#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 >:

Public Types
typedef BSplineTransformType::Pointer	BSplineTransformPointer

typedef itk::AdvancedBSplineDeformableTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension, __VSplineOrder >	BSplineTransformType

typedef Superclass2::CombinationTransformType	CombinationTransformType

typedef Superclass2::ConfigurationPointer	ConfigurationPointer

typedef Superclass2::ConfigurationType	ConfigurationType

typedef itk::SmartPointer< const Self >	ConstPointer

typedef BSplineTransformType::ContinuousIndexType	ContinuousIndexType

typedef Superclass2::CoordRepType	CoordRepType

typedef itk::ImageFileWriter< VectorImageType >	DeformationFieldWriterType

typedef DiffusionFilterType::Pointer	DiffusionFilterPointer

typedef itk::VectorMeanDiffusionImageFilter< VectorImageType, GrayValueImageType >	DiffusionFilterType

typedef itk::Image< short, itkGetStaticConstMacro(SpaceDimension) >	DummyImageType

typedef itk::ImageRegionConstIterator< DummyImageType >	DummyIteratorType

typedef Superclass2::ElastixPointer	ElastixPointer

typedef Superclass2::ElastixType	ElastixType

typedef ElastixType::FixedImageType	FixedImageELXType

typedef Superclass2::FixedImageType	FixedImageType

typedef Superclass1::Superclass	GenericDeformationFieldRegulizer

typedef itk::ImageRegionIterator< GrayValueImageType >	GrayValueImageIteratorType

typedef GrayValueImageType::Pointer	GrayValueImagePointer

typedef GrayValueImageReaderType::Pointer	GrayValueImageReaderPointer

typedef itk::ImageFileReader< GrayValueImageType >	GrayValueImageReaderType

typedef FixedImageELXType	GrayValueImageType

typedef itk::ImageFileWriter< GrayValueImageType >	GrayValueImageWriterType

typedef GrayValueImageType::PixelType	GrayValuePixelType

typedef BSplineTransformType::ImagePointer	ImagePointer

typedef BSplineTransformType::ImageType	ImageType

typedef BSplineTransformType::IndexType	IndexType

typedef Superclass1::InputCovariantVectorType	InputCovariantVectorType

typedef Superclass1::InputPointType	InputPointType

typedef Superclass1::InputVectorType	InputVectorType

typedef Superclass1::InputVnlVectorType	InputVnlVectorType

typedef Superclass1::IntermediaryDFTransformType	IntermediaryDFTransformType

typedef InterpolatorType::Pointer	InterpolatorPointer

typedef itk::BSplineInterpolateImageFunction< GrayValueImageType >	InterpolatorType

typedef Superclass2::ITKBaseType	ITKBaseType

typedef Superclass1::JacobianType	JacobianType

typedef itk::MaximumImageFilter< GrayValueImageType, GrayValueImageType, GrayValueImageType >	MaximumImageFilterType

typedef ElastixType::MovingImageType	MovingImageELXType

typedef Superclass2::MovingImageType	MovingImageType

typedef BSplineTransformType::OriginType	OriginType

typedef Superclass1::OutputCovariantVectorType	OutputCovariantVectorType

typedef Superclass1::OutputPointType	OutputPointType

typedef Superclass1::OutputVectorType	OutputVectorType

typedef Superclass1::OutputVnlVectorType	OutputVnlVectorType

typedef BSplineTransformType::ParameterIndexArrayType	ParameterIndexArrayType

typedef Superclass1::ParametersType	ParametersType

typedef itk::SmartPointer< Self >	Pointer

typedef VectorImageType::SizeType	RadiusType

typedef BSplineTransformType::RegionType	RegionType

typedef Superclass2::RegistrationPointer	RegistrationPointer

typedef Superclass2::RegistrationType	RegistrationType

typedef ResamplerType1::Pointer	ResamplerPointer1

typedef ResamplerType2::Pointer	ResamplerPointer2

typedef itk::ResampleImageFilter< MovingImageELXType, GrayValueImageType, CoordRepType >	ResamplerType1

typedef itk::ResampleImageFilter< GrayValueImageType, GrayValueImageType, CoordRepType >	ResamplerType2

typedef Superclass1::ScalarType	ScalarType

typedef BSplineTransformWithDiffusion	Self

typedef BSplineTransformType::SizeType	SizeType

typedef BSplineTransformType::SpacingType	SpacingType

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

typedef elx::TransformBase< TElastix >	Superclass2

typedef itk::ImageRegionIterator< VectorImageType >	VectorImageIteratorType

typedef VectorImageType::Pointer	VectorImagePointer

typedef Superclass1::VectorImageType	VectorImageType

typedef itk::ImageFileReader< VectorImageType >	VectorReaderType

typedef VectorImageType::PixelType	VectorType

typedef BSplineTransformType::WeightsFunctionType	WeightsFunctionType

typedef BSplineTransformType::WeightsType	WeightsType

Public Types inherited from itk::DeformationFieldRegulizer< itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::InputCovariantVectorType	InputCovariantVectorType

