Closes #2 Updated to MQ

buschmais · Jul 27, 2017 · e02df09 · e02df09
1 parent 3232fb3
commit e02df09
Show file tree

Hide file tree

Showing 8 changed files with 104 additions and 12 deletions.
diff --git a/src/main/java/com/buchmais/sarf/benchmark/ModularizationQualityCalculator.java b/src/main/java/com/buchmais/sarf/benchmark/ModularizationQualityCalculator.java
@@ -0,0 +1,56 @@
+package com.buchmais.sarf.benchmark;
+
+import com.buchmais.sarf.SARFRunner;
+import com.buchmais.sarf.repository.MetricRepository;
+
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+
+/**
+ * @author Stephan Pirnbaum
+ */
+public class ModularizationQualityCalculator {
+
+    public static Double computeSimilarityBasedMQ(Map<Long, Set<Long>> decomposition) {
+        Double intraConnectivity = 0d;
+        Double interConnectivity = 0d;
+        MetricRepository metricRepository = SARFRunner.xoManager.getRepository(MetricRepository.class);
+        for (Map.Entry<Long, Set<Long>> component1 : decomposition.entrySet()) {
+            long[] ids1 = component1.getValue().stream().mapToLong(l -> l).toArray();
+            int denominator = ids1.length == 1 ? 1 : ((ids1.length * (ids1.length - 1)) / 2);
+            intraConnectivity += metricRepository.computeSimilarityCohesionInComponent(ids1) / denominator;
+            for (Map.Entry<Long, Set<Long>> component2 : decomposition.entrySet()) {
+                if (!Objects.equals(component1.getKey(), component2.getKey())) {
+                    long[] ids2 = component2.getValue().stream().mapToLong(l -> l).toArray();
+                    denominator = ((ids1.length + ids2.length) * (ids1.length + ids2.length - 1)) / 2;
+                    interConnectivity += metricRepository.computeSimilarityCouplingBetweenComponents(ids1, ids2) / denominator;
+                }
+            }
+        }
+        intraConnectivity /= decomposition.size();
+        interConnectivity /= (decomposition.size() * (decomposition.size() - 1)) / 2;
+        return intraConnectivity - interConnectivity;
+    }
+
+    public static Double computeCouplingBasedMQ(Map<Long, Set<Long>> decomposition) {
+        Double intraConnectivity = 0d;
+        Double interConnectivity = 0d;
+        MetricRepository metricRepository = SARFRunner.xoManager.getRepository(MetricRepository.class);
+        for (Map.Entry<Long, Set<Long>> component1 : decomposition.entrySet()) {
+            long[] ids1 = component1.getValue().stream().mapToLong(l -> l).toArray();
+            int denominator = ids1.length == 1 ? 1 : ((ids1.length * (ids1.length - 1)) / 2);
+            intraConnectivity += metricRepository.computeCouplingCohesionInComponent(ids1) / denominator;
+            for (Map.Entry<Long, Set<Long>> component2 : decomposition.entrySet()) {
+                if (!Objects.equals(component1.getKey(), component2.getKey())) {
+                    long[] ids2 = component2.getValue().stream().mapToLong(l -> l).toArray();
+                    denominator = ((ids1.length + ids2.length) * (ids1.length + ids2.length - 1)) / 2;
+                    interConnectivity += metricRepository.computeCouplingBetweenComponents(ids1, ids2) / denominator;
+                }
+            }
+        }
+        intraConnectivity /= decomposition.size();
+        interConnectivity /= (decomposition.size() * (decomposition.size() - 1));
+        return intraConnectivity - interConnectivity;
+    }
+}
diff --git a/...ain/java/com/buchmais/sarf/classification/criterion/cohesion/LongObjectiveChromosome.java b/...ain/java/com/buchmais/sarf/classification/criterion/cohesion/LongObjectiveChromosome.java
@@ -2,6 +2,7 @@
 
 import com.buchmais.sarf.SARFRunner;
 import com.buchmais.sarf.benchmark.MoJoCalculator;
+import com.buchmais.sarf.benchmark.ModularizationQualityCalculator;
 import com.buchmais.sarf.repository.MetricRepository;
 import com.google.common.collect.Sets;
 import org.jenetics.LongChromosome;
@@ -34,6 +35,8 @@ public abstract class LongObjectiveChromosome extends LongChromosome {
 
     private Double componentRangeObjective = 0d;
 
