Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jan 20 17:42
    matthiasLEBEC commented #82
  • Jan 20 17:41
    matthiasLEBEC commented #82
  • Jan 20 17:41
    matthiasLEBEC commented #82
  • Jan 20 17:41
    matthiasLEBEC commented #82
  • Jan 20 17:40
    matthiasLEBEC commented #82
  • Jan 17 16:25
    tinevez assigned #23
  • Jan 17 16:25
    tinevez opened #23
  • Jan 10 15:15

    tinevez on TrackMate_-5.2.0

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

  • Jan 10 15:15

    tinevez on master

    Bump to next development cycle … (compare)

  • Jan 10 15:13

    tinevez on label-img-exporter

    (compare)

  • Jan 10 15:13

    tinevez on master

    An action to export tracking re… Export label image: add methods… Export label image: add methods… and 4 more (compare)

  • Jan 10 15:13
    tinevez closed #147
  • Jan 10 15:04
    tinevez edited #147
  • Jan 10 14:59
    tinevez synchronize #147
  • Jan 10 14:59

    tinevez on label-img-exporter

    Export label image: add methods… Export to label image: options … Add a main method as a demo. and 1 more (compare)

  • Jan 10 08:12
    tinevez opened #147
  • Jan 10 08:08

    tinevez on label-img-exporter

    Export label image: add methods… (compare)

  • Jan 09 13:22

    tinevez on label-img-exporter

    An action to export tracking re… (compare)

  • Jan 09 12:11

    tinevez on label-img-exporter

    WIP: An action to export tracki… (compare)

  • Dec 26 2019 15:37
    ctrueden commented #223
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
odinsbane
@odinsbane
When I go into the Fiji.app folder, they're under jars/macosx/ Then there are four of them.
Varun Kapoor
@kapoorlab
Oh yeah the 3D viewer works in Fiji, just not on eclipse
odinsbane
@odinsbane
I spent a little time trying to get Intellij to work with the native jar files and not unpack them, but I just ended up unpacking them and it worked.
Varun Kapoor
@kapoorlab
I c, so I have to point these jars on the java build path for the repo I want to use the 3D viewer in, right?
odinsbane
@odinsbane
The only way I could get it to work was to unpack the jarfiles and then when I run the program include an argument to the jvm. -Djava.library.path=/path/to/folder/with/jnilibs
Hopefully somebody chimes in with the correct way to do this. I would much prefer to just include the jarfiles.
Varun Kapoor
@kapoorlab
No it works that way, I just did this to trackmate in eclipse: Right click on repo, -> Build Path -> Add external Archives -> Then add all the four jars in the Fiji macos folder that you mentioned and then it works
Curtis Rueden
@ctrueden
@odinsbane It should not be necessary to manually unpack natives from JARs in IntelliJ. The Java code is supposed to provide magic to take care of that for you. Maybe @skalarproduktraum has some insight?
Jean-Yves Tinevez
@tinevez
Hi all.
I am having troubles creating a new update site for Fiji.
I successfully created the TrackMateCSVImporteraccount on the wiki, and validated my email. But when I try to create the corresponding update site in Fiji updater, it does not work.
I cliked on Add my site in the updater, and input TrackMateCSVImporter as account name. The updater then asks me for my password, but it rejects it and this message appears in the console:
Did not get a token!
Did I do something wrong?
Jan Eglinger
@imagejan
You did set the upload password in addition to your wiki password, right?
Jean-Yves Tinevez
@tinevez

And another question: (sorry for the spam).
I meet a enforcer-related compile error for this very project.
It depends on the bioformats_plugin artifact, and it generate the following error:

[WARNING] Rule 3: org.apache.maven.plugins.enforcer.BanDuplicateClasses failed with message:
No Duplicate Classes Allowed!
- For duplicate transitive dependencies, add dependency exclusions.
- For duplications between direct dependencies, resolve or add
  ignored classes to this rule's configuration.

  Found in:
    commons-io:commons-io:jar:2.6:compile
    ch.systems.cisd:jhdf5:jar:14.12.0:compile
  Duplicate classes:
    org/apache/commons/io/FileCleaningTracker.class
    org/apache/commons/io/comparator/SizeFileComparator.class
    org/apache/commons/io/output/ProxyWriter.class

which is fine I guess. But how to skip this?

@imagejan .... no
Where do you do this?
Jan Eglinger
@imagejan
Also note that it's better to ask @ctrueden to add upload permissions to your existing personal account, instead of creating a new account...
Sorry, on mobile. ...
Jean-Yves Tinevez
@tinevez
ok.
Jan Eglinger
@imagejan
Special page set upload password on the wiki.
Jean-Yves Tinevez
@tinevez
aaaaaaah
Jan Eglinger
@imagejan
Re enforcer: you can add exclude statements to your pom, no?
It should all be documented somewhere on the wiki :smile:
Jean-Yves Tinevez
@tinevez
this one is a tough nut to crack even with google.
Curtis Rueden
@ctrueden
<properties><enforcer.skip>true</enforcer.skip></properties>
But then we come to your house with torches and pitchforks.
For testing and development, it is temporarily OK. But better to fix with exclusions as mentioned in the error message.
The problem is that ch.systems.cisd:jhdf5 is an uber-JAR.

You can avoid the error by adding:

<exclusions>
  <exclusion>
    <groupId>commons-io</groupId>
    <artifactId>commons-io</artifactId>
  </exclusion>
</exclusions>

in the <dependency> block of whatever dependency is pulling in commons-io.

Best fix would be for us to deploy a new jhdf5 that does not do this evilness.
Jean-Yves Tinevez
@tinevez
ok thanks this is clear.
Curtis Rueden
@ctrueden
Regarding the update site: as @imagejan said, I can create whatever update site you want, without you needing to make a wiki account, if you ask. And I can grant JeanYvesTinevez and/or other users permission to push to it .
Jean-Yves Tinevez
@tinevez
I did not know. What do you favor?
Curtis Rueden
@ctrueden
I have a weak preference to avoid creating dummy wiki accounts solely for the side effect of making an update site. But I do not care a lot—I fully appreciate that you can do it right now without waiting for other humans by doing that.
Jean-Yves Tinevez
@tinevez
Agreed.