typedef Superclass::InputPointType	InputPointType

typedef Superclass::InputVectorType	InputVectorType

typedef Superclass::InputVnlVectorType	InputVnlVectorType

typedef IntermediaryDFTransformType::Pointer	IntermediaryDFTransformPointer

typedef DeformationVectorFieldTransform< ScalarType, itkGetStaticConstMacro(InputSpaceDimension) >	IntermediaryDFTransformType

typedef ImageRegionIterator< VectorImageType >	IteratorType

typedef Superclass::JacobianType	JacobianType

typedef VectorImageType::PointType	OriginType

typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType

typedef Superclass::OutputPointType	OutputPointType

typedef Superclass::OutputVectorType	OutputVectorType

typedef Superclass::OutputVnlVectorType	OutputVnlVectorType

typedef Superclass::ParametersType	ParametersType

typedef SmartPointer< Self >	Pointer

typedef VectorImageType::RegionType	RegionType

typedef Superclass::ScalarType	ScalarType

typedef DeformationFieldRegulizer	Self

typedef VectorImageType::SpacingType	SpacingType

typedef itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >	Superclass

typedef IntermediaryDFTransformType::CoefficientVectorImageType	VectorImageType

typedef VectorImageType::PixelType	VectorPixelType

Public Types inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
typedef SmartPointer< const Self >	ConstPointer

typedef CurrentTransformType::ConstPointer	CurrentTransformConstPointer

typedef CurrentTransformType::InverseTransformBasePointer	CurrentTransformInverseTransformBasePointer

typedef CurrentTransformType::InverseTransformBaseType	CurrentTransformInverseTransformBaseType

typedef CurrentTransformType::Pointer	CurrentTransformPointer

typedef Superclass	CurrentTransformType

typedef Superclass::DerivativeType	DerivativeType

typedef void(Self::*	EvaluateJacobianWithImageGradientProductFunctionPointer) (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const

typedef Superclass::FixedParametersType	FixedParametersType

typedef void(Self::*	GetJacobianOfSpatialHessianFunctionPointer) (const InputPointType &, JacobianOfSpatialHessianType &, NonZeroJacobianIndicesType &) const

typedef void(Self::*	GetJacobianOfSpatialHessianFunctionPointer2) (const InputPointType &, SpatialHessianType &, JacobianOfSpatialHessianType &, NonZeroJacobianIndicesType &) const

typedef void(Self::*	GetJacobianOfSpatialJacobianFunctionPointer) (const InputPointType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const

typedef void(Self::*	GetJacobianOfSpatialJacobianFunctionPointer2) (const InputPointType &, SpatialJacobianType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const

typedef void(Self::*	GetSparseJacobianFunctionPointer) (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const

typedef void(Self::*	GetSpatialHessianFunctionPointer) (const InputPointType &, SpatialHessianType &) const

typedef void(Self::*	GetSpatialJacobianFunctionPointer) (const InputPointType &, SpatialJacobianType &) const

typedef InitialTransformType::ConstPointer	InitialTransformConstPointer

typedef InitialTransformType::InverseTransformBasePointer	InitialTransformInverseTransformBasePointer

typedef InitialTransformType::InverseTransformBaseType	InitialTransformInverseTransformBaseType

typedef InitialTransformType::Pointer	InitialTransformPointer

typedef Superclass	InitialTransformType

typedef Superclass::InputCovariantVectorType	InputCovariantVectorType

typedef Superclass::InputPointType	InputPointType

typedef Superclass::InputVectorType	InputVectorType

typedef Superclass::InputVnlVectorType	InputVnlVectorType

typedef Superclass::InternalMatrixType	InternalMatrixType

typedef Superclass::InverseTransformBasePointer	InverseTransformBasePointer

typedef Superclass::InverseTransformBaseType	InverseTransformBaseType

typedef Superclass::JacobianOfSpatialHessianType	JacobianOfSpatialHessianType

typedef Superclass::JacobianOfSpatialJacobianType	JacobianOfSpatialJacobianType

typedef Superclass::JacobianType	JacobianType

typedef Superclass::MovingImageGradientType	MovingImageGradientType

typedef Superclass::MovingImageGradientValueType	MovingImageGradientValueType

typedef Superclass::NonZeroJacobianIndicesType	NonZeroJacobianIndicesType

typedef Superclass::NumberOfParametersType	NumberOfParametersType

typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType

typedef Superclass::OutputPointType	OutputPointType

typedef Superclass::OutputVectorType	OutputVectorType

typedef Superclass::OutputVnlVectorType	OutputVnlVectorType

typedef Superclass::ParametersType	ParametersType

typedef Superclass::ParametersValueType	ParametersValueType

typedef SmartPointer< Self >	Pointer

typedef Superclass::ScalarType	ScalarType

typedef AdvancedCombinationTransform	Self

typedef Superclass::SpatialHessianType	SpatialHessianType

typedef Superclass::SpatialJacobianType	SpatialJacobianType

typedef AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >	Superclass

typedef Superclass::TransformCategoryEnum	TransformCategoryEnum

typedef OutputPointType(Self::*	TransformPointFunctionPointer) (const InputPointType &) const

