1 | #region License Information
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2 | /* HeuristicLab
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3 | * Copyright (C) 2002-2012 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
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4 | *
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5 | * This file is part of HeuristicLab.
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6 | *
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7 | * HeuristicLab is free software: you can redistribute it and/or modify
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8 | * it under the terms of the GNU General Public License as published by
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9 | * the Free Software Foundation, either version 3 of the License, or
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10 | * (at your option) any later version.
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11 | *
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12 | * HeuristicLab is distributed in the hope that it will be useful,
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13 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 | * GNU General Public License for more details.
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16 | *
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17 | * You should have received a copy of the GNU General Public License
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18 | * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
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19 | */
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20 | #endregion
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21 |
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22 | using System;
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23 | using System.Collections.Generic;
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24 | using System.Globalization;
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25 | using System.Linq;
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26 | using HeuristicLab.Common;
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27 | using HeuristicLab.Core;
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28 | using HeuristicLab.Data;
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29 | using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
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30 | using HeuristicLab.Operators;
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31 | using HeuristicLab.Optimization;
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32 | using HeuristicLab.Parameters;
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33 | using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
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34 |
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35 | using TreeCacheType = HeuristicLab.Core.ItemList<HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.ISymbolicExpressionTree>;
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36 | using CloneMapType = HeuristicLab.Core.ItemDictionary<HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.ISymbolicExpressionTree,
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37 | HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.ISymbolicExpressionTree>;
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38 | using TraceMapType = HeuristicLab.Core.ItemDictionary<HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.ISymbolicExpressionTree,
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39 | HeuristicLab.Core.IItemArray<HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.ISymbolicExpressionTree>>;
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40 |
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41 | namespace HeuristicLab.EvolutionaryTracking {
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42 | /// <summary>
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43 | /// An operator that tracks the genealogy of every individual
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44 | /// </summary>
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45 | [Item("SymbolicExpressionTreeGenealogyAnalyzer", "An operator that tracks tree lengths of Symbolic Expression Trees")]
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46 | [StorableClass]
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47 | public sealed class SymbolicExpressionTreeGenealogyAnalyzer : SingleSuccessorOperator, IAnalyzer {
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48 | private const string SymbolicExpressionTreeParameterName = "SymbolicExpressionTree";
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49 | private const string UpdateIntervalParameterName = "UpdateInterval";
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50 | private const string UpdateCounterParameterName = "UpdateCounter";
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51 | private const string ResultsParameterName = "Results";
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52 | private const string ElitesParameterName = "Elites";
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53 | private const string GenerationsParameterName = "Generations";
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54 | private const string MaximumGenerationsParameterName = "MaximumGenerations";
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55 | private const string MaximumSelectionPressureParameterName = "MaximumSelectionPressure";
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56 | private const string SelectionPressureParameterName = "SelectionPressure";
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57 | private const string GlobalTreeCacheParameterName = "GlobalTreeCache";
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58 | private const string GlobalTraceMapParameterName = "GlobalTraceMap";
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59 | private const string GlobalCloneMapParameterName = "GlobalCloneMap";
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60 | private const string PopulationGraphResultParameterName = "PopulationGraph";
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61 | private const string PopulationGraphResultParameterDescription = "Individual lineages";
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62 |
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63 | #region Parameter properties
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64 | public ValueParameter<IntValue> UpdateIntervalParameter {
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65 | get { return (ValueParameter<IntValue>)Parameters[UpdateIntervalParameterName]; }
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66 | }
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67 | public ValueParameter<IntValue> UpdateCounterParameter {
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68 | get { return (ValueParameter<IntValue>)Parameters[UpdateCounterParameterName]; }
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69 | }
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70 | public LookupParameter<ResultCollection> ResultsParameter {
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71 | get { return (LookupParameter<ResultCollection>)Parameters[ResultsParameterName]; }
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72 | }
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73 | public LookupParameter<IntValue> ElitesParameter {
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74 | get { return (LookupParameter<IntValue>)Parameters[ElitesParameterName]; }
