#include <svkGEPFileMapper.h>

Inheritance diagram for svkGEPFileMapper:

Public Types
enum	MapperBehavior { UNDEFINED = 0, LOAD_RAW, LOAD_RAW_UNSUPPRESSED, LOAD_RAW_SUPPRESSED, LOAD_AVG_UNSUPPRESSED, LOAD_AVG_SUPPRESSED, LOAD_EPSI }

Public Member Functions
	vtkTypeMacro (svkGEPFileMapper, vtkObject)

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

virtual void	ReadData (vtkStringArray pFileNames, svkImageData data)

string	GetProgressText ()

void	SetProgressText (string progressText)

void	SetPfileName (string pfileName)

Static Public Member Functions
static svkGEPFileMapper *	New ()

static string	ConvertGEDateToDICOM (string geDate)

Protected Member Functions
	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	InitMRSpectroscopyModule ()

virtual string	GetVolumeLocalizationTechnique ()

virtual void	InitVolumeLocalizationSeq ()

virtual void	InitMRSpectroscopyDataModule ()

virtual void	InitK0Sampled (svkDcmHeader *hdr)

virtual void	InitSatBandsFromXML ()

virtual void	GetCenterFromRawFile (double *center)

virtual float	GetFrequencyOffset ()

int	GetNumVoxelsInVol ()

virtual void	GetNumVoxels (int numVoxels[3])

virtual int	GetNumKSpacePoints ()

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])

virtual float	GetPPMRef ()

bool	IsSwapOn ()

bool	Is2D ()

virtual bool	IsChopOn ()

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)

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

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])

Protected Attributes
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 pfile header to DICOM IOD/SOP Class instance.

Member Enumeration Documentation

enum MapperBehavior

Data Loading Behavior options:

Enumerator
UNDEFINED
LOAD_RAW
LOAD_RAW_UNSUPPRESSED
LOAD_RAW_SUPPRESSED
LOAD_AVG_UNSUPPRESSED
LOAD_AVG_SUPPRESSED
LOAD_EPSI

Constructor & Destructor Documentation

svkGEPFileMapper ( )

protected

References svkGEPFileMapper::chopVal, and svkGEPFileMapper::progress.

~svkGEPFileMapper ( )

protected

Member Function Documentation

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

protected

Determine whether to add a dummy scan. The assumption is that the number of dummy scans should be equal to the number of coils or numCoils * numTimePts (e.g. for a spectral editing sequence). If true, then the an FID worth of data should be skipped over when reading data (e.g. frame_size * numComponents, or numFreqPts * numComponents)

References svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetNumCoils(), svkGEPFileMapper::GetNumDummyScans(), svkGEPFileMapper::GetNumKSpacePoints(), and svkGEPFileMapper::GetNumTimePoints().

Referenced by svkGEPFileMapper::ReadData().

string ConvertGEDateToDICOM ( string geDate )

static

Referenced by svkGEPFileMapper::InitGeneralStudyModule(), and svkGEPFileMapper::InitMultiFrameFunctionalGroupsModule().

void GetCenterFromRawFile ( double * center )

protectedvirtual

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0, and svkGEPFileMapperUCSFfidcsi.

References svkGEPFileMapper::GetHeaderValueAsFloat(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro(), and svkGEPFileMapper::InitPerFrameFunctionalGroupMacros().

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

protected

Get the data dcos

References svkGEPFileMapper::GetHeaderValueAsFloat(), and svkGEPFileMapper::ModifyForPatientEntry().

Referenced by svkGEPFileMapper::GetSelBoxSize(), svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), svkGEPFileMapper::InitPlaneOrientationMacro(), and svkGEPFileMapper::InitVolumeLocalizationSeq().

void GetFOV ( float fov[3] )

protected

Get the voxel spacing in 3D. Note that the slice spacing may include a skip. Swaps the FOV if necessary based on freq_dir setting.

References svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::Is2D(), svkGEPFileMapper::IsSwapOn(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapperUCSFProseProstate::GetVoxelSpacing(), svkGEPFileMapper::GetVoxelSpacing(), and svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro().

float GetFrequencyOffset ( )

protectedvirtual

Returns the spectral frquency offset

References svkGEPFileMapper::GetHeaderValueAsFloat(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitMRSpectroscopyModule().

float GetHeaderValueAsFloat ( string key )

protected

returns the value for the specified key as a float.

References svkGEPFileMapper::pfMap.

int GetHeaderValueAsInt ( string key )

protected

returns the value for the specified key as an int.

References svkGEPFileMapper::pfMap.

long long int GetHeaderValueAsLongInt ( string key )

protected

returns the value for the specified key as a long long int. An int may be 4 or 8 bytes, but long int should be 8 as needed.

References svkGEPFileMapper::pfMap.

Referenced by svkGEPFileMapper::GetNumDummyScans(), and svkGEPFileMapper::GetNumTimePoints().

string GetHeaderValueAsString ( string key )

protected

returns the value for the specified key as a string.

References svkGEPFileMapper::pfMap.

bool GetInputArgBoolValue	(	string	argName,
		bool *	argValue
	)

protected

Sets the inputArg value for the specified key as a string. If the value is not set, then argValue is not modified. Return value is true if the arg was found, or false if not set.

References svkGEPFileMapper::inputArgs, and svkGEPFileMapper::isInputArgSet().

Referenced by svkGEPFileMapperMBrease::IsChopOn(), and svkGEPFileMapper::IsChopOn().

bool GetInputArgStringValue	(	string	argName,
		string *	argValue
	)

protected

Sets the inputArg value for the specified key as a string. If the value is not set, then argValue is not modified. Return value is true if the arg was found, or false if not set.

References svkGEPFileMapper::inputArgs, and svkGEPFileMapper::isInputArgSet().

string GetNucleus ( )

protected

References svkGEPFileMapper::GetHeaderValueAsFloat().

Referenced by svkGEPFileMapper::GetPPMRef(), and svkGEPFileMapper::InitMRSpectroscopyModule().

int GetNumberSuppressedAcquisitions ( )

protectedvirtual

For single voxel acquisitions, return the number of suppressed acquisitions.

Reimplemented in svkGEPFileMapperMBrease.

References svkGEPFileMapper::GetHeaderValueAsFloat().

Referenced by svkGEPFileMapper::ModifyBehavior().

int GetNumberUnsuppressedAcquisitions ( )

protectedvirtual

For single voxel acquisitions, return the number of unsuppressed acquisitions.

Reimplemented in svkGEPFileMapperMBrease.

References svkGEPFileMapper::GetHeaderValueAsFloat().

Referenced by svkGEPFileMapper::ModifyBehavior().

int GetNumCoils ( )

protected

Determine number of coils of data in the PFile.

References svkGEPFileMapper::GetHeaderValueAsInt().

Referenced by svkGEPFileMapper::AddDummy(), svkGEPFileMapper::GetNumDummyScans(), svkGEPFileMapper::GetNumFrames(), svkGEPFileMapper::GetNumTimePoints(), svkGEPFileMapper::InitMRReceiveCoilMacro(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), svkGEPFileMapper::ModifyBehavior(), and svkGEPFileMapper::ReadData().

int GetNumDummyScans ( )

protectedvirtual

Determine number of dummy scans (FIDs) in the data block. This is the difference between the raw pass size and the expected size of the data based on numCoils, numTimePts, numKSpacePts and numFreqPts.

Reimplemented in svkGEPFileMapperMPCSIOBL.

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetHeaderValueAsLongInt(), svkGEPFileMapper::GetNumCoils(), svkGEPFileMapper::GetNumKSpacePoints(), svkGEPFileMapper::GetNumTimePoints(), and svkDcmHeader::GetStringValue().

