Bug 465 – Trackmate - missing Save dialog for Export tracks to XML

Bug 465 - Trackmate - missing Save dialog for Export tracks to XML


Summary:	Trackmate - missing Save dialog for Export tracks to XML

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P2 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2012-08-14 01:16 CDT by Ron Rock
Modified:	2014-08-22 12:00 CDT
CC List:	4 users (show)

See Also:

Description Ron Rock 2012-08-14 01:16:23 CDT

Hi JY,
We've run into a new (and weird) problem with the "Export to XML file" action at the end.  This problem showed up aroud the same time as the problem with the Fiji updater a couple of weeks ago.   The progress bar appears and runs to completion, but the save dialog never shows up.    The console gives me:

8/13/12 5:10:37.740 PM [0x0-0x6a16a1].org.fiji: Exception in thread "TrackMate action thread" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
8/13/12 5:10:37.740 PM [0x0-0x6a16a1].org.fiji: 	at java.lang.String.substring(String.java:1937)
8/13/12 5:10:37.740 PM [0x0-0x6a16a1].org.fiji: 	at fiji.plugin.trackmate.action.ExportTracksToXML.execute(ExportTracksToXML.java:58)
8/13/12 5:10:37.740 PM [0x0-0x6a16a1].org.fiji: 	at fiji.plugin.trackmate.gui.ActionChooserPanel$1$1.run(ActionChooserPanel.java:116)

Funny thing is that this only shows up for some of our movie files.  With other movies, we can go all the way to the end without a problem.  I have a trackmate XML file (the big one) that reproduces the problem, if you'd like that.

Thanks for fixing the earlier UI issues a few months ago.  I can confirm that one problem I had was low RAM / VM thrashing.  New computer is on it's way to replace this 5-yr old beast...

Cheers,
Ron


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.app

Comment 1 Johannes Schindelin 2012-08-14 02:16:19 CDT

Hey Ron, it would be helpful if you could upload said movie via Help>Upload Sample Image. Especially since you claim that the problem occurs only with that movie...

Comment 2 Ron Rock 2012-08-14 21:28:42 CDT

Ok, I've sorted one more thing out which may help.  The uploaded movie "MYO (problem).tif" demonstrates the issue.  "MYO.tif" does not have the issue.  The only difference is that I took MYO (problem).tif, re-ordered the hyperstack swapping z and t, and saved.  Odd that the problem shows up all the way at the end.

For tracking, I used:
blob diameter 5 px
Initial threshold: leave ~2700 spots
No filters on spots
LAP tracker, max distance 5 px, no gap closing
No filters

Console gives the same error as before with MYO (problem).tif.

Hope this helps.

Cheers,
Ron

Comment 3 Jean-Yves Tinevez 2012-08-20 14:23:53 CDT

Ok I downloaded the 2 movies.
But I miss the metadata: is it 3D over time or 2D over time? Can you give me the dimensionality of the images? I fail to guess it.
best
jy

Comment 4 Johannes Schindelin 2013-07-07 09:54:50 CDT

Closing due to missing feedback.

Comment 5 tero.p.heikkinen 2014-08-19 05:05:27 CDT

This bug is easy to reproduce with following

1) Get a czi files for example, that needs to be stiched
2) Use stiching (grid/collection stiching) to open image
3) Use trackmate and try to export XML track

Or simply split channels and try running tracking to one channel.

If I save stiched file and then do tracking, XML saving works. So it seems that when you are doing things "on fly", like stiching, splitting, etc, XML saving does not work. Maybe because save dialog tries to open folder where current file is located and when there is no file, we end up unexpected behaviour.

Comment 6 Johannes Schindelin 2014-08-19 08:12:44 CDT

Tero, this was crucial information, but since it has been such a long time, you will probably agree that you expected others to do substantially more than you were actually prepared to do on your end. That is unfortunately an unsustainable concept, so if you really want to see this bug resolved, you need to provide a (small!) czi file and then provide *exact* instructions (including, for example, the exact values of the parameters you chose) to reproduce. Remember, this is not commercial software, you must not expect other people to spend more time than you do, just to help you resolve *your* problem.

