elastix::AdvancedBSplineTransform< TElastix > Class Template Reference

#include <elxAdvancedBSplineTransform.h>

Detailed Description

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

A transform based on the itkAdvancedBSplineTransform.

This transform is a B-spline transformation, commonly used for nonrigid registration.

The parameters used in this class are:

Parameters

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

BSplineTransformSplineOrder: choose a B-spline order 1,2, or 3.
example: (BSplineTransformSplineOrder 3)
Default value: 3 (cubic B-splines).

FinalGridSpacingInVoxels: the grid spacing of the B-spline transform for each dimension.
example: (FinalGridSpacingInVoxels 8.0 8.0 8.0)
If only one argument is given, that factor is used for each dimension. The spacing is not in millimeters, but in "voxel size units". The default is 16.0 in every dimension.

FinalGridSpacingInPhysicalUnits: the grid spacing of the B-spline transform for each dimension.
example: (FinalGridSpacingInPhysicalUnits 8.0 8.0 8.0)
If only one argument is given, that factor is used for each dimension. The spacing is specified in millimeters. If not specified, the FinalGridSpacingInVoxels is used, or the FinalGridSpacing, to compute a FinalGridSpacingInPhysicalUnits. If those are not specified, the default value for FinalGridSpacingInVoxels is used to compute a FinalGridSpacingInPhysicalUnits. If an affine transformation is provided as initial transformation, the control grid will be scaled to cover the fixed image domain in the space defined by the initial transformation.

GridSpacingSchedule: the grid spacing downsampling factors for the B-spline transform for each dimension and each resolution.
example: (GridSpacingSchedule 4.0 4.0 2.0 2.0 1.0 1.0)
Which is an example for a 2D image, using 3 resolutions.
For convenience, you may also specify only one value for each resolution:
example: (GridSpacingSchedule 4.0 2.0 1.0 )
which is equivalent to the example above.

PassiveEdgeWidth: the width of a band of control points at the border of the B-spline coefficient image that should remain passive during optimisation.
Can be specified for each resolution.
example: (PassiveEdgeWidth 0 1 2)
The default is zero for all resolutions. A value of 4 will avoid all deformations at the edge of the image. Make sure that 2*PassiveEdgeWidth < ControlPointGridSize in each dimension.

UseCyclicTransform: use the cyclic version of the B-spline transform which ensures that the B-spline polynomials wrap around in the slowest varying dimension. This is useful for dynamic imaging data in which the motion is assumed to be cyclic, for example in ECG-gated or respiratory gated CTA. For more information see the paper: Nonrigid registration of dynamic medical imaging data using nD+t B-splines and a groupwise optimization approach, C.T. Metz, S. Klein, M. Schaap, T. van Walsum and W.J. Niessen, Medical Image Analysis, in press.

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

Transform Parameters

GridSize: stores the size of the B-spline grid.
example: (GridSize 16 16 16)

GridIndex: stores the index of the B-spline grid.
example: (GridIndex 0 0 0)

GridSpacing: stores the spacing of the B-spline grid.
example: (GridSpacing 16.0 16.0 16.0)

GridOrigin: stores the origin of the B-spline grid.
example: (GridOrigin 0.0 0.0 0.0)

GridDirection: stores the direction cosines of the B-spline grid.
The matrix elements must be specified in column-major order.
example: (GridDirection 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.1)

BSplineTransformSplineOrder: stores the B-spline order 1,2, or 3.
example: (BSplineTransformSplineOrder 3) Default value: 3 (cubic B-splines).

UseCyclicTransform: use the cyclic version of the B-spline transform which ensures that the B-spline polynomials wrap around in the slowest varying dimension. This is useful for dynamic imaging data in which the motion is assumed to be cyclic, for example in ECG-gated or respiratory gated CTA. For more information see the paper: Nonrigid registration of dynamic medical imaging data using nD+t B-splines and a groupwise optimization approach, C.T. Metz, S. Klein, M. Schaap, T. van Walsum and W.J. Niessen, Medical Image Analysis, in press.

Todo

It is unsure what happens when one of the image dimensions has length 1.

Definition at line 110 of file elxAdvancedBSplineTransform.h.

