#include <svkImageReader2.h>

Inheritance diagram for svkImageReader2:

Public Types
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 }

Public Member Functions
	vtkTypeMacro (svkImageReader2, vtkImageReader2)

svkImageData *	GetOutput ()

svkImageData *	GetOutput (int)

svkDcmHeader *	GetDcmHeader (const char *fileName)

void	OnlyReadOneInputFile ()

void	OnlyGlobFiles ()

void	GlobFileNames ()

void	OnlyReadHeader (bool onlyReadHeader)

virtual svkImageReader2::ReaderType	GetReaderType ()=0

Static Public Member Functions
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)

Protected Member Functions
	svkImageReader2 ()

	~svkImageReader2 ()

virtual int	FillOutputPortInformation (int port, vtkInformation *info)

virtual svkDcmHeader::DcmPixelDataFormat	GetFileType ()=0

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)

virtual void	SetProvenance ()

virtual string	GetFileSeriesDescription (string fileName)

void	SetReadLength (int length)

Protected Attributes
vtkDataArray *	dataArray

bool	readOneInputFile

bool	onlyGlobFiles

bool	onlyReadHeader

Member Enumeration Documentation

enum ReaderType

Enumerator
UNDEFINED
DICOM_MRS
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

Constructor & Destructor Documentation

svkImageReader2 ( )

protected

References svkImageReader2::dataArray, svkMrsImageData::NewObject(), svkMriImageData::NewObject(), svkImageReader2::onlyGlobFiles, svkImageReader2::onlyReadHeader, and svkImageReader2::readOneInputFile.

~svkImageReader2 ( )

protected

References svkImageReader2::dataArray.

Member Function Documentation

int FillOutputPortInformation	(	int	port,
		vtkInformation *	info
	)

protectedvirtual

Reimplemented in svkGEPFileReader, svkSiemensRdaReader, svkIdfVolumeReader, svkGESigna5XReader, svkFdfVolumeReader, svkVarianFidReader, svkPhilipsSReader, svkDcmEnhancedVolumeReader, svkDdfVolumeReader, svkBrukerDCMMRSReader, svkSdbmVolumeReader, svkDcmRawDataReader, svkDcmMriVolumeReader, svkDcmMrsVolumeReader, svkGEPostageStampReader, svkDcmSegmentationVolumeReader, svkLCModelCoordReader, svkLCModelCSVReader, and svkLCModelTableReader.

svkDcmHeader * GetDcmHeader ( const char * fileName )

References svkImageData::GetDcmHeader(), and svkImageReader2::GetOutput().

Referenced by svkDcmEnhancedVolumeReader::GetPixelTransform(), svkGEPostageStampReader::InitDcmHeader(), svkDcmMriVolumeReader::InitDcmHeader(), svkBrukerDCMMRSReader::InitDcmHeader(), svkGESigna5XReader::InitDcmHeader(), and svkDcmEnhancedVolumeReader::IsDataFloatingPoint().

string GetFileExtension ( const char * fname )

static

Returns the file root without extension or NULL if no extension found.

Referenced by svkDdfVolumeReader::CanReadFile(), svkPhilipsSReader::CanReadFile(), and svkImageReader2::GlobFileNames().

string GetFileNameWithoutPath ( const char * fname )

static

Returns the file name without path: everything after the last "/".

Referenced by svkLCModelReader::GetVoxelIndexFromFileName(), and svkImageReader2::GlobFileNames().

string GetFilePath ( const char * fname )

static

Returns the file path: everything before the last "/".

Referenced by svkImageReader2::GlobFileNames(), svkGESigna5XReader::InitDcmHeader(), and svkDcmVolumeReader::InitFileNames().

string GetFileRoot ( const char * fname )

static

Returns the file root without extension (will include any path elements)

Referenced by svkPhilipsSMapper::ReadSDATFile(), and svkImageWriter::SetFileName().

string GetFileSeriesDescription ( string fileName )

protectedvirtual

get the series description for this file for globbing purposes:

Reimplemented in svkGEPFileReader, and svkLCModelReader.