typedef Superclass::TransformType	TransformType

typedef TransformType::ConstPointer	TransformTypeConstPointer

typedef TransformType::Pointer	TransformTypePointer

Public Types inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DerivativeType	DerivativeType

typedef Superclass::FixedParametersType	FixedParametersType

typedef Superclass::InputCovariantVectorType	InputCovariantVectorType

typedef Superclass::InputPointType	InputPointType

typedef Superclass::InputVectorType	InputVectorType

typedef Superclass::InputVnlVectorType	InputVnlVectorType

typedef SpatialJacobianType::InternalMatrixType	InternalMatrixType

typedef Superclass::InverseTransformBasePointer	InverseTransformBasePointer

typedef Superclass::InverseTransformBaseType	InverseTransformBaseType

typedef std::vector< SpatialHessianType >	JacobianOfSpatialHessianType

typedef std::vector< SpatialJacobianType >	JacobianOfSpatialJacobianType

typedef Superclass::JacobianType	JacobianType

typedef OutputCovariantVectorType	MovingImageGradientType

typedef MovingImageGradientType::ValueType	MovingImageGradientValueType

typedef std::vector< unsigned long >	NonZeroJacobianIndicesType

typedef Superclass::NumberOfParametersType	NumberOfParametersType

typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType

typedef Superclass::OutputPointType	OutputPointType

typedef Superclass::OutputVectorType	OutputVectorType

typedef Superclass::OutputVnlVectorType	OutputVnlVectorType

typedef Superclass::ParametersType	ParametersType

typedef Superclass::ParametersValueType	ParametersValueType

typedef SmartPointer< Self >	Pointer

typedef Superclass::ScalarType	ScalarType

typedef AdvancedTransform	Self

typedef FixedArray< Matrix< ScalarType, InputSpaceDimension, InputSpaceDimension >, OutputSpaceDimension >	SpatialHessianType

typedef Matrix< ScalarType, OutputSpaceDimension, InputSpaceDimension >	SpatialJacobianType

typedef Transform< elx::TransformBase< TElastix >::CoordRepType, NInputDimensions, NOutputDimensions >	Superclass

typedef Transform< elx::TransformBase< TElastix >::CoordRepType, NInputDimensions, NOutputDimensions >	TransformType

typedef TransformType::ConstPointer	TransformTypeConstPointer

typedef TransformType::Pointer	TransformTypePointer

Public Types inherited from elastix::TransformBase< TElastix >
typedef itk::AdvancedCombinationTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension) >	CombinationTransformType

typedef ConfigurationType::CommandLineArgumentMapType	CommandLineArgumentMapType

typedef ConfigurationType::CommandLineEntryType	CommandLineEntryType

typedef ComponentDatabase	ComponentDatabaseType

typedef ComponentDatabaseType::ComponentDescriptionType	ComponentDescriptionType

typedef Configuration::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef ElastixType::CoordRepType	CoordRepType

typedef itk::Image< VectorPixelType, FixedImageDimension >	DeformationFieldImageType

typedef itk::WeakPointer< ElastixType >	ElastixPointer

typedef TElastix	ElastixType

typedef ElastixType::FixedImageType	FixedImageType

typedef CombinationTransformType::InitialTransformType	InitialTransformType

typedef ITKBaseType::InputPointType	InputPointType

typedef itk::AdvancedTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension), itkGetStaticConstMacro(MovingImageDimension) >	ITKBaseType

typedef RegistrationType::ITKBaseType	ITKRegistrationType

typedef ElastixType::MovingImageType	MovingImageType

typedef itk::Object	ObjectType

typedef ITKRegistrationType::OptimizerType	OptimizerType

typedef ITKBaseType::OutputPointType	OutputPointType

typedef ElastixType::ParameterMapType	ParameterMapType

typedef ITKBaseType::ParametersType	ParametersType

typedef elx::ProgressCommand	ProgressCommandType

typedef ComponentDatabase::PtrToCreator	PtrToCreator

typedef RegistrationType *	RegistrationPointer

typedef ElastixType::RegistrationBaseType	RegistrationType

typedef OptimizerType::ScalesType	ScalesType

typedef TransformBase	Self

typedef BaseComponentSE< TElastix >	Superclass

typedef ParametersType::ValueType	ValueType

typedef itk::Vector< float, FixedImageDimension >	VectorPixelType

Public Types inherited from elastix::BaseComponentSE< TElastix >
typedef Configuration::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef itk::WeakPointer< ElastixType >	ElastixPointer

typedef TElastix	ElastixType

typedef RegistrationType *	RegistrationPointer

typedef ElastixType::RegistrationBaseType	RegistrationType

typedef BaseComponentSE	Self

typedef BaseComponent	Superclass

Public Member Functions
void	AfterEachIteration (void) override

void	AfterRegistration (void) override

void	BeforeEachResolution (void) override

void	BeforeRegistration (void) override

void	DiffuseDeformationField (void)

	elxClassNameMacro ("BSplineTransformWithDiffusion")

virtual const char *	GetClassName () const

virtual void	IncreaseScale (void)

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

	itkStaticConstMacro (SplineOrder, unsigned int, __VSplineOrder)

void	ReadFromFile (void) override

virtual void	SetInitialGrid (bool upsampleGridOption)

