#include <svkGEPFileMapperUCSFfidcsiDev0.h>

Inheritance diagram for svkGEPFileMapperUCSFfidcsiDev0:

Public Member Functions
	vtkTypeMacro (svkGEPFileMapperUCSFfidcsiDev0, svkGEPFileMapperUCSF)

virtual void	ReadData (vtkStringArray pFileNames, svkImageData data)

Public Member Functions inherited from svkGEPFileMapperUCSF
	vtkTypeMacro (svkGEPFileMapperUCSF, svkGEPFileMapper)

Public Member Functions inherited from svkGEPFileMapper
	vtkTypeMacro (svkGEPFileMapper, vtkObject)

virtual void	InitializeDcmHeader (map< string, vector< string > > pfMap, svkDcmHeader header, float pfileVersion, int swapBytes, map< string, void > inputArgs)

string	GetProgressText ()

void	SetProgressText (string progressText)

void	SetPfileName (string pfileName)

Static Public Member Functions
static svkGEPFileMapperUCSFfidcsiDev0 *	New ()

static void	RedimensionData (svkImageData data, int numVoxelsOriginal, int *numVoxelsReordered, int numFreqPts)

Static Public Member Functions inherited from svkGEPFileMapperUCSF
static svkGEPFileMapperUCSF *	New ()

Static Public Member Functions inherited from svkGEPFileMapper
static svkGEPFileMapper *	New ()

static string	ConvertGEDateToDICOM (string geDate)

Protected Member Functions
	svkGEPFileMapperUCSFfidcsiDev0 ()

	~svkGEPFileMapperUCSFfidcsiDev0 ()

virtual vtkstd::string	GetVolumeLocalizationTechnique ()

virtual void	GetSelBoxCenter (float selBoxCenter[3])

virtual void	GetSelBoxSize (float selBoxSize[3])

virtual void	GetCenterFromRawFile (double *center)

virtual bool	IsChopOn ()

void	ModifyForPatientEntry (svkImageData *data)

void	InitMRSpectroscopyModule ()

float	GetPPMRef ()

Protected Member Functions inherited from svkGEPFileMapperUCSF
	svkGEPFileMapperUCSF ()

	~svkGEPFileMapperUCSF ()

virtual int	GetNumKSpacePoints ()

virtual bool	WasIndexSampled (int xIndex, int yIndex, int zIndex)

virtual void	InitSatBandsFromXML ()

Protected Member Functions inherited from svkGEPFileMapper
	svkGEPFileMapper ()

	~svkGEPFileMapper ()

void	InitPatientModule ()

void	InitGeneralStudyModule ()

void	InitGeneralSeriesModule ()

void	InitFrameOfReferenceModule ()

void	InitGeneralEquipmentModule ()

void	InitEnhancedGeneralEquipmentModule ()

virtual void	InitMultiFrameFunctionalGroupsModule ()

virtual void	InitAcquisitionContextModule ()

virtual void	InitMRSpectroscopyPulseSequenceModule ()

virtual void	InitSharedFunctionalGroupMacros ()

virtual void	InitPerFrameFunctionalGroupMacros ()

virtual void	InitPixelMeasuresMacro ()

virtual void	InitPlaneOrientationMacro ()

virtual void	InitMRSpectroscopyFrameTypeMacro ()

virtual void	InitMRTimingAndRelatedParametersMacro ()

virtual void	InitMRSpectroscopyFOVGeometryMacro ()

virtual void	InitMREchoMacro ()

virtual void	InitMRModifierMacro ()

virtual void	InitMRReceiveCoilMacro ()

virtual void	InitMRTransmitCoilMacro ()

virtual void	InitMRAveragesMacro ()

virtual void	InitMRSpatialSaturationMacro ()

virtual void	InitSatBand (float satRAS[3], float translation)

virtual void	InitVolumeLocalizationSeq ()

virtual void	InitMRSpectroscopyDataModule ()

virtual void	InitK0Sampled (svkDcmHeader *hdr)

virtual float	GetFrequencyOffset ()

