#include <elxBSplineStackTransform.h>

Detailed Description

template<class TElastix>
class elastix::BSplineStackTransform< TElastix >

A B-spline transform based on the itkStackTransform.

This transform is a B-spline transformation, with for every time point a separate D-1 dimensional B-spline transform. Calls to TransformPoint and GetJacobian are redirected to the appropriate sub transform based on the last dimension (time) index.

This transform uses the size, spacing and origin of the last dimension of the fixed image to set the number of sub transforms the origin of the first transform and the spacing between the transforms.

When supplying the B-spline parameters (grid) make sure to provide dimension - 1 elements.

The parameters used in this class are:

Parameters

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

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.

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.
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).

StackSpacing: stores the spacing between the sub transforms.
exanoke: (StackSpacing 1.0)

StackOrigin: stores the origin of the first sub transform.
exanoke: (StackOrigin 0.0)

NumberOfSubTransforms: stores the number of sub transforms.
exanoke: (NumberOfSubTransforms 10)

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

Definition at line 112 of file elxBSplineStackTransform.h.

Inheritance diagram for elastix::BSplineStackTransform< TElastix >:

[legend]

Public Types
using	BSplineTransformBasePointer = typename BSplineTransformBaseType::Pointer

using	BSplineTransformBaseType

using	CombinationTransformType = typename Superclass2::CombinationTransformType

using	ConstPointer = itk::SmartPointer<const Self>

using	CoordRepType

using	DirectionType = typename BSplineTransformBaseType::DirectionType

using	FixedImageType

using	GridScheduleComputerPointer = typename GridScheduleComputerType::Pointer

using	GridScheduleComputerType = itk::GridScheduleComputer<CoordRepType, ReducedSpaceDimension>

using	GridScheduleType = typename GridScheduleComputerType ::VectorGridSpacingFactorType

using	GridUpsamplerPointer = typename GridUpsamplerType::Pointer

using	GridUpsamplerType = itk::UpsampleBSplineParametersFilter<ParametersType, ReducedDimensionImageType>

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	ParameterMapType

using	ParameterValueType = std::vector<std::string>

using	Pointer = itk::SmartPointer<Self>

using	ReducedDimensionBSplineTransformBasePointer = typename ReducedDimensionBSplineTransformBaseType::Pointer

using	ReducedDimensionBSplineTransformBaseType

using	ReducedDimensionDirectionType = typename ReducedDimensionImageType::DirectionType

using	ReducedDimensionImageType = itk::Image<PixelType, Self::ReducedSpaceDimension>

using	ReducedDimensionIndexType = typename ReducedDimensionRegionType::IndexType

using	ReducedDimensionOriginType = typename ReducedDimensionImageType::PointType

using	ReducedDimensionRegionType = itk::ImageRegion<Self::ReducedSpaceDimension>

using	ReducedDimensionSizeType = typename ReducedDimensionRegionType::SizeType

using	ReducedDimensionSpacingType = typename ReducedDimensionImageType::SpacingType

using	RegionType = typename BSplineTransformBaseType::RegionType

using	Self = BSplineStackTransform

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	InverseTransformBaseType = typename Superclass::InverseTransformBaseType

using	Pointer = SmartPointer<Self>

using	Self = AdvancedCombinationTransform

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<CoordRepType, Self::FixedImageDimension>

using	CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType

using	CommandLineEntryType = Configuration ::CommandLineEntryType

using	ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType

using	CoordRepType = ElastixBase::CoordRepType

using	DeformationFieldImageType = itk::Image<VectorPixelType, FixedImageDimension>

using	FixedImageType = typename TElastix::FixedImageType

using	InitialTransformType = typename CombinationTransformType::InitialTransformType

using	InputPointType = typename ITKBaseType::InputPointType

using	ITKBaseType = CombinationTransformType

using	ITKRegistrationType = typename RegistrationType::ITKBaseType

using	MovingImageType = typename TElastix::MovingImageType

using	OptimizerType = typename ITKRegistrationType::OptimizerType

using	OutputPointType = typename ITKBaseType::OutputPointType

using	ParameterMapType = typename TElastix::ParameterMapType

using	ParametersType = itk::OptimizerParameters<ValueType>

using	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 ("BSplineStackTransform")

virtual const char *	GetClassName () const

virtual void	IncreaseScale ()

