Bug 723 – TrackMate unable to do tracking in Windows7

Bug 723 - (TrackingFail) TrackMate unable to do tracking in Windows7

(TrackingFail)
Summary:	TrackMate unable to do tracking in Windows7

Status:	RESOLVED FIXED

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

Importance:	P5 trivial
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-03-27 16:03 CDT by Marcia Yoshida
Modified:	2014-05-23 11:29 CDT
CC List:	4 users (show)

See Also:

Attachments
What TrackMate panel looks like after choosing tracker settings (39.99 KB, image/png) 2014-03-27 16:03 CDT, Marcia Yoshida
Debug-mode-log before I updated JAVA (539.64 KB, text/plain) 2014-03-31 06:19 CDT, Marcia Yoshida
Debug-mode-log after I installed JAVA version 7 update 51 (539.55 KB, text/plain) 2014-03-31 06:20 CDT, Marcia Yoshida
Debug-mode-log after I changed international decimal settings from comma to dot (554.10 KB, text/plain) 2014-04-01 13:34 CDT, Marcia Yoshida
Debug mode after I updated TrackMate-dev site (540.00 KB, text/plain) 2014-04-07 17:38 CDT, Marcia Yoshida
Debug mode after updating TrackMate-dev website. (1.25 MB, text/plain) 2014-05-23 10:39 CDT, Marcia Yoshida
Debug mode while I was updating TrackMate (99.52 KB, text/plain) 2014-05-23 10:43 CDT, Marcia Yoshida
Show Obsolete (5) Add an attachment (proposed patch, testcase, etc.)

Description Marcia Yoshida 2014-03-27 16:03:18 CDT

Created attachment 137
What TrackMate panel looks like after choosing tracker settings

TrackMate (ver. 2.2.0 for both 32-bit and 64-bit versions of Windows7) does not perform tracking after choosing tracker settings.

Steps to reproduce:
1)Open Fiji on Windows7
2)Follow tutorial http://fiji.sc/Getting_started_with_TrackMate

Actual results:
After choosing the LAP tracker settings, the log panel does not appear, the parameters are reset to 0 (or other values depending on the parameter) and the 'next' button is disabled. (see picture)

Expected results:
Successful tracking of dummy tracks (as in the tutorial).

Date of first encounter with the bug: 27 March 2014
Hardware used: Windows 7 Ultimate
Additional info: Bug does not occur on Microsoft Windows XP professional

I hope this is helpful :) I am extremely sorry if this is not a real bug. D:
Thanks in advance!

Comment 1 Curtis Rueden 2014-03-27 16:15:20 CDT

Note that Marcia also wrote to the ImageJ mailing list; see:
https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;1b62bb72.1403

Comment 2 Marcia Yoshida 2014-03-27 16:44:11 CDT

I am sorry for double-posting. I was not sure whether this was a bug or not so I posted on the forum, but then thought that maybe posting here would have been more appropriate.

Also, an update: I used TrackMate with one of my videos and again the tracking does not work, but it does not reset the settings I had chosen to 0.

(Sorry, Mr. Rueden, I don't know how to reply to a comment)

Comment 3 Marcia Yoshida 2014-03-31 06:19:17 CDT

Created attachment 138
Debug-mode-log before I updated JAVA

Comment 4 Marcia Yoshida 2014-03-31 06:20:27 CDT

Created attachment 139
Debug-mode-log after I installed JAVA version 7 update 51

Comment 5 Jean-Yves Tinevez 2014-03-31 06:27:37 CDT

Hey thank you Marcia. It's very helpful.

I see at LEAST two categories of problem in the log you sent. 

1.
All the SciJava TrackMate modules discovery generated a java.lang.ClassCastException. 
This one I do not understand. You told us you were able to reach the tracking panel right? This means that the module discoveries kind of happened ok.

2.
The most likely reason for your error is this:

err >Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "15,0"
err >	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1222)

You have a international system where the decimal separator is the coma. TrackMAte expects it to be the dot. So it fails because it does not know how to interpret 15,0. 

We have been receiving bug reports for this for ages, and I never have been able to safely tackle it. 

Any chance you could change your international settings to US for instance, just to confirm?

Comment 6 Marcia Yoshida 2014-03-31 06:34:29 CDT

wow

Thank you, Mr. Tivenez!
That was quick! 
Yes, I could reach the tracking panel (if that is the one shown in the picture I attached); I just could not perform the actual tracking.

Ok, I will try doing that! That makes a lot of sense! Once I learn how to change my international settings, I will give you an uodate!

Again, 
Thank you very much!

Comment 7 Marcia Yoshida 2014-03-31 11:25:19 CDT

Hello,

I have changed the international settings for the decimal separator to be dot instead of comma. After that I restarted the computer and opened Trackmate again, but unfortunatelly it does the same thing again, and does not run the tracking.

