#include <SlidingTransformation.h>

Inheritance diagram for SlidingTransformation:

Collaboration diagram for SlidingTransformation:

Public Types
typedef Transformation::PrecisionType	PrecisionType

Public Types inherited from Transformation
typedef float	PrecisionType

Public Member Functions
	SlidingTransformation (std::shared_ptr< Transformation >transformationAIn, std::shared_ptr< Transformation >transformationBIn, nifti_image *defSpaceImage, unsigned int numberOfLevels, unsigned int numberOfLevelsToPerform)

	SlidingTransformation (const SlidingTransformation &transformToCopy)

	~SlidingTransformation ()

virtual void	InitialiseLevel (unsigned int level)

void	SetParameters (PrecisionType *parametersIn, bool parametersAreDisplacements)

virtual nifti_image *	GetDeformationVectorField (nifti_image *targetImageIn)

virtual SlidingTransformation::PrecisionType *	GetDVFGradientWRTTransformationParameters (nifti_image *denseDVFIn)

virtual SlidingTransformation::PrecisionType *	GetConstraintGradientWRTTransformationParameters ()

double	GetConstraintValue ()

virtual PrecisionType *	GetCopyOfParameters ()

std::shared_ptr< Transformation >	DeepCopy ()

void	DisplayTransformationParameters ()

virtual PrecisionType	GetSumOfPenaltyWeights ()

virtual PrecisionType	GetMaxTransformationParameterLength (PrecisionType *parametersIn)

std::vector< nifti_image * >	GetTransformationAsImage ()

void	SetGapOverlapConstraintWeight (double gapOverlabConstraintWeightIn)

void	SetSignedDistanceMapImage (nifti_image *signedDistanceMapImageIn)

Public Member Functions inherited from Transformation
virtual	~Transformation ()

virtual void	InitialiseLevel (unsigned int level)=0

virtual PrecisionType *	GetCopyOfParameters ()=0

virtual unsigned int	GetNumberOfParameters ()

virtual void	SetParameters (PrecisionType *paramsIn, bool parametersAreDisplacements)=0

virtual nifti_image *	GetDeformationVectorField (nifti_image *targetImageIn)=0

virtual PrecisionType *	GetDVFGradientWRTTransformationParameters (nifti_image *denseDVFIn)=0

virtual PrecisionType *	GetConstraintGradientWRTTransformationParameters ()=0

virtual double	GetConstraintValue ()=0

void	TransformImage (nifti_image sourceImage, nifti_image warpedImage)

void	TransformImageAdjoint (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

virtual std::shared_ptr< Transformation >	DeepCopy ()=0

virtual void	DisplayTransformationParameters ()=0

virtual PrecisionType	GetSumOfPenaltyWeights ()=0

virtual void	GetImageGradientWRTDVF (nifti_image sourceImage, nifti_image outWarpedGradientImage)

void	ReorientateVectorImage (nifti_image *vectorFieldToReorientate, mat44 reorientationMatrix)

virtual PrecisionType	GetMaxTransformationParameterLength (PrecisionType *parametersIn)=0

virtual std::vector< nifti_image * >	GetTransformationAsImage ()=0

PrecisionType	GetPaddingValue ()

Private Member Functions
void	ClearSignedDistanceMap ()

void	ClearTransformedSignedDistanceMaps ()

void	AllocateTransformedSignedDistanceMaps (nifti_image *targetImage)

double	CalculateGapOverlapConstraintTerm ()

bool	TransformedSignedDistMapsCanBeUsedForConstraintCalculations ()

Private Attributes
std::shared_ptr< Transformation >	transformA
	The transformation defining the inside, i.e. SDT < 0. More...

std::shared_ptr< Transformation >	transformB
	The transformation defining the outside, i.e. SDT > 0. More...

nifti_image *	signedDistMapImage
	Nifti image holding the singed distance image in source-image space for the current level. More...

std::shared_ptr< ImagePyramid< PrecisionType > >	defSpaceImagePyramid
	The image pyramid holding the images in which the transformation is defined. Should correspond with those used to initilase the transfomrations A and B. Will be generated during construction. More...

nifti_image *	curDefSpaceImage
	Pointer to the current image within the defSpaceImagePyramid. More...

int	lastInitialisedLevel
	The last initialised level. This determines which level of the def space image pyramid is accessed. Will be set to -1 before initialisation. More...

nifti_image *	signedDistMapImageTransformedA
	Nfiti image holdeing the signed distance map transformed with transformA. More...

nifti_image *	signedDistMapImageTransformedB
	Nfiti image holdeing the signed distance map transformed with transformA. More...

double	gapOverlapConstraintWeight
	The gap-overlap-constraint weight. More...

