APTFileIO.cpp File Reference

#include "APTFileIO.h"
#include "ionhit.h"
#include "../../common/stringFuncs.h"
#include "../../common/basics.h"
#include "../../common/translation.h"
#include <cstring>
#include <new>

Include dependency graph for APTFileIO.cpp:

Macros
#define	USE_SEEKING_LIMITLOAD

Enumerations
enum	{   TEXT_ERR_OPEN =1, TEXT_ERR_ONLY_HEADER, TEXT_ERR_REOPEN, TEXT_ERR_READ_CONTENTS,   TEXT_ERR_FORMAT, TEXT_ERR_ALLOC_FAIL, TEXT_ERR_ENUM_END }
enum	{   LAWATAP_ATO_OPEN_FAIL =1, LAWATAP_ATO_EMPTY_FAIL, LAWATAP_ATO_SIZE_ERR, LAWATAP_ATO_VERSIONCHECK_ERR,   LAWATAP_ATO_MEM_ERR, LAWATAP_ATO_BAD_ENDIAN_DETECT, LAWATAP_ATO_ENUM_END }
enum	{ TAPSIM_ERR_FILE_FORMAT_FAIL, TAPSIM_ERR_FILE_OPEN_FAIL, TAPSIM_ERR_ABORTED }

Functions
unsigned int	LimitLoadPosFile (unsigned int inputnumcols, unsigned int outputnumcols, const unsigned int index[], vector< IonHit > &posIons, const char *posFile, size_t limitCount, unsigned int &progress, ATOMIC_BOOL &wantAbort, bool strongSampling)
unsigned int	GenericLoadFloatFile (unsigned int inputnumcols, unsigned int outputnumcols, const unsigned int index[], vector< IonHit > &posIons, const char *posFile, unsigned int &progress, ATOMIC_BOOL &wantAbort)
	Load a pos file directly into a single ion list. More...
unsigned int	limitLoadTextFile (unsigned int maxCols, vector< vector< float > > &data, const char *textFile, const char *delim, const size_t limitCount, unsigned int &progress, ATOMIC_BOOL &wantAbort, bool strongRandom)
unsigned int	LoadATOFile (const char *fileName, vector< IonHit > &ions, unsigned int &progress, ATOMIC_BOOL &wantAbort, unsigned int forceEndian)
unsigned int	loadTapsimBinFile (const char *fileName, unsigned int &progress, ATOMIC_BOOL &wantAbort, vector< IonHit > &posIons)

Variables
const size_t	PROGRESS_REDUCE =5000
const char *	TEXT_LOAD_ERR_STRINGS []
const char *	POS_ERR_STRINGS []
const char *	ION_TEXT_ERR_STRINGS []
const char *	LAWATAP_ATO_ERR_STRINGS []
const char *	TAPSIM_ERR_STRINGS []

Macro Definition Documentation

USE_SEEKING_LIMITLOAD

#define USE_SEEKING_LIMITLOAD

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
TEXT_ERR_OPEN
TEXT_ERR_ONLY_HEADER
TEXT_ERR_REOPEN
TEXT_ERR_READ_CONTENTS
TEXT_ERR_FORMAT
TEXT_ERR_ALLOC_FAIL
TEXT_ERR_ENUM_END

anonymous enum

anonymous enum

Enumerator
LAWATAP_ATO_OPEN_FAIL
LAWATAP_ATO_EMPTY_FAIL
LAWATAP_ATO_SIZE_ERR
LAWATAP_ATO_VERSIONCHECK_ERR
LAWATAP_ATO_MEM_ERR
LAWATAP_ATO_BAD_ENDIAN_DETECT
LAWATAP_ATO_ENUM_END

anonymous enum

anonymous enum

Enumerator
TAPSIM_ERR_FILE_FORMAT_FAIL
TAPSIM_ERR_FILE_OPEN_FAIL
TAPSIM_ERR_ABORTED

Function Documentation

GenericLoadFloatFile()

unsigned int GenericLoadFloatFile	(	unsigned int	inputnumcols,
		unsigned int	outputnumcols,
		const unsigned int	index[],
		vector< IonHit > &	posIons,
		const char *	posFile,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort
	)

Load a pos file directly into a single ion list.

Pos files are fixed record size files, with data stored as 4byte big endian floating point. (IEEE 574?). Data is stored as x,y,z,mass/charge. Load a pos file into a T of IonHits

References ASSERT, IonHit::DATA_SIZE, IonHit::hasInf(), IonHit::hasNaN(), POS_ABORT_FAIL, POS_ALLOC_FAIL, POS_EMPTY_FAIL, POS_INF_LOAD_ERROR, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_MODULUS_ERR, PROGRESS_REDUCE, and IonHit::setHit().

Referenced by LimitLoadPosFile(), ExternalProgramFilter::refresh(), DataLoadFilter::refresh(), and SpatialAnalysisFilter::refresh().

Here is the caller graph for this function:

LimitLoadPosFile()

unsigned int LimitLoadPosFile	(	unsigned int	inputnumcols,
		unsigned int	outputnumcols,
		const unsigned int	index[],
		vector< IonHit > &	posIons,
		const char *	posFile,
		size_t	limitCount,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		bool	strongSampling
	)

References ASSERT, ATOMIC_BOOL, GenericLoadFloatFile(), getFilesize(), RandNumGen::initTimer(), LimitLoadPosFile(), POS_ABORT_FAIL, POS_ALLOC_FAIL, POS_EMPTY_FAIL, POS_INF_LOAD_ERROR, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_MODULUS_ERR, PROGRESS_REDUCE, and randomDigitSelection().

