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:
- the driver is definitely compatible
- the example is not requesting any extensions
- 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
- i have fixed all gpu memory leaks i could find, and there are no more errors reported by the validations layers
- 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,...?
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😎
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)
and just for your info @NicoKiaru, @moreApi is just working on syncronising transformations between bdv and sciview
<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>
(which corresponds to inverting Y and Z)
(BDV also uses right-handed system, with Z pointing "into the screen")
then
second column * -1 and third column * -1
"negative x points to the left, negative y points downwards"
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
:-D
just for completeness, it's the same convention opengl uses
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
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
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