[ImageJ-bugs] [Bug 999] New: When Fiji is launched using Miji, then the GDSC (or FindFoci) plugin is missing

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=999

            Bug ID: 999
           Summary: When Fiji is launched using Miji, then the GDSC (or
                    FindFoci) plugin is missing
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: westerveld2 at gmx.com
                CC: westerveld2 at gmx.com

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

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