#include <elxBSplineTransformWithDiffusion.h>

Detailed Description

template<class TElastix>
class elastix::BSplineTransformWithDiffusion< TElastix >

This class combines a B-spline transform with the diffusion/filtering of the deformation field.

Every n iterations the deformation field is diffused using the VectorMeanDiffusionImageFilter. The total transformation of a point is determined by adding the B-spline deformation to the deformation field arrow. Filtering of the deformation field is based on some 'stiffness coefficient' image.

Todo: : this Transform has not been tested for images with Direction cosines matrix other than the identity matrix.

Warning: Using this transform in with the option (HowToCombineTranforms "Compose"). May give unpredictable results. Especially if the initial transformation is large. This is because the coefficient grid is not properly initialized. Better use (HowToCombineTranforms "Add").

The parameters used in this class are:

Parameters

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

FinalGridSpacing: the grid spacing of the B-spline transform part of this transform for each dimension.
example: (FinalGridSpacing 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 8.0 in every dimension.

UpsampleGridOption: whether or not the B-spline grid should be upsampled from one resolution level to another. Choose from {true, false}.
example: (UpsampleGridOption "true") The default is "true".

FilterPattern: defines according to what schedule/pattern the deformation field should be filtered. Choose from {1,2}, where FilterPattern 1 is diffusion every "DiffusionEachNIterations" iterations, and where FilterPattern 2 filters more frequent in the beginning and less frequent at the end of a resolution.
example: (FilterPattern 1) The default is filter pattern 1.

DiffusionEachNIterations: defines for FilterPattern 1 after how many iterations of the optimiser there should be a filtering step.
example: (DiffusionEachNIterations 5) The default is 1.

AfterIterations: defines for FilterPattern 2 after how many iterations of the optimiser the filter frequency should be increased.
example: (AfterIterations 100 200) The default is 50 and 100.

HowManyIterations: defines to what frequency the filtering should be increased.
example: (HowManyIterations 1 5 10) The default is 1, 5 and 10.

NumberOfDiffusionIterations: defines the number of times the adaptive filtering is performed.
example: (NumberOfDiffusionIterations 10) The default is 1.

Radius: defines the radius of the filter.
example: (Radius 1) The default is 1.

ThresholdBool: defines whether or not the stiffness coefficient image should be thresholded. Choose from {true, false}.
example: (ThresholdBool "true") The default is "true".

ThresholdHU: if it is thresholded, this defines the threshold in Houndsfield units.
example: (ThresholdHU 150) The default is 150.

WriteDiffusionFiles: defines whether or not the stiffness coefficient image, the deformation field and the filtered field should be written to file. Choose from {true, false}.
example: (WriteDiffusionFiles "true") The default is "false".

GrayValueImageAlsoBasedOnFixedImage: defines whether or not the stiffness coefficient image should also be based on the fixed image. Choose from {true, false}.
example: (GrayValueImageAlsoBasedOnFixedImage "true") The default is "true".

UseFixedSegmentation: defines whether or not the stiffness coefficient image should be based on some prior defined segmentation of rigid structures in the fixed image, instead on a thresholding. Choose from {true, false}.
example: (UseFixedSegmentation "true") The default is "false".

FixedSegmentationFileName: the filename of this segmentation.
example: (FixedSegmentationFileName "somestring")

UseMovingSegmentation: defines whether or not the stiffness coefficient image should be based on some prior defined segmentation of rigid structures in the moving image, instead on a thresholding. Choose from {true, false}.
example: (UseMovingSegmentation "true") The default is "false".

MovingSegmentationFileName: the filename of this segmentation.
example: (MovingSegmentationFileName "somestring")

DefaultPixelValueForGVI: the default pixel value, when resampling the grayvalueimage. example: (DefaultPixelValueForGVI 0) The default is 0.

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

Transform Parameters

DeformationFieldFileName: stores the name of the deformation field.
example: (DeformationFieldFileName "defField.mhd")

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)

Definition at line 159 of file elxBSplineTransformWithDiffusion.h.

