Bug 460 – TrackMate plugin has stopped working

Bug 460 - TrackMate plugin has stopped working


Summary:	TrackMate plugin has stopped working

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P2 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2012-08-03 16:34 CDT by Alison Twelvetrees
Modified:	2012-08-11 12:55 CDT
CC List:	0 users

See Also:

Description Alison Twelvetrees 2012-08-03 16:34:13 CDT

Following the recent (large) update, the TrackMate plugin was stopped working on my system. The plugin stalls after the initial LoG segmentation is run - the graph for removing particles based on quality does not appear in the window and it's not possible to progress to the next section. This is true for all data sets, including ones that ran through fine previously. It also cannot load the xml backup files for previously susccessful operations.

Also my in app bug report failed...

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

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.7.4
  java.version => 1.6.0_33
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_33-b03-424-11M3720
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.8-b03-424
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji old.app

Comment 1 Jean-Yves Tinevez 2012-08-03 17:34:53 CDT

I managed to reproduce the bug on my computer. 
It is apparently linked to a JFreeChart problem I will investigate. 
Here is what I get in the console:

03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: Exception in thread "AWT-EventQueue-0" java.lang.AbstractMethodError: org.jfree.chart.annotations.XYTextSimpleAnnotation.addChangeListener(Lorg/jfree/chart/event/AnnotationChangeListener;)V
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at org.jfree.chart.plot.XYPlot.addAnnotation(XYPlot.java:2968)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at org.jfree.chart.plot.XYPlot.addAnnotation(XYPlot.java:2951)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.FilterPanel.createHistogramPlot(FilterPanel.java:339)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.FilterPanel.initGUI(FilterPanel.java:228)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.FilterPanel.<init>(FilterPanel.java:88)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.FilterPanel.<init>(FilterPanel.java:93)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.InitFilterPanel.regenerateThresholdPanel(InitFilterPanel.java:199)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.InitFilterPanel.access$100(InitFilterPanel.java:33)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at fiji.plugin.trackmate.gui.InitFilterPanel$1.done(InitFilterPanel.java:136)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at javax.swing.Timer.fireActionPerformed(Timer.java:291)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventQueue.access$000(EventQueue.java:85)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventQueue$1.run(EventQueue.java:643)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventQueue$1.run(EventQueue.java:641)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.security.AccessController.doPrivileged(Native Method)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
03/08/12 10:02:16,280 [0x0-0x3bf3bf].org.fiji: 	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Comment 2 Johannes Schindelin 2012-08-03 18:23:22 CDT

Ouch. I am genuinely sorry, this was my mistake: we serve jfreechart from the ImageJ update site instead of the Fiji update site, and apparently the former is an older version.

Comment 3 Johannes Schindelin 2012-08-03 18:30:04 CDT

Actually, further investigation reveals that Fiji used to have jfreechart-1.0.13 but ImageJ already has jfreechart-1.0.14. I'll see what I can do to fix the compilation against 1.0.14 and push to a topic branch. J-Y, I will ask you to have a look over it when I am done.

Comment 4 Johannes Schindelin 2012-08-03 18:43:29 CDT

J-Y, could you have a look at https://github.com/fiji/fiji/commit/526d0bc0806ab7280b2753397b23ab88d94542c7 and merge at will?

Comment 5 Jean-Yves Tinevez 2012-08-03 21:41:34 CDT

Thanks Johannes, I tested it and your fix works. I merged and pushed, but cannot upload right now. On win64 I get a "Missing uploader for protocol ssh:.
I leave the bug open until I can.

Comment 6 Johannes Schindelin 2012-08-04 18:09:44 CDT

That is too bad... I tested my change to auto-install the ssh uploader also on Windows, but apparently there are many things to consider when you want things to work on all Windowses.

Could you go to advanced mode, type 'ssh' in the search box and "View all plugins" in the view mode, and mark ij-updater-ssh for install? After installing it, you should be able to upload again. Sorry for that.

Comment 7 Jean-Yves Tinevez 2012-08-04 23:10:19 CDT

Ok I met another problem:
As I upload from a full build of Fiji I have plenty of conflocts, which I leave as is generally ('do not upload ' etc). But the last one is:

Conflict: jars/netcdf-java-4.0.41.jar
Depends on plugins/visad-lite-2.0.20070828.jar which was not uploaded.

Clicking on the button 'break the dependency' has actually no effect.
Do you want to pursue this issue on another bug number or later? For TrackMate, I can update from another computer later.
Best!

Comment 8 Johannes Schindelin 2012-08-06 22:27:35 CDT

The upload bug should be fixed now (see http://trac.imagej.net/ticket/1372).

Comment 9 Johannes Schindelin 2012-08-10 22:27:05 CDT

J-Y, do you want me to upload?

Comment 10 Jean-Yves Tinevez 2012-08-10 22:44:03 CDT

Yes sorry you will have to.
On the win64 machine I still have a problem when uploading. I do not get a chance to fill in my login, and I am asked for "Password for @fiji.sc".

Comment 11 Curtis Rueden 2012-08-10 22:50:47 CDT

J-Y: Did you try using "tinevez@fiji.sc" instead of just "fiji.sc" for your SSH host?

Comment 12 Johannes Schindelin 2012-08-10 23:01:25 CDT

To clarify: this setting needs to be updated in the advanced mode of the updater, under "Manage update sites". Make sure that "For uploading" is checked and click on the Fiji site and then on the "Edit" button.

Sorry for that, I forgot that the updater no longer infers the user name automatically.

Comment 13 Jean-Yves Tinevez 2012-08-10 23:04:13 CDT

My bad, I forgot about that.
I just uploaded. However, I will not close the bug right now: I have some troubles with the install version that prevents me from checking that everything is 100% ok. Will do tomorrow, I'm dead now.
Thanks guys.

Comment 14 Jean-Yves Tinevez 2012-08-11 12:55:58 CDT

Tested: the fix works even on clean installs. Thanks Johannes!