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Bug 999 - (Miji_and_GDSC_plugin) When Fiji is launched using Miji, then the GDSC (or FindFoci) plugin is missing
(Miji_and_GDSC_plugin)
When Fiji is launched using Miji, then the GDSC (or FindFoci) plugin is missing
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-02-03 08:08 CST by westerveld2
Modified: 2015-02-06 12:02 CST
2 users (show)

See Also:

Description westerveld2 2015-02-03 08:08:02 CST
Dear Sir/Madam,

PROBLEM:
When I launch Fiji from Matlab using the Miji (MIJ) plugin, the GDSC plugins (including FindFoci) do not show in the Plugins toolbar. Also, I can not run FindFoci from a macro or from the Matlab MIJ.run() command.

DIAGNOSE:
When I launch Fiji normally, everything works fine.
I am able to start FindFoci using: Toolbar => Plugins => GDSC => FindFoci
I am able to start FindFoci using the test macro shown below.

When I launch Fiji via Matlab / Miji interface:
Run in Matlab: > Miji
The GDSC plugins including FindFoci are missing from the Toolbar => Plugins menu.
When I start the test macro shown below, I get the error "Unrecognized command: FindFoci"
When I start the command described in the test macro using MIJ.run(), I get the same error "Unrecognized command: FindFoci"
Other Fiji operations work fine, e.g., MIJ.run('Invert');
Other plugins work fine, e.g., MIJ.run('Classic Watershed', 'input=131_mode9_abs mask=None use min=0 max=255');

TEST MACRO:
run("FindFoci", "mask=[None] background_method=[Std.Dev above mean] background_parameter=3 auto_threshold=Otsu statistics_mode=Both search_method=[Above background] search_parameter=0.30 minimum_size=5 minimum_above_saddle minimum_peak_height=[Relative above background] peak_parameter=0.50 sort_method=[Total intensity] maximum_peaks=50 show_mask=[Peaks above saddle] fraction_parameter=0.50 show_table mark_maxima show_peak_maxima_as_dots show_log_messages remove_edge_maxima results_directory=[] gaussian_blur=0 centre_method=[Max value (search image)] centre_parameter=2");

MORE DETAILS:
MIJ version: 1.3.6-fiji

When I start Miji, the following .jar packages are listed (among many others):
beansbinding-1.2.1.jar, gdsc-1.0.1-SNAPSHOT.jar

This problem was also reported on the mailing list, but I could not find it in the bug tracker.
https://groups.google.com/forum/#!topic/fiji-devel/LefVwBOOs-g
Entry of Chen Huang.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Wouter\Programs\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Wouter\Programs\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150122114514)
Fiji: http://fiji.sc/update/ (last check:20150130182536)
GDSC: http://sites.imagej.net/GDSC/ (last check:20141118185052)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20150121082658 jars/jpedalSTD.jar
  2b7aa66b (LOCAL_ONLY) 20150130115802 plugins/MorphoLibJ_-1.0.6.jar
  5f60d96e (LOCAL_ONLY) 20150130135907 plugins/Watershed_.jar
Comment 1 westerveld2 2015-02-05 01:20:04 CST
The author of the GDSC plugin, Alex Herbert, has fixed this problem. I would like to thank him very much for his very quick fix. 

Hereby his anwer:

I have looked at this using the Miji plugin and the problem was solved by renaming the plugin from:

gdsc-1.0.1-SNAPSHOT.jar to gdsc_-1.0.1-SNAPSHOT.jar

It used to be ImageJ convention to have an underscore in the filename of plugins. This convention is obviously still necessary for Miji.

You can update the GDSC plugin using the Fiji update mechanism. This should remove the old plugin and install a new one with the correct name.
Comment 2 Curtis Rueden 2015-02-06 12:02:46 CST
Thanks to Alex. For anyone else interested, the relevant bug-fix is here:
https://github.com/aherbert/GDSC/commit/67803449f81a4c47217fce0c68a15bcb47268b58