massspec/map_tk.h File Reference

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Data Structures
struct	Map2D
Defines
#define	MAP_VALUE_NOT_SEGMENT   FLT_MIN
Typedefs
typedef Map2D	Map2D
Enumerations
enum	{ REMOVE_EDGES, INCLUDE_EDGES }
enum	{ RT_DIMENSION, MZ_DIMENSION }
enum	{ MAP2D_POINT_INDEX, MAP2D_POINT_SAMPLING, MAP2D_POINT_REAL }
enum	{ MASS_TYPE_MOZ, MASS_TYPE_BIN, MASS_TYPE_MZJ }
enum	{ RT_TYPE_MIN, RT_TYPE_SCAN, RT_TYPE_RTI }
Functions
Map2D *	Map2D_new ()
void	Map2D_mallocAbundanceMatrix (Map2D *map)
void	Map2D_mallocScanArray (Map2D *map)
void	Map2D_mallocDim (Map2D *map, Dimensions2i dim)
void	Map2D_malloc (Map2D *map, int no_of_scans, int no_of_bins)
void	Map2D_initHeader (Map2D *map)
void	Map2D_initAbundance (Map2D *map, float value)
void	initMap (Map2D *MP)
void	initMapWithValue (Map2D *MP, float value)
void	Map2D_setHeader (Map2D *map, Experiment *expmnt, Rectangle4i rect)
void	Map2D_setSamplingArrays (Map2D *map, Rectangle4i *rect)
void	Map2D_setBorders (Map2D *map, int x_start, int x_stop, int y_start, int y_stop)
void	Map2D_setProcScript (Map2D *map, ProcScript PS)
int	Map2D_fprintHeader (FILE *fp, Map2D *map)
void	Map2D_fprintAbundanceMatrix (FILE *fp, Map2D *map, int format)
void	Map2D_fprintAbundanceSubMatrix (FILE *fp, Map2D *map, Rectangle4i *rect)
void	Map2D_printHeader (Map2D *map, char *mapname)
void	Map2D_copyHeader (Map2D *source, Map2D *dest)
void	Map2D_copy (Map2D *dest, Map2D *source)
void	Map2D_create (Map2D *map, Experiment *expmnt, Rectangle4i rect)
void	Map2D_createUsingTemplate (Map2D *template_map, Map2D *output_map, float init_value)
Map2D	Map2D_createBinaryMap (Map2D *map, float threshold)
void	Map2D_destroy (Map2D *map)
void	Map2D_invert_new (Map2D *out, Map2D *in)
float	Map2D_calcArea (Map2D *map)
float	Map2D_getResidualVolume (Map2D *original, Map2D *fitted)
void	Map2D_subtractMaps (Map2D *one, Map2D *two, Map2D *diff)
void	Map2D_mergeMaps (Map2D *one, Map2D *two, Map2D *result)
void	Map2D_applyLinearInterpolation (Map2D *map)
int	Map2D_applyErosion (Map2D *OMAP, Map2D *IMAP, char *szStructElemName)
int	Map2D_applyDilation (Map2D *OMAP, Map2D *IMAP, char *szStructElemName)
int	Map2D_applyClosing (Map2D *map, char *szStructElemName)
int	Map2D_applyClosingUsingOriginal (Map2D *out, Map2D *in, char *szStructElemName)
int	Map2D_applyOpening (Map2D *map, char *szStructElemName)
int	Map2D_isMOZValid (Map2D *map, float MOZ)
int	Map2D_isRTValid (Map2D *map, float RT)
int	Map2D_isMassBinValid (Map2D *map, int mass_bin)
int	Map2D_isScanValid (Map2D *map, int rt_bin)
int	Map2D_isMassIndexValid (Map2D *map, int mass_index)
int	Map2D_isRTIndexValid (Map2D *map, int rt_index)
float *	Map2D_getAbundanceArrayFromMassChrm (Map2D *map, int size, float index_value, int index_type)
float *	Map2D_getAbundanceArrayFromMassSpec (Map2D *map, int size, float index_value, int index_type)
float *	Map2D_getAbundancePointerFromScan (Map2D *map, int scan)
float *	Map2D_getAbundancePointerFromIndex (Map2D *map, int scanIndex)
float *	getAbundanceArrayOfMassSpecAtRTI (Map2D *map, int rt_index, int start, int stop)
void	putMassChrmToMap2D_BIN (Map2D *MP, int bin, float *array, int size)
void	putMassChrmToMap2D_MZI (Map2D *MP, int mz_index, float *array, int size)
void	putMassSpecToMap2D_RTI (Map2D *MP, int rt_index, float *array, int size)
Map2D	Map2D_extractSubMap (Map2D *map, Rectangle4i *rect)
float *	getRTSamplingArrayFromMap2D (Map2D *MP)
float *	getMSSamplingArrayFromMap2D (Map2D *MP)
void	Map2D_transformPeak2i (Map2D *map, Peak2i *peak, int type)
void	Map2D_transformPeak2iArray (Map2D *map, Peak2i *peaks, int npeaks, int type)
void	Map2D_transformRectangle4i (Map2D *map, Rectangle4i *target, int type)
float	Map2D_getValue (Map2D *map, Peak2i peak)
