#include <elxSplineKernelTransform.h>

Inheritance diagram for elastix::SplineKernelTransform< TElastix >:

Collaboration diagram for elastix::SplineKernelTransform< TElastix >:

Public Types
typedef Superclass2::CombinationTransformType	CombinationTransformType
typedef Superclass2::ConfigurationPointer	ConfigurationPointer
typedef Superclass2::ConfigurationType	ConfigurationType
typedef 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 KernelTransform2 < typename elx::TransformBase < TElastix >::CoordRepType, elx::TransformBase< TElastix > ::FixedImageDimension >	KernelTransformType
typedef Superclass2::MovingImageType	MovingImageType
typedef Superclass1::OutputCovariantVectorType	OutputCovariantVectorType
typedef Superclass1::OutputPointType	OutputPointType
typedef Superclass1::OutputVectorType	OutputVectorType
typedef Superclass1::OutputVnlVectorType	OutputVnlVectorType
typedef Superclass1::ParametersType	ParametersType
typedef 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 AdvancedCombinationTransform < typename elx::TransformBase < TElastix >::CoordRepType, elx::TransformBase< TElastix > ::FixedImageDimension >	Superclass1
typedef elx::TransformBase < TElastix >	Superclass2
Public Member Functions
virtual int	BeforeAll (void)
virtual void	BeforeRegistration (void)
	elxClassNameMacro ("SplineKernelTransform")
virtual const char *	GetClassName () const
	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)
virtual void	ReadFromFile (void)
virtual void	WriteToFile (const ParametersType &param) const
Static Public Member Functions
static Pointer	New ()
Protected Types
typedef ElasticBodySplineKernelTransform2 < CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	EBKernelTransformType
typedef ElasticBodyReciprocalSplineKernelTransform2 < CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	EBRKernelTransformType
typedef ThinPlateSplineKernelTransform2 < CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	TPKernelTransformType
typedef ThinPlateR2LogRSplineKernelTransform2 < CoordRepType, itkGetStaticConstMacro(SpaceDimension) >	TPRKernelTransformType
typedef 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 ()
virtual	~SplineKernelTransform ()
Protected Attributes
KernelTransformPointer	m_KernelTransform
Private Member Functions
void	operator= (const Self &)
	SplineKernelTransform (const Self &)
Private Attributes
std::string	m_SplineKernelType

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")

Parameters:: 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.

Parameters:: 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.

Parameters:: 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.

Command line arguments:: -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")

Transform Parameters:: 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")
*

Transform Parameters:: 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 )
*

Transform Parameters:: 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.

Transform Parameters:: 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 113 of file elxSplineKernelTransform.h.

Member Typedef Documentation

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 175 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 168 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 167 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 134 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 171 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef ElasticBodySplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) > elastix::SplineKernelTransform< TElastix >::EBKernelTransformType [protected]

Definition at line 216 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef ElasticBodyReciprocalSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) > elastix::SplineKernelTransform< TElastix >::EBRKernelTransformType [protected]

Definition at line 218 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 166 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Typedef's from the TransformBase class.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 165 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 172 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 157 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 161 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 155 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 159 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 174 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 154 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Extra typedefs

Definition at line 178 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef 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 132 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 173 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 158 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 162 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 156 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 160 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 153 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 133 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Definition at line 180 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Definition at line 179 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 170 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 169 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Typedefs inherited from the superclass.

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

Definition at line 152 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Standard ITK-stuff.

Reimplemented from elastix::TransformBase< TElastix >.

Definition at line 121 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Definition at line 124 of file elxSplineKernelTransform.h.

template<class TElastix >

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

Definition at line 125 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef ThinPlateSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) > elastix::SplineKernelTransform< TElastix >::TPKernelTransformType [protected]

Definition at line 207 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef ThinPlateR2LogRSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) > elastix::SplineKernelTransform< TElastix >::TPRKernelTransformType [protected]

Definition at line 212 of file elxSplineKernelTransform.h.

template<class TElastix >

typedef VolumeSplineKernelTransform2< CoordRepType, itkGetStaticConstMacro(SpaceDimension) > elastix::SplineKernelTransform< TElastix >::VKernelTransformType [protected]

Definition at line 214 of file elxSplineKernelTransform.h.

Constructor & Destructor Documentation

template<class TElastix >

elastix::SplineKernelTransform< TElastix >::SplineKernelTransform ( ) [protected]

The constructor.

template<class TElastix >

virtual elastix::SplineKernelTransform< TElastix >::~SplineKernelTransform ( ) [inline, protected, virtual]

The destructor.

Definition at line 207 of file elxSplineKernelTransform.h.

template<class TElastix >

elastix::SplineKernelTransform< TElastix >::SplineKernelTransform ( const Self & ) [private]

The private constructor.

Member Function Documentation

template<class TElastix >

virtual int elastix::SplineKernelTransform< TElastix >::BeforeAll ( void ) [virtual]

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.

template<class TElastix >

virtual void elastix::SplineKernelTransform< TElastix >::BeforeRegistration ( void ) [virtual]

Execute stuff before the actual registration:

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

Reimplemented from elastix::BaseComponent.

template<class TElastix >

virtual void elastix::SplineKernelTransform< TElastix >::DetermineSourceLandmarks ( void ) [protected, virtual]

Read source landmarks from fp file

Try reading -fp file

template<class TElastix >

virtual bool elastix::SplineKernelTransform< TElastix >::DetermineTargetLandmarks ( void ) [protected, virtual]

Read target landmarks from mp file or load identity.

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

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")

template<class TElastix >

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

Run-time type information (and related methods).

Reimplemented from elastix::TransformBase< TElastix >.

template<class TElastix >

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

Dimension of the domain space.

template<class TElastix >

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

Method for creation through the object factory.

Reimplemented from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >.

template<class TElastix >

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

The private copy constructor.

template<class TElastix >

virtual void elastix::SplineKernelTransform< TElastix >::ReadFromFile ( void ) [virtual]

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

template<class TElastix >

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