This describes the revision history of the Seg2Dgel program of
released or soon to be released versions. Generally, only the most
recent versions are kept on the Web site (see Version). Documentation for
unresolved bugs and requested functionality is found in the status Web page.
V.0.5.11 11-07-2005: Changed installer paradigm to use
launch4j. Also, new manifest for
Seg2Dgel.jar file that now includes the Class-Path so the demo .bat
and .sh scripts were simplified in this release. The (Edit menu |
Resize memory limits) command was depricated - see
Increasing or decreasing the
allowable memory used by Seg2Dgel in the Reference manual.
V.0.5.10 05-11-2005: Rebuilt after refactored
O2Plibrary.
V.0.5.9 04-20-2005: Fixed bugs in library and
synchronized with O2Plibrary.
V.0.5.7 03-21-2005: Fixed bug in -usage and -version
switches. Changed SSF output files so it generates
<sample-name>-SSL.xml rather than <sample-name>.xml.
V.0.5.4 01-19-2005: Fixed bug that failed for
some combinations of segmenting a new image if the prior image
used the -accessionDB option.
V.0.5.3 01-18-2005: Changed the Image Viewer so it
now has a zoom function (1X, 2X, 3X, or 4X). Fixed bug histogram
display. Fixed bug when switch input images. Changed menu. Now
you must specify (in -gui mode) changes in the Edit Options popup
rather than from the File menu.
V.0.4.7 12-08-2004: Cleanup and using new O2Plib
methods.
V.0.4.5 11-29-2004: Updated and edited documentation in
Reference Manual.
V.0.4.5 11-23-2004: Added documentation in Reference
Manual to show how to
segmenter under batch processing with either Windows or Unix.
V.0.4.5 11-22-2004: Fixed bug with histogram display.
Cleanup and refactored code so uses new O2Plib methods. Added new switch
-dtd (default is -nodtd) to add (omit) Open2Dprot-SSF.dtd
when generate the SSF files.
V.0.4.4 11-09-2004: Cleanup and refactored code into
O2Plib. Fixed histogram problem when used with data filtering that
was introduced when went to the O2Plib. Removed cal/ calibration
directory. Added consistent O2Plib project subdirectory code
to test and create (batch/ cache/ ppx/ rdbms/ tmp/ and xml/)
subdirectories.
V.0.4.3 11-03-2004: Fixed a bug where it would not write
out images that were not square (introduced with new library). Fixed a
few other minor bugs. Added ImageViewer (View |Show spot
numbers) as an image overlay and (Histogram | Sx/Sy ratio)
histogram filter.
V.0.4.1 11-01-2004: Added new
-laplacian:{H|V},{height},{width} line filter switch for
locating flat Horizontal or Vertical spots more easily. Also changed
some switch names for consistency as well as other cleanup. Added
switches -thrSxSyRatio:{s1,s2} switch to do additional spot
thresholding by the ratio of the density-weighted spot sizes Sx and
Sy, Sx/Sy. This is useful for better separating flat horizontal or
vertical spots. Added switches -drawMinEnclRect:{P|O} switch to
draw minimum enclosing rectangle spot overlays.
V.0.3.3 10-21-2004: Problem with zoom code. Was
sometimes not accessing correct image in Image Viewer after
segmentation. Stepped back and disabled zoom code (left it in the
code) until the zoom functionality is finished.
V.0.3.1 10-13-2004: Moved code from Seg2Dgel and other
applications into the new Open2Dprot common library O2Plib.
V.0.2.5 08-25-2004: enabled the command line processing
using the Seg2Dgel.exe file for running it in batch. Run the command
with "-nodemo" and other switches you need as well as the gel image
or gel sample name (if using the -accession file option). A new switch
-default was added to give you the -demo options but with -nogui and
with no gel name.
V.0.2.3 08-10-2004: Enabled the
-accessionDB:accession file option. If a gel is not in the
accession file, then (currently) use the -demo defaults and continue
processing.
V.0.2.2 08-10-2004: Changed accession database input
file format so that the sample name is now "Sample" instead of
"PubPixFileName".
V.0.1.3 08-1-2004: Changed (Gel Segmentation File, GSF,
.gsf) to (Sample Spot-list File, SSF, .ssf) to be compatible with the
rest of Open2Dprot. NOTE: Version V.0.1.X is NOT compatible with
Version 0.0.XX. You must download a new version of the installer. The
(File | Update from Web server | *) will not do the full
update.
V.0.0.25 07-28-2004: Change some of the tab-delimited
(-gsfFormat:F) GSF Epilogue section to more descriptive correct
symbols.
V.0.0.24 07-27-2004: Change some of the XML
(-gsfFormat:X) GSF Epilogue section to more descriptive correct
symbols.