void	Peak2i_fprintlnWithMapValue (FILE *fp, Peak2i peak, Map2D *map)
void	Peak2i_fprintlnWithMapValues (FILE *fp, Peak2i peak, Map2D *map)
void	Peak2iArray_fprintWithMapValues (FILE *fp, Peak2i *peaks, int start, int stop, Map2D *map)
void	Peak2iArray_fprintWithMapValue (FILE *fp, Peak2i *peaks, int start, int stop, struct Map2D *map)
int	Map2D_getIndexFromScan (Map2D *map, int scan)
int	Map2D_getIndexFromMassBin (Map2D *map, int bin)
int	Map2D_getIndexFromRT (Map2D *map, float RT)
int	Map2D_getIndexFromMOZ (Map2D *map, float MOZ)
int	Map2D_getScanFromIndex (Map2D *map, int index)
int	Map2D_getMassBinFromIndex (Map2D *map, int binIndex)
float	Map2D_getFloatScanFromIndex (Map2D *map, int scanIndex)
float	Map2D_getFloatMassBinFromIndex (Map2D *map, int binIndex)
float	Map2D_getRTFromScan (Map2D *map, int scanNumber)
float	Map2D_getMOZFromMassBin (Map2D *map, int binNumber)
float	Map2D_getRTFromIndex (Map2D *map, int scanIndex)
float	Map2D_getMOZFromIndex (Map2D *map, int binIndex)
int	Map2D_findHighestIntensityScan (Map2D *map)
void	Map2D_findMinMax (Map2D *map, float *max, float *min)
void	Map2D_findMinMaxMultiple (Experiment *expmnt, char *szSession, char *type, float *max, float *min)
int *	Map2D_getHistogramMultiple (Experiment *expmnt, char *szSession, char *type, float max, int *nbins)
int *	Map2D_getHistogram (Map2D *map, float max, int *nBinSize, int *nbins)
int	Map2D_getNumberOfSegmentsMultiple (Experiment *expmnt, char *szSessionName)
Segment *	Map2D_getSegmentArray (Map2D *map, int nMode, int *nSegment)
void	Map2D_saveRawInfo (char *szPath, char *szMap2D, Map2D *map)
int	Map2D_isPeakInMap (Map2D *map, int scan, int bin)
float *	Map2D_collapseToTIC (Map2D *map, int *nSize)
int	Map2D_alignMaps (Map2D *map1, Map2D *map2)
void	Map2D_trimEdges (Map2D *map, float value)
void	Map2D_eliminateNegativeValues (Map2D *map)
void	Map2D_tile (Map2D *map, float mz_width)
void	Map2D_tileUsingSize (Map2D *map, float tile_size)
int	Map2D_getNumberOfTiles (Experiment *expmnt, char *szSession)
int	Map2D_aIsText (char *filename)
int	Map2D_pIsText (char *path, char *mapname, char *type)
int	Map2D_snIsText (Experiment *expmnt, char *szSession, char *szName)
Peak3iif *	Map2D_getPeak3iifArray (Map2D *MAP, int *npeaks, int type)
char *	Map2D_getFullHeaderName (Experiment *expmnt, char *szSession, char *type)
int	Map2D_deconvolveUsingWienerFilter (Map2D *pMap, float dSD, int nDimension, int signal_scan, int noisy_scan)
int	Map2D_deconvolve (Map2D *pMap, float dSD, int nDimension)
int	Map2D_getStatFromMassChrm (Map2D *map, int index_type, void *index_value, DescriptiveStatistics *stat)
int	Map2D_getStatFromMassSpec (Map2D *map, int index_type, void *index_value, DescriptiveStatistics *stat)
int	Map2D_loadMS2Data (Map2D *map, Experiment *ms2_expmnt)
DescriptiveStatistics	Stat_getDescriptiveStatForMap2D (Map2D *map)
DescriptiveStatistics	Stat_getDescriptiveStatForSubMap2D (Map2D *map, Rectangle4i *rect)
float	Stat_getMedianForMap2D (Map2D *map, int mode)
float	Stat_getMeanForMap2D (Map2D *map, int mode)
float	Stat_getAvgAbsDevFromValueForMap2D (Map2D *map, float median, int mode)
float	Stat_getMedianAbsDevFromValueForMap2D (Map2D *map, float median, int mode)
float	Stat_getSDForMap2D (Map2D *map, float mean, int mode)
int	Map2D_isMassSpecSignalConstant (Map2D *map, int index_type, void *index_value)
BaselineMark	Map2D_getBaselineForPeak (Map2D *map, Peak2i *peak, int dimension)
BaselineMark *	Map2D_getBaselineForPeak2iArray (Map2D *map, Peak2i *peakarray, int nsize, int dimension)
void	Map2D_getPeakEndsInRT (Map2D *map, int scan, int bin, int *left, int *right)
DescriptiveStatistics	Stat_getDescriptiveStatForMap2DNonZero (Map2D *map)
Variables
float	MAP2D_MAX_SIZE_IN_POINTS

