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  • Sep 17 17:39

    Domino2357 on protein_builder

    VRControllerExample.kt,VRSelect… VRControllerExample.kt,VRGRab.k… SelectionWheel: move wheel node… and 18 more (compare)

  • Sep 17 15:18

    ctrueden on scijava-bom

    WIP: use pom-scijava as impleme… (compare)

  • Sep 17 11:29

    kephale on scijava-common

    Hard code scijava-common versio… (compare)

  • Sep 14 20:30

    kephale on kotlin-versions

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  • Sep 14 20:29

    kephale on master

    Test kotlinx-coroutines-core 1.… Fix version Update versions for kotlin-stdl… and 1 more (compare)

  • Sep 14 20:29
    kephale closed #401
  • Sep 14 20:29
    kephale opened #401
  • Sep 14 20:20

    kephale on kotlin-versions

    Update versions for kotlin-stdl… (compare)

  • Sep 14 15:13

    kephale on kotlin-versions

    Fix version (compare)

  • Sep 14 15:07

    kephale on kotlin-versions

    Test kotlinx-coroutines-core 1.… (compare)

  • Sep 14 14:30

    kephale on master

    Find -bom and make dependency t… Fix bom dependency finding Add jackson fix and 1 more (compare)

  • Sep 14 14:30
    kephale closed #400
  • Sep 14 14:29
    kephale opened #400
  • Sep 14 14:14
    kephale closed #443
  • Sep 14 14:14
    kephale opened #443
  • Sep 14 13:50

    kephale on pom-bom-fix

    Add jackson fix (compare)

  • Sep 14 13:37

    kephale on pom-bom-fix

    Fix bom dependency finding (compare)

  • Sep 14 12:41

    kephale on pom-bom-fix

    Find -bom and make dependency t… (compare)

  • Sep 14 11:37

    kephale on master

    Remove hardcoded log.level from… (compare)

  • Sep 14 11:31

    kephale on jitpack-pom

    (compare)

Kyle I S Harrington
@kephale
it looks like pom-scijava is behind on kotlin though
@hanslovsky you're using 1.4.30?
happy to align the update site to match ntakt for now
Philipp Hanslovsky
@hanslovsky

would it be possible to align via pom-scijava insteadl?

Last time I checked it was on 1.4.20 or older so I would rather not do that. It will likely be more complicated than that because scripting-kotlin needs to be distributed as a shaded jar including kotlin-compiler-embeddable and shaded JetBrains fork of trove. Otherwise, the compiler will fetch the incorrect classes from standard GNU trove. We could have a kotlin-compiler-embeddable-shaded jar in SciJava space that both SciView and scripting-kotlin could depend on. (Other dependencies may have kotlin-compiler-embeddable as runtime dependency, making things a little hairy when installing into scijava.app.directory)

@hanslovsky you're using 1.4.30?

Yes. I could update to 1.4.31 and see if that works

Kyle I S Harrington
@kephale
arg i see
ok if you want to push to 1.4.31 or 1.4.32 then we can go up to those as well (i'd have to check first of course)
Philipp Hanslovsky
@hanslovsky
Yeah, the annoying JetBrains fork of trove is what makes everything so hard and they do not show any intent of shading it themselves. It would not be a problem if they forked version 3 but they forked version 1...
Ulrik Günther
@skalarproduktraum
maybe we should push them towards thaat
i actually have a version of that included with sciview, but i changed the group id so it doesn't clash with anything :-D
Philipp Hanslovsky
@hanslovsky

maybe we should push them towards thaat

Would be great if they changed it :thumbsup:

