itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar > Class Template Reference

Base class for deformable transforms. More...

Inheritance diagram for itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >:

Collaboration diagram for itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >:

Public Types
typedef DeformableTransform	Self
typedef Transform< TScalarType, NDimensions, NDimensions >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::ScalarType	ScalarType
typedef Superclass::NumberOfParametersType	NumberOfParametersType
typedef Superclass::ParametersType	ParametersType
typedef Superclass::ParametersValueType	ParametersValueType
typedef Array < ParametersValueType >	DerivativeType
typedef Superclass::OutputPointType	OutputPointType
typedef Superclass::InputPointType	InputPointType
typedef Superclass::InputVectorType	InputVectorType
typedef Superclass::OutputVectorType	OutputVectorType
typedef Superclass::InputCovariantVectorType	InputCovariantVectorType
typedef Superclass::OutputCovariantVectorType	OutputCovariantVectorType
typedef Superclass::InputVnlVectorType	InputVnlVectorType
typedef Superclass::OutputVnlVectorType	OutputVnlVectorType
typedef Vector < TDeformationScalar, NDimensions >	VectorFieldPixelType
typedef Image < VectorFieldPixelType, NDimensions >	VectorFieldImageType
typedef VectorFieldImageType::Pointer	VectorFieldImagePointer
typedef VectorFieldImageType::SizeType	VectorFieldSizeType
typedef ImageRegionIterator < VectorFieldImageType >	VectorFieldIteratorType
typedef ImageRegionConstIterator < VectorFieldImageType >	VectorFieldConstIteratorType
typedef VectorFieldPixelType	DeformationFieldPixelType
typedef VectorFieldImageType	DeformationFieldType
typedef DeformationFieldType::Pointer	DeformationFieldPointer
typedef ImageRegion< NDimensions >	DeformationFieldRegionType
typedef DeformationFieldRegionType::IndexType	DeformationFieldIndexType
typedef DeformationFieldRegionType::SizeType	DeformationFieldSizeType
typedef DeformationFieldType::SpacingType	DeformationFieldSpacingType
typedef DeformationFieldType::DirectionType	DeformationFieldDirectionType
typedef DeformationFieldType::PointType	DeformationFieldOriginType
typedef Image < TDeformationScalar, NDimensions >	DeformationFieldComponentImageType
typedef TFixedImage	FixedImageType
typedef FixedImageType::ConstPointer	FixedImagePointer
typedef Transform< TScalarType, itkGetStaticConstMacro(SpaceDimension), itkGetStaticConstMacro(SpaceDimension)>	GlobalTransformType
typedef GlobalTransformType::ConstPointer	GlobalTransformPointer
typedef DisplacementFieldJacobianDeterminantFilter < DeformationFieldType, TScalarType >	JacobianDeterminantFilterType
typedef JacobianDeterminantFilterType::Pointer	JacobianDeterminantFilterPointer
typedef Superclass::JacobianType	JacobianType