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Detailed Description

Author:

Kyriacos C. Leptos

Date:

2004-05-04

A file that has the definitions of Map2D

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Function Documentation

void Map2D_initHeader (  Map2D *  map  )

Initializing the header of data structure map. That means it initializes all fields apart from allocating memory for the abundance matrix. Parameters: map

void Map2D_malloc (  Map2D *  map, int  no_of_scans, int  no_of_bins )

Allocating memory for abundance matrix based on the values of no_of_scans and no_of_bins Parameters: map  pointer to the map2D no_of_scans  no_of_bins

void Map2D_mallocAbundanceMatrix (  Map2D *  map  )

Allocating memory for abundance matrix based on the values of map->dim.SCAN_SIZE and map->dim.BIN_SIZE Parameters: map

void Map2D_mallocDim (  Map2D *  map, Dimensions2i  dim )

Allocating memory for abundance matrix based on the values of dim.SCAN_SIZE and dim.BIN_SIZE Parameters: map  dim

void Map2D_mallocScanArray (  Map2D *  map  )

Parameters: map

Map2D* Map2D_new (   )

Allocating memory to a Map2D pointer Returns: a pointer to the structure Map2D

void Map2D_setHeader (  Map2D *  map, Experiment *  expmnt, Rectangle4i  rect )

Sets the map header's borders and dimensions. It also sets experiment and sampling array.information Parameters: map  expmnt  rect

DescriptiveStatistics Stat_getDescriptiveStatForMap2D (  Map2D *  map  )

Parameters: map  the map to be used in the analysis Returns: returns a structure of Descriptive Statistics

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