Additional Inherited Members
Protected Member Functions inherited from Transformation
bool	CheckDVFImageUpdateRequired (nifti_image *targetImageIn)

bool	CheckImageGeometryEquality (nifti_image img1, nifti_image img2)

virtual void	ClearDeformationVectorFieldImage ()

void	CubicSplineTransformImage3D (nifti_image sourceImage, nifti_image warpedImage)

void	CubicSplineTransformImage2D (nifti_image sourceImage, nifti_image warpedImage)

void	NearestNeighbourTransformImage3D (nifti_image sourceImage, nifti_image warpedImage)

void	NearestNeighbourTransformImage2D (nifti_image sourceImage, nifti_image warpedImage)

void	TrilinearTransformImage (nifti_image sourceImage, nifti_image warpedImage)

void	BilinearTransformImage (nifti_image sourceImage, nifti_image warpedImage)

void	CubicSplineTransformImageAdjoint3D (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	CubicSplineTransformImageAdjoint2D (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	NearestNeighbourTransformImageAdjoint3D (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	NearestNeighbourTransformImageAdjoint2D (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	TrilinearTransformImageAdjoint (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	BilinearTransformImageAdjoint (nifti_image sourceImage, nifti_image sourceWeightsImage, nifti_image warpedImage, nifti_image warpedWeightsImage)

void	TrilinearImageGradient (nifti_image sourceImage, nifti_image resultGradientImage)

void	BilinearImageGradient (nifti_image sourceImage, nifti_image resultGradientImage)

void	CubicSplineImageGradient3D (nifti_image sourceImage, nifti_image resultGradientImage)

void	CubicSplineImageGradient2D (nifti_image sourceImage, nifti_image resultGradientImage)

Protected Attributes inherited from Transformation
bool	dvfImageUpdateRequired
	Indicates if the DVF requires re-calculation when it is required. More...

unsigned int	numberOfParameters
	The total number of parameters needed to describe the transformation. More...

int	interpolation
	Type of interpolation used. More...

PrecisionType	warpedPaddingValue
	Padding value for the warped image. More...

nifti_image *	deformationVectorFieldImage
	The deformation vector field image. More...

Detailed Description

Class implementing the sliding transformation

Member Typedef Documentation

◆ PrecisionType

typedef Transformation::PrecisionType SlidingTransformation::PrecisionType

Constructor & Destructor Documentation

◆ SlidingTransformation() [1/2]

SlidingTransformation::SlidingTransformation	(	std::shared_ptr< Transformation >	transformationAIn,
		std::shared_ptr< Transformation >	transformationBIn,
		nifti_image *	defSpaceImage,
		unsigned int	numberOfLevels,
		unsigned int	numberOfLevelsToPerform
	)

Constructor to generate a sliding transformation object.

The sliding transformation is defined by two individual transformation objects, i.e. transformationA and transformationB.

Parameters

transformationAIn	Pointer to the first transformation.
transformationBIn	Pointer to the second transformation.
defSpaceImage	Image defining the area where the sliding-transformation specific constraint term will be calculated.
numberOfLevels	Number of pyramid levels. Required to correctly calculate the image pyramid of defSpaceImage.
numberOfLevelsToPerform	Number of levels to perform. See numberOfLevels.

◆ SlidingTransformation() [2/2]

SlidingTransformation::SlidingTransformation ( const SlidingTransformation & transformToCopy )

Copy constructor.

Parameters

transformToCopy Reference to the sliding transformation object to copy.

◆ ~SlidingTransformation()

SlidingTransformation::~SlidingTransformation ( )

Destructor.