Public Member Functions
virtual const char *	GetClassName () const
	itkStaticConstMacro (SpaceDimension, unsigned int, NDimensions)
virtual void	SetGlobalTransform (const GlobalTransformType *_arg)
virtual const GlobalTransformType *	GetGlobalTransform ()
virtual void	SetInverseSearchRadius (double _arg)
virtual double	GetInverseSearchRadius ()
virtual const ParametersType &	GetParameters (void) const
virtual void	SetParameters (const ParametersType &parameters)
virtual NumberOfParametersType	GetNumberOfParameters (void) const
virtual void	SetParametersFromField (const VectorFieldImagePointer &image, bool force=false)
virtual DeformationFieldType *	GetDeformationField () const
TScalarType	ComputeMaxDeformation ()
TScalarType	ComputeMinDeformation ()
TScalarType	ComputeMaxJacobian ()
TScalarType	ComputeMinJacobian ()
TScalarType	GetSumLogJacobianDeterminant ()
virtual void	WriteTransform (std::string filename)
virtual void	WriteParameters (std::string filename)
void	WriteJacobianImage (std::string filename)
void	WriteMidasStrImage (std::string filename, int origin[NDimensions], typename TFixedImage::RegionType paddedDesiredRegion, const typename JacobianDeterminantFilterType::OutputImageType *jacobianImage)
void	ReadMidasStrImage (std::string filename, int origin[NDimensions], typename TFixedImage::RegionType paddedDesiredRegion, typename JacobianDeterminantFilterType::OutputImageType *jacobianImage)
void	WriteMidasVecImage (std::string filename, int origin[NDimensions], typename TFixedImage::RegionType paddedDesiredRegion)
void	WriteVectorImage (std::string filename)
virtual void	SetIdentity ()
void	Initialize (FixedImagePointer image)
virtual OutputPointType	TransformPoint (const InputPointType &point) const
virtual OutputVectorType	TransformVector (const InputVectorType &) const
virtual OutputVnlVectorType	TransformVector (const InputVnlVectorType &) const
virtual OutputCovariantVectorType	TransformCovariantVector (const InputCovariantVectorType &) const
virtual bool	IsLinear () const
virtual bool	IsIdentity ()
virtual const ParametersType &	GetFixedParameters (void) const
virtual void	SetFixedParameters (const ParametersType &parameters)
bool	GetInverse (Self *inverse) const
void	ConcatenateAfterGivenTransform (Self *givenTransform)
virtual bool	IsRegridable () const
virtual void	UpdateRegriddedDeformationParameters (ParametersType &regriddedParameters, const ParametersType &currentPosition)
void	SetUseForwardDifferenceJacobianCalculation ()
void	InitialiseGlobalTransformation ()
JacobianDeterminantFilterType::OutputImageType *	GetJacobianImage () const
void	ExtractComponents ()
void	InvertUsingIterativeFixedPoint (typename Self::Pointer invertedTransform, int maxIterations, int maxOuterIterations, double tol)
virtual void	ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const

Protected Member Functions
	DeformableTransform ()
virtual	~DeformableTransform ()
void	PrintSelf (std::ostream &os, Indent indent) const
unsigned long int	GetNumberOfParametersImpliedByImage (const VectorFieldImagePointer image)
void	ResizeParametersArray (const VectorFieldImagePointer image)
void	MarshallParametersToImage (VectorFieldImagePointer image)
void	MarshallImageToParameters (const VectorFieldImagePointer image, ParametersType &parameters)
virtual JacobianDeterminantFilterType::OutputImageRegionType	GetValidJacobianRegion () const

Protected Attributes
DeformationFieldType::Pointer	m_DeformationField
GlobalTransformPointer	m_GlobalTransform
JacobianDeterminantFilterPointer	m_JacobianFilter
double	m_InverseSearchRadius
double	m_InverseVoxelTolerance
double	m_InverseIterationTolerance
double	m_MaxNumberOfInverseIterations
DeformationFieldComponentImageType::Pointer	m_DeformationFieldComponent [NDimensions]

Detailed Description

template<class TFixedImage, class TScalarType, unsigned int NDimensions, class TDeformationScalar>
class itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >

Base class for deformable transforms.

For both UCLBSplineTransform and FluidDeformableTransform, the transformation is represented as an image of vectors, one vector per voxel. Its parameterisation depends on derived classes. So, for Fluid, you are actually working at the voxel level, and for BSpline/FFD based transformation, the transformation is parameterized by the control point grid, and interpolated to each voxel.

The optimizer API requires SetParameters() and GetParameters(). So, this class provides protected utility methods GetNumberOfParametersImpliedByImage, ResizeParametersArray and MarshallParametersToImage to marshall parameters from the array representation to an image. In both cases, the transformation owns its internal parameter array, and should be responsible for resizing it, and deciding if its the right size.

Don't forget that even though the transformation owns its internal parameter array, such that GetParameters returns a reference to the parameters contained herein, the optimizer class provides new parameters arrays throughout the optimisation. This means that when the optimizer calls transform->SetParameters(&parameters), then the argument is passed by reference, and the parameters are copied to the parameters array within this class.