Inheritance diagram for elastix::AdvancedBSplineTransform< TElastix >:

Public Types
using	BSplineTransformBasePointer = typename BSplineTransformBaseType::Pointer
using	BSplineTransformBaseType
using	CombinationTransformType = typename Superclass2::CombinationTransformType
using	ConstPointer = itk::SmartPointer<const Self>
using	ContinuousIndexType = typename BSplineTransformBaseType::ContinuousIndexType
using	CoordinateType
using	CyclicGridScheduleComputerType = itk::CyclicGridScheduleComputer<CoordinateType, SpaceDimension>
using	DirectionType = typename BSplineTransformBaseType::DirectionType
using	FixedImageType
using	GridScheduleComputerPointer = typename GridScheduleComputerType::Pointer
using	GridScheduleComputerType = itk::GridScheduleComputer<CoordinateType, SpaceDimension>
using	GridScheduleType = typename GridScheduleComputerType ::VectorGridSpacingFactorType
using	GridUpsamplerPointer = typename GridUpsamplerType::Pointer
using	GridUpsamplerType = itk::UpsampleBSplineParametersFilter<ParametersType, ImageType>
using	ImagePointer = typename BSplineTransformBaseType::ImagePointer
using	ImageType = typename BSplineTransformBaseType::ImageType
using	IndexType = typename BSplineTransformBaseType::IndexType
using	ITKBaseType = typename Superclass2::ITKBaseType
using	MovingImageType
using	OriginType = typename BSplineTransformBaseType::OriginType
using	ParameterIndexArrayType = typename BSplineTransformBaseType::ParameterIndexArrayType
using	ParameterMapType
using	Pointer = itk::SmartPointer<Self>
using	RegionType = typename BSplineTransformBaseType::RegionType
using	Self = AdvancedBSplineTransform
using	SizeType = typename BSplineTransformBaseType::SizeType
using	SpacingType = typename BSplineTransformBaseType::SpacingType
using	Superclass1
using	Superclass2 = elx::TransformBase<TElastix>
Public Types inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
using	ConstPointer = SmartPointer<const Self>
using	CurrentTransformConstPointer = typename CurrentTransformType::ConstPointer
using	CurrentTransformInverseTransformBasePointer = typename CurrentTransformType::InverseTransformBasePointer
using	CurrentTransformInverseTransformBaseType = typename CurrentTransformType::InverseTransformBaseType
using	CurrentTransformPointer = typename CurrentTransformType::Pointer
using	CurrentTransformType = Superclass
using	InitialTransformConstPointer = typename InitialTransformType::ConstPointer
using	InitialTransformInverseTransformBasePointer = typename InitialTransformType::InverseTransformBasePointer
using	InitialTransformInverseTransformBaseType = typename InitialTransformType::InverseTransformBaseType
using	InitialTransformPointer = typename InitialTransformType::Pointer
using	InitialTransformType = Superclass
using	InternalMatrixType
using	InverseTransformBaseType = typename Superclass::InverseTransformBaseType
using	JacobianOfSpatialHessianType
using	JacobianOfSpatialJacobianType
using	MovingImageGradientType
using	MovingImageGradientValueType
using	NonZeroJacobianIndicesType
using	Pointer = SmartPointer<Self>
using	Self = AdvancedCombinationTransform
using	SpatialHessianType
using	SpatialJacobianType
using	Superclass = AdvancedTransform<TScalarType, NDimensions, NDimensions>
using	TransformType = typename Superclass::TransformType
using	TransformTypeConstPointer = typename TransformType::ConstPointer
using	TransformTypePointer = typename TransformType::Pointer
Public Types inherited from itk::AdvancedTransform< TScalarType, 3, 3 >
using	ConstPointer
using	InternalMatrixType
using	InverseTransformBaseType
using	JacobianOfSpatialHessianType
using	JacobianOfSpatialJacobianType
using	MovingImageGradientType
using	MovingImageGradientValueType
using	NonZeroJacobianIndicesType
using	Pointer
using	Self
using	SpatialHessianType
using	SpatialJacobianType
using	Superclass
using	TransformType
using	TransformTypeConstPointer
using	TransformTypePointer
Public Types inherited from elastix::TransformBase< TElastix >
using	CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, Self::FixedImageDimension>
using	CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType
using	CommandLineEntryType = Configuration ::CommandLineEntryType
using	ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
using	CoordinateType = ElastixBase::CoordinateType
using	DeformationFieldImageType = itk::Image<VectorPixelType, FixedImageDimension>
using	FixedImageType = typename TElastix::FixedImageType
using	InitialTransformType = typename CombinationTransformType::InitialTransformType
using	InputPointType = typename ITKBaseType::InputPointType
using	ITKBaseType = CombinationTransformType
using	ITKRegistrationType = typename RegistrationType::ITKBaseType
using	MovingImageType = typename TElastix::MovingImageType
using	OptimizerType = typename ITKRegistrationType::OptimizerType
using	OutputPointType = typename ITKBaseType::OutputPointType
using	ParameterMapType = typename TElastix::ParameterMapType
using	ParametersType = itk::OptimizerParameters<ValueType>
using	PtrToCreator = ComponentDatabase::PtrToCreator
using	RegistrationType
using	ScalesType = itk::Optimizer::ScalesType
using	Self = TransformBase
using	SpatialJacobianDeterminantImageType = itk::Image<float, FixedImageDimension>
using	SpatialJacobianMatrixImageType
using	Superclass = BaseComponentSE<TElastix>
using	ValueType = double
using	VectorPixelType = itk::Vector<float, FixedImageDimension>
Public Types inherited from elastix::BaseComponentSE< TElastix >
using	ElastixType = TElastix
using	RegistrationType = typename ElastixType::RegistrationBaseType
using	Self = BaseComponentSE
using	Superclass = BaseComponent