Referenced by LimitLoadPosFile(), and DataLoadFilter::refresh().

Here is the caller graph for this function:

limitLoadTextFile()

unsigned int limitLoadTextFile	(	unsigned int	maxCols,
		vector< vector< float > > &	data,
		const char *	textFile,
		const char *	delim,
		const size_t	limitCount,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		bool	strongRandom
	)

References ASSERT, RandNumGen::initTimer(), loadTextData(), POS_ABORT_FAIL, randomDigitSelection(), splitStrsRef(), stream_cast(), stripZeroEntries(), TEXT_ERR_ALLOC_FAIL, TEXT_ERR_FORMAT, TEXT_ERR_ONLY_HEADER, TEXT_ERR_OPEN, TEXT_ERR_READ_CONTENTS, and TEXT_ERR_REOPEN.

Referenced by DataLoadFilter::refresh().

Here is the caller graph for this function:

LoadATOFile()

unsigned int LoadATOFile	(	const char *	fileName,
		vector< IonHit > &	ions,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		unsigned int	forceEndian
	)

References ASSERT, floatSwapBytes(), RandNumGen::initTimer(), LAWATAP_ATO_EMPTY_FAIL, LAWATAP_ATO_MEM_ERR, LAWATAP_ATO_OPEN_FAIL, LAWATAP_ATO_SIZE_ERR, LAWATAP_ATO_VERSIONCHECK_ERR, and randomDigitSelection().

Referenced by loadTapsimBinFile(), and DataLoadFilter::refresh().

Here is the caller graph for this function:

loadTapsimBinFile()

unsigned int loadTapsimBinFile	(	const char *	fileName,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		vector< IonHit > &	posIons
	)

References ASSERT, ATOMIC_BOOL, floatSwapBytes(), genRandomFilename(), LoadATOFile(), IonHit::makePosData(), rmFile(), IonHit::setMassToCharge(), IonHit::setPos(), shortSwapBytes(), splitStrsRef(), stream_cast(), TAPSIM_ERR_ABORTED, TAPSIM_ERR_FILE_FORMAT_FAIL, TAPSIM_ERR_FILE_OPEN_FAIL, TEST, and WARN.

Referenced by DataLoadFilter::refresh().

Here is the caller graph for this function:

Variable Documentation

ION_TEXT_ERR_STRINGS

const char* ION_TEXT_ERR_STRINGS[]

Initial value:

= { "",
                                        NTRANS("Error opening file"),
                                        NTRANS("No numerical data found"),
                                        NTRANS("Error re-opening file, after first scan"),
                                        NTRANS("Unable to read file contents after open"),
                                        NTRANS("Error interpreting field in file"),
                                        NTRANS("Incorrect number of fields in file"),
                                        NTRANS("Unable to allocate memory to store data"),
                                        }

LAWATAP_ATO_ERR_STRINGS

const char* LAWATAP_ATO_ERR_STRINGS[]

Initial value:

= { "",
                                NTRANS("Error opening file"),
                                NTRANS("File is empty"),
                                NTRANS("Filesize does not match expected format"),
                                NTRANS("File version number not <4, as expected"),
                                NTRANS("Unable to allocate memory to store data"),

                                }

Referenced by DataLoadFilter::refresh().

POS_ERR_STRINGS

const char* POS_ERR_STRINGS[]

Initial value:

= { "",
                                NTRANS("Memory allocation failure on POS load"),
                                NTRANS("Error opening pos file"),
                                NTRANS("Pos file empty"),
                                NTRANS("Pos file size appears to have non-integer number of entries"),
                                NTRANS("Error reading from pos file (after open)"),
                                NTRANS("Error - Found NaN in pos file"),
                                NTRANS("Error - Found Inf in pos file"),

}

Referenced by DataLoadFilter::refresh().

PROGRESS_REDUCE

const size_t PROGRESS_REDUCE =5000

Referenced by GenericLoadFloatFile(), LimitLoadPosFile(), TransformFilter::refresh(), CropHelper::runFilter(), and ClusterAnalysisFilter::setPropFromBinding().

TAPSIM_ERR_STRINGS

const char* TAPSIM_ERR_STRINGS[]

Initial value:

= {"",
                        NTRANS("Error interpreting file contents"),
                        NTRANS("Error opening file"),
                        NTRANS("Aborted opening file"),
                        }

Referenced by DataLoadFilter::refresh().

TEXT_LOAD_ERR_STRINGS

const char* TEXT_LOAD_ERR_STRINGS[]

Initial value:

= { "",
                                        NTRANS("Error opening file"),
                                        NTRANS("Only found header, no data"),
                                        NTRANS("Unable to reopen file after first scan"),
                                        NTRANS("Error whilst reading file contents"),
                                        NTRANS("Unexpected file format"),
                                        NTRANS("Unexpected file format"),
                                        NTRANS("Insufficient memory to continue"),
                                        }

Referenced by DataLoadFilter::refresh().