OutputPointType	TransformPoint (const InputPointType &point) const override

void	WriteToFile (const ParametersType &param) const override

Public Member Functions inherited from itk::DeformationFieldRegulizer< itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > >
virtual const char *	GetClassName () const

virtual const IntermediaryDFTransformType *	GetIntermediaryDeformationFieldTransform ()

void	InitializeDeformationFields (void)

	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 itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
void	EvaluateJacobianWithImageGradientProduct (const InputPointType &ipp, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

virtual const char *	GetClassName () const

const FixedParametersType &	GetFixedParameters (void) const override

bool	GetHasNonZeroSpatialHessian (void) const override

virtual bool	GetInverse (Self *inverse) const

void	GetJacobian (const InputPointType &ipp, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

void	GetJacobianOfSpatialHessian (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

void	GetJacobianOfSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override

virtual const TransformTypePointer	GetNthTransform (SizeValueType n) const

NumberOfParametersType	GetNumberOfNonZeroJacobianIndices (void) const override

NumberOfParametersType	GetNumberOfParameters (void) const override

virtual SizeValueType	GetNumberOfTransforms (void) const

const ParametersType &	GetParameters (void) const override

void	GetSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh) const override

void	GetSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj) const override

TransformCategoryEnum	GetTransformCategory () const override

virtual bool	GetUseAddition () const

virtual bool	GetUseComposition () const

virtual bool	HasNonZeroJacobianOfSpatialHessian (void) const

bool	IsLinear (void) const override

	itkGetModifiableObjectMacro (CurrentTransform, CurrentTransformType)

	itkGetModifiableObjectMacro (InitialTransform, InitialTransformType)

	itkStaticConstMacro (SpaceDimension, unsigned int, NDimensions)

virtual void	SetCurrentTransform (CurrentTransformType *_arg)

void	SetFixedParameters (const FixedParametersType &fixedParam) override

virtual void	SetInitialTransform (InitialTransformType *_arg)

void	SetParameters (const ParametersType &param) override

void	SetParametersByValue (const ParametersType &param) override

virtual void	SetUseAddition (bool _arg)

virtual void	SetUseComposition (bool _arg)

OutputCovariantVectorType	TransformCovariantVector (const InputCovariantVectorType &) const override

OutputPointType	TransformPoint (const InputPointType &point) const override

OutputVectorType	TransformVector (const InputVectorType &) const override

OutputVnlVectorType	TransformVector (const InputVnlVectorType &) const override

Public Member Functions inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
void	ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const override

virtual void	EvaluateJacobianWithImageGradientProduct (const InputPointType &ipp, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

virtual const char *	GetClassName () const

virtual bool	GetHasNonZeroJacobianOfSpatialHessian () const

virtual bool	GetHasNonZeroSpatialHessian () const

virtual void	GetJacobian (const InputPointType &ipp, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0

virtual void	GetJacobianOfSpatialHessian (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0

virtual void	GetJacobianOfSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0

virtual void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0

virtual void	GetJacobianOfSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const=0

virtual NumberOfParametersType	GetNumberOfNonZeroJacobianIndices (void) const

virtual void	GetSpatialHessian (const InputPointType &ipp, SpatialHessianType &sh) const=0

virtual void	GetSpatialJacobian (const InputPointType &ipp, SpatialJacobianType &sj) const=0

	itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)

	itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)

Public Member Functions inherited from elastix::TransformBase< TElastix >
void	AfterRegistrationBase (void) override

int	BeforeAllBase (void) override

virtual int	BeforeAllTransformix (void)

void	BeforeRegistrationBase (void) override

virtual void	ComputeDeterminantOfSpatialJacobian (void) const

virtual void	ComputeSpatialJacobian (void) const

virtual void	CreateTransformParametersMap (const ParametersType &param, ParameterMapType *paramsMap) const

DeformationFieldImageType::Pointer	GenerateDeformationFieldImage (void) const

virtual CombinationTransformType *	GetAsCombinationTransform (void)

virtual const CombinationTransformType *	GetAsCombinationTransform (void) const

virtual ITKBaseType *	GetAsITKBaseType (void)

virtual const ITKBaseType *	GetAsITKBaseType (void) const

virtual const char *	GetClassName () const

virtual const InitialTransformType *	GetInitialTransform (void) const

virtual const char *	GetTransformParametersFileName () const

	ITK_DISALLOW_COPY_AND_ASSIGN (TransformBase)

	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)

	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)

virtual void	ReadFromFile (void)

virtual void	ReadInitialTransformFromFile (const char *transformParameterFileName)

virtual void	ReadInitialTransformFromVector (const vcl_size_t index)

virtual void	SetFinalParameters (void)

virtual void	SetInitialTransform (InitialTransformType *_arg)

virtual void	SetReadWriteTransformParameters (const bool _arg)

virtual void	SetTransformParametersFileName (const char *filename)

virtual void	TransformPoints (void) const

virtual void	TransformPointsAllPoints (void) const

virtual void	TransformPointsSomePoints (const std::string filename) const

virtual void	TransformPointsSomePointsVTK (const std::string filename) const

void	WriteDeformationFieldImage (typename DeformationFieldImageType::Pointer) const

virtual void	WriteToFile (const ParametersType &param) const

virtual void	WriteToFile (void) const

Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
ConfigurationType *	GetConfiguration (void) const

