TrackMate Saving Bug!

[Olivier Burri]

Dear Fiji/TrackMate Developers,

TrackMate is unable to save files under Win7!

After finishing a detection, the "Save" button just locks the TrackMate window. No save dialog, nothing.
Similarily, when We reach the point where we can export to XML, after "Execute", the log window says "Preparing XML File" and then nothing again...

It's rather unfortunate we cannot use it as it's impossible to save any results except for the exported result tables. We were hoping to import the tracks into Matlab, as per your tutorial suggestions.

Also when launching "Load a TrackMate File", just to try, the following error appears:

(Fiji Is Just) ImageJ 1.48s; Java 1.7.0_25 [64-bit]; Windows 7 6.1; 123MB of 22000MB (<1%)
 
java.lang.NullPointerException
        at fiji.plugin.trackmate.LoadTrackMatePlugIn_.run(LoadTrackMatePlugIn_.java:74)
        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:724)


Best

Oli

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[dscho]

Hi Olivier,

On Mon, 10 Mar 2014, Burri Olivier wrote:

> After finishing a detection, the "Save" button just locks the TrackMate
> window. No save dialog, nothing.

Any console output? And: what TrackMate version are you using?

Ciao,
Johannes

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[Olivier Burri]

Hi Johannes,


I was using TrackMate v2.2.0 snapshot. No console output.

Seems the latest update of Fiji solved things for me. Either that or restarting my machine, seeing as it crashed between my email and now.

Best

Oli


Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

> -----Original Message-----
> From: Johannes Schindelin [mailto:[hidden email]]
> Sent: lundi 10 mars 2014 11:12
> To: Burri Olivier
> Cc: [hidden email]
> Subject: Re: TrackMate Saving Bug!
>
> Hi Olivier,
>
> On Mon, 10 Mar 2014, Burri Olivier wrote:
>
> > After finishing a detection, the "Save" button just locks the
> > TrackMate window. No save dialog, nothing.
>
> Any console output? And: what TrackMate version are you using?
>
> Ciao,
> Johannes

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[dscho]

Hi Olivier,

On Mon, 10 Mar 2014, Burri Olivier wrote:

> Also when launching "Load a TrackMate File", just to try, the following error appears:
>
> (Fiji Is Just) ImageJ 1.48s; Java 1.7.0_25 [64-bit]; Windows 7 6.1; 123MB of 22000MB (<1%)
>  
> java.lang.NullPointerException
> at fiji.plugin.trackmate.LoadTrackMatePlugIn_.run(LoadTrackMatePlugIn_.java:74)

Guessing that you did not activate the TrackMate-dev update site, and
further guessing that your TrackMate was up-to-date as per the update
site, I tried to fix this bug. Please activate the TrackMate-dev update
site and try again.

Ciao,
Johannes

P.S.: The fix is here: https://github.com/fiji/TrackMate/commit/7d3c56e5

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[dscho]

Hi Olivier,

On Mon, 10 Mar 2014, Burri Olivier wrote:

> I was using TrackMate v2.2.0 snapshot.

Please note that this is imprecise because snapshot versions can change a
lot. The best idea would be to open a Fiji bug report because it
automatically lists what your current files' versions are.

> No console output.

Then it probably hang due to some mutually blocking GUI threads.

> Seems the latest update of Fiji solved things for me. Either that or
> restarting my machine, seeing as it crashed between my email and now.

Please be more careful about the terms. When telling a software developer
that a software "crashed", the developer will always imply that the
software quit without warning. That is almost definitely not what happened
in your case: it hang.

Think about it this way: if you talk to a biologist and you use the term
"confocal" to refer to, say, OPT, the biologist will be left very confused
as what you try to tell her. Same thing here, I went back to your original
mail and found no trace of a crash, only to suspect that you wanted to say
"hang".

Just sayin.
Johannes

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[Olivier Burri]

Dear Johannes,

> Please note that this is imprecise because snapshot versions can change a lot.
> The best idea would be to open a Fiji bug report because it automatically lists
> what your current files' versions are.
Noted. I'll make sure to do this next time!

> Please be more careful about the terms. When telling a software developer
> that a software "crashed", the developer will always imply that the software
> quit without warning. That is almost definitely not what happened in your
> case: it hang.
>
> Think about it this way: if you talk to a biologist and you use the term
> "confocal" to refer to, say, OPT, the biologist will be left very confused as
> what you try to tell her. Same thing here, I went back to your original mail
> and found no trace of a crash, only to suspect that you wanted to say "hang".

Indeed, I apologize for that. Chock it up to Monday mornings. I had indeed meant a hang and not a crash.
Apologies for the mistakes and thank you for clearing everything out for me!

Best

Oli

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[dscho]

Hi Olivier,

On Mon, 10 Mar 2014, Burri Olivier wrote:

> > Please be more careful about the terms. When telling a software
> > developer that a software "crashed", the developer will always imply
> > that the software quit without warning. That is almost definitely not
> > what happened in your case: it hang.
> >
> > Think about it this way: if you talk to a biologist and you use the
> > term "confocal" to refer to, say, OPT, the biologist will be left very
> > confused as what you try to tell her. Same thing here, I went back to
> > your original mail and found no trace of a crash, only to suspect that
> > you wanted to say "hang".
>
> Indeed, I apologize for that. Chock it up to Monday mornings. I had
> indeed meant a hang and not a crash.

Just in case it was not utterly clear already: my intent was not to make
you feel bad. To the contrary, I wanted you to feel good about the
efficient way we converse from now on ;-)

If my mail did not make it clear that I just wanted to be helpful, maybe I
can ask you to chalk it up to Monday mornings, too? ;-)

Ciao,
Johannes

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