::ElastixType	ElastixType
typedef Superclass2::FixedImageType	FixedImageType
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 KernelTransformType::Pointer	KernelTransformPointer
typedef itk::KernelTransform2< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >	KernelTransformType
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 Superclass1::ParametersType	ParametersType
typedef itk::SmartPointer< Self >	Pointer
typedef PointSetType::Pointer	PointSetPointer
typedef KernelTransformType::PointSetType	PointSetType
typedef Superclass2::RegistrationPointer	RegistrationPointer
typedef Superclass2::RegistrationType	RegistrationType
typedef Superclass1::ScalarType	ScalarType
typedef SplineKernelTransform	Self
typedef itk::AdvancedCombinationTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >	Superclass1
typedef elx::TransformBase< TElastix >	Superclass2
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
int	BeforeAll (void) override
void	BeforeRegistration (void) override
	elxClassNameMacro ("SplineKernelTransform")
virtual const char *	GetClassName () const
	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
void	ReadFromFile (void) override
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 Types
typedef itk::ElasticBodySplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	EBKernelTransformType
typedef itk::ElasticBodyReciprocalSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	EBRKernelTransformType
typedef itk::ThinPlateSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	TPKernelTransformType
typedef itk::ThinPlateR2LogRSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	TPRKernelTransformType
typedef itk::VolumeSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	VKernelTransformType

Protected Member Functions
virtual void	DetermineSourceLandmarks (void)
virtual bool	DetermineTargetLandmarks (void)
virtual void	ReadLandmarkFile (const std::string &filename, PointSetPointer &landmarkPointSet, const bool &landmarksInFixedImage)
virtual bool	SetKernelType (const std::string &kernelType)
	SplineKernelTransform ()
	~SplineKernelTransform () 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

Protected Attributes
KernelTransformPointer	m_KernelTransform
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 {}

Private Member Functions
void	operator= (const Self &)
	SplineKernelTransform (const Self &)

Private Attributes
std::string	m_SplineKernelType

Member Typedef Documentation

CombinationTransformType

template<class TElastix >

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

Definition at line 178 of file elxSplineKernelTransform.h.

ConfigurationPointer

template<class TElastix >

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

Definition at line 171 of file elxSplineKernelTransform.h.

ConfigurationType

template<class TElastix >

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

Definition at line 170 of file elxSplineKernelTransform.h.

ConstPointer

template<class TElastix >

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

Definition at line 136 of file elxSplineKernelTransform.h.

CoordRepType

template<class TElastix >

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

Definition at line 174 of file elxSplineKernelTransform.h.

EBKernelTransformType

template<class TElastix >

typedef itk::ElasticBodySplineKernelTransform2< CoordRepType, itkGetStaticConstMacro( SpaceDimension ) > elastix::SplineKernelTransform< TElastix >::EBKernelTransformType

protected

Definition at line 219 of file elxSplineKernelTransform.h.

EBRKernelTransformType

template<class TElastix >

typedef itk::ElasticBodyReciprocalSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro( SpaceDimension ) > elastix::SplineKernelTransform< TElastix >::EBRKernelTransformType

protected

Definition at line 221 of file elxSplineKernelTransform.h.

ElastixPointer

template<class TElastix >

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

Definition at line 169 of file elxSplineKernelTransform.h.

ElastixType

template<class TElastix >

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

Typedef's from the TransformBase class.

Definition at line 168 of file elxSplineKernelTransform.h.

FixedImageType

template<class TElastix >

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

Definition at line 175 of file elxSplineKernelTransform.h.

InputCovariantVectorType

template<class TElastix >

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

Definition at line 160 of file elxSplineKernelTransform.h.

InputPointType

template<class TElastix >

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

Definition at line 164 of file elxSplineKernelTransform.h.

InputVectorType

template<class TElastix >

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

Definition at line 158 of file elxSplineKernelTransform.h.

InputVnlVectorType

template<class TElastix >

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

Definition at line 162 of file elxSplineKernelTransform.h.

ITKBaseType

template<class TElastix >

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

Definition at line 177 of file elxSplineKernelTransform.h.

JacobianType

template<class TElastix >

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

Definition at line 157 of file elxSplineKernelTransform.h.

KernelTransformPointer

template<class TElastix >

typedef KernelTransformType::Pointer elastix::SplineKernelTransform< TElastix >::KernelTransformPointer

Extra typedefs

Definition at line 181 of file elxSplineKernelTransform.h.

KernelTransformType

template<class TElastix >

typedef itk::KernelTransform2< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > elastix::SplineKernelTransform< TElastix >::KernelTransformType

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

Definition at line 134 of file elxSplineKernelTransform.h.

MovingImageType

template<class TElastix >

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

Definition at line 176 of file elxSplineKernelTransform.h.

NumberOfParametersType

template<class TElastix >

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

Definition at line 156 of file elxSplineKernelTransform.h.

OutputCovariantVectorType

template<class TElastix >

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

Definition at line 161 of file elxSplineKernelTransform.h.

OutputPointType

template<class TElastix >

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

Definition at line 165 of file elxSplineKernelTransform.h.

OutputVectorType

template<class TElastix >

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

Definition at line 159 of file elxSplineKernelTransform.h.

OutputVnlVectorType

template<class TElastix >

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

Definition at line 163 of file elxSplineKernelTransform.h.

ParametersType

template<class TElastix >

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

Definition at line 155 of file elxSplineKernelTransform.h.