ElastixType *	GetElastix (void) const

RegistrationPointer	GetRegistration (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponentSE)

void	SetConfiguration (ConfigurationType *_arg)

void	SetElastix (ElastixType *_arg)

Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration (void)

virtual void	AfterEachIterationBase (void)

virtual void	AfterEachResolution (void)

virtual void	AfterEachResolutionBase (void)

virtual void	AfterRegistration (void)

virtual void	AfterRegistrationBase (void)

virtual int	BeforeAll (void)

virtual int	BeforeAllBase (void)

virtual void	BeforeEachResolution (void)

virtual void	BeforeEachResolutionBase (void)

virtual void	BeforeRegistration (void)

virtual void	BeforeRegistrationBase (void)

virtual const char *	elxGetClassName (void) const

const char *	GetComponentLabel (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponent)

	itkTypeMacroNoParent (BaseComponent)

void	SetComponentLabel (const char *label, unsigned int idx)

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::DeformationFieldRegulizer< itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > >
static Pointer	New ()

Static Public Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
static Pointer	New ()

Static Public Member Functions inherited from elastix::BaseComponent
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Protected Member Functions
	BSplineTransformWithDiffusion ()

	~BSplineTransformWithDiffusion () override

Protected Member Functions inherited from itk::DeformationFieldRegulizer< itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension > >
	DeformationFieldRegulizer ()

	~DeformationFieldRegulizer () override

Protected Member Functions inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
	AdvancedCombinationTransform ()

void	EvaluateJacobianWithImageGradientProductNoCurrentTransform (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const

void	EvaluateJacobianWithImageGradientProductNoInitialTransform (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const

void	EvaluateJacobianWithImageGradientProductUseAddition (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const

void	EvaluateJacobianWithImageGradientProductUseComposition (const InputPointType &, const MovingImageGradientType &, DerivativeType &, NonZeroJacobianIndicesType &) const

void	GetJacobianNoCurrentTransform (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const

void	GetJacobianNoInitialTransform (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const

void	GetJacobianOfSpatialHessianNoCurrentTransform (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianNoCurrentTransform (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianNoInitialTransform (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianUseAddition (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &ipp, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

virtual void	GetJacobianOfSpatialHessianUseComposition (const InputPointType &ipp, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianNoCurrentTransform (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianNoInitialTransform (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianUseAddition (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &ipp, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianOfSpatialJacobianUseComposition (const InputPointType &ipp, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const

void	GetJacobianUseAddition (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const

void	GetJacobianUseComposition (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const

void	GetSpatialHessianNoCurrentTransform (const InputPointType &ipp, SpatialHessianType &sh) const

void	GetSpatialHessianNoInitialTransform (const InputPointType &ipp, SpatialHessianType &sh) const

void	GetSpatialHessianUseAddition (const InputPointType &ipp, SpatialHessianType &sh) const

void	GetSpatialHessianUseComposition (const InputPointType &ipp, SpatialHessianType &sh) const

void	GetSpatialJacobianNoCurrentTransform (const InputPointType &ipp, SpatialJacobianType &sj) const

void	GetSpatialJacobianNoInitialTransform (const InputPointType &ipp, SpatialJacobianType &sj) const

void	GetSpatialJacobianUseAddition (const InputPointType &ipp, SpatialJacobianType &sj) const

void	GetSpatialJacobianUseComposition (const InputPointType &ipp, SpatialJacobianType &sj) const

virtual void	NoCurrentTransformSet (void) const

OutputPointType	TransformPointNoCurrentTransform (const InputPointType &point) const

OutputPointType	TransformPointNoInitialTransform (const InputPointType &point) const

OutputPointType	TransformPointUseAddition (const InputPointType &point) const

OutputPointType	TransformPointUseComposition (const InputPointType &point) const

virtual void	UpdateCombinationMethod (void)

	~AdvancedCombinationTransform () override

Protected Member Functions inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
	AdvancedTransform ()

	AdvancedTransform (NumberOfParametersType numberOfParameters)

	~AdvancedTransform () override

Protected Member Functions inherited from elastix::TransformBase< TElastix >
void	AutomaticScalesEstimation (ScalesType &scales) const

void	AutomaticScalesEstimationStackTransform (const unsigned int &numSubTransforms, ScalesType &scales) const

	TransformBase ()=default

	~TransformBase () override=default

Protected Member Functions inherited from elastix::BaseComponentSE< TElastix >
	BaseComponentSE ()=default

	~BaseComponentSE () override=default

Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default

virtual	~BaseComponent ()=default

Protected Attributes
SpacingType	m_GridSpacingFactor

Protected Attributes inherited from itk::AdvancedCombinationTransform< elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension >
CurrentTransformPointer	m_CurrentTransform

InitialTransformPointer	m_InitialTransform

EvaluateJacobianWithImageGradientProductFunctionPointer	m_SelectedEvaluateJacobianWithImageGradientProductFunction