Comment 7 tero.p.heikkinen 2014-08-20 06:03:01 CDT

Easiest way to reproduce *my problem* that is *in my professional opinion* a bug that is rather annoying. Like I said problem is based on a fact that the file does not actually exist and dialog itself does not know where it should open. 

I would fix this by myself but I don't have time to start studying how every piece of open source software that I occasionally need to use. Also no need to fix it since it can be circumvented just by saving manually stiched / splitted layers. It just rather annoying when files are tens of gigabytes...

But here I give you very easy way to reproduce issue without any need to get any czi files etc.

1) file->open samples->tracks for trackmate
2) image->duplicate->check duplicate stack and use whole range->ok
3) close the original file
4) Now you should be working with FakeTracks-1.tif (or some other number)
5) Plugins->Tracking->TrackMate and click next until you reach end of the process
6) Select action->export tracks to XML file

Experienced behaviour: No dialog is opened
Expected behaviour: Open dialog eg to the "root folder" or if possible last used folder. It really does not matter if I get to save the XML somewhere at least.

br, Tero

Comment 8 Johannes Schindelin 2014-08-20 06:21:17 CDT

Sorry, that's not the way this project works (or for that matter, how it could work in a sustainable manner).

Comment 9 Curtis Rueden 2014-08-21 14:23:36 CDT

@Tero: Very sorry for the earlier rudeness, and thank you very much for the recipe to reproduce. However, following your instructions with a fully updated Fiji, I was successfully able to export the tracks to an XML file on my OS X machine.

That said, I did look at the source code relating to the original stack trace that Ron posted, and am fairly confident what the problem is, so I committed a tentative fix:

https://github.com/fiji/TrackMate/commit/588e9780acc343b36d6193ddef92c138201c0469

If you enable the TrackMate-dev update site, you should receive the fix. Please reopen the issue if you still experience the problem.

Comment 10 Jean-Yves Tinevez 2014-08-21 15:41:17 CDT

@Tero: I could not reproduce the bug either, on win7, following your recipe and using the v2.4.0 (falsely named v2.4.0-SNAPSHOT in the title bar). 

However there have been a bug like this in v2.2.0 or prior (not sure) linked indeed to working on images not existing on the filesystem. Just to be sure: with what version have you been generating this bug?

Comment 11 tero.p.heikkinen 2014-08-22 05:01:19 CDT

@Jean-Yves 
I was using Fiji with following specs: Win7 + Trackmate v2.4.0-snapshot + ImageJ 1.49e

@Curtis no problem with rudeness. I'm was not just used to that kind of reaction with open source projects, when reporting a bug.

I also last night tried to look from the source and was looking the same java-file for bug. Unfortunately my Java skills are no longer fresh...

I tried to start fiji after using Trackmate-dev update site and now software crashes on startup. I think there was too many dev-packages coming in. I'll try later again with fresh installation. I'll report my test findings. And just to be sure I'll test with Os X and Win 7 because file systems between them are bit different.

Is the communication of fiji and plugins now in github or here in bugzilla?

Comment 12 Curtis Rueden 2014-08-22 12:00:31 CDT

> Is the communication of fiji and plugins
> now in github or here in bugzilla?

Wherever you are more comfortable, Tero. The bugzilla is more "user facing" while the GitHub Issues are more "developer facing". Also, as a rule of thumb, we tend to file a GitHub Issue whenever anything here on the Bugzilla turns into more of a feature request. There is also only one Bugzilla, and it is connected to the "Report a Bug" plugin, which is handy, whereas every ImageJ and Fiji component has its own GitHub issue tracker, making it more complex to locate issues there (though GitHub does have a very nice global search feature).