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    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
    Hadrien Mary
    @hadim
    Last hing @ctrueden , I need your opinion on this
    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.
    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 !
    tpietzsch
    @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)
    But it always returns null.
    (that's why I fallback and use RoiManager)
    Any workaround to get the active ROI waiting for the new Overlay API.
    1. About fiji/KymographBuilder#1. Any idea what is the best way to merge two dataset along the CHANNEL axis ?
    Curtis Rueden
    @ctrueden
    @hadim I don't know the answer. But that question sounds super familiar. Did you ask it somewhere else? Or did someone else ask it on the forum maybe awhile back?
    Hadrien Mary
    @hadim
    @ctrueden I found nothing (Google or the forum)
    Curtis Rueden
    @ctrueden
    Maybe this thread? Not sure.
    Hadrien Mary
    @hadim
    All code there is IJ1 only
    Curtis Rueden
    @ctrueden
    For the second question: maybe Views.stack)?
    Hadrien Mary
    @hadim
    I am pretty sure the issue is related to IJ1/IJ2 conversion.
    I use this ImagePlus imp = ij.convert().convert(dataset, ImagePlus.class); to get the ImagePlus
    And getRoi return the correct Roi in jython...
    I'll have a look at Views.stack. Thanks
    Curtis Rueden
    @ctrueden
    The nice thing about Views is that it won't need to copy your pixels.
    But you'd have to rewrap it into a new Dataset afterward.
    Hadrien Mary
    @hadim
    Ok good to know.
    Curtis Rueden
    @ctrueden
    OK, regarding the getRoi being null: a Dataset cannot have a ROI. It can be part of an ImageDisplay which also includes other objects such as overlays. So if you convert directly from Dataset to ImagePlus then the resulting ImagePlus will never have a ROI.
    Hadrien Mary
    @hadim
    Ok so the only solution is to retrieve the ImagePlus via the IJ namespace I guess.
    Curtis Rueden
    @ctrueden
    Well, at the moment, the intended IJ2 way is to use the OverlayService to get the active overlay of an ImageDisplay.
    The ImageDisplay class is really more analogous to ImagePlus.