source: trunk/HeuristicLab.Analysis/3.3/AlleleFrequencyAnalysis/AlleleFrequencyAnalyzer.cs @ 18242

#region License Information
/* HeuristicLab
 * Copyright (C) Heuristic and Evolutionary Algorithms Laboratory (HEAL)
 *
 * This file is part of HeuristicLab.
 *
 * HeuristicLab is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * HeuristicLab is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
 */
#endregion

using System;
using System.Collections.Generic;
using System.Linq;
using HeuristicLab.Common;
using HeuristicLab.Core;
using HeuristicLab.Data;
using HeuristicLab.Operators;
using HeuristicLab.Optimization;
using HeuristicLab.Parameters;
using HEAL.Attic;

namespace HeuristicLab.Analysis {
  /// <summary>
  /// An operator for analyzing the frequency of alleles.
  /// </summary>
  [Item("AlleleFrequencyAnalyzer", "An operator for analyzing the frequency of alleles.")]
  [StorableType("FB4ABEB4-E94E-4B79-9356-8AC48D8F77BE")]
  public abstract class AlleleFrequencyAnalyzer<T> : SingleSuccessorOperator, IAnalyzer, ISingleObjectiveOperator where T : class, IItem {
    public virtual bool EnabledByDefault {
      get { return false; }
    }

    public LookupParameter<BoolValue> MaximizationParameter {
      get { return (LookupParameter<BoolValue>)Parameters["Maximization"]; }
    }
    public ScopeTreeLookupParameter<T> SolutionParameter {
      get { return (ScopeTreeLookupParameter<T>)Parameters["Solution"]; }
    }
    public ScopeTreeLookupParameter<DoubleValue> QualityParameter {
      get { return (ScopeTreeLookupParameter<DoubleValue>)Parameters["Quality"]; }
    }
    public LookupParameter<T> BestKnownSolutionParameter {
      get { return (LookupParameter<T>)Parameters["BestKnownSolution"]; }
    }
    public ValueLookupParameter<ResultCollection> ResultsParameter {
      get { return (ValueLookupParameter<ResultCollection>)Parameters["Results"]; }
    }
    public ValueParameter<BoolValue> StoreHistoryParameter {
      get { return (ValueParameter<BoolValue>)Parameters["StoreHistory"]; }
    }
    public ValueParameter<IntValue> UpdateIntervalParameter {
      get { return (ValueParameter<IntValue>)Parameters["UpdateInterval"]; }
    }
    public LookupParameter<IntValue> UpdateCounterParameter {
      get { return (LookupParameter<IntValue>)Parameters["UpdateCounter"]; }
    }

    [StorableConstructor]
    protected AlleleFrequencyAnalyzer(StorableConstructorFlag _) : base(_) { }
    protected AlleleFrequencyAnalyzer(AlleleFrequencyAnalyzer<T> original, Cloner cloner) : base(original, cloner) { }
    public AlleleFrequencyAnalyzer()
      : base() {
      Parameters.Add(new LookupParameter<BoolValue>("Maximization", "True if the problem is a maximization problem."));
      Parameters.Add(new ScopeTreeLookupParameter<T>("Solution", "The solutions whose alleles should be analyzed."));
      Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>("Quality", "The qualities of the solutions which should be analyzed."));
      Parameters.Add(new LookupParameter<T>("BestKnownSolution", "The best known solution."));
      Parameters.Add(new ValueLookupParameter<ResultCollection>("Results", "The result collection where the allele frequency analysis results should be stored."));
      Parameters.Add(new ValueParameter<BoolValue>("StoreHistory", "True if the history of the allele frequency analysis should be stored.", new BoolValue(false)));
      Parameters.Add(new ValueParameter<IntValue>("UpdateInterval", "The interval in which the allele frequency analysis should be applied.", new IntValue(1)));
      Parameters.Add(new LookupParameter<IntValue>("UpdateCounter", "The value which counts how many times the operator was called since the last update.", "AlleleFrequencyAnalyzerUpdateCounter"));

