Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • May 24 22:17
    aryaman-gupta commented #474
  • May 24 12:21

    RuoshanLan on eyetracking-update

    AtomicSimulation: Remove unnece… Protein: Refactor throw/catch b… OpenGLSwapchain: Remove superfl… and 18 more (compare)

  • May 24 11:28
    skalarproduktraum opened #477
  • May 24 11:28

    skalarproduktraum on lwjgl-3.3.1

    Gradle: Bump lwjgl to 3.3.1 (compare)

  • May 19 20:41

    RuoshanLan on eyetracking-utilization

    WIP: use pom-scijava as impleme… Initialize with more required s… Add method to check the availab… and 67 more (compare)

  • May 18 19:47

    RuoshanLan on eyetracking-update

    add raivoulmesampling example a… (compare)

  • May 18 09:25
    skalarproduktraum commented #432
  • May 17 15:43
    moreApi commented #432
  • May 17 07:58
    elect86 commented #431
  • May 13 12:54

    moreApi on branch-of-jan

    (buffered)Volume: check if volu… (compare)

  • May 12 11:32
    skalarproduktraum ready_for_review #396
  • May 12 11:31
    skalarproduktraum commented #431
  • May 12 11:30
    skalarproduktraum commented #434
  • May 12 11:29
    skalarproduktraum commented #446
  • May 12 11:29

    skalarproduktraum on spirv_version

    (compare)

  • May 12 11:28

    skalarproduktraum on master

    ShaderCompiler: changes spirv v… (compare)

  • May 12 11:28
    skalarproduktraum closed #473
  • May 12 11:27
    skalarproduktraum commented #474
  • May 11 12:14

    moreApi on branch-of-jan

    SceneryBase.kt, VolumeManager.k… (compare)

  • May 09 16:21

    moreApi on branch-of-jan

    Settings: jvmOverloads for cons… (compare)

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
now i get a hard crash in the c runtime :-D
Kyle I S Harrington
@kephale
jgo's directory naming probably makes sense but seems a little silly
Ulrik Günther
@skalarproduktraum
same behaviour btw from git bash and cmd.exe, just checked for testing
Kyle I S Harrington
@kephale
if only it was the string's hash or smth
Ulrik Günther
@skalarproduktraum
windows 10 should not have a problem with that anymore (see link), but the behaviour is opt-in
nevertheless, there's a cpp exception uncaught:
Stack: [0x0000001459600000,0x00000014597f0000],  sp=0x00000014597e7630,  free space=1949k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [KERNELBASE.dll+0x34b59]
C  [VCRUNTIME140.dll+0x4411]
C  [ntdll.dll+0xa1406]
C  [_jpype.cp38-win_amd64.pyd+0x392ce]
C  [_jpype.cp38-win_amd64.pyd+0x3d3d2]
C  [_jpype.cp38-win_amd64.pyd+0x32585]
C  0x000001abcfb1ef97

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j  org.jpype.JPypeContext.newWrapper(J)V+16
v  ~StubRoutines::call_stub
j  org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j  org.jpype.JPypeContext.newWrapper(J)V+16
v  ~StubRoutines::call_stub
j  org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j  org.jpype.JPypeContext.newWrapper(J)V+16
v  ~StubRoutines::call_stub

siginfo: EXCEPTION_UNCAUGHT_CXX_EXCEPTION (0xe06d7363), ExceptionInformation=0x0000000019930520 0x00000014597ec660 0x00007ff99217e7d0 0x00007ff992100000