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75 | }
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76 | public LookupParameter<IntValue> GenerationsParameter {
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77 | get { return (LookupParameter<IntValue>)Parameters[GenerationsParameterName]; }
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78 | }
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79 | public LookupParameter<IntValue> MaximumGenerationsParameter {
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80 | get { return (LookupParameter<IntValue>)Parameters[MaximumGenerationsParameterName]; }
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81 | }
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82 | public LookupParameter<DoubleValue> SelectionPressureParameter {
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83 | get { return (LookupParameter<DoubleValue>)Parameters[SelectionPressureParameterName]; }
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84 | }
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85 | public LookupParameter<DoubleValue> MaximumSelectionPressureParameter {
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86 | get { return (LookupParameter<DoubleValue>)Parameters[MaximumSelectionPressureParameterName]; }
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87 | }
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88 | // genealogy global parameters
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89 | public LookupParameter<TreeCacheType> GlobalTreeCacheParameter {
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90 | get { return (LookupParameter<TreeCacheType>)Parameters[GlobalTreeCacheParameterName]; }
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91 | }
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92 | public LookupParameter<TraceMapType> GlobalTraceMapParameter {
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93 | get { return (LookupParameter<TraceMapType>)Parameters[GlobalTraceMapParameterName]; }
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94 | }
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95 | public LookupParameter<CloneMapType> GlobalCloneMapParameter {
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96 | get { return (LookupParameter<CloneMapType>)Parameters[GlobalCloneMapParameterName]; }
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97 | }
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98 | #endregion
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99 |
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100 | #region Properties
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101 | public bool EnabledByDefault {
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102 | get { return true; }
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103 | }
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104 | public IntValue UpdateInterval {
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105 | get { return UpdateIntervalParameter.Value; }
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106 | }
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107 | public IntValue UpdateCounter {
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108 | get { return UpdateCounterParameter.Value; }
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109 | }
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110 | public ResultCollection Results {
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111 | get { return ResultsParameter.ActualValue; }
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112 | }
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113 | public IntValue Elites {
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114 | get { return ElitesParameter.ActualValue; }
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115 | }
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116 | public IntValue Generations {
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117 | get { return GenerationsParameter.ActualValue; }
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118 | }
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119 | public IntValue MaximumGenerations {
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120 | get { return MaximumGenerationsParameter.ActualValue; }
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121 | }
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122 | public DoubleValue SelectionPressure {
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123 | get { return SelectionPressureParameter.ActualValue; }
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124 | }
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125 | public DoubleValue MaximumSelectionPressure {
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126 | get { return MaximumSelectionPressureParameter.ActualValue; }
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127 | }
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128 | public ItemList<ISymbolicExpressionTree> GlobalTreeCache {
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129 | get { return GlobalTreeCacheParameter.ActualValue; }
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130 | }
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131 | public ItemDictionary<ISymbolicExpressionTree, ISymbolicExpressionTree> GlobalCloneMap {
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132 | get { return GlobalCloneMapParameter.ActualValue; }
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133 | }
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134 | public ItemDictionary<ISymbolicExpressionTree, IItemArray<ISymbolicExpressionTree>> GlobalTraceMap {
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135 | get { return GlobalTraceMapParameter.ActualValue; }
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136 | }
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137 | #endregion
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138 |
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139 | [StorableConstructor]
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140 | private SymbolicExpressionTreeGenealogyAnalyzer(bool deserializing)
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141 | : base() {
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142 | }
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143 | private SymbolicExpressionTreeGenealogyAnalyzer(SymbolicExpressionTreeGenealogyAnalyzer original, Cloner cloner)
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144 | : base(original, cloner) {
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145 | }
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146 | public override IDeepCloneable Clone(Cloner cloner) {
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147 | return new SymbolicExpressionTreeGenealogyAnalyzer(this, cloner);
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148 | }
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149 | public SymbolicExpressionTreeGenealogyAnalyzer()
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150 | : base() {
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151 | Parameters.Add(new ScopeTreeLookupParameter<ISymbolicExpressionTree>(SymbolicExpressionTreeParameterName, "The symbolic expression tree whose length should be calculated."));
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152 | Parameters.Add(new LookupParameter<IntValue>(ElitesParameterName, "The number of elites."));
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153 | Parameters.Add(new LookupParameter<IntValue>(GenerationsParameterName, "The number of generations so far."));