      MaximizationParameter.Hidden = true;
      SolutionParameter.Hidden = true;
      QualityParameter.Hidden = true;
      BestKnownSolutionParameter.Hidden = true;
      ResultsParameter.Hidden = true;
      UpdateCounterParameter.Hidden = true;
    }

    #region Equality Comparers
    private class AlleleIdEqualityComparer : IEqualityComparer<Allele> {
      public bool Equals(Allele x, Allele y) {
        return x.Id == y.Id;
      }
      public int GetHashCode(Allele obj) {
        return obj.Id.GetHashCode();
      }
    }
    private class AlleleFrequencyIdEqualityComparer : IEqualityComparer<AlleleFrequency> {
      public bool Equals(AlleleFrequency x, AlleleFrequency y) {
        return x.Id == y.Id;
      }
      public int GetHashCode(AlleleFrequency obj) {
        return obj.Id.GetHashCode();
      }
    }
    #endregion

    public override IOperation Apply() {
      int updateInterval = UpdateIntervalParameter.Value.Value;
      IntValue updateCounter = UpdateCounterParameter.ActualValue;
      if (updateCounter == null) {
        updateCounter = new IntValue(updateInterval);
        UpdateCounterParameter.ActualValue = updateCounter;
      } else updateCounter.Value++;

      if (updateCounter.Value == updateInterval) {
        updateCounter.Value = 0;

        bool max = MaximizationParameter.ActualValue.Value;
        ItemArray<T> solutions = SolutionParameter.ActualValue;
        double[] qualities = QualityParameter.ActualValue.Select(x => x.Value).ToArray();
        T bestKnownSolution = BestKnownSolutionParameter.ActualValue;
        bool storeHistory = StoreHistoryParameter.Value.Value;

        // calculate index of current best solution
        int bestIndex = -1;
        if (!max) {
          bestIndex = qualities
            .Select((x, i) => new { Index = i, Value = x })
            .OrderBy(x => x.Value)
            .First().Index;
        } else {
          bestIndex = qualities
            .Select((x, i) => new { Index = i, Value = x })
            .OrderByDescending(x => x.Value)
            .First().Index;
        }

        // calculate allels of current best and (if available) best known solution
        Allele[] bestAlleles = CalculateAlleles(solutions[bestIndex]);
        Allele[] bestKnownAlleles = null;
        if (bestKnownSolution != null)
          bestKnownAlleles = CalculateAlleles(bestKnownSolution);

        // calculate allele frequencies
        var frequencies = solutions.SelectMany((s, index) => CalculateAlleles(s).Select(a => new { Allele = a, Quality = qualities[index] })).
                          GroupBy(x => x.Allele.Id).
                          Select(x => new AlleleFrequency(x.Key,
                                                          x.Count() / ((double)solutions.Length),
                                                          x.Average(a => a.Allele.Impact),
                                                          x.Average(a => a.Quality),
                                                          bestKnownAlleles == null ? false : bestKnownAlleles.Any(a => a.Id == x.Key),
                                                          bestAlleles.Any(a => a.Id == x.Key)));

        // calculate dummy allele frequencies of alleles of best known solution which did not occur
        if (bestKnownAlleles != null) {
          var bestKnownFrequencies = bestKnownAlleles.Select(x => new AlleleFrequency(x.Id, 0, x.Impact, 0, true, false)).Except(frequencies, new AlleleFrequencyIdEqualityComparer());
          frequencies = frequencies.Concat(bestKnownFrequencies);
        }

        // fetch results collection
        ResultCollection results;
        if (!ResultsParameter.ActualValue.ContainsKey(Name + " Results")) {
          results = new ResultCollection();
          ResultsParameter.ActualValue.Add(new Result(Name + " Results", results));
        } else {
          results = (ResultCollection)ResultsParameter.ActualValue[Name + " Results"].Value;
        }

