svkVarianUCSFEPSI2DMapper Class Reference

#include <svkVarianUCSFEPSI2DMapper.h>

Inheritance diagram for svkVarianUCSFEPSI2DMapper:

Public Member Functions
	vtkTypeMacro (svkVarianUCSFEPSI2DMapper, svkVarianFidMapper)
Public Member Functions inherited from svkVarianFidMapper
	vtkTypeMacro (svkVarianFidMapper, vtkObject)
virtual void	InitializeDcmHeader (map< string, vector< vector< string > > > procparMap, svkDcmHeader *header, svkMRSIOD *iod, int swapBytes)

Static Public Member Functions
static svkVarianUCSFEPSI2DMapper *	New ()

Protected Member Functions
	svkVarianUCSFEPSI2DMapper ()
	~svkVarianUCSFEPSI2DMapper ()
virtual void	InitMRSpectroscopyPulseSequenceModule ()
virtual void	InitPixelMeasuresMacro ()
virtual void	InitPerFrameFunctionalGroupMacros ()
virtual void	InitMRSpectroscopyDataModule ()
virtual void	InitMRSpectroscopyModule ()
virtual void	InitMultiFrameFunctionalGroupsModule ()
virtual void	ReadFidFile (string fidFileName, svkImageData *data)
void	ReorderEPSIData (svkImageData *data)
void	RemoveArrays (svkImageData *data)
void	RedimensionData (svkImageData *data, int *numVoxelsOriginal, int *numVoxelsReordered, int numFreqPts)
virtual void	SetCellSpectrum (vtkImageData *data, int x, int y, int z, int timePt, int coilNum)
Protected Member Functions inherited from svkVarianFidMapper
	svkVarianFidMapper ()
	~svkVarianFidMapper ()
void	InitPatientModule ()
void	InitGeneralStudyModule ()
void	InitGeneralSeriesModule ()
void	InitGeneralEquipmentModule ()
virtual void	InitMultiFrameDimensionModule ()
virtual void	InitAcquisitionContextModule ()
virtual void	InitSharedFunctionalGroupMacros ()
virtual void	InitMRModifierMacro ()
virtual void	InitMRTransmitCoilMacro ()
virtual void	InitMRAveragesMacro ()
virtual void	InitPlaneOrientationMacro ()
virtual void	InitMREchoMacro ()
virtual void	InitMRTimingAndRelatedParametersMacro ()
virtual void	InitMRReceiveCoilMacro ()
virtual void	InitMRSpectroscopyFOVGeometryMacro ()
string	GetDcmPatientPositionString ()
virtual void	ConvertCmToMm ()
int	GetHeaderValueAsInt (string keyString, int valueIndex=0, int procparRow=0)
float	GetHeaderValueAsFloat (string keyString, int valueIndex=0, int procparRow=0)
string	GetHeaderValueAsString (string keyString, int valueIndex=0, int procparRow=0)

Additional Inherited Members
Protected Attributes inherited from svkVarianFidMapper
map< string, vector< vector < string > > >	procparMap
svkDcmHeader *	dcmHeader
float *	specData
svkDcmHeader::DcmDataOrderingDirection	dataSliceOrder
int	numSlices
int	numFrames
svkMRSIOD *	iod
int	swapBytes

Detailed Description

Concrete mapper for C13 UCSF 2D EPSI Varian sequence written by Sukumar Subramaniam, PhD (UCSF Surbeck Lab).

contributors to the development of the 2D C13 EPSI sequence and software : Sukumar Subramaniam, PhD (UCSF Surbeck Lab) Jason C. Crane, PhD (UCSF Surbeck Lab) Sarah J. Nelson, PhD (UCSF Surbeck Lab) Dan B. Vigneron, PhD (UCSF Surbeck Lab) John Kurhanewicz, PhD (UCSF Surbeck Lab)

Supported by: NIH P41EB013598

Constructor & Destructor Documentation

svkVarianUCSFEPSI2DMapper ( )

protected

References svkVarianFidMapper::specData.

~svkVarianUCSFEPSI2DMapper ( )

protected

References svkVarianFidMapper::specData.

