Posted by
Tim Schäfer on
Feb 05, 2014; 2:24pm
URL: http://imagej.273.s1.nabble.com/Running-the-Register-Virtual-Stack-Slices-plug-in-headless-tp5006424.html
Dear list,
we have been using the 'Register Virtual Stack Slices' Fiji plugin here
at Goethe-University Frankfurt and it worked well so far. Now, we would
like to be able to run our imaging pipeline headless on a cluster and
ran into some problems.
We used the jython script given at
http://fiji.sc/wiki/index.php/Register_Virtual_Stack_Slices#Scripting_.2F_PlugIn.
All works fine and the images get registered when we run the script
normally, e.g.:
/path_to/Fiji.app/ImageJ-linux64 ~/our_jython_script.py
But when using Fiji in headless mode (as described at
http://fiji.sc/wiki/index.php/Headless) like this:
/path_to/Fiji.app/ImageJ-linux64 --headless ~/our_jython_script.py
we get the error message attached to the bottom of this message.
Is it even possible to run 'Register Virutal Stack Slides' in headless
mode? Has anybody done this? Or are we doing something wrong?
(We are using the latest version of Fiji under 64bit Linux. Please ask
if you need more information on our installation, I will provide it
asap.)
Greetings from Germany and thanks in advance for your help,
--
Tim Schäfer
PhD student
Johann Wolfgang Goethe-University Frankfurt
Institute of Computer Science, Molecular Bioinformatics
+49 69 798-24655
www.bioinformatik.uni-frankfurt.de
---ERROR MESSAGE---
/path_to/Fiji.app/ImageJ-linux64 --headless ~/our_jython_script.py
Traceback (most recent call last):
File
"/home/patrick/improWorkspace/5806/ImproImageRegistrationPlugin/regexec.py",
line 1, in <module>
from register_virtual_stack import Register_Virtual_Stack_MT
java.lang.VerifyError: (class:
register_virtual_stack/Register_Virtual_Stack_MT, method: run signature:
(Ljava/lang/String;)V) Incompatible argument to function
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at
org.python.core.SyspathJavaLoader.loadClass(SyspathJavaLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
at org.python.core.Py.findClass(Py.java:774)
at
org.python.core.JavaImportHelper.isJavaClass(JavaImportHelper.java:182)
at
org.python.core.JavaImportHelper.tryAddPackage(JavaImportHelper.java:41)
at org.python.core.imp.import_next(imp.java:640)
at org.python.core.imp.import_name(imp.java:746)
at org.python.core.imp.importName(imp.java:806)
at
org.python.core.ImportFunction.__call__(__builtin__.java:1232)
at org.python.core.PyObject.__call__(PyObject.java:367)
at
org.python.core.__builtin__.__import__(__builtin__.java:1202)
at org.python.core.imp.importFromAs(imp.java:884)
at org.python.core.imp.importFrom(imp.java:860)
at
org.python.pycode._pyx0.f$0(/home/patrick/improWorkspace/5806/ImproImageRegistrationPlugin/regexec.py:14)
at
org.python.pycode._pyx0.call_function(/home/patrick/improWorkspace/5806/ImproImageRegistrationPlugin/regexec.py)
at org.python.core.PyTableCode.call(PyTableCode.java:165)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1204)
at
org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:200)
at org.python.util.jython.run(jython.java:246)
at org.python.util.jython.main(jython.java:129)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at imagej.ClassLauncher.launch(ClassLauncher.java:222)
at imagej.ClassLauncher.run(ClassLauncher.java:159)
at imagej.ClassLauncher.main(ClassLauncher.java:72)
java.lang.VerifyError: java.lang.VerifyError: (class:
register_virtual_stack/Register_Virtual_Stack_MT, method: run signature:
(Ljava/lang/String;)V) Incompatible argument to function
--
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