[7128] | 1 | using System;
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| 2 | using System.Collections.Generic;
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| 3 | using System.Drawing;
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| 4 | using System.Linq;
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[16573] | 5 | using HEAL.Attic;
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[7128] | 6 | using HeuristicLab.Common;
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| 7 | using HeuristicLab.Core;
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| 8 | using HeuristicLab.Data;
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| 9 | using HeuristicLab.Operators;
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| 10 | using HeuristicLab.Optimization;
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| 11 | using HeuristicLab.Optimization.Operators;
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| 12 | using HeuristicLab.Parameters;
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| 13 | using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
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| 14 |
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| 15 | namespace HeuristicLab.Analysis.FitnessLandscape.Evolvability {
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| 16 |
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| 17 | [Item("Evolvability Analyzer", "Compares two sets of scopes containing the original population and the evolved population generating several evolvability measures.")]
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[16573] | 18 | [StorableType("6B05CC43-161A-45C6-9B08-A4CC2235A96B")]
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[7128] | 19 | public class EvolvabilityAnalyzer : AlgorithmOperator, IAnalyzer {
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| 20 |
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[16573] | 21 | public bool EnabledByDefault
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| 22 | {
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[7176] | 23 | get { return false; }
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| 24 | }
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| 25 |
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[7128] | 26 | #region Parameters
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[16573] | 27 | public LookupParameter<DoubleValue> QualityParameter
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| 28 | {
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[7128] | 29 | get { return (LookupParameter<DoubleValue>)Parameters["Quality"]; }
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| 30 | }
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[16573] | 31 | public LookupParameter<IntValue> SampleSizeParameter
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| 32 | {
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[7128] | 33 | get { return (LookupParameter<IntValue>)Parameters["SampleSize"]; }
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| 34 | }
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[16573] | 35 | public LookupParameter<HeatMap> EvolvabilityPlotParameter
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| 36 | {
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[7128] | 37 | get { return (LookupParameter<HeatMap>)Parameters["EvolvabilityPlot"]; }
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| 38 | }
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[16573] | 39 | public LookupParameter<VariableCollection> ResultsParameter
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| 40 | {
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[7128] | 41 | get { return (LookupParameter<VariableCollection>)Parameters["Results"]; }
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| 42 | }
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[16573] | 43 | public LookupParameter<ScatterPlot> FitnessCloudParameter
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| 44 | {
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[7128] | 45 | get { return (LookupParameter<ScatterPlot>)Parameters["FitnessCloud"]; }
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| 46 | }
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[16573] | 47 | public LookupParameter<DataTable> EvolvabilityPortraitParameter
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| 48 | {
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[7128] | 49 | get { return (LookupParameter<DataTable>)Parameters["EvolvabilityPortrait"]; }
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| 50 | }
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[16573] | 51 | public ValueLookupParameter<IntValue> NrOfBinsParameter
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| 52 | {
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[7128] | 53 | get { return (ValueLookupParameter<IntValue>)Parameters["NrOfBins"]; }
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| 54 | }
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[16573] | 55 | public ScopeParameter ScopeParameter
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| 56 | {
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[7128] | 57 | get { return (ScopeParameter)Parameters["Scope"]; }
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| 58 | }
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| 59 | #endregion
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| 60 |
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| 61 | #region Constructors
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| 62 | public EvolvabilityAnalyzer() {
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| 63 | Parameters.Add(new LookupParameter<DoubleValue>("Quality", "The qualities of evolved and unevolved solution candidates"));
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| 64 | Parameters.Add(new LookupParameter<IntValue>("SampleSize", "The number of samples or population size for evolvability analysis"));
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| 65 | Parameters.Add(new LookupParameter<HeatMap>("EvolvabilityPlot", "Collected evolvability values"));