Member Function Documentation

◆ AllocateTransformedSignedDistanceMaps()

void SlidingTransformation::AllocateTransformedSignedDistanceMaps ( nifti_image * targetImage )

private

Allocate the transfomred signed distance maps

Parameters

targetImage The target image defines the size of the allocated signed distance maps.

◆ CalculateGapOverlapConstraintTerm()

double SlidingTransformation::CalculateGapOverlapConstraintTerm ( )

private

Calculate the gap and overlap constraint term from the transfomred signed distance maps.

Note: The function GetDeformationVectorField() has to be called before this can be computed.

◆ ClearSignedDistanceMap()

void SlidingTransformation::ClearSignedDistanceMap ( )

private

Delete this objet's copy of the signed distance image used.

◆ ClearTransformedSignedDistanceMaps()

void SlidingTransformation::ClearTransformedSignedDistanceMaps ( )

private

Delete the transfomred signed distance maps

◆ DeepCopy()

std::shared_ptr< Transformation > SlidingTransformation::DeepCopy ( )

virtual

Function to create a deep copy of this object.

Implements Transformation.

◆ DisplayTransformationParameters()

void SlidingTransformation::DisplayTransformationParameters ( )

virtual

Display function to print the transformation parameters to the standard output

Implements Transformation.

◆ GetConstraintGradientWRTTransformationParameters()

SlidingTransformation::PrecisionType * SlidingTransformation::GetConstraintGradientWRTTransformationParameters ( )

virtual

Calculate the gradient of the constraint term (regularisation) for the transformation with the current parameters.

Implements Transformation.

◆ GetConstraintValue()

double SlidingTransformation::GetConstraintValue ( )

virtual

Get the constraint value for the transformation with the current parameters.

Implements Transformation.

◆ GetCopyOfParameters()

SlidingTransformation::PrecisionType * SlidingTransformation::GetCopyOfParameters ( )

virtual

Return a pointer to the parameters of the transformation

Implements Transformation.

◆ GetDeformationVectorField()

nifti_image * SlidingTransformation::GetDeformationVectorField ( nifti_image * targetImageIn )

virtual

For a given target image, calculate a deformation vector field (DVF).

Parameters

targetImageIn The target image defines the geometry of the DVF, or the voxel locations for which deformation vectors are calculated.

ToDo: make parallel

Implements Transformation.

◆ GetDVFGradientWRTTransformationParameters()

SlidingTransformation::PrecisionType * SlidingTransformation::GetDVFGradientWRTTransformationParameters ( nifti_image * denseDVFIn )

virtual

Calculates the gradient of an image for a given deformation vector field.

Parameters

denseDVFIn Deformation vector field

Implements Transformation.

◆ GetMaxTransformationParameterLength()

SlidingTransformation::PrecisionType SlidingTransformation::GetMaxTransformationParameterLength ( PrecisionType * parametersIn )

virtual

Calculate the maximum control-point displacement value for the given transformation parametes.

Implements Transformation.

◆ GetSumOfPenaltyWeights()

SlidingTransformation::PrecisionType SlidingTransformation::GetSumOfPenaltyWeights ( )

virtual

Calculates the sum of the penalty term weights. Responsibility of the correct scaling of the penalty term lies with the generating function.

Implements Transformation.

◆ GetTransformationAsImage()

std::vector< nifti_image * > SlidingTransformation::GetTransformationAsImage ( )

virtual

Returns the transformation as an image.

Implements Transformation.

◆ InitialiseLevel()

void SlidingTransformation::InitialiseLevel ( unsigned int level )

virtual

Initialise a given level. Call the initialisation for the individual transformations and update the current defSpaceImage.

Parameters

level Defines the level that is to be initialised.

Implements Transformation.

◆ SetGapOverlapConstraintWeight()

void SlidingTransformation::SetGapOverlapConstraintWeight ( double gapOverlabConstraintWeightIn )

Set the sliding-transformation specific constraint weight. Higher values will result in less gaps and overlaps.

Parameters

gapOverlabConstraintWeightIn Weight of the gap-overlap constraint term.

