svkVarianReader Class Reference

#include <svkVarianReader.h>

Inheritance diagram for svkVarianReader:

Public Member Functions
	vtkTypeMacro (svkVarianReader, svkImageReader2)
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)
virtual svkImageReader2::ReaderType	GetReaderType ()=0

Static Public Member Functions
static void	UserToMagnet (double *user, double *magnet, double dcos[3][3])
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)

Protected Member Functions
	svkVarianReader ()
	~svkVarianReader ()
int	GetNumPixelsInVol ()
int	GetNumSlices ()
void	ParseProcpar (string path)
int	GetProcparKeyValuePair ()
void	ReadLine (ifstream *fs, istringstream *iss)
void	ParseAndSetProcparStringElements (string key, string valueArray1, string valueArray2)
void	PrintProcparKeyValuePairs ()
int	GetNumberOfProcparElements (string *valueString)
void	GetProcparValueArray (string *valueString)
void	RemoveStringQuotes (string *input)
void	AssignProcparVectorElements (vector< string > *procparVector, string valueArray)
Protected Member Functions inherited from svkImageReader2
	svkImageReader2 ()
	~svkImageReader2 ()
virtual int	FillOutputPortInformation (int port, vtkInformation *info)
virtual svkDcmHeader::DcmPixelDataFormat	GetFileType ()=0
void	SetupOutputInformation ()
void	SetupOutputExtent ()
void	SetupOutputScalarData ()
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
ifstream *	procparFile
map< string, vector< vector < string > > >	procparMap
int	numSlices
long	procparFileSize
svkDcmHeader::DcmDataOrderingDirection	dataSliceOrder
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

Varian reader base class.

Constructor & Destructor Documentation

svkVarianReader ( )

protected

References svkVarianReader::procparFile.

~svkVarianReader ( )

protected

References svkVarianReader::procparFile.

Member Function Documentation

void AssignProcparVectorElements ( vector< string > *  procparVector, string  valueArray  )

protected

References svkVarianReader::RemoveStringQuotes().

Referenced by svkVarianReader::ParseAndSetProcparStringElements().

int GetNumberOfProcparElements ( string *  valueString )

protected

Utility method to determine how many space delimited elements are in current propcar string.

Referenced by svkVarianReader::GetProcparValueArray().

int GetNumPixelsInVol ( )

protected

Referenced by svkFdfVolumeReader::ExecuteDataWithInformation().

int GetNumSlices ( )

protected

Not sure if this is always extent 5 if the data is coronal and sagital for example

int GetProcparKeyValuePair ( )

protected

Utility function to read key/values from procpar file and set the delimited key/value pair into the stl map. Returns -1 if can't parse line.

References svkVarianReader::GetProcparValueArray(), svkVarianReader::ParseAndSetProcparStringElements(), svkVarianReader::procparFile, svkVarianReader::procparFileSize, and svkVarianReader::ReadLine().

Referenced by svkVarianReader::ParseProcpar().

void GetProcparValueArray ( string *  valueString )

protected

Read lines from propcar until all elements of value have been parsed.

References svkVarianReader::GetNumberOfProcparElements(), svkVarianReader::procparFile, svkVarianReader::ReadLine(), and svkImageReader2::StripWhite().

Referenced by svkVarianReader::GetProcparKeyValuePair().

void ParseAndSetProcparStringElements ( string  key, string  valueArray1, string  valueArray2  )

protected

Push key value pairs into the map's value vector: mapFor values that are space delimited lists, put each element into the value vector.

References svkVarianReader::AssignProcparVectorElements(), and svkVarianReader::procparMap.

Referenced by svkVarianReader::GetProcparKeyValuePair().

void ParseProcpar ( string  path )

protected

Parses the procpar file if present. The format appears to be: keyName numElements1 space_separated_values numElements2 space_separated_values

References svkImageReader2::GetFileSize(), svkVarianReader::GetProcparKeyValuePair(), svkVarianReader::procparFile, and svkVarianReader::procparFileSize.

void PrintProcparKeyValuePairs ( )

protected

Prints the key value pairs parsed from the header.

References svkVarianReader::procparMap.

void ReadLine ( ifstream *  fs, istringstream *  iss  )

protectedvirtual

Utility function to read a single line from the fdf file stream.

Reimplemented from svkImageReader2.

Referenced by svkVarianReader::GetProcparKeyValuePair(), and svkVarianReader::GetProcparValueArray().

void RemoveStringQuotes ( string *  input )

protected

Remove any quotation marks from the string

Referenced by svkVarianReader::AssignProcparVectorElements().

void UserToMagnet ( double *  user, double *  magnet, double  dcos[3][3]  )

static

Referenced by svkVarianUCSF2DcsiMapper::InitPerFrameFunctionalGroupMacros(), svkVarianUCSFEPSI2DMapper::InitPerFrameFunctionalGroupMacros(), and svkVarianFidMapper::InitPerFrameFunctionalGroupMacros().

vtkTypeMacro	(	svkVarianReader	,
		svkImageReader2
	)

Member Data Documentation

svkDcmHeader::DcmDataOrderingDirection dataSliceOrder

protected

int numSlices

protected

ifstream* procparFile

protected

Referenced by svkVarianReader::GetProcparKeyValuePair(), svkVarianReader::GetProcparValueArray(), svkVarianReader::ParseProcpar(), svkFdfVolumeReader::svkFdfVolumeReader(), svkVarianFidReader::svkVarianFidReader(), svkVarianReader::svkVarianReader(), svkFdfVolumeReader::~svkFdfVolumeReader(), svkVarianFidReader::~svkVarianFidReader(), and svkVarianReader::~svkVarianReader().

long procparFileSize

protected

Referenced by svkVarianReader::GetProcparKeyValuePair(), and svkVarianReader::ParseProcpar().

map<string, vector < vector<string> > > procparMap

protected

Referenced by svkVarianReader::ParseAndSetProcparStringElements(), and svkVarianReader::PrintProcparKeyValuePairs().

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

• svkVarianReader.h
• svkVarianReader.cc