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154 | Parameters.Add(new LookupParameter<IntValue>(MaximumGenerationsParameterName, "The maximum number of generations"));
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155 | Parameters.Add(new LookupParameter<DoubleValue>(SelectionPressureParameterName, "The current selection (ony for OSGA)"));
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156 | Parameters.Add(new LookupParameter<DoubleValue>(MaximumSelectionPressureParameterName, "Maximum allowed value of selection pressure."));
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157 | Parameters.Add(new ValueParameter<IntValue>(UpdateIntervalParameterName, "The interval in which the tree length analysis should be applied.", new IntValue(1)));
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158 | Parameters.Add(new ValueParameter<IntValue>(UpdateCounterParameterName, "The value which counts how many times the operator was called since the last update", new IntValue(0)));
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159 | Parameters.Add(new LookupParameter<TreeCacheType>(GlobalTreeCacheParameterName, "A global list holding all trees from all generations."));
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160 | Parameters.Add(new LookupParameter<TraceMapType>(GlobalTraceMapParameterName, "A global cache containing the whole genealogy."));
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161 | Parameters.Add(new LookupParameter<CloneMapType>(GlobalCloneMapParameterName, "A global map keeping track of trees and their clones (made during selection)."));
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162 | Parameters.Add(new ValueLookupParameter<ResultCollection>(ResultsParameterName, "The results collection where the analysis values should be stored."));
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163 |
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164 | UpdateCounterParameter.Hidden = true;
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165 | UpdateIntervalParameter.Hidden = true;
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166 | }
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167 |
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168 | [StorableHook(HookType.AfterDeserialization)]
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169 | private void AfterDeserialization() {
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170 | // check if all the parameters are present and accounted for
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171 | if (!Parameters.ContainsKey(UpdateIntervalParameterName)) {
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172 | Parameters.Add(new ValueParameter<IntValue>(UpdateIntervalParameterName,
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173 | "The interval in which the tree length analysis should be applied.",
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174 | new IntValue(1)));
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175 | }
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176 | //necessary code to correct UpdateCounterParameter - type was changed from LookupParameter to ValueParameter
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177 | if (Parameters.ContainsKey(UpdateCounterParameterName) &&
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178 | (Parameters[UpdateCounterParameterName] is LookupParameter<IntValue>))
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179 | Parameters.Remove(UpdateCounterParameterName);
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180 | if (!Parameters.ContainsKey(UpdateCounterParameterName)) {
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181 | Parameters.Add(new ValueParameter<IntValue>(UpdateCounterParameterName,
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182 | "The value which counts how many times the operator was called since the last update",
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183 | new IntValue(0)));
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184 | UpdateCounterParameter.Hidden = true;
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185 | }
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186 | }
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187 |
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188 | #region IStatefulItem members
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189 | public override void InitializeState() {
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190 | base.InitializeState();
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191 | UpdateCounter.Value = 0;
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192 | }
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193 |
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194 | public override void ClearState() {
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195 | base.ClearState();
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196 | UpdateCounter.Value = 0;
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197 | }
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198 | #endregion
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199 |
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200 | public override IOperation Apply() {
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201 | UpdateCounter.Value++;
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202 | // the analyzer runs periodically, every 'updateInterval' times
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203 | if (UpdateCounter.Value == UpdateInterval.Value) {
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204 | UpdateCounter.Value = 0; // reset counter
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205 |
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206 | var gScope = ExecutionContext.Scope;
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207 | while (gScope.Parent != null) gScope = gScope.Parent;
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208 |
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209 | GenealogyGraph _graph;
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210 | if (!Results.ContainsKey(PopulationGraphResultParameterName)) {
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211 | _graph = new GenealogyGraph();
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212 | Results.Add(new Result(PopulationGraphResultParameterName, PopulationGraphResultParameterDescription, _graph));
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213 | } else {
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214 | _graph = (GenealogyGraph)Results[PopulationGraphResultParameterName].Value;
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215 | }
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216 |
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217 | var treeQualities = (from s in gScope.SubScopes
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218 | let tree = (SymbolicExpressionTree)s.Variables["SymbolicExpressionTree"].Value
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219 | let quality = (DoubleValue)s.Variables["Quality"].Value
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220 | orderby quality.Value descending
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221 | select new Tuple<ISymbolicExpressionTree, DoubleValue>(tree, quality)).ToList();
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222 | // add all individuals to the evolutionary graph
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223 | for (int i = 0; i != treeQualities.Count; ++i) {
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224 | var tree = treeQualities[i].Item1;
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225 | var quality = treeQualities[i].Item2;
