From e26434979adc33bd949566ba7bf02dff64e80a3e Mon Sep 17 00:00:00 2001
From: Chris Dyer <cdyer@cab.ark.cs.cmu.edu>
Date: Tue, 2 Oct 2012 00:19:43 -0400
Subject: cdec cleanup, remove bayesian stuff, parsing stuff

---
 .../src/optimization/util/Interpolation.java       |  37 ---
 .../prjava/src/optimization/util/Logger.java       |   7 -
 .../prjava/src/optimization/util/MathUtils.java    | 339 ---------------------
 .../prjava/src/optimization/util/MatrixOutput.java |  28 --
 .../prjava/src/optimization/util/StaticTools.java  | 180 -----------
 5 files changed, 591 deletions(-)
 delete mode 100644 gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java
 delete mode 100644 gi/posterior-regularisation/prjava/src/optimization/util/Logger.java
 delete mode 100644 gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java
 delete mode 100644 gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java
 delete mode 100644 gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java

(limited to 'gi/posterior-regularisation/prjava/src/optimization/util')

diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java b/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java
deleted file mode 100644
index cdbdefc6..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package optimization.util;
-
-public class Interpolation {
-
-	/**
-	 * Fits a cubic polinomyal to a function given two points,
-	 * such that either gradB is bigger than zero or funcB >= funcA
-	 * 
-	 * NonLinear Programming appendix C
-	 * @param funcA
-	 * @param gradA
-	 * @param funcB
-	 * @param gradB
-	 */
-	public final static double cubicInterpolation(double a, 
-			double funcA, double gradA, double b,double funcB, double gradB ){
-		if(gradB < 0 && funcA > funcB){
-			System.out.println("Cannot call cubic interpolation");
-			return -1;
-		}
-		
-		double z = 3*(funcA-funcB)/(b-a) + gradA + gradB;
-		double w = Math.sqrt(z*z - gradA*gradB);
-		double min = b -(gradB+w-z)*(b-a)/(gradB-gradA+2*w);
-		return min;
-	}
-	
-	public final static double quadraticInterpolation(double initFValue, 
-			double initGrad, double point,double pointFValue){
-				double min = -1*initGrad*point*point/(2*(pointFValue-initGrad*point-initFValue));
-		return min;
-	}
-	
-	public static void main(String[] args) {
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java b/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java
deleted file mode 100644
index 5343a39b..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package optimization.util;
-
-public class Logger {
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java b/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java
deleted file mode 100644
index af66f82c..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java
+++ /dev/null
@@ -1,339 +0,0 @@
-package optimization.util;
-
-import java.util.Arrays;
-
-
-
-public class MathUtils {
-	
-	/**
-	 * 
-	 * @param vector
-	 * @return
-	 */
-	public static double L2Norm(double[] vector){
-		double value = 0;
-		for(int i = 0; i < vector.length; i++){
-			double v = vector[i];
-			value+=v*v;
-		}
-		return Math.sqrt(value);
-	}
-	
-	public static double sum(double[] v){
-		double sum = 0;
-		for (int i = 0; i < v.length; i++) {
-			sum+=v[i];
-		}
-		return sum;
-	}
-	
-	
-	
-	
-	/**
-	 * w = w + v
-	 * @param w
-	 * @param v
-	 */
-	public static void plusEquals(double[] w, double[] v) {
-		for(int i=0; i<w.length;i++){
-			w[i] += w[i] + v[i];
-		}		
-	}
-	
-	/**
-	 * w[i] = w[i] + v
-	 * @param w
-	 * @param v
-	 */
-	public static void plusEquals(double[] w, double v) {
-		for(int i=0; i<w.length;i++){
-			w[i] += w[i] + v;
-		}		
-	}
-	
-	/**
-	 * w[i] = w[i] - v
-	 * @param w
-	 * @param v
-	 */
-	public static void minusEquals(double[] w, double v) {
-		for(int i=0; i<w.length;i++){
-			w[i] -= w[i] + v;
-		}		
-	}
-	
-	/**
-	 * w = w + a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void plusEquals(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			w[i] += a*v[i];
