SciView cannot install on Fiji

turko9999 · December 23, 2020, 7:52am

I already updated my ImageJ and SciView but it gives me that error? What should i do?

3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily

C:\Users\TURKER'S PC\.ImageJ_3D_Viewer.props (Sistem belirtilen dosyayı bulamıyor)
nFrames = 1
nFrames = 1
nFrames = 1
nFrames = 1
Started application as PID 9196
[WARN] No such log level: İNFO
This is sciview 0.2.0-beta-9-SNAPSHOT (12709a0d) ) / scenery 0.7.0-beta-8-SNAPSHOT (9747a221) ( (12709a0d)  /  (9747a221))
Resetting language to Python
java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at sc.iview.DefaultSciViewService.makeSciView(DefaultSciViewService.java:127)
	at sc.iview.DefaultSciViewService.getOrCreateActiveSciView(DefaultSciViewService.java:175)
	at sc.iview.commands.LaunchViewer.run(LaunchViewer.kt:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	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$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ExceptionInInitializerError
	at org.python.core.PySystemState.<clinit>(PySystemState.java:73)
	at org.python.util.PythonInterpreter.threadLocalStateInterpreter(PythonInterpreter.java:80)
	at org.python.jsr223.PyScriptEngine.<init>(PyScriptEngine.java:27)
	at org.python.jsr223.PyScriptEngineFactory.getScriptEngine(PyScriptEngineFactory.java:85)
	at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:137)
	at org.scijava.script.DefaultScriptInterpreter.<init>(DefaultScriptInterpreter.java:104)
	at org.scijava.script.DefaultScriptInterpreter.<init>(DefaultScriptInterpreter.java:88)
	at org.scijava.script.ScriptREPL.lang(ScriptREPL.java:277)
	at org.scijava.script.ScriptREPL.lang(ScriptREPL.java:266)
	at sc.iview.ui.REPLEditor.setREPLLanguage(REPLEditor.java:150)
	at sc.iview.ui.REPLPane.<init>(REPLPane.java:94)
	at sc.iview.ui.SwingMainWindow.<init>(SwingMainWindow.kt:160)
	at sc.iview.SciView.init(SciView.kt:382)
	at graphics.scenery.SceneryBase.sceneryMain$suspendImpl(SceneryBase.kt:217)
	at graphics.scenery.SceneryBase.sceneryMain(SceneryBase.kt)
	at graphics.scenery.SceneryBase$main$1.invokeSuspend(SceneryBase.kt:491)
	at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
	at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:56)
	at kotlinx.coroutines.EventLoopImplBase.processNextEvent(EventLoop.common.kt:274)
	at kotlinx.coroutines.BlockingCoroutine.joinBlocking(Builders.kt:84)
	at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking(Builders.kt:59)
	at kotlinx.coroutines.BuildersKt.runBlocking(Unknown Source)
	at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking$default(Builders.kt:38)
	at kotlinx.coroutines.BuildersKt.runBlocking$default(Unknown Source)
	at graphics.scenery.SceneryBase.main(SceneryBase.kt:491)
	at sc.iview.DefaultSciViewService.lambda$makeSciView$0(DefaultSciViewService.java:114)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	... 4 more
Caused by: java.lang.IllegalArgumentException: Cannot create PyString with non-byte value
	at org.python.core.PyString.<init>(PyString.java:57)
	at org.python.core.PyString.<init>(PyString.java:70)
	at org.python.core.PyString.<init>(PyString.java:74)
	at org.python.core.Py.newString(Py.java:643)
	at org.python.core.PyJavaType.init(PyJavaType.java:543)
	at org.python.core.PyType$Registry.createType(PyType.java:477)
	at org.python.core.PyType$Registry.addFromClass(PyType.java:426)
	at org.python.core.PyType$Registry.resolveType(PyType.java:352)
	at org.python.core.PyType$Registry$1.computeValue(PyType.java:208)
	at org.python.core.PyType$Registry$1.computeValue(PyType.java:202)
	at java.lang.ClassValue.getFromHashMap(ClassValue.java:227)
	at java.lang.ClassValue.getFromBackup(ClassValue.java:209)
	at java.lang.ClassValue.get(ClassValue.java:115)
	at org.python.core.PyType.fromClass(PyType.java:2137)
	at org.python.core.PyObject.<init>(PyObject.java:85)
	at org.python.core.PySingleton.<init>(PySingleton.java:9)
	at org.python.core.PyNotImplemented.<init>(PyNotImplemented.java:10)
	at org.python.core.Py.<clinit>(Py.java:66)
	... 32 more