This class also provides a Global transform. This can be any parametric transform using the standard ITK Transform class hierarchy. If this has been set then calling TransformPoint will multiply the point by the Global transform (for example an affine one), and then add the deformation vector onto the point.

TODO: We haven't tested this Global transform. I think you would actually need to interpolate the vector field. So, in most cases, you are better off sorting out your affine transform, resampling, and then just doing deformable stuff on pre-registered images.

See also

UCLBSplineTransform, FluidDeformableTransform.

Member Typedef Documentation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef SmartPointer<const Self> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ConstPointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Image<TDeformationScalar, NDimensions> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldComponentImageType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldType::DirectionType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldDirectionType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldRegionType::IndexType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldIndexType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldType::PointType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldOriginType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef VectorFieldPixelType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldPixelType

Both Fluid and FFD will represent the deformation field as a vector at each point in an image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldType::Pointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldPointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef ImageRegion<NDimensions> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldRegionType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldRegionType::SizeType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldSizeType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformationFieldType::SpacingType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldSpacingType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef VectorFieldImageType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Array<ParametersValueType> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DerivativeType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef FixedImageType::ConstPointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::FixedImagePointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef TFixedImage itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::FixedImageType

The deformation field is defined over the fixed image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef GlobalTransformType::ConstPointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GlobalTransformPointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Transform<TScalarType, itkGetStaticConstMacro(SpaceDimension), itkGetStaticConstMacro(SpaceDimension)> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GlobalTransformType

Typedef of the bulk transform, i.e. we set up an affine transform.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::InputCovariantVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InputCovariantVectorType

Standard covariant vector type for this class

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::InputPointType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InputPointType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::InputVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InputVectorType

Standard vector type for this class.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::InputVnlVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InputVnlVectorType

Standard vnl_vector type for this class.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef JacobianDeterminantFilterType::Pointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::JacobianDeterminantFilterPointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DisplacementFieldJacobianDeterminantFilter< DeformationFieldType, TScalarType > itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::JacobianDeterminantFilterType

Typedef for Jacobian Calculator.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::JacobianType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::JacobianType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::NumberOfParametersType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::NumberOfParametersType

Standard parameters container.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::OutputCovariantVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::OutputCovariantVectorType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::OutputPointType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::OutputPointType

Standard coordinate point type for this class.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::OutputVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::OutputVectorType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::OutputVnlVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::OutputVnlVectorType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::ParametersType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ParametersType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::ParametersValueType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ParametersValueType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef SmartPointer<Self> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::Pointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Superclass::ScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ScalarType

Standard scalar type for this class.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef DeformableTransform itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::Self

Standard class typedefs.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Transform< TScalarType, NDimensions, NDimensions > itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::Superclass

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef ImageRegionConstIterator<VectorFieldImageType> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldConstIteratorType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef VectorFieldImageType::Pointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldImagePointer

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Image< VectorFieldPixelType, NDimensions > itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldImageType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef ImageRegionIterator<VectorFieldImageType> itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldIteratorType

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef Vector< TDeformationScalar, NDimensions > itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldPixelType

These are so we can marshall parameters into an image of either control points, or voxels.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

typedef VectorFieldImageType::SizeType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::VectorFieldSizeType

Constructor & Destructor Documentation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformableTransform ( )

protected

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::~DeformableTransform ( )

protectedvirtual

Member Function Documentation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeJacobianWithRespectToParameters ( const InputPointType &  , JacobianType &    ) const

inlinevirtual

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

TScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeMaxDeformation

(

)

Actually run through the deformation field, and calculate the max deformation. This is the maximum magnitude of a deformation vector (not of the individual component in x,y,z).

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

TScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeMaxJacobian

(

)

Actually run through the deformation field, and calculate the max jacobian.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

TScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeMinDeformation

(

)

Actually run through the deformation field, and calculate the min deformation. This is the minimum magnitude of a deformation vector (not of the individual component in x,y,z).