GetJacobianOfSpatialHessianFunctionPointer	m_SelectedGetJacobianOfSpatialHessianFunction

GetJacobianOfSpatialHessianFunctionPointer2	m_SelectedGetJacobianOfSpatialHessianFunction2

GetJacobianOfSpatialJacobianFunctionPointer	m_SelectedGetJacobianOfSpatialJacobianFunction

GetJacobianOfSpatialJacobianFunctionPointer2	m_SelectedGetJacobianOfSpatialJacobianFunction2

GetSparseJacobianFunctionPointer	m_SelectedGetSparseJacobianFunction

GetSpatialHessianFunctionPointer	m_SelectedGetSpatialHessianFunction

GetSpatialJacobianFunctionPointer	m_SelectedGetSpatialJacobianFunction

TransformPointFunctionPointer	m_SelectedTransformPointFunction

bool	m_UseAddition

bool	m_UseComposition

Protected Attributes inherited from itk::AdvancedTransform< elx::TransformBase< TElastix >::CoordRepType, NDimensions, NDimensions >
bool	m_HasNonZeroJacobianOfSpatialHessian

bool	m_HasNonZeroSpatialHessian

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

ElastixPointer	m_Elastix {}

RegistrationPointer	m_Registration {}

Private Member Functions
	BSplineTransformWithDiffusion (const Self &)

void	operator= (const Self &)

Private Attributes
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 >

typedef BSplineTransformType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::BSplineTransformPointer

Definition at line 266 of file elxBSplineTransformWithDiffusion.h.

◆ BSplineTransformType

template<class TElastix >

typedef itk::AdvancedBSplineDeformableTransform< typename elx::TransformBase< TElastix >::CoordRepType, elx::TransformBase< TElastix >::FixedImageDimension, __VSplineOrder > elastix::BSplineTransformWithDiffusion< TElastix >::BSplineTransformType

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

Definition at line 189 of file elxBSplineTransformWithDiffusion.h.

◆ CombinationTransformType

template<class TElastix >

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

Definition at line 250 of file elxBSplineTransformWithDiffusion.h.

◆ ConfigurationPointer

template<class TElastix >

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

Definition at line 243 of file elxBSplineTransformWithDiffusion.h.

◆ ConfigurationType

template<class TElastix >

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

Definition at line 242 of file elxBSplineTransformWithDiffusion.h.

◆ ConstPointer

template<class TElastix >

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

Definition at line 192 of file elxBSplineTransformWithDiffusion.h.

◆ ContinuousIndexType

template<class TElastix >

typedef BSplineTransformType::ContinuousIndexType elastix::BSplineTransformWithDiffusion< TElastix >::ContinuousIndexType

Definition at line 236 of file elxBSplineTransformWithDiffusion.h.

◆ CoordRepType

template<class TElastix >

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

Definition at line 246 of file elxBSplineTransformWithDiffusion.h.

◆ DeformationFieldWriterType

template<class TElastix >

typedef itk::ImageFileWriter< VectorImageType > elastix::BSplineTransformWithDiffusion< TElastix >::DeformationFieldWriterType

Definition at line 300 of file elxBSplineTransformWithDiffusion.h.

◆ DiffusionFilterPointer

template<class TElastix >

typedef DiffusionFilterType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::DiffusionFilterPointer

Definition at line 284 of file elxBSplineTransformWithDiffusion.h.

◆ DiffusionFilterType

template<class TElastix >

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

Definition at line 283 of file elxBSplineTransformWithDiffusion.h.

◆ DummyImageType

template<class TElastix >

typedef itk::Image< short, itkGetStaticConstMacro( SpaceDimension ) > elastix::BSplineTransformWithDiffusion< TElastix >::DummyImageType

Other typedef's.

Definition at line 263 of file elxBSplineTransformWithDiffusion.h.

◆ DummyIteratorType

template<class TElastix >

typedef itk::ImageRegionConstIterator< DummyImageType > elastix::BSplineTransformWithDiffusion< TElastix >::DummyIteratorType

Definition at line 265 of file elxBSplineTransformWithDiffusion.h.

◆ ElastixPointer

template<class TElastix >

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

Definition at line 241 of file elxBSplineTransformWithDiffusion.h.

◆ ElastixType

template<class TElastix >

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

Typedef's from TransformBase.

Definition at line 240 of file elxBSplineTransformWithDiffusion.h.

◆ FixedImageELXType

template<class TElastix >

typedef ElastixType::FixedImageType elastix::BSplineTransformWithDiffusion< TElastix >::FixedImageELXType

References to the fixed and moving image types.

Definition at line 258 of file elxBSplineTransformWithDiffusion.h.

◆ FixedImageType

template<class TElastix >

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

Definition at line 247 of file elxBSplineTransformWithDiffusion.h.

