Running a Jython Script from the Command Prompt

Posted by MChapman on Feb 14, 2017; 10:05pm
URL: http://imagej.273.s1.nabble.com/Running-a-Jython-Script-from-the-Command-Prompt-tp5018100.html

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