Referenced by svkGEPFileMapper::AddDummy(), and svkGEPFileMapper::ReadData().

int GetNumEPSIAcquisitions ( )

protectedvirtual

References svkGEPFileMapper::inputArgs, svkEPSIReorder::INTERLEAVED, and svkEPSIReorder::SYMMETRIC.

Referenced by svkGEPFileMapper::ReorderEPSI().

int GetNumFrames ( )

protected

Number of frames is number of slices * numCoils * numTimePoints

References svkGEPFileMapper::GetNumCoils(), svkGEPFileMapper::GetNumTimePoints(), and svkGEPFileMapper::GetNumVoxels().

int GetNumKSpacePoints ( )

protectedvirtual

Determine the number of sampled k-space points in the data set. This may differ from the number of voxels in the rectalinear grid, for example if elliptical or another non rectangular acquisition sampling strategy was employed. GE product sequences pad the reduced k-space data with zeros so the number of k-space points is the same as the number of voxels, but that may not be true for custom sequences.

Reimplemented in svkGEPFileMapperUCSF.

References svkGEPFileMapper::GetNumVoxelsInVol().

Referenced by svkGEPFileMapper::AddDummy(), svkGEPFileMapper::GetNumDummyScans(), svkGEPFileMapper::GetNumTimePoints(), svkGEPFileMapper::InitMRSpectroscopyPulseSequenceModule(), and svkGEPFileMapper::ReadData().

int GetNumTimePoints ( )

protectedvirtual

Determine number of time points in the PFile. Number of time points is determined from the file size, number of voxels and number of coils.

Reimplemented in svkGEPFileMapperMPCSIOBL, and svkGEPFileMapperMBrease.

References svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetHeaderValueAsLongInt(), svkGEPFileMapper::GetNumCoils(), svkGEPFileMapper::GetNumKSpacePoints(), and svkGEPFileMapper::GetNumVoxelsInVol().

Referenced by svkGEPFileMapper::AddDummy(), svkGEPFileMapper::GetNumDummyScans(), svkGEPFileMapper::GetNumFrames(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), svkGEPFileMapper::ModifyBehavior(), svkGEPFileMapper::ReadData(), and svkGEPFileMapper::RedimensionModifiedSVData().

void GetNumVoxels ( int numVoxels[3] )

protectedvirtual

Get the 3D spatial dimensionality of the data set Returns an int array with 3 dimensions. Swaps if necessary based on freq_dir setting.

Reimplemented in svkGEPFileMapperMPCSIOBL.

References svkGEPFileMapper::GetHeaderValueAsInt(), and svkGEPFileMapper::IsSwapOn().

Referenced by svkGEPFileMapper::GetFOV(), svkGEPFileMapper::GetNumFrames(), svkGEPFileMapperUCSF::GetNumKSpacePoints(), svkGEPFileMapper::GetNumVoxelsInVol(), svkGEPFileMapperUCSFProseProstate::GetVoxelSpacing(), svkGEPFileMapper::GetVoxelSpacing(), svkGEPFileMapper::GetXYZIndices(), svkGEPFileMapper::InitMRSpectroscopyDataModule(), svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro(), svkGEPFileMapper::InitMRSpectroscopyPulseSequenceModule(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), svkGEPFileMapper::InitPixelMeasuresMacro(), svkGEPFileMapper::ModifyBehavior(), svkGEPFileMapper::ReadData(), and svkGEPFileMapperUCSF::WasIndexSampled().

int GetNumVoxelsInVol ( )

protected

References svkGEPFileMapper::GetNumVoxels().

Referenced by svkGEPFileMapperUCSF::GetNumKSpacePoints(), svkGEPFileMapper::GetNumKSpacePoints(), svkGEPFileMapper::GetNumTimePoints(), and svkGEPFileMapper::InitMRSpectroscopyPulseSequenceModule().

float GetPPMRef ( )

protectedvirtual

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

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0, and svkGEPFileMapperUCSFfidcsiDev07t.

References svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetNucleus(), svkSpecUtils::GetPPMRef(), svkGEPFileMapper::inputArgs, and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitMRSpectroscopyModule().

string GetProgressText ( )

References svkGEPFileMapper::progressText.

void GetSelBoxCenter ( double selBoxCenter[3] )

protectedvirtual

References svkGEPFileMapper::GetHeaderValueAsFloat().

Referenced by svkGEPFileMapper::InitVolumeLocalizationSeq().

void GetSelBoxSize ( double selBoxSize[3] )

protectedvirtual

References svkGEPFileMapper::GetDcos(), svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::IsSwapOn(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitPixelMeasuresMacro(), and svkGEPFileMapper::InitVolumeLocalizationSeq().

string GetVolumeLocalizationTechnique ( )

protectedvirtual

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0, and svkGEPFileMapperUCSFfidcsi.

References svkGEPFileMapper::GetHeaderValueAsFloat(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitMRSpectroscopyModule(), and svkGEPFileMapper::InitPixelMeasuresMacro().

void GetVoxelSpacing ( double voxelSpacing[3] )

protectedvirtual

Get the voxel spacing in 3D. Note that the slice spacing may include a skip.

Reimplemented in svkGEPFileMapperUCSFProseProstate.

References svkGEPFileMapper::GetFOV(), svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetNumVoxels(), and svkGEPFileMapper::pfileVersion.

Referenced by svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), and svkGEPFileMapper::InitPixelMeasuresMacro().

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

protectedvirtual

If swapping is turned on, the data will need to get mapped correctly from the input data buffer read from disk (specData) to the correct svkImageData arrays. If swap is true, then the data indices are swapped and ky is flipped.

References svkGEPFileMapper::GetNumVoxels(), and svkGEPFileMapper::IsSwapOn().

Referenced by svkGEPFileMapper::ReadData().

void InitAcquisitionContextModule ( )

protectedvirtual

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitEnhancedGeneralEquipmentModule ( )

protected

initialize

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

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitFrameOfReferenceModule ( )

protected

initialize

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

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitGeneralEquipmentModule ( )

protected

initialize

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

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitGeneralSeriesModule ( )

protected

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetHeaderValueAsString(), and svkDcmHeader::InitGeneralSeriesModule().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitGeneralStudyModule ( )

protected

References svkGEPFileMapper::ConvertGEDateToDICOM(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsString(), svkDcmHeader::InitGeneralStudyModule(), and svkImageReader2::RemoveDelimFromDate().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

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

virtual

Initializes the svkDcmHeader adapter to a specific IOD type and initizlizes the svkDcmHeader member of the svkImageData object.

void InitK0Sampled ( svkDcmHeader * hdr )

protectedvirtual

Initializes the parameter SVK_K0Sampled based on symmetry and dimensions of the dataset (odd/even).

References svkGEPFileMapper::GetHeaderValueAsString(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfSlices(), svkGEPFileMapper::pfileVersion, and svkDcmHeader::SetValue().

Referenced by svkGEPFileMapper::InitMRSpectroscopyDataModule(), and svkGEPFileMapperUCSFfidcsiDev0::ReadData().

void InitMRAveragesMacro ( )

protectedvirtual

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, and svkGEPFileMapper::GetHeaderValueAsFloat().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMREchoMacro ( )

protectedvirtual

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitMREchoMacro().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRModifierMacro ( )

protectedvirtual

Inversion timing and other acquisition params

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitMRModifierMacro().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRReceiveCoilMacro ( )

protectedvirtual

Should work for single vs multi-coil, but will not currently differentiate between volume, surface, body coils

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsString(), and svkGEPFileMapper::GetNumCoils().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRSpatialSaturationMacro ( )

protectedvirtual

Initialize sat band information:

from pfile Header: image.user25-48
additional sat bands encoded in xml (.dat) file

