Documenation update in statistics package.

refs #2

src/eva2/optimization/statistics/EvAStatisticalEvaluation.java

@@ -8,9 +8,7 @@ import eva2.tools.StringTools;
 import eva2.tools.math.Mathematics;
 
 import java.text.DecimalFormat;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.LinkedList;
-import java.util.List;
 import java.util.logging.Logger;
 
 /**
@@ -270,6 +268,53 @@ public class EvAStatisticalEvaluation {
         return "" + t;
     }
 
+    /**
+     * ToDo: Figure out why this gives different results than jsc.independentsamples.MannWhitneyTest#getSP
+     * @param field The field for which the test should be executed for.
+     * @param job1 First job to test
+     * @param job2 Second job to test
+     * @return
+     */
+    private static String calculateMannWhitneyU(String field, OptimizationJob job1, OptimizationJob job2) {
+        double[] dat1 = job1.getDoubleDataColumn(field);
+        double[] dat2 = job2.getDoubleDataColumn(field);
+        double t = Double.NaN;
+
+        // We can't compute the MannWhitney test if one of the samples is empty
+        if (dat1 != null && dat2 != null) {
+            double n1 = dat1.length;
+            double n2 = dat2.length;
+
+            ArrayList<Double> sortedValues = new ArrayList<>();
+            // This is stupid. Find a better way.
+            for (Double d : dat1) {
+                sortedValues.add(d);
+            }
+            for (Double d : dat2) {
+                sortedValues.add(d);
+            }
+            Collections.sort(sortedValues);
+            double tA = 0.0;
+            for (Double value : dat1) {
+                tA += (sortedValues.indexOf(value) + 1.0 + sortedValues.lastIndexOf(value) + 1.0) / 2.0;;
+            }
+            double tB = 0.0;
+            for (Double value : dat2) {
+                tB += (sortedValues.indexOf(value) + 1 + sortedValues.lastIndexOf(value) + 1) / 2.0;
+            }
+            double uA = (n1 * n2) + ((0.5 * n1) * (n1 + 1.0)) - tA;
+            double uB = (n1 * n2) + ((0.5 * n2) * (n2 + 1.0)) - tB;
+
+            assert(uA + uB == n1 * n2);
+            double u = Math.min(uA, uB);
+            double mU = (n1 * n2) / 2;
+            double omegaU = Math.sqrt((n1*n2*(n1 + n2 + 1.0))/12.0);
+
+            t = (u - mU) / omegaU;
+        }
+        return "" + t;
+    }
+
     private static String compare(String field, OptimizationJob job1, OptimizationJob job2) {
 //		TODO do some statistical test
         int numRuns1 = job1.getNumRuns();

src/eva2/optimization/statistics/OptimizationJob.java

@@ -124,7 +124,7 @@ public class OptimizationJob implements Serializable, InterfaceStatisticsListene
         return multiRunFinalObjectData;
     }
 
-    public InterfaceOptimizationParameters getGOParams() {
+    public InterfaceOptimizationParameters getOptimizationParameters() {
         return params;
     }
 
@@ -197,14 +197,15 @@ public class OptimizationJob implements Serializable, InterfaceStatisticsListene
      * Retrieve a single column of double data indicated by a field name. If the field is unknown
      * or there is no double data, null is returned.
      *
-     * @param field
+     * @param field Field name
-     * @return
+     * @return An array of values from the field provided
      */
     public double[] getDoubleDataColumn(String field) {
         int index = getFieldIndex(field);
+        int numRuns = getNumRuns();
         if (index >= 0) {
-            double[] data = new double[getNumRuns()];
+            double[] data = new double[numRuns];
-            for (int i = 0; i < getNumRuns(); i++) {
+            for (int i = 0; i < numRuns; i++) {
                 Object o = multiRunFinalObjectData.get(i)[index];
                 try {
                     if ((o instanceof Double)) {

src/eva2/optimization/statistics/OptimizationJobList.java

@@ -141,7 +141,7 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
      */
     public OptimizationJob getJobOf(InterfaceOptimizationParameters params) {
         for (OptimizationJob job : getObjects()) {
-            if (job.getGOParams() == params) {
+            if (job.getOptimizationParameters() == params) {
                 return job;
             }
         }
@@ -206,7 +206,7 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
                 if (jobs.size() == 1) {
                     OptimizationJob job = jobs.get(0);
                     AbstractOptimizationParameters curParams = (AbstractOptimizationParameters) ((AbstractModuleAdapter) jobList.module).getOptimizationParameters();
-                    curParams.setSameParams((AbstractOptimizationParameters) job.getGOParams());
+                    curParams.setSameParams((AbstractOptimizationParameters) job.getOptimizationParameters());
                     ((GenericModuleAdapter) jobList.module).setOptimizationParameters(curParams);
                     ((GenericModuleAdapter) jobList.module).getStatistics().getStatisticsParameter().setMultiRuns(job.getNumRuns());
                     ((GenericModuleAdapter) jobList.module).getStatistics().getStatisticsParameter().setFieldSelection(job.getFieldSelection(((GenericModuleAdapter) jobList.module).getStatistics().getStatisticsParameter().getFieldSelection()));

src/eva2/optimization/strategies/HillClimbing.java

@@ -217,7 +217,7 @@ public class HillClimbing implements InterfaceOptimizer, java.io.Serializable {
      */
     @Override
     public String getName() {
-        return "MS-HC" + getIdentifier();
+        return "MS-HC";
     }
 
     @Override

src/eva2/tools/math/Mathematics.java

@@ -683,7 +683,7 @@ public class Mathematics {
     /**
      * Computes the 2-norm of an array of doubles.
      *
-     * @param doubles the array of double
+     * @param d the array of double
      * @return the 2-norm of the elements
      */
     public static double norm(double[] d) {
@@ -698,7 +698,7 @@ public class Mathematics {
      * Normalizes the doubles in the array by their sum, so that they add up to
      * one.
      *
-     * @param doubles the array of double
+     * @param d the array of double
      * @throws IllegalArgumentException if sum is Zero or NaN
      */
     public static double[] normalizeSum(double[] v) {
@@ -711,7 +711,7 @@ public class Mathematics {
      * Normalizes the doubles in the array by their sum, so that they add up to
      * one.
      *
-     * @param doubles the array of double
+     * @param v the array of double
      * @throws IllegalArgumentException if sum is Zero or NaN
      */
     public static void normalizeSum(double[] v, double[] res) {