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| 66 | Parameters.Add(new LookupParameter<VariableCollection>("Results", "The collection of all results of this algorithm"));
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| 67 | Parameters.Add(new LookupParameter<ScatterPlot>("FitnessCloud", "A fitness cloud of the original vs. evolved sample."));
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| 68 | Parameters.Add(new LookupParameter<DataTable>("EvolvabilityPortrait", "Evolvability Portrait as described in Smith et. al (2002). Evol Comput 10:1–34"));
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| 69 | Parameters.Add(new ValueLookupParameter<IntValue>("NrOfBins", "Nr of bins for evolvability portrait analysis", new IntValue(25)));
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| 70 | Parameters.Add(new ScopeParameter("Scope", "The current scope"));
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| 71 |
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| 72 | var resultsCollector = new ResultsCollector();
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| 73 | resultsCollector.CollectedValues.Add(new LookupParameter<HeatMap>(EvolvabilityPlotParameter.Name));
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| 74 | resultsCollector.CollectedValues.Add(new LookupParameter<ScatterPlot>(FitnessCloudParameter.Name));
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| 75 | resultsCollector.CollectedValues.Add(new LookupParameter<DataTable>(EvolvabilityPortraitParameter.Name));
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| 76 |
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| 77 | OperatorGraph.InitialOperator = resultsCollector;
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| 78 | resultsCollector.Successor = null;
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| 79 | }
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| 80 |
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| 81 | [StorableConstructor]
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[16573] | 82 | protected EvolvabilityAnalyzer(StorableConstructorFlag _) : base(_) { }
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[7128] | 83 |
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| 84 | protected EvolvabilityAnalyzer(EvolvabilityAnalyzer original, Cloner cloner)
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| 85 | : base(original, cloner) {
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| 86 | }
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| 87 | #endregion
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| 88 |
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| 89 | public override IDeepCloneable Clone(Cloner cloner) {
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| 90 | return new EvolvabilityAnalyzer(this, cloner);
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| 91 | }
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| 92 |
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| 93 | public override IOperation Apply() {
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| 94 | var points = GenerateQualityPairs(ScopeParameter.ActualValue);
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| 95 | GetOrCreateEvolvabilityPlot().Add(points);
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| 96 | GetOrCreateScatterPlot().Add(points);
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| 97 | CreateEvolvabilityPortrait(ScopeParameter.ActualValue);
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| 98 | return base.Apply();
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| 99 | }
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| 100 |
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| 101 | private IEnumerable<PointF> GenerateQualityPairs(IScope globalScope) {
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| 102 | foreach (IScope sampleScope in globalScope.SubScopes) {
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| 103 | double originalQuality = ((DoubleValue)sampleScope.Variables[QualityParameter.ActualName].Value).Value;
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| 104 | foreach (IScope evolvedScope in sampleScope.SubScopes) {
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| 105 | double evolvedQuality = ((DoubleValue)evolvedScope.Variables[QualityParameter.ActualName].Value).Value;
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| 106 | yield return new PointF((float)originalQuality, (float)evolvedQuality);
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| 107 | }
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| 108 | }
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| 109 | }
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| 110 |
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| 111 | private HeatMap GetOrCreateEvolvabilityPlot() {
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| 112 | HeatMap evolvabilityPlot = EvolvabilityPlotParameter.ActualValue as HeatMap;
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| 113 | if (evolvabilityPlot == null) {
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| 114 | evolvabilityPlot = new HeatMap();
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| 115 | evolvabilityPlot.Name = "Evolvability";
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| 116 | EvolvabilityPlotParameter.ActualValue = evolvabilityPlot;
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| 117 | }
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| 118 | return evolvabilityPlot;
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| 119 | }
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| 120 |
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| 121 | private ScatterPlot GetOrCreateScatterPlot() {
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| 122 | ScatterPlot scatterPlot = FitnessCloudParameter.ActualValue as ScatterPlot;
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| 123 | if (scatterPlot == null) {
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| 124 | scatterPlot = new ScatterPlot();
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| 125 | scatterPlot.Name = "Fitness Cloud";
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| 126 | scatterPlot.XAxisName = "Parent Fitness";
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| 127 | scatterPlot.YAxisName = "Offspring Fitness";