	ITK_DISALLOW_COPY_AND_MOVE (BSplineStackTransform)

	itkStaticConstMacro (ReducedSpaceDimension, unsigned int, Superclass2::FixedImageDimension - 1)

	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)

	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)

	itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)

	itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)

Public Member Functions inherited from elastix::TransformBase< TElastix >
int	BeforeAllTransformix ()

void	ComputeAndWriteSpatialJacobianDeterminantImage () const

void	ComputeAndWriteSpatialJacobianMatrixImage () const

SpatialJacobianDeterminantImageType::Pointer	ComputeSpatialJacobianDeterminantImage () const

SpatialJacobianMatrixImageType::Pointer	ComputeSpatialJacobianMatrixImage () const

void	CreateTransformParameterMap (const ParametersType &param, ParameterMapType &parameterMap, const bool includeDerivedTransformParameters=true) const

ITKBaseType *	GetAsITKBaseType ()

const ITKBaseType *	GetAsITKBaseType () const

	ITK_DISALLOW_COPY_AND_MOVE (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)

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)

	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< 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
	BSplineStackTransform ()

virtual void	PreComputeGridInformation ()

	~BSplineStackTransform () 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 Types
using	StackTransformType = itk::BSplineStackTransform<SpaceDimension>

Private Member Functions
ParameterMapType	CreateDerivedTransformParameterMap () const override

unsigned int	InitializeBSplineTransform ()

void	InitializeTransform ()

Private Attributes
	elxOverrideGetSelfMacro

ReducedDimensionBSplineTransformBasePointer	m_DummySubTransform

GridScheduleComputerPointer	m_GridScheduleComputer

GridUpsamplerPointer	m_GridUpsampler

unsigned int	m_NumberOfSubTransforms

unsigned int	m_SplineOrder

double	m_StackOrigin

double	m_StackSpacing

const StackTransformType::Pointer	m_StackTransform { StackTransformType::New() }

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<class TElastix >

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

Definition at line 150 of file elxBSplineStackTransform.h.

◆ BSplineTransformBaseType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::BSplineTransformBaseType

Initial value:

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

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

Definition at line 147 of file elxBSplineStackTransform.h.

◆ CombinationTransformType

template<class TElastix >

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

Definition at line 181 of file elxBSplineStackTransform.h.

◆ ConstPointer

template<class TElastix >

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

Definition at line 126 of file elxBSplineStackTransform.h.

◆ CoordRepType

template<class TElastix >

using elastix::TransformBase< TElastix >::CoordRepType

Elastix typedef's.

Definition at line 156 of file elxTransformBase.h.

◆ DirectionType

template<class TElastix >

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

Definition at line 172 of file elxBSplineStackTransform.h.

◆ FixedImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::FixedImageType

Definition at line 157 of file elxTransformBase.h.

◆ GridScheduleComputerPointer

template<class TElastix >

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

Definition at line 194 of file elxBSplineStackTransform.h.

◆ GridScheduleComputerType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::GridScheduleComputerType = itk::GridScheduleComputer<CoordRepType, ReducedSpaceDimension>

Typedef's for the GridScheduleComputer and the UpsampleBSplineParametersFilter.

Definition at line 193 of file elxBSplineStackTransform.h.

◆ GridScheduleType

template<class TElastix >

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

Definition at line 195 of file elxBSplineStackTransform.h.

◆ GridUpsamplerPointer

template<class TElastix >

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

Definition at line 197 of file elxBSplineStackTransform.h.