kephale · December 23, 2020, 7:45am

Hi @turko9999

Which version of Java are you using?

turko9999 · December 23, 2020, 10:52am

Version 8 Update 261
Edit: Now I updated to 271 but still giving same error message.

skalarproduktraum · December 23, 2020, 11:37am

Hi @turko9999 and welcome to the forum! This seems to be an issue with the Python/Jython interpreter. I’ll investigate and get back to you Sorry for the trouble!

skalarproduktraum · December 23, 2020, 11:46am

So it looks like Jython is choking on some non-ASCII characters. As there is this warning I am quoting here, could you check where this is set and remove it? If that doesn’t help, could you send me the output of Fiji’s Plugins > Debug > System Information in a private message please? Thanks!

turko9999 · December 23, 2020, 11:58am

Hello im so new on this forum, i cannot find the private message section. Yeah actually my username has an (’) I don’t know how can i make it happen but it also makes me sick

I think Im new user and forum is limiting my abilities, if u have a chance send me private message and i reply to you

skalarproduktraum · December 23, 2020, 11:57am

Just click on my name, and then on message

turko9999 · December 23, 2020, 11:59am

I think Im new user and forum is limiting my abilities, if u have a chance send me private message and i reply to you, when i get into my message box.

skalarproduktraum · December 23, 2020, 12:41pm

Hey! I sent you a private message, can you see it?

skalarproduktraum · December 23, 2020, 1:04pm

Okay, the system info you sent me looks good. Have you found where some log level is being set to İNFO?

turko9999 · December 23, 2020, 1:10pm

actually no, theres no İNFO thing on my computer, even in fiji’s folder

turko9999 · December 23, 2020, 1:22pm

I actully need SciView because of isosurface. Im making 3d model from layers, when im in 3d viewer try to export STL but i give “No meshes to export!” error. I search in the forum, someone said you need to do isosurface command first, then you can export as STL file.

kephale · December 23, 2020, 1:40pm

Move your Fiji to a directory that does not have special characters.

I can confirm that this is an error in SciJava’s Jython interpreter and not a direct issue with sciview. I will report the error there and link it to this thread.

kephale · December 23, 2020, 1:45pm

For completeness, you can find the issue/bug report here Jython error when script is stored in directory with non-standard characters · Issue #11 · scijava/scripting-jython · GitHub

turko9999 · December 23, 2020, 3:53pm

UMM still no. I moved in main directory in my D:/, so its location now D:/Fiji/ but still same error

