From 05ae0a7f1926dd499532cca42208467c21745c0f Mon Sep 17 00:00:00 2001
From: Kota Miura <miura@embl.de>
Date: Thu, 24 May 2012 10:31:23 +0200
Subject: [PATCH] changed the package name to gmm

---
 .../ext/GrayLevelClassMixtureModeling.java    | 224 ------------------
 .../gmm/GrayLevelClassMixtureModeling.java    | 224 ++++++++++++++++++
 .../{ext => gmm}/MixtureModeling_.java        |   2 +-
 3 files changed, 225 insertions(+), 225 deletions(-)
 delete mode 100644 src/emblcmci/ext/GrayLevelClassMixtureModeling.java
 create mode 100644 src/emblcmci/gmm/GrayLevelClassMixtureModeling.java
 rename src/emblcmci/{ext => gmm}/MixtureModeling_.java (99%)

diff --git a/src/emblcmci/ext/GrayLevelClassMixtureModeling.java b/src/emblcmci/ext/GrayLevelClassMixtureModeling.java
deleted file mode 100644
index 100b534..0000000
--- a/src/emblcmci/ext/GrayLevelClassMixtureModeling.java
+++ /dev/null
@@ -1,224 +0,0 @@
-package emblcmci.ext;
-
-/*
- * Mixture Modeling algorithm
- *
- * Copyright (c) 2003 by Christopher Mei (christopher.mei@sophia.inria.fr)
- *                    and Maxime Dauphin
- *
- * This plugin is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License version 2 
- * as published by the Free Software Foundation.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this plugin; if not, write to the Free Software
- * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
- */
-/* This code was downloaded from
- * http://rsbweb.nih.gov/ij/plugins/mixture-modeling.html
- * 
- */
-
-import java.util.*;
-import ij.*;
-import ij.process.*;
-
-/** This class implements a GrayLevelClassMixtureModeling.
- **/
-
-public class GrayLevelClassMixtureModeling {
-  public static int[] histogram;
-    /** The index must vary between 1 and 253
-	C1 : [0;index]
-	C2 : [index+1; 255]
-    **/
-    private int index;
-    private float mu1, mu2;
-    private float sigma2_1, sigma2_2;
-    private float mult1, mult2;
-    private float twoVariance1, twoVariance2;
-    private float max1, max2;
-    private int cardinal1, cardinal2;
-    private int cardinal;
-
-    private int INDEX_MIN = 1;
-    private int INDEX_MAX = 253;
-    private int MIN = 0;
-    public static final int MAX = 255;
-    
-    public GrayLevelClassMixtureModeling(ByteProcessor img) {
-	cardinal = img.getWidth()*img.getHeight();
-	histogram = img.getHistogram();
-	index = INDEX_MIN-1;
-	//setValues();
-    }
-
-    public boolean addToIndex() {
-	index++;
-
-	if(!(index<=INDEX_MAX))
-	    return false;	
-
-	setValues();
-	return true;
-    }
-
-    private float calculateMax(int index) {
-	float sum = histogram[index];
-	float num = 1;
-	if(index-1>=0) {
-	    sum += histogram[index-1];
-	    num++;
-	}
-	if(index+1<MAX) {
-	    sum += histogram[index+1];
-	    num++;
-	}
-	return sum/num;
-    }
-
-    public String toString() {
-	StringBuffer ret = new StringBuffer();
-	
-	ret.append("Index : "+index+"\n");
-	ret.append("Max1 : "+max1+" ");
-	ret.append("Max2 : "+max2+"\n");
-	ret.append("Mu1 : "+mu1+" ");
-	ret.append("Mu2 : "+mu2+"\n");
-	ret.append("Cardinal1 : "+cardinal1+" ");
-	ret.append("Cardinal2 : "+cardinal2+"\n");
-	ret.append("Variance1 : "+sigma2_1+" ");
-	ret.append("Variance2 : "+sigma2_2+"\n");
-	
-	return ret.toString();