◆ GridUpsamplerType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::GridUpsamplerType = itk::UpsampleBSplineParametersFilter<ParametersType, ReducedDimensionImageType>

Definition at line 196 of file elxBSplineStackTransform.h.

◆ ImagePointer

template<class TElastix >

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

Definition at line 166 of file elxBSplineStackTransform.h.

◆ ImageType

template<class TElastix >

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

Definition at line 165 of file elxBSplineStackTransform.h.

◆ IndexType

template<class TElastix >

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

Definition at line 168 of file elxBSplineStackTransform.h.

◆ ITKBaseType

template<class TElastix >

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

Definition at line 180 of file elxBSplineStackTransform.h.

◆ MovingImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::MovingImageType

Definition at line 158 of file elxTransformBase.h.

◆ OriginType

template<class TElastix >

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

Definition at line 171 of file elxBSplineStackTransform.h.

◆ ParameterMapType

template<class TElastix >

using elastix::TransformBase< TElastix >::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 199 of file elxTransformBase.h.

◆ ParameterValueType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ParameterValueType = std::vector<std::string>

Typedef's creation of parameter map

Definition at line 200 of file elxBSplineStackTransform.h.

◆ Pointer

template<class TElastix >

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

Definition at line 125 of file elxBSplineStackTransform.h.

◆ ReducedDimensionBSplineTransformBasePointer

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionBSplineTransformBasePointer = typename ReducedDimensionBSplineTransformBaseType::Pointer

Definition at line 156 of file elxBSplineStackTransform.h.

◆ ReducedDimensionBSplineTransformBaseType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionBSplineTransformBaseType

Initial value:

 
    itk::AdvancedBSplineDeformableTransformBase<typename elx::TransformBase<TElastix>::CoordRepType,
                                                Self::ReducedSpaceDimension>

The ITK-class for the sub transforms, which have a reduced dimension.

Definition at line 153 of file elxBSplineStackTransform.h.

◆ ReducedDimensionDirectionType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionDirectionType = typename ReducedDimensionImageType::DirectionType

Definition at line 189 of file elxBSplineStackTransform.h.

◆ ReducedDimensionImageType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionImageType = itk::Image<PixelType, Self::ReducedSpaceDimension>

Reduced dimension image typedefs.

Definition at line 184 of file elxBSplineStackTransform.h.

◆ ReducedDimensionIndexType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionIndexType = typename ReducedDimensionRegionType::IndexType

Definition at line 187 of file elxBSplineStackTransform.h.

◆ ReducedDimensionOriginType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionOriginType = typename ReducedDimensionImageType::PointType

Definition at line 190 of file elxBSplineStackTransform.h.

◆ ReducedDimensionRegionType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionRegionType = itk::ImageRegion<Self::ReducedSpaceDimension>

Definition at line 185 of file elxBSplineStackTransform.h.

◆ ReducedDimensionSizeType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionSizeType = typename ReducedDimensionRegionType::SizeType

Definition at line 186 of file elxBSplineStackTransform.h.

◆ ReducedDimensionSpacingType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::ReducedDimensionSpacingType = typename ReducedDimensionImageType::SpacingType

Definition at line 188 of file elxBSplineStackTransform.h.

◆ RegionType

template<class TElastix >

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

Definition at line 167 of file elxBSplineStackTransform.h.

◆ Self

template<class TElastix >

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

Standard ITK-stuff.

Definition at line 121 of file elxBSplineStackTransform.h.

◆ SizeType

template<class TElastix >

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

Definition at line 169 of file elxBSplineStackTransform.h.

◆ SpacingType

template<class TElastix >

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

Definition at line 170 of file elxBSplineStackTransform.h.

◆ StackTransformType

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::StackTransformType = itk::BSplineStackTransform<SpaceDimension>

private

The deleted copy constructor and assignment operator. Typedef for stack transform.

Definition at line 278 of file elxBSplineStackTransform.h.

