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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!
The text was updated successfully, but these errors were encountered:
Hi,
For my cellpose segmentation, I wanted to try out the labelsToRois plugin, but it doesn't want to start, raising a java exception.
The text was updated successfully, but these errors were encountered: