#include <svkMRSAutoPhase.h>

Inheritance diagram for svkMRSAutoPhase:

Public Types
enum	PhasingModel { UNDEFINED_PHASE_MODEL = 0, FIRST_POINT_0 = 1, MAX_PEAK_HTS_0 = 2, MAX_PEAK_HT_ONE_PEAK_0 = 3, LAST_MODEL }

Public Member Functions
	vtkTypeMacro (svkMRSAutoPhase, svkThreadedImageAlgorithm)

void	OnlyUseSelectionBox ()

virtual svkImageData *	GetOutput (int port)

Public Member Functions inherited from svkThreadedImageAlgorithm
	vtkTypeMacro (svkThreadedImageAlgorithm, vtkThreadedImageAlgorithm)

svkImageData *	GetOutput ()

svkImageData *	GetImageDataInput (int port)

Protected Member Functions
	svkMRSAutoPhase ()

	~svkMRSAutoPhase ()

virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

int	SVKRequestDataPreExec (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

int	SVKRequestDataPostExec (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual void	ThreadedRequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector, vtkImageData *inData, vtkImageData outData, int extent[6], int threadId)

virtual void	ValidateInput ()

virtual int	FillInputPortInformation (int vtkNotUsed(port), vtkInformation *info)

virtual int	FillOutputPortInformation (int vtkNotUsed(port), vtkInformation *info)

void	ZeroData ()

virtual void	UpdateProvenance ()

void	AutoPhaseExecute (int *outExt, int id)

virtual void	AutoPhaseSpectrum (int cellID)

virtual void	FitPhase (int cellID)=0

virtual void	PrePhaseSetup ()=0

virtual void	PostPhaseCleanup ()=0

void	SyncPointsFromCells ()

virtual void	SetMapSeriesDescription ()

virtual void	InitOptimizer (int cellID, itk::ParticleSwarmOptimizer::Pointer itkOptimizer)=0

Protected Member Functions inherited from svkThreadedImageAlgorithm
	svkThreadedImageAlgorithm ()

	~svkThreadedImageAlgorithm ()

int	SplitExtent (int splitExt[6], int startExt[6], int num, int total)

Protected Attributes
int	numTimePoints

svkMRSAutoPhase::PhasingModel	phaseModelType

bool	onlyUseSelectionBox

short *	selectionBoxMask

bool	isSpectralFFTRequired

string	seriesDescription

vtkDataArray *	mapArrayZeroOrderPhase

Static Protected Attributes
static int *	progress

Detailed Description

Algorithm for automatic phase correction of MR spectra.

Member Enumeration Documentation

enum PhasingModel

Enumerator
UNDEFINED_PHASE_MODEL
FIRST_POINT_0
MAX_PEAK_HTS_0
MAX_PEAK_HT_ONE_PEAK_0
LAST_MODEL

Constructor & Destructor Documentation

svkMRSAutoPhase ( )

protected

References svkMRSAutoPhase::onlyUseSelectionBox, and svkMRSAutoPhase::progress.

~svkMRSAutoPhase ( )

protected

Member Function Documentation

void AutoPhaseExecute	(	int *	ext,
		int	id
	)

protected

Loop through spectra within the specified sub-extent and apply auto phase algo to each.

References svkMRSAutoPhase::AutoPhaseSpectrum(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetDimensionVectorIndexFromCellID(), svkThreadedImageAlgorithm::GetImageDataInput(), svkDcmHeader::GetNumberOfCells(), svkDcmHeader::GetNumSpatialVoxels(), svkThreadedImageAlgorithm::GetOutput(), svk4DImageData::IsIndexInExtent(), loopVector, svkMRSAutoPhase::progress, and svkMRSAutoPhase::ValidateInput().

Referenced by svkMRSAutoPhase::ThreadedRequestData().

void AutoPhaseSpectrum ( int cellID )

protectedvirtual

References svkMRSAutoPhase::FitPhase(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetDimensionVectorIndexFromCellID(), svkThreadedImageAlgorithm::GetImageDataInput(), svkDcmHeader::GetSpatialCellIDFromDimensionVectorIndex(), svkMRSAutoPhase::numTimePoints, svkMRSAutoPhase::onlyUseSelectionBox, and svkMRSAutoPhase::selectionBoxMask.

