scenerygraphics/SciView

Come for the sciview, stay for the scenery -- we are phasing out gitter, come join our fancy new Zulip stream at https://imagesc.zulipchat.com/#narrow/stream/327495-scenery.2Bsciview :+1:

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

Kyle I S Harrington

@kephale

@skalarproduktraum https://github.com/scenerygraphics/sciview/blob/python-scripts/scripts/python_basic.py

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

okay, there seems to be a workaround: https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=cmd

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

Kyle I S Harrington

@kephale

jpype-project/jpype#928 ?

i wonder if it could be the jvm version as well

Ulrik Günther

@skalarproduktraum

@kephale that issues looks spot-on

and the jvm is the 11 azul jdk it's probably getting via conda

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