References svkImageReaderFactory::CreateImageReader2(), svkImageData::GetDcmHeader(), svkImageReader2::GetOutput(), svkImageReader2::GetReaderType(), svkDcmHeader::GetStringValue(), svkImageReader2::OnlyReadHeader(), and svkImageReader2::OnlyReadOneInputFile().

Referenced by svkImageReader2::GlobFileNames().

long GetFileSize ( ifstream * fs )

static

Return the file size.

Referenced by svkVarianReader::ParseProcpar().

virtual svkDcmHeader::DcmPixelDataFormat GetFileType ( )

protectedpure virtual

Implemented in svkGEPFileReader, svkVariableFlipDatReader, svkSiemensRdaReader, svkIdfVolumeReader, svkGESigna5XReader, svkFdfVolumeReader, svkDdfVolumeReader, svkSdbmVolumeReader, svkBrukerDCMMRSReader, svkDcmEnhancedVolumeReader, svkDcmMriVolumeReader, svkDcmMrsVolumeReader, svkGEPostageStampReader, svkDcmSegmentationVolumeReader, and svkLCModelReader.

Referenced by svkImageReader2::SetupOutputScalarData().

svkImageData * GetOutput ( )

svkImageData * GetOutput ( int port )

void GlobFileNames ( )

References svkImageReader2::GetFileExtension(), svkImageReader2::GetFileNameWithoutPath(), svkImageReader2::GetFilePath(), svkImageReader2::GetFileSeriesDescription(), svkImageReader2::onlyGlobFiles, and svkImageReader2::readOneInputFile.

Referenced by svkLCModelCoordReader::ExecuteDataWithInformation(), and svkGEPFileReader::ReadGEPFile().

void OnlyGlobFiles ( )

Only list the files in the data set, then exit.

References svkImageReader2::onlyGlobFiles.

void OnlyReadHeader ( bool onlyReadHeader )

If only the idf header is to be read. Sometimes this acts as a template for processing, but
- there isn't an associated data file.

References svkImageReader2::onlyReadHeader.

Referenced by svkGEPFileReader::Deidentify(), svkGEPFileReader::GetFileSeriesDescription(), svkImageReader2::GetFileSeriesDescription(), svkGEPFileReader::ModifyRawField(), svkImageReaderFactory::QuickParse(), and svkDICOMRawDataWriter::Write().

void OnlyReadOneInputFile ( )

Only read the one specified input file. Otherwise the default behavior is to read all the files in the group.

References svkImageReader2::readOneInputFile.

Referenced by svkGEPFileReader::GetFileSeriesDescription(), svkImageReader2::GetFileSeriesDescription(), svkImageAlgorithmPipeline::InitializeAlgorithmForTag(), and svkDataModel::LoadFile().

void ReadLine	(	ifstream *	hdr,
		istringstream *	iss
	)

protectedvirtual

Utility function to read a single line from the volume file.

Reimplemented in svkVarianReader.

Referenced by svkSiemensRdaReader::CanReadFile(), svkImageReader2::ReadLineIgnore(), svkImageReader2::ReadLineKeyValue(), svkImageReader2::ReadLineSubstr(), and svkImageReader2::ReadLineValue().

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

protected

Utility function to read a single line from the volume file. and ignore all characters up to the specified delimiting character.

References svkImageReader2::ReadLine().

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

protected

Read the value part of a delimited key value line in a file:

Returns: 0 on success, 1 if can't parse line with delimiter into key/value pair

References svkImageReader2::ReadLine(), and svkImageReader2::StripWhite().

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

protected

Utility function for extracting a substring with white space removed from LHS.

References svkImageReader2::ReadLine().

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

protected

Read the value part of a delimited key value line in a file:

References svkImageReader2::ReadLine().

Referenced by svkVariableFlipDatReader::InitDatReader().

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

static

Remove slashes from idf date and reorder for DICOM compliance: 07/25/2007 -> 20070725 assumes input order is month, day, year output order is year, month, day

References svkImageReader2::StripWhite().

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

void SetProvenance ( )

protectedvirtual

Appends algo info to provenance record.

Reimplemented in svkGEPFileReader.

References svkImageReader2::GetOutput().

void SetReadLength ( int length )

protected

void SetupOutputExtent ( )

protected

References svkImageData::GetDcmHeader(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfSlices(), and svkImageReader2::GetOutput().