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226 | if (!_graph.HasNode(tree)) {
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227 | _graph.AddNode(tree, quality.Value, (Generations.Value * treeQualities.Count + i + 1).ToString(CultureInfo.InvariantCulture));
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228 | } else {
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229 | _graph.GetNode(tree).Label += "\\n" + (Generations.Value * treeQualities.Count + i + 1).ToString(CultureInfo.InvariantCulture);
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230 | }
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231 |
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232 | if (GlobalTraceMap == null || !GlobalTraceMap.ContainsKey(tree))
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233 | continue;
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234 | // get number of parents and adjust label (2 parents => crossover, 1 parent => mutation)
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235 | var parents = GlobalTraceMap[tree];
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236 | string label = (parents.Count == 2) ? "c" : "m";
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237 | foreach (var parent in parents) {
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238 | _graph.AddArc(parent, tree, label);
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239 | }
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240 | }
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241 | if (GlobalTraceMap != null)
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242 | GlobalTraceMap.Clear();
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243 |
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244 | // mark elites
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245 | for (int i = 0; i != Elites.Value; ++i)
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246 | _graph.GetNode(treeQualities[i].Item1).IsElite = true;
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247 |
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248 | // if we've reached the end of the run
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249 | if (Generations.Value == MaximumGenerations.Value ||
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250 | (SelectionPressureParameter != null && SelectionPressure.Value >= MaximumSelectionPressure.Value)) {
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251 |
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252 | var path = Environment.GetFolderPath(Environment.SpecialFolder.UserProfile);
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253 |
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254 | // write whole graph to a dot file
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255 | WriteDot(path + @"\lineage.dot", _graph);
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256 |
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257 | // get genealogy of the best solution
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258 | var bestSolution = treeQualities.First().Item1;
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259 | var genealogy = _graph.GetNode(bestSolution).Genealogy();
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260 | WriteDot(path + @"\bestlineage.dot", genealogy);
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261 |
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262 | // trim the graph
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263 | // exclude the individuals of the last generation
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264 | var individuals = _graph.Keys.Except(treeQualities.Select(x => x.Item1)).ToList();
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265 | bool done = false;
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266 | while (!done) {
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267 | done = true;
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268 | foreach (var ind in individuals) {
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269 | // if node has no outgoing connections (absence of offspring), remove it from the graph
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270 | var node = _graph.GetNode(ind);
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271 | if (node == null) continue;
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272 | if (node.OutEdges == null) {
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273 | done = false; // we still have "dead" nodes
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274 | _graph.RemoveNode(ind);
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275 | }
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276 | }
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277 | }
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278 | WriteDot(path + @"\trimmedlineage.dot", _graph);
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279 | }
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280 | }
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281 | return base.Apply();
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282 | }
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283 |
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284 | private static void WriteDot(string path, GenealogyGraph graph) {
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285 | using (var file = new System.IO.StreamWriter(path)) {
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286 | string nl = Environment.NewLine;
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287 | file.WriteLine("digraph \"lineage " + graph.AverageDegree.ToString() + "\" {" + nl +
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288 | "ratio=auto;" + nl +
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289 | "mincross=2.0");
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290 | file.WriteLine("\tnode [shape=circle,label=\"\",style=filled]");
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291 |
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292 | foreach (var node in graph.Values) {
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293 | var quality = node.Quality;
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294 | string fillColor = String.Format("#{0:x2}{1:x2}{2:x2}", (int)(255 - 255 * quality), (int)(255 * quality), (int)(100 * quality));
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295 | if (node.IsElite)
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296 | fillColor = String.Format("#{0:x2}{1:x2}{2:x2}", (int)(255 - 255 * quality), (int)(255 * quality), (int)(255 * quality));
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297 | file.WriteLine("\t\"" + node.Id + "\" [fillcolor=\"" + fillColor + "\",label=\"" + node.Label + "\"];");
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298 | if (node.InEdges == null)
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299 | continue;
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300 | foreach (var edge in node.InEdges)
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301 | file.WriteLine("\t\"" + edge.Target.Id + "\" -> \"" + node.Id + "\" [arrowsize=.5, color=\"" + fillColor + "\"];");
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302 | }
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303 | file.WriteLine("}");
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304 | }
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305 | }
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306 | }
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307 | }
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