Pointer

template<class TElastix >

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

Definition at line 135 of file elxSplineKernelTransform.h.

PointSetPointer

template<class TElastix >

typedef PointSetType::Pointer elastix::SplineKernelTransform< TElastix >::PointSetPointer

Definition at line 183 of file elxSplineKernelTransform.h.

PointSetType

template<class TElastix >

typedef KernelTransformType::PointSetType elastix::SplineKernelTransform< TElastix >::PointSetType

Definition at line 182 of file elxSplineKernelTransform.h.

RegistrationPointer

template<class TElastix >

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

Definition at line 173 of file elxSplineKernelTransform.h.

RegistrationType

template<class TElastix >

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

Definition at line 172 of file elxSplineKernelTransform.h.

ScalarType

template<class TElastix >

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

Typedefs inherited from the superclass.

Definition at line 154 of file elxSplineKernelTransform.h.

Self

template<class TElastix >

typedef SplineKernelTransform elastix::SplineKernelTransform< TElastix >::Self

Standard ITK-stuff.

Definition at line 123 of file elxSplineKernelTransform.h.

Superclass1

template<class TElastix >

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

Definition at line 126 of file elxSplineKernelTransform.h.

Superclass2

template<class TElastix >

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

Definition at line 127 of file elxSplineKernelTransform.h.

TPKernelTransformType

template<class TElastix >

typedef itk::ThinPlateSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro( SpaceDimension ) > elastix::SplineKernelTransform< TElastix >::TPKernelTransformType

protected

Definition at line 213 of file elxSplineKernelTransform.h.

TPRKernelTransformType

template<class TElastix >

typedef itk::ThinPlateR2LogRSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro( SpaceDimension ) > elastix::SplineKernelTransform< TElastix >::TPRKernelTransformType

protected

Definition at line 215 of file elxSplineKernelTransform.h.

VKernelTransformType

template<class TElastix >

typedef itk::VolumeSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro( SpaceDimension ) > elastix::SplineKernelTransform< TElastix >::VKernelTransformType

protected

Definition at line 217 of file elxSplineKernelTransform.h.

Constructor & Destructor Documentation

SplineKernelTransform() [1/2]

template<class TElastix >

elastix::SplineKernelTransform< TElastix >::SplineKernelTransform ( )

protected

The constructor.

~SplineKernelTransform()

template<class TElastix >

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

inlineoverrideprotected

The destructor.

Definition at line 210 of file elxSplineKernelTransform.h.

SplineKernelTransform() [2/2]

template<class TElastix >

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

private

The private constructor.

Member Function Documentation

BeforeAll()

template<class TElastix >

int elastix::SplineKernelTransform< TElastix >::BeforeAll ( void  )

overridevirtual

Execute stuff before everything else:

• Check if -fp command line argument was given
• Check if -mp command line argument was given

Reimplemented from elastix::BaseComponent.

BeforeRegistration()

template<class TElastix >

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

overridevirtual

Execute stuff before the actual registration:

• Setup transform
• Determine fixed image (source) landmarks
• Determine moving image (target) landmarks
• Call InitializeTransform.

Reimplemented from elastix::BaseComponent.

DetermineSourceLandmarks()

template<class TElastix >

virtual void elastix::SplineKernelTransform< TElastix >::DetermineSourceLandmarks ( void  )

protectedvirtual

Read source landmarks from fp file

• Try reading -fp file

DetermineTargetLandmarks()

template<class TElastix >

virtual bool elastix::SplineKernelTransform< TElastix >::DetermineTargetLandmarks ( void  )

protectedvirtual

Read target landmarks from mp file or load identity.

• Try reading -mp file
• If no -mp file was given, place landmarks as identity.

elxClassNameMacro()

template<class TElastix >

elastix::SplineKernelTransform< TElastix >::elxClassNameMacro

(

"SplineKernelTransform< TElastix >"

)

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

GetClassName()

template<class TElastix >

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

virtual

Run-time type information (and related methods).

Reimplemented from elastix::TransformBase< TElastix >.

itkStaticConstMacro()

template<class TElastix >

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

Dimension of the domain space.

New()

template<class TElastix >

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

static

Method for creation through the object factory.

operator=()

template<class TElastix >

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

private

The private copy constructor.

ReadFromFile()

template<class TElastix >

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

overridevirtual

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

ReadLandmarkFile()

template<class TElastix >

virtual void elastix::SplineKernelTransform< TElastix >::ReadLandmarkFile ( const std::string &  filename, PointSetPointer &  landmarkPointSet, const bool &  landmarksInFixedImage  )

protectedvirtual

General function to read all landmarks.

SetKernelType()

template<class TElastix >

virtual bool elastix::SplineKernelTransform< TElastix >::SetKernelType ( const std::string &  kernelType )

protectedvirtual

Create an instance of a kernel transform. Returns false if the kernelType is unknown.

WriteToFile()

template<class TElastix >

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

overridevirtual

Function to write transform-parameters to a file.

Reimplemented from elastix::TransformBase< TElastix >.

Field Documentation

m_KernelTransform

template<class TElastix >

KernelTransformPointer elastix::SplineKernelTransform< TElastix >::m_KernelTransform

protected

The itk kernel transform.

Definition at line 246 of file elxSplineKernelTransform.h.

m_SplineKernelType

template<class TElastix >

std::string elastix::SplineKernelTransform< TElastix >::m_SplineKernelType

private

Definition at line 255 of file elxSplineKernelTransform.h.