-		}		
-	}
-	
-	/**
-	 * w = w - a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void minusEquals(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			w[i] -= a*v[i];
-		}		
-	}
-	/**
-	 * v = w - a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void minusEqualsInverse(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			v[i] = w[i] - a*v[i];
-		}		
-	}
-	
-	public static double dotProduct(double[] w, double[] v){
-		double accum = 0;
-		for(int i=0; i<w.length;i++){
-			accum += w[i]*v[i];
-		}
-		return accum;
-	}
-	
-	public static double[] arrayMinus(double[]w, double[]v){
-		double result[] = w.clone();
-		for(int i=0; i<w.length;i++){
-			result[i] -= v[i];
-		}
-		return result;
-	}
-	
-	public static double[] arrayMinus(double[] result , double[]w, double[]v){
-		for(int i=0; i<w.length;i++){
-			result[i] = w[i]-v[i];
-		}
-		return result;
-	}
-	
-	public static double[] negation(double[]w){
-		double result[]  = new double[w.length];
-		for(int i=0; i<w.length;i++){
-			result[i] = -w[i];
-		}
-		return result;
-	}
-	
-	public static double square(double value){
-		return value*value;
-	}
-	public static double[][] outerProduct(double[] w, double[] v){
-		double[][] result = new double[w.length][v.length];
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < v.length; j++){
-				result[i][j] = w[i]*v[j];
-			}
-		}
-		return result;
-	}
-	/**
-	 * results = a*W*V
-	 * @param w
-	 * @param v
-	 * @param a
-	 * @return
-	 */
-	public static double[][] weightedouterProduct(double[] w, double[] v, double a){
-		double[][] result = new double[w.length][v.length];
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < v.length; j++){
-				result[i][j] = a*w[i]*v[j];
-			}
-		}
-		return result;
-	}
-	
-	public static double[][] identity(int size){
-		double[][] result = new double[size][size];
-		for(int i = 0; i < size; i++){
-			result[i][i] = 1;
-		}
-		return result;
-	}
-	
-	/**
-	 * v -= w
-	 * @param v
-	 * @param w
-	 */
-	public static void minusEquals(double[][] w, double[][] v){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] -= v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v[i][j] -= a*w[i][j]
-	 * @param v
-	 * @param w
-	 */
-	public static void minusEquals(double[][] w, double[][] v, double a){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] -= a*v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v += w
-	 * @param v
-	 * @param w
-	 */
-	public static void plusEquals(double[][] w, double[][] v){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] += v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v[i][j] += a*w[i][j]
-	 * @param v
-	 * @param w
-	 */
-	public static void plusEquals(double[][] w, double[][] v, double a){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] += a*v[i][j];
-			}
-		}
-	}
-	
-	
-	/**
-	 * results = w*v
-	 * @param w
-	 * @param v
-	 * @return
-	 */
-	public static  double[][] matrixMultiplication(double[][] w,double[][] v){
-		int w1 = w.length;
-		int w2 = w[0].length;
-		int v1 = v.length;
-		int v2 = v[0].length;
-		
-		if(w2 != v1){
-			System.out.println("Matrix dimensions do not agree...");
-			System.exit(-1);
-		}
-		
-		double[][] result = new double[w1][v2];
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-			for(int v_i2 = 0; v_i2 < v2; v_i2++){
-				double sum = 0;
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						sum += w[w_i1 ][w_i2]*v[w_i2][v_i2];	
-				}
-				result[w_i1][v_i2] = sum;
-			}
-		}
-		return result;
-	}
-	
-	/**
-	 * w = w.*v
-	 * @param w
-	 * @param v
-	 */
-	public static  void matrixScalarMultiplication(double[][] w,double v){
-		int w1 = w.length;
-		int w2 = w[0].length;	
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						w[w_i1 ][w_i2] *= v;	
-				}
-		}
-	}
-	
-	public static  void scalarMultiplication(double[] w,double v){
-		int w1 = w.length;
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-			w[w_i1 ] *= v;	
-		}
-		
-	}
-	
-	public static  double[] matrixVector(double[][] w,double[] v){
-		int w1 = w.length;
-		int w2 = w[0].length;
-		int v1 = v.length;
-		
-		if(w2 != v1){
-			System.out.println("Matrix dimensions do not agree...");
-			System.exit(-1);
-		}
-		
-		double[] result = new double[w1];
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-				double sum = 0;
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						sum += w[w_i1 ][w_i2]*v[w_i2];	
-				}
-				result[w_i1] = sum;
-		}
-		return result;
-	}
-	
-	public static boolean allPositive(double[] array){
-		for (int i = 0; i < array.length; i++) {
-			if(array[i] < 0) return false;
-		}
-		return true;
-	}
-	
-	
-	
-	
-	
-		public static void main(String[] args) {
-			double[][] m1 = new double[2][2];
-			m1[0][0]=2;
-			m1[1][0]=2;
-			m1[0][1]=2;
-			m1[1][1]=2;
-			MatrixOutput.printDoubleArray(m1, "m1");
-			double[][] m2 = new double[2][2];
-			m2[0][0]=3;
-			m2[1][0]=3;
-			m2[0][1]=3;
-			m2[1][1]=3;
-			MatrixOutput.printDoubleArray(m2, "m2");
-			double[][] result = matrixMultiplication(m1, m2);
-			MatrixOutput.printDoubleArray(result, "result");
-			matrixScalarMultiplication(result, 3);
-			MatrixOutput.printDoubleArray(result, "result after multiply by 3");
-		}
-	
-		public static boolean almost(double a, double b, double prec){
-			return Math.abs(a-b)/Math.abs(a+b) <= prec || (almostZero(a) && almostZero(b));
-		}
-
-		public static boolean almost(double a, double b){
-			return Math.abs(a-b)/Math.abs(a+b) <= 1e-10 || (almostZero(a) && almostZero(b));
-		}
-
-		public static boolean almostZero(double a) {
-			return Math.abs(a) <= 1e-30;
-		}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java b/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java
deleted file mode 100644
index 9fbdf955..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package optimization.util;
-
-
-public class MatrixOutput {
-	public static void printDoubleArray(double[][] array, String arrayName) {
-		int size1 = array.length;
-		int size2 = array[0].length;
-		System.out.println(arrayName);
-		for (int i = 0; i < size1; i++) {
-			for (int j = 0; j < size2; j++) {
-				System.out.print(" " + StaticTools.prettyPrint(array[i][j],
-						"00.00E00", 4) + " ");
-
-			}
-			System.out.println();
-		}
-		System.out.println();
-	}
-	
-	public static void printDoubleArray(double[] array, String arrayName) {
-		System.out.println(arrayName);
-		for (int i = 0; i < array.length; i++) {
-				System.out.print(" " + StaticTools.prettyPrint(array[i],
-						"00.00E00", 4) + " ");
-		}
-		System.out.println();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java b/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java
deleted file mode 100644
index bcabee06..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java
+++ /dev/null
@@ -1,180 +0,0 @@
-package optimization.util;
-
-
-import java.io.File;
-import java.io.PrintStream;
-
-public class StaticTools {
-
-	static java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-
-	public static void createDir(String directory) {
-
-		File dir = new File(directory);
-		if (!dir.isDirectory()) {
-			boolean success = dir.mkdirs();
-			if (!success) {
-				System.out.println("Unable to create directory " + directory);
-				System.exit(0);
-			}
-			System.out.println("Created directory " + directory);
-		} else {
-			System.out.println("Reusing directory " + directory);
-		}
-	}
-
-	/*
-	 * q and p are indexed by source/foreign Sum_S(q) = 1 the same for p KL(q,p) =
-	 * Eq*q/p
-	 */
-	public static double KLDistance(double[][] p, double[][] q, int sourceSize,
-			int foreignSize) {
-		double totalKL = 0;
-		// common.StaticTools.printMatrix(q, sourceSize, foreignSize, "q",
-		// System.out);
-		// common.StaticTools.printMatrix(p, sourceSize, foreignSize, "p",
-		// System.out);
-		for (int i = 0; i < sourceSize; i++) {
-			double kl = 0;
-			for (int j = 0; j < foreignSize; j++) {
-				assert !Double.isNaN(q[i][j]) : "KLDistance q:  prob is NaN";
-				assert !Double.isNaN(p[i][j]) : "KLDistance p:  prob is NaN";
-				if (p[i][j] == 0 || q[i][j] == 0) {
-					continue;
-				} else {
-					kl += q[i][j] * Math.log(q[i][j] / p[i][j]);
-				}
-
-			}
-			totalKL += kl;
-		}
-		assert !Double.isNaN(totalKL) : "KLDistance: prob is NaN";
-		if (totalKL < -1.0E-10) {
-			System.out.println("KL Smaller than zero " + totalKL);
-			System.out.println("Source Size" + sourceSize);
-			System.out.println("Foreign Size" + foreignSize);
-			StaticTools.printMatrix(q, sourceSize, foreignSize, "q",
-					System.out);
-			StaticTools.printMatrix(p, sourceSize, foreignSize, "p",
-					System.out);
-			System.exit(-1);
-		}
-		return totalKL / sourceSize;
-	}
-
-	/*
-	 * indexed the by [fi][si]
-	 */
-	public static double KLDistancePrime(double[][] p, double[][] q,
-			int sourceSize, int foreignSize) {
-		double totalKL = 0;
-		for (int i = 0; i < sourceSize; i++) {
-			double kl = 0;
-			for (int j = 0; j < foreignSize; j++) {
-				assert !Double.isNaN(q[j][i]) : "KLDistance q:  prob is NaN";
-				assert !Double.isNaN(p[j][i]) : "KLDistance p:  prob is NaN";
-				if (p[j][i] == 0 || q[j][i] == 0) {
-					continue;
-				} else {
-					kl += q[j][i] * Math.log(q[j][i] / p[j][i]);
-				}
-
-			}
-			totalKL += kl;
-		}
-		assert !Double.isNaN(totalKL) : "KLDistance: prob is NaN";
-		return totalKL / sourceSize;
-	}
-
-	public static double Entropy(double[][] p, int sourceSize, int foreignSize) {
-		double totalE = 0;
-		for (int i = 0; i < foreignSize; i++) {
-			double e = 0;
-			for (int j = 0; j < sourceSize; j++) {
-				e += p[i][j] * Math.log(p[i][j]);
-			}
-			totalE += e;
-		}
-		return totalE / sourceSize;
-	}
-
-	public static double[][] copyMatrix(double[][] original, int sourceSize,
-			int foreignSize) {
-		double[][] result = new double[sourceSize][foreignSize];
-		for (int i = 0; i < sourceSize; i++) {
-			for (int j = 0; j < foreignSize; j++) {
-				result[i][j] = original[i][j];
-			}
-		}
-		return result;
-	}
-
-	public static void printMatrix(double[][] matrix, int sourceSize,
-			int foreignSize, String info, PrintStream out) {
-
-		java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-		fmt.setMaximumFractionDigits(3);
-		fmt.setMaximumIntegerDigits(3);
-		fmt.setMinimumFractionDigits(3);
-		fmt.setMinimumIntegerDigits(3);
-
-		out.println(info);
-
-		for (int i = 0; i < foreignSize; i++) {
-			for (int j = 0; j < sourceSize; j++) {
-				out.print(prettyPrint(matrix[j][i], ".00E00", 6) + " ");
-			}
-			out.println();
-		}
-		out.println();
-		out.println();
-	}
-
-	public static void printMatrix(int[][] matrix, int sourceSize,
-			int foreignSize, String info, PrintStream out) {
-
-		out.println(info);
-		for (int i = 0; i < foreignSize; i++) {
-			for (int j = 0; j < sourceSize; j++) {
-				out.print(matrix[j][i] + " ");
-			}
-			out.println();
-		}
-		out.println();
-		out.println();
-	}
-
-	public static String formatTime(long duration) {
-		StringBuilder sb = new StringBuilder();
-		double d = duration / 1000;
-		fmt.applyPattern("00");
-		sb.append(fmt.format((int) (d / (60 * 60))) + ":");
-		d -= ((int) d / (60 * 60)) * 60 * 60;
-		sb.append(fmt.format((int) (d / 60)) + ":");
-		d -= ((int) d / 60) * 60;
-		fmt.applyPattern("00.0");
-		sb.append(fmt.format(d));
-		return sb.toString();
-	}
-
-	public static String prettyPrint(double d, String patt, int len) {
-		fmt.applyPattern(patt);
-		String s = fmt.format(d);
-		while (s.length() < len) {
-			s = " " + s;
-		}
-		return s;
-	}
-	
-	
-	public static long getUsedMemory(){
-		System.gc();
-		return (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/ (1024 * 1024);
-	}
-	
-	public final static boolean compareDoubles(double d1, double d2){
-		return Math.abs(d1-d2) <= 1.E-10;
-	}
-	
-	
-}
-- 
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