◆ Superclass1

template<class TElastix >

using elastix::BSplineStackTransform< TElastix >::Superclass1

Initial value:

itk::AdvancedCombinationTransform<typename elx::TransformBase<TElastix>::CoordRepType,

elx::TransformBase<TElastix>::FixedImageDimension>

elastix::TransformBase

This class is the elastix base class for all Transforms.

Definition elxTransformBase.h:138

itk::AdvancedCombinationTransform

This class combines two transforms: an 'initial transform' with a 'current transform'.

Definition itkAdvancedCombinationTransform.h:57

Definition at line 122 of file elxBSplineStackTransform.h.

◆ Superclass2

template<class TElastix >

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

Definition at line 124 of file elxBSplineStackTransform.h.

Constructor & Destructor Documentation

◆ BSplineStackTransform()

template<class TElastix >

elastix::BSplineStackTransform< TElastix >::BSplineStackTransform ( )

inlineprotected

The constructor.

Definition at line 252 of file elxBSplineStackTransform.h.

◆ ~BSplineStackTransform()

template<class TElastix >

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

overrideprotecteddefault

The destructor.

Member Function Documentation

◆ BeforeAll()

template<class TElastix >

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

overridevirtual

Execute stuff before anything else is done:

Initialize the right BSplineTransform.
Initialize the right grid schedule computer.
Initialize upsample filter.

Reimplemented from elastix::BaseComponent.

◆ BeforeEachResolution()

template<class TElastix >

void elastix::BSplineStackTransform< 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<class TElastix >

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

overridevirtual

Execute stuff before the actual registration:

Create an initial B-spline grid.
Set the stack transform parameters.
Set initial sub transforms.
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<class TElastix >

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

overrideprivatevirtual

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

Implements elastix::TransformBase< TElastix >.

◆ elxClassNameMacro()

template<class TElastix >

elastix::BSplineStackTransform< TElastix >::elxClassNameMacro ( "BSplineStackTransform< TElastix >" )

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

◆ GetClassName()

template<class TElastix >

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::AdvancedCombinationTransform< TScalarType, NDimensions >.

◆ IncreaseScale()

template<class TElastix >

virtual void elastix::BSplineStackTransform< 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 for all sub transforms.
Set these coefficients as InitialParametersOfNextLevel in the registration object. Called by BeforeEachResolution().

◆ InitializeBSplineTransform()

template<class TElastix >

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

private

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

◆ InitializeTransform()

template<class TElastix >

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

private

Method to set the initial B-spline grid and grid scheduler 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<class TElastix >

elastix::BSplineStackTransform< TElastix >::ITK_DISALLOW_COPY_AND_MOVE ( BSplineStackTransform< TElastix > )

◆ itkStaticConstMacro() [1/2]

template<class TElastix >

elastix::BSplineStackTransform< TElastix >::itkStaticConstMacro	(	ReducedSpaceDimension	,
		unsigned int	,
		Superclass2::FixedImageDimension -	1 )

◆ itkStaticConstMacro() [2/2]

template<class TElastix >

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

(Reduced) dimension of the fixed image.

◆ New()

template<class TElastix >

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

static

Method for creation through the object factory.

◆ PreComputeGridInformation()

template<class TElastix >

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

protectedvirtual

Read user-specified gridspacing and call the itkGridScheduleComputer.

◆ ReadFromFile()

template<class TElastix >

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

overridevirtual

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

◆ SetOptimizerScales()

template<class TElastix >

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

virtual

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

Field Documentation

◆ elxOverrideGetSelfMacro

template<class TElastix >

elastix::BSplineStackTransform< TElastix >::elxOverrideGetSelfMacro

private

Definition at line 262 of file elxBSplineStackTransform.h.

◆ m_DummySubTransform

template<class TElastix >

ReducedDimensionBSplineTransformBasePointer elastix::BSplineStackTransform< TElastix >::m_DummySubTransform

private

Dummy sub transform to be used to set sub transforms of stack transform.