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::InitSatBand(), and svkGEPFileMapper::InitSatBandsFromXML().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyDataModule ( )

protectedvirtual

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::InitK0Sampled(), and svkDcmHeader::SetValue().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitMRSpectroscopyFOVGeometryMacro ( )

protectedvirtual

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetCenterFromRawFile(), svkGEPFileMapper::GetDcos(), svkGEPFileMapper::GetFOV(), svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::GetVoxelSpacing(), and svkGEPFileMapper::IsSwapOn().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyFrameTypeMacro ( )

protectedvirtual

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

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyModule ( )

protectedvirtual

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0.

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetFrequencyOffset(), svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetHeaderValueAsString(), svkGEPFileMapper::GetNucleus(), svkGEPFileMapper::GetPPMRef(), svkGEPFileMapper::GetVolumeLocalizationTechnique(), svkGEPFileMapper::InitVolumeLocalizationSeq(), and svkDcmHeader::SetValue().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitMRSpectroscopyPulseSequenceModule ( )

protectedvirtual

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsString(), svkGEPFileMapper::GetNumKSpacePoints(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::GetNumVoxelsInVol(), svkGEPFileMapper::IsChopOn(), and svkDcmHeader::SetValue().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitMRTimingAndRelatedParametersMacro ( )

protectedvirtual

Specific to sequence, may need to be overridden in sub-class for a specific acquisition.

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetHeaderValueAsInt(), and svkDcmHeader::InitMRTimingAndRelatedParametersMacro().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMRTransmitCoilMacro ( )

protectedvirtual

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

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitMultiFrameFunctionalGroupsModule ( )

protectedvirtual

References svkGEPFileMapper::ConvertGEDateToDICOM(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsString(), svkGEPFileMapper::InitPerFrameFunctionalGroupMacros(), svkGEPFileMapper::InitSharedFunctionalGroupMacros(), svkImageReader2::RemoveDelimFromDate(), and svkDcmHeader::SetValue().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitPatientModule ( )

protected

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetHeaderValueAsInt(), svkGEPFileMapper::GetHeaderValueAsString(), and svkDcmHeader::InitPatientModule().

Referenced by svkGEPFileMapper::InitializeDcmHeader().

void InitPerFrameFunctionalGroupMacros ( )

protectedvirtual

References svkDcmHeader::AddDimensionIndex(), svkDcmHeader::CHANNEL_INDEX, svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetCenterFromRawFile(), svkGEPFileMapper::GetDcos(), svkDcmHeader::GetDimensionIndexVector(), svkGEPFileMapper::GetNumCoils(), svkGEPFileMapper::GetNumTimePoints(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::GetVoxelSpacing(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SLICE_INDEX, and svkDcmHeader::TIME_INDEX.

Referenced by svkGEPFileMapper::InitMultiFrameFunctionalGroupsModule().

void InitPixelMeasuresMacro ( )

protectedvirtual

Pixel Spacing:

References svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::GetSelBoxSize(), svkGEPFileMapper::GetVolumeLocalizationTechnique(), svkGEPFileMapper::GetVoxelSpacing(), and svkDcmHeader::InitPixelMeasuresMacro().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

void InitPlaneOrientationMacro ( )

protectedvirtual

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dataSliceOrder, svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetDcos(), svkDcmHeader::GetNormalVector(), svkDcmHeader::INCREMENT_ALONG_NEG_NORMAL, svkDcmHeader::INCREMENT_ALONG_POS_NORMAL, and svkDcmHeader::SetSliceOrder().

Referenced by svkGEPFileMapper::InitSharedFunctionalGroupMacros().

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

protectedvirtual

Add a sat band to the SpatialSaturationSequence: RAS: vector of the normal to the sat band with length equal to the band thickness in RAS coordinates. translation : translation along that vector from origin to sat band location (slab farthest from origin)

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, and svkDcmHeader::GetNumberOfItemsInSequence().

