#include <Supremo.h>

Public Types
typedef float	VoxelType

Public Member Functions
	Supremo ()

	~Supremo ()

void	FitMotionModelAndReconstruct ()

void	SetDynamicImages (nifti_image **dynamicImagesIn, int numberOfDynamicImagesIn)

void	SetReferenceStateImage (nifti_image *referenceStateImageIn)

void	SetSurrogateSignals (float *surrogateSignalsIn, int numberOfSurrogateSignalsIn)

void	SetDefSpaceImage (nifti_image *defSpaceImageIn)

void	SetImageAcquisition (std::shared_ptr< ImageAcquisition > imageAcquisitionIn)

void	SetMotionCompensatedReconstruction (std::shared_ptr< MoCoRecon > mocoReconstructionIn)

void	SetInterMCROutputFolder (const std::string &outputFolder)

void	SetInterGradOutputFolder (const std::string &outputFolder)

void	SetTransformationType (t_transformationType transformationTypeIn)

void	SetSlidingTrafoDistanceMap (nifti_image *slidingTrafoDistanceMapIn)

void	SetSlidingGapOverlapConstraintWeight (float gapOverlapConstraintWeightIn)

void	SetBSplineCPGSpacing (float sx, float sy, float sz)

void	SetBSplineBendingEnergy (float be)

void	SetBSplineLinearEnergy (float le)

void	SetNumberOfPyramidLevels (unsigned int numberOfLevelsIn)

void	SetNumberOfPyramidLevelsToPerform (unsigned int numberOfLevelsToPerformIn)

void	SetMaxModelFittingIterationNumber (unsigned int maxModelFittingIterations)

void	SetMaxSwitchIterationNumber (unsigned int maxSwitchIterations)

void	SetInputRCMImages (const std::vector< nifti_image * > &inputRCMImgs)

std::vector< nifti_image * >	GetCorrespondenceModelAsImage ()

nifti_image *	GetMotionCompensatedReconstructedImage ()

std::vector< nifti_image * >	SimulateDynamicImages ()

std::vector< nifti_image * >	GenerateDVFsFromCorrespondenceModel ()

Private Member Functions
void	Initialise ()

void	CheckParameters ()

void	DisplayCurrentLevelParameters (unsigned int level)

void	SaveInterMCRToImage (nifti_image *mcrImage)

Private Attributes
unsigned int	numberOfSurrogateSignals
	Number of surrogate signals (per dynamic image) More...

unsigned int	numberOfDynamicImages
	Total number of dynamic images. More...

nifti_image **	allDynamicImages
	Pointer to all dynamic nifti images available. More...

nifti_image *	referenceStateImage
	Pointer to the reference state image \( \mathbf{I}_0 \). More...

nifti_image *	finalMoCoReconImage
	Pointer holding the final motion-compensated reconstruction image after fit and reconstruct. More...

std::vector< std::vector< float > >	surrogateSignals
	Vector of vector containing the the surrogate signals. First index for time point, second for surrogate signal number. More...

nifti_image *	defSpaceImage
	Pointer to image that defines the space of the deformed images. More...

std::vector< nifti_image * >	inputRCMImages
	The vector holding the pointer to the respiratory correspondence model images. Will be used as a starting point of the optimisation. More...

unsigned int	maxSwitchIterationNumber
	Maximum number of times to iterate between motion compensated reconstruction and fitting the respiratory correspondence model. More...

unsigned int	maxModelFitIterationNumber
	Maximum number of respiratory correspondence model fitting iterations. More...

unsigned int	numberOfLevels
	The total number of levels. More...

unsigned int	numberOfLevelsToPerform
	The number of levels that are used in the fitting/reconstruction process. More...

unsigned int	currentLevel
	The current level that is being processed. More...

t_transformationType	transformationType
	The transformation type used to deform the reference-state image. More...

float	bSplineCPGSpacing [3]
	B-spline control point spacing (used if b-spline transformation is used) More...

float	bSplineBendingEnergyWeight
	Bending energy weight to constrain a b-spline transformation. More...

float	bSplineLinearEnergyWeight
	Linear energy weight to constrain a b-spline transformation. More...

nifti_image *	slidingSignedDistanceMapImage
	Image required by the sliding transformation to determine the regions involved. More...