Inheritance diagram for elastix::BSplineTransformWithDiffusion< TElastix >:

[legend]

Public Types
using	BSplineTransformPointer = typename BSplineTransformType::Pointer

using	BSplineTransformType

using	CombinationTransformType = typename Superclass2::CombinationTransformType

using	ConstPointer = itk::SmartPointer<const Self>

using	ContinuousIndexType = typename BSplineTransformType::ContinuousIndexType

using	CoordRepType

using	DiffusionFilterPointer = typename DiffusionFilterType::Pointer

using	DiffusionFilterType = itk::VectorMeanDiffusionImageFilter<VectorImageType, GrayValueImageType>

using	DummyImageType = itk::Image<short, Self::SpaceDimension>

using	DummyIteratorType = itk::ImageRegionConstIterator<DummyImageType>

using	FixedImageELXType = typename ElastixType::FixedImageType

using	FixedImageType

using	GenericDeformationFieldRegulizer = typename Superclass1::Superclass

using	GrayValueImageIteratorType = itk::ImageRegionIterator<GrayValueImageType>

using	GrayValueImagePointer = typename GrayValueImageType::Pointer

using	GrayValueImageReaderPointer = typename GrayValueImageReaderType::Pointer

using	GrayValueImageReaderType = itk::ImageFileReader<GrayValueImageType>

using	GrayValueImageType = FixedImageELXType

using	GrayValuePixelType = typename GrayValueImageType::PixelType

using	ImagePointer = typename BSplineTransformType::ImagePointer

using	ImageType = typename BSplineTransformType::ImageType

using	IndexType = typename BSplineTransformType::IndexType

using	IntermediaryDFTransformType

using	InterpolatorPointer = typename InterpolatorType::Pointer

using	InterpolatorType = itk::BSplineInterpolateImageFunction<GrayValueImageType>

using	ITKBaseType = typename Superclass2::ITKBaseType

using	MaximumImageFilterType = itk::MaximumImageFilter<GrayValueImageType, GrayValueImageType, GrayValueImageType>

using	MovingImageELXType = typename ElastixType::MovingImageType

using	MovingImageType

using	OriginType = typename BSplineTransformType::OriginType

using	ParameterIndexArrayType = typename BSplineTransformType::ParameterIndexArrayType

using	ParameterMapType

using	Pointer = itk::SmartPointer<Self>

using	RadiusType = typename VectorImageType::SizeType

using	RegionType = typename BSplineTransformType::RegionType

using	ResamplerPointer1 = typename ResamplerType1::Pointer

using	ResamplerPointer2 = typename ResamplerType2::Pointer

using	ResamplerType1 = itk::ResampleImageFilter<MovingImageELXType, GrayValueImageType, CoordRepType>

using	ResamplerType2 = itk::ResampleImageFilter<GrayValueImageType, GrayValueImageType, CoordRepType>

using	Self = BSplineTransformWithDiffusion

using	SizeType = typename BSplineTransformType::SizeType

using	SpacingType = typename BSplineTransformType::SpacingType

using	Superclass1

using	Superclass2 = elx::TransformBase<TElastix>

using	VectorImageIteratorType = itk::ImageRegionIterator<VectorImageType>

using	VectorImagePointer = typename VectorImageType::Pointer

using	VectorImageType

using	VectorReaderType = itk::ImageFileReader<VectorImageType>

using	VectorType = typename VectorImageType::PixelType

using	WeightsFunctionType = typename BSplineTransformType::WeightsFunctionType

using	WeightsType = typename BSplineTransformType::WeightsType

Public Types inherited from itk::DeformationFieldRegulizer< TAnyITKTransform >
using	ConstPointer = SmartPointer<const Self>

using	IntermediaryDFTransformPointer = typename IntermediaryDFTransformType::Pointer

using	IntermediaryDFTransformType = DeformationVectorFieldTransform<ScalarType, Self::InputSpaceDimension>