I actually just manually changed come to dot in the control panel part for languages and region. I am not sure if that does not solve the problem. Should I upload another log file?

Thank you very much,
Marcia

Comment 8 Johannes Schindelin 2014-03-31 11:33:27 CDT

> Should I upload another log file?

Yes, please!

Comment 9 Curtis Rueden 2014-03-31 11:42:05 CDT

Regarding the ClassCastExceptions: I think this is unrelated to TrackMate since they are all relating to io.scif.tools.SCIFIOToolCommand. (I am not sure why we are seeing those since that plugin type is part of scifio-tools, not scifio core -- and scifio-tools is not currently part of Fiji...)

As for the comma problem: my Fiji PR #22 (https://github.com/fiji/fiji/pull/22) from last year did not solve it, eh? Too bad.

Comment 10 Jean-Yves Tinevez 2014-03-31 14:17:31 CDT

@Curtis: I am amazed to find that it did not make it through to v2.2.0. I guess I deleted or reverted it for some reason. I am good to try that again now...

Comment 11 Curtis Rueden 2014-03-31 15:07:43 CDT

J-Y: Well, it *did* make it into 2.2.0; see:
https://github.com/fiji/TrackMate/commit/2aefe8bc81c718929e3b4f0f4272ef832e9b177c

But then there were some changes reorganizing the AbstractProvider and many other things, and now "git grep NumberParser" no longer shows any results.

The offending commit seems to be:
https://github.com/fiji/TrackMate/commit/bee71a0831caf77192a19c445535080349c1a05c

Shouldn't be too hard to reinstate my patch in the correct place, but I fear my changes were probably not the only changes lost by the above merge commit...

Comment 12 Marcia Yoshida 2014-04-01 13:34:40 CDT

Created attachment 140
Debug-mode-log after I changed international decimal settings from comma to dot

Comment 13 Johannes Schindelin 2014-04-01 14:23:59 CDT

Thank you!

This looks to me as if the persistent settings were using locales... J-Y, we need to look into that...

Comment 14 Johannes Schindelin 2014-04-01 14:29:04 CDT

Okay, I take it back. It should be fixed with the pull request we were discussing this morning. It's the problem that the value of a JNumericTextField is parsed using Double.parseDouble() instead of NumberParser.parseDouble().

In preparation for this fix, I will upload the current (fixed) fiji-lib.

Comment 15 Johannes Schindelin 2014-04-02 15:34:30 CDT

Marcia, could you please run Help>Update Fiji, click on "Manage update sites", check the "TrackMate-dev" update site, click the "Close" button followed by the "Apply changes" button and try again?

Hopefully this fixes your problem!

Comment 16 Marcia Yoshida 2014-04-07 17:04:27 CDT

Dear Mr. Schindelin,

I am sorry for taking so long. I checked and updated the "TrackMate-dev" site, restarted Fiji and started working on the sample video again. However, again the program stopped before tracking. Here I upload another log file in case I did something wrong. 

Thank you very much
Marcia

Comment 17 Marcia Yoshida 2014-04-07 17:38:40 CDT

Created attachment 142
Debug mode after I updated TrackMate-dev site

Comment 18 Johannes Schindelin 2014-04-29 11:18:46 CDT

Hmm. From the stack trace, it does not look as if the latest TrackMate version is used. In particular, it reports that the getSettings() method of JPanelTrackerSettingsMain still calls Double.parseDouble() directly, when the current developer version actually calls NumberParser.parseDouble() instead...

Can you start the updater, go to the advanced mode, "View all files", type "trackmate" in the search box, then click on the appropriate line in the list and verify that it is up-to-date and then verify that the file details state that it is from the TrackMate-dev update site?

Comment 19 Marcia Yoshida 2014-05-23 10:38:09 CDT

Hello everyone, sorry for taking so long!

But I am very excited! The updater worked and now TrackMate works exactely like the tutorial! :D

It seems that the update I tried earlier did not work. I tried again and checked the update site and there were two update sites: fiji and TrackMate-dev. I will send you another log file in case something is missing, but the tracks were successfully detected this time! 

Thank you very much for your pacience.
Marcia

Comment 20 Marcia Yoshida 2014-05-23 10:39:39 CDT

Created attachment 152
Debug mode after updating TrackMate-dev website.

Comment 21 Marcia Yoshida 2014-05-23 10:43:04 CDT

Created attachment 153
Debug mode while I was updating TrackMate

It seems there were some errors while the updater was working, so here I upload a log file of the updating process, in case it is important.

Comment 22 Curtis Rueden 2014-05-23 11:29:23 CDT

The "Debug mode while I was updating TrackMate" log looks just fine. There is a lot of debugging output of course, but no unexpected errors. (The only error, the ClassCastException, is known and harmless, though we will be fixing it later today nonetheless.)

Same for the "Debug mode after updating TrackMate-dev website" log, as far as I could tell. So no worries!

Thanks for following up!