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

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::AdvancedCombinationTransform< TScalarType, NDimensions >
static Pointer	New ()
Static Public Member Functions inherited from elastix::BaseComponent
template<typename TBaseComponent>
static auto	AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())
static void	InitializeElastixExecutable ()
static bool	IsElastixLibrary ()

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

Private Member Functions
ParameterMapType	CreateDerivedTransformParameterMap () const override
unsigned int	InitializeBSplineTransform ()
void	InitializeTransform ()

Private Attributes
	elxOverrideGetSelfMacro
BSplineTransformBasePointer	m_BSplineTransform
bool	m_Cyclic
GridScheduleComputerPointer	m_GridScheduleComputer
GridUpsamplerPointer	m_GridUpsampler
unsigned int	m_SplineOrder

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

Member Typedef Documentation

BSplineTransformBasePointer

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::BSplineTransformBasePointer = typename BSplineTransformBaseType::Pointer

Definition at line 147 of file elxAdvancedBSplineTransform.h.

BSplineTransformBaseType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::BSplineTransformBaseType

Initial value:

 
itk::AdvancedBSplineDeformableTransformBase<typename elx::TransformBase<TElastix>::CoordinateType,
                                            Self::SpaceDimension>

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

Definition at line 144 of file elxAdvancedBSplineTransform.h.

CombinationTransformType

template<typename TElastix>

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

Definition at line 183 of file elxAdvancedBSplineTransform.h.

ConstPointer

template<typename TElastix>

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

Definition at line 124 of file elxAdvancedBSplineTransform.h.

ContinuousIndexType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::ContinuousIndexType = typename BSplineTransformBaseType::ContinuousIndexType

Definition at line 173 of file elxAdvancedBSplineTransform.h.

CoordinateType

template<typename TElastix>

using elastix::TransformBase< TElastix >::CoordinateType

Elastix typedef's.

Definition at line 163 of file elxTransformBase.h.

CyclicGridScheduleComputerType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::CyclicGridScheduleComputerType = itk::CyclicGridScheduleComputer<CoordinateType, SpaceDimension>

Definition at line 187 of file elxAdvancedBSplineTransform.h.

DirectionType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::DirectionType = typename BSplineTransformBaseType::DirectionType

Definition at line 172 of file elxAdvancedBSplineTransform.h.

FixedImageType

template<typename TElastix>

using elastix::TransformBase< TElastix >::FixedImageType

Definition at line 164 of file elxTransformBase.h.

GridScheduleComputerPointer

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::GridScheduleComputerPointer = typename GridScheduleComputerType::Pointer

Definition at line 188 of file elxAdvancedBSplineTransform.h.

GridScheduleComputerType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::GridScheduleComputerType = itk::GridScheduleComputer<CoordinateType, SpaceDimension>

Typedef's for the GridScheduleComputer and the UpsampleBSplineParametersFilter.

