[ImageJ-devel] Problem getting the context

[Mark Hiner]

Hi Thorsten,

>The static initializer did not help.

Unfortunately the static initializer error message is missing some critical
information: you can't launch from a class that will cause ImageJ 1.x
classes to be loaded. TrackMatePlugin_.java contains fields that will cause
ImageJ 1.x classes to be loaded, so a main method in that class will not be
able to use an ImageJ2 context. Also, Curtis and I both prefer using
Debug.run instead of a static initializer to launch from Eclipse.

So I would recommend using the Main class in the test directory of
TrackMate[1] to avoid premature IJ 1.x class loading. The existing
runFilter call didn't work for me, but if you use: "Debug.run("Tracks for
TrackMate (807K)", null);" in the main method then it will open Fiji, open
the TrackMate sample image, and then you can run TrackMate and test
FindMaxima.

Hope that helps. Let me know if you run into problems.

Best,
Mark

[1]
https://github.com/fiji/TrackMate/blob/v2.7.4/src/test/java/fiji/plugin/trackmate/Main.java

On Tue, Jul 14, 2015 at 10:20 AM, Thorsten Wagner <
wagner at biomedical-imaging.de> wrote:

> Dear Mark,
>
> thank you for your willingness to help me.
>
> No, we are not using the latest TrackMate master. I'm implementing the
> find-maxima detector for TrackMate and therefore I'm using a modified
> version [1] (this is the version which produces the exception) of the
> find-maxima branch of TrackMate [2] .
>
> To reproduce this error (sorry that I've forgotten this important
> information in my last mail!):
>  - Start TrackMate with the Main Method in the TrackMatePlugIn_.java (I'm
> using eclipse and select "Run as -> Java Application")
>  - Select "Next" in TrackMate
>  - Select the "Find Maxima" detector
>  - Select a arbitary threshold
>  - Press Preview
>
> The static initializer did not help.
>
> Thank you for your help!
>
> Cheers,
> Thorsten
>
> [1]
> https://github.com/thorstenwagner/TrackMate/tree/master/src/main/java/fiji/plugin/trackmate/detection/findmaxima (These
> classes containing all changes that I've made)
> [2] https://github.com/fiji/TrackMate/tree/find-maxima
>
> Am Dienstag, den 14.07.2015, 09:45 -0500 schrieb Mark Hiner:
>
> Hi Thorsten,
>
> >For some reasons we have to start TrackMate by the following main method:
>
> How exactly are you trying to launch TrackMate? Are you using the latest
> TrackMate master[1]? When I run this class in Eclipse, it works for me -
> launching TrackMate and opening the sample image (although I did have to
> change the path to http://fiji.sc/samples/FakeTracks.tif)
>
> >This is the exception:
> >http://pastebin.com/A3N5LQBw
>
> Note that this exception message includes suggested debugging and
> workaround options. It may be sufficient to add the suggested static
> initializer.
>
> >However, this just leads to another exception:
> >http://pastebin.com/m0VCTZ4S
>
> My first guess would be a class path problem with the way you are
> launching TrackMate. Also, it may be helpful to lean on the Fiji Debug
> launcher[2] to set things up properly. If you can share the exact command
> you used to launch (or your IDE environment) I can try to reproduce and
> debug.
>
> Best,
> Mark
>
> [1] https://github.com/fiji/TrackMate/commits/master
> [2] http://imagej.net/Developing_Fiji_in_Eclipse#Running_and_Debugging
>
> On Sat, Jul 11, 2015 at 4:17 AM, Thorsten Wagner <
> wagner at biomedical-imaging.de> wrote:
>
> Just an additional information:
>
> I tried to start it by imagej2:
>
> net.imagej.Main.main(args);
> new TrackMatePlugIn_().run( "/home/thorsten/samples/FakeTracks.tif" );
>
> However, this just leads to another exception:
> http://pastebin.com/m0VCTZ4S
>
> Cheers,
> Thorsten
>
> Am Samstag, den 11.07.2015, 11:14 +0200 schrieb Thorsten Wagner:
> > Dear List, dear Brian,
> >
> > we currently came across problems with ImageJ-OPs and TrackMate.
> >
> > For some reasons we have to start TrackMate by the following main
> > method:
> > https://github.com/thorstenwagner/TrackMate/blob/master/src/main/java
> > /f
> > iji/plugin/trackmate/TrackMatePlugIn_.java#L134
> >
> > However, this always leads to the a exception at this line:
> > https://github.com/thorstenwagner/TrackMate/blob/master/src/main/java
> > /f
> > iji/plugin/trackmate/detection/findmaxima/FindMaximaSpotDetector.java
> > #L
> > 123
> >
> > This is the exception:
> > http://pastebin.com/A3N5LQBw
> >
> > Any ideas?
> >
> > Cheers,
> > Thorsten
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel at imagej.net
> http://imagej.net/mailman/listinfo/imagej-devel
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20150715/b57106bf/attachment.html>