Tracking process failed to plot feature

debugging
imagej
trackmate

#1

Hi Friends,
I think I may have encountered a bug in Trackmate plugin. While everything else was normal, Trackmate failed to ‘Plot Feature’ and showed such error text:

Exception in thread "TrackMate plot spot features thread" java.lang.NoClassDefFoundError: com/itextpdf/text/DocumentException
	at fiji.plugin.trackmate.features.SpotFeatureGrapher.render(SpotFeatureGrapher.java:115)
	at fiji.plugin.trackmate.gui.GrapherPanel.plotSpotFeatures(GrapherPanel.java:189)
	at fiji.plugin.trackmate.gui.GrapherPanel.access$100(GrapherPanel.java:29)
	at fiji.plugin.trackmate.gui.GrapherPanel$1$1.run(GrapherPanel.java:122)
Caused by: java.lang.ClassNotFoundException: com.itextpdf.text.DocumentException
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
	... 4 more

Any ideas about what has gone wrong? I sincerely appreciate any suggestion and advice.

Best regards,
Da


Trackmate/ImageJ issues
#2

Hi @DidasW

I checked and could not reproduce your problem.

I just updated and got TrackMate v.3.5.1-SNAPSHOT. Could you check that you have this version? Normally NoClassDefFoundError indicate a missing dependency in your Fiji. If nothing works, could you try to redownload a fresh Fiji.app, update and retry?


#3

Dear Tinevez, thanks for such promptly response. I was taking more data in the lab till now. Will try your suggestion the very first thing next morning and let you know right afterwards.

Best regards,
Da


#4

Hi Tinevez,
Here is what I found:

  1. The Fiji I have is downloaded several days ago from https://imagej.net/Fiji/Downloads; and was updated fully.

  2. But I realized that my Trackmate is of version 2.8.1 (as I found in the update site http://update.fiji.sc/plugins/, that the latest version is 2.8.1)

  3. I went to download Trackmate 3.5.3 from the site below and replaced the jar file in Fiji.app/plugins/…
    http://maven.imagej.net/index.html#nexus-search;gav~sc.fiji~TrackMate
    ~3.5.3~~~kw,versionexpand
    (…/sc/fiji/TrackMate_/3.5.3/TrackMate_-3.5.3.jar)
    BTW: I tried 3.5.1 too, the error was the same

  4. The problem I now have is that in the plugin menu I cannot start Trackmate. The error message

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51o; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 82MB of 6067MB (1%)
java.lang.UnsupportedClassVersionError: fiji/plugin/trackmate/TrackMateRunner_ : Unsupported major.minor version 52.0
This plugin requires Java 1.8 or later.
My OS is Win7 64 and the Java version I have is Java8 update 131

  1. I then tried the function in the menu. While showing ‘Trackmate 3.5.3 is installed successfully’, there were actually errors:
    D:\PROGRA~2\Fiji.app\plugins\TrackMate_-3.5.3.jar: java.util.zip.ZipException: error in opening zip file
    D:\PROGRA~2\Fiji.app\plugins\TrackMate_-3.5.3.jar: java.util.zip.ZipException: error in opening zip file
    And track mate is no where to be found.

I supposed I must have done something stupid. Any suggestion on how to proceed?
Thanks a lot


#5

Yep, you did not have the Java8 update site activated.

Just redownload Fiji.app from scratch, and make sure that in thee Update sites of the Fiji updater, the Java8 site is activated.


#6

Hey @DidasW.
Did it work?


#7

Yes, thanks a lot.
I included java8 as one of the update site. In the first place there were a lot to update (though the Java8 update 131 was the most recent release). After this ImageJ stopped working altogether.
But after re-installation and restart, repeating each procedure again, it works now.
And only now did I realize that you said ’ Trackmate 3.5.1-SNAPSHOT’ is actually a name of a version. I was thinking ‘SNAPSHOT’ as certain function.

Your timely help is sincerely appreciated.
Best regards,
Da