1 files changed, 186 insertions, 0 deletions
diff --git a/gi/posterior-regularisation/prjava/src/util/ArrayMath.java b/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
new file mode 100644
index 00000000..398a13a2
--- /dev/null
+++ b/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
@@ -0,0 +1,186 @@
+package util;
+
+import java.util.Arrays;
+
+public class ArrayMath {
+
+	public static double dotProduct(double[] v1, double[] v2) {
+		assert(v1.length == v2.length);
+		double result = 0;
+		for(int i = 0; i < v1.length; i++)
+			result += v1[i]*v2[i];
+		return result;
+	}
+
+	public static double twoNormSquared(double[] v) {
+		double result = 0;
+		for(double d : v)
+			result += d*d;
+		return result;
+	}
+
+	public static boolean containsInvalid(double[] v) {
+		for(int i = 0; i < v.length; i++)
+			if(Double.isNaN(v[i]) || Double.isInfinite(v[i]))
+				return true;
+		return false;
+	}
+
+
+	
+	public static double safeAdd(double[] toAdd) {
+		// Make sure there are no positive infinities
+		double sum = 0;
+		for(int i = 0; i < toAdd.length; i++) {
+			assert(!(Double.isInfinite(toAdd[i]) && toAdd[i] > 0));
+			assert(!Double.isNaN(toAdd[i]));
+			sum += toAdd[i];
+		}
+		
+		return sum;
+	}
+
+	/* Methods for filling integer and double arrays (of up to four dimensions) with the given value. */
+	
+	public static void set(int[][][][] array, int value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(int[][][] array, int value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(int[][] array, int value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(int[] array, int value) {
+		Arrays.fill(array, value);
+	}
+	
+	
+	public static void set(double[][][][] array, double value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(double[][][] array, double value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(double[][] array, double value) {
+		for(int i = 0; i < array.length; i++) {
+			set(array[i], value);
+		}
+	}
+	
+	public static void set(double[] array, double value) {
+		Arrays.fill(array, value);
+	}
+
+	public static void setEqual(double[][][][] dest, double[][][][] source){
+		for (int i = 0; i < source.length; i++) {
+			setEqual(dest[i],source[i]);
+		}
+	}
+
+	
+	public static void setEqual(double[][][] dest, double[][][] source){
+		for (int i = 0; i < source.length; i++) {
+			set(dest[i],source[i]);
+		}
+	}
+
+	
+	public static void set(double[][] dest, double[][] source){
+		for (int i = 0; i < source.length; i++) {
+			setEqual(dest[i],source[i]);
+		}
+	}
+
+	public static void setEqual(double[] dest, double[] source){
+		System.arraycopy(source, 0, dest, 0, source.length);
+	}
+
+	public static void plusEquals(double[][][][] array, double val){
+		for (int i = 0; i < array.length; i++) {
+			plusEquals(array[i], val);
+		}
+	}	
+	
+	public static void plusEquals(double[][][] array, double val){
+		for (int i = 0; i < array.length; i++) {
+			plusEquals(array[i], val);
+		}
+	}	
+	
+	public static void plusEquals(double[][] array, double val){
+		for (int i = 0; i < array.length; i++) {
+			plusEquals(array[i], val);
+		}
+	}	
+	
+	public static void plusEquals(double[] array, double val){
+		for (int i = 0; i < array.length; i++) {
+			array[i] += val;
+		}
+	}
+
+	
+	public static double sum(double[] array) {
+		double res = 0;
+		for (int i = 0; i < array.length; i++) res += array[i];
+		return res;
+	}
+
+
+	
+	public static  double[][] deepclone(double[][] in){
+		double[][] res = new double[in.length][];
+		for (int i = 0; i < res.length; i++) {
+			res[i] = in[i].clone();
+		}
+		return res;
+	}
+
+	
+	public static  double[][][] deepclone(double[][][] in){
+		double[][][] res = new double[in.length][][];
+		for (int i = 0; i < res.length; i++) {
+			res[i] = deepclone(in[i]);
+		}
+		return res;
+	}
+
+	public static double cosine(double[] a,
+			double[] b) {
+		return (dotProduct(a, b)+1e-5)/(Math.sqrt(dotProduct(a, a)+1e-5)*Math.sqrt(dotProduct(b, b)+1e-5));
+	}
+
+	public static double max(double[] ds) {
+		double max = Double.NEGATIVE_INFINITY;
+		for(double d:ds) max = Math.max(d,max);
+		return max;
+	}
+
+	public static void exponentiate(double[] a) {
+		for (int i = 0; i < a.length; i++) {
+			a[i] = Math.exp(a[i]);
+		}
+	}
+
+	public static int sum(int[] array) {
+		int res = 0;
+		for (int i = 0; i < array.length; i++) res += array[i];
+		return res;
+	}
+}