Removed, downloaded, installed.Making updates and still i have this

Started application as PID 18000
[WARN] No such log level: İNFO
This is sciview 0.2.0-beta-9-SNAPSHOT (12709a0d) ) / scenery 0.7.0-beta-8-SNAPSHOT (9747a221) ( (12709a0d)  /  (9747a221))
Resetting language to Python
java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at sc.iview.DefaultSciViewService.makeSciView(DefaultSciViewService.java:127)
	at sc.iview.DefaultSciViewService.getOrCreateActiveSciView(DefaultSciViewService.java:175)
	at sc.iview.commands.LaunchViewer.run(LaunchViewer.kt:60)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	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$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ExceptionInInitializerError
	at org.python.core.PySystemState.<clinit>(PySystemState.java:73)
	at org.python.util.PythonInterpreter.threadLocalStateInterpreter(PythonInterpreter.java:80)
	at org.python.jsr223.PyScriptEngine.<init>(PyScriptEngine.java:27)
	at org.python.jsr223.PyScriptEngineFactory.getScriptEngine(PyScriptEngineFactory.java:85)
	at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:137)
	at org.scijava.script.DefaultScriptInterpreter.<init>(DefaultScriptInterpreter.java:104)
	at org.scijava.script.DefaultScriptInterpreter.<init>(DefaultScriptInterpreter.java:88)
	at org.scijava.script.ScriptREPL.lang(ScriptREPL.java:277)
	at org.scijava.script.ScriptREPL.lang(ScriptREPL.java:266)
	at sc.iview.ui.REPLEditor.setREPLLanguage(REPLEditor.java:150)
	at sc.iview.ui.REPLPane.<init>(REPLPane.java:94)
	at sc.iview.ui.SwingMainWindow.<init>(SwingMainWindow.kt:160)
	at sc.iview.SciView.init(SciView.kt:382)
	at graphics.scenery.SceneryBase.sceneryMain$suspendImpl(SceneryBase.kt:217)
	at graphics.scenery.SceneryBase.sceneryMain(SceneryBase.kt)
	at graphics.scenery.SceneryBase$main$1.invokeSuspend(SceneryBase.kt:491)
	at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
	at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:56)
	at kotlinx.coroutines.EventLoopImplBase.processNextEvent(EventLoop.common.kt:274)
	at kotlinx.coroutines.BlockingCoroutine.joinBlocking(Builders.kt:84)
	at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking(Builders.kt:59)
	at kotlinx.coroutines.BuildersKt.runBlocking(Unknown Source)
	at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking$default(Builders.kt:38)
	at kotlinx.coroutines.BuildersKt.runBlocking$default(Unknown Source)
	at graphics.scenery.SceneryBase.main(SceneryBase.kt:491)
	at sc.iview.DefaultSciViewService.lambda$makeSciView$0(DefaultSciViewService.java:114)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	... 4 more
Caused by: java.lang.IllegalArgumentException: Cannot create PyString with non-byte value
	at org.python.core.PyString.<init>(PyString.java:57)
	at org.python.core.PyString.<init>(PyString.java:70)
	at org.python.core.PyString.<init>(PyString.java:74)
	at org.python.core.Py.newString(Py.java:643)
	at org.python.core.PyJavaType.init(PyJavaType.java:543)
	at org.python.core.PyType$Registry.createType(PyType.java:477)
	at org.python.core.PyType$Registry.addFromClass(PyType.java:426)
	at org.python.core.PyType$Registry.resolveType(PyType.java:352)
	at org.python.core.PyType$Registry$1.computeValue(PyType.java:208)
	at org.python.core.PyType$Registry$1.computeValue(PyType.java:202)
	at java.lang.ClassValue.getFromHashMap(ClassValue.java:227)
	at java.lang.ClassValue.getFromBackup(ClassValue.java:209)
	at java.lang.ClassValue.get(ClassValue.java:115)
	at org.python.core.PyType.fromClass(PyType.java:2137)
	at org.python.core.PyObject.<init>(PyObject.java:85)
	at org.python.core.PySingleton.<init>(PySingleton.java:9)
	at org.python.core.PyNotImplemented.<init>(PyNotImplemented.java:10)
	at org.python.core.Py.<clinit>(Py.java:66)
	... 32 more

2020-12-23_18-50-28|690x111

turko9999 · December 23, 2020, 3:57pm

Im installing another computer, and boom, still giving same error

turko9999 · December 23, 2020, 4:04pm

Both PCs have installed python, i think python installation causes this error

turko9999 · December 23, 2020, 4:17pm

By the way, is there any option to export stl model without isosurface/sciview command in 3D viewer section?