| 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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