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Bug 711 - FIJI no longer recognises ImageJ Macro files in Macro editor
FIJI no longer recognises ImageJ Macro files in Macro editor
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P5 enhancement
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-03-07 07:36 CST by Steve J. West
Modified: 2014-03-10 09:53 CDT
1 user (show)

See Also:

Attachments
A replacement ij-legacy hopefully fixing the issue (125.94 KB, application/java-archive)
2014-03-07 15:09 CST, Johannes Schindelin

Description Steve J. West 2014-03-07 07:36:30 CST 
With the new FIJI update (version 1.48r) on Debian Wheezy (7.4.0), whenever I open a macro window, FIJI throws the following exception:

(Fiji Is Just) ImageJ 1.48r; Java 1.6.0_24 [64-bit]; Linux 3.2.0-4-amd64; 12MB of 15000MB (<1%)
 
java.lang.NullPointerException
	at imagej.script.editor.EditorPane.setFileName(EditorPane.java:273)
	at imagej.script.editor.TextEditor.setFileName(TextEditor.java:1855)
	at imagej.script.editor.TextEditor.createNewDocument(TextEditor.java:790)
	at imagej.legacy.plugin.DefaultLegacyEditor.create(DefaultLegacyEditor.java:98)
	at imagej.legacy.DefaultLegacyHooks.createInEditor(DefaultLegacyHooks.java:326)
	at ij.plugin.NewPlugin.createMacro(NewPlugin.java:91)
	at ij.plugin.NewPlugin.run(NewPlugin.java:71)
	at ij.IJ.runPlugIn(IJ.java:169)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)


In the macro window, the ImageJ Macro Language is no longer available, and I am no longer able to run any macros from this window.

I havent checked whether I can run them as a plugin, but I think that is not affected.

Any help would be greatly appreciited with this bug!  In the meantime, is there any way I can revert to the previous version of FIJI?

Cheers,

Steve.
Comment 1 Johannes Schindelin 2014-03-07 07:56:08 CST 
The problem is that the Script Editor version from ImageJ2 (not quite ready yet) is used instead of the Fiji version (obsolete, but works with ImageJ Macros).

I cannot reproduce the problem here, but I urge you to make sure (via the advanced mode of the updater) that your ij1-patcher, ij-legacy and fiji-compat files are all up-to-date with a Release date of 03 Mar 2014.
Comment 2 Steve J. West 2014-03-07 08:17:33 CST 
Hi Johannes,

Thanks for the prompt reply.  I have checked the ij1-patcher, ij-legacy & fiji-compat fles and htrey are all up to date (release date 03 March 2014).  I have installed/updated fiji-lin64 and the ij.jar files, and still have the bug...

Should I just revert to version 1.47 using the ImageJ Updater until this bug is fixed?  Do you need any more information to try to re-create the bug?

Cheers,

Steve.
Comment 3 Johannes Schindelin 2014-03-07 08:53:56 CST 
Could you rename the ImageJ-launcher to "debug", start Fiji again (no need to start the script editor, the bug happens much earlier) and paste the console output here?
Comment 4 Johannes Schindelin 2014-03-07 15:09:59 CST 
Created attachment 134
A replacement ij-legacy hopefully fixing the issue
Comment 5 Johannes Schindelin 2014-03-07 15:12:10 CST 
Could you drag 'n drop the attached ij-legacy.jar to your Fiji? This is the only guess I have at a fix, after staring at the code for quite a bit of time. (The bug you reported does not appear here, neither on my machine nor any machine I got my hands on...).
Comment 6 Johannes Schindelin 2014-03-07 18:07:53 CST 
For what it's worth, I uploaded the new file to the update site. Again, hopefully this fixes the problem you identified.
Comment 7 Johannes Schindelin 2014-03-08 10:01:51 CST 
I mark this as fixed, tentatively, and ask you to reopen if you find that it is not fixed. Thank you!
Comment 8 Steve J. West 2014-03-10 09:19:13 CDT 
Hi Johannes,

Sorry for the late reply - I have been away this weekend.

I re-ran the update, got the new ij-legacy.jar file, and now it seems to work.  So whatever you changed seems to have solved the problem.

Thanks very much for fixing it!

Best,

Steve West.
Comment 9 Johannes Schindelin 2014-03-10 09:53:28 CDT 
That's fine, I sometimes release something on a Friday afternoon and then leave immediately for a two-week vacation without internet access.

Thanks for the feedback!