Philipp Hanslovsky
@hanslovsky
So I deleted all jars with kotlin version 1.4.20 in Fiji.app/jars and kotlin-scripting worked inside the Script Interpreter but not in SciView (NullPointerException). Gotta run now
Ulrik Günther
@skalarproduktraum
@hanslovsky that's the same issue i had :(
Tobias Pietzsch
@tpietzsch
Is there a ntakt gitter channel?
Ulrik Günther
@skalarproduktraum
what is ntakt?
Kyle I S Harrington
@kephale
ntakt == imklib2
Jan Eglinger
@imagejan
If you guys get scripting-kotlin work reliably, it would be awesome to have it shipped with core Fiji (i.e. on the Java-8 update site) — and bump kotlin to 1.4.31 in pom-scijava — so that it’s accessible as script language for all users!
Philipp Hanslovsky
@hanslovsky
Yes, that is the plan in the long term. It works reliably if installed on its own but there will always be issues if another jar depends on kotlin-compiler-embeddable. Probably best to create a shaded jar of that in the SciJava org and then have downstream depend on that
@skalarproduktraum https://github.com/saalfeldlab/ntakt fka imklib
Ulrik Günther
@skalarproduktraum
@hanslovsky supercool! i saw you're having publishing to maven in the pipeline, if you need inspiration, check out the scenery build scripts that @elect86 built, they support signing and everything needed to publish to sonatype :+1:
Ulrik Günther
@skalarproduktraum
new docs, everyone! this time on gamepad input handling: https://docs.scenery.graphics/scenery/controls-and-input-handling/gamepads
Domino2357
@Domino2357
Pretty cool article, thanks for sharing!
Ulrik Günther
@skalarproduktraum
your are most welcome, @Domino2357 :+1:
Domino2357
@Domino2357
Does gitter have some sort of search function?
Giuseppe Barbieri
@elect86
yes, but it suxs
left corner, on top
Domino2357
@Domino2357
seems to work better than threading at least :D
thanks!
Aryaman Gupta
@aryaman-gupta
I am facing issues with using the composite build of sciview and scenery, and I would appreciate any suggestions
I am using the composite build as is available on the latest version of sciview, with scenery included in the settings.gradle.kts file. However, while scenery seems to be imported by gradle, and I can see both scenery and sciview tasks in the Gradle window on the right of IntelliJ, scenery does not appear in the project view on the left and I cannot open scenery source files
Does anyone know what may be wrong?
Giuseppe Barbieri
@elect86
It might not perform the substitution at the end, can I have a look sometimes tomorrow or so?
2 replies
Giuseppe Barbieri
@elect86
@skalarproduktraum it looks like we might have a dep issue with imagej:mesh, https://github.com/scenerygraphics/sciview/commit/622d0dba6ab829f7d5b1da0539294bc909ebbfb7#r50038119
Domino2357
@Domino2357
Maybe @skalarproduktraum or @elect86 you can have a quick glance at #415 ? This is probably trivial, but I am not seeing it at the moment.
1 reply
Ulrik Günther
@skalarproduktraum
@Domino2357 see my reply :+1:
Giuseppe Barbieri
@elect86

Maybe @skalarproduktraum or @elect86 you can have a quick glance at #415 ? This is probably trivial, but I am not seeing it at the moment.

404

Ulrik Günther
@skalarproduktraum
Domino2357
@Domino2357

@Domino2357 see my reply :+1:

Wow, that was quick! Thanks!

Ulrik Günther
@skalarproduktraum
@Domino2357 i was puzzled by the same issue a while ago :-D
Jan T
@moreApi
How can I make SciView respect origin = Origin.Centerof a volume?
Ulrik Günther
@skalarproduktraum

sooooooooo, here's a puzzle for everyone: i am currently preparing docker images to run scenery and sciview (and our graphical CI stuff), and i have encountered an issue there: after 34 (of 38) integration tests/examples, the next example fails at creating a vulkan instance, either complaining that the driver is incompatible, or that i requested an extension that's not available. i have figured out/done:

  1. the driver is definitely compatible
  2. the example is not requesting any extensions
  3. it doesn't matter in which order the examples run, random or not, example 35 fails -- actually both on my local machine and on the ci xD
  4. i have fixed all gpu memory leaks i could find, and there are no more errors reported by the validations layers
  5. the time is also set correctly (this one is for @elect86 :-D)

any ideas? is it the moon? the constellation of the planets? solar winds?

55 replies
@moreApi what kind of volume is it? raivolume, bufferedvolume,...?
Jan T
@moreApi
im setting the world matrix of the volume directly if that might be an issue
same for bufferd or rai
also setting the inverse of the viewmatrix as the world of the volume looks promising for the bdv <> sciview thing😎
Ulrik Günther
@skalarproduktraum
that would be the issue, yes. the only place where the origin plays a role is in the composeModel function
Jan T
@moreApi
ok thanks then I probatly have to dive in the way sciview builds volumes and squeze a pivot node in there
Ulrik Günther
@skalarproduktraum
you could probably still squeeze that shift in, because that's the last mult that's happening to the model matrix of the volume.
Jan T
@moreApi
I will have a look tomorrow but I am hopeful :)
Jan T
@moreApi
sadly its the second to last mult. Scale comes afterwards
NicoKiaru
@NicoKiaru
Hi everybody, I regularly (let's say once every 6 months) try to catch-up with sciview in order to see if sciview can communicate with bigdataviewer-playground. So, if @kephale or @skalarproduktraum or anybody else has time to investigate, I'd be pleased to know if you can make this demo work : https://github.com/bigdataviewer/bigdataviewer-playground/blob/sciview/src/test/src/sc/fiji/bdvpg/sciview/SciViewDemo.java ? Cheers (currently on my setup I get errors on sciview startup)