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

TScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeMinJacobian

(

)

Actually run through the deformation field, and calculate the min jacobian.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ConcatenateAfterGivenTransform

(

Self *

givenTransform

)

Concatenate the current deformation field after the given deformation field

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ExtractComponents

(

)

Extract the x, y, z components of the vector deformation field into 3 images.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual const char* itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetClassName ( ) const

virtual

Run-time type information (and related methods).

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >, and itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual DeformationFieldType* itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetDeformationField ( ) const

inlinevirtual

Get the deformation field pointer.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual const ParametersType& itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetFixedParameters ( void  ) const

virtual

Get the fixed parameters for saving.

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual const GlobalTransformType* itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetGlobalTransform ( )

virtual

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

bool itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetInverse

(

Self *

inverse

)

const

Create inverse of a deformable transformation according to Methods for inverting dense displacement fields: Evaluation in brain image registration, Crum et al, MICCAI, 2007.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual double itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetInverseSearchRadius ( )

virtual

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

JacobianDeterminantFilterType::OutputImageType* itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetJacobianImage ( ) const

inline

Get the Jacobian image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual NumberOfParametersType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetNumberOfParameters ( void  ) const

inlinevirtual

Return the number of parameters that completely define the Transfom

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

unsigned long int itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetNumberOfParametersImpliedByImage ( const VectorFieldImagePointer  image )

protected

Works out the number of parameters implied by the image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual const ParametersType& itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetParameters ( void  ) const

inlinevirtual

Return the transformation parameters.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

TScalarType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetSumLogJacobianDeterminant

(

)

Calculate the log of the jacobian determinant at each voxel.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual JacobianDeterminantFilterType::OutputImageRegionType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetValidJacobianRegion ( ) const

inlineprotectedvirtual

To get the valid Jacobian region - because for fluid Diriac boundary condition - the deformation around the edge is 0.

Reimplemented in itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InitialiseGlobalTransformation

(

)

Iniitilise the deformation field with the global transformation.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::Initialize

(

FixedImagePointer

image

)

Convenience method to set up internal deformation field to the same size as the supplied image. In this method, we can't set up a corresponding m_Parameters array, as different subclasses will have different requirements.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InvertUsingIterativeFixedPoint	(	typename Self::Pointer	invertedTransform,
		int	maxIterations,
		int	maxOuterIterations,
		double	tol
	)

Invert using fixed point iteration.

Recommended values: maxIterations=30 maxOuterIterations=5 tol=0.001

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual bool itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::IsIdentity ( )

virtual

Returns true if we are currently equal to Identity transform.

Reimplemented in itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual bool itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::IsLinear ( ) const

inlinevirtual

Indicates that this transform is linear. That is, given two points P and Q, and scalar coefficients a and b, then

      T( a*P + b*Q ) = a * T(P) + b * T(Q)

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual bool itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::IsRegridable ( ) const

inlinevirtual

Return true if the deformable is regriddable. This then requires the implementation the Regrid function.

Reimplemented in itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::itkStaticConstMacro	(	SpaceDimension	,
		unsigned	int,
		NDimensions
	)

Dimension of the domain space.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::MarshallImageToParameters ( const VectorFieldImagePointer  image, ParametersType &  parameters  )

protected

To Convert image to parameters array.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::MarshallParametersToImage ( VectorFieldImagePointer  image )

protected

To Convert parameters array to an image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protected

Print contents of an FluidDeformableTransform.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ReadMidasStrImage	(	std::string	filename,
		int	origin[NDimensions],
		typename TFixedImage::RegionType	paddedDesiredRegion,
		typename JacobianDeterminantFilterType::OutputImageType *	jacobianImage
	)

Write the Midas jacobian image of the deformation field out to the given filename.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ResizeParametersArray ( const VectorFieldImagePointer  image )

protected

Makes the parameters array match the size of the image, and resets everything.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetFixedParameters ( const ParametersType &  parameters )

virtual

Set the fixed paramters for loading

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetGlobalTransform ( const GlobalTransformType *  _arg )

virtual

This method specifies the bulk transform to be applied.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetIdentity ( )

virtual

Set the parameters array to Identity. Doesn't affect the Global transform. Doesn't resize anything either.

