Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jan 26 20:35

    moreApi on synchronization-volume

    Volume: Fix build for Java 8 by… (compare)

  • Jan 26 16:54

    moreApi on synchronization-volume

    build.gradle: fix tests for jav… (compare)

  • Jan 24 17:27
    skalarproduktraum pinned #470
  • Jan 24 17:27
    skalarproduktraum edited #470
  • Jan 24 17:27
    skalarproduktraum labeled #470
  • Jan 24 17:27
    skalarproduktraum labeled #470
  • Jan 24 17:24
    skalarproduktraum opened #470
  • Jan 24 15:53

    moreApi on synchronization-volume

    SlicingPlane: syncs correctly (compare)

  • Jan 24 15:51

    moreApi on synchronization-volume

    DefaultNode: (post)update list … DefaultSpatial.kt: "Parent" nod… SlicingPlane: syncs correctly (compare)

  • Jan 23 13:02

    Domino2357 on peptide_chain

    ProteinForge: fixed first pictu… minor changes (compare)

  • Jan 23 08:39

    Domino2357 on peptide_chain

    StickAndBallProteinModel: fixed… (compare)

  • Jan 23 08:10

    Domino2357 on peptide_chain

    Proteinforge: prototype 2, work… ProteinforgeExample: make pictu… (compare)

  • Jan 23 07:31

    Domino2357 on peptide_chain

    AminoAcidTreeList: added code f… MoleculeTree: changed according… MoleculeMesh and CzclicMolecule… (compare)

  • Jan 21 15:06

    moreApi on better-access-to-vr-wheel-menu

    (compare)

  • Jan 21 15:06

    moreApi on master

    VR*SelectionWheel.kt: Make acti… Merge pull request #469 from sc… (compare)

  • Jan 21 15:06
    moreApi closed #469
  • Jan 21 13:19
    moreApi synchronize #469
  • Jan 21 13:19

    moreApi on better-access-to-vr-wheel-menu

    VR*SelectionWheel.kt: Make acti… (compare)

  • Jan 21 13:19
    moreApi review_requested #469
  • Jan 21 13:19
    moreApi opened #469
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)
gradle version doesnt work from python
but i think that is still a transitive dependency issue
Ulrik Günther
@skalarproduktraum
@kephale this one i know, it usually comes from mismatched kotlin versions
Kyle I S Harrington
@kephale
ok, that makes sense
Ulrik Günther
@skalarproduktraum
so transitive dependency issue is within possibilities as well
Kyle I S Harrington
@kephale
the dependency management through python seems to be more driven by pom-scijava than normal dependency management
but the gradle one just doesnt work
it gives
Traceback (most recent call last):
  File "ClassLoader.java", line 522, in java.lang.ClassLoader.loadClass
  File "ClassLoaders.java", line 178, in jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass
  File "BuiltinClassLoader.java", line 581, in jdk.internal.loader.BuiltinClassLoader.loadClass
java.lang.ClassNotFoundException: java.lang.ClassNotFoundException: com.sun.jna.Library

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "org.jpype.manager.TypeManager.java", line -1, in org.jpype.manager.TypeManager.findClassByName
  File "org.jpype.manager.TypeManager.java", line -1, in org.jpype.manager.TypeManager.lookupByName
  File "Class.java", line 398, in java.lang.Class.forName
  File "Class.java", line -2, in java.lang.Class.forName0
  File "SceneryBase.kt", line 507, in graphics.scenery.SceneryBase.<clinit>
  File "LazyLogger.kt", line 26, in graphics.scenery.utils.LazyLoggerKt.LazyLogger
  File "LazyLogger.kt", line 8, in graphics.scenery.utils.LazyLoggerKt.unwrapCompanionClass
  File "Class.java", line 1517, in java.lang.Class.getEnclosingClass
  File "Class.java", line -2, in java.lang.Class.getDeclaringClass0
  File "ClassLoader.java", line 522, in java.lang.ClassLoader.loadClass
  File "ClassLoaders.java", line 178, in jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass
  File "BuiltinClassLoader.java", line 579, in jdk.internal.loader.BuiltinClassLoader.loadClass
  File "BuiltinClassLoader.java", line 621, in jdk.internal.loader.BuiltinClassLoader.loadClassOrNull
  File "BuiltinClassLoader.java", line 698, in jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull
  File "BuiltinClassLoader.java", line 800, in jdk.internal.loader.BuiltinClassLoader.defineClass
  File "SecureClassLoader.java", line 174, in java.security.SecureClassLoader.defineClass
  File "ClassLoader.java", line 1017, in java.lang.ClassLoader.defineClass
  File "ClassLoader.java", line -2, in java.lang.ClassLoader.defineClass1
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "scripts/python_basic.py", line 42, in <module>
    SciView = jimport('sc.iview.SciView')
  File "/home/kharrin/anaconda3/envs/sciview/lib/python3.8/site-packages/scyjava/__init__.py", line 151, in jimport
    return jpype.JClass(class_name)
  File "/home/kharrin/anaconda3/envs/sciview/lib/python3.8/site-packages/jpype/_jclass.py", line 99, in __new__
    return _jpype._getClass(jc)
java.lang.NoClassDefFoundError: java.lang.NoClassDefFoundError: com/sun/jna/Library
Ulrik Günther
@skalarproduktraum
so what are you running? that's your python stuff right? i always wanted to try that, here's your chance :-D
Kyle I S Harrington
@kephale
you sir are right, it was a kotlin mismatch
but still gradle issue
link coming in a sec
the BDV version is mismatched for sciview_ageratum, but should be right for sciview
i'm just testing out a simple layer instead of the callback stuff we had before
Ulrik Günther
@skalarproduktraum
installing internet
Ulrik Günther
@skalarproduktraum
@kephale i am getting
$ python scripts/python_basic.py
Traceback (most recent call last):
  File "scripts/python_basic.py", line 43, in <module>
    HashMap = jimport('java.util.HashMap')
  File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\scyjava\__init__.py", line 150, in jimport
    start_jvm()
  File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\scyjava\__init__.py", line 45, in start_jvm
    _, workspace = jgo.resolve_dependencies(
  File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\jgo\jgo.py", line 426, in resolve_dependencies

    os.makedirs(workspace, exist_ok=True)
  File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\os.py", line 223, in makedirs
    mkdir(name, mode)
FileNotFoundError: [WinError 3] The system cannot find the path specified: 'C:\\Users\\ulrik\\.jgo\\net.imagej\\imagej\\2.1.0+graphics.scenery-scenery-5de0b1e+ome-formats-bsd-6.1.1+ome-formats-gpl-6.1.1+org.jetbrains.kotlin-kotlin-stdlib-jdk8-1.4.20+org.jetbrains.kotlinx-kotlinx-coroutines-core-1.3.9+sc.fiji-bigdataviewer-core-10.1.1-SNAPSHOT+sc.iview-sciview-92add67'
(the jgo folder is empty)
(python 3.8.8, on miniconda, just fyi)
Kyle I S Harrington
@kephale
@skalarproduktraum hm ok i dont know what the deal is on windows, but i do get past that on linux
jgo is supposed to link files from m2 into the jgo directory
but i'll note that it was insanely slow to fetch the dependencies
especially given that they were already present in my m2
15 minutes or so
but your error looks like some os specific issue since it is failing on a mkdir call
Ulrik Günther
@skalarproduktraum
ya just saw it actually fails on the mkdir
i created that dir manually but it still fails
aha, found the issue Error: Current working directory has a path longer than allowed for a Win32 working directory.
Ulrik Günther
@skalarproduktraum