⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 1043 - (Jeff) The align rgb planes plug in does not work
(Jeff)
The align rgb planes plug in does not work
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-31 14:27 CDT by jeff.spector
Modified: 2015-04-06 11:30 CDT
4 users (show)

See Also:
Description jeff.spector 2015-03-31 14:27:58 CDT 
When I load an image and run the "align RGB planes" plugin (downloaded from your website) the text in the imageJ bar flashes very quickly (so fast I can not read it) and then nothing happens and the plugin does nothing. 
I installed the same plugin files to a "regular" imageJ and the plugin worked perfectly (I tested it using the same image) 

so something is causing it to not work when using FIJI. 
If it helps, when I run it in FIJI the align rgb planes GUI never appears...

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: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150328005348)
Fiji: http://fiji.sc/update/ (last check:20150324232333)

Files not up-to-date:
  b732dbf2 (MODIFIED) 20150213144220 Contents/Info.plist
  bdc88860 (LOCAL_ONLY) 20140611190441 jars/MultipleKymograph_.class
  6128cb23 (LOCAL_ONLY) 20140611190442 jars/MultipleOverlay_ (2).class
  07c683b2 (LOCAL_ONLY) 20140611190442 jars/StackDifference_ (2).class
  8821a474 (LOCAL_ONLY) 20140611190443 jars/WalkingAverage_ (2).class
  1ad3be0d (LOCAL_ONLY) 20131114111332 jars/jpedalSTD.jar
  8f675b7b (LOCAL_ONLY) 20080612095048 plugins/Align_RGB_planes.class
  455de238 (LOCAL_ONLY) 20141110190011 plugins/Jama-1.0.3 copy.jar
  a5d02cb7 (LOCAL_ONLY) 20140612120910 plugins/Kymo_graph1001.jar
  aa5aa145 (LOCAL_ONLY) 20140619180813 plugins/MMReader_.jar
  946ffba8 (LOCAL_ONLY) 20140611190441 plugins/MultipleKymograph_.class
  1cc35aff (LOCAL_ONLY) 20140611194446 plugins/MultipleOverlay_ (2).class
  8fb74bae (LOCAL_ONLY) 20140611190442 plugins/MultipleOverlay_class.class
  77bb5c2d (LOCAL_ONLY) 20141110083600 plugins/SpeckleLib.jar
  87786c25 (LOCAL_ONLY) 20140611194503 plugins/StackDifference_ (2).class
  98992cd2 (LOCAL_ONLY) 20140611190442 plugins/StackDifference_class.class
  d3721d57 (LOCAL_ONLY) 20140611190443 plugins/WalkingAverage_.class
Comment 1 Mark Hiner 2015-04-01 08:15:49 CDT 
Thanks for the report, Jeff!

Gabriel - I added you to the CC list since you're listed as the maintainer on the wiki: http://fiji.sc/Align_RGB_planes

Does the parenthetical (ImageJ) on that page indicate this plugin is only supported in pure ImageJ 1.x?
Comment 2 G. Landini 2015-04-01 08:34:58 CDT 
It works here... I copied the align RGB planes class file to an arbitrary (e.g. /plugins/macros) folder and I see it in the menu as well as being able to run it.

If you copied the *.java file as well, you might try deleting and keeping only the class file. I think Fiji handles plugins slightly different than ImageJ.
Comment 3 jeff.spector 2015-04-06 09:00:12 CDT 
Thanks. This seems to have corrected the problem. I had to create a new folder for it in the plugins directory. When i had the .class and .java file in the fiji/plugins directory it didn't work, but by creating a new dir /fiji/lugins/aignrgbplanes and placing the .class file there it is now working.
thanks.