Changeset 11227 for branches

Timestamp:

07/29/14 02:17:14 (10 years ago)

Author:

bburlacu

Message:

#1772: Added storable attributes to all the tracking operators. Added an additional method in the genealogy analyzer which computes the relative reproductive success for each individual in the population as the ratio of its offspring which make it into the next generation.

Location:

branches/HeuristicLab.EvolutionTracking

Files:

• HeuristicLab.EvolutionTracking.Views/3.4/HeuristicLab.EvolutionTracking.Views-3.4.csproj (modified) (1 diff)
• HeuristicLab.EvolutionTracking/3.4/Analyzers/GenealogyAnalyzer.cs (modified) (12 diffs)
• HeuristicLab.EvolutionTracking/3.4/HeuristicLab.EvolutionTracking-3.4.csproj (modified) (1 diff)
• HeuristicLab.EvolutionTracking/3.4/Operators/AfterCrossoverOperator.cs (modified) (1 diff)
• HeuristicLab.EvolutionTracking/3.4/Operators/AfterManipulatorOperator.cs (modified) (1 diff)
• HeuristicLab.EvolutionTracking/3.4/Operators/BeforeCrossoverOperator.cs (modified) (1 diff)
• HeuristicLab.EvolutionTracking/3.4/Operators/BeforeManipulatorOperator.cs (modified) (2 diffs)
• HeuristicLab.EvolutionTracking/3.4/Operators/EvolutionTrackingOperator.cs (modified) (2 diffs)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisGenealogyAnalyzer.cs (modified) (1 diff)

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking.Views/3.4/HeuristicLab.EvolutionTracking.Views-3.4.csproj

@@ -105 +105 @@
     <Compile Include="Plugin.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
-    <Compile Include="GenealogyGraphView.cs" />
+    <Compile Include="GenealogyGraphView.cs">
+      <SubType>UserControl</SubType>
+    </Compile>
     <Compile Include="GenealogyGraphView.Designer.cs">
       <DependentUpon>GenealogyGraphView.cs</DependentUpon>

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Analyzers/GenealogyAnalyzer.cs

@@ -21 +21 @@
 
 using System.Linq;
+using HeuristicLab.Analysis;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
@@ -34 +35 @@
   public class GenealogyAnalyzer<T> : SingleSuccessorOperator, IAnalyzer
   where T : class,IItem {
+    #region parameter names
     private const string GenerationsParameterName = "Generations";
     private const string ResultsParameterName = "Results";
@@ -53 +55 @@
     private const string EnableManipulatorTrackingParameterName = "EnableManipulatorTracking";
     private const string EnableSolutionCreatorTrackingParameterName = "EnableSolutionCreatorTracking"; // should always be enabled. maybe superfluous
+    #endregion
 
     #region parameter properties
@@ -140 +143 @@
 
     public GenealogyAnalyzer() {
+      #region add parameters
       // the instrumented operators
       Parameters.Add(new LookupParameter<ICrossover>(CrossoverParameterName, "The crossover operator."));
@@ -157 +161 @@
       Parameters.Add(new ValueParameter<IManipulatorOperator<T>>(BeforeManipulatorOperatorParameterName));
       Parameters.Add(new ValueParameter<IManipulatorOperator<T>>(AfterManipulatorOperatorParameterName));
+      #endregion
     }
     public override IDeepCloneable Clone(Cloner cloner) {
@@ -164 +169 @@
       : base(original, cloner) {
     }
+
+    [StorableConstructor]
+    protected GenealogyAnalyzer(bool deserializing) : base(deserializing) { }
+
     [StorableHook(HookType.AfterDeserialization)]
     private void AfterDeserialization() {
@@ -232 +241 @@
 
     public override IOperation Apply() {
-      var population = PopulationParameter.ActualValue.ToList();
+      var population = PopulationParameter.ActualValue;
       var qualities = QualityParameter.ActualValue.ToList();
 
