Changeset 10755 for branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking

Timestamp:

04/16/14 17:15:33 (10 years ago)

Author:

bburlacu

Message:

#1772: Simplified genealogy graph and fragment graph creation:

• the genealogy graph now has a 1-1 mapping between content and vertices (as opposed to 1-n as it was previously, to account for elites); this required changes to the directed graph implementation
• the fragment graph only contains bifurcation points (where the subtree contains the fragment so tracing must be done both ways (in the root parent AND in the other parent). in the other cases, tracing is restarted from the parent genealogy graph node.

Location:

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4

Files:

• Analyzers/GenealogyAnalyzer.cs (modified) (3 diffs)
• DirectedGraph/DirectedGraph.cs (modified) (4 diffs)
• DirectedGraph/Interfaces/IDirectedGraph.cs (modified) (1 diff)
• Fragment.cs (modified) (2 diffs)
• GenealogyGraph/GenealogyGraph.cs (modified) (3 diffs)
• Interfaces/IFragment.cs (modified) (1 diff)
• Operators/BeforeManipulatorOperator.cs (modified) (2 diffs)

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

@@ -191 +191 @@
         instrumentedManipulator.AfterExecutionOperators.Clear();
         instrumentedManipulator.BeforeExecutionOperators.Clear();
-        if (EnableManipulatorTracking.Value && Manipulator != null) {
+
+        if (EnableManipulatorTracking.Value) {
           if (BeforeManipulatorOperator != null) {
             BeforeManipulatorOperator.ChildParameter.ActualName = ManipulatorChildParameterName;
@@ -222 +223 @@
         if (elite != null) {
           var vertex = new GenealogyGraphNode<T> {
-            Content = elite,
+            Content = (T)elite.Clone(),
             Rank = Generations.Value,
             IsElite = true
           };
-          var previousVertex = (IGenealogyGraphNode<T>)GenealogyGraph[elite].Last();
+          var previousVertex = (IGenealogyGraphNode<T>)GenealogyGraph[elite];
           GenealogyGraph.AddVertex(vertex);
           previousVertex.AddForwardArc(vertex);
           vertex.AddReverseArc(previousVertex);
           vertex.Id = previousVertex.Id; // another way would be to introduce the vertex.Id into the scope of the elite
+          vertex.Quality = previousVertex.Quality;
+
           if (previousVertex.InArcs.Any()) {
             vertex.InArcs.Last().Data = previousVertex.InArcs.Last().Data; // save the fragment in case there is one
@@ -238 +241 @@
       // update qualities
       for (int i = 0; i < population.Count; ++i) {
-        var individual = population[i];
-        foreach (var vertex in GenealogyGraph[individual].Cast<IGenealogyGraphNode<T>>()) {
-          vertex.Quality = qualities[i].Value;
-        }
+        var vertex = (IGenealogyGraphNode)GenealogyGraph[population[i]];
+        vertex.Quality = qualities[i].Value;
       }
 

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/DirectedGraph/DirectedGraph.cs

@@ -38 +38 @@
     }
     [Storable]
-    private readonly Dictionary<object, List<IVertex>> contentMap;
+    private readonly Dictionary<object, IVertex> contentMap;
     public DirectedGraph() {
       nodes = new List<IVertex>();
-      contentMap = new Dictionary<object, List<IVertex>>();
+      contentMap = new Dictionary<object, IVertex>();
     }
     [StorableConstructor]
@@ -50 +50 @@
       : base(original, cloner) {
       nodes = new List<IVertex>(original.Nodes);
-      contentMap = new Dictionary<object, List<IVertex>>(original.contentMap);
+      contentMap = new Dictionary<object, IVertex>(original.contentMap);
     }
     public override IDeepCloneable Clone(Cloner cloner) {
@@ -62 +62 @@
       return contentMap.ContainsKey(content);
     }
-    public List<IVertex> this[object key] {
+    public IVertex this[object key] {
       get {
-        List<IVertex> result;
+        IVertex result;
         contentMap.TryGetValue(key, out result);
         return result;
@@ -80 +80 @@
     }
     public virtual void AddVertex(IVertex vertex) {
+      if (contentMap.ContainsKey(vertex.Content)) {
+        throw new Exception("Content already exists in the graph.");
+      }
+      contentMap[vertex.Content] = vertex;
       Nodes.Add(vertex);
-      if (!contentMap.ContainsKey(vertex.Content))
-        contentMap[vertex.Content] = new List<IVertex>();
-      contentMap[vertex.Content].Add(vertex);
     }
 

