[ImageJ-bugs] [Bug 1242] New: We are running a batch files and seem to get the occasional zero-intensity value image when using run("RGB Color")

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1242

            Bug ID: 1242
           Summary: We are running a batch files and seem to get the
                    occasional zero-intensity value image when using
                    run("RGB Color")
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: gcolarus at ucalgary.ca
                CC: gcolarus at ucalgary.ca

We use Process-Batch-Marco:

path=File.directory+File.name;
run("Brightness/Contrast...");
setMinAndMax(500, 20000);
run("RGB Color");

The resulting files have occasional (0,0,0) files when they should be
non-black. There is no reproducibility that we can find on which files will be
written as "black." It seems to be random. We have tested this on 3 Mac laptops
(2 running El Cap and one running Yosemite with the  the El Cap running latest
version of FIJI as of today) while the Yosemite is using 1.50e. The PC seems to
be fine- no black images. 

I am sending this bug report from Yosemite 10.8.5
Please note
that we tested the same data set when trouble-shooting though it happens with
all data sets.
We also tried:
-pausing after the RGB command:
waitForUser( "Pause","Some \n Dialog"); 
-one one laptop running Yosemite, there seemed to be a correlation with slowing
down the process and better results (few black images)
-we are reading and writing directly from the computers- no external drives

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.5
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151221191554)
Fiji: http://update.fiji.sc/ (last check:20151221212403)

Files not up-to-date:
  c295a4c5 (OBSOLETE_UNINSTALLED) 20140702174714 jars/jdom-2.0.2.jar
  64241209 (OBSOLETE_UNINSTALLED) 20140702174714 jars/jdom-contrib.jar
  1ad3be0d (LOCAL_ONLY) 20140703084714 jars/jpedalSTD.jar
  d2af3ac9 (OBSOLETE_UNINSTALLED) 20140702174714 jars/kryo-2.21-shaded.jar
  e3f588d6 (LOCAL_ONLY) 20160310183321 macros/BatchMacro.ijm
  7f373f94 (LOCAL_ONLY) 20140708115900 macros/MicroTubBleachTool.txt
  77d1ae42 (LOCAL_ONLY) 20140707003705 plugins/EMBL_sampleimages-1.0.0.jar
  3960cab8 (LOCAL_ONLY) 20140708115900 plugins/MicroTubBleachTool.txt
  f84c20e3 (LOCAL_ONLY) 20140706091027 plugins/Mosaic_ToolSuite.jar
  4fe1cfd7 (LOCAL_ONLY) 20140714081951 plugins/SNR_.jar
  12f0acc6 (OBSOLETE_UNINSTALLED) 20150213222520
plugins/Threshold_Colour-2.0.1.jar
  71331805 (LOCAL_ONLY) 20160309095328 plugins/jacop_.jar
  739a58eb (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$1.class
  3595fc8b (LOCAL_ONLY) 20140706082321
plugins/mser/MSER$ConnectedComponent.class
  b0fd6d19 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$GrowHistory.class
  74ed5b1e (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$OffsetsPostions.class
  7d2d0830 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER$Parameters.class
  f42c66b1 (LOCAL_ONLY) 20140706082321 plugins/mser/MSER.class
  1b4b766b (LOCAL_ONLY) 20140706082321 plugins/mser/Region.class
  ff26cb9f (LOCAL_ONLY) 20140706082321 plugins/mser/RegionFactory.class

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