float	slidingGapOverlapConstraintWeight
	The weight with which the gaps and overlaps will be constrained. More...

std::string	outputInterMCRFolder
	Folder to which intermediate MCRs will be saved. More...

std::string	outputInterGradientFolder
	Folder to which intermediate objective function gradients will be saved. More...

bool	initialised
	Control parameter indicating if the fit-and-reconstruct method was initialised. More...

std::shared_ptr< ImagePyramid< VoxelType > >	referenceStatePyramid
	Pointer holding the reference state image pyramid. More...

std::vector< std::shared_ptr< ImagePyramid< VoxelType > > >	allDynamicPyramids
	Vector of pointers holding all the dynamic image pyramids. More...

nifti_image *	currentReferenceStateImage

std::shared_ptr< Transformation >	transform
	Pointer to the transformation used (e.g. b-spline) More...

std::shared_ptr< CorrespondenceModel >	correspondenceModel
	Pointer to the correspondence model. More...

std::shared_ptr< ImageSimilarity >	similarityMeasure
	Pointer to the image similarity measure used. More...

std::shared_ptr< ImageAcquisition >	imageAcquisition
	Pointer to the image acquisition used. More...

std::shared_ptr< MoCoRecon >	mocoReconstructor
	The motion-compensated image reconstruction object. More...

std::string	levelID
	String holding an ID to differentiate file output from various multi-resolution levels and MCR iterations. More...

Detailed Description

Class that implements the generalised motion modelling framework by McClelland et al. (2017). This class implements the generalised motion modelling framework and is the main class that determines flow control, data handling etc.

Member Typedef Documentation

◆ VoxelType

typedef float Supremo::VoxelType

Constructor & Destructor Documentation

◆ Supremo()

Supremo::Supremo ( )

Constructor

◆ ~Supremo()

Supremo::~Supremo ( )

Destructor

Member Function Documentation

◆ CheckParameters()

void Supremo::CheckParameters ( )

private

Checks that all parameters for fitting and reconstruction were provided correctly.

◆ DisplayCurrentLevelParameters()

void Supremo::DisplayCurrentLevelParameters ( unsigned int level )

private

Display some parameters of the current levels including image resolution, transformation parameters, etc.

Parameters

level The level number

◆ FitMotionModelAndReconstruct()

void Supremo::FitMotionModelAndReconstruct ( )

Fit a motion model and perform motion compensated image reconstruction

◆ GenerateDVFsFromCorrespondenceModel()

std::vector< nifti_image * > Supremo::GenerateDVFsFromCorrespondenceModel ( )

Once a motion model was fitted (or input), use the results to calculate the deformation vector fields. The requested DVFs will have the size of the dynamic images.

Returns: A vector holding the pointers to the DVFs for the defined surrogate values.

◆ GetCorrespondenceModelAsImage()

std::vector< nifti_image * > Supremo::GetCorrespondenceModelAsImage ( )

Get the respiratory correspondence model after model fitting

Returns: Vecotr with pointers to the nifti images representing the correspondence model. These will usually be a 5d nifti images.

Note: The correspondence model image depends on the transformation model used.

◆ GetMotionCompensatedReconstructedImage()

nifti_image * Supremo::GetMotionCompensatedReconstructedImage ( )

inline

Get the resulting motion-compensated reconstructed image.

Returns: Pointer to the image holding the final MCR iamge. This image will be deallocated by this class on destruction.

◆ Initialise()

void Supremo::Initialise ( )

private

Initillise the fitting and reconstruction method

Checks that all parameters were set correctly.
Generates the image pyramids.

Todo: Remove transform. Does not need to be a member variable!

◆ SaveInterMCRToImage()

void Supremo::SaveInterMCRToImage ( nifti_image * mcrImage )

private

Save the current MCR image to file. The string levelID info will be used to determine the output

Parameters

mcrImage The reconstructed image that will be saved to the defined output directory.

