gistfile1.clj

(ns edu.harvard.connectome.convert-tiff-to-png
  (:gen-class)
  (:import [ij IJ ImagePlus])
  (:use [clojure.contrib io seq string :as s]))

(defn only-tiff (proxy [java.io.FilenameFilter] []
		  (accept [file name] (.endsWith name "tif"))))

(defn replace-extension [file old-ext new-ext]
  (.replace (str file) old-ext new-ext))

(defn convert [in-dir out-dir]
  (loop [tiffs (seq (.listFiles in-dir only-tiff))]
    (-> (first tiffs)
	.getAbsolutePath
	IJ/openImage
	(IJ/save (str out-dir (replace-extension tiff "tif" "png"))))
    (recur (rest tiffs))))