        // store allele frequencies
        AlleleFrequencyCollection frequenciesCollection = new AlleleFrequencyCollection(frequencies);
        if (!results.ContainsKey("Allele Frequencies"))
          results.Add(new Result("Allele Frequencies", frequenciesCollection));
        else
          results["Allele Frequencies"].Value = frequenciesCollection;

        // store allele frequencies history
        if (storeHistory) {
          if (!results.ContainsKey("Allele Frequencies History")) {
            AlleleFrequencyCollectionHistory history = new AlleleFrequencyCollectionHistory();
            history.Add(frequenciesCollection);
            results.Add(new Result("Allele Frequencies History", history));
          } else {
            ((AlleleFrequencyCollectionHistory)results["Allele Frequencies History"].Value).Add(frequenciesCollection);
          }
        }

        // store alleles data table
        DataTable allelesTable;
        if (!results.ContainsKey("Alleles")) {
          allelesTable = new DataTable("Alleles");
          allelesTable.VisualProperties.XAxisTitle = "Iteration";
          allelesTable.VisualProperties.YAxisTitle = "Number of Alleles";
          allelesTable.VisualProperties.SecondYAxisTitle = "Number of Alleles";

          allelesTable.Rows.Add(new DataRow("Unique Alleles"));
          allelesTable.Rows["Unique Alleles"].VisualProperties.StartIndexZero = true;

          allelesTable.Rows.Add(new DataRow("Unique Alleles of Best Known Solution", null));
          allelesTable.Rows["Unique Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
          allelesTable.Rows["Unique Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;

          allelesTable.Rows.Add(new DataRow("Fixed Alleles", null));
          allelesTable.Rows["Fixed Alleles"].VisualProperties.SecondYAxis = true;
          allelesTable.Rows["Fixed Alleles"].VisualProperties.StartIndexZero = true;

          allelesTable.Rows.Add(new DataRow("Fixed Alleles of Best Known Solution", null));
          allelesTable.Rows["Fixed Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
          allelesTable.Rows["Fixed Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;

          allelesTable.Rows.Add(new DataRow("Lost Alleles of Best Known Solution", null));
          allelesTable.Rows["Lost Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
          allelesTable.Rows["Lost Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;

          results.Add(new Result("Alleles", allelesTable));
        } else {
          allelesTable = (DataTable)results["Alleles"].Value;
        }

        int fixedAllelesCount = frequenciesCollection.Where(x => x.Frequency == 1).Count();
        var relevantAlleles = frequenciesCollection.Where(x => x.ContainedInBestKnownSolution);
        int relevantAllelesCount = relevantAlleles.Count();
        int fixedRelevantAllelesCount = relevantAlleles.Where(x => x.Frequency == 1).Count();
        int lostRelevantAllelesCount = relevantAlleles.Where(x => x.Frequency == 0).Count();
        int uniqueRelevantAllelesCount = relevantAllelesCount - lostRelevantAllelesCount;
        allelesTable.Rows["Unique Alleles"].Values.Add(frequenciesCollection.Count);
        allelesTable.Rows["Unique Alleles of Best Known Solution"].Values.Add(uniqueRelevantAllelesCount);
        allelesTable.Rows["Fixed Alleles"].Values.Add(fixedAllelesCount);
        allelesTable.Rows["Fixed Alleles of Best Known Solution"].Values.Add(fixedRelevantAllelesCount);
        allelesTable.Rows["Lost Alleles of Best Known Solution"].Values.Add(lostRelevantAllelesCount);

        // store alleles values
        if (!results.ContainsKey("Unique Alleles"))
          results.Add(new Result("Unique Alleles", new DoubleValue(frequenciesCollection.Count)));
        else
          ((DoubleValue)results["Unique Alleles"].Value).Value = frequenciesCollection.Count;

        if (!results.ContainsKey("Unique Alleles of Best Known Solution"))
          results.Add(new Result("Unique Alleles of Best Known Solution", new DoubleValue(uniqueRelevantAllelesCount)));
        else
          ((DoubleValue)results["Unique Alleles of Best Known Solution"].Value).Value = uniqueRelevantAllelesCount;