using	IteratorType = ImageRegionIterator<VectorImageType>

using	OriginType = typename VectorImageType::PointType

using	Pointer = SmartPointer<Self>

using	RegionType = typename VectorImageType::RegionType

using	Self = DeformationFieldRegulizer

using	SpacingType = typename VectorImageType::SpacingType

using	Superclass = TAnyITKTransform

using	VectorImageType = typename IntermediaryDFTransformType ::CoefficientVectorImageType

using	VectorPixelType = typename VectorImageType::PixelType

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
void	AfterEachIteration () override

void	AfterRegistration () override

void	BeforeEachResolution () override

void	BeforeRegistration () override

void	DiffuseDeformationField ()

	elxClassNameMacro ("BSplineTransformWithDiffusion")

virtual const char *	GetClassName () const

virtual void	IncreaseScale ()

	ITK_DISALLOW_COPY_AND_MOVE (BSplineTransformWithDiffusion)

	itkStaticConstMacro (SpaceDimension, unsigned int, Superclass2::FixedImageDimension)

	itkStaticConstMacro (SplineOrder, unsigned int, __VSplineOrder)

void	ReadFromFile () override

virtual void	SetInitialGrid (bool upsampleGridOption)

OutputPointType	TransformPoint (const InputPointType &point) const override

Public Member Functions inherited from itk::DeformationFieldRegulizer< TAnyITKTransform >
virtual const IntermediaryDFTransformType *	GetIntermediaryDeformationFieldTransform ()

void	InitializeDeformationFields ()

	ITK_DISALLOW_COPY_AND_MOVE (DeformationFieldRegulizer)

	itkStaticConstMacro (InputSpaceDimension, unsigned int, Superclass::InputSpaceDimension)

	itkStaticConstMacro (OutputSpaceDimension, unsigned int, Superclass::OutputSpaceDimension)

virtual void	SetDeformationFieldOrigin (OriginType _arg)

virtual void	SetDeformationFieldRegion (RegionType _arg)

virtual void	SetDeformationFieldSpacing (SpacingType _arg)

OutputPointType	TransformPoint (const InputPointType &inputPoint) const override

virtual void	UpdateIntermediaryDeformationFieldTransform (typename VectorImageType::Pointer vecImage)

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	AfterEachIterationBase ()

virtual void	AfterEachResolution ()

virtual void	AfterEachResolutionBase ()

virtual int	BeforeAll ()

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::DeformationFieldRegulizer< TAnyITKTransform >
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
	BSplineTransformWithDiffusion ()

	~BSplineTransformWithDiffusion () override=default

Protected Member Functions inherited from itk::DeformationFieldRegulizer< TAnyITKTransform >
	DeformationFieldRegulizer ()

	~DeformationFieldRegulizer () 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

Protected Attributes
SpacingType	m_GridSpacingFactor

Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
Configuration::ConstPointer	m_Configuration {}

itk::WeakPointer< TElastix >	m_Elastix {}

RegistrationType *	m_Registration {}

Private Member Functions
ParameterMapType	CreateDerivedTransformParameterMap () const override

void	WriteDerivedTransformDataToFile () const override

Private Attributes
	elxOverrideGetSelfMacro

bool	m_AlsoFixed

ParametersType	m_BSplineParameters

BSplineTransformPointer	m_BSplineTransform

VectorImagePointer	m_DeformationField

OriginType	m_DeformationOrigin

RegionType	m_DeformationRegion

SpacingType	m_DeformationSpacing

VectorImagePointer	m_DiffusedField

DiffusionFilterPointer	m_Diffusion

std::string	m_FixedSegmentationFileName

GrayValueImagePointer	m_FixedSegmentationImage

GrayValueImageReaderPointer	m_FixedSegmentationReader

GrayValueImagePointer	m_GrayValueImage1

GrayValueImagePointer	m_GrayValueImage2

InterpolatorPointer	m_Interpolator

std::string	m_MovingSegmentationFileName

GrayValueImagePointer	m_MovingSegmentationImage

GrayValueImageReaderPointer	m_MovingSegmentationReader

ResamplerPointer1	m_Resampler1

ResamplerPointer2	m_Resampler2

bool	m_ThresholdBool

GrayValuePixelType	m_ThresholdHU

bool	m_UseFixedSegmentation

bool	m_UseMovingSegmentation

bool	m_WriteDiffusionFiles

Member Typedef Documentation

◆ BSplineTransformPointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::BSplineTransformPointer = typename BSplineTransformType::Pointer

Definition at line 256 of file elxBSplineTransformWithDiffusion.h.