◆ GenericDeformationFieldRegulizer

template<class TElastix >

typedef Superclass1::Superclass elastix::BSplineTransformWithDiffusion< TElastix >::GenericDeformationFieldRegulizer

Definition at line 267 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageIteratorType

template<class TElastix >

typedef itk::ImageRegionIterator< GrayValueImageType > elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageIteratorType

Definition at line 278 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImagePointer

template<class TElastix >

typedef GrayValueImageType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImagePointer

Definition at line 275 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageReaderPointer

template<class TElastix >

typedef GrayValueImageReaderType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageReaderPointer

Definition at line 298 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageReaderType

template<class TElastix >

typedef itk::ImageFileReader< GrayValueImageType > elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageReaderType

Definition at line 297 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageType

template<class TElastix >

typedef FixedImageELXType elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageType

Definition at line 274 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValueImageWriterType

template<class TElastix >

typedef itk::ImageFileWriter< GrayValueImageType > elastix::BSplineTransformWithDiffusion< TElastix >::GrayValueImageWriterType

Definition at line 299 of file elxBSplineTransformWithDiffusion.h.

◆ GrayValuePixelType

template<class TElastix >

typedef GrayValueImageType::PixelType elastix::BSplineTransformWithDiffusion< TElastix >::GrayValuePixelType

Definition at line 276 of file elxBSplineTransformWithDiffusion.h.

◆ ImagePointer

template<class TElastix >

typedef BSplineTransformType::ImagePointer elastix::BSplineTransformWithDiffusion< TElastix >::ImagePointer

Definition at line 228 of file elxBSplineTransformWithDiffusion.h.

◆ ImageType

template<class TElastix >

typedef BSplineTransformType::ImageType elastix::BSplineTransformWithDiffusion< TElastix >::ImageType

Definition at line 227 of file elxBSplineTransformWithDiffusion.h.

◆ IndexType

template<class TElastix >

typedef BSplineTransformType::IndexType elastix::BSplineTransformWithDiffusion< TElastix >::IndexType

Definition at line 230 of file elxBSplineTransformWithDiffusion.h.

◆ InputCovariantVectorType

template<class TElastix >

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

Definition at line 218 of file elxBSplineTransformWithDiffusion.h.

◆ InputPointType

template<class TElastix >

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

Definition at line 222 of file elxBSplineTransformWithDiffusion.h.

◆ InputVectorType

template<class TElastix >

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

Definition at line 216 of file elxBSplineTransformWithDiffusion.h.

◆ InputVnlVectorType

template<class TElastix >

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

Definition at line 220 of file elxBSplineTransformWithDiffusion.h.

◆ IntermediaryDFTransformType

template<class TElastix >

typedef Superclass1::IntermediaryDFTransformType elastix::BSplineTransformWithDiffusion< TElastix >::IntermediaryDFTransformType

Other typedef's inherited from Superclass1.

Definition at line 253 of file elxBSplineTransformWithDiffusion.h.

◆ InterpolatorPointer

template<class TElastix >

typedef InterpolatorType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::InterpolatorPointer

Definition at line 296 of file elxBSplineTransformWithDiffusion.h.

◆ InterpolatorType

template<class TElastix >

typedef itk::BSplineInterpolateImageFunction< GrayValueImageType > elastix::BSplineTransformWithDiffusion< TElastix >::InterpolatorType

Definition at line 295 of file elxBSplineTransformWithDiffusion.h.

◆ ITKBaseType

template<class TElastix >

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

Definition at line 249 of file elxBSplineTransformWithDiffusion.h.

◆ JacobianType

template<class TElastix >

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

Definition at line 215 of file elxBSplineTransformWithDiffusion.h.

◆ MaximumImageFilterType

template<class TElastix >

typedef itk::MaximumImageFilter< GrayValueImageType, GrayValueImageType, GrayValueImageType > elastix::BSplineTransformWithDiffusion< TElastix >::MaximumImageFilterType

Definition at line 281 of file elxBSplineTransformWithDiffusion.h.

◆ MovingImageELXType

template<class TElastix >

typedef ElastixType::MovingImageType elastix::BSplineTransformWithDiffusion< TElastix >::MovingImageELXType

Definition at line 259 of file elxBSplineTransformWithDiffusion.h.

◆ MovingImageType

template<class TElastix >

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

Definition at line 248 of file elxBSplineTransformWithDiffusion.h.

◆ OriginType

template<class TElastix >

typedef BSplineTransformType::OriginType elastix::BSplineTransformWithDiffusion< TElastix >::OriginType

Definition at line 233 of file elxBSplineTransformWithDiffusion.h.

◆ OutputCovariantVectorType

template<class TElastix >

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

Definition at line 219 of file elxBSplineTransformWithDiffusion.h.

◆ OutputPointType

template<class TElastix >

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

Definition at line 223 of file elxBSplineTransformWithDiffusion.h.

◆ OutputVectorType

template<class TElastix >

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

Definition at line 217 of file elxBSplineTransformWithDiffusion.h.

◆ OutputVnlVectorType

template<class TElastix >

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

Definition at line 221 of file elxBSplineTransformWithDiffusion.h.

◆ ParameterIndexArrayType

template<class TElastix >

typedef BSplineTransformType::ParameterIndexArrayType elastix::BSplineTransformWithDiffusion< TElastix >::ParameterIndexArrayType

Definition at line 237 of file elxBSplineTransformWithDiffusion.h.

