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  • Apr 03 13:43

    tpietzsch on master

    clean up (compare)

  • Apr 02 15:58

    tpietzsch on mastodon-1.0.0-beta-15

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

  • Apr 02 15:58

    tpietzsch on master

    Bump to next development cycle … (compare)

  • Apr 02 15:53

    tpietzsch on update-bdv-core

    (compare)

  • Apr 02 15:53

    tpietzsch on master

    Update ui-behaviour version to … WIP: adopt new BDV UI Fix key event dispatch All sho… and 1 more (compare)

  • Apr 02 15:53
    tpietzsch closed #114
  • Apr 02 15:53
    tpietzsch opened #114
  • Apr 02 15:52

    tpietzsch on update-bdv-core

    Update ui-behaviour version to … WIP: adopt new BDV UI Fix key event dispatch All sho… and 1 more (compare)

  • Apr 02 15:50

    tpietzsch on generalize-plugin-annotations

    (compare)

  • Apr 02 15:50

    tpietzsch on absolute-paths

    (compare)

  • Apr 02 15:50

    tpietzsch on master

    POM: update dependency versions… Maintain the absolute/relative … Don't just fail when opening a … (compare)

  • Apr 02 15:50
    tpietzsch closed #113
  • Apr 02 15:49

    tpietzsch on master

    Use more general type in all @P… Merge pull request #112 from ma… (compare)

  • Apr 02 15:49
    tpietzsch closed #112
  • Mar 31 10:47
    tpietzsch synchronize #113
  • Mar 31 10:47

    tpietzsch on absolute-paths

    POM: update dependency versions… Maintain the absolute/relative … Don't just fail when opening a … (compare)

  • Mar 31 10:35
    tpietzsch opened #113
  • Mar 31 10:33

    tpietzsch on absolute-paths

    POM: update dependency versions… Maintain the absolute/relative … Don't just fail when opening a … (compare)

  • Mar 30 17:36

    tinevez on update-bdv-core

    Update ui-behaviour version to … WIP: Try to update to the new B… (compare)

  • Mar 30 15:47
    tpietzsch opened #112
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.
Curtis Rueden
@ctrueden
@tinevez It looks like you already were able to successfully upload to TrackMateCSVImporter?
But just in case, I granted JeanYvesTinevez user the permission as well, for the future.
Jean-Yves Tinevez
@tinevez
yep. I had forgotten about the upload password. @imagejan reminded me and everything rolled.
Jean-Yves Tinevez
@tinevez
The exclusions fix does not have an effect. I think I may have to live with -Dskip.enforcer=true for a while.
Curtis Rueden
@ctrueden
I'd suggest checking the dependency tree using the Dependency Hierarchy tab of the pom.xml in Eclipse.
You can search it for where the commons-io is coming in.
You need to plug all holes in your metaphorical boat.
Jean-Yves Tinevez
@tinevez
I should frame this and hang it in the lab.
Jean-Yves Tinevez
@tinevez
@ctrueden fixed, thanks!
Curtis Rueden
@ctrueden
👍
Philipp Hanslovsky
@hanslovsky
:plus1:
For people who prefer command line, you can also run:
mvn dependency:tree
Curtis Rueden
@ctrueden
@hanslovsky Beware: mvn dependency:tree does pruning, unlike the Eclipse UI.
Philipp Hanslovsky
@hanslovsky
@ctrueden I am not 100% sure what that means but definitely good to know (and somewhat unexpected).
Curtis Rueden
@ctrueden

@hanslovsky It means the dependency tree listed by dependency:tree can be incomplete compared to the one given by Eclipse. For example, the dependency:tree for net.imagej:imagej says:

[INFO] +- net.imagej:imagej-legacy:jar:0.29.0:runtime (optional)
[INFO] |  +- net.imagej:ij1-patcher:jar:0.12.8:runtime (optional)
[INFO] |  +- net.imagej:ij:jar:1.51s:runtime (optional)
[INFO] |  +- net.imglib2:imglib2-ij:jar:2.0.0-beta-39:runtime (optional)
[INFO] |  +- org.scijava:scijava-search:jar:0.4.0:runtime (optional)
[INFO] |  +- org.scijava:scijava-ui-awt:jar:0.1.6:runtime
[INFO] |  +- org.scijava:scijava-ui-swing:jar:0.9.5:runtime
[INFO] |  |  +- org.scijava:swing-checkbox-tree:jar:1.0.2:runtime
[INFO] |  |  \- net.sourceforge.jdatepicker:jdatepicker:jar:1.3.2:runtime
[INFO] |  \- org.javassist:javassist:jar:3.22.0-GA:runtime (optional)

But imagej-legacy has additional dependencies such as imagej-common. The imagej-common dependency is not shown because it is already a direct dependency of imagej. So even though it is also inherited transitively, this fact is not visible from the output. So if your goal is to add exclusions to stop all leakage of a particular dependency, this tool is only sufficient if you check the tree iteratively.

Philipp Hanslovsky
@hanslovsky
Ugh, that's frustrating. Thanks for the clarification @ctrueden
Jan Eglinger
@imagejan
Would using mvn dependency:tree -Dverbose make any difference?
Curtis Rueden
@ctrueden
@imagejan "Verbose not supported since maven-dependency-plugin 3.0"
My understanding, from my time reading the Maven mailing list, is that the dependency resolution mechanism was changed rather deeply between Maven 2 and Maven 3, and in particular the maven-dependency-plugin works quite differently between v2 and v3. I guess v2 was hackier but better in some ways, whereas v3 is more well architected but ends up being less flexible/powerful? That might be a misrepresentation/oversimplification, though.
Jean-Yves Tinevez
@tinevez
@hadim Could you check the FilamentDetector plugin?
I can launch the GUI but as soon as I trigger any kind of processing, Fiji hangs with 0% CPU and I have to kill -9 Fiji to get it back. I can reproduce on all computers I have access to.
Hadrien Mary
@hadim
@tinevez I'll have a look today.
Did you install it from the update site or from Eclipse?
Hadrien Mary
@hadim
@tinevez I tried to install it from a fresh Fiji installation with the update site and it works fine for me.
(on Linux)
Which OS did you used?
Jean-Yves Tinevez
@tinevez
Macosx.
True I did not try on another is.
I installed it from the update site. I will give another try on another os.
Hadrien Mary
@hadim
Ok. For me it works on Windows and Linux (never tried on Macosx).
Shuang
@27hushuang_twitter
Did anyone have the problem that when you setup the readFromCD, the study did not show up under the Read. It's PET/CT data from Triumph PET/CT small animal scanner
Curtis Rueden
@ctrueden
@27hushuang_twitter Could you please give some context? Are you talking about something in Fiji? If so, which plugin? What steps did you take?
Shuang
@27hushuang_twitter
Thanks for replying. I am using the PET/CT view in Fiji. I followed the tutorial from https://www.youtube.com/watch?v=BK8tG6odVXg&feature=youtu.be , After setup the the Dicom path, there's no information under Read. Based on my understanding, after choosing the path, the data should automatically appear under Read?
Curtis Rueden
@ctrueden
@27hushuang_twitter The authors of that plugin, Ilan Tal and Salim Kanoun, are not in this Gitter channel. Could you please post a new thread on forum.imagej.net and mention @Salim_Kanoun in your message? Hopefully he can help you!
Shuang
@27hushuang_twitter
@ctrueden Got it, thank you.
Jean-Yves Tinevez
@tinevez
@hadim Apologies: I could get it to run on Windows. I will investigate Macs.
Hadrien Mary
@hadim
@tinevez glad you get it to work. Let me know how it goes.