I want to use ImageJ to do some processing of several thousand images.

Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically?

For example, say I want to take my thousand images and apply a polar transformation to each---

A polar transformation plugin for ImageJ can be found here:

http://rsbweb.nih.gov/ij/plugins/polar-transformer.html

Great! Let's use it. From:

[http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog]

I find that I can apply a plugin using the following:

(defn x-polar 
     [imageP]
     (let [thread (Thread/currentThread)
       options ""]
       (.setName thread "Run$_polar-transform")
       (Macro/setOptions thread options)
       (IJ/runPlugIn imageP "Polar_Transformer" "")))

This is good because it suppresses the dialog which would otherwise pop up for every image. But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image.

The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying.

Does what I want but is absolutely retarded:

(defn x-polar 
     [imageP]
     (let [thread (Thread/currentThread)
       options ""]
       (.setName thread "Run$_polar-transform")
       (Macro/setOptions thread options)
       (IJ/runPlugIn imageP "Polar_Transformer" "")
       (let [return-image (IJ/getImage)]
     (.hide return-image)
     return-image)))

I'm obviously missing something about how to use imageJ plugins in a programming context. Does anyone know the right way to do this?

Thanks, --Robert McIntyre