#include <svkGEPFileReader.h>

Inheritance diagram for svkGEPFileReader:

Public Member Functions
	vtkTypeMacro (svkGEPFileReader, svkImageReader2)

virtual int	CanReadFile (const char *fname)

svkGEPFileMapper *	GetMapper ()

void	SetMapperBehavior (svkGEPFileMapper::MapperBehavior type)

void	SetDeidentify (svkDcmHeader::PHIType phiType)

void	SetDeidentify (svkDcmHeader::PHIType phiType, string deidentificationId)

void	SetDeidentify (svkDcmHeader::PHIType phiType, string patientId, string studyId)

void	SetDeidentificationStudyUID (string deidStudyUID)

void	SetDeidentificationSeriesUID (string deidSeriesUID)

void	SetDeidentificationInstanceUID (string deidImageUID)

void	SetDeidentificationLandmarkUID (string deidLandmarkUID)

void	SetTemperature (float temp)

void	SetChop (bool chop)

void	PrintHeader ()

void	PrintShortHeader ()

void	SetEPSIParams (svkEPSIReorder::EPSIType type, svkEPSIReorder::EPSIAxis axis, int first, int numLobes, int numSkip)

void	Deidentify ()

void	ModifyRawField (string rawField, string value)

void	SetPSDLogic (string psdName)

map< string, vector< string > >	GetPFMap ()

virtual const char *	GetDescriptiveName ()

virtual svkImageReader2::ReaderType	GetReaderType ()

Public Member Functions inherited from svkImageReader2
	vtkTypeMacro (svkImageReader2, vtkImageReader2)

svkImageData *	GetOutput ()

svkImageData *	GetOutput (int)

svkDcmHeader *	GetDcmHeader (const char *fileName)

void	OnlyReadOneInputFile ()

void	OnlyGlobFiles ()

void	GlobFileNames ()

void	OnlyReadHeader (bool onlyReadHeader)

Static Public Member Functions
static svkGEPFileReader *	New ()

static float	LookupRawVersion (float rdbmRev, float rdbmRevSwapped)

Static Public Member Functions inherited from svkImageReader2
static string	StripWhite (string in)

static string	RemoveDelimFromDate (string *slashDate, char delimChar= '/')

static string	GetFileRoot (const char *fname)

static string	GetFileExtension (const char *fname)

static string	GetFilePath (const char *fname)

static string	GetFileNameWithoutPath (const char *fname)

static long	GetFileSize (ifstream *fs)

Public Attributes
bool	checkSeriesUID

Protected Member Functions
	svkGEPFileReader ()

	~svkGEPFileReader ()

virtual int	FillOutputPortInformation (int port, vtkInformation *info)

virtual void	ExecuteInformation ()

virtual void	ExecuteDataWithInformation (vtkDataObject output, vtkInformation outInfo)

virtual svkDcmHeader::DcmPixelDataFormat	GetFileType ()

void	ReadGEPFile ()

void	ParsePFile ()

void	InitOffsetsMap ()

virtual void	SetProvenance ()

virtual string	GetFileSeriesDescription (string fileName)

Protected Member Functions inherited from svkImageReader2
	svkImageReader2 ()

	~svkImageReader2 ()

void	SetupOutputInformation ()

void	SetupOutputExtent ()

void	SetupOutputScalarData ()

virtual void	ReadLine (ifstream hdr, istringstream iss)

void	ReadLineIgnore (ifstream hdr, istringstream iss, char delim)

string	ReadLineSubstr (ifstream hdr, istringstream iss, int start, int stop)

string	ReadLineValue (ifstream hdr, istringstream iss, char delim)

int	ReadLineKeyValue (ifstream hdr, istringstream iss, char delim, string key, string value)

void	SetReadLength (int length)

Protected Attributes
map< string, vector< string > >	pfMap

Protected Attributes inherited from svkImageReader2
vtkDataArray *	dataArray

bool	readOneInputFile

bool	onlyGlobFiles

bool	onlyReadHeader

Additional Inherited Members
Public Types inherited from svkImageReader2
enum	ReaderType { UNDEFINED = -1, DICOM_MRS =0, DICOM_MRI, DICOM_ENHANCED_MRI, DICOM_SEGMENTATION, DICOM_RAW, SIEMENS_RDA, VARIAN_FID, VARIAN_FDF, GE_PFILE, GE_SDBM, GE_POSTAGE_STAMP, GE_SIGNA_LX2, GE_SIGNA_5X, LC_MODEL_COORD, LC_MODEL_CSV, LC_MODEL_TABLE, VARIABLE_FLIP_DAT, BRUKER_MRS, PHILIPS_S, DDF, IDF, LAST_TYPE = IDF }

Detailed Description

This is an svkImageReader2 for reading GE P-files. The reader supports 9.x - 20.x raw file versions. The reader reads fields from GE P-files, putting the content into a string map. The reader then obtains a svkGEPFileMapper for the specific PSD in order to map that content to an svkMrsImageData object (and svkDcmHeader representing a DICOM MR Spectroscopy SOP Class UID). The mapping will depend on the specific psd context, for example because of variability in meaning of user cvs.

