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Changeset 12017


Ignore:
Timestamp:
02/16/15 16:52:52 (9 years ago)
Author:
bburlacu
Message:

#1772:

  • Added missing cloning constructors to the phenotypic and bottom-up similarity analyzers
  • Added missing cloning of private members in the PhenotypicSimilarityCalculator cloning constructor
  • Merged trunk changes into the SymbolicExpressionTreeBottomUpSimilarityCalculator
  • Minor layout fixes to the SymbolicDataAnalysisGenealogyGraphView
Location:
branches/HeuristicLab.EvolutionTracking
Files:
8 edited

Legend:

Unmodified
Added
Removed

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic.Views/3.4/HeuristicLab.Problems.DataAnalysis.Symbolic.Views-3.4.csproj

    r11925 r12017  
    367367      <SubType>Designer</SubType>
    368368    </EmbeddedResource>
     369    <EmbeddedResource Include="Tracking\SymbolicDataAnalysisGenealogyGraphView.resx">
     370      <DependentUpon>SymbolicDataAnalysisGenealogyGraphView.cs</DependentUpon>
     371    </EmbeddedResource>
    369372  </ItemGroup>
    370373  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic.Views/3.4/Tracking/SymbolicDataAnalysisGenealogyGraphView.Designer.cs

    r11864 r12017  
    6363      // splitContainer
    6464      //
     65      this.splitContainer.Size = new System.Drawing.Size(1241, 700);
     66      this.splitContainer.SplitterDistance = 617;
     67      //
     68      // viewHost
     69      //
     70      this.viewHost.Size = new System.Drawing.Size(617, 697);
    6571      //
    6672      // genealogyGraphChart
    6773      //
    68       this.genealogyGraphChart.Size = new System.Drawing.Size(692, 697);
     74      this.genealogyGraphChart.Size = new System.Drawing.Size(614, 697);
    6975      //
    7076      // groupBox1

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic.Views/3.4/Tracking/SymbolicDataAnalysisGenealogyGraphView.cs