Definition at line 284 of file elxBSplineStackTransform.h.

◆ m_GridScheduleComputer

template<class TElastix >

GridScheduleComputerPointer elastix::BSplineStackTransform< TElastix >::m_GridScheduleComputer

private

Grid schedule computer and grid upsampler.

Definition at line 287 of file elxBSplineStackTransform.h.

◆ m_GridUpsampler

template<class TElastix >

GridUpsamplerPointer elastix::BSplineStackTransform< TElastix >::m_GridUpsampler

private

Definition at line 288 of file elxBSplineStackTransform.h.

◆ m_NumberOfSubTransforms

template<class TElastix >

unsigned int elastix::BSplineStackTransform< TElastix >::m_NumberOfSubTransforms

private

Stack variables.

Definition at line 294 of file elxBSplineStackTransform.h.

◆ m_SplineOrder

template<class TElastix >

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

private

Variable to remember order of B-spline transform.

Definition at line 291 of file elxBSplineStackTransform.h.

◆ m_StackOrigin

template<class TElastix >

double elastix::BSplineStackTransform< TElastix >::m_StackOrigin

private

Definition at line 295 of file elxBSplineStackTransform.h.

◆ m_StackSpacing

template<class TElastix >

double elastix::BSplineStackTransform< TElastix >::m_StackSpacing

private

Definition at line 295 of file elxBSplineStackTransform.h.

◆ m_StackTransform

template<class TElastix >

const StackTransformType::Pointer elastix::BSplineStackTransform< TElastix >::m_StackTransform { StackTransformType::New() }

private

The B-spline stack transform.

Definition at line 281 of file elxBSplineStackTransform.h.

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BSplineTransformBasePointer

◆ BSplineTransformBaseType

◆ CombinationTransformType

◆ ConstPointer

◆ CoordRepType

◆ DirectionType

◆ FixedImageType

◆ GridScheduleComputerPointer

◆ GridScheduleComputerType

◆ GridScheduleType

◆ GridUpsamplerPointer

◆ GridUpsamplerType

◆ ImagePointer

◆ ImageType

◆ IndexType

◆ ITKBaseType

◆ MovingImageType

◆ OriginType

◆ ParameterMapType

◆ ParameterValueType

◆ Pointer

◆ ReducedDimensionBSplineTransformBasePointer

◆ ReducedDimensionBSplineTransformBaseType

◆ ReducedDimensionDirectionType

◆ ReducedDimensionImageType

◆ ReducedDimensionIndexType

◆ ReducedDimensionOriginType

◆ ReducedDimensionRegionType

◆ ReducedDimensionSizeType

◆ ReducedDimensionSpacingType

◆ RegionType

◆ Self

◆ SizeType

◆ SpacingType

◆ StackTransformType

◆ Superclass1

◆ Superclass2

Constructor & Destructor Documentation

◆ BSplineStackTransform()

◆ ~BSplineStackTransform()

Member Function Documentation

◆ BeforeAll()

◆ BeforeEachResolution()

◆ BeforeRegistration()

◆ CreateDerivedTransformParameterMap()

◆ elxClassNameMacro()

◆ GetClassName()

◆ IncreaseScale()

◆ InitializeBSplineTransform()

◆ InitializeTransform()

◆ ITK_DISALLOW_COPY_AND_MOVE()

◆ itkStaticConstMacro() [1/2]

◆ itkStaticConstMacro() [2/2]

◆ New()

◆ PreComputeGridInformation()

◆ ReadFromFile()

◆ SetOptimizerScales()

Field Documentation

◆ elxOverrideGetSelfMacro

◆ m_DummySubTransform

◆ m_GridScheduleComputer

◆ m_GridUpsampler

◆ m_NumberOfSubTransforms

◆ m_SplineOrder

◆ m_StackOrigin

◆ m_StackSpacing

◆ m_StackTransform