Referenced by svkMRSAutoPhase::AutoPhaseExecute().

int FillInputPortInformation	(	int	vtkNotUsedport,
		vtkInformation *	info
	)

protectedvirtual

input port 0 is required. .

Reimplemented from svkThreadedImageAlgorithm.

int FillOutputPortInformation	(	int	vtkNotUsedport,
		vtkInformation *	info
	)

protectedvirtual

Output from this algo is 1: image of applied phases The phased MRS data is in place applied to the input object.

Reimplemented from svkThreadedImageAlgorithm.

virtual void FitPhase ( int cellID )

protectedpure virtual

Implemented in svkMRSFirstPointPhase, svkMRSFirstOrderPhase, and svkMRSZeroOrderPhase.

Referenced by svkMRSAutoPhase::AutoPhaseSpectrum().

svkImageData * GetOutput ( int port )

virtual

Wire input to output for in place filters

Reimplemented from svkThreadedImageAlgorithm.

virtual void InitOptimizer	(	int	cellID,
		itk::ParticleSwarmOptimizer::Pointer	itkOptimizer
	)

protectedpure virtual

void OnlyUseSelectionBox ( )

Only fit phase inside selection box

References svkMRSAutoPhase::onlyUseSelectionBox.

virtual void PostPhaseCleanup ( )

protectedpure virtual

Implemented in svkMRSFirstPointPhase, and svkMRSZeroOrderPhase.

Referenced by svkMRSAutoPhase::SVKRequestDataPostExec().

virtual void PrePhaseSetup ( )

protectedpure virtual

Implemented in svkMRSFirstPointPhase, and svkMRSZeroOrderPhase.

Referenced by svkMRSAutoPhase::SVKRequestDataPreExec().

int RequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protectedvirtual

Copy the Dcm Header and Provenance from the input to the output.

Reimplemented in svkMRSZeroOrderPhase.

References vtkImageThreadStruct::Filter, vtkImageThreadStruct::Inputs, vtkImageThreadStruct::InputsInfo, vtkImageThreadStruct::Outputs, vtkImageThreadStruct::OutputsInfo, vtkImageThreadStruct::Request, svkMRSAutoPhase::SVKRequestDataPostExec(), and svkMRSAutoPhase::SVKRequestDataPreExec().

int RequestInformation	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protectedvirtual

Resets the origin and extent for correct initialization of output svkMriImageData object from input svkMrsImageData object.

References svkImageData::GetDcmHeader(), svkThreadedImageAlgorithm::GetImageDataInput(), and svkDcmHeader::GetOrigin().

void SetMapSeriesDescription ( )

protectedvirtual

References svkImageData::GetDcmHeader(), svkThreadedImageAlgorithm::GetOutput(), svkMRSAutoPhase::seriesDescription, and svkDcmHeader::SetValue().

Referenced by svkMRSAutoPhase::SVKRequestDataPreExec().

int SVKRequestDataPostExec	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protected

References svkMRSAutoPhase::PostPhaseCleanup(), svkMRSAutoPhase::progress, svkMRSAutoPhase::selectionBoxMask, and svkMRSAutoPhase::UpdateProvenance().

Referenced by svkMRSAutoPhase::RequestData().

int SVKRequestDataPreExec	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

protected

Copy the Dcm Header and Provenance from the input to the output.

References svk4DImageData::GetArray(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkThreadedImageAlgorithm::GetImageDataInput(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfCells(), svkDcmHeader::GetNumSpatialVoxels(), svkThreadedImageAlgorithm::GetOutput(), svkMrsImageData::GetSelectionBoxMask(), svk4DImageData::GetZeroImage(), svkDcmHeader::InsertUniqueUID(), svkMRSAutoPhase::numTimePoints, svkMRSAutoPhase::PrePhaseSetup(), svkMRSAutoPhase::progress, svkDcmHeader::Redimension(), svkMRSAutoPhase::selectionBoxMask, and svkMRSAutoPhase::SetMapSeriesDescription().

Referenced by svkMRSAutoPhase::RequestData().

void SyncPointsFromCells ( )

protected

Sync Point Data from Cell Data

References svkImageData::GetNumberOfVoxels(), and svkThreadedImageAlgorithm::GetOutput().

void ThreadedRequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector,
		vtkImageData ***	inData,
		vtkImageData **	outData,
		int	extent[6],
		int	threadId
	)