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| 128 | FitnessCloudParameter.ActualValue = scatterPlot;
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| 129 | }
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| 130 | return scatterPlot;
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| 131 | }
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| 132 |
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| 133 | private DataTable GetOrCreateEvolvabilityPortrait() {
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| 134 | DataTable evolvabilityPortrait = EvolvabilityPortraitParameter.ActualValue as DataTable;
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| 135 | if (evolvabilityPortrait == null) {
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| 136 | evolvabilityPortrait = new DataTable("Evolvability Portrait");
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| 137 | evolvabilityPortrait.Rows.Add(new DataRow("E_a", "Probability of non-deleterious mutation"));
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| 138 | evolvabilityPortrait.Rows.Add(new DataRow("E_b", "Average expected offspring fitness"));
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| 139 | evolvabilityPortrait.Rows.Add(new DataRow("E_c", "Top offspring fitness"));
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| 140 | evolvabilityPortrait.Rows.Add(new DataRow("E_d", "Bottom offspring fitness"));
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| 141 | EvolvabilityPortraitParameter.ActualValue = evolvabilityPortrait;
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| 142 | }
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| 143 | return evolvabilityPortrait;
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| 144 | }
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| 145 |
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| 146 | private double GetQuality(IScope scope) {
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| 147 | return ((DoubleValue)scope.Variables[QualityParameter.ActualName].Value).Value;
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| 148 | }
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| 149 |
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| 150 | private void CreateEvolvabilityPortrait(IScope globalScope) {
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| 151 | DataTable table = GetOrCreateEvolvabilityPortrait();
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| 152 | var e_a = table.Rows["E_a"].Values;
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| 153 | var e_b = table.Rows["E_b"].Values;
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| 154 | var e_c = table.Rows["E_c"].Values;
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| 155 | var e_d = table.Rows["E_d"].Values;
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| 156 | var qualities = globalScope.SubScopes.Select(s => GetQuality(s));
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| 157 | double min = qualities.Min();
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| 158 | double max = qualities.Max();
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| 159 | double range = max - min;
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| 160 | double stepSize = range / NrOfBinsParameter.ActualValue.Value;
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| 161 | double threshold = min + stepSize;
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| 162 |
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| 163 | int n_not_worse = 0;
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| 164 | int n = 0;
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| 165 | double totalOffspringQuality = 0;
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| 166 | double best = double.MinValue;
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| 167 | double worst = double.MaxValue;
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| 168 | foreach (IScope sampleScope in globalScope.SubScopes) {
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| 169 | double originalQuality = GetQuality(sampleScope);
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| 170 | foreach (IScope evolvedScope in sampleScope.SubScopes) {
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| 171 | double evolvedQuality = GetQuality(evolvedScope);
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| 172 | if (evolvedQuality >= originalQuality)
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| 173 | n_not_worse++;
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| 174 | n++;
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| 175 | totalOffspringQuality += evolvedQuality;
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| 176 | best = Math.Max(best, evolvedQuality);
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| 177 | worst = Math.Min(worst, evolvedQuality);
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| 178 | }
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| 179 | if (originalQuality > threshold) {
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| 180 | threshold += stepSize;
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| 181 | e_a.Add(1.0 * n_not_worse / n);
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| 182 | e_b.Add(totalOffspringQuality / n);
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| 183 | e_c.Add(best);
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| 184 | e_d.Add(worst);
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| 185 | n_not_worse = 0;
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| 186 | n = 0;
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| 187 | totalOffspringQuality = 0;
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| 188 | best = double.MinValue;
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| 189 | worst = double.MaxValue;
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| 190 | }
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| 191 | }
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| 192 | }
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| 193 | }
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| 194 | }
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