◆ SetBSplineBendingEnergy()

void Supremo::SetBSplineBendingEnergy ( float be )

Set the bending energy weight for the B-spline regularisation

Parameters

be	Bending energy weight to set

◆ SetBSplineCPGSpacing()

void Supremo::SetBSplineCPGSpacing	(	float	sx,
		float	sy,
		float	sz
	)

Set the control point spacing of the B-spline control point grid

Parameters

sx	Control point spacing in x direction
sy	Control point spacing in y direction
sz	Control point spacing in z direction

◆ SetBSplineLinearEnergy()

void Supremo::SetBSplineLinearEnergy ( float le )

Set the linear energy weight for the B-spline regularisation

Parameters

le	Linear energy weight to set

◆ SetDefSpaceImage()

void Supremo::SetDefSpaceImage ( nifti_image * defSpaceImageIn )

Set an image to define the space of the deformed images. Image used to define the space of the deformed images. This image is used to define the extent and resolution (if specified in voxels) of the model and transform CPGs. If a defSpace image is not specified the reference state image will be used.

Parameters

defSpaceImageIn Pointer to a nifti image that defines the space of the deforemd images.

◆ SetDynamicImages()

void Supremo::SetDynamicImages	(	nifti_image **	dynamicImagesIn,
		int	numberOfDynamicImagesIn
	)

Set all dynamic images. Used to set a number of externally loaded dynamic images.

Parameters

dynamicImagesIn	Pointer to the dynamic images.
numberOfDynamicImagesIn	Number of dynamic images, i.e. length of the pointer above.

◆ SetImageAcquisition()

void Supremo::SetImageAcquisition ( std::shared_ptr< ImageAcquisition > imageAcquisitionIn )

Set an image acquisition object. Has to be created externally.

◆ SetInputRCMImages()

void Supremo::SetInputRCMImages ( const std::vector< nifti_image * > & inputRCMImgs )

inline

Set the input RCM correspondence model. The values of this image/these image(s) will be used as a starting point of the optimisation. Multiple RCMs can occur if the sliding transforation was used.

Parameters

inputRCMImgs Vector holding image pointers to the input respiratory correspondence model images.

◆ SetInterGradOutputFolder()

void Supremo::SetInterGradOutputFolder ( const std::string & outputFolder )

Set the folder to which intermediate objective function gradients will be saved

Parameters

outputFolder

◆ SetInterMCROutputFolder()

void Supremo::SetInterMCROutputFolder ( const std::string & outputFolder )

Set the folder to which intermediate MCR results will be saved

Parameters

outputFolder

◆ SetMaxModelFittingIterationNumber()

void Supremo::SetMaxModelFittingIterationNumber ( unsigned int maxModelFittingIterations )

inline

Set the number of iterations used to fit the motion model.

Parameters

maxModelFittingIterations Maximum number of model fitting iterations

◆ SetMaxSwitchIterationNumber()

void Supremo::SetMaxSwitchIterationNumber ( unsigned int maxSwitchIterations )

inline

Set the number of switch iterations. Determines how often the method iterates between model fitting and motion-compensated image reconstruction.

Parameters

maxSwitchIterations Maximum number of switch iterations

◆ SetMotionCompensatedReconstruction()

void Supremo::SetMotionCompensatedReconstruction ( std::shared_ptr< MoCoRecon > mocoReconstructionIn )

Set the motion compensated image reconstruction object.

Note: The image acquisition has to be passed on to the reconstruction externally - no longer set internally by SuPReMo.

Parameters

mocoReconstructionIn Object that implements a motion compensated image reconstruction.

◆ SetNumberOfPyramidLevels()

void Supremo::SetNumberOfPyramidLevels ( unsigned int numberOfLevelsIn )

inline

Set the number of pyramid levels

Parameters

numberOfLevelsIn Total number of pyramid levels

◆ SetNumberOfPyramidLevelsToPerform()

void Supremo::SetNumberOfPyramidLevelsToPerform ( unsigned int numberOfLevelsToPerformIn )

inline

Set the number of pyramid levels on which a computation should be performed.

Parameters

numberOfLevelsToPerformIn Nmber of pyramid levels. Has to be equal or smaller than the value set with SetNumberOfPyramidLevels().

◆ SetReferenceStateImage()

void Supremo::SetReferenceStateImage ( nifti_image * referenceStateImageIn )

Set the reference state image \( \mathbf{I}_0 \). This image was known as static or source image.

Parameters

referenceStateImageIn Pointer to the nifti_image holding the static image.