Definition at line 186 of file elxAdvancedBSplineTransform.h.

GridScheduleType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::GridScheduleType = typename GridScheduleComputerType ::VectorGridSpacingFactorType

Definition at line 189 of file elxAdvancedBSplineTransform.h.

GridUpsamplerPointer

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::GridUpsamplerPointer = typename GridUpsamplerType::Pointer

Definition at line 191 of file elxAdvancedBSplineTransform.h.

GridUpsamplerType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::GridUpsamplerType = itk::UpsampleBSplineParametersFilter<ParametersType, ImageType>

Definition at line 190 of file elxAdvancedBSplineTransform.h.

ImagePointer

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::ImagePointer = typename BSplineTransformBaseType::ImagePointer

Definition at line 166 of file elxAdvancedBSplineTransform.h.

ImageType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::ImageType = typename BSplineTransformBaseType::ImageType

Definition at line 165 of file elxAdvancedBSplineTransform.h.

IndexType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::IndexType = typename BSplineTransformBaseType::IndexType

Definition at line 168 of file elxAdvancedBSplineTransform.h.

ITKBaseType

template<typename TElastix>

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

Definition at line 182 of file elxAdvancedBSplineTransform.h.

MovingImageType

template<typename TElastix>

using elastix::TransformBase< TElastix >::MovingImageType

Definition at line 165 of file elxTransformBase.h.

OriginType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::OriginType = typename BSplineTransformBaseType::OriginType

Definition at line 171 of file elxAdvancedBSplineTransform.h.

ParameterIndexArrayType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::ParameterIndexArrayType = typename BSplineTransformBaseType::ParameterIndexArrayType

Definition at line 174 of file elxAdvancedBSplineTransform.h.

ParameterMapType

template<typename TElastix>

using elastix::TransformBase< TElastix >::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 206 of file elxTransformBase.h.

Pointer

template<typename TElastix>

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

Definition at line 123 of file elxAdvancedBSplineTransform.h.

RegionType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::RegionType = typename BSplineTransformBaseType::RegionType

Definition at line 167 of file elxAdvancedBSplineTransform.h.

Self

template<typename TElastix>

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

Standard ITK-stuff.

Definition at line 119 of file elxAdvancedBSplineTransform.h.

SizeType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::SizeType = typename BSplineTransformBaseType::SizeType

Definition at line 169 of file elxAdvancedBSplineTransform.h.

SpacingType

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::SpacingType = typename BSplineTransformBaseType::SpacingType

Definition at line 170 of file elxAdvancedBSplineTransform.h.

Superclass1

template<typename TElastix>

using elastix::AdvancedBSplineTransform< TElastix >::Superclass1

Initial value:

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

Definition at line 120 of file elxAdvancedBSplineTransform.h.

Superclass2

template<typename TElastix>

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

Definition at line 122 of file elxAdvancedBSplineTransform.h.

Constructor & Destructor Documentation

AdvancedBSplineTransform()

template<typename TElastix>

elastix::AdvancedBSplineTransform< TElastix >::AdvancedBSplineTransform ( )

protecteddefault

The constructor.

~AdvancedBSplineTransform()

template<typename TElastix>

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

overrideprotecteddefault

The destructor.

Member Function Documentation

BeforeAll()

template<typename TElastix>

int elastix::AdvancedBSplineTransform< TElastix >::BeforeAll ( )

overridevirtual

Execute stuff before anything else is done:

• Initialize the right BSplineTransform.
• Initialize the right grid schedule computer.

Reimplemented from elastix::BaseComponent.

BeforeEachResolution()

template<typename TElastix>

void elastix::AdvancedBSplineTransform< TElastix >::BeforeEachResolution ( )

overridevirtual

Execute stuff before each new pyramid resolution:

• In the first resolution call InitializeTransform().
• In next resolutions upsample the B-spline grid if necessary (so, call IncreaseScale())

Reimplemented from elastix::BaseComponent.

BeforeRegistration()

template<typename TElastix>

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

overridevirtual

Execute stuff before the actual registration:

• Create an initial B-spline grid.
• Create initial registration parameters.
• PrecomputeGridInformation Initially, the transform is set to use a 1x1x1 grid, with deformation (0,0,0). In the method BeforeEachResolution() this will be replaced by the right grid size. This seems not logical, but it is required, since the registration class checks if the number of parameters in the transform is equal to the number of parameters in the registration class. This check is done before calling the BeforeEachResolution() methods.