-      int currentGeneration = GenerationsParameter.ActualValue.Value;
-      if (currentGeneration == 0) {
+      int generation = GenerationsParameter.ActualValue.Value;
+      if (generation == 0) {
         ConfigureTrackingOperators();
 
-        for (int i = 0; i < population.Count; ++i) {
+        for (int i = 0; i < population.Length; ++i) {
           var individual = population[i];
-          var vertex = new GenealogyGraphNode<T>(individual) { Rank = currentGeneration };
+          var vertex = new GenealogyGraphNode<T>(individual) { Rank = generation };
           GenealogyGraph.AddVertex(vertex);
           // save the vertex id in the individual scope (so that we can identify graph indices)
@@ -249 +258 @@
         int index = 0;
         T elite = null;
-        for (int i = 0; i < population.Count; ++i) {
+        for (int i = 0; i < population.Length; ++i) {
           if (GenealogyGraph.Contains(population[i])) {
             elite = population[i];
             index = i;
-          }
-          break;
-        }
-
+            break;
+          }
+        }
+
+        #region add elite in the graph and connect it with the previous elite
         if (elite != null) {
           var prevVertex = (IGenealogyGraphNode<T>)GenealogyGraph.GetVertex(elite);
@@ -264 +274 @@
 
           var vertex = new GenealogyGraphNode<T>(prevVertex.Content) {
-            Rank = currentGeneration,
+            Rank = generation,
             Quality = prevVertex.Quality,
             IsElite = false
@@ -272 +282 @@
           // inject the graph node unique id to the scope
           ExecutionContext.Scope.SubScopes[index].Variables["Id"].Value = new StringValue(vertex.Id);
-
           GenealogyGraph.AddVertex(vertex);
-
           GenealogyGraph.AddArc(prevVertex, vertex); // connect current elite with previous elite
 
@@ -281 +289 @@
           }
         }
+        #endregion
+
+        ComputeSuccessRatios();
       }
       // update qualities
-      for (int i = 0; i < population.Count; ++i) {
+      for (int i = 0; i < population.Length; ++i) {
         var vertex = (IGenealogyGraphNode)GenealogyGraph.GetVertex(population[i]);
         vertex.Quality = qualities[i].Value;
@@ -289 +300 @@
 
       // remove extra graph nodes (added by the instrumented operators in the case of offspring selection)
-      var discardedOffspring = GenealogyGraph.Ranks[currentGeneration].Select(x => (T)x.Content).Except(population).ToList();
-      foreach (var individual in discardedOffspring) {
-        var vertex = GenealogyGraph.GetVertex(individual);
+      var discardedOffspring = GenealogyGraph.Ranks[generation].Select(x => (T)x.Content).Except(population).ToList();
+      foreach (var vertex in discardedOffspring.Select(individual => GenealogyGraph.GetVertex(individual))) {
         GenealogyGraph.RemoveVertex(vertex);
       }
 
       return base.Apply();
+    }
+
+    private void ComputeSuccessRatios() {
+      var population = PopulationParameter.ActualValue;
+      var generation = GenerationsParameter.ActualValue.Value;
+      // compute the weight of each genealogy graph node as the ratio (produced offspring) / (surviving offspring)
+      foreach (var ind in population) {
+        var v = (IGenealogyGraphNode)GenealogyGraph.GetVertex(ind);
+        foreach (var p in v.Parents)
+          p.Weight++;
+      }
+      foreach (var v in GenealogyGraph.Ranks[generation - 1]) {
+        if (v.OutDegree > 0)
+          v.Weight /= v.OutDegree;
+      }
+
+      var results = ResultsParameter.ActualValue;
+      DataTable table;
+      if (!results.ContainsKey("Successful offspring ratio")) {
+        table = new DataTable("Successful offspring ratio");
+        results.Add(new Result("Successful offspring ratio", table));
+        table.Rows.Add(new DataRow("Successful offspring ratio") { VisualProperties = { ChartType = DataRowVisualProperties.DataRowChartType.Columns, StartIndexZero = true } });
+      } else {
+        table = (DataTable)results["Successful offspring ratio"].Value;
+      }
+      var row = table.Rows["Successful offspring ratio"];
+      row.Values.Replace(GenealogyGraph.Ranks[generation - 1].OrderByDescending(x => x.Quality).Select(x => x.Weight));
     }
   }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/HeuristicLab.EvolutionTracking-3.4.csproj

