http://imagej.273.s1.nabble.com/Running-the-Register-Virtual-Stack-Slices-plug-in-headless-tp5006424p5006435.html
I find the same error. Can you use a batch mode?
> 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
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>