    r11927 r12017  
    3939    private readonly ISymbolicExpressionTreeNodeEqualityComparer comparer;
    4040
     41    private ISymbolicExpressionTreeNode selectedSubtree;
     42    private ISymbolicExpressionTreeNode SelectedSubtree {
     43      get {
     44        return selectedSubtree;
     45      }
     46      set {
     47        if (selectedSubtree == value) return;
     48        selectedSubtree = value;
     49        ClonedSubtree = (ISymbolicExpressionTreeNode)selectedSubtree.Clone();
     50      }
     51    }
     52
     53    private ISymbolicExpressionTreeNode ClonedSubtree { get; set; }
     54
    4155    public SymbolicDataAnalysisGenealogyGraphView() {
    4256      InitializeComponent();
    … …  
    100114          var nodes = graphNode.Data.IterateNodesPrefix().ToList();
    101115          treeChart_HighlightSubtree(nodes[td.LastSubtreeIndex], Color.Orange);
    102           treeChart_HighlightSubtree(nodes[td.LastFragmentIndex], Color.DodgerBlue);
     116          treeChart_HighlightSubtree(nodes[td.LastFragmentIndex], null, Color.PowderBlue);
    103117        }
    104118      }
    … …  
    114128      bool trace = genealogyGraphChart.TraceFragments; // check whether we are in 'trace' or 'match' mode
    115129
    116       if (trace) {
    117         // perform fragment tracing
    118         var graphNode = (IGenealogyGraphNode<ISymbolicExpressionTree>)genealogyGraphChart.SelectedGraphNode;
    119         var subtreeIndex = graphNode.Data.IterateNodesPrefix().ToList().IndexOf(subtree);
    120         var traceGraph = TraceCalculator.TraceSubtree(graphNode, subtreeIndex);
    121         if (traceGraph.Vertices.Any()) {
    122           genealogyGraphChart.UpdateEnabled = false;
    123           genealogyGraphChart.ClearArcs();
    124           var genealogyNodes = traceGraph.Vertices.Select(v => Content.GetByContent(v.Data));
    125           genealogyGraphChart.HighlightNodes(genealogyNodes, Color.Black, false);
    126           genealogyGraphChart.UpdateEnabled = true;
    127           genealogyGraphChart.EnforceUpdate();
    128           MainFormManager.MainForm.ShowContent(traceGraph); // display the fragment graph on the screen
    129         }
    130       } else {
    131         // perform matching like it was done before
    132         // currently there is no possibility to specify the subtree matching criteria
    133         var trees = Content.Vertices.Select(x => x.Data);
    134         var matchingTrees = trees.Where(x => x.Root.ContainsSubtree(subtree, comparer));
    135 
    136         var matchingVertices = matchingTrees.Select(x => Content.GetByContent(x));
    137         graphChart_HighlightMatchingVertices(matchingVertices);
     130      switch (args.Button) {
     131        case MouseButtons.Left:
     132          SelectedSubtree = subtree;
     133          if (trace) {
     134            // perform fragment tracing
     135            var graphNode = (IGenealogyGraphNode<ISymbolicExpressionTree>)genealogyGraphChart.SelectedGraphNode;
     136            var subtreeIndex = graphNode.Data.IterateNodesPrefix().ToList().IndexOf(subtree);
     137            var traceGraph = TraceCalculator.TraceSubtree(graphNode, subtreeIndex);
     138            if (traceGraph.Vertices.Any()) {
     139              genealogyGraphChart.UpdateEnabled = false;
     140              genealogyGraphChart.ClearArcs();
     141              var genealogyNodes = traceGraph.Vertices.Select(v => Content.GetByContent(v.Data));
     142              genealogyGraphChart.HighlightNodes(genealogyNodes, Color.Black, false);
     143              genealogyGraphChart.UpdateEnabled = true;
     144              genealogyGraphChart.EnforceUpdate();
     145              MainFormManager.MainForm.ShowContent(traceGraph); // display the fragment graph on the screen
     146            }
     147          } else {
     148            // perform matching like it was done before
     149            // currently there is no possibility to specify the subtree matching criteria
     150            var trees = Content.Vertices.Select(x => x.Data);
     151            var matchingTrees = trees.Where(x => x.Root.ContainsSubtree(subtree, comparer));
     152
     153            var matchingVertices = matchingTrees.Select(x => Content.GetByContent(x));
     154            graphChart_HighlightMatchingVertices(matchingVertices);
     155          }
     156          break;
     157        case MouseButtons.Middle:
     158          var index = SelectedSubtree.IterateNodesPrefix().ToList().IndexOf(subtree);
     159          if (index > 0) {
     160            var s = ClonedSubtree.NodeAt(index);
     161            s.Parent.RemoveSubtree(s.Parent.IndexOfSubtree(s));
     162
     163            var trees = Content.Vertices.Select(x => x.Data);
     164            var matchingTrees = trees.Where(x => x.Root.ContainsSubtree(ClonedSubtree, comparer));
     165
     166            var matchingVertices = matchingTrees.Select(x => Content.GetByContent(x));
     167            treeChart_HighlightSubtree(subtree, Color.Black, Color.White);
     168            graphChart_HighlightMatchingVertices(matchingVertices);
     169          }
     170          break;
    138171      }
    139172    }
    … …  
    158191    }
    159192
    160     private void treeChart_HighlightSubtree(ISymbolicExpressionTreeNode subtree, Color? color = null) {
    161       Color myColor = color ?? Color.RoyalBlue;
     193    private void treeChart_HighlightSubtree(ISymbolicExpressionTreeNode subtree, Color? lineColor = null, Color? fillColor = null) {
     194      var lc = lineColor ?? Color.RoyalBlue;
     195      var fc = fillColor ?? Color.White;
    162196      foreach (var s in subtree.IterateNodesPrefix()) {
    163197        var visualNode = SymbolicExpressionTreeChart.GetVisualSymbolicExpressionTreeNode(s);
    164         visualNode.LineColor = myColor;
     198        visualNode.LineColor = lc;
     199        visualNode.FillColor = fc;
    165200
    166201        foreach (var c in s.Subtrees) {
    167202          var visualArc = SymbolicExpressionTreeChart.GetVisualSymbolicExpressionTreeNodeConnection(s, c);
    168           visualArc.LineColor = myColor;
     203          visualArc.LineColor = lc;
    169204        }
    170205      }

