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

Deformable transform using a fluid representation. More...

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

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

Public Types
typedef FluidDeformableTransform	Self
typedef DeformableTransform < TFixedImage, TScalarType, NDimensions, TDeformationScalar >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::ScalarType	ScalarType
typedef Superclass::ParametersType	ParametersType
typedef Superclass::JacobianType	JacobianType
typedef Superclass::OutputPointType	OutputPointType
typedef Superclass::InputPointType	InputPointType
typedef Superclass::DeformationFieldPixelType	DeformationFieldPixelType
typedef Superclass::DeformationFieldType	DeformationFieldType
typedef TFixedImage	FixedImageType
typedef TFixedImage::ConstPointer	FixedImagePointer
typedef Superclass::VectorFieldImageType	DeformableParameterType
typedef DeformableParameterType::Pointer	DeformableParameterPointerType
Public Types inherited from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >
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	Initialize (FixedImagePointer fixedImage)
virtual void	SetIdentity ()
virtual void	SetParameters (const ParametersType &parameters)
virtual void	SetDeformableParameters (DeformableParameterPointerType parameters)
virtual DeformableParameterPointerType	GetDeformableParameters ()
virtual void	InterpolateNextGrid (FixedImagePointer image)
virtual bool	IsRegridable () const
virtual void	UpdateRegriddedDeformationParameters (DeformableParameterPointerType regriddedParameters, DeformableParameterPointerType currentPosition, double factor)
virtual bool	IsIdentity ()
void	InvertUsingGradientDescent (typename Self::Pointer invertedTransform, unsigned int maxIteration, double tol)
void	ComputeSquareRoot (typename Self::Pointer sqrtTransform, unsigned int maxInverseIteration, unsigned int maxIteration, double tol)
Public Member Functions inherited from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >
	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 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)
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 const ParametersType &	GetFixedParameters (void) const
virtual void	SetFixedParameters (const ParametersType &parameters)
bool	GetInverse (Self *inverse) const
void	ConcatenateAfterGivenTransform (Self *givenTransform)
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

Static Public Member Functions
static Pointer	New ()
static DeformableParameterPointerType	DuplicateDeformableParameters (const DeformableParameterType *deformableParameters)

Protected Member Functions
	FluidDeformableTransform ()
virtual	~FluidDeformableTransform ()
void	PrintSelf (std::ostream &os, Indent indent) const
virtual Superclass::JacobianDeterminantFilterType::OutputImageRegionType	GetValidJacobianRegion () const
Protected Member Functions inherited from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >
	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)

Additional Inherited Members
Protected Attributes inherited from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >
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::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >

Deformable transform using a fluid representation.

Member Typedef Documentation

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

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

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

typedef DeformableParameterType::Pointer itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformableParameterPointerType

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

typedef Superclass::VectorFieldImageType itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformableParameterType

Use our own deformable parameter type to save memory.

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

typedef Superclass::DeformationFieldPixelType itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldPixelType

Typedefs for the deformation field.

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

typedef Superclass::DeformationFieldType itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DeformationFieldType

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

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

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

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

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

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

Standard Jacobian container.

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

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

Standard coordinate point type for this class.

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

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

Standard parameters container.

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

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

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

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

Standard scalar type for this class.

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

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

Standard class typedefs.

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

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

Constructor & Destructor Documentation

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

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

protected

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

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

protectedvirtual

Member Function Documentation

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

void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::ComputeSquareRoot	(	typename Self::Pointer	sqrtTransform,
		unsigned int	maxInverseIteration,
		unsigned int	maxIteration,
		double	tol
	)

Compute the square root of the deformation.

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

static DeformableParameterPointerType itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::DuplicateDeformableParameters ( const DeformableParameterType *  deformableParameters )

static

Return a copy of the deformable parameters.

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

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

virtual DeformableParameterPointerType itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::GetDeformableParameters ( )

inlinevirtual

Return the current deformable parameters, which is just the deformation field. Nice and easy!

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

virtual Superclass::JacobianDeterminantFilterType::OutputImageRegionType itk::FluidDeformableTransform< 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 from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

virtual void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::Initialize ( FixedImagePointer  fixedImage )

virtual

Convenience method to set up internal images. Sets the internal deformation field to the same size as fixed image. Sets the parameters array to the right size, and then calls SetIdentity().

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

virtual void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InterpolateNextGrid ( FixedImagePointer  image )

virtual

Interpolate the deformation fluid when moving to a bigger image.

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

void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::InvertUsingGradientDescent	(	typename Self::Pointer	invertedTransform,
		unsigned int	maxIteration,
		double	tol
	)

Invert using gradient descent.

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

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

virtual

Returns true if we are currently equal to Identity transform.

Reimplemented from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

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

inlinevirtual

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

Reimplemented from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

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

Get the number of dimensions.

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

static Pointer itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::New ( )

static

New macro for creation of through the object factory.

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

void itk::FluidDeformableTransform< 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 >

virtual void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::SetDeformableParameters ( DeformableParameterPointerType  parameters )

virtual

This method sets the parameters of the transform. For a fluid transformation, the parameters are displacement vectors for each voxel.

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

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

virtual

Set the deformation field to Identity. Doesn't affect the Global transform. Doesn't resize anything either.

Reimplemented from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

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

inlinevirtual

This method sets the parameters of the transform. For a fluid transformation, the parameters are displacement vectors for each voxel.

Reimplemented from itk::DeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >.

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

virtual void itk::FluidDeformableTransform< TFixedImage, TScalarType, NDimensions, TDeformationScalar >::UpdateRegriddedDeformationParameters ( DeformableParameterPointerType  regriddedParameters, DeformableParameterPointerType  currentPosition, double  factor  )

virtual

Regrid and compose the new regridded deformation Note that this function destroys the content of currentPosition.

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

• itkFluidDeformableTransform.h