◆ BSplineTransformType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::BSplineTransformType

Initial value:

 
    itk::AdvancedBSplineDeformableTransform<typename elx::TransformBase<TElastix>::CoordRepType,
                                            elx::TransformBase<TElastix>::FixedImageDimension,
                                            3>

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

Definition at line 181 of file elxBSplineTransformWithDiffusion.h.

◆ CombinationTransformType

template<class TElastix >

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

Definition at line 242 of file elxBSplineTransformWithDiffusion.h.

◆ ConstPointer

template<class TElastix >

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

Definition at line 187 of file elxBSplineTransformWithDiffusion.h.

◆ ContinuousIndexType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ContinuousIndexType = typename BSplineTransformType::ContinuousIndexType

Definition at line 231 of file elxBSplineTransformWithDiffusion.h.

◆ CoordRepType

template<class TElastix >

using elastix::TransformBase< TElastix >::CoordRepType

Elastix typedef's.

Definition at line 156 of file elxTransformBase.h.

◆ DiffusionFilterPointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::DiffusionFilterPointer = typename DiffusionFilterType::Pointer

Definition at line 269 of file elxBSplineTransformWithDiffusion.h.

◆ DiffusionFilterType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::DiffusionFilterType = itk::VectorMeanDiffusionImageFilter<VectorImageType, GrayValueImageType>

Definition at line 268 of file elxBSplineTransformWithDiffusion.h.

◆ DummyImageType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::DummyImageType = itk::Image<short, Self::SpaceDimension>

Other typedef's.

Definition at line 254 of file elxBSplineTransformWithDiffusion.h.

◆ DummyIteratorType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::DummyIteratorType = itk::ImageRegionConstIterator<DummyImageType>

Definition at line 255 of file elxBSplineTransformWithDiffusion.h.

◆ FixedImageELXType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::FixedImageELXType = typename ElastixType::FixedImageType

References to the fixed and moving image types.

Definition at line 250 of file elxBSplineTransformWithDiffusion.h.

◆ FixedImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::FixedImageType

Definition at line 157 of file elxTransformBase.h.

◆ GenericDeformationFieldRegulizer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GenericDeformationFieldRegulizer = typename Superclass1::Superclass

Definition at line 257 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageIteratorType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageIteratorType = itk::ImageRegionIterator<GrayValueImageType>

Definition at line 266 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImagePointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImagePointer = typename GrayValueImageType::Pointer

Definition at line 264 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageReaderPointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageReaderPointer = typename GrayValueImageReaderType::Pointer

Definition at line 278 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageReaderType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageReaderType = itk::ImageFileReader<GrayValueImageType>

Definition at line 277 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageType = FixedImageELXType

Definition at line 263 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValuePixelType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::GrayValuePixelType = typename GrayValueImageType::PixelType

Definition at line 265 of file elxBSplineTransformWithDiffusion.h.

◆ ImagePointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ImagePointer = typename BSplineTransformType::ImagePointer

Definition at line 223 of file elxBSplineTransformWithDiffusion.h.

◆ ImageType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ImageType = typename BSplineTransformType::ImageType

Definition at line 222 of file elxBSplineTransformWithDiffusion.h.

◆ IndexType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::IndexType = typename BSplineTransformType::IndexType

Definition at line 225 of file elxBSplineTransformWithDiffusion.h.

◆ IntermediaryDFTransformType

template<class TElastix >

using itk::DeformationFieldRegulizer< TAnyITKTransform >::IntermediaryDFTransformType

Typedef's needed in this class.

Definition at line 77 of file itkDeformationFieldRegulizer.h.

