Running the 'Register Virtual Stack Slices' plug-in headless

[Tim Schäfer]

 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
 [phone]
  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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Dear Tim,

I find the same error. Can you use a batch mode?

./ImageJ -batch ~/our_jython_script.py

ignacio


On Wed, Feb 5, 2014 at 3:24 PM, Tim <[hidden email]> wrote:

> 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
> [phone]
>  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
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Ignacio,

On Thu, 6 Feb 2014, Ignacio Arganda-Carreras wrote:

> I find the same error.

If you make an easy-to-reproduce package for me, I will fix it.

Ciao,
Dscho

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Hello Johannes,

I cannot attach a script file to this e-mail, so just copy the following
two lines to a script call "test-dscho.bsh":


import register_virtual_stack.Register_Virtual_Stack_MT;

p = new Register_Virtual_Stack_MT.Param();


And run it like this:

$ ImageJ --headless test-dscho.bsh

It seems the headless mode doesn't like the call to the constructor of the
inner class "Param".

Thanks for your help!


On Thu, Feb 6, 2014 at 4:01 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Ignacio,
>
> On Thu, 6 Feb 2014, Ignacio Arganda-Carreras wrote:
>
> > I find the same error.
>
> If you make an easy-to-reproduce package for me, I will fix it.
>
> Ciao,
> Dscho
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: [phone]
> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Ignacio,

On Sat, 8 Feb 2014, Ignacio Arganda-Carreras wrote:

> Here you are a script that reproduces the error. Just run it like this:
>
> $ ImageJ --headless test-dscho.bsh
>
> It seems the headless mode doesn't like the call to the constructor of the
> inner class "Param".

Here is what I did: keeping in mind that a VerifyError is thrown when
bytecode is loaded into a class loader (*long* before it is executed, if
it is executed at all), I commented out method by method, returning true
or null when necessary, and running your script every single time, until
the error went away.

Then I reverted the comments partially, until I got at the offending
lines.

See https://github.com/fiji/fiji/pull/68

Ciao,
Dscho

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