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >, and itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetInverseSearchRadius ( double  _arg )

virtual

Set/Get the search radius (voxel unit) for computing the inverse.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetParameters ( const ParametersType &  parameters )

inlinevirtual

Set the transformation parameters.

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >, and itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetParametersFromField ( const VectorFieldImagePointer &  image, bool  force = false  )

virtual

Sets the transformation parameters from an image. The parameter 'force' is to force parameter array to the right size. If force is false, and the parameters array is the wrong size, an exception is thrown. If force is true, the parameters array is resized.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetUseForwardDifferenceJacobianCalculation ( )

inline

Call to set the Jacobian calculation to be using the forward difference. This function should be called immediately after constructing the deformable transform.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual OutputCovariantVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::TransformCovariantVector ( const InputCovariantVectorType &  ) const

inlinevirtual

Method to transform a CovariantVector - not applicable for this type of transform

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual OutputPointType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::TransformPoint ( const InputPointType &  point ) const

virtual

Declared virtual in base class, transform points

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual OutputVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::TransformVector ( const InputVectorType &  ) const

inlinevirtual

Method to transform a vector - not applicable for this type of transform.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual OutputVnlVectorType itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::TransformVector ( const InputVnlVectorType &  ) const

inlinevirtual

Method to transform a vnl_vector - not applicable for this type of transform

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::UpdateRegriddedDeformationParameters ( ParametersType &  regriddedParameters, const ParametersType &  currentPosition  )

inlinevirtual

Regrid and compose the new regridded deformation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteJacobianImage

(

std::string

filename

)

Write the jacobian image of the deformation field out to the given filename.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteMidasStrImage	(	std::string	filename,
		int	origin[NDimensions],
		typename TFixedImage::RegionType	paddedDesiredRegion,
		const typename JacobianDeterminantFilterType::OutputImageType *	jacobianImage
	)

Write the Midas jacobian image of the deformation field out to the given filename.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteMidasVecImage	(	std::string	filename,
		int	origin[NDimensions],
		typename TFixedImage::RegionType	paddedDesiredRegion
	)

Write the Midas vector image of the deformation field out to the given filename.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteParameters ( std::string  filename )

inlinevirtual

Write parameters, so subclass can override if necessary. Default implementation is suitable for Fluid.

Reimplemented in itk::UCLBSplineTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

virtual void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteTransform ( std::string  filename )

inlinevirtual

Write transform, so subclass can override it if necessary. Default implementation is suitable for Fluid.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

void itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::WriteVectorImage

(

std::string

filename

)

Write the vector image of the deformation field out to the given filename.

Member Data Documentation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

DeformationFieldType::Pointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_DeformationField

protected

The deformation/displacement field, represented as an image.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

DeformationFieldComponentImageType::Pointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_DeformationFieldComponent[NDimensions]

protected

Hold the x, y, z components of the deformation field.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

GlobalTransformPointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_GlobalTransform

protected

The global transform.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

double itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_InverseIterationTolerance

protected

Tolerance for checking in the iteration if the forward transformation is close to the source image grid.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

double itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_InverseSearchRadius

protected

Search radius for calculating the inverse transformation

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

double itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_InverseVoxelTolerance

protected

Tolerance for checking if the forward transformation hits the source image grid.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

JacobianDeterminantFilterPointer itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_JacobianFilter

protected

Jacobian Filter. Currently no need to expose this publically, so no Setter/Getter.

template<class TFixedImage , class TScalarType , unsigned int NDimensions, class TDeformationScalar >

double itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::m_MaxNumberOfInverseIterations

protected

Maximum number of iteration in the inverse computaion.

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The documentation for this class was generated from the following file:

• itkDeformableTransform.h