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisBottomUpDiversityAnalyzer.cs

    r11965 r12017  
    11#region License Information
    22/* HeuristicLab
    3  * Copyright (C) 2002-2014 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
     3 * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
    44 *
    55 * This file is part of HeuristicLab.
    … …  
    2121
    2222using HeuristicLab.Analysis;
     23using HeuristicLab.Common;
    2324using HeuristicLab.Core;
    2425using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
    2526
    2627namespace HeuristicLab.Problems.DataAnalysis.Symbolic.Analyzers {
    27   [Item("SymbolicDataAnalysisBottomUpDiversityAnalyzer", "A diversity analyzer based on the bottom-up similarity between trees.")]
     28  [Item("SymbolicDataAnalysisBottomUpDiversityAnalyzer", "A diversity analyzer based on the bottom-up distance between trees.")]
    2829  [StorableClass]
    2930  public class SymbolicDataAnalysisBottomUpDiversityAnalyzer : SingleObjectivePopulationDiversityAnalyzer {
    … …  
    3132    protected SymbolicDataAnalysisBottomUpDiversityAnalyzer(bool deserializing) : base(deserializing) { }
    3233
    33     [StorableHook(HookType.AfterDeserialization)]
    34     private void AfterDeserialization() {
     34    private SymbolicDataAnalysisBottomUpDiversityAnalyzer(SymbolicDataAnalysisBottomUpDiversityAnalyzer original, Cloner cloner)
     35      : base(original, cloner) {
     36    }
     37
     38    public override IDeepCloneable Clone(Cloner cloner) {
     39      return new SymbolicDataAnalysisBottomUpDiversityAnalyzer(this, cloner);
    3540    }
    3641

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisPhenotypicDiversityAnalyzer.cs

    r11291 r12017  
    2222using System.Linq;
    2323using HeuristicLab.Analysis;
     24using HeuristicLab.Common;
    2425using HeuristicLab.Core;
    2526using HeuristicLab.Data;
    … …  
    2930
    3031namespace HeuristicLab.Problems.DataAnalysis.Symbolic.Analyzers {
    31   [Item("SymbolicDataAnalysisPhenotypicDiversityAnalyzer", "An analyzer which calculates diversity based on the phenotypic similarity between trees")]
     32  [Item("SymbolicDataAnalysisPhenotypicDiversityAnalyzer", "An analyzer which calculates diversity based on the phenotypic distance between trees")]
    3233  [StorableClass]
    3334  public class SymbolicDataAnalysisPhenotypicDiversityAnalyzer : SingleObjectivePopulationDiversityAnalyzer {
     35    #region parameter names
    3436    private const string SymbolicExpressionTreeParameterName = "SymbolicExpressionTree";
    3537    private const string EvaluatedValuesParameterName = "EstimatedValues";
    … …  
    3739    private const string ProblemDataParameterName = "ProblemData";
    3840    private const string EstimationLimitsParameterName = "EstimationLimits";
     41    #endregion
    3942
     43    #region parameter properties
    4044    public IScopeTreeLookupParameter<ISymbolicExpressionTree> SymbolicExpressionTreeParameter {
    4145      get { return (IScopeTreeLookupParameter<ISymbolicExpressionTree>)Parameters[SymbolicExpressionTreeParameterName]; }
    … …  
    5660      get { return (IValueLookupParameter<DoubleLimit>)Parameters[EstimationLimitsParameterName]; }
    5761    }
     62    #endregion
    5863
    5964    public SymbolicDataAnalysisPhenotypicDiversityAnalyzer() {
    6065      SimilarityCalculator = new PhenotypicSimilarityCalculator { SolutionVariableName = "SymbolicExpressionTree" };
    61 
     66      #region add parameters
    6267      Parameters.Add(new ScopeTreeLookupParameter<ISymbolicExpressionTree>(SymbolicExpressionTreeParameterName, "The symbolic expression trees."));
    6368      Parameters.Add(new ScopeTreeLookupParameter<DoubleArray>(EvaluatedValuesParameterName, "Intermediate estimated values to be saved in the scopes."));
    … …  
    6570      Parameters.Add(new ValueLookupParameter<IDataAnalysisProblemData>(ProblemDataParameterName, "The problem data on which the symbolic data analysis solution should be evaluated."));
    6671      Parameters.Add(new ValueLookupParameter<DoubleLimit>(EstimationLimitsParameterName, "The upper and lower limit that should be used as cut off value for the output values of symbolic data analysis trees."));
     72      #endregion
     73    }
     74
     75    [StorableConstructor]
     76    protected SymbolicDataAnalysisPhenotypicDiversityAnalyzer(bool deserializing)
     77      : base(deserializing) {
     78    }
     79
     80    public override IDeepCloneable Clone(Cloner cloner) {
     81      return new SymbolicDataAnalysisPhenotypicDiversityAnalyzer(this, cloner);
     82    }
     83
     84    private SymbolicDataAnalysisPhenotypicDiversityAnalyzer(SymbolicDataAnalysisPhenotypicDiversityAnalyzer original, Cloner cloner)
     85      : base(original, cloner) {
    6786    }
    6887

