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trunk Directory Reference


Files

file  anacutoff.h
 defines a struct to hold cutoffs and constants for the program, and define their default values as well.
file  asymmetry.c
 contains function to calculate, sort and evaluate the asymmetry score in each lane
file  asymmetry.h
 header file for asymmetry.c, contains functions for calculating and evaluating the asymmetry in each lane
file  border.c
 contains function to find the outer most lanes by first finding the outer most marker lanes.
file  border.h
 header file for border.c, contains function to find the outer most lanes by first finding the outer most marker lanes.
file  checknogrowths.c
 contains functions to extract the median row for each lane and outputs the thresholded roughness and maxdiff to a file
file  checknogrowths.h
 header file for checknogrowths.c, contains functions to extract the median row for each lane and outputs the thresholded roughness and maxdiff to a file
file  checkresult.c
file  checkresult.h
file  diagnostic.c
 contains function to write a PNG of the gel with node and peak position information overlaid. Interpolated peaks are shown in red for diagnostic purposes
file  diagnostic.h
 header file for diagnostic.c, contains function to write a PNG of the gel with node and peak position information overlaid. Interpolated peaks are shown in red for diagnostic purposes
file  fftw3.h
file  findlanes.c
 file holding the main for findlanes
file  findlanes.h
 header file for findlanes.c holds the default gel parameters
file  gelinfo.h
file  mapto8bits.c
 contains functino to map a 16 bit image to 8 bit and stretches its dymanic range to be full scale
file  mapto8bits.h
 header file for mapto8bits.c, maps a 16 bit image to 8 bit and stretches its dymanic range to be full scale
file  medianfilter.c
 implements a 3x3 then 1x9 median filter for a PIX
file  medianfilter.h
 header file for medianfilter.c, implements a 3x3 then 1x9 median filter for a PIX
file  node.c
 implements functions for extrapolating nodes to the edge, adjusting the boundary nodes, and writing lanes information to file
file  node.h
 header file for node.c, implements functions for extrapolating nodes to the edge, adjusting the boundary nodes, and writing lanes information to file
file  noisedetect.c
 contains functions to find multi-lane noise
file  noisedetect.h
 header file for noisedetect.c, contains functions to find multi-lane noise
file  peaks.c
 contains function for finding guassian-like peaks in a vector of intensity
file  peaks.h
 header file for peak.c, contains function for finding guassian-like peaks in a vector of intensity
file  position.c
 contains functions for peak matching and curvature calculations and output
file  position.h
 header file for position.c, contains functions for peak matching and curvature calculations and output
file  readlanes.c
 read and parse lanes file in gel directory for node and peak positions for generation of traces16 without re-lanetracking
file  readlanes.h
 header file for readlanes.h, read and parse lanes file in gel directory for node and peak positions for generation of traces16 without re-lanetracking
file  readtiff.c
 holds function to read in 16bit tiff file (image.tif)
file  readtiff.h
 header file for readtiff.c, holds function to read in 16bit tiff file (image.tif)
file  spacing.c
 contains algorithm for finding the dominant lane spacing in the gel as well as the dominant spacing of each zone
file  spacing.h
 header file for spacing.c, contains algorithm for finding the dominant lane spacing in the gel as well as the dominant spacing of each zone
file  toneadjust.c
 holds functions for tone mapping for contrast enhancement using a bezier curve
file  toneadjust.h
 header file for toneadjust.c, has function for tone mapping for contrast enhancement using a bezier curve
file  traces16.c
 contains function to write lane straightened image to traces16 file
file  traces16.h
 header file for traces16.c, contains function to write lane straightened image to traces16 file
file  zone.c
 contains functions related to the initialization operations of zone boundary, nodes, and zoneprojection
file  zone.h
 header file for zone.c, contains functions related to the initialization operations of zone boundary, nodes, and zoneprojection

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