-    }
-
-    public float getCardinal() {
-	return cardinal;
-    }
-
-    public float getMu1() {
-	return mu1;
-    }
-
-    public float getMu2() {
-	return mu2;
-    }
-
-    public float getMax1() {
-	return max1;
-    }
-
-    public float getMax2() {
-	return max2;
-    }
-
-    public float getVariance1() {
-	return sigma2_1;
-    }
-
-    public float getVariance2() {
-	return sigma2_2;
-    }
-
-    public float getCardinal1() {
-	return cardinal1;
-    }
-
-    public float getCardinal2() {
-	return cardinal2;
-    }
-
-    public int getThreshold() {
-	return index;
-    }
-
-    public void setIndex(int index) {
-	this.index = index;
-	setValues();
-    }
-
-    private void setValues() {	
-	mu1 = 0; mu2 = 0;
-	sigma2_1 = 0; sigma2_2 = 0;
-	max1 = 0; max2 = 0;
-	cardinal1 = 0; cardinal2 = 0;
-
-	for(int i=MIN; i<=index ; i++) {
-	    cardinal1 +=  histogram[i];
-	    mu1 +=  i*histogram[i];
-	}
-    
-	for(int i=index+1; i<=MAX ; i++) {
-	    cardinal2 +=  histogram[i];
-	    mu2 +=  i*histogram[i];
-	}
-    
-	if(cardinal1 == 0) {
-	    mu1 = 0;
-	    sigma2_1 = 0;
-
-	}
-	else 
-	    mu1 /= (float)cardinal1; 
-
-	if(cardinal2 == 0) {
-	    mu2 = 0;
-	    sigma2_2 = 0;
-	}
-	else 
-	    mu2 /= (float)cardinal2; 
-
-	if( mu1 != 0 ) {
-	    for(int i=MIN; i<=index ; i++) 
-		sigma2_1 += histogram[i]*Math.pow(i-mu1,2);
-	    
-	    sigma2_1 /= (float)cardinal1;
-	
-	    max1 = calculateMax((int) mu1);
-
-	    mult1 = (float) max1;
-	    twoVariance1 = 2*sigma2_1; 
-	}
-	if( mu2 != 0 ) {
-	    for(int i=index+1; i<=MAX ; i++) 
-		sigma2_2 += histogram[i]*Math.pow(i-mu2,2);
-	    
-	    sigma2_2 /= (float)cardinal2;
-	
-	    max2 = calculateMax((int) mu2);
-
-	    mult2 = (float) max2;
-	    twoVariance2 = 2*sigma2_2; 
-	}
-    }
-
-    public final float gamma1(int i) {
-	if(sigma2_1 == 0) 
-	    return 0;
-	return (float)(mult1*Math.exp(-(Math.pow((float)i-mu1,2))/twoVariance1));
-    }
-
-    public final float gamma2(int i) {
-	if(sigma2_2 == 0) 
-	    return 0;
-	return (float)(mult2*Math.exp(-(Math.pow((float)i-mu2,2))/twoVariance2));
-    }
-
-    public float gamma(int i) {
-	return gamma1(i)+gamma2(i);
-    }
-
-    public float differenceGamma(int i) {
-	return gamma1(i)-gamma2(i);
-    }
-
-    public static int getHistogram(int i) {
-	return histogram[i];
-    }
-}
diff --git a/src/emblcmci/gmm/GrayLevelClassMixtureModeling.java b/src/emblcmci/gmm/GrayLevelClassMixtureModeling.java
new file mode 100644
index 0000000..4ff4ab3
--- /dev/null
+++ b/src/emblcmci/gmm/GrayLevelClassMixtureModeling.java
@@ -0,0 +1,224 @@
+package emblcmci.gmm;
+
+/*
+ * Mixture Modeling algorithm
+ *
+ * Copyright (c) 2003 by Christopher Mei (christopher.mei@sophia.inria.fr)
+ *                    and Maxime Dauphin
+ *
+ * This plugin is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 2 
+ * as published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this plugin; if not, write to the Free Software
+ * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+/* This code was downloaded from
+ * http://rsbweb.nih.gov/ij/plugins/mixture-modeling.html
+ * 
+ */
+
+import java.util.*;
+import ij.*;
+import ij.process.*;
+
+/** This class implements a GrayLevelClassMixtureModeling.
+ **/
+
+public class GrayLevelClassMixtureModeling {
+	public static int[] histogram;
+	/** The index must vary between 1 and 253
+	C1 : [0;index]
+	C2 : [index+1; 255]
+	 **/
+	private int index;
+	private float mu1, mu2;
+	private float sigma2_1, sigma2_2;
+	private float mult1, mult2;
+	private float twoVariance1, twoVariance2;
+	private float max1, max2;
+	private int cardinal1, cardinal2;
+	private int cardinal;
+
+	private int INDEX_MIN = 1;
+	private int INDEX_MAX = 253;
+	private int MIN = 0;
+	public static final int MAX = 255;
+
+	public GrayLevelClassMixtureModeling(ByteProcessor img) {
+		cardinal = img.getWidth()*img.getHeight();
+		histogram = img.getHistogram();
+		index = INDEX_MIN-1;
+		//setValues();
+	}
+
+	public boolean addToIndex() {
+		index++;
+
+		if(!(index<=INDEX_MAX))
+			return false;	
+
+		setValues();
+		return true;
+	}
+
+	private float calculateMax(int index) {
+		float sum = histogram[index];
+		float num = 1;
+		if(index-1>=0) {
+			sum += histogram[index-1];
+			num++;
+		}
+		if(index+1<MAX) {
+			sum += histogram[index+1];
+			num++;
+		}
+		return sum/num;
+	}
+
+	public String toString() {
+		StringBuffer ret = new StringBuffer();
+
+		ret.append("Index : "+index+"\n");
+		ret.append("Max1 : "+max1+" ");
+		ret.append("Max2 : "+max2+"\n");
+		ret.append("Mu1 : "+mu1+" ");
+		ret.append("Mu2 : "+mu2+"\n");
+		ret.append("Cardinal1 : "+cardinal1+" ");
+		ret.append("Cardinal2 : "+cardinal2+"\n");
+		ret.append("Variance1 : "+sigma2_1+" ");
+		ret.append("Variance2 : "+sigma2_2+"\n");
+
+		return ret.toString();
+	}
+
+	public float getCardinal() {
+		return cardinal;
+	}
+
+	public float getMu1() {
+		return mu1;
+	}
+
+	public float getMu2() {
+		return mu2;
+	}
+
+	public float getMax1() {
+		return max1;
+	}
+
+	public float getMax2() {
+		return max2;
+	}
+
+	public float getVariance1() {
+		return sigma2_1;
+	}
+
+	public float getVariance2() {
+		return sigma2_2;
+	}
+
+	public float getCardinal1() {
+		return cardinal1;
+	}
+
+	public float getCardinal2() {
+		return cardinal2;
+	}
+
+	public int getThreshold() {
+		return index;
+	}
+
+	public void setIndex(int index) {
+		this.index = index;
+		setValues();
+	}
+
+	private void setValues() {	
+		mu1 = 0; mu2 = 0;
+		sigma2_1 = 0; sigma2_2 = 0;
+		max1 = 0; max2 = 0;
+		cardinal1 = 0; cardinal2 = 0;
+
+		for(int i=MIN; i<=index ; i++) {
+			cardinal1 +=  histogram[i];
+			mu1 +=  i*histogram[i];
+		}
+
+		for(int i=index+1; i<=MAX ; i++) {
+			cardinal2 +=  histogram[i];
+			mu2 +=  i*histogram[i];
+		}
+
+		if(cardinal1 == 0) {
+			mu1 = 0;
+			sigma2_1 = 0;
+
+		}
+		else 
+			mu1 /= (float)cardinal1; 
+
+		if(cardinal2 == 0) {
+			mu2 = 0;
+			sigma2_2 = 0;
+		}
+		else 
+			mu2 /= (float)cardinal2; 
+
+		if( mu1 != 0 ) {
+			for(int i=MIN; i<=index ; i++) 
+				sigma2_1 += histogram[i]*Math.pow(i-mu1,2);
+
+			sigma2_1 /= (float)cardinal1;
+
+			max1 = calculateMax((int) mu1);
+
+			mult1 = (float) max1;
+			twoVariance1 = 2*sigma2_1; 
+		}
+		if( mu2 != 0 ) {
+			for(int i=index+1; i<=MAX ; i++) 
+				sigma2_2 += histogram[i]*Math.pow(i-mu2,2);
+
+			sigma2_2 /= (float)cardinal2;
+
+			max2 = calculateMax((int) mu2);
+
+			mult2 = (float) max2;
+			twoVariance2 = 2*sigma2_2; 
+		}
+	}
+
+	public final float gamma1(int i) {
+		if(sigma2_1 == 0) 
+			return 0;
+		return (float)(mult1*Math.exp(-(Math.pow((float)i-mu1,2))/twoVariance1));
+	}
+
+	public final float gamma2(int i) {
+		if(sigma2_2 == 0) 
+			return 0;
+		return (float)(mult2*Math.exp(-(Math.pow((float)i-mu2,2))/twoVariance2));
+	}
+
+	public float gamma(int i) {
+		return gamma1(i)+gamma2(i);
+	}
+
+	public float differenceGamma(int i) {
+		return gamma1(i)-gamma2(i);
+	}
+
+	public static int getHistogram(int i) {
+		return histogram[i];
+	}
+}
diff --git a/src/emblcmci/ext/MixtureModeling_.java b/src/emblcmci/gmm/MixtureModeling_.java
similarity index 99%
rename from src/emblcmci/ext/MixtureModeling_.java
rename to src/emblcmci/gmm/MixtureModeling_.java
index 91f7e23..8e94efc 100644
--- a/src/emblcmci/ext/MixtureModeling_.java
+++ b/src/emblcmci/gmm/MixtureModeling_.java
@@ -1,4 +1,4 @@
-package emblcmci.ext;
+package emblcmci.gmm;
 
 /*
  * Mixture Modeling algorithm