◆ SetParameters()

void SlidingTransformation::SetParameters	(	SlidingTransformation::PrecisionType *	parametersIn,
		bool	parametersAreDisplacements
	)

virtual

Set the parameters that define the sliding transformation.

Parameters

parametersIn	Pointer to the parameters that will be copied to the internal transformation parameters.
parametersAreDisplacements	Set to true if the parameters are displacements.

Implements Transformation.

◆ SetSignedDistanceMapImage()

void SlidingTransformation::SetSignedDistanceMapImage ( nifti_image * signedDistanceMapImageIn )

Set the signed distance map image used to determine the sliding boundary. This function generates a local copy of this image

Parameters

signedDistanceMapImageIn Nifti image of the signed distance map in the source image space.

◆ TransformedSignedDistMapsCanBeUsedForConstraintCalculations()

bool SlidingTransformation::TransformedSignedDistMapsCanBeUsedForConstraintCalculations ( )

private

Checks the geometry of the transformed signed distance map and the (current) image defining the space where the sliding constraint is calculated.

Member Data Documentation

◆ curDefSpaceImage

nifti_image* SlidingTransformation::curDefSpaceImage

private

Pointer to the current image within the defSpaceImagePyramid.

◆ defSpaceImagePyramid

std::shared_ptr<ImagePyramid<PrecisionType> > SlidingTransformation::defSpaceImagePyramid

private

The image pyramid holding the images in which the transformation is defined. Should correspond with those used to initilase the transfomrations A and B. Will be generated during construction.

◆ gapOverlapConstraintWeight

double SlidingTransformation::gapOverlapConstraintWeight

private

The gap-overlap-constraint weight.

◆ lastInitialisedLevel

int SlidingTransformation::lastInitialisedLevel

private

The last initialised level. This determines which level of the def space image pyramid is accessed. Will be set to -1 before initialisation.

◆ signedDistMapImage

nifti_image* SlidingTransformation::signedDistMapImage

private

Nifti image holding the singed distance image in source-image space for the current level.

◆ signedDistMapImageTransformedA

nifti_image* SlidingTransformation::signedDistMapImageTransformedA

private

Nfiti image holdeing the signed distance map transformed with transformA.

◆ signedDistMapImageTransformedB

nifti_image* SlidingTransformation::signedDistMapImageTransformedB

private

Nfiti image holdeing the signed distance map transformed with transformA.

◆ transformA

std::shared_ptr<Transformation> SlidingTransformation::transformA

private

The transformation defining the inside, i.e. SDT < 0.

◆ transformB

std::shared_ptr<Transformation> SlidingTransformation::transformB

private

The transformation defining the outside, i.e. SDT > 0.

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

motion-lib/SlidingTransformation.h
motion-lib/SlidingTransformation.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PrecisionType

Constructor & Destructor Documentation

◆ SlidingTransformation() [1/2]

◆ SlidingTransformation() [2/2]

◆ ~SlidingTransformation()

Member Function Documentation

◆ AllocateTransformedSignedDistanceMaps()

◆ CalculateGapOverlapConstraintTerm()

◆ ClearSignedDistanceMap()

◆ ClearTransformedSignedDistanceMaps()

◆ DeepCopy()

◆ DisplayTransformationParameters()

◆ GetConstraintGradientWRTTransformationParameters()

◆ GetConstraintValue()

◆ GetCopyOfParameters()

◆ GetDeformationVectorField()

◆ GetDVFGradientWRTTransformationParameters()

◆ GetMaxTransformationParameterLength()

◆ GetSumOfPenaltyWeights()

◆ GetTransformationAsImage()

◆ InitialiseLevel()

◆ SetGapOverlapConstraintWeight()

◆ SetParameters()

◆ SetSignedDistanceMapImage()

◆ TransformedSignedDistMapsCanBeUsedForConstraintCalculations()

Member Data Documentation

◆ curDefSpaceImage

◆ defSpaceImagePyramid

◆ gapOverlapConstraintWeight

◆ lastInitialisedLevel

◆ signedDistMapImage

◆ signedDistMapImageTransformedA

◆ signedDistMapImageTransformedB

◆ transformA

◆ transformB