Referenced by svkGEPFileMapper::InitMRSpatialSaturationMacro(), and svkGEPFileMapperUCSF::InitSatBandsFromXML().

void InitSatBandsFromXML ( )

protectedvirtual

Reimplemented in svkGEPFileMapperUCSF.

Referenced by svkGEPFileMapper::InitMRSpatialSaturationMacro().

void InitSharedFunctionalGroupMacros ( )

protectedvirtual

Referenced by svkGEPFileMapper::InitMultiFrameFunctionalGroupsModule().

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

protectedvirtual

Virtual method for initializing the spectrum array for a given cell. Some data sets have time/frequency reversed

Reimplemented in svkGEPFileMapperUCSFfidcsiDev07t.

Referenced by svkGEPFileMapper::SetCellSpectrum().

void InitVolumeLocalizationSeq ( )

protectedvirtual

Initializes the VolumeLocalizationSequence in the MRSpectroscopy DICOM object for PRESS excitation.

References svkDcmHeader::AddSequenceItemElement(), svkGEPFileMapper::dcmHeader, svkGEPFileMapper::GetDcos(), svkGEPFileMapper::GetSelBoxCenter(), svkGEPFileMapper::GetSelBoxSize(), and svkDcmHeader::InsertEmptyElement().

Referenced by svkGEPFileMapper::InitMRSpectroscopyModule().

bool Is2D ( )

protected

Is this a 2D or 3D data set (spatial dimensions)?

References svkGEPFileMapper::GetHeaderValueAsInt().

Referenced by svkGEPFileMapper::GetFOV().

bool IsChopOn ( )

protectedvirtual

Is data chopped?

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0, and svkGEPFileMapperMBrease.

References svkGEPFileMapper::GetHeaderValueAsFloat(), svkGEPFileMapper::GetHeaderValueAsInt(), and svkGEPFileMapper::GetInputArgBoolValue().

Referenced by svkGEPFileMapper::InitMRSpectroscopyPulseSequenceModule(), svkGEPFileMapper::ReadData(), and svkGEPFileMapper::SetCellSpectrum().

bool isInputArgSet ( string argName )

protected

Returns true if the inputArgs map key is set

References svkGEPFileMapper::inputArgs.

Referenced by svkGEPFileMapper::GetInputArgBoolValue(), and svkGEPFileMapper::GetInputArgStringValue().

bool IsSwapOn ( )

protected

Is freq dir swapped?

References svkGEPFileMapper::GetHeaderValueAsInt().

Referenced by svkGEPFileMapper::GetFOV(), svkGEPFileMapperMPCSIOBL::GetNumVoxels(), svkGEPFileMapper::GetNumVoxels(), svkGEPFileMapper::GetSelBoxSize(), svkGEPFileMapper::GetXYZIndices(), and svkGEPFileMapper::InitMRSpectroscopyFOVGeometryMacro().

void ModifyBehavior ( svkImageData * data )

protectedvirtual

Modify the data loading behavior. For single voxel multi-acq data this means return the averaged (suppresssed data, if applicable).

Referenced by svkGEPFileMapper::ReadData().

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

protected

Modifies the dcos to reflect the patient entry.

References svkGEPFileMapper::GetHeaderValueAsInt().

Referenced by svkGEPFileMapper::GetDcos().

static svkGEPFileMapper* New ( )

static

void ReadData	(	vtkStringArray *	pFileNames,
		svkImageData *	data
	)

virtual

This method reads data from the pfile and puts the data into the CellData arrays. if elliptical k-space sampling was used, the data is zero-padded. Other reduced k-space sampling strategies aren't supported yet.

Reimplemented in svkGEPFileMapperUCSFfidcsiDev0.