◆ SetSlidingGapOverlapConstraintWeight()

void Supremo::SetSlidingGapOverlapConstraintWeight ( float gapOverlapConstraintWeightIn )

Set the gap/overlap constraint weight. This weight only has an effect if the sliding transformation is being used.

Parameters

gapOverlapConstraintWeightIn Gap/overlap constraint weight.

◆ SetSlidingTrafoDistanceMap()

void Supremo::SetSlidingTrafoDistanceMap ( nifti_image * slidingTrafoDistanceMapIn )

Set the distance map for the sliding transformation

Parameters

slidingTrafoDistanceMapIn Pointer to the nifti image structure holding the sliding transformation

◆ SetSurrogateSignals()

void Supremo::SetSurrogateSignals	(	float *	surrogateSignalsIn,
		int	numberOfSurrogateSignalsIn
	)

Set the surrogate data.

Note: This function must be called after the dynamic images were set.

Parameters

surrogateSignalsIn	Pointer to the surrogate data. Has to be of size numberOfSurrogateSignalsIn*numberOfDynamicImages.
numberOfSurrogateSignalsIn	Number of surrogate signals per dynamic image.

◆ SetTransformationType()

void Supremo::SetTransformationType ( t_transformationType transformationTypeIn )

Set the transformation type used

Parameters

transformationTypeIn Transformation type

◆ SimulateDynamicImages()

std::vector< nifti_image * > Supremo::SimulateDynamicImages ( )

Once a motion model was fitted (or input), use the results to simulate the dynamic images

Returns: A vector holding the pointers to the simulated dynamic images

Member Data Documentation

◆ allDynamicImages

nifti_image** Supremo::allDynamicImages

private

Pointer to all dynamic nifti images available.

◆ allDynamicPyramids

std::vector<std::shared_ptr<ImagePyramid<VoxelType> > > Supremo::allDynamicPyramids

private

Vector of pointers holding all the dynamic image pyramids.

◆ bSplineBendingEnergyWeight

float Supremo::bSplineBendingEnergyWeight

private

Bending energy weight to constrain a b-spline transformation.

◆ bSplineCPGSpacing

float Supremo::bSplineCPGSpacing[3]

private

B-spline control point spacing (used if b-spline transformation is used)

◆ bSplineLinearEnergyWeight

float Supremo::bSplineLinearEnergyWeight

private

Linear energy weight to constrain a b-spline transformation.

◆ correspondenceModel

std::shared_ptr<CorrespondenceModel> Supremo::correspondenceModel

private

Pointer to the correspondence model.

◆ currentLevel

unsigned int Supremo::currentLevel

private

The current level that is being processed.

◆ currentReferenceStateImage

nifti_image* Supremo::currentReferenceStateImage

private

◆ defSpaceImage

nifti_image* Supremo::defSpaceImage

private

Pointer to image that defines the space of the deformed images.

◆ finalMoCoReconImage

nifti_image* Supremo::finalMoCoReconImage

private

Pointer holding the final motion-compensated reconstruction image after fit and reconstruct.

◆ imageAcquisition

std::shared_ptr<ImageAcquisition> Supremo::imageAcquisition

private

Pointer to the image acquisition used.

◆ initialised

bool Supremo::initialised

private

Control parameter indicating if the fit-and-reconstruct method was initialised.

◆ inputRCMImages

std::vector<nifti_image*> Supremo::inputRCMImages

private

The vector holding the pointer to the respiratory correspondence model images. Will be used as a starting point of the optimisation.

◆ levelID

std::string Supremo::levelID

private

String holding an ID to differentiate file output from various multi-resolution levels and MCR iterations.

◆ maxModelFitIterationNumber

unsigned int Supremo::maxModelFitIterationNumber

private

Maximum number of respiratory correspondence model fitting iterations.

◆ maxSwitchIterationNumber

unsigned int Supremo::maxSwitchIterationNumber

private

Maximum number of times to iterate between motion compensated reconstruction and fitting the respiratory correspondence model.

◆ mocoReconstructor

std::shared_ptr<MoCoRecon> Supremo::mocoReconstructor

private

The motion-compensated image reconstruction object.

◆ numberOfDynamicImages

unsigned int Supremo::numberOfDynamicImages

private

Total number of dynamic images.

◆ numberOfLevels

unsigned int Supremo::numberOfLevels

private

The total number of levels.