int	GetNumVoxelsInVol ()

virtual void	GetNumVoxels (int numVoxels[3])

virtual void	GetVoxelSpacing (double voxelSpacing[3])

void	GetFOV (float fov[3])

int	GetNumCoils ()

int	GetNumFrames ()

virtual int	GetNumTimePoints ()

virtual int	GetNumDummyScans ()

virtual int	GetNumEPSIAcquisitions ()

bool	AddDummy (int offset, int coilNum, int timePt)

void	GetDcos (double dcos[3][3])

bool	IsSwapOn ()

bool	Is2D ()

virtual void	GetXYZIndices (int dataIndex, int x, int y, int *z)

void	UpdateProgress (double amount)

virtual void	ModifyBehavior (svkImageData *data)

void	RedimensionModifiedSVData (svkImageData *data)

virtual int	GetNumberUnsuppressedAcquisitions ()

virtual int	GetNumberSuppressedAcquisitions ()

virtual void	GetSelBoxCenter (double selBoxCenter[3])

virtual void	GetSelBoxSize (double selBoxSize[3])

void	SetCellSpectrum (vtkImageData *data, bool wasSampled, int offset, int index, int x, int y, int z, int timePoint=0, int channel=0)

virtual void	InitSpecTuple (int numFreqPts, int freqPt, float tuple, vtkDataArray dataArray)

int	GetHeaderValueAsInt (string key)

long long int	GetHeaderValueAsLongInt (string key)

float	GetHeaderValueAsFloat (string key)

string	GetHeaderValueAsString (string key)

bool	isInputArgSet (string argName)

bool	GetInputArgStringValue (string argName, string *argValue)

bool	GetInputArgBoolValue (string argName, bool *argValue)

virtual void	ReorderEPSI (svkMrsImageData *data)

string	GetNucleus ()

void	ModifyForPatientEntry (double dcos[3][3])

Additional Inherited Members
Public Types inherited from svkGEPFileMapper
enum	MapperBehavior { UNDEFINED = 0, LOAD_RAW, LOAD_RAW_UNSUPPRESSED, LOAD_RAW_SUPPRESSED, LOAD_AVG_UNSUPPRESSED, LOAD_AVG_SUPPRESSED, LOAD_EPSI }

Protected Attributes inherited from svkGEPFileMapper
string	progressText

map< string, vector< string > >	pfMap

svkDcmHeader *	dcmHeader

float	pfileVersion

int *	specData

svkDcmHeader::DcmDataOrderingDirection	dataSliceOrder

int	chopVal

map< string, void * >	inputArgs

int	swapBytes

svkMRSIOD *	iod

double	progress

string	pfileName

Detailed Description

Mapper from a GE P-file header to a DICOM MRS SOP Class. This concrete svkGEPFileMapper overrides the default product sequence logic with specifics required for reading symmetric EPSI data acquired with the fidcsi_ucsf_dev0 research PSD developed by Peder Larson, PhD, UCSF Department of Radiology and Biomedical Imaging. This mapper outputs a regular cartesian grid of k-space data suitable for Fourier transform reconstruction.

Non-uniformly sampled Symmetric EPSI ramp data is sampled onto a cartesian grid using a "Gridding" algorithm based on a Kaiser-Bessel convolving function as described in references 1 and 2.

Portions of this implementation are based on a MATLAB implementation of the regridding algorithm developed by Brian Hargreaves, Ph.D. (Stanford University) that is available at the following URL:

http://www-mrsrl.stanford.edu/~brian/gridding/
http://mrsrl.stanford.edu/~brian/mritools.html The license on this MATLAB implementation is reproduced here from the above web-site: "All code on these pages is available free of charge for any use."

