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  • 09:53

    kephale on scijava-compatible-pom

    Adjust way lwjgl natives are us… (compare)

  • 08:24

    kephale on scijava-compatible-pom

    Fix versions and repositories f… (compare)

  • 08:04

    kephale on scijava-compatible-pom

    Add more artifacts to version (compare)

  • Oct 16 19:17

    kephale on pyimagej-compatibility

    Update scenery version for Debo… (compare)

  • Oct 16 18:54

    kephale on scijava-compatible-pom

    build.gradle.kts: use pom-scija… Merge remote-tracking branch 'o… (compare)

  • Oct 16 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)

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?
then second column * -1 and third column * -1
which is rotation aroound x by 180deg as tobias said :)
Ulrik Günther
@skalarproduktraum
@axtimwalde x points to the right, y upwards, negative z into the screen
Stephan Saalfeld
@axtimwalde
"negative z into the screen" XD
"negative x points to the left, negative y points downwards"
Ulrik Günther
@skalarproduktraum
maybe i don't get the joke here, @axtimwalde ...?
Stephan Saalfeld
@axtimwalde
I noticed
I find it incredibly funny to describe the orientation of a vector by describing the direction it doesn't point at
but thanks for the clarification
Ulrik Günther
@skalarproduktraum
i also use not white as default background color
:-D
just for completeness, it's the same convention opengl uses
Stephan Saalfeld
@axtimwalde
excellent
the great thing with this is that the screen coordinate system actually never matters
if you make a camera at 0:x,0:y,-1:z that looks at 0:x,0:y,0:z, then you get the BDV/ ImgLib2/ image processing friendly right handed coordinate system with x pointing right, y pointing down, z pointing into the screen
Kyle I S Harrington
@kephale
hmm running into this with sciview from python
ScriptEngineManager providers.next(): javax.script.ScriptEngineFactory: Provider kotlin.script.experimental.jsr223.KotlinJsr223DefaultScriptEngineFactory could not be instantiated
ScriptEngineManager providers.next(): javax.script.ScriptEngineFactory: Provider kotlin.script.experimental.jsr223.KotlinJsr223DefaultScriptEngineFactory could not be instantiated
ScriptEngineManager providers.next(): javax.script.ScriptEngineFactory: Provider kotlin.script.experimental.jsr223.KotlinJsr223DefaultScriptEngineFactory could not be instantiated
ScriptEngineManager providers.next(): javax.script.ScriptEngineFactory: Provider kotlin.script.experimental.jsr223.KotlinJsr223DefaultScriptEngineFactory could not be instantiated
ScriptEngineManager providers.next(): javax.script.ScriptEngineFactory: Provider kotlin.script.experimental.jsr223.KotlinJsr223DefaultScriptEngineFactory could not be instantiated
waiting[ERROR] Module threw error
java.lang.NoSuchMethodError: 'void kotlin.jvm.internal.MutablePropertyReference1Impl.<init>(java.lang.Class, java.lang.String, java.lang.String, int)'
    at graphics.scenery.Node.<clinit>(Node.kt)
    at graphics.scenery.SceneryBase.<init>(SceneryBase.kt:54)
    at sc.iview.SciView.<init>(SciView.kt:234)
    at sc.iview.DefaultSciViewService.makeSciView(DefaultSciViewService.java:112)
    at sc.iview.DefaultSciViewService.getOrCreateActiveSciView(DefaultSciViewService.java:175)
    at sc.iview.ActiveSciViewPreprocessor.getValue(ActiveSciViewPreprocessor.java:64)
    at sc.iview.ActiveSciViewPreprocessor.getValue(ActiveSciViewPreprocessor.java:48)
    at net.imagej.display.process.SingleInputPreprocessor.process(SingleInputPreprocessor.java:83)
    at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:154)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:834)