Re: trakEM jython script does not work in newer versions of Fiji

Posted by Mark Hiner on Oct 17, 2014; 2:02pm
URL: http://imagej.273.s1.nabble.com/trakEM-jython-script-does-not-work-in-newer-versions-of-Fiji-tp5010088p5010093.html

Hi all,

>Fiji does no longer autoimport classes

Sorry if this is off-topic, but this seemed like a good time to clarify
that this is no longer strictly the case.

There is now a plugin mechanism for Script Headers
<https://github.com/scijava/scijava-common/blob/master/src/main/java/org/scijava/script/ScriptHeader.java>.
These are per-language, and multiple headers can co-exist.

Apologies that this was not clear earlier, and is completely undocumented.
I will put something up on the wiki
<http://imagej.net/Script_Editor_Auto_Import> in the next hour or so and
link it in with the rest of the scripting documentation
<http://imagej.net/Scripting>.

Best,
Mark

On Fri, Oct 17, 2014 at 6:48 AM, Kirschmann, Moritz <
[hidden email]> wrote:

> Dear Albert,
>
> Thank you! Perfect!
>
> Best Moritz
>
> -----Original Message-----
> From: Albert Cardona [mailto:[hidden email]]
> Sent: Friday, October 17, 2014 11:34 AM
> To: <[hidden email]>; Kirschmann, Moritz
> Subject: Re: trakEM jython script does not work in newer versions of Fiji
>
> Hi Moritz,
>
> Fiji does no longer autoimport classes. Add this to the top:
>
> from ini.trakem2.display import Display
>
>
> ... and the jython script will work again.
>
> Best regards,
>
> Albert
>
>
> > On Oct 16, 2014, at 7:45 AM, "Kirschmann, Moritz" <
> [hidden email]> wrote:
> >
> > Dear TrakEM developers and experts,
> >
> > A jython script which has worked just fine for years, is broken by new
> versions of imagej and Fiji.
> > In the line of code
> > front = Display.getFront()
> > I get the message:
> > NameError: name 'Display' is not defined Is there a workaround for
> > this or a bug fix in sight, besides keeping an old version of Fiji?
> > Below is the full error message.
> >
> > Thank you very much for your help!
> >
> > Best regards from Switzerland, Moritz
> >
> >
> >
> >
> >
> >
> > Started Selectcolorinmultiplelayersver5_2mo.py at Wed Oct 15 15:57:40
> > CEST 2014 Traceback (most recent call last):
> >  File
> "C:\Users\kirsmori\Dropbox\FMI\Imagej_macros\EM_related\Selectcolorinmultiplelayersver5_2mo.py",
> line 79, in <module>
> >    front = Display.getFront()
> > NameError: name 'Display' is not defined
> >
> >               at
> org.python.core.PyException.fillInStackTrace(PyException.java:70)
> >               at java.lang.Throwable.<init>(Throwable.java:181)
> >               at java.lang.Exception.<init>(Exception.java:29)
> >               at
> java.lang.RuntimeException.<init>(RuntimeException.java:32)
> >               at org.python.core.PyException.<init>(PyException.java:46)
> >               at org.python.core.PyException.<init>(PyException.java:43)
> >               at org.python.core.PyException.<init>(PyException.java:61)
> >               at org.python.core.Py.NameError(Py.java:260)
> >               at org.python.core.PyFrame.getname(PyFrame.java:257)
> >               at
> org.python.pycode._pyx2.f$0(C:\Users\kirsmori\Dropbox\FMI\Imagej_macros\EM_related\Selectcolorinmultiplelayersver5_2mo.py:148)
> >               at
> org.python.pycode._pyx2.call_function(C:\Users\kirsmori\Dropbox\FMI\Imagej_macros\EM_related\Selectcolorinmultiplelayersver5_2mo.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:1275)
> >               at
> org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
> >               at
> org.scijava.script.ScriptModule.run(ScriptModule.java:175)
> >               at
> org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
> >               at
> org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
> >               at
> org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
> >               at
> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
> >               at
> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
> >               at java.util.concurrent.FutureTask.run(FutureTask.java:138)
> >               at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
> >               at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
> >               at java.lang.Thread.run(Thread.java:619)
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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