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java.lang.Object Seg2Dgel.Sg2glb Seg2Dgel.Sg2data
public class Sg2data
Class sg2data splits large saturated or near saturated spots by Boundary, Run-Projection-Map (boundary) or Threshold methods for the 2D gel spot segmenter.
This code was derived and refactored from GELLAB-II sg2gii C language files.
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.
Field Summary | |
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private static int |
areaTot
working area total |
private static float |
densTot
total spot density NOT corrected for background |
private static float |
dMax
Maximum pixel OD density within a spot |
private static float |
dMin
Minimum pixel OD density within a spot |
private static boolean |
FPU_ROUNDS
should be removed later... |
static DbBoundary |
spotDbugBnd
holds spot boundary as well as current debugging boundary for -DRAWSPOT:B. |
private static float |
sXsYRatio
Estimate of spot shape (r.sx/r.sy) if r.sy!=0 |
Constructor Summary | |
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Sg2data()
Sg2data() - Constructor |
Method Summary | |
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boolean |
calcFeaturesAndNewSpot()
calcFeaturesAndNewSpot() - Compute the features of the current spot in the Final Blob List and save the values in global variables and create a new spot in the spotList[]. |
boolean |
lookupMeanBackgroundForAllSpots()
lookupMeanBackgroundForAllSpots() - if using background correction, then lookup the mean background for each spot at its centroid in the mean background image (pix6), then map it through the and save the results for all spots r as (r.mnBkgrdGrayvalue, r.mnBackground). |
private int |
okAreaDensityDensRange()
okAreaDensityDensRange() - test area, density and density range features in the global variables areaTot, densTot, dMax-dMin against the thresholds. |
boolean |
removeInvalidSpots()
removeInvalidSpots() - remove invalid spots from the pix5 output image |
static boolean |
writeEntireSSF()
writeEntireSSF() - write the entire SSF file. |
Methods inherited from class Seg2Dgel.Sg2glb |
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get2D, get2D, getPixLineBuf, getPixLineBuf, initGlb, isDBwindow, isDBwindow, put2Dbuf, resetGlb, set2D, set2D, setPixLineBuf, setPixLineBuf, showReportStatus |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private static final boolean FPU_ROUNDS
private static int areaTot
private static float densTot
private static float dMax
private static float dMin
private static float sXsYRatio
public static DbBoundary spotDbugBnd
Constructor Detail |
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public Sg2data()
Method Detail |
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public boolean calcFeaturesAndNewSpot()
private int okAreaDensityDensRange()
areaTot range is [t1Area : t2Area] densTot range is [t1Density : t2Density] (dMax-dMin) range is [t1Range : t2Range] (if using OD calibration)
public boolean removeInvalidSpots()
public boolean lookupMeanBackgroundForAllSpots()
public static boolean writeEntireSSF()
bannerTitle
- is optional title to put into output file header if
not null.swList
- is optional list of program switches used by the
SSF generating program if not null.projDir
- is optional project directory if not null.ssfOutputFile
- is the SSF output format mode
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