Referenced by svkGEPFileReader::ExecuteDataWithInformation().

void RedimensionModifiedSVData ( svkImageData * data )

protected

Remove extra arrays and redimension the DICOM frames to reflect that the single voxel acquisitions have been averaged.

References svkDcmHeader::CHANNEL_INDEX, svkImageData::DeepCopy(), svkDcmHeader::GetDataDcos(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetNumberOfCoils(), svkDcmHeader::GetNumberOfSlices(), svkImageData::GetNumberOfVoxels(), svkGEPFileMapper::GetNumTimePoints(), svkDcmHeader::GetOrigin(), svkDcmHeader::GetPixelSpacing(), svkMrsImageData::GetSpectrum(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkDcmHeader::PrintDcmHeader(), svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SLICE_INDEX, and svkDcmHeader::TIME_INDEX.

Referenced by svkGEPFileMapper::ModifyBehavior().

void ReorderEPSI ( svkMrsImageData * data )

protectedvirtual

Modify behavior for EPSI data.

References svkDcmHeader::AddDimensionIndex(), svkImageData::DeepCopy(), svkDcmHeader::EPSI_ACQ_INDEX, svkFastCellData::FastAddArray(), svkFastCellData::FinishFastAdd(), svk4DImageData::GetArray(), svkDcmHeader::GetCellIDFromDimensionVectorIndex(), svkImageData::GetDcmHeader(), svkDcmHeader::GetDimensionIndexVector(), svkDcmHeader::GetDimensionVectorIndexFromCellID(), svkDcmHeader::GetDimensionVectorValue(), svkDcmHeader::GetNumberOfCells(), svkGEPFileMapper::GetNumEPSIAcquisitions(), svkImageInPlaceFilter::GetOutput(), svkGEPFileMapper::inputArgs, svkEPSIReorder::New(), svkMrsImageData::New(), svkImageData::RemoveArrays(), svk4DImageData::SetArrayName(), svkDcmHeader::SetDimensionIndexSize(), svkDcmHeader::SetDimensionVectorValue(), svkEPSIReorder::SetEPSIAxis(), svkEPSIReorder::SetEPSIType(), svkEPSIReorder::SetFirstSample(), svkEPSIReorder::SetNumEPSILobes(), svkEPSIReorder::SetNumSamplesToSkip(), svkImageData::ShallowCopy(), and svkDcmHeader::TIME_INDEX.

Referenced by svkGEPFileMapper::ModifyBehavior().

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

protected

References svkGEPFileMapper::chopVal, svkGEPFileMapper::dcmHeader, svkDcmHeader::GetIntValue(), svkDcmHeader::GetStringValue(), svkGEPFileMapper::InitSpecTuple(), svkGEPFileMapper::IsChopOn(), and svkGEPFileMapper::specData.

Referenced by svkGEPFileMapper::ReadData().

void SetPfileName ( string pfileName )

References svkGEPFileMapper::pfileName.

void SetProgressText ( string progressText )

References svkGEPFileMapper::progressText.

Referenced by svkGEPFileMapper::ReadData(), and svkGEPFileMapperUCSFfidcsiDev0::ReadData().

void UpdateProgress ( double amount )

protected

Referenced by svkGEPFileMapper::ReadData(), and svkGEPFileMapperUCSFfidcsiDev0::ReadData().

vtkTypeMacro	(	svkGEPFileMapper	,
		vtkObject
	)

bool WasIndexSampled	(	int	indexX,
		int	indexY,
		int	indexZ
	)

protectedvirtual

Determines whether a voxel (index) was sampled (or a zero padded point is present in the data set), or not, i.e. was it within the elliptical sampling volume if reduced k-space elliptical sampling was used. Could be extended to support other sparse sampling trajectories. Note that for product sequences this always returns true since GE zero-pads reduced k-space data to a full rectilinear grid.

Reimplemented in svkGEPFileMapperUCSF.

Referenced by svkGEPFileMapper::ReadData().