A mapper factory will ultimatly be developed to obtain the appropriate svkPFileMapper for a given Pfile.

Thanks to Mike Figueira of GE Medical for helful discussions about the class design. Many thanks also to Sanjay Joshi( GE Medical recon ), Mike Figueira (GEMS) and Katie McMillan (GEMS) for their help making this possible.

Acknowledgments: Dr. Ping-Hong Yeh for providing sample data for validating 21.x support.

Constructor & Destructor Documentation

svkGEPFileReader ( )

protected

References svkGEPFileReader::checkSeriesUID, svkImageReader2::onlyReadHeader, svkDcmHeader::PHI_IDENTIFIED, UNASSIGNED_ID, and UNASSIGNED_UID.

~svkGEPFileReader ( )

protected

Member Function Documentation

int CanReadFile ( const char * fname )

virtual

Check to see if this is a GE pfile. If so, try to open the file for reading. If that works, then return a success code. Return Values: 1 if can read the file, 0 otherwise.

References svkGEPFileReader::InitOffsetsMap(), svkImageReader2::onlyReadHeader, and svkGEPFileReader::ReadGEPFile().

void Deidentify ( )

References svkDcmHeader::GenerateUniqueUID(), svkImageData::GetDcmHeader(), svkImageReader2::GetOutput(), svkTypeUtils::IntToString(), svkImageReader2::OnlyReadHeader(), svkDcmHeader::PHI_DEIDENTIFIED, svkGEPFileReader::ReadGEPFile(), UNASSIGNED_ID, and UNASSIGNED_UID.

void ExecuteDataWithInformation	(	vtkDataObject *	output,
		vtkInformation *	outInfo
	)

protectedvirtual

Side effect of Update() method. Used to load pixel data and initialize vtkImageData Called after ExecuteInformation()

References svkDcmHeader::GetDataDcos(), svkImageData::GetDcmHeader(), svkImageReader2::GetOutput(), svkImageReader2::onlyReadHeader, svkGEPFileMapper::ReadData(), svkImageData::SetDcos(), svkGEPFileReader::SetProvenance(), and svkImageReader2::SetupOutputInformation().

void ExecuteInformation ( )

protectedvirtual

Side effect of Update() method. Used to load pixel data and initialize vtkImageData Called before ExecuteData()

References svkImageReader2::onlyReadHeader, and svkImageReader2::SetupOutputInformation().

int FillOutputPortInformation	(	int	port,
		vtkInformation *	info
	)

protectedvirtual

Reimplemented from svkImageReader2.

virtual const char* GetDescriptiveName ( )

inlinevirtual

string GetFileSeriesDescription ( string fileName )

protectedvirtual

get the series description for this file for globbing purposes:

Reimplemented from svkImageReader2.

References svkGEPFileReader::checkSeriesUID, svkGEPFileReader::GetPFMap(), svkGEPFileReader::New(), svkImageReader2::OnlyReadHeader(), and svkImageReader2::OnlyReadOneInputFile().

svkDcmHeader::DcmPixelDataFormat GetFileType ( )

protectedvirtual

Returns the file root without extension

Implements svkImageReader2.

References svkDcmHeader::SIGNED_FLOAT_4.

svkGEPFileMapper * GetMapper ( )

returns the mapper

map< string, vector< string > > GetPFMap ( )

References svkGEPFileReader::pfMap.

Referenced by svkGEPFileReader::GetFileSeriesDescription(), and svkDICOMRawDataWriter::Write().

virtual svkImageReader2::ReaderType GetReaderType ( )

inlinevirtual

Implements svkImageReader2.

References svkImageReader2::GE_PFILE.

void InitOffsetsMap ( )

protected

Initialize map of field names to dataType, size and offset. This map is used to parse GE Pfile:

// fieldName nativeType numElements offset stringValue // -------------------------------------------------------— // rhr.rh_rdbm_rev , FLOAT_4, 1 , 0 value // rhr.rh_logo , CHAR , 10 , 34 value

References svkGEPFileReader::pfMap, and svkImageReader2::StripWhite().

Referenced by svkGEPFileReader::CanReadFile(), and svkGEPFileReader::ParsePFile().

float LookupRawVersion	(	float	rdbmRev,
		float	rdbmRevSwapped
	)

static

Lookup version from rdbmRev:

void ModifyRawField	(	string	rawField,
		string	value
	)

References svkImageReader2::OnlyReadHeader(), and svkGEPFileReader::ReadGEPFile().

static svkGEPFileReader* New ( )

static

Referenced by svkImageReaderFactory::CreateImageReader2(), svkGEPFileReader::GetFileSeriesDescription(), and svkImageReaderFactory::svkImageReaderFactory().

void ParsePFile ( )

protected

Initializes the map of pfile offsets and data types, parses the pfile header and sets the field value in the map to a string representation of the header field.