#include <BSplineTransformation.h>

Inheritance diagram for BSplineTransformation:

Collaboration diagram for BSplineTransformation:

Public Types
typedef Transformation::PrecisionType	PrecisionType

Public Types inherited from Transformation
typedef float	PrecisionType

Public Member Functions
	BSplineTransformation (nifti_image referenceImageIn, unsigned int numberOfLevelsToPerform, float finalControlPointGridSpacing)

	BSplineTransformation (const BSplineTransformation &transformToCopy)

	~BSplineTransformation ()

virtual void	InitialiseLevel (unsigned int level)

void	SetParameters (PrecisionType *parametersIn, bool parametersAreDisplacements)

virtual nifti_image *	GetDeformationVectorField (nifti_image *targetImageIn)

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

virtual BSplineTransformation::PrecisionType *	GetConstraintGradientWRTTransformationParameters ()

double	GetConstraintValue ()

virtual PrecisionType *	GetCopyOfParameters ()

void	SetLinearEnergyWeight (double linearEnergyWeightIn)

void	SetBendingEnergyWeight (double bendingEnergyWeightIn)

std::shared_ptr< Transformation >	DeepCopy ()

void	DisplayTransformationParameters ()

virtual PrecisionType	GetSumOfPenaltyWeights ()

virtual PrecisionType	GetMaxTransformationParameterLength (PrecisionType *parametersIn)

std::vector< nifti_image * >	GetTransformationAsImage ()

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 ()

Protected Member Functions
void	CPGToDVF2D (nifti_image *denseVectorFieldImage)

void	CPGToDVF3D (nifti_image *denseVectorFieldImage)

void	DVFToCPG2D (nifti_image controlPointGridImage, nifti_image denseVectorFieldImage, bool normaliseKernel)

void	DVFToCPG3D (nifti_image controlPointGridImage, nifti_image denseVectorFieldImage, bool normaliseKernel)

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
nifti_image *	controlPointGridImage
	‍** Function to reorientate vectors in 5D nifti image. More...

double	bendingEnergyWeight
	The bending-energy weight. More...

double	linearEnergyWeight
	The linear energy weight. More...

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...

Private Attributes
int	lastInitialisedLevel
	The level taht was last requested to be initialised. More...

unsigned int	numberOfLevelsToPerform
	The total number of levels that are used to fit the model. Parameter needed to correctly scale constraints. More...

Detailed Description

Class implementing the standard b-spline transformation

Member Typedef Documentation

◆ PrecisionType

typedef Transformation::PrecisionType BSplineTransformation::PrecisionType

Constructor & Destructor Documentation

◆ BSplineTransformation() [1/2]

BSplineTransformation::BSplineTransformation	(	nifti_image *	referenceImageIn,
		unsigned int	numberOfLevelsToPerform,
		float *	finalControlPointGridSpacing
	)

Constructor. Requires the reference image to define the space in which the transformation is valid, the number of levels to update the bending energy correctly as well as the final control-point grid spacing.

Parameters

referenceImageIn	Pointer to the reference image
numberOfLevelsToPerform	Number of levels to perform
finalControlPointGridSpacing	Pointer to the final control-point grid spacing if negative, the spacing is assumed to be given as multiples of the voxel spacing

◆ BSplineTransformation() [2/2]

BSplineTransformation::BSplineTransformation ( const BSplineTransformation & transformToCopy )

Copy constructor.

Parameters

transformToCopy Reference to the B-spline transformation object to copy

◆ ~BSplineTransformation()

BSplineTransformation::~BSplineTransformation ( )

Destructor.

Member Function Documentation

◆ CPGToDVF2D()

void BSplineTransformation::CPGToDVF2D ( nifti_image * denseVectorFieldImage )

protected

Compute a dense vector field (DVF) from a B-spline control point grid (CPG). This function assumes the axes of the DVF is aligned with axes of the CPG

Parameters

denseVectorFieldImage A nifti image that will be filled with the DVF

◆ CPGToDVF3D()

void BSplineTransformation::CPGToDVF3D ( nifti_image * denseVectorFieldImage )

protected

Compute a dense vector field (DVF) from a B-spline control point grid (CPG). This function assumes the axes of the DVF is aligned with axes of the CPG

Parameters

denseVectorFieldImage A nifti image that will be filled with the DVF

◆ DeepCopy()

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

virtual

Function to create a deep copy of this object.

Implements Transformation.

◆ DisplayTransformationParameters()

void BSplineTransformation::DisplayTransformationParameters ( )

virtual

Display function to print the transformation parameters to the standard output

Implements Transformation.