Member Function Documentation

void InitMRSpectroscopyDataModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), svkVarianFidMapper::GetHeaderValueAsInt(), and svkDcmHeader::SetValue().

void InitMRSpectroscopyModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), and svkDcmHeader::SetValue().

void InitMRSpectroscopyPulseSequenceModule ( )

protectedvirtual

Implements svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsInt(), svkVarianFidMapper::GetHeaderValueAsString(), and svkDcmHeader::SetValue().

void InitMultiFrameFunctionalGroupsModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsInt(), svkVarianFidMapper::GetHeaderValueAsString(), svkVarianUCSFEPSI2DMapper::InitPerFrameFunctionalGroupMacros(), svkVarianFidMapper::InitSharedFunctionalGroupMacros(), svkVarianFidMapper::numFrames, svkVarianFidMapper::numSlices, and svkDcmHeader::SetValue().

void InitPerFrameFunctionalGroupMacros ( )

protectedvirtual

The FID toplc is the center of the first voxel.

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dataSliceOrder, svkVarianFidMapper::dcmHeader, svkDcmHeader::GetDataDcos(), svkDcmHeader::GetDimensionIndexVector(), svkVarianFidMapper::GetHeaderValueAsFloat(), svkDcmHeader::GetPixelSize(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkVarianFidMapper::numFrames, svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SetSliceOrder(), svkDcmHeader::SLICE_INDEX, and svkVarianReader::UserToMagnet().

Referenced by svkVarianUCSFEPSI2DMapper::InitMultiFrameFunctionalGroupsModule().

void InitPixelMeasuresMacro ( )

protectedvirtual

Pixel Spacing:

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitPixelMeasuresMacro().

static svkVarianUCSFEPSI2DMapper* New ( )

static

void ReadFidFile ( string  fidFileName, svkImageData *  data  )

protectedvirtual

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 svkVarianFidMapper.

References svkImageData::DeepCopy(), svkMrsImageData::New(), svkVarianUCSFEPSI2DMapper::ReorderEPSIData(), and svkImageData::SyncVTKImageDataToDcmHeader().

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

protected

Redimension after reordering epsi dimension. Should have 2 lobes at this point.

References svkDcmHeader::CHANNEL_INDEX, svkDcmHeader::GetCenterFromOrigin(), svkDcmHeader::GetDataDcos(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetNumberOfTimePoints(), svkDcmHeader::GetOrigin(), svkDcmHeader::GetOriginFromCenter(), svkDcmHeader::GetPixelSpacing(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SetValue(), svkDcmHeader::SLICE_INDEX, svkImageData::SyncVTKImageDataToDcmHeader(), and svkDcmHeader::TIME_INDEX.

Referenced by svkVarianUCSFEPSI2DMapper::ReorderEPSIData().

void RemoveArrays ( svkImageData *  data )

protected

Remove the original EPSI arrays from the svkImageData. at this point.

References svkImageData::GetDcmHeader(), svkDcmHeader::GetNumberOfCoils(), svkDcmHeader::GetNumberOfTimePoints(), and svkImageData::GetNumberOfVoxels().

Referenced by svkVarianUCSFEPSI2DMapper::ReorderEPSIData().

void ReorderEPSIData ( svkImageData *  data )

protected

References svkImageData::DeepCopy(), svkImageData::GetDcmHeader(), svkDcmHeader::GetIntValue(), svkImageData::GetNumberOfVoxels(), svkDcmHeader::GetStringValue(), svkMrsImageData::New(), svkVarianUCSFEPSI2DMapper::RedimensionData(), and svkVarianUCSFEPSI2DMapper::RemoveArrays().

Referenced by svkVarianUCSFEPSI2DMapper::ReadFidFile().

void SetCellSpectrum ( vtkImageData *  data, int  x, int  y, int  z, int  timePt, int  coilNum  )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfSlices(), svkDcmHeader::GetStringValue(), and svkVarianFidMapper::specData.

vtkTypeMacro	(	svkVarianUCSFEPSI2DMapper	,
		svkVarianFidMapper
	)

---

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

• svkVarianUCSFEPSI2DMapper.h
• svkVarianUCSFEPSI2DMapper.cc