Main Page | Data Structures | File List | Data Fields | Globals

findlanes.h File Reference

header file for findlanes.c holds the default gel parameters More...

#include "allheaders.h"
#include "gelinfo.h"
#include "anacutoff.h"
#include "readtiff.h"
#include "mapto8bits.h"
#include "medianfilter.h"
#include "zone.h"
#include "toneadjust.h"
#include "spacing.h"
#include "readlanes.h"
#include "position.h"
#include "diagnostic.h"
#include "border.h"
#include "node.h"
#include "checkresult.h"
#include "checknogrowths.h"
#include "noisedetect.h"

Go to the source code of this file.

Defines

#define DEFAULT_NLANES   121
 default number of expected lanes in the gel
#define DEFAULT_MARKERPERIOD   5
 default marker period of the gel
#define DEFAULT_MARKEROFFSET   0
 location of first marker lane
#define DEFAULT_LASTMARKEROFFSET   0
 distance from last marker to last lane
#define DEFAULT_NZONES   10
 default number of zones used for lane tracking
#define DEFAULT_SIZEFACTOR   10
 default factor which determines how big the structural element is for closing
#define DEFAULT_WELL_EDGE   0
 default position of the well edge (0=left, 1=top, 2=right, 3=bottom
#define DEFAULT_GELSPANFACTOR   0.75
 default fraction of the image that a gel is expected to take up
#define DEFAULT_GELNAME   "image.tif"
 default name of the image file
#define DEFAULT_PROJECTDIR   "."
 default project directory
#define DEFAULT_MINPSIZEFACTOR   0.0
 default minimum psize factor below which is peak is not accepted.
#define DEFAULT_FLAGOUT_NAME   "LR_data.out"
 dault name of the file to be used as a data dump
#define DEFAULT_ERROROUT_NAME   "LR_error.out"
 default name of the file to store error comment(s)
#define DEFAULT_NOGROW_NAME   "LR_no_grow.out"
 dault name of the file to store no grow detection results
#define DEFAULT_TRACES_NAME   "traces16_auto"
 default name for traces16 file
#define DEFAULT_LANES_NAME   "lanes"
 default names for output lanes file
#define DEFAULT_IN_LANES_NAME   "lanes"
 default names for input lanes file
#define DEFAULT_LIMS_NAME   "LR_LIMS.out"
 default name of the file to hold gel inspection parameters

Functions

PIX * adjustTone (PIX *pixGel, INT32 **ZoneProjection, struct GelInfo *GelInfo, int *ZoneID, int *ToneAdjusted, int Verbose)
 for a given gel image tone adjust zones of low density using a point transformation with a monotonic Bezier curve


Detailed Description

header file for findlanes.c holds the default gel parameters


Function Documentation

PIX* adjustTone PIX *  pixGel,
INT32 **  ZoneProjection,
struct GelInfo GelInfo,
int *  ZoneID,
int *  ToneAdjusted,
int  Verbose
 

for a given gel image tone adjust zones of low density using a point transformation with a monotonic Bezier curve

The bezier curve is adjusted using the mean intensity of the zone

Parameters:
pixGel pix of gel image
ZoneProjection points to 1D y-projection in each of the zone, to be replaced in tone adjusted zones
GelInfo holds various gel parameters
ZoneID array noting the zone number for each column
ToneAdjusted array to note which zone has been tone adjusted
Verbose turn on text output to screen
Returns:
version of pixGel that has been toneadjusted in large zones


Generated on Fri Apr 20 16:43:06 2007 for LaneRuler by  doxygen 1.3.9.1