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  • Sep 20 08:02
    erjel closed #22
  • Sep 20 08:02
    erjel commented #22
  • Sep 19 19:42
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  • Sep 19 09:59
    erjel opened #22
  • Sep 19 08:18

    tpietzsch on master

    Create Simi/TGMM import dialogs… Add TODO (compare)

  • Sep 19 05:43
    tischi commented #26
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    ctrueden commented #26
  • Sep 18 12:16

    tpietzsch on serialize-feature-model2

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  • Sep 18 12:16

    tpietzsch on master

    Implements the Contextual metho… Interface for classes that can … Feature serialization service a… and 36 more (compare)

  • Sep 18 12:16
    tpietzsch closed #106
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    tpietzsch on serialize-feature-model2

    Make UpdateStackSerializationTe… Make TrackMateImporterTest work… Make MaMuTExporterTest work hea… (compare)

  • Sep 18 12:09
    jburel opened #237
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    jburel opened #236
  • Sep 18 11:37
    tischi commented #26
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    tpietzsch synchronize #106
  • Sep 18 11:13

    tpietzsch on serialize-feature-model2

    Make TrackMateImporterTest work… Make MaMuTExporterTest work hea… (compare)

  • Sep 17 21:46
    tpietzsch synchronize #106
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    tpietzsch on serialize-feature-model2

    Make UpdateStackSerializationTe… (compare)

Brian Northan
@bnorthan
So I think there is a place for some simpler examples aimed at ImageJers interested in learning about KNIME. I have a few examples that are a bit simpler (3-10 nodes, no meta nodes) that may be useful.
Curtis Rueden
@ctrueden
@bnorthan Would it make sense to put the notebooks into imagej-tutorials, scifio-tutorials, etc., as appropriate? Then we wouldn't need a new repo for each org.
Especially since as of now, the Scala notebook is really just a (fancier) port of an existing ImageJ tutorial. Keeping them together might (hopefully) help keep things in better sync.
I really like this idea. The only case I can imagine with notebooks not being appropriate for the tutorials repos is if the notebook is intended for something other than illustrating how to do stuff... like if they somehow start being used to do "real science" instead of training.
And in that case, we can create new repo(s) then, if it happens.
I'll try to be more responsive tomorrow so we can discuss further during work hours.
Kyle I S Harrington
@kephale
is there a wiki page with a list of data types for @ annotations in scripts (looking for how to trigger a checkbox)?
Kyle I S Harrington
@kephale
well it was kind of obvious as boolean, but it still might be useful to have a list of those data types (if one doesn't already exist, i couldnt find it via plugin pages on the wiki)
Kyle I S Harrington
@kephale
and a related thing, if i'm developing a script that uses annotations to grab inputs and testing it out by coding it in a separate project by symlinking the script into plugins/Scripts, then I can test code logic changes because the script is reread from file on each call, but the annotations seem to get read at menu generation time, so i end up restarting Fiji if I modify the input annotations to the script
loving this way of writing scripts for the biologists though, just making observations about the process
Curtis Rueden
@ctrueden
@kephale I made a short list in my workshop with @bnorthan in September: https://imagej.github.io/presentations/2015-09-04-imagej2-scripting/#/3/2
Please feel free to transcribe that onto the wiki! I suggest the script parameters page.
Kyle I S Harrington
@kephale
Cool! thanks!!!
Curtis Rueden
@ctrueden
Concrete classes that implement the org.scijava.widget.InputWidget interface will extend that though, of course.
Kyle I S Harrington
@kephale
1 related question: is there a way to add a static text field via @ annotation? i.e. to provide some instructions that shouldn't appear in an editable text area
Richard Domander
@rimadoma
@kephale use the option @Parameter(visibility = ItemVisibility.MESSAGE)
Kyle I S Harrington
@kephale
@rimadoma awesome, thanks
Curtis Rueden
@ctrueden
@kephale Why yes there is! Set the visibility to MESSAGE.
Oh sorry, I missed your reply, @rimadoma. Thanks.
Richard Domander
@rimadoma
:+1:
To include more things closer to the WidgetDemo.java I linked above.
In particular, multiple choice widgets (since those work now), and the message visibility thing.
Kyle I S Harrington
@kephale
zomg UIs are so easy now
done by lunchtime
Curtis Rueden
@ctrueden
Woot! :sparkles:
Curtis Rueden
@ctrueden
Jean-Yves Tinevez
@tinevez
This wiki page just became realler
Ulrik Günther
@skalarproduktraum
i like the testimonial part of that wiki page a lot :D
Jean-Yves Tinevez
@tinevez
@ctrueden Continuing from the github issue: How can I have the System Information command from something I launched from Eclipse with a main() method?
Jean-Yves Tinevez
@tinevez
There is a net.imagej.patcher.Debug, but I have an initialization error when I use it.
Ok signing off for today. See you!
Curtis Rueden
@ctrueden
Sorry I missed you, @tinevez. The System Information command is part of scijava-plugins-commands IIRC. So just add a runtime dependency on that temporarily.
Curtis Rueden
@ctrueden
@hinerm I released scijava stuff (pom-scijava, scijava-common), imagej stuff (pom-imagej, imagej-legacy, imagej-ops), and fiji stuff (pom-fiji).
Next, we need to: 1. release imagej-launcher 4.0.4 (fixes Win10 32-bit, thanks to @stelfrich); 2. release TrackMate, Simple_Neurite_Tracer and IO; 3. update imagej/imagej and fiji/fiji accordingly (which I guess means another pom-imagej and pom-fiji, oops...); 4. test and upload all to Java-8.
This update will: 1. fix Win10 32-bit memory allocation as mentioned above; 2. fix the preprocessor cancelation bug; 3. eliminate the batik uber-JAR, closing fiji/fiji#83 and addressing this forum post; 4. fix the "1 errors during plugin discovery" message some people have noticed, and relatedly, fix execution of ImageJ1 plugins from the script editor and via --run again.
Curtis Rueden
@ctrueden
Item 2 above (releasing the fiji components) is now done.
Jean-Yves Tinevez
@tinevez
@ctrueden sorry I was super tired.
I tried to run SystemInformation, but could not have a proper Service set to initialise from the main method. They are all null.
I have tried to run net.imagej.Main, etc up to no avail. I remember fighting this a while ago but could not retrieve the way to make it work.
This reminds me a bit of Quantum Theory: a snippet that creates the conditions in which you cannot determine why it is working.
Jean-Yves Tinevez
@tinevez
fiji/fiji#83 Thanks @ctrueden
Curtis Rueden
@ctrueden
@hinerm There are some remaining class clashes I am working out across Fiji relating to the XML classes. However, I think it is safe to upload the new scijava-common to the Java-8 update site any time. The imagej/imagej and fiji/fiji master branches will "catch up" to it very soon.
I will be in to the office ~1:30pm today, but feel free to upload it earlier if you wish.
Also, if you could cut the new release of imagej-launcher, that would be awesome. I didn't do it yet.
Curtis Rueden
@ctrueden
Then all that remains will be to release new poms again that fix the class clashes (probably via exclusions; researching now), and bump the version of net.imagej:imagej itself.
Kyle I S Harrington
@kephale
@ctrueden LMAO
@kmader ok i'm stumped about the notebook displays (given that I'm puttering at this in Clojure), I see that the jupyter-scala package is providing the display function but it is behind so many layers of abstraction that i'm having trouble figuring out where the actual code is
although it looks like the scala world solved this, do you happen to know anything about how you trigger an image to be rendered, like does one actually need to hook into the Jupyter ZeroMQ instance and send a MIME encoded image via JSON?