search

ariel-waisman / LabelsToROIs

A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
GNU General Public License v3.0
21 stars 9 forks source link

java error IOException: Mark invalid #13

Open tralfalmadaan opened 2 years ago

tralfalmadaan commented 2 years ago

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!