◆ InterpolatorPointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::InterpolatorPointer = typename InterpolatorType::Pointer

Definition at line 276 of file elxBSplineTransformWithDiffusion.h.

◆ InterpolatorType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::InterpolatorType = itk::BSplineInterpolateImageFunction<GrayValueImageType>

Definition at line 275 of file elxBSplineTransformWithDiffusion.h.

◆ ITKBaseType

template<class TElastix >

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

Definition at line 241 of file elxBSplineTransformWithDiffusion.h.

◆ MaximumImageFilterType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::MaximumImageFilterType = itk::MaximumImageFilter<GrayValueImageType, GrayValueImageType, GrayValueImageType>

Definition at line 267 of file elxBSplineTransformWithDiffusion.h.

◆ MovingImageELXType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::MovingImageELXType = typename ElastixType::MovingImageType

Definition at line 251 of file elxBSplineTransformWithDiffusion.h.

◆ MovingImageType

template<class TElastix >

using elastix::TransformBase< TElastix >::MovingImageType

Definition at line 158 of file elxTransformBase.h.

◆ OriginType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::OriginType = typename BSplineTransformType::OriginType

Definition at line 228 of file elxBSplineTransformWithDiffusion.h.

◆ ParameterIndexArrayType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ParameterIndexArrayType = typename BSplineTransformType::ParameterIndexArrayType

Definition at line 232 of file elxBSplineTransformWithDiffusion.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.

◆ Pointer

template<class TElastix >

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

Definition at line 186 of file elxBSplineTransformWithDiffusion.h.

◆ RadiusType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::RadiusType = typename VectorImageType::SizeType

Definition at line 270 of file elxBSplineTransformWithDiffusion.h.

◆ RegionType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::RegionType = typename BSplineTransformType::RegionType

Definition at line 224 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerPointer1

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerPointer1 = typename ResamplerType1::Pointer

Definition at line 272 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerPointer2

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerPointer2 = typename ResamplerType2::Pointer

Definition at line 274 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerType1

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerType1 = itk::ResampleImageFilter<MovingImageELXType, GrayValueImageType, CoordRepType>

Definition at line 271 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerType2

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerType2 = itk::ResampleImageFilter<GrayValueImageType, GrayValueImageType, CoordRepType>

Definition at line 273 of file elxBSplineTransformWithDiffusion.h.

◆ Self

template<class TElastix >

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

Standard ITK-stuff.

Definition at line 172 of file elxBSplineTransformWithDiffusion.h.

◆ SizeType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::SizeType = typename BSplineTransformType::SizeType

Definition at line 226 of file elxBSplineTransformWithDiffusion.h.

◆ SpacingType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::SpacingType = typename BSplineTransformType::SpacingType

Definition at line 227 of file elxBSplineTransformWithDiffusion.h.

◆ Superclass1

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::Superclass1

Initial value:

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

Definition at line 173 of file elxBSplineTransformWithDiffusion.h.

◆ Superclass2

template<class TElastix >

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

Definition at line 176 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImageIteratorType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::VectorImageIteratorType = itk::ImageRegionIterator<VectorImageType>

Definition at line 262 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImagePointer

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::VectorImagePointer = typename VectorImageType::Pointer

Definition at line 247 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImageType

template<class TElastix >

using itk::DeformationFieldRegulizer< TAnyITKTransform >::VectorImageType

Definition at line 79 of file itkDeformationFieldRegulizer.h.

◆ VectorReaderType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::VectorReaderType = itk::ImageFileReader<VectorImageType>

Typedef's for the diffusion of the deformation field.

Definition at line 260 of file elxBSplineTransformWithDiffusion.h.

◆ VectorType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::VectorType = typename VectorImageType::PixelType

Definition at line 261 of file elxBSplineTransformWithDiffusion.h.

◆ WeightsFunctionType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::WeightsFunctionType = typename BSplineTransformType::WeightsFunctionType

Definition at line 229 of file elxBSplineTransformWithDiffusion.h.

