Recipe11.15.Implementing an ImageJ Plug-in in Jython

Recipe 11.15. Implementing an ImageJ Plug-in in Jython

Credit: Ferdinand Jamitzky, Edoardo "Dado" Marcora

Problem

You perform image processing using the excellent free program ImageJ and need to extend it with your own plug-ins, but you want to code those plug-ins in Jython rather than in Java.

Solution

Jython can do all that Java can, but with Python's elegance and high productivity. For example, here is an ImageJ plug-in that implements a simple image inverter:

import ij class Inverter_py(ij.plugin.filter.PlugInFilter):     def setup(self, arg, imp):         """@sig public int setup(String arg, ij.ImagePlus imp)"""         return ij.plugin.filter.PlugInFilter.DOES_8G     def run(self,ip):         """@sig public void run(ij.process.ImageProcessor ip)"""         pixels = ip.getPixels( )         width = ip.getWidth( )         r = ip.getRoi( )         for y in range(r.y, r.y+r.height):             for x in range(r.x, r.x+r.width):                 i = y*width + x                 pixels[i] = 255-pixels[i]

Discussion

To make this plug-in usable from ImageJ, all you need to do is compile it into a Java bytecode class using the jythonc command with the appropriate command-line option switches. For example, I use IBM's open source Java compiler, jikes, and I have placed it into the C:\ImageJ directory, which also holds the plugins and jre subdirectories. So, in my case, the command line to use is:

# jythonc -w C:\ImageJ\plugins\Jython -C C:\ImageJ\jikes   -J "-bootclasspath C:\ImageJ\jre\lib\rt.jar -nowarn"

If you use Sun's Java SDK, or other Java implementations, you just change the -C argument, which indicates the path of your Java compiler and the -J argument, which specifies the options to pass to your Java compiler.

Recipe11.15.Implementing an ImageJ Plug-in in Jython