Running ThunderSTORM headless ?

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Ian M

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Jun 15, 2016, 11:16:09 AM6/15/16
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Hello All 

I hope that somebody can help me?
. I'm attempting to run ThunderSTORM using Imagej's --headless option with the goal of running on a cluster.

However I am getting a java.lang.RuntimeException: java.awt.HeadlessException
at cz.cuni.lf1.lge.ThunderSTORM.results.IJResultsTable.getResultsTable(IJResultsTable.java:56)

when it tries to instantiate an IJResultsTable which makes sense as this extends ResultsTableWindow
I don't suppose anyone has had any success doing this?

Best Wishes

Ian


Felix Wäldchen

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Jun 28, 2018, 7:35:05 AM6/28/18
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Hi Ian,

just following up on this (I know it's been 2 years...). Did you manage to run Thunderstorm on your cluster? I'm facing the same problem right now.

Best,
Felix

MajkaH

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Feb 4, 2019, 9:49:42 AM2/4/19
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Hi,

I'm using the virtual desktop Xvnc4, so it is not running headless, but I get java.lang.RuntimeException: java.lang.NullPointerException (see below). Does anybody have an idea why it is happening?

Thank you very much,
Maria

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release

java.lang.RuntimeException: java.lang.NullPointerException
at cz.cuni.lf1.lge.ThunderSTORM.results.IJResultsTable.getResultsTable(IJResultsTable.java:46)
at cz.cuni.lf1.lge.ThunderSTORM.AnalysisPlugIn.storeFits(AnalysisPlugIn.java:272)
at cz.cuni.lf1.lge.ThunderSTORM.AnalysisPlugIn.run(AnalysisPlugIn.java:251)
at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
at ij.IJ.runUserPlugIn(IJ.java:230)
at ij.IJ.runPlugIn(IJ.java:192)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:308)
at ij.IJ.run(IJ.java:364)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:188)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:206)
at org.python.core.PyObject.__call__(PyObject.java:515)
at org.python.core.PyObject.__call__(PyObject.java:519)
at org.python.pycode._pyx0.f$0(/fsimb/groups/imb-microscopycf/Maria/data/Kirsten/Lars/cluster_test/thunderstorm_3d.py:23)
at org.python.pycode._pyx0.call_function(/fsimb/groups/imb-microscopycf/Maria/data/Kirsten/Lars/cluster_test/thunderstorm_3d.py)
at org.python.core.PyTableCode.call(PyTableCode.java:171)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1614)
at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:296)
at org.python.util.jython.run(jython.java:362)
at org.python.util.jython.main(jython.java:142)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
Caused by: java.lang.NullPointerException
at cz.cuni.lf1.lge.ThunderSTORM.results.GenericTableWindow.<init>(GenericTableWindow.java:56)
at cz.cuni.lf1.lge.ThunderSTORM.results.ResultsTableWindow.<init>(ResultsTableWindow.java:63)
at cz.cuni.lf1.lge.ThunderSTORM.results.IJResultsTable.<init>(IJResultsTable.java:70)
at cz.cuni.lf1.lge.ThunderSTORM.results.IJResultsTable$1.run(IJResultsTable.java:40)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:301)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

lhj...@gmail.com

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May 6, 2019, 1:17:09 PM5/6/19
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Hi

I am trying to run ThunderSTORM using ImageJ's --headless option too. I had the problem as same as yours. So I was wondering if you figured out how to deal with this?

Best,
Luhong

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