V.0.0.22 07-06-2004: Refactored code and fixed bug in
-gsfFormat:F option.
V.0.0.21 07-06-2004: Added support code for -accessionDB
switch (working but disabled for now).
V.0.0.20 07-02-2004: Added support code (disabled for
now) for -accessionDB switch.
V.0.0.18 06-10-2004: Fixed bug with
-laplacian:B,P,gridSize - however the -laplacian:B,C,gridSize is not
working. Fixed bug with Options wizard window so now the text fields
and the pulldown choices are synchronized.
V.0.0.17 06-10-2004: Optimized memory some more. Now
draw interpolation lines in horizontal and vertical slices so it is
easier to see. Added spot finder abort on ill-formed spots if the size
of the central core is > the upper area sizing threshold. This helps
avoid hanging up the segmenter on impossible spots that may be created
if the gel image is saturated in regions. Saturation, results in the
laplacian not being accurate with the result that spots might be
merged together. This will result in some spots missed and bogus spots
being formed from the remnants of these aborted spots. However, the
real problem is that the spot images are saturated. Other algorithms
could be added (such as the -splitSpot that is being debugged) to deal
with this problem. Garbage in - garbage out.
V.0.0.16 06-09-2004: Optimized memory some more. Fixed
ImageViewer list of images when switched paradigm in Version V.0.0.14.
V.0.0.15 06-08-2004: Cleanup.
V.0.0.14 06-07-2004: Added ability to add/remove the
histogram display in the Image Viewer (when in -gui mode). The
"-histGUI" ("-nohistGUI) switch can be used to add (remove) it from
the command line. The (View | Add histogram to Image Viewer)
checkbox menu command or the popup options wizard window can also be
used to change it.
V.0.0.12 06-04-2004: Added pull-down menus to Image
Viewer window. Added a histogram display in the Image Viewer. This may
be useful for setting the threshold parameters. The user may select a
feature from a list including image density under the region of
interest (ROI) as well as spot features (area, mean background
density/spot, mean spot density/spot, total spot density, total spot
D', minD/spot, maxD/spot, spot density range (maxD - minD)). Also
added horizontal or vertical image line slice histograms (i.e., image
slices). You can do rudimentary spot data filtering (if enabled in the
Histogram menu of the Image Viewer) where spots passing the selected
histogram-bin filter are indicated in the image. If filtering is
enabled, you click on a bin in the histogram and the filter will show
spots (with a cyan "+") GEQ or LEQ the bin value you selected.
V.0.0.9 05-05-2004: Fixed bug where Option Window would
lockup if you used it more 2 times in a row. Added ability to modify
the Region of Interest by redefining it for the (-cw, -pixdump, and
-debug regions). Note: in the Image Viewer first select the ROI as
either CW, -dbug ROI, or -pixdump ROI. Then click on the upper
left-hand corner of the new region and type Control-U. Then click on
the upper lower left-hand corner of the new region and type Control-L.
This will then redefine the selected ROI and use it the next time you
run the segmenter from the Report Window.
V.0.0.8 05-05-2004: The -gsfFormat:mode options have
been refined so that Full tab-delimited mode packages the
tab-delimited spot list within searchable delimiters strings
###START-OF-SPOTLIST### and ###END-OF-SPOTLIST###. It includes the
preface (gel accession and parameters data) and an epilog (statistics
on spots segmented). The Options Window has been refactored so that it
now has explicit choices for switches like -gsfFormat:{F |
G | T | X}, and the
-projDir:directory-path and
-propertiesFile:alternate-properties-file.
V.0.0.7 05-02-2004: It can now generate XML with an
internal DTD. Added a (View menu | Show GSF report) to look at the
generated GSF file in the Report Window. Added a (View menu | Show GSF
browser) to look at the generated GSF file in a popup browser. Changed
the -gsfFormat:mode options so that they are now {F | G
| T | X}. They define the output format for the Gel
Segmentation File (GSF) where mode is: 'F' for full tab-delimited
(default .txt), 'G' for GELLAB-II (.gsf), 'T' for tab-delimited (.txt)
spots-only, and 'X' for XML (.xml). (Default is -gsfFormat:X).
V.0.0.6 04-29-2004: Moved the local documentation files
to the Web site so that all documentation now comes from the Web site
where it is easier to update. Various cleanups including adding
-ccMinSize:nbrPixels and -saturateSpots:percentThreshold
options threshold sliders to the Option Window.
V.0.0.5 04-27-2004: This version will handle moderate
resolution TIFF, JPEG, GIF images. The DBUG_TEST_IMAGE option is
enabled in this release which means it will reset the switches to a
known state and ignore the Seg2Dgel.properties file for now. You must
explicitly change the options using the (Edit menu | Options | Edit
Options) or press the Edit options button to change options for
now. Not all options work. See the Status
page for more details.