◆ ParametersType

template<class TElastix >

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

Definition at line 214 of file elxBSplineTransformWithDiffusion.h.

◆ Pointer

template<class TElastix >

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

Definition at line 191 of file elxBSplineTransformWithDiffusion.h.

◆ RadiusType

template<class TElastix >

typedef VectorImageType::SizeType elastix::BSplineTransformWithDiffusion< TElastix >::RadiusType

Definition at line 285 of file elxBSplineTransformWithDiffusion.h.

◆ RegionType

template<class TElastix >

typedef BSplineTransformType::RegionType elastix::BSplineTransformWithDiffusion< TElastix >::RegionType

Definition at line 229 of file elxBSplineTransformWithDiffusion.h.

◆ RegistrationPointer

template<class TElastix >

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

Definition at line 245 of file elxBSplineTransformWithDiffusion.h.

◆ RegistrationType

template<class TElastix >

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

Definition at line 244 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerPointer1

template<class TElastix >

typedef ResamplerType1::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerPointer1

Definition at line 289 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerPointer2

template<class TElastix >

typedef ResamplerType2::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::ResamplerPointer2

Definition at line 293 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerType1

template<class TElastix >

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

Definition at line 288 of file elxBSplineTransformWithDiffusion.h.

◆ ResamplerType2

template<class TElastix >

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

Definition at line 292 of file elxBSplineTransformWithDiffusion.h.

◆ ScalarType

template<class TElastix >

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

Typedefs inherited from the superclass.

Definition at line 213 of file elxBSplineTransformWithDiffusion.h.

◆ Self

template<class TElastix >

typedef BSplineTransformWithDiffusion elastix::BSplineTransformWithDiffusion< TElastix >::Self

Standard ITK-stuff.

Definition at line 173 of file elxBSplineTransformWithDiffusion.h.

◆ SizeType

template<class TElastix >

typedef BSplineTransformType::SizeType elastix::BSplineTransformWithDiffusion< TElastix >::SizeType

Definition at line 231 of file elxBSplineTransformWithDiffusion.h.

◆ SpacingType

template<class TElastix >

typedef BSplineTransformType::SpacingType elastix::BSplineTransformWithDiffusion< TElastix >::SpacingType

Definition at line 232 of file elxBSplineTransformWithDiffusion.h.

◆ Superclass1

template<class TElastix >

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

Definition at line 180 of file elxBSplineTransformWithDiffusion.h.

◆ Superclass2

template<class TElastix >

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

Definition at line 181 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImageIteratorType

template<class TElastix >

typedef itk::ImageRegionIterator< VectorImageType > elastix::BSplineTransformWithDiffusion< TElastix >::VectorImageIteratorType

Definition at line 273 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImagePointer

template<class TElastix >

typedef VectorImageType::Pointer elastix::BSplineTransformWithDiffusion< TElastix >::VectorImagePointer

Definition at line 255 of file elxBSplineTransformWithDiffusion.h.

◆ VectorImageType

template<class TElastix >

typedef Superclass1::VectorImageType elastix::BSplineTransformWithDiffusion< TElastix >::VectorImageType

Definition at line 254 of file elxBSplineTransformWithDiffusion.h.

◆ VectorReaderType

template<class TElastix >

typedef itk::ImageFileReader< VectorImageType > elastix::BSplineTransformWithDiffusion< TElastix >::VectorReaderType

Typedef's for the diffusion of the deformation field.

Definition at line 270 of file elxBSplineTransformWithDiffusion.h.

◆ VectorType

template<class TElastix >

typedef VectorImageType::PixelType elastix::BSplineTransformWithDiffusion< TElastix >::VectorType

Definition at line 271 of file elxBSplineTransformWithDiffusion.h.

◆ WeightsFunctionType

template<class TElastix >

typedef BSplineTransformType::WeightsFunctionType elastix::BSplineTransformWithDiffusion< TElastix >::WeightsFunctionType

Definition at line 234 of file elxBSplineTransformWithDiffusion.h.

◆ WeightsType

template<class TElastix >

typedef BSplineTransformType::WeightsType elastix::BSplineTransformWithDiffusion< TElastix >::WeightsType

Definition at line 235 of file elxBSplineTransformWithDiffusion.h.

Constructor & Destructor Documentation

◆ BSplineTransformWithDiffusion() [1/2]

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 ( )

inlineoverrideprotected

The destructor.

Definition at line 367 of file elxBSplineTransformWithDiffusion.h.

◆ BSplineTransformWithDiffusion() [2/2]

template<class TElastix >

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

private

The private constructor.

Member Function Documentation

◆ AfterEachIteration()

template<class TElastix >

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

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 ( void )

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 ( void )

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 ( void )

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.

◆ DiffuseDeformationField()

template<class TElastix >

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

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 elastix::TransformBase< TElastix >.

◆ IncreaseScale()

template<class TElastix >

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

virtual

Upsample the B-spline grid.

◆ 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.

◆ operator=()

template<class TElastix >

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

private

The private copy constructor.

◆ ReadFromFile()

template<class TElastix >

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

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).