Posted by
ctrueden on
Feb 15, 2017; 10:05am
URL: http://imagej.273.s1.nabble.com/Running-a-Jython-Script-from-the-Command-Prompt-tp5018100p5018103.html
Hi Mike,
> os.popen('"C:\Program Files\Fiji.app\ImageJ-win64.exe" -jython --run
"SomeScript.py"')
I think that this flag "-jython" is valid. There is an undocumented flag
"--jython" with two dashes which the ImageJ Launcher supports, but like all
the language-specific flags (e.g., --javascript, --clojure, etc.), it was
added before we switched to the unified SciJava script framework. So it
actually launches Java quite differently than using "--run", and it does
not make sense to mix the two.
The current way, according to the Scripting Headless [1] page, is to use:
ImageJ-win64.exe --ij2 --headless --run "SomeScript.py"
'sigma=5,label="GFP"'
where the "sigma" etc. argument is a list of key/value pairs corresponding
to the @ parameters of your script [2]. (Of course, if you have no such
parameters, you do not need to pass anything after the name of your script.)
Like you said, Jython+Windows+headless has (had?) a bug [3] which prevents
it from working. However, since that bug report, we have upgraded from
Jython 2.5.3 to 2.7.0—so it would actually be awesome if you could test now
whether it works. And if so, we can close that bug and remove the warning
from the wiki.
You could also try the old "--jython" flag and see if it works for you, but
in that case I would try something like:
ImageJ-win64.exe --jython "SomeScript.py"
And you will not be able to use the SciJava @ parameters.
Regards,
Curtis
[1]
http://imagej.net/Scripting_Headless[2]
http://imagej.net/Script_Parameters[3]
https://github.com/imagej/imagej/issues/114--
Curtis Rueden
LOCI software architect -
https://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
https://imagej.net/User:RuedenDid you know ImageJ has a forum?
http://forum.imagej.net/On Tue, Feb 14, 2017 at 10:05 PM, MChapman <
[hidden email]> wrote:
> Hello again,
>
> I have a set of image processing codes that go between Python and ImageJ by
> calling macro scripts from Python through the command prompt. One of these
> calls looks like:
>
> os.popen('"C:\Program Files\Fiji.app\ImageJ-win64.exe" --headless -macro
> "SomeScript.ijm"')
>
> In attempting to integrate "Register Virtual Stack Slices" the only way
> that
> I could figure out how to script it to work autonomously was with a Jython
> script. The script works fine on its own, but when I try to call it from
> Python it won't execute, it just opens up the script in the script editor
> instead of executing. The call looks like this:
>
> os.popen('"C:\Program Files\Fiji.app\ImageJ-win64.exe" --headless -jython
> "SomeScript.py"')
>
> I saw on the wiki that there is a known bug with jython and running
> headless, so I tried:
>
> os.popen('"C:\Program Files\Fiji.app\ImageJ-win64.exe" -jython
> "SomeScript.py"')
> os.popen('"C:\Program Files\Fiji.app\ImageJ-win64.exe" -jython --run
> "SomeScript.py"')
>
> but neither worked.
>
> Any advice on how to get this to execute properly?
>
> Thanks!
> Mike
>
>
>
>
> --
> View this message in context:
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> com/Running-a-Jython-Script-from-the-Command-Prompt-tp5018100.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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