◆ DVFToCPG2D()

void BSplineTransformation::DVFToCPG2D	(	nifti_image *	controlPointGridImage,
		nifti_image *	denseVectorFieldImage,
		bool	normaliseKernel
	)

protected

Compute a B-spline control point grid (CPG) from the B-spline convolution of a dense 2D vector field (DVF), i.e. the CPG will be the B-spline parameterisation that best approximates the DVF. This function assumes the axes of the DVF are aligned with axes of the CPG

Parameters

controlPointGridImage	A nifti image that will be filled with the B-spline CPG
denseVectorFieldImage	A nifti image containing the DVF
normaliseKernel	If true each B-spline kernel will be normalised to have a sum of 1

◆ DVFToCPG3D()

void BSplineTransformation::DVFToCPG3D	(	nifti_image *	controlPointGridImage,
		nifti_image *	denseVectorFieldImage,
		bool	normaliseKernel
	)

protected

Compute a B-spline control point grid (CPG) from the B-spline convolution of a dense 3D vector field (DVF), i.e. the CPG will be the B-spline parameterisation that best approximates the DVF. This function assumes the axes of the DVF are aligned with axes of the CPG

Parameters

controlPointGridImage	A nifti image that will be filled with the B-spline CPG
denseVectorFieldImage	A nifti image containing the DVF
normaliseKernel	If true each B-spline kernel will be normalised to have a sum of 1

◆ GetConstraintGradientWRTTransformationParameters()

BSplineTransformation::PrecisionType * BSplineTransformation::GetConstraintGradientWRTTransformationParameters ( )

virtual

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

Implements Transformation.

◆ GetConstraintValue()

double BSplineTransformation::GetConstraintValue ( )

virtual

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

Implements Transformation.

◆ GetCopyOfParameters()

BSplineTransformation::PrecisionType * BSplineTransformation::GetCopyOfParameters ( )

virtual

Get a pointer to a copy of the current transformation parameters. Receiving function will need to free the memory after usage.

Implements Transformation.

◆ GetDeformationVectorField()

nifti_image * BSplineTransformation::GetDeformationVectorField ( nifti_image * targetImageIn )

virtual

For a given target image, calculate a deformation field.

Parameters

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

Implements Transformation.

◆ GetDVFGradientWRTTransformationParameters()

BSplineTransformation::PrecisionType * BSplineTransformation::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()

BSplineTransformation::PrecisionType BSplineTransformation::GetMaxTransformationParameterLength ( PrecisionType * parametersIn )

virtual

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

Implements Transformation.

◆ GetSumOfPenaltyWeights()

BSplineTransformation::PrecisionType BSplineTransformation::GetSumOfPenaltyWeights ( )

virtual

Calculates the sum of the penalty term weights. Curretnly the bending energy weight and the linear energy weight are added. Responsibility of the correct scaling of the penalty term lies with the generating function.

Implements Transformation.

◆ GetTransformationAsImage()

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

virtual

Returns the b-spline control-point grind as an image.

Implements Transformation.

◆ InitialiseLevel()

void BSplineTransformation::InitialiseLevel ( unsigned int level )

virtual

Initialise a given level, i.e. perform a grid refinement. If the same level was initialised before, no refinement will be performed. Currently it is not checked, if a coarser level is requested.

Parameters

level Defines the level that is to be initialised.

Implements Transformation.

◆ SetBendingEnergyWeight()

void BSplineTransformation::SetBendingEnergyWeight ( double bendingEnergyWeightIn )

B-spline specific regularisation term weight. Penalises the bending energy.

Parameters

bendingEnergyWeightIn Input weight

◆ SetLinearEnergyWeight()

void BSplineTransformation::SetLinearEnergyWeight ( double linearEnergyWeightIn )

B-spline specific regularisation term weight. Penalises the linear energy.

Parameters

linearEnergyWeightIn Input weight

◆ SetParameters()

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

virtual

Set the parameters that define the b-spline 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 (i.e. relative to control-point position and NOT absolute positions)

Implements Transformation.

Member Data Documentation

◆ bendingEnergyWeight

double BSplineTransformation::bendingEnergyWeight

protected

The bending-energy weight.

◆ controlPointGridImage

nifti_image* BSplineTransformation::controlPointGridImage

protected

‍** Function to reorientate vectors in 5D nifti image.

The control-point grid image

◆ lastInitialisedLevel

int BSplineTransformation::lastInitialisedLevel

private

The level taht was last requested to be initialised.

◆ linearEnergyWeight

double BSplineTransformation::linearEnergyWeight

protected

The linear energy weight.

◆ numberOfLevelsToPerform

unsigned int BSplineTransformation::numberOfLevelsToPerform

private

The total number of levels that are used to fit the model. Parameter needed to correctly scale constraints.

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

motion-lib/BSplineTransformation.h
motion-lib/BSplineTransformation.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

◆ PrecisionType

Constructor & Destructor Documentation

◆ BSplineTransformation() [1/2]

◆ BSplineTransformation() [2/2]

◆ ~BSplineTransformation()

Member Function Documentation

◆ CPGToDVF2D()

◆ CPGToDVF3D()

◆ DeepCopy()

◆ DisplayTransformationParameters()

◆ DVFToCPG2D()

◆ DVFToCPG3D()

◆ GetConstraintGradientWRTTransformationParameters()

◆ GetConstraintValue()

◆ GetCopyOfParameters()

◆ GetDeformationVectorField()

◆ GetDVFGradientWRTTransformationParameters()

◆ GetMaxTransformationParameterLength()

◆ GetSumOfPenaltyWeights()

◆ GetTransformationAsImage()

◆ InitialiseLevel()

◆ SetBendingEnergyWeight()

◆ SetLinearEnergyWeight()

◆ SetParameters()

Member Data Documentation

◆ bendingEnergyWeight

◆ controlPointGridImage

◆ lastInitialisedLevel

◆ linearEnergyWeight

◆ numberOfLevelsToPerform