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/DirectedGraph/Interfaces/IDirectedGraph.cs

@@ -32 +32 @@
     void RemoveVertex(IVertex vertex);
     List<IVertex> Nodes { get; }
-    List<IVertex> this[object content] { get; }
+    IVertex this[object content] { get; }
     bool Contains(object content);
   }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Fragment.cs

@@ -8 +8 @@
   public class Fragment : Item, IFragment {
     [Storable]
-    public int Index { get; set; }
+    public int Index1 { get; set; }
 
     [Storable]
-    public int OldIndex { get; set; }
+    public int Index2 { get; set; }
 
     [Storable]
@@ -23 +23 @@
       : base(original, cloner) {
       Root = original.Root;
-      Index = original.Index;
-      OldIndex = original.OldIndex;
+      Index1 = original.Index1;
+      Index2 = original.Index2;
     }
     public override IDeepCloneable Clone(Cloner cloner) {

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/GenealogyGraph/GenealogyGraph.cs

@@ -71 +71 @@
     }
 
-    public new List<IGenealogyGraphNode> this[object content] {
+    public new IGenealogyGraphNode this[object content] {
       get {
         var result = base[content];
-        return result != null ? result.Cast<IGenealogyGraphNode>().ToList() : null;
+        return result == null ? null : (IGenealogyGraphNode)result;
       }
     }
@@ -112 +112 @@
     public override void AddVertex(IVertex vertex) {
       var node = (IGenealogyGraphNode<T>)vertex;
-      if (!Ranks.ContainsKey(node.Rank))
+      if (!Ranks.ContainsKey(node.Rank)) {
         Ranks[node.Rank] = new LinkedList<IGenealogyGraphNode>();
+      }
       Ranks[node.Rank].AddLast(node);
       base.AddVertex(vertex);
@@ -134 +135 @@
       if (updated != null) updated(sender, args);
     }
-    public new List<IGenealogyGraphNode<T>> this[object content] {
+    public new IGenealogyGraphNode<T> this[object content] {
       get {
         var result = base[content];
-        return result != null ? result.Cast<IGenealogyGraphNode<T>>().ToList() : null;
+        return result == null ? null : (IGenealogyGraphNode<T>)result;
       }
     }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.EvolutionTracking/3.4/Interfaces/IFragment.cs

@@ -25 +25 @@
   public interface IFragment : IItem {
     object Root { get; set; }
-    int Index { get; set; }
-    int OldIndex { get; set; }
+    int Index1 { get; set; }
+    int Index2 { get; set; }
   }
 

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

@@ -49 +49 @@
     public override IOperation Apply() {
       if (GenealogyGraph.Contains(ChildParameter.ActualValue)) {
+        // if the graph already contains a vertex representing the child, it means that the child is a product of crossover
+        // when mutation follows after crossover, some changes need to be made
         var child = ChildParameter.ActualValue;
         var clone = (T)child.Clone();
-        var vChild = (IGenealogyGraphNode<T>)GenealogyGraph[child].Last();
+        var vChild = (IGenealogyGraphNode<T>)GenealogyGraph[child];
         var vClone = new GenealogyGraphNode<T> { Content = clone, Rank = vChild.Rank - 0.5 };
         GenealogyGraph.AddVertex(vClone);
         // adjust parent-child(clone) relationship in the graph
-        var parents = vChild.InArcs.Select(a => a.Source);
+        var parents = vChild.Parents;
+        // if there's a fragment, save it 
+        IFragment fragment = null;
+        if (vChild.InArcs.Last().Data != null) {
+          fragment = (IFragment<T>)vChild.InArcs.Last().Data;
+        }
         vChild.InArcs = new List<IGenealogyGraphArc>();
         foreach (var p in parents) {
-          foreach (var a in p.OutArcs) {
-            if (a.Target == vChild)
-              a.Target = vClone;
+          foreach (var a in p.OutArcs.Where(a => a.Target == vChild)) {
+            a.Target = vClone;
           }
           vClone.AddReverseArc(p);
@@ -66 +72 @@
         vChild.AddReverseArc(vClone);
         vClone.AddForwardArc(vChild);
+        vClone.InArcs.Last().Data = fragment;
       } else { // this needs to be checked
         var vChild = new GenealogyGraphNode<T> { Content = ChildParameter.ActualValue, Rank = Generations.Value };