The following people contributed to the development, implementation and validation of this class:

Peder E.Z. Larson, PhD (UCSF Department of Radiology and Biomedical Imaging)
Jason C. Crane, PhD (UCSF Department of Radiology and Biomedical Imaging) 
Sarah J. Nelson, PhD (UCSF Department of Radiology and Biomedical Imaging)
Daniel Vigneron, PhD (UCSF Department of Radiology and Biomedical Imaging)
Mathew L. Zierhut, PhD (UCSF Department of Radiology and Biomedical Imaging)

References:

John I. Jackson, Craig H. Meyer, Dwight G. Nishimura and Albert Macovski Selection of a Convolution Function for Fourier Inversion Using Gridding IEEE TRANSACTIONS ON MEDICAL IMAGING. VOL. 10. NO. 3 , SEPTEMBER 1991
Philip J. Beatty, Dwight G. Nishimura, John M. Pauly, Rapid Gridding Reconstruction With a Minimal Oversampling Ratio IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 24, NO. 6, JUNE 2005

Constructor & Destructor Documentation

svkGEPFileMapperUCSFfidcsiDev0 ( )

protected

~svkGEPFileMapperUCSFfidcsiDev0 ( )

protected

Member Function Documentation

void GetCenterFromRawFile ( double * center )

protectedvirtual

Gets the center of the acquisition grid. May vary between sequences.

Reimplemented from svkGEPFileMapper.

References svkGEPFileMapper::GetHeaderValueAsFloat().

float GetPPMRef ( )

protectedvirtual

Gets the chemical shift reference taking into account acquisition frequency offset and the acquisition sample temperature.

Reimplemented from svkGEPFileMapper.

void GetSelBoxCenter ( float selBoxCenter[3] )

protectedvirtual

References svkGEPFileMapper::GetHeaderValueAsFloat().

void GetSelBoxSize ( float selBoxSize[3] )

protectedvirtual

For FIDCSI make the press box occupy the whole volume. There isnt't full 3D PRESS, just a single slab of selection (1D selective).

References svkGEPFileMapper::GetHeaderValueAsFloat().

string GetVolumeLocalizationTechnique ( )

protectedvirtual

Reimplemented from svkGEPFileMapper.

void InitMRSpectroscopyModule ( )

protectedvirtual

Reimplemented from svkGEPFileMapper.

References svkGEPFileMapper::dcmHeader, and svkDcmHeader::SetValue().

bool IsChopOn ( )

protectedvirtual

Chop is off for UCSF fid dev0 (EPSI)

Reimplemented from svkGEPFileMapper.

void ModifyForPatientEntry ( svkImageData * data )

protected

Reorder axes if patient entry is not HFS:

References svkDcmHeader::GetCenterFromOrigin(), svkDcmHeader::GetDataDcos(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkGEPFileMapper::GetHeaderValueAsInt(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfSlices(), svkDcmHeader::GetOrigin(), svkDcmHeader::GetOriginFromCenter(), svkDcmHeader::GetPixelSpacing(), svkDcmHeader::GetStringValue(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), and svkImageData::SyncVTKImageDataToDcmHeader().

static svkGEPFileMapperUCSFfidcsiDev0* New ( )

static

void ReadData	(	vtkStringArray *	pFileNames,
		svkImageData *	data
	)

virtual

This method reads data from the pfile and puts the data into the CellData arrays. Non-uniform k-space sampling requires regridding to rectaliniear k-space array here.

Reimplemented from svkGEPFileMapper.

References svkImageData::DeepCopy(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfCells(), svkDcmHeader::GetStringValue(), svkGEPFileMapper::InitK0Sampled(), svkMrsImageData::New(), svkGEPFileMapper::progress, svkImageData::RemoveArrays(), svkDcmHeader::SetDimensionIndexSize(), svkGEPFileMapper::SetProgressText(), svkImageData::SyncVTKImageDataToDcmHeader(), svkDcmHeader::TIME_INDEX, and svkGEPFileMapper::UpdateProgress().

static void RedimensionData	(	svkImageData *	data,
		int *	numVoxelsOriginal,
		int *	numVoxelsReordered,
		int	numFreqPts
	)

static

vtkTypeMacro	(	svkGEPFileMapperUCSFfidcsiDev0	,
		svkGEPFileMapperUCSF
	)

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation