cdec cleanup, remove bayesian stuff, parsing stuff

1 files changed, 0 insertions, 339 deletions

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;
-		}
-	
-}