Merge branch 'master' of https://github.com/nno/burstiDAtor

.gitignore

@@ -3,5 +3,8 @@
 *.m~
 .git.bfg-report
 build
+bin
 *.jar
 .*.sw?
+.classpath
+.project

Makefile

@@ -10,20 +10,11 @@ ENTRY_POINT = burstiDAtor/BurstiDAtor
 
 BUILD_DIR = build/java
 
-SOURCE_FILES = \
-java/burstiDAtor/Burst.java \
-java/burstiDAtor/BurstWizard.java \
-java/burstiDAtor/BurstiDAtor.java \
-java/burstiDAtor/Bursts.java \
-java/burstiDAtor/Props.java \
-java/burstiDAtor/Settings.java \
-java/burstiDAtor/Spikes.java \
-java/burstiDAtor/Utils.java
+SOURCE_FILES = $(wildcard java/burstiDAtor/*.java)
 
 JAVAC = javac
 JFLAGS = -encoding UTF-8
 
-
 vpath %.class build/java
 vpath %.java java
 
@@ -37,7 +28,7 @@ Default:
 	@echo "make run: run your app."
 	@echo "make jar: package your project into a executable jar."
 
-build: $(SOURCE_FILES:.java=.class) 
+build: ${BUILD_DIR} $(SOURCE_FILES:.java=.class)
 
 # pattern rule
 %.class: %.java
@@ -58,7 +49,7 @@ clean:
 run: build
 	java -cp build/java $(ENTRY_POINT)
 
-jar: build
+jar: clean build
 	jar cvfe $(JAR_PKG) $(ENTRY_POINT) -C build/java .
 
 

java/burstiDAtor/AutoCorr.java

@@ -0,0 +1,82 @@
+package burstiDAtor;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import javax.imageio.ImageIO;
+
+public class AutoCorr extends Histogram {
+    public AutoCorr(Spikes spikes) {
+	super();
+	int n_spikes = spikes.length();
+
+	Settings settings = Settings.getInstance();
+	SpikeDelta min_isi = SpikeDelta.fromString(settings.getS("autocorr_min"));
+	SpikeDelta max_isi = SpikeDelta.fromString(settings.getS("autocorr_max"));
+	SpikeDelta binwidth = SpikeDelta.fromString(settings.getS("autocorr_binwidth"));
+
+	int n_bins = max_isi.subtract(min_isi).divideCeil(binwidth);
+
+	for (int i = 0; i <= n_bins; i++) {
+	    bins.add((double) i);
+	    if (i<n_bins) {
+	    	counts.add(0);
+	    }
+	}
+
+	if (n_spikes<2) {
+	    return;
+	}
+
+	for (int i = 0; i < n_spikes; i++) {
+	    for (int j = i + 1; j < spikes.length(); j++) {
+		SpikeDelta delta = new SpikeDelta(spikes.get(i), spikes.get(j));
+		int bin = getBin(min_isi, binwidth, delta);
+		boolean too_small = bin < 0;
+		boolean too_large = bin >= n_bins;
+		boolean keep = !(too_small || too_large);
+		if (keep) {
+		    counts.set(bin, 1 + counts.get(bin));
+		}
+		if (too_large) {
+		    break;
+		}
+	    }
+	}
+    }
+
+    public static int getBin(SpikeDelta t_onset, SpikeDelta binwidth, SpikeDelta t) {
+	int bin = t.subtract(t_onset).divideFloor(binwidth);
+	return bin;
+    }
+
+    public BufferedImage getPlot() {
+	return super.getPlot("time (ms)");
+    }
+
+
+    public static void main(String... _) throws Exception {
+	String d = "/Users/nick/tmp/";
+
+	String[] fns = { "neuron 1 651542.txt", "neuron 2 653286.txt", "Neuron 3 653284.txt" };
+
+	for (int i = 0; i < fns.length; i++) {
+
+	    String fn = "/Users/nick/tmp/" + fns[i];
+	    File f = new File(fn);
+	    Spikes spikes = new Spikes(f);
+	    AutoCorr ac = new AutoCorr(spikes);
+
+	    BufferedImage img = ac.getPlot();
+
+	    try {
+		// Save as PNG
+		File file = new File("/Users/nick/tmp/neuron" + (i + 1) + ".png");
+		ImageIO.write(img, "png", file);
+
+	    } catch (IOException e) {
+	    }
+
+	}
+    }
+}

java/burstiDAtor/Burst.java

@@ -4,9 +4,9 @@
 
 /**
  * Contains onset information of spikes in a burst
- * 
+ *
  * @author nick
- * 
+ *
  */
 public class Burst {
     Vector<Double> onsets;
@@ -20,7 +20,7 @@ public Burst() {
 
     /**
      * add a spike to the burst
-     * 
+     *
      * @param onset
      *            time of the spike
      */
@@ -30,7 +30,7 @@ public void add(double onset) {
 
     /**
      * Compute statistics for this burst
-     * 
+     *
      * @param fs
      *            Optional list of property keys to return. If null or empty
      *            then all keys are returned.