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java error IOException: Mark invalid #13

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tralfalmadaan opened this issue Oct 3, 2022 · 0 comments
Open

java error IOException: Mark invalid #13

tralfalmadaan opened this issue Oct 3, 2022 · 0 comments

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@tralfalmadaan
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Hi,
For my cellpose segmentation, I wanted to try out the labelsToRois plugin, but it doesn't want to start, raising a java exception.

  Warning AbstractCLIJ2Plugin.setCLIJ is deprecated. Use setCLIJ2 instead.

  [ERROR] java.io.IOException: Mark invalid
	  at java.io.BufferedReader.reset(BufferedReader.java:512)
	  at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:133)
	  at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:321)
	  at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:317)
	  at org.python.jsr223.PyScriptEngine.compileScript(PyScriptEngine.java:90)
	  at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
	  at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	  at org.scijava.script.ScriptModule.run(ScriptModule.java:164)
	  at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
	  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)
  java.io.IOException: java.io.IOException: Mark invalid 


	at org.python.core.Py.JavaError(Py.java:547)
	at org.python.core.ParserFacade.fixParseError(ParserFacade.java:107)
	at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:136)
	at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:321)
	at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:317)
	at org.python.jsr223.PyScriptEngine.compileScript(PyScriptEngine.java:90)
	at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:164)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
	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.io.IOException: Mark invalid
	at java.io.BufferedReader.reset(BufferedReader.java:512)
	at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:133)
	... 14 more
'''

I'm running 
Fiji (IJ 1.52t Java 1.8.0_172 64-bit) on Windows 11
I copied Labels_To_Rois.py to my plugin folder.

This is not a CLIJ vs CLIJ2 error is it?

Thanks!
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