Re: calling python script from macro

Posted by Aryeh Weiss on Nov 16, 2015; 11:14am
URL: http://imagej.273.s1.nabble.com/calling-python-script-from-macro-tp5014952p5014957.html

Many thanks to Pariksheet and Wayne. Both methods work.

The first time I ran them, I was prompted to download Jython.jar to the
plugins folder.
Then, I think ImageJ attempted to refresh menus, but as I run Fiji, I
had to restart the program.
Then my test script for running python from a macro worked.

Best regards,
--aryeh

On 16/11/2015 3:02 AM, Rasband, Wayne (NIH/NIMH) [E] wrote:

>> On Nov 15, 2015, at 5:16 PM, Pariksheet Nanda <[hidden email]> wrote:
>>
>> Hi Aryeh,
>>
>> On Sun, Nov 15, 2015 at 2:40 PM, Aryeh Weiss <[hidden email]> wrote:
>>> Is there a way to run a python script form a macro?
>>> i tried
>>> call(ij.plugin.Macro_Runner.runPython(pathToPythonScript, "");
>>> but that did not work.
> You can also run a python script using the eval() macro function, for example:
>
>     script = File.openAsString(pathToPythonScript);
>     eval("python", script);
>
> -wayne
>
>
>> There were 2 things that needed to be changed:
>>
>>     jythonText = File.openAsString(pathToPythonScript);
>>     call("ij.plugin.Macro_Runner.runPython", jythonText, "");
>>
>> ... namely:
>> 1) One needs to put quotes around the first class.method parameter to
>> call(...) as described in the function reference
>> (http://imagej.nih.gov/ij/developer/macro/functions.html#C).
>> 2) Instead of passing the path to the Jython file, one must instead
>> read in the file text for runPython(...) to interpret.
>>
>>
>> On the other hand if you are not trying to run an ImageJ Jython script
>> (e.g. using ImageJ specific imports, etc) and are instead running a
>> CPython script (https://learnwithtina.wordpress.com/2014/07/20/what-is-the-difference-between-python-and-cpython/)
>> in a "traditional" Python interpreter outside of ImageJ in a separate
>> process one would use exec(...):
>>
>>     exec("python", pathToPythonScript).
>>
>> Note with exec(...) one must use commas to separate any part of the
>> command that requires spaces.  For example while one may normally run
>> "python -c print(123)" on the command-line, in exec it is:
>>
>>     output = exec("python", "-c", "print(123)");
>>     print(output);
>>
>> Also note that "output" only seems to contain stdout not stderr *.
>> See the exec(...) examples here:
>> http://imagej.nih.gov/ij/macros/ExecExamples.txt
>>
>>
>>> --aryeh
>> Pariksheet
>>
>>
>> * Maybe to also see stderr one should use e.g. 2>&1 redirection, but
>> my weird system hangs on exec("sh", "-c", "ls") alone although
>> exec("ls") works fine.  A mystery for another time.
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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