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  • 09:45

    elect86 on tunePom

    done (compare)

  • Oct 15 22:14
    Domino2357 synchronize #434
  • Oct 15 22:14

    Domino2357 on sidechains_new

    Added a new proteins package to… Rainbow; RainbowTests: correcte… (compare)

  • Oct 15 21:54
    Domino2357 synchronize #434
  • Oct 15 21:54

    Domino2357 on sidechains_new

    SpaceFillingExample: changed ac… (compare)

  • Oct 15 21:50
    Domino2357 synchronize #434
  • Oct 15 21:50

    Domino2357 on sidechains_new

    VRSidechainsExample: refactored… (compare)

  • Oct 15 21:31
    Domino2357 synchronize #434
  • Oct 15 21:31

    Domino2357 on sidechains_new

    Remaining changes from moving p… (compare)

  • Oct 15 21:31
    Domino2357 synchronize #434
  • Oct 15 21:31

    Domino2357 on sidechains_new

    Put everything proteins related… StickandBallProteinModel: chang… AminoAcidsStickandBall: fixed f… and 1 more (compare)

  • Oct 15 21:18
    Domino2357 synchronize #428
  • Oct 15 21:18

    Domino2357 on space_filling_diagram

    PubChemElemens_all.json: moved … (compare)

  • Oct 15 21:13
    Domino2357 synchronize #418
  • Oct 15 21:13

    Domino2357 on boundingBoxBugBrotein

    Curve: added bounding box again… RibbondiagramTests: fixed tests… (compare)

  • Oct 15 20:53
    Domino2357 synchronize #428
  • Oct 15 20:53

    Domino2357 on space_filling_diagram

    SpaceFillingDiagramExample: som… (compare)

  • Oct 15 20:50
    Domino2357 synchronize #428
  • Oct 15 20:50

    Domino2357 on space_filling_diagram

    SpaceFillingDiagramExample: cha… (compare)

  • Oct 15 20:45
    Domino2357 synchronize #418
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)
Jan T
@moreApi
I need a bit of linear algebra help. How does one convert a rotation to a "regular" righthand coordinate system (SciView) from a (x,-y,z)-system (BDV)? Simply multiplying the second colum of the transformation matrix with -1 like someone on SA metioned does not work.
Ulrik Günther
@skalarproduktraum
@NicoKiaru do you have some more specific info what errors you get? apart from that, i'm also happy to have a look at your demo soon
and just for your info @NicoKiaru, @moreApi is just working on syncronising transformations between bdv and sciview
NicoKiaru
@NicoKiaru
Great, thanks! Sure I think the first issue is to get the current dependencies right. Right now I have:
<sciview.version>121e036</sciview.version>
        <scenery.version>5de0b1e</scenery.version>

        <kotlin.version>1.4.20</kotlin.version>
        <kotlinx-coroutines-core.version>1.3.9</kotlinx-coroutines-core.version>
        <kotlin.compiler.jvmTarget>1.8</kotlin.compiler.jvmTarget>
Ulrik Günther
@skalarproduktraum
the kotlin things should actually come from sciview as transitive dependency
Tobias Pietzsch
@tpietzsch
@moreApi rotate by 180 degree about the X axis
(which corresponds to inverting Y and Z)
(BDV also uses right-handed system, with Z pointing "into the screen")
Stephan Saalfeld
@axtimwalde
sciview's y points upwards?