@@ -56 +56 @@
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="HeuristicLab.Analysis-3.3, Version=3.3.0.0, Culture=neutral, PublicKeyToken=ba48961d6f65dcec, processorArchitecture=MSIL">
+      <SpecificVersion>False</SpecificVersion>
+      <HintPath>..\..\..\..\trunk\sources\bin\HeuristicLab.Analysis-3.3.dll</HintPath>
+      <Private>False</Private>
+    </Reference>
     <Reference Include="HeuristicLab.Collections-3.3">
       <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Collections-3.3.dll</HintPath>

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Operators/AfterCrossoverOperator.cs

@@ -45 +45 @@
       return new AfterCrossoverOperator<T>(this, cloner);
     }
+    [StorableConstructor]
+    protected AfterCrossoverOperator(bool deserializing) : base(deserializing) { }
 
     public AfterCrossoverOperator() {

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Operators/AfterManipulatorOperator.cs

@@ -41 +41 @@
       return new AfterManipulatorOperator<T>(this, cloner);
     }
+    [StorableConstructor]
+    protected AfterManipulatorOperator(bool deserializing) : base(deserializing) { }
 
     public AfterManipulatorOperator() {

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Operators/BeforeCrossoverOperator.cs

@@ -54 +54 @@
     }
 
+    [StorableConstructor]
+    protected BeforeCrossoverOperator(bool deserializing) : base(deserializing) { }
+
     public BeforeCrossoverOperator() {
       Parameters.Add(new ScopeTreeLookupParameter<T>(ParentsParameterName));

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Operators/BeforeManipulatorOperator.cs

@@ -30 +30 @@
   [Item("AfterCrossoverOperator", "Performs an action after the crossover operator is applied.")]
   public class BeforeManipulatorOperator<T> : EvolutionTrackingOperator<T>, IManipulatorOperator<T> where T : class,IItem {
-
     private const string ChildParameterName = "Child";
 
@@ -43 +42 @@
       return new BeforeManipulatorOperator<T>(this, cloner);
     }
+    [StorableConstructor]
+    protected BeforeManipulatorOperator(bool deserializing) : base(deserializing) { }
 
     public BeforeManipulatorOperator() {

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Operators/EvolutionTrackingOperator.cs

@@ -26 +26 @@
 using HeuristicLab.Optimization;
 using HeuristicLab.Parameters;
+using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
 
 namespace HeuristicLab.EvolutionTracking {
+  [Item("EvolutionTrackingOperator", "A base operator which facilitates access to the genealogy graph.")]
+  [StorableClass]
   public class EvolutionTrackingOperator<T> : SingleSuccessorOperator where T : class,IItem {
     // evolution tracking-related parameters
@@ -69 +72 @@
       return new EvolutionTrackingOperator<T>(this, cloner);
     }
+    [StorableConstructor]
+    protected EvolutionTrackingOperator(bool deserializing) : base(deserializing) { }
   }
 }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisGenealogyAnalyzer.cs

@@ -4 +4 @@
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
 
-namespace HeuristicLab.Problems.DataAnalysis.Symbolic.Analyzers {
+namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
+  [Item("SymbolicDataAnalysisGenealogyAnalyzer", "")]
   [StorableClass]
-  [Item("SymbolicDataAnalysisGenealogyAnalyzer", "")]
   public class SymbolicDataAnalysisGenealogyAnalyzer : GenealogyAnalyzer<ISymbolicExpressionTree> {
+    public SymbolicDataAnalysisGenealogyAnalyzer() { }
+
+    [StorableConstructor]
+    protected SymbolicDataAnalysisGenealogyAnalyzer(bool deserializing) : base(deserializing) { }
   }
 }