        if (!results.ContainsKey("Fixed Alleles"))
          results.Add(new Result("Fixed Alleles", new DoubleValue(fixedAllelesCount)));
        else
          ((DoubleValue)results["Fixed Alleles"].Value).Value = fixedAllelesCount;

        if (!results.ContainsKey("Fixed Alleles of Best Known Solution"))
          results.Add(new Result("Fixed Alleles of Best Known Solution", new DoubleValue(fixedRelevantAllelesCount)));
        else
          ((DoubleValue)results["Fixed Alleles of Best Known Solution"].Value).Value = fixedRelevantAllelesCount;

        if (!results.ContainsKey("Lost Alleles of Best Known Solution"))
          results.Add(new Result("Lost Alleles of Best Known Solution", new DoubleValue(lostRelevantAllelesCount)));
        else
          ((DoubleValue)results["Lost Alleles of Best Known Solution"].Value).Value = lostRelevantAllelesCount;

        // calculate contained alleles of best known solution and relative quality
        if (bestKnownAlleles != null) {
          double qualityRange = Math.Abs(qualities.Max() - qualities.Min());
          var points = solutions.Select((s, index) => new Point2D<double>(CalculateAlleles(s).Intersect(bestKnownAlleles, new AlleleIdEqualityComparer()).Count(),
                                                                          Math.Abs(qualities[index] - qualities[bestIndex]) / qualityRange));
          var avgContainedReleventAlleles = points.Select(x => x.X).Average();

          var plot = new ScatterPlot("Contained Alleles of Best Known Solution and Relative Solution Qualtiy", null);
          plot.VisualProperties.XAxisTitle = "Contained Alleles of Best Known Solution";
          plot.VisualProperties.YAxisTitle = "Relative Solution Quality";
          plot.VisualProperties.XAxisMinimumAuto = false;
          plot.VisualProperties.XAxisMinimumFixedValue = 0.0;
          plot.VisualProperties.XAxisMaximumAuto = false;
          plot.VisualProperties.XAxisMaximumFixedValue = bestKnownAlleles.Length;
          plot.VisualProperties.YAxisMinimumAuto = false;
          plot.VisualProperties.YAxisMinimumFixedValue = 0.0;
          plot.VisualProperties.YAxisMaximumAuto = false;
          plot.VisualProperties.YAxisMaximumFixedValue = 1.0;
          var row = new ScatterPlotDataRow("Solutions of Current Generation", null, points);
          row.VisualProperties.PointStyle = ScatterPlotDataRowVisualProperties.ScatterPlotDataRowPointStyle.Circle;
          row.VisualProperties.PointSize = 5;
          plot.Rows.Add(row);

          if (!results.ContainsKey("Scatter Plot"))
            results.Add(new Result("Scatter Plot", plot));
          else
            results["Scatter Plot"].Value = plot;
          if (storeHistory) {
            if (!results.ContainsKey("Scatter Plot History")) {
              results.Add(new Result("Scatter Plot History", new ScatterPlotHistory()));
            }
            ((ScatterPlotHistory)results["Scatter Plot History"].Value).Add(plot);
          }

          if (!allelesTable.Rows.ContainsKey("Average Contained Alleles of Best Known Solution")) {
            allelesTable.Rows.Add(new DataRow("Average Contained Alleles of Best Known Solution", null));
            allelesTable.Rows["Average Contained Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
            allelesTable.Rows["Average Contained Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;
          }
          allelesTable.Rows["Average Contained Alleles of Best Known Solution"].Values.Add(avgContainedReleventAlleles);

          if (!results.ContainsKey("Average Contained Alleles of Best Known Solution"))
            results.Add(new Result("Average Contained Alleles of Best Known Solution", new DoubleValue(avgContainedReleventAlleles)));
          else
            ((DoubleValue)results["Average Contained Alleles of Best Known Solution"].Value).Value = avgContainedReleventAlleles;
        }
      }
      return base.Apply();
    }

    protected abstract Allele[] CalculateAlleles(T solution);
  }
}