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noisedetect.c File Reference

contains functions to find multi-lane noise More...

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "noisedetect.h"

Functions

PIX * pixGraySubtract (PIX *pix1, PIX *pix2)
 gray scale subtract two 8 bit pixs, negative values are set to 0
PIX * subtractBG (PIX *pixIn, int morphElement, int Verbose)
 subtract background extracted with open operation
PIX * extractFG (PIX *pixIn, int morphElement, int Verbose)
 extract fore ground with a closing operation
float averageLaneSpacing (float **PeakPosition, struct GelInfo *GelInfo)
 calculate average lane spacing over gel given a set of peak positions
PIX * pickBadPoints (PIX *pixNoise, PIX *pixFG, float noise_to_FG_ratio, int min_FG, int laneWidth, int Verbose)
 returns 8 bit pix with 255's labelled at points with noise galaxy content
void extractLanes (PIX *pixIn, float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo, int **values)
void detectNoise (PIX *pixIn, float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, int *noisePresent, int Verbose)
 count the number of lanes with noise galaxy present
int countMaxConsec (int *noise, int nlanes, float cutoff)
 counts the maximum span of values over a cutoff


Detailed Description

contains functions to find multi-lane noise


Function Documentation

float averageLaneSpacing float **  PeakPosition,
struct GelInfo GelInfo
 

calculate average lane spacing over gel given a set of peak positions

Parameters:
PeakPosition holds y position for all nodes
GelInfo holds various gel parameters

int countMaxConsec int *  noise,
int  nlanes,
float  cutoff
 

counts the maximum span of values over a cutoff

Parameters:
noise array of values
nlanes size of array
cutoff cutoff to use
Returns:
the maximum number of consecutive values over the cutoff

void detectNoise PIX *  pixIn,
float **  PeakPosition,
float *  NodePosition,
struct GelInfo GelInfo,
struct AnaCutoff AnaCutoff,
int *  noisePresent,
int  Verbose
 

count the number of lanes with noise galaxy present

Parameters:
pixIn pix of the gel on which noise is to be detected
PeakPosition holds y position of all nodes
NodePosition holds x position of nodes in each zone
GelInfo holds various gel parameters
AnaCutoff holds various analysis cutoff
noisePresent array to store amount of noisy pixels is found in the center of each lane
Verbose turn on text output to screen

PIX* extractFG PIX *  pixIn,
int  morphElement,
int  Verbose
 

extract fore ground with a closing operation

Parameters:
pixIn input pix
morphElement size of the structural element used for closing for foreground extraction
Verbose turns on text output
Returns:
foreground pix

void extractLanes PIX *  pixIn,
float **  PeakPosition,
float *  NodePosition,
struct GelInfo GelInfo,
int **  values
 

brief extract a center of lane for every lane from an image

Parameters:
pixIn pix to extract from
PeakPosition holds y position of all nodes
NodePosition holds x position of nodes in each zone
GelInfo holds various gel parameters
values 2D array where results are returned

PIX* pickBadPoints PIX *  pixNoise,
PIX *  pixFG,
float  noise_to_FG_ratio,
int  min_FG,
int  laneWidth,
int  Verbose
 

returns 8 bit pix with 255's labelled at points with noise galaxy content

Parameters:
pixNoise pix of image with bands removed, leaving only large noise patches
pixFG pix of foreground (closed image)
noise_to_FG_ratio minimum noise to FG ratio for a point to be labelled as having noise
min_FG minimum foreground intensity for a the noise to FG ratio to be valid
laneWidth the width of a lane
Verbose turn on text output to screen
Returns:
pix with 255 highlighting where the noise is located on a gel

PIX* pixGraySubtract PIX *  pix1,
PIX *  pix2
 

gray scale subtract two 8 bit pixs, negative values are set to 0

Parameters:
pix1 pix to subtract from
pix2 pix to subtract with
Returns:
pix of the difference

PIX* subtractBG PIX *  pixIn,
int  morphElement,
int  Verbose
 

subtract background extracted with open operation

Parameters:
pixIn input pix
morphElement size of the structural element used for opening for background extraction
Verbose turns on text output
Returns:
background subtracted pix


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