#include "allheaders.h"
#include "gelinfo.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 | TOLERANCEFACTOR 3.0 |
factor used to determine the maximum difference between a peak and template in a match | |
#define | MAXCURVATUREFACTOR 1.6 |
factor used to determine the maximum allowed curvature of a node | |
Functions | |
int | findPeakPosition (FILE *FLAGOUT_FILE, float **PeakPosition, INT32 **ZoneProjection, struct GelInfo *GelInfo, float *Spacing, float minpsizefactor, int Markerinc, int Verbose) |
Find peaks in ZoneProjections and match with nodes by closest distance to the template. | |
void | writeCurvature (FILE *FLAGOUT_FILE, float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo) |
calculates curvature of a set of peak position and node position for all lanes and all zones | |
int | correctOutlierPeaks (float **PeakPosition, float *NodePosition, struct GelInfo *GelInfo, int Verbose) |
finds nodes showing high curvature and correct for them by forcing them to be in a straight line with their neighbours in neighbouring zones | |
void | smoothPeaks (float **PeakPosition, struct GelInfo *GelInfo, int Verbose) |
compare each peak with the mean position of all other nodes in the lane and smooth the overall results by applying a 3 lane x 3 zones median filters to these differences | |
void | fillEmpties (float *PeakPosition, struct GelInfo *GelInfo) |
interpolate for any unplaced nodes (peak position == 0) |
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factor used to estimate the width of a peak based on generic spacing
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sigma value used for peak finding
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finds nodes showing high curvature and correct for them by forcing them to be in a straight line with their neighbours in neighbouring zones
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interpolate for any unplaced nodes (peak position == 0)
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Find peaks in ZoneProjections and match with nodes by closest distance to the template. unmatch nodes are interpolated, which are marked using negative numbers
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compare each peak with the mean position of all other nodes in the lane and smooth the overall results by applying a 3 lane x 3 zones median filters to these differences
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calculates curvature of a set of peak position and node position for all lanes and all zones
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