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching/SymbolicExpressionTreeBottomUpSimilarityCalculator.cs

    r11965 r12017  
    11#region License Information
    22/* HeuristicLab
    3  * Copyright (C) 2002-2014 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
     3 * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
    44 *
    55 * This file is part of HeuristicLab.
    … …  
    8181
    8282      // visit nodes in order of decreasing height to ensure correct mapping
    83       var nodes1 = n1.IterateNodesPrefix().ToList();
     83      var nodes1 = n1.IterateNodesPrefix().OrderByDescending(x => x.GetDepth()).ToList();
    8484      var nodes2 = n2.IterateNodesPrefix().ToList();
    8585      for (int i = 0; i < nodes1.Count; ++i) {
    … …  
    9898        if (w == null) continue;
    9999
    100         // at this point we know that v and w are isomorphic, however, the mapping cannot be done directly (as in the paper) because the trees are unordered (subtree order might differ)
    101         // the solution is to sort subtrees by label using IterateBreadthOrdered (this will work because the subtrees are isomorphic!) and simultaneously iterate over the two subtrees
     100        // at this point we know that v and w are isomorphic, however, the mapping cannot be done directly
     101        // (as in the paper) because the trees are unordered (subtree order might differ). the solution is
     102        // to sort subtrees from under commutative labels (this will work because the subtrees are isomorphic!)
     103        // while iterating over the two subtrees
    102104        var vv = IterateBreadthOrdered(v, comparer).ToList();
    103105        var ww = IterateBreadthOrdered(w, comparer).ToList();
    … …  
    133135      foreach (var n in nodes) {
    134136        if (n.SubtreeCount == 0) {
    135           var label = Label(n);
     137          var label = GetLabel(n);
    136138          if (!labelMap.ContainsKey(label)) {
    137139            var z = new GraphNode { SymbolicExpressionTreeNode = n, Label = label };
    … …  
    209211    }
    210212
    211     private static string Label(ISymbolicExpressionTreeNode node) {
     213    private static string GetLabel(ISymbolicExpressionTreeNode node) {
    212214      if (node.SubtreeCount > 0)
    213215        return node.Symbol.Name;

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching/SymbolicExpressionTreePhenotypicSimilarityCalculator.cs

    r11927 r12017  
    3434    public ISymbolicDataAnalysisExpressionTreeInterpreter Interpreter { get; set; }
    3535
     36    [StorableConstructor]
     37    protected PhenotypicSimilarityCalculator(bool deserializing) : base(deserializing) { }
     38
    3639    public PhenotypicSimilarityCalculator(PhenotypicSimilarityCalculator original, Cloner cloner)
    3740      : base(original, cloner) {
     41      this.ProblemData = original.ProblemData;
     42      this.Interpreter = original.Interpreter;
    3843    }
    39 
    40     public PhenotypicSimilarityCalculator() { }
    41 
    42     [StorableConstructor]
    43     protected PhenotypicSimilarityCalculator(bool deserializing) : base(deserializing) { }
    4444
    4545    public override IDeepCloneable Clone(Cloner cloner) {
    4646      return new PhenotypicSimilarityCalculator(this, cloner);
    4747    }
     48
     49    public PhenotypicSimilarityCalculator() { }
    4850
    4951    public double CalculateSimilarity(ISymbolicExpressionTree t1, ISymbolicExpressionTree t2) {

  • branches/HeuristicLab.EvolutionTracking/HeuristicLab.Tracking.sln

    r11968 r12017  
    1010    Local.testsettings = Local.testsettings
    1111    Performance1.psess = Performance1.psess
     12    Performance2.psess = Performance2.psess
    1213    Performance3.psess = Performance3.psess
    1314    PreBuildEvent.cmd = PreBuildEvent.cmd
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