Reimplemented from elastix::BaseComponent.

CreateDerivedTransformParameterMap()

template<typename TElastix>

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

overrideprivatevirtual

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

Implements elastix::TransformBase< TElastix >.

elxClassNameMacro()

template<typename TElastix>

elastix::AdvancedBSplineTransform< TElastix >::elxClassNameMacro

(

"BSplineTransform"

)

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

IncreaseScale()

template<typename TElastix>

virtual void elastix::AdvancedBSplineTransform< TElastix >::IncreaseScale ( )

virtual

Method to increase the density of the B-spline grid.

• Determine the new B-spline coefficients that describe the current deformation field.
• Set these coefficients as InitialParametersOfNextLevel in the registration object. Called by BeforeEachResolution().

InitializeBSplineTransform()

template<typename TElastix>

unsigned int elastix::AdvancedBSplineTransform< TElastix >::InitializeBSplineTransform ( )

private

Initialize the right B-spline transform based on the spline order and periodicity.

InitializeTransform()

template<typename TElastix>

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

private

Method to set the initial B-spline grid and initialize the parameters (to 0).

• Define the initial grid region, origin and spacing, using the precomputed grid information.
• Set the initial parameters to zero and set then as InitialParametersOfNextLevel in the registration object. Called by BeforeEachResolution().

ITK_DISALLOW_COPY_AND_MOVE()

template<typename TElastix>

elastix::AdvancedBSplineTransform< TElastix >::ITK_DISALLOW_COPY_AND_MOVE

(

AdvancedBSplineTransform< TElastix >

)

itkOverrideGetNameOfClassMacro()

template<typename TElastix>

elastix::AdvancedBSplineTransform< TElastix >::itkOverrideGetNameOfClassMacro

(

AdvancedBSplineTransform< TElastix >

)

Run-time type information (and related methods).

itkStaticConstMacro()

template<typename TElastix>

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

Dimension of the fixed image.

New()

template<typename TElastix>

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

static

Method for creation through the object factory.

PreComputeGridInformation()

template<typename TElastix>

virtual void elastix::AdvancedBSplineTransform< TElastix >::PreComputeGridInformation ( )

protectedvirtual

Read user-specified grid spacing and call the itkGridScheduleComputer.

ReadFromFile()

template<typename TElastix>

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

overridevirtual

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

SetOptimizerScales()

template<typename TElastix>

virtual void elastix::AdvancedBSplineTransform< TElastix >::SetOptimizerScales ( const unsigned int edgeWidth )

virtual

Set the scales of the edge B-spline coefficients to zero.

Member Data Documentation

elxOverrideGetSelfMacro

template<typename TElastix>

elastix::AdvancedBSplineTransform< TElastix >::elxOverrideGetSelfMacro

private

Definition at line 252 of file elxAdvancedBSplineTransform.h.

m_BSplineTransform

template<typename TElastix>

BSplineTransformBasePointer elastix::AdvancedBSplineTransform< TElastix >::m_BSplineTransform

private

Private variables.

Definition at line 267 of file elxAdvancedBSplineTransform.h.

m_Cyclic

template<typename TElastix>

bool elastix::AdvancedBSplineTransform< TElastix >::m_Cyclic

private

Definition at line 273 of file elxAdvancedBSplineTransform.h.

m_GridScheduleComputer

template<typename TElastix>

GridScheduleComputerPointer elastix::AdvancedBSplineTransform< TElastix >::m_GridScheduleComputer

private

Definition at line 268 of file elxAdvancedBSplineTransform.h.

m_GridUpsampler

template<typename TElastix>

GridUpsamplerPointer elastix::AdvancedBSplineTransform< TElastix >::m_GridUpsampler

private

Definition at line 269 of file elxAdvancedBSplineTransform.h.

m_SplineOrder

template<typename TElastix>

unsigned int elastix::AdvancedBSplineTransform< TElastix >::m_SplineOrder

private

Variables to remember order and periodicity of B-spline transform.

Definition at line 272 of file elxAdvancedBSplineTransform.h.