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Bug 241 - RefreshScripts can throw an exception on start up
RefreshScripts can throw an exception on start up
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-10-15 19:35 CDT by Albert Cardona
Modified: 2011-03-23 17:23 CDT
1 user (show)

See Also:

Description Albert Cardona 2010-10-15 19:35:13 CDT
Just launching Fiji, I got:

java.lang.ArrayIndexOutOfBoundsException: 18 >= 18
	at java.util.Vector.elementAt(Vector.java:427)
	at java.awt.Menu.getItemImpl(Menu.java:230)
	at java.awt.Menu.getItem(Menu.java:222)
	at common.RefreshScripts.maybeAddFile(RefreshScripts.java:143)
	at common.RefreshScripts.addFromDirectory(RefreshScripts.java:307)
	at common.RefreshScripts.addFromDirectory(RefreshScripts.java:297)
	at common.RefreshScripts.addFromDirectory(RefreshScripts.java:297)
	at common.RefreshScripts.addFromDirectory(RefreshScripts.java:277)
	at common.RefreshScripts.run(RefreshScripts.java:378)
	at Clojure.Refresh_Clojure_Scripts.run(Refresh_Clojure_Scripts.java:16)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at fiji.User_Plugins.runPlugIn(User_Plugins.java:108)
	at fiji.User_Plugins.installScripts(User_Plugins.java:119)
	at fiji.User_Plugins.run(User_Plugins.java:77)
	at fiji.Main.setup(Main.java:331)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.macro.Functions.call(Functions.java:3465)
	at ij.macro.Functions.getStringFunction(Functions.java:250)
	at ij.macro.Interpreter.getStringTerm(Interpreter.java:1155)
	at ij.macro.Interpreter.getString(Interpreter.java:1134)
	at ij.macro.Interpreter.doStatement(Interpreter.java:246)
	at ij.macro.Interpreter.doStatements(Interpreter.java:189)
	at ij.macro.Interpreter.run(Interpreter.java:100)
	at ij.macro.Interpreter.run(Interpreter.java:72)
	at ij.macro.Interpreter.run(Interpreter.java:82)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:94)
	at ij.IJ.runMacro(IJ.java:106)
	at ij.IJ.runMacro(IJ.java:93)
	at ij.ImageJ.main(ImageJ.java:623)
	at fiji.Main.main(Main.java:363)


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.32-24-generic
  java.version => 1.6.0_20
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 16.3-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2010-10-15 20:11:32 CDT
Did you change the way Fiji operates? I.e. did you multi-thread the refresh scripts startup? Because the exception you see can only happen when the menus are _shrunk_ while refresh scripts runs. And I can only see that happening when _multiple_ refresh scripts try to do their thing at the same time.

If this is the issue, the multi-threading must go. There is simply no way you can allow that code to be multi-threaded. (It's not only hard in this case, but impossible!)
Comment 2 Albert Cardona 2010-10-15 20:24:28 CDT
(In reply to comment #1)
> Did you change the way Fiji operates? I.e. did you multi-thread the refresh
> scripts startup? Because the exception you see can only happen when the menus
> are _shrunk_ while refresh scripts runs. And I can only see that happening when
> _multiple_ refresh scripts try to do their thing at the same time.


I have not touched that part of fiji in over a year or more. So no, I haven't.

I suspect that the 1.6.0_21 JVM event dispatch thread is being clever and perhaps running operations in parallel on occasions. Bizarre as it sounds--I've seen weird GUI effects in trakem2 that I had never seen before. Otherwise no clue.

Albert
Comment 3 Johannes Schindelin 2011-03-23 15:30:44 CDT
Does this bug persist?
Comment 4 Albert Cardona 2011-03-23 17:23:52 CDT
(In reply to comment #3)
> Does this bug persist?


Can't reproduce it anymore.