Accession file input file format mode set by the command line switch
-accessionDB:accession.txt or
-accessionDB:accession.xml
This then gets mapped to either FileIO.IO_FORMAT_XML or
IO_FORMAT_TAB_DELIMITED.
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[].
dbugPixNxNcode() - print window of size (n X n) of current char[] picture
if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of
[dbx1:dbx2, dby1:dby2] to ssfFD.
drawBoundariesForSpots() - If generating the segmented spot image
in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set,
draw a white boundary around each spot in the 'O'riginal or segmented
'Z' image (-DRAWSPOTS:BO default).
drawBoundariesForSpots() - If generating the segmented spot image
in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set,
draw a white boundary around each spot in the 'O'riginal or segmented
'Z' image (-DRAWSPOTS:BO default).
drawDotsInSpots() - If generating the segmented spot image
in pix5, and the -drawDots, -drawPlus, -drawBoundary, -drawMinEnclRect,
or -drawSxSyEllipse switch was set, then
draw a color dot or plus in the center of each spot.
drawOverLays() - paint the scrollable image canvas which includes
the image, optional ROI's, overlay spots, optional histogram
that is repainted in another class.
drawTextInPix() - Display the string 'str' starting at (x0,y0) in
specified 'gray' value in either of two charcter sizes 4x6
(upper case only: font=0); or 5x7 (upper/lower case: font=1)
and a 'zoom' factor of 1X (default) to 64X.
drawTextInPix() - Display the string 'str' starting at (x0,y0) in
specified 'gray' value in either of two charcter sizes 4x6
(upper case only: font=0); or 5x7 (upper/lower case: font=1)
and a 'zoom' factor of 1X (default) to 64X.
dumpCCppx() - debugging tool to dump the CC image in gellab/tmp file
with name: "CCfile-nnn-tag" + pixFileExtn
where 'nnn' is the current iteration # incremented if incNflag is set
and 'tag' is a short string.
fillCorners() - fill corners such that the central pixel (C) is
in [2:MAX_CC_CODE] and the 4-ngh pixels (N) are cc+PCC_BASE_CODE
and the diagonal (E) to be filled is either BKGRD_CODE (i.e., 0),
or KILL_SPOT_CODE, or ISOLATED_PIXEL_CODE in the central core image.
findAllSpots() - Find and segment all the spots in the image marking
both the various images central-core and propagated-central-core
and output image as well as computing the features which are
saved in the next spot record.
findSpot() - Given a new spot pixel (x,y,ccLookForCode) find all
(x,y) pairs that are 4-neighbor connected to this spot with central
core pixel ccLookForCode.
itemStateChanged() - handle item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and CheckboxMenuItems.
itemStateChanged() - handle item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and CheckboxMenuItems.
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).
maxPropagate() - Do 4-neighbor propagation of all CC's in Final
Blob List to to PCCs to fill in any concavities on the edge of the
spot so the spot is round as would be expected.
Project directory that is either userDir, specified
by -projDir:{path}, or extracted from the input file
path it the image is in a "/ppx/" subdirectory.
propSaturatedSpots() - propagate saturated spots using the histogram
glbPercentThr of the MAX g in 'gHist[0:maxGrayPixel]' generated in
the averagePix() of the averaged gel data.
propSpotTo2ndDrivMaxima() - Propagate the value CC+PCC_BASE_CODE
in the central core image (with pixel value CC) from (x1,y1)
using (dx,dy) as the propagated central core image starting
position until either see a UNLABELED_CC_CODE (i.e.
rmvConcavities() - Remove UNLABELED_CC_CODE's concavities of the
central core image by searching for the following pattern
(in four 90-degree combinations) and replacing it with another pattern.
setupC13x13Gaussian() - create the 2D Gaussian convolution matrix
Sg2glb.{cxy} of the ellipse or circle (depending on which G13(x,y) macro
is used below).
Setupc13x17gaussian() - create the 2D Gaussian convolution matrix
Sg2glb.{cxy} of the ellipse or circle (depending on which G13(x,y) macro
is used below).
setupDemo2Kx2KSwitches() - setup "demo/ppx/testGel-2Kx2K.gif" for
special debug image "demo/ppx/testGel-2Kx2K.gif" which is a
2000x2000 pixel 8-bit/pixel image with some saturated spots.
setupDemo3Kx3KSwitches() - setup "demo/ppx/testGel-3Kx3K.gif" for
special debug image "demo/ppx/testGel-3Kx3K.gif" which is a
3100x3100 pixel 8-bit/pixel image with some saturated spots.
setupDemo_2DLCMS_Switches() - setup "demo/ppx/2D-LC-MS-01.gif" for
special debug image that is a 868x612 pixel 8-bit/pixel image
with some saturated spots.
Class sg2data splits large saturated or near saturated spots
by Boundary, Run-Projection-Map (boundary) or Threshold methods for the
2D gel spot segmenter.