Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Hadrien Mary
    @hadim
    Yes indeed. Python is what I use when I can
    Analyzing data with python/jupyter is just amazing
    I do Java because I have to :-) But I Have to a admit that IJ2 API and Java 8 make the process very smooth
    Much better than few years ago :-0
    Curtis Rueden
    @ctrueden
    @hadim KymographBuilder Jenkins job is ready.
    Hadrien Mary
    @hadim
    You are now admin
    Sure we could talk about that somedays
    If you can't backport issues to the fiji repo I'll do it tonight
    Curtis Rueden
    @ctrueden
    @hadim It looks like push access is not enough; I need admin to move it.
    Hadrien Mary
    @hadim
    @ctrueden done
    Curtis Rueden
    @ctrueden
    Thank you!
    Your testimonial! ;-) (If you don't like it, I can delete it. But these things are actually very helpful!)
    Hadrien Mary
    @hadim
    ahah
    no I like it
    Curtis Rueden
    @ctrueden
    OK, we have it! https://github.com/fiji/KymographBuilder
    You should still have admin—please let me know ASAP if not.
    Hadrien Mary
    @hadim
    Seems to be ok
    Curtis Rueden
    @ctrueden
    And the first jenkins build even passed! Whoa! (This never happens.)
    Hadrien Mary
    @hadim
    Thank for that @ctrueden
    Good
    Curtis Rueden
    @ctrueden
    And here it is in the Maven repo
    Hadrien Mary
    @hadim
    Last hing @ctrueden , I need your opinion on this
    I use a test tif file in resources https://github.com/fiji/KymographBuilder/tree/master/src/main/resources/testdata
    Which 8 Mo and make the JAR files big for nothing (at least for the end user)
    Curtis Rueden
    @ctrueden
    Umm, is it just for unit tests?
    If so, put it in src/test/resources instead.
    Hadrien Mary
    @hadim
    Well for now it's just for me
    Curtis Rueden
    @ctrueden
    Ideally you wouldn't even commit it to the git repository at all, though. It bloats the clones.
    Hadrien Mary
    @hadim
    ok
    Curtis Rueden
    @ctrueden
    There is a tool called git-annex for managing large associated binaries, but I haven't used it.
    Hadrien Mary
    @hadim
    yeah but it makes the testing very convenient
    hum ok I'll think about this
    Curtis Rueden
    @ctrueden
    If it isn't needed for automated tests either, then I would just commit to /data or something. If you really want it committed at all, as I said.
    Hadrien Mary
    @hadim
    I use it for this https://github.com/fiji/KymographBuilder/blob/master/src/main/java/fiji/plugin/kymographbuilder/KymographBuilder.java#L131
    Curtis Rueden
    @ctrueden
    @hadim I suggest splitting out that main method to a separate Main class in src/test/java and then put the TIFF into src/test/resources and then it will keep working. Alternately, you can use just hardcode a relative file path to ../../../../../data/mt.tif or whatever instead of using Class.getResource. If it's in your test code, it isn't very important.
    @hadim Your user profile now exists on the wiki.
    Hadrien Mary
    @hadim
    I'll do that. Thanks for the profile.
    Curtis Rueden
    @ctrueden
    I pushed some POM changes. I am done for now. The deps could use some tweaking but it's not urgent.
    FYI:
    $ mvn dependency:analyze
...
[WARNING] Used undeclared dependencies found:
[WARNING]    org.scijava:scijava-common:jar:2.56.0:compile
[WARNING]    io.scif:scifio:jar:0.27.2:compile
[WARNING]    net.imglib2:imglib2:jar:2.7.0:compile
[WARNING]    net.imagej:imagej-ops:jar:0.29.0:compile
[WARNING]    net.imagej:imagej-common:jar:0.20.1:compile
[WARNING] Unused declared dependencies found:
[WARNING]    net.imagej:imagej-legacy:jar:0.20.0:runtime
[WARNING]    junit:junit:jar:4.11:test
    I would also suggest making imagej-legacy <optional>true</optional> because you don't want others to inherit that from you.
    Hadrien Mary
    @hadim
    Ok
    Curtis Rueden
    @ctrueden
    @tpietzsch Maybe this helps you: scijava/scijava-scripts@1386a7b
    Curtis Rueden
    @ctrueden
    @hadim I totally lied about being done cleaning up that repo. I pushed some more commits. Hopefully everything is in order now. :smile:
    Hadrien Mary
    @hadim
    Nice changes. Thanks !
    Tobias Pietzsch
    @tpietzsch
    @ctrueden That's perfect, thanks! I'll try this the next time I do a bigger release
    Curtis Rueden
    @ctrueden
    @tpietzsch Great, let me know how it goes when you do. I didn't bother to explain the -v or -f or -s options but they should be simple to understand. In particular -s is nice to verify that it even constructs the pot the way you expect.
    Hadrien Mary
    @hadim
    Few questions for you @ctrueden (or anyone that can answer)
    1. I use ImagePlus.getRoi() to get the active ROI on the image. See https://github.com/fiji/KymographBuilder/blob/master/src/main/java/fiji/plugin/kymographbuilder/Utils.java#L148
    But it always returns null.
    (that's why I fallback and use RoiManager)