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Bug 700 - NullPointerException on Load TrackMate File
NullPointerException on Load TrackMate File
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: Jean-Yves Tinevez
Depends on:
Blocks:
 
Reported: 2014-02-05 12:27 CST by Kris Sheets
Modified: 2015-04-14 02:01 CDT
2 users (show)

See Also:
Description Kris Sheets 2014-02-05 12:27:48 CST 
Successfully launched Load Trackmate File a single time.  Everytime after that it produces a NullPointer crash.  Have tried restarting Fiji, restarting computer, upgrading Fiji, creating new Trackmate file to attempt loading from.  Nothing works.  I had noticed problems in the TrackMate interface with saving files.  Many times it will just report "Saving" to the log but never brings up the file browser dialog window.  Possibly a common error between the two as the LoadTrackMate_.java uses a non-default file browser.  Possible that both save and load use same browser and that problem lies within the IOUtils.askForFileForLoading

**LOG***
(Fiji Is Just) ImageJ 1.48q; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.1; 28MB of 11887MB (<1%)
 
java.lang.NullPointerException
	at fiji.plugin.trackmate.LoadTrackMatePlugIn_.run(LoadTrackMatePlugIn_.java:89)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.1
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

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Comment 1 Kris Sheets 2014-02-06 16:32:20 CST 
Bug occurs following:
- incomplete xml write from Trackmate plugin. 
- continuation of work after save without clicking the "Resume" button in logger
- save action that only logs, but doesn't load file browser for save
- save action that loads file browser then locks up, mandating force quit 


Workaround is to reset the plugin by the following
1. load any time series image (mitosis sample)
2. run Trackmate plugin
3. save TrackMate file from the plugin after it loads (mitosis.xml)
4. quit the plugin and close time series image
5. Now you can load desired Trackmate xml from the "Load TrackMate File" plugin.
Comment 2 Jean-Yves Tinevez 2014-02-07 04:37:49 CST 
Hi Kris.

I am about to release the next version of TrackMate anyway. Would you care to test whether this problem reproduces with the RC of v2.2.0?

The instructions to get this version are here:
http://fiji.sc/2013-02-25_-_TrackMate_v2.0.0_released

best
jy
Comment 3 Kris Sheets 2014-02-07 17:34:58 CST 
I believe this problem exists in the v2.2 plugin. Inspection of the saved trackmate xml files show the tag <TrackMate version="2.2.0-rc3">.  The problems described in this bug have all occurred with this TrackMate version.
Comment 4 Jean-Yves Tinevez 2014-02-13 03:26:58 CST 
Hi Kris

Thanks for the details. I have been trying stuff without success.
As I cannot reproduce, I need to ask you clarifications about your bug report:

> Bug occurs following:
> - incomplete xml write from Trackmate plugin. 

Ok what do you mean by "incomplete"?

> - continuation of work after save without clicking the "Resume" button in logger

You normally can't. The "Resume" button should be the only one activated after saving. If not, please tell me at what stage in the GUI are you (just after detection?, after tracking?, etc...)

> - save action that only logs, but doesn't load file browser for save

This I do not understand. How do you reach this step?

> - save action that loads file browser then locks up, mandating force quit 

Same question.

best
jy
Comment 5 Kris Sheets 2014-02-13 08:51:35 CST 
- Incomplete xml write
   - save action that only logs, but doesn't load file browser for save
   - save action that loads file browser then locks up, mandating force quit

I characterized the overall issue as a bad xml write action.  My initial belief was that something in the xml write was incomplete or corrupted.  However, if the xml write occurs and a file is written, inspection of the xml file doesn't show any differences or obviously corrupted information.  

I have grouped the two save actions under this header as those are the failed write actions.  Specifically there are instances when clicking save from the Trackmate panel results in the panel switching to the info window (Logger) and displaying "Saving data ...". The file browser dialog which normally follows to facilitate designating the filename and path to save is never displayed and no 'Resume' button is enabled.  This situation requires me to quit the plugin and lose all work. I also do not recall seeing the log stating the computations of edge and track features which follow "Saving data...". I haven't had this version of the error happen in a while so I cannot verify the absence of the computation log listings.

Other times, the file browser dialog for saving does display but freezes the entire Fiji program.  My computer is not frozen, just everything under the Fiji application.  I cannot edit the filename string, choose path locations, or cancel the file browser dialog. This error requires a force-quit of the Fiji application. This seems to occur when I have made significant amount of changes to the spots and tracks - either by reorganizing/linking spots, or by adding new spots. So maybe this is an error in feature calculations which prevents the subsequent save action.


- continuation of work after save without clicking the "Resume" button in logger

Initially this seemed to be problematic, but I have done it a couple times now without generating any errors. Initially, I had the Track scheme window open when saving, then after saving I would continue making changes to the spots and links.  When saving another time, it would generate one of the two errors above.  I don't know if it was spot deletion, whole track deletion, or editing links that made this happen. This mainly occurred when I used the auto-detection features (found >4000 spots in 30 frames, filtered down to ~1500 spots and ~125 tracks) and needed to manually eliminate many spots/tracks. I now use the manual spot tool and the semi-auto tracking.  It is possible to add/edit spots with this while the Trackmate panel is in the logger window with the 'Resume' button. Also, if the Track scheme window was open when saving, it is still possible to edit in the Track scheme window without clicking the 'Resume' button.

Currently I am using Trackmate extensively. I am manually adding spots and tracking with the semi-auto feature of the Trackmate Tools. I save regularly, usually after addition of <3 tracks. By using Trackmate in this way, I have not had a recurrence of either of the two save errors. This has not prevented the null pointer error though. Using the 'Load Trackmate File' plugin after launch of Fiji results in null pointer error every time without fail, regardless of my avoidance of save errors. Thus, after every new launch of Fiji, I must rest the Trackmate loading with my workaround of opening mitosis sample, run Trackmate, save as mitosis.xml, quit Trackmate, close mitosis.  After this, I am able to open my desired trackmate xml file without problem. Closing and restarting Fiji at this point restores the erro and necessitates the reset procedure.

I hope this more detailed info helps. Let me know if you need any more info.
Comment 6 Jean-Yves Tinevez 2014-02-13 08:58:57 CST 
Woa thank you this is very detailed. 
I will look into it. 
For the random freezing of Fiij, your are right, this looks like a problem with feature calculation.
I'll look.
Comment 7 Jean-Yves Tinevez 2014-08-24 13:11:04 CDT 
Hi Kris,
I plan to work on this before we release v2.5.0
Could you update me with the status of the bug? We released v2.3.0 and v2.4.0 since. I would like to know if you still notice the random behavior.
Best
jy