duncanmak

var doTree = function (tree, func) { 
    func (tree.value); 
    for (var child in tree.children) { doTree (child); } 
};

var makeNode = function (i) { return { value: i, children: [] };};

var numTree = { value: 42, children: [makeNode (1), makeNode (2)]};

var sumTree = function (i) { if (this.sum == undefined) this.sum = 0; else this.sum += i; };

duncanmak

(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))

duncanmak

(ns edu.harvard.connectome.convert-tiff-to-png
  (:gen-class)
  (:import [edu.harvard.connectome Dataset IterationCallback]
	   [ij IJ]))

(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))

duncanmak

ij> describe app.markup;
COLUMN_NAME         |TYPE_NAME|DEC&|NUM&|COLUM&|COLUMN_DEF|CHAR_OCTE&|IS_NULL&
------------------------------------------------------------------------------
ID                  |INTEGER  |0   |10  |10    |GENERATED&|NULL      |NO
PROCESS_ID          |INTEGER  |0   |10  |10    |NULL      |NULL      |NO
SECTION_ID          |INTEGER  |0   |10  |10    |NULL      |NULL      |NO
RED                 |SMALLINT |0   |10  |5     |NULL      |NULL      |NO
GREEN               |SMALLINT |0   |10  |5     |NULL      |NULL      |NO
BLUE                |SMALLINT |0   |10  |5     |NULL      |NULL      |NO
ALPHA               |SMALLINT |0   |10  |5     |NULL      |NULL      |YES

duncanmak

Test successful
Profiler: top 3 stack trace(s) of 595217 ms [build-139]:
11750/11786
at java.io.RandomAccessFile.writeBytes(Native Method)
at java.io.RandomAccessFile.write(Unknown Source)
at org.h2.store.FileStore.write(FileStore.java:332)
at org.h2.store.PageStore.checkpoint(PageStore.java:389)
at org.h2.store.PageStore.openExisting(PageStore.java:317)
at org.h2.store.PageStore.open(PageStore.java:264)
at org.h2.engine.Database.getPageStore(Database.java:2059)

duncanmak

class Test {
    
    public static abstract class Base {
	
	public Base (int x) { initialize (x); }

	protected String value;

	private void initialize (int x) {
	    

duncanmak

mac:foo duncan$ cat src/foo/core.clj
(ns foo.core (:require clojure.java.io))

(defn foo [] (println (file (System/getProperty "user.home"))))

mac:foo duncan$ java -cp "lib/*" clojure.main src/foo/core.clj
Exception in thread "main" java.lang.Exception: Unable to resolve symbol: file in this context (core.clj:3)
	at clojure.lang.Compiler.analyze(Compiler.java:5205)
	at clojure.lang.Compiler.analyze(Compiler.java:5151)
	at clojure.lang.Compiler$InvokeExpr.parse(Compiler.java:3036)

duncanmak

(ns ScriptIJ.distance-matrix
  (:import [java.awt.geom Point2D$Double]))

(defn ->point [m]
  (Point2D$Double. (Double/parseDouble (get m "XM"))
		   (Double/parseDouble (get m "YM"))))

(defn compute-matrix [table]
  (partition (count table)
	     (for [a table, b table]

duncanmak

(defmulti distance #(vector (class %1) (class %2)))
(defmethod distance [IPersistentVector IPersistentVector]
  [p q]
  (let [[x1 y1] p, [x2 y2] q]
      (.distance (Point. x1 y1) (Point. x2 y2))))

(defmethod distance [Point Point]
  [p q] (.distance p q))

duncanmak

(defn rotations [s]
  (map #(take (count s) (drop % (cycle s)))
       (range (count s)))