◆ WeightsType

template<class TElastix >

using elastix::BSplineTransformWithDiffusion< TElastix >::WeightsType = typename BSplineTransformType::WeightsType

Definition at line 230 of file elxBSplineTransformWithDiffusion.h.

Constructor & Destructor Documentation

◆ BSplineTransformWithDiffusion()

template<class TElastix >

elastix::BSplineTransformWithDiffusion< TElastix >::BSplineTransformWithDiffusion ( )

protected

Method to transform a point with extra arguments. Just calls the Superclass1's implementation. Has to be present here since it is an overloaded function.

virtual void TransformPoint( const InputPointType & inputPoint, OutputPointType & outputPoint, WeightsType & weights, ParameterIndexArrayType & indices, bool & inside ) const; The constructor.

◆ ~BSplineTransformWithDiffusion()

template<class TElastix >

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

overrideprotecteddefault

The destructor.

Member Function Documentation

◆ AfterEachIteration()

template<class TElastix >

void elastix::BSplineTransformWithDiffusion< TElastix >::AfterEachIteration ( )

overridevirtual

Execute stuff after each iteration:

Do a diffusion of the deformation field.

Reimplemented from elastix::BaseComponent.

◆ AfterRegistration()

template<class TElastix >

void elastix::BSplineTransformWithDiffusion< TElastix >::AfterRegistration ( )

overridevirtual

Execute stuff after registration:

Destroy things that are not needed anymore in order to free memory.

Reimplemented from elastix::BaseComponent.

◆ BeforeEachResolution()

template<class TElastix >

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

overridevirtual

Execute stuff before each new pyramid resolution:

upsample the B-spline grid.

Reimplemented from elastix::BaseComponent.

◆ BeforeRegistration()

template<class TElastix >

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

overridevirtual

Execute stuff before the actual registration:

Create an initial B-spline grid.
Create initial registration parameters.
Setup stuff for the diffusion of the deformation field.

Reimplemented from elastix::BaseComponent.

◆ CreateDerivedTransformParameterMap()

template<class TElastix >

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

overrideprivatevirtual

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

Implements elastix::TransformBase< TElastix >.

◆ DiffuseDeformationField()

template<class TElastix >

void elastix::BSplineTransformWithDiffusion< TElastix >::DiffuseDeformationField ( )

Diffuse the deformation field.

◆ elxClassNameMacro()

template<class TElastix >

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

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

◆ GetClassName()

template<class TElastix >

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::DeformationFieldRegulizer< TAnyITKTransform >.

◆ IncreaseScale()

template<class TElastix >

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

virtual

Upsample the B-spline grid.

◆ ITK_DISALLOW_COPY_AND_MOVE()

template<class TElastix >

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

◆ itkStaticConstMacro() [1/2]

template<class TElastix >

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

Dimension of the domain space.

◆ itkStaticConstMacro() [2/2]

template<class TElastix >

elastix::BSplineTransformWithDiffusion< TElastix >::itkStaticConstMacro	(	SplineOrder	,
		unsigned int	,
		__VSplineOrder	)

The B-spline order.

◆ New()

template<class TElastix >

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

static

Method for creation through the object factory.

◆ ReadFromFile()

template<class TElastix >

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

overridevirtual

Function to read transform-parameters from a file.

Reimplemented from elastix::TransformBase< TElastix >.

◆ SetInitialGrid()

template<class TElastix >

virtual void elastix::BSplineTransformWithDiffusion< TElastix >::SetInitialGrid ( bool upsampleGridOption )

virtual

Set the initial B-spline grid.

◆ TransformPoint()

template<class TElastix >

OutputPointType elastix::BSplineTransformWithDiffusion< TElastix >::TransformPoint ( const InputPointType & point ) const

override

Method to transform a point. This method just calls the implementation from the GenericDeformationFieldRegulizer. This is necessary, since: The DeformationFieldRegulizerFor is used which expects that its template argument is a BSplineDeformableTransform. This is not the case, because we gave it a BSplineCombinationTransform. This last class has a slightly different behavior of the TransformPoint() method (it does not call the TransformPoint() with with 5 arguments, as the BSplineDeformableTransform does).