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  • Nov 19 22:22
    imagejan synchronize #90
  • Nov 19 12:16
    MaximeMaW commented #140
  • Nov 19 11:59
    tinevez closed #139
  • Nov 19 11:59
    tinevez commented #139
  • Nov 19 11:56
    tinevez commented #133
  • Nov 19 11:56
    tinevez closed #126
  • Nov 19 11:56
    tinevez commented #126
  • Nov 19 11:55

    tinevez on TrackMate_-5.0.2

    [maven-release-plugin] prepare … (compare)

  • Nov 19 11:55
    tinevez closed #140
  • Nov 19 11:55

    tinevez on master

    Fix bug in Capture action. The… Bump to next development cycle … (compare)

  • Nov 19 09:47
    MaximeMaW edited #140
  • Nov 19 07:24
    tinevez assigned #140
  • Nov 19 07:24
    tinevez labeled #140
  • Nov 19 07:24
    tinevez commented #140
  • Nov 18 21:19
    imagejan assigned #90
  • Nov 18 15:42
    MaximeMaW opened #140
  • Nov 14 19:00
    ctrueden commented #223
  • Nov 10 22:12
    SarenT opened #139
  • Nov 09 15:13

    ctrueden on master

    Bump to next development cycle … (compare)

  • Nov 09 15:13

    ctrueden on TrackMate_-5.0.1

    [maven-release-plugin] prepare … (compare)

Kabouik
@Kabouik
Alright it seems to work with the button "RUN" from the script editor (and "#@"), but not from Plugins/Macros/Run (weird, because I have another script that works from there). And I needed to edit the first lines to replace "style" with "value" to prefill the window asking for input and output paths.
Kabouik
@Kabouik
Thanks @imagejan, @ctrueden, for pointing into the right direction.
amirffff
@amirffff
Hi everyone
does someone programming with imageJ/Jthon and can help me please?
Curtis Rueden
@ctrueden
@Kabouik The Plugins/Macros/Run is an ImageJ 1.x command, which has not been tested with ImageJ2 scripts. Sorry for the confusion there.
@Kabouik The syntax looks correct, apart from the style attribute being used incorrectly, yeah.
The script should work if you press Run in script editor, and it should work if you place it into $IMAGEJ_DIR/scripts/Foo/Bar. Then it will appear in the Foo > Bar menu and should work from the menus, as well.
Curtis Rueden
@ctrueden
NOTICE: The ImageJ server infrastructure will be going down within the next few minutes. Downtime should be short (less than 10 minutes).
Curtis Rueden
@ctrueden
Servers should all be back online; please ping if you notice otherwise.
li8
@liberium_li8_twitter
I have taken several microscopy images through a camera but I can't upload then to Image J unless I use bio-format importing. The problem is that in this way I can't apply the color threshold, as it doesn't work properly, with all 3 items (Hue, saturation and brightness) appearing blank. Any ideas?
Jan Eglinger
@imagejan
@liberium_li8_twitter bio-formats will import as multi-channel hyperstack. Try converting to RGB first before using color threshold.
li8
@liberium_li8_twitter
It worked! Thank you very much! Have a nice day!
Varun Kapoor
@kapoorlab
Hi, what do I have to write in my pom.xml so that I can write import fiji.plugin* in my java code?
Jan Eglinger
@imagejan
@kapoorlab you can search http://maven.imagej.net for the classname you want to import, it will give the the necessary xml snippet for your POM
(and you shouldn't use wildcard imports, of course ;-)
Varun Kapoor
@kapoorlab
@imagejan Thanks :) no wildcards, ok am getting an error which I do not understand:
Failure to transfer sc.fiji:TrackMate_:jar:3.6.1 from http://maven.imagej.net/content/groups/public was cached in the local repository, resolution will not be reattempted until the update interval of imagej.public has elapsed or updates are forced.
tpietzsch
@tpietzsch
That means maven tried to download sc.fiji:TrackMate_:jar:3.6.1 and failed for some reason
It will not reattempt to download for some period of time
instead remember that this failed
you can force it retry by running with -U option
(e.g. mvn clean package -U)
@kapoorlab
Varun Kapoor
@kapoorlab
@tpietzsch yeah it is the reason thats bugging me, i will try force, clean with/without wifi/ethernet. Thanks Tobias
Curtis Rueden
@ctrueden
@kapoorlab If you still have trouble, you can also rm -rf ~/.m2/repository/sc/fiji/TrackMate_. This is sometimes necessary if a JAR file is corrupted during download.
amirffff
@amirffff
HI can I ask a question the manager of this Chat?
Niko Ehrenfeuchter
@ehrenfeu
@amirffff this is an open community, you can ask your question right here.
Varun Kapoor
@kapoorlab
@ctrueden Thanks Curtis, I got it working. About the 3D displayer, is it out already? When I try to use it I get: java.lang.NoClassDefFoundError: org/scijava/java3d/utils/universe/SimpleUniverse, Is hyperstack viewer the only other option left?
odinsbane
@odinsbane
Is there a way for providing an incremental update without updating an update site?
Jan Eglinger
@imagejan
@kapoorlab the class org.scijava.java3d.utils.universe.SimpleUniverse is in the org.scijava.j3dutils artifact: http://maven.imagej.net/#nexus-search;classname~org.scijava.java3d.utils.universe.SimpleUniverse
AFAICT, this is related to the 'old' 3D Viewer, and not SciView (if this is what you meant with "3D displayer"). SciView can be used via separate update site.
Jan Eglinger
@imagejan
@odinsbane what do you mean by incremental update? There's currently no possibility to define "inter-dependencies" between update sites. You can also point people to jar files built automatically by Travis and uploaded to the maven repository.
(If it's just for testing etc)
Why not uploading to the existing update site?
odinsbane
@odinsbane
I am doing some work with the plugin, so I might have more updates in the near future. Ill probably just upload to the existing site though.
I don't really have a good reason not to. It is just a pretty small change.
Varun Kapoor
@kapoorlab
@imagejan Thanks, I did that and now I get a new error: java.util.concurrent.ExecutionException: java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/PreProcessingSuite/natives/macosx-universal//gluegen-rt
There is no directory called natives in my PreProcessingSuite folder
Varun Kapoor
@kapoorlab
Maybe I will just try SciView
Varun Kapoor
@kapoorlab
@tinevez Same error in Trackmate when I try to run it from Eclipse as a cloned repo (execture TrackMatePLugin_.java): Exception in thread "TrackMate view rendering thread" java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/TrackMate/natives/macosx-universal//gluegen-rt
odinsbane
@odinsbane
@kapoorlab they should be in a jar file something along the line of gluegen-natives-rt or some such thing.
I don't know why, but for working with Intellij I had to unpack the jarfiles and then add the libraries to the java.library.path when I run programs with java3d.
Varun Kapoor
@kapoorlab
@odinsbane where did you get those jar files from?
odinsbane
@odinsbane
The all platforms will have everything, including other platforms. I just use the natives-macosx-universal.jar (s) Four of them.
On linux the native jar files load fine, but on osx, for some reason I had to unpack them. Although I think fiji/3d viewer works out of the box for me.
Varun Kapoor
@kapoorlab
The file has an extension of 7z, how do you unpack such a file?
odinsbane
@odinsbane
There is a program 7zip.
@kapoorlab Do you have a version of fiji working with the 3D viewer? If so it will have the jar files you need.
Varun Kapoor
@kapoorlab
Ah let me check