◆ numberOfLevelsToPerform

unsigned int Supremo::numberOfLevelsToPerform

private

The number of levels that are used in the fitting/reconstruction process.

◆ numberOfSurrogateSignals

unsigned int Supremo::numberOfSurrogateSignals

private

Number of surrogate signals (per dynamic image)

◆ outputInterGradientFolder

std::string Supremo::outputInterGradientFolder

private

Folder to which intermediate objective function gradients will be saved.

◆ outputInterMCRFolder

std::string Supremo::outputInterMCRFolder

private

Folder to which intermediate MCRs will be saved.

◆ referenceStateImage

nifti_image* Supremo::referenceStateImage

private

Pointer to the reference state image \( \mathbf{I}_0 \).

◆ referenceStatePyramid

std::shared_ptr<ImagePyramid<VoxelType> > Supremo::referenceStatePyramid

private

Pointer holding the reference state image pyramid.

◆ similarityMeasure

std::shared_ptr<ImageSimilarity> Supremo::similarityMeasure

private

Pointer to the image similarity measure used.

◆ slidingGapOverlapConstraintWeight

float Supremo::slidingGapOverlapConstraintWeight

private

The weight with which the gaps and overlaps will be constrained.

◆ slidingSignedDistanceMapImage

nifti_image* Supremo::slidingSignedDistanceMapImage

private

Image required by the sliding transformation to determine the regions involved.

◆ surrogateSignals

std::vector<std::vector<float> > Supremo::surrogateSignals

private

Vector of vector containing the the surrogate signals. First index for time point, second for surrogate signal number.

surrogateSignals[time][surrNumber]

◆ transform

std::shared_ptr<Transformation> Supremo::transform

private

Pointer to the transformation used (e.g. b-spline)

◆ transformationType

t_transformationType Supremo::transformationType

private

The transformation type used to deform the reference-state image.

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

motion-lib/Supremo.h
motion-lib/Supremo.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ VoxelType

Constructor & Destructor Documentation

◆ Supremo()

◆ ~Supremo()

Member Function Documentation

◆ CheckParameters()

◆ DisplayCurrentLevelParameters()

◆ FitMotionModelAndReconstruct()

◆ GenerateDVFsFromCorrespondenceModel()

◆ GetCorrespondenceModelAsImage()

◆ GetMotionCompensatedReconstructedImage()

◆ Initialise()

◆ SaveInterMCRToImage()

◆ SetBSplineBendingEnergy()

◆ SetBSplineCPGSpacing()

◆ SetBSplineLinearEnergy()

◆ SetDefSpaceImage()

◆ SetDynamicImages()

◆ SetImageAcquisition()

◆ SetInputRCMImages()

◆ SetInterGradOutputFolder()

◆ SetInterMCROutputFolder()

◆ SetMaxModelFittingIterationNumber()

◆ SetMaxSwitchIterationNumber()

◆ SetMotionCompensatedReconstruction()

◆ SetNumberOfPyramidLevels()

◆ SetNumberOfPyramidLevelsToPerform()

◆ SetReferenceStateImage()

◆ SetSlidingGapOverlapConstraintWeight()

◆ SetSlidingTrafoDistanceMap()

◆ SetSurrogateSignals()

◆ SetTransformationType()

◆ SimulateDynamicImages()

Member Data Documentation

◆ allDynamicImages

◆ allDynamicPyramids

◆ bSplineBendingEnergyWeight

◆ bSplineCPGSpacing

◆ bSplineLinearEnergyWeight

◆ correspondenceModel

◆ currentLevel

◆ currentReferenceStateImage

◆ defSpaceImage

◆ finalMoCoReconImage

◆ imageAcquisition

◆ initialised

◆ inputRCMImages

◆ levelID

◆ maxModelFitIterationNumber

◆ maxSwitchIterationNumber

◆ mocoReconstructor

◆ numberOfDynamicImages

◆ numberOfLevels

◆ numberOfLevelsToPerform

◆ numberOfSurrogateSignals

◆ outputInterGradientFolder

◆ outputInterMCRFolder

◆ referenceStateImage

◆ referenceStatePyramid

◆ similarityMeasure

◆ slidingGapOverlapConstraintWeight

◆ slidingSignedDistanceMapImage

◆ surrogateSignals

◆ transform

◆ transformationType