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border.h File Reference

header file for border.c, contains function to find the outer most lanes by first finding the outer most marker lanes. More...

#include "allheaders.h"
#include "gelinfo.h"
#include "anacutoff.h"

Go to the source code of this file.

Defines

#define SIGMA_CUTOFF   4
 sigma value used for peak finding
#define FWHM_FACTOR   5.0/9.0
 factor used to estimate the width of a peak based on generic spacing
#define ZONE_PROJECTION_FACTOR   3
 determines the number of zones to include in border finding
#define BORDERTOLERANCEFACTOR   0.4
 factor used to calculate the tolerance we allow from the expected spacing between lanes
#define OFFSETFACTOR   40
 factor used to determine along lane (x) offset allowed for correlation calculation

Functions

void findBorder (FILE *FLAGOUT_FILE, PIX *pixGel, INT32 **ZoneProjection, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, int *ToneAdjusted, int Verbose)
 finds the outer most lanes by extrapolating from the outermost marker lanes.
float correlation (PIX *pixGel, int row1, int row2, int start, int stop, int maxoffset)
float roughness (PIX *pixGel, int row, int start, int stop)
 calculates a roughness measure in a row in a PIX, defined as the sum of the absolute difference between neighbouring points normalized by the dynamic range of the pix


Detailed Description

header file for border.c, contains function to find the outer most lanes by first finding the outer most marker lanes.

These are tested for similary and roughness before accepted. Correlation and roughness code are also found here, which is also used for result checking.


Define Documentation

#define FWHM_FACTOR   5.0/9.0
 

factor used to estimate the width of a peak based on generic spacing

See also:
specFindPeak()

#define OFFSETFACTOR   40
 

factor used to determine along lane (x) offset allowed for correlation calculation

See also:
correlation()

#define SIGMA_CUTOFF   4
 

sigma value used for peak finding

See also:
specFindPeak()


Function Documentation

float correlation PIX *  pixGel,
int  row1,
int  row2,
int  start,
int  stop,
int  maxoffset
 

brief calculates the uncentered correlation between two rows in a PIX while allowing for a offset.

Parameters:
pixGel pix representation of the gel image
row1 the y position of the first row to be compared
row2 the y position of the second row to be compared
start the leftmost column included in the comparison
stop the rightmost column included in the comparison
maxoffset the maximum offset allowed between the two rows
Returns:
the uncentered correlation between the two specified vectors

void findBorder FILE *  FLAGOUT_FILE,
PIX *  pixGel,
INT32 **  ZoneProjection,
struct GelInfo GelInfo,
struct AnaCutoff AnaCutoff,
int *  ToneAdjusted,
int  Verbose
 

finds the outer most lanes by extrapolating from the outermost marker lanes.

Using the generic spacing, we estimate the distance between the outermost markers. A number of the first zones after the first data zone is chosen. Tone adjusted zones are not included, unless all zones considered have been tone adjusted From the sum of zone projection of these zones, we find two peaks close to the estimated distance apart. The data in these two rows are check for correlation with each other (with translational offset allowed) and with their respective neighbour marker lanes. The data is also checked for roughness. The results will be stored in GelInfo->LowYBorder and GelInfo->HighYBorder

Parameters:
FLAGOUT_FILE writable file handle to data dump
pixGel pix representation of the gel image
ZoneProjection points to 1D y-projection in each of the zone
GelInfo holds various gel parameters
AnaCutoff holds various analysis cutoff
ToneAdjusted a vector stating if a zone has been tone adjusted
Verbose turn on text output to screen

float roughness PIX *  pixGel,
int  row,
int  start,
int  stop
 

calculates a roughness measure in a row in a PIX, defined as the sum of the absolute difference between neighbouring points normalized by the dynamic range of the pix

Parameters:
pixGel pix representation of the gel image
row the row to be measured
start the leftmost column included in the measure
stop the rightmost column included in the measure
Returns:
the roughness measure


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