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    Ulrik Günther
    @skalarproduktraum
    hey everyone! quick question on commands: I'd like to have a dropdown of the open images in fiji, how do i declare this?
    (also -- somewhat belated -- a very happy new year to all of you!)
    Curtis Rueden
    @ctrueden

    Hi @skalarproduktraum :wave: :smile: Try this:

    @Parameter(autoFill = false)
    Dataset dataset;

    Or ImagePlus or Img or RandomAccessibleInterval.

    Ulrik Günther
    @skalarproduktraum
    ah, the autoFill is key. supercool, thanks!
    Curtis Rueden
    @ctrueden
    If you declare two such parameters, then you don't need the autoFill = false. But with only one, it fills in the currently "active image" (i.e. the one with the window in the foreground).
    :+1:
    Gabriel Selzer
    @gselzer
    @ctrueden @imagejan what's the status of the Batch search actions? I can't seem to find any chance to use them in Fiji, and they keep throwing errors when I try to run them in napari-imagej
    23 replies
    As far as napari-imagej goes, I can't tell if they just aren't working, or if that error is on me
    Jan Eglinger
    @imagejan
    @ctrueden I forgot what’s the recommended way to initialize a scijava command: 1) use an initializer = attribute in the @Plugin annotation of a DynamicCommand, or 2) implement org.scijava.Initializable?
    I vaguely remember there were some discussions about this, but was unsure.
    1 reply
    (maybe relevant: scijava/scijava-common#181)
    Mark Kittisopikul
    @mkitti
    I'm a bit confused if the scijava-pom is supposed to load javafx dependencies or not.
    9 replies
    Mark Kittisopikul
    @mkitti
    I'm making some progress on scijava/pom-scijava#181
    Mark Kittisopikul
    @mkitti
    In scijava/pom-scijava#181 above, some of the projects in a list have an exclusion: https://github.com/fiji/register_virtual_stack_slices/blob/c6dc334fde7f764f029c3965ec165c204eba4d83/pom.xml#L156-L160
    I'm assuming nothing has to be done there with regard to jhdf5 19.04?
    Mark Kittisopikul
    @mkitti
    Good morning @ctrueden , I sent some PRs related to scijava/pom-scijava#181 . Let me know if you would to discuss these at some point.
    Mark Kittisopikul
    @mkitti
    Is cisd.jhdf5.version preferred over jhdf5.version ?
    Tobias Pietzsch
    @tpietzsch
    Is cisd.jhdf5.version preferred over jhdf5.version ?
    Mark Kittisopikul
    @mkitti
    @ctrueden , what else needs to be done for scijava/pom-scijava#181 ? I have pull requests for most of the initial list and have a general idea how to fix other cases.
    Nicolas Chiaruttini
    @NicoKiaru
    @tinevez I remembered that you had a sort of graphical 'progress logger' for multiple long running tasks. Where is it ? Is it easy to use ? Thanks!
    Jean-Yves Tinevez
    @tinevez
    This guy?
    Nicolas Chiaruttini
    @NicoKiaru
    Yes!!
    Stiff ongoing ?
    still
    Jean-Yves Tinevez
    @tinevez
    Nope, I miss time for Mastodon nowadays, but I will come back to it soooooooon
    In the meantime feel free to cut it out of Mastodon for yourself.
    Nicolas Chiaruttini
    @NicoKiaru
    It would be super nice to have it in a more general repo. Scijava-common ?
    Jean-Yves Tinevez
    @tinevez
    If I can help ask
    Nicolas Chiaruttini
    @NicoKiaru
    Perfect, thanks
    Curtis Rueden
    @ctrueden
    @NicoKiaru @tinevez About the progress bars: my vision was to have a TaskService that lets you register Task objects and a task can have subtasks recursively, and then we can have a GUI that shows a progress bar for a task with an expandable triangle widget to show the next layer of progress bars below it. And to replace ImageJ's current progress bar with this better one. But as with so much in SciJava, this work was never completed.
    Gabriel Selzer
    @gselzer
    The experimental scijava-progress may or may not be of relevance here
    (But it is likely not practical for a little while :sweat_smile:)
    Jean-Yves Tinevez
    @tinevez
    @ctrueden do you wish for us to do it? But never dared to ask?
    We are your minions, you can.
    Curtis Rueden
    @ctrueden
    @tinevez It was started—there is a TaskService in SciJava Common now with Task objects that you can create—and the DownloadService uses it. I'd be happy to chat about requirements and whatnot any time, if you or @NicoKiaru or anyone has time and interest to develop it further. Perhaps all that would be needed is the user-interface portion of it now.
    Nicolas Chiaruttini
    @NicoKiaru
    @ctrueden cool! But how can I display the task with a progress bar ? Should I use the display service ?
    Curtis Rueden
    @ctrueden
    @NicoKiaru That was my point: these Task objects have no GUI support yet.
    I wrote some code for ImageJ-TensorFlow that hooks up the DownloadService tasks to the StatusService.
    This is totally the wrong place for logic like this... but until SciJava Common and SciJava UI Swing have better support for the TaskService directly, this is where we are.
    21 replies
    Nicolas Chiaruttini
    @NicoKiaru
    Thanks for the fast feedback. I'm not super familiar with 'events' in scijava. That's why I posted my initial thoughts. I'll look at how TaskEvent and EventHandler work first.
    Curtis Rueden
    @ctrueden
    TIL: attempting to outsmart limitations of the GitHub issue transfer mechanism is not a good idea! I had five issues in imagej/imagej-ui-swing with label component:script-editor, from back when the Script Editor lived in imagej-ui-swing. Since then, it moved to its own repository at scijava/script-editor, since it is more general than images. I wanted to transfer those five issues from imagej-ui-swing to script-editor, but you can only transfer an issue between repos of the same org. So! I created a new repo imagej/scijava-issue-shuttle and moved the five issues there. Then transferred scijava-issue-shuttle from imagej to scijava. But now, I'm not able to transfer the issues again from scijava-issue-shuttle to script-editor; no repositories appear on the list. Furthermore, two of the issues seem to have partially incomplete transfers, such that they still say they are "transferring" at the bottom. I fear they may be hosed now. So the end result is five deleted issues, i.e. five broken links, without successfully landing them at their new destinations in the end.
    Jean-Yves Tinevez
    @tinevez
    Could it be temporary and related to the issues GitHub has right now?
    Curtis Rueden
    @ctrueden
    Could be! I hope so.
    Curtis Rueden
    @ctrueden
    I solved it! I tried using gh issue transfer command line function, and it gave me an informative error: "Old issue cannot be transferred from private repository to public repository". Once I changed scijava-issue-shuttle to public, I was able to move them to the script-editor repo. Next time I'll try that command directly across orgs, and see if it works.
    Jan Eglinger
    @imagejan
    :blue_heart:
    Nicolas Chiaruttini
    @NicoKiaru
    @imagejan I'd like to try adding a progress bar (through the task service) on the batch module you wrote. Do you know where I could add this? There should be somewhere a main loop that goes through all the inputs, no?
    Nicolas Chiaruttini
    @NicoKiaru
    :+1:
    Nicolas Chiaruttini
    @NicoKiaru
    Above you can see a small demo of multiple progress bars for async tasks. It seems to work quite well. I will probably do an experimental demo update site and a forum post for those who want to test it. I've included it in by default in the batch processor, but with little effort, such a task specific progress bar can be added to any script or command.