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Bug 704 - Error Message when starting Fiji when the application from an external application
Error Message when starting Fiji when the application from an external applic...
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Windows
: P3 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-02-20 04:47 CST by Sebastian Rhode
Modified: 2014-06-16 16:35 CDT
4 users (show)

See Also:

Description Sebastian Rhode 2014-02-20 04:47:51 CST
Hi guys,

I am not really sure if this a bug, but nevertheless it is strange.

When I start today´s Fiji (2014_02_20) and open an CZI file, it works fine. When I use the ImageJ extension of ZEN Blue to start Fiji and open the same file I get an error. But the file opens correctly.

My question is, what causes this error, because we may start Fiji in the "wrong" manner now. Until today this problem was not there, so I have no idea, what the reason might be.

System: Windows7, 64bit, Java 1.7.0_21 (64bit)

Any help is really appreciated,

Cheers, Sebi


(Fiji Is Just) ImageJ 1.48r; Java 1.7.0_21 [64-bit]; Windows 7 6.1; 21MB of 6102MB (<1%)
 
java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:601)
	at ij.macro.Functions.call(Functions.java:3833)
	at ij.macro.Functions.getStringFunction(Functions.java:264)
	at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283)
	at ij.macro.Interpreter.getString(Interpreter.java:1262)
	at ij.macro.Interpreter.doStatement(Interpreter.java:277)
	at ij.macro.Interpreter.doStatements(Interpreter.java:214)
	at ij.macro.Interpreter.run(Interpreter.java:111)
	at ij.macro.Interpreter.run(Interpreter.java:81)
	at ij.macro.Interpreter.run(Interpreter.java:92)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:123)
	at ij.IJ.runMacro(IJ.java:115)
	at ij.IJ.runMacro(IJ.java:104)
	at ij.OtherInstance$Implementation.sendArgument(OtherInstance.java:65)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:601)
	at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
	at sun.rmi.transport.Transport$1.run(Transport.java:177)
	at sun.rmi.transport.Transport$1.run(Transport.java:174)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 5 >= 2
	at java.util.Vector.elementAt(Vector.java:470)
	at java.awt.Menu.getItemImpl(Menu.java:255)
	at java.awt.Menu.getItem(Menu.java:247)
	at java.awt.Menu.remove(Menu.java:410)
	at common.RefreshScripts.removeFromMenu(RefreshScripts.java:233)
	at common.RefreshScripts.removeFromMenu(RefreshScripts.java:224)
	at common.RefreshScripts.run(RefreshScripts.java:312)
	at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at fiji.Main.runGently(Main.java:47)
	at fiji.Main.runGently(Main.java:35)
	at fiji.MenuRefresher.installScripts(MenuRefresher.java:58)
	at fiji.MenuRefresher.run(MenuRefresher.java:39)
	at fiji.Main.setup(Main.java:112)
	... 32 more
Comment 1 Johannes Schindelin 2014-03-05 15:43:20 CST
Unfortunately I do not have access to ZEN Blue nor its Fiji extension, therefore I cannot reproduce. I would need to know the exact startup procedure used by ZEN Blue to get a vague idea how to try to make it happen here...
Comment 2 Jean-Yves Tinevez 2014-03-06 02:02:06 CST
Hi Johannes, all.
My facility will get Zen Blue, around the end of this year. Then I can help and investigate. But in the meantime, this problem will remain.
I am at your command. 
jy
Comment 3 Johannes Schindelin 2014-03-06 04:07:26 CST
J-Y, thanks for the offer!

However, I thought that if Zeiss wants to improve the situation and cannot spare resources to debug it themselves, they might want to provide us with a (possibly time-limited) Zeiss Blue installation to play with.

I'd even VNC into a machine if that is the best option for Zeiss.
Comment 4 Jean-Yves Tinevez 2014-03-06 04:10:44 CST
Ok. You know I am willing to have external and industry players come into the playground. I would suggest to really wait so that we have this installation as a permanent resource of the facility. Then I can fiddle in all serenity. 
Do we have someone on Zeiss side to talk to?
Comment 5 Johannes Schindelin 2014-03-06 04:14:04 CST
J-Y, I know. And you know, too, that I haven't the slightest problem to work with industry, either.

Our contact into Zeiss is... *drumroll* Sebastian (who reported this bug).

:-)
Comment 6 Jean-Yves Tinevez 2014-03-06 04:25:22 CST
Ohhhhh... ok. I guess I need to learn to read. 
So Sebastian: can you wait a little bit for us? My facility plan on acquiring 2 Zen Blue licenses through normal commercial ways, but probably around the end of the year. Then I would have the time and resources to work on the issue. 

This is if you can wait on your side, of course. If not, then I would ask for a demo license.
Comment 7 Sebastian Rhode 2014-03-13 04:03:40 CDT
Hi Johannes and JY,

the provides jar by Johannes fixed this issue for ZEN Blue as well (i posted this here: https://groups.google.com/forum/#!topic/fiji-devel/nNLFDZ01stA)

But I am more than happy to see this tested from real user,not someone like me working for the dark side ... :-).

And maybe you have some ideas on how to even make this workflow better. What I do quite often is the following.

1) Acquire data in ZEN Blue
2) Send them to Fiji and do some special analysis (that we do not have)
3) Import the results to ZEN and modify the next experiment according to the results
4) Run the modifies experiment

The whole workflow is controlled from within an ZEN Blue IronPython script, which allows us to use all of ZEN Blue (and .NET) objects, since ZEN Blue is written in C#.

Let me know, when you need help or support.

Cheers,  Sebi


Ohhhhh... ok. I guess I need to learn to read. 
So Sebastian: can you wait a little bit for us? My facility plan on acquiring 2 Zen Blue licenses through normal commercial ways, but probably around the end of the year. Then I would have the time and resources to work on the issue. 

This is if you can wait on your side, of course. If not, then I would ask for a demo license.
Comment 8 Curtis Rueden 2014-06-16 16:35:59 CDT
Since all evidence points to this bug being fixed, I'm closing it. Please feel free to reopen (with details) if anyone hears any reports of the problem persisting in any circumstances.