+    private Double mQ = 0d;
+
     protected LongObjectiveChromosome(ISeq<LongGene> genes) {
         super(genes);
     }
@@ -73,7 +76,7 @@ private void evaluate() {
                 }
             }
         }
-        this.couplingObjective /= (identifiedComponents.size() * (identifiedComponents.size() - 1)) / 2; // TODO: 22.07.2017 Improve
+        this.couplingObjective /= (identifiedComponents.size() * (identifiedComponents.size() - 1)) / 2; // TODO: 27.07.2017 Similarity undirected, coupling directed
         this.cohesionObjective /= identifiedComponents.size();
         //SARFRunner.xoManager.currentTransaction().commit();
         // minimize the difference between min and max component size
@@ -86,6 +89,7 @@ private void evaluate() {
                 identifiedComponents.size() <= 0.25 * Partitioner.ids.length ?
                         (identifiedComponents.size() / (Partitioner.ids.length / 4d)) :
                         (Partitioner.ids.length - identifiedComponents.size()) / (0.75 * Partitioner.ids.length);
+        this.mQ = computeMQ(identifiedComponents);
         if (MoJoCalculator.reference != null) {
             writeBenchmarkLine(identifiedComponents);
         }
@@ -97,6 +101,8 @@ private void evaluate() {
 
     abstract Double computeCoupling(MetricRepository mR, long[] ids1, long[] ids2);
 
+    abstract Double computeMQ(Map<Long, Set<Long>> decomposition);
+
     protected Double getCohesionObjective() {
         if (!this.evaluated) evaluate();
         return this.cohesionObjective;
@@ -122,6 +128,11 @@ protected Double getComponentCountObjective() {
         return this.componentCountObjective;
     }
 
+    protected Double getMQ() {
+        if (!this.evaluated) evaluate();
+        return this.mQ;
+    }
+
     /**
      *
      * @param chromosome
@@ -168,6 +179,8 @@ private void writeBenchmarkLine(Map<Long, Set<Long>> identifiedComponents) {
         Long mojoPlus = Math.min(mojoPlusCompRef, mojoPlusRefComp);
         Double fitness = this.cohesionObjective + this.couplingObjective + this.componentCountObjective +
                 this.componentRangeObjective + this.componentSizeObjective;
+        Double mQSim = ModularizationQualityCalculator.computeSimilarityBasedMQ(identifiedComponents);
+        Double mQCoup = ModularizationQualityCalculator.computeCouplingBasedMQ(identifiedComponents);
         try(FileWriter fw = new FileWriter("benchmark.csv", true);
             BufferedWriter bw = new BufferedWriter(fw);
             PrintWriter out = new PrintWriter(bw)) {
@@ -181,6 +194,8 @@ private void writeBenchmarkLine(Map<Long, Set<Long>> identifiedComponents) {
             out.print(mojo + ", ");
             out.print(mojoFm + ", ");
             out.print(mojoPlus + ", ");
+            out.print(mQSim + ", ");
+            out.print(mQCoup + ", ");
             out.println(fitness);
         } catch (IOException e) {
         }

diff --git a/.../com/buchmais/sarf/classification/criterion/cohesion/LongObjectiveCouplingChromosome.java b/.../com/buchmais/sarf/classification/criterion/cohesion/LongObjectiveCouplingChromosome.java
@@ -1,10 +1,14 @@
 package com.buchmais.sarf.classification.criterion.cohesion;
 
+import com.buchmais.sarf.benchmark.ModularizationQualityCalculator;
 import com.buchmais.sarf.repository.MetricRepository;
 import org.jenetics.LongGene;
 import org.jenetics.util.ISeq;
 import org.jenetics.util.LongRange;
 
+import java.util.Map;
+import java.util.Set;
+
 /**
  * @author Stephan Pirnbaum
  */
@@ -24,12 +28,18 @@ public LongObjectiveCouplingChromosome(Long min, Long max) {
 
     @Override
     Double computeCohesion(MetricRepository mR, long[] ids) {
-        return mR.computeCouplingCohesionInComponent(ids) / ids.length;
+        int denominator = ids.length == 1 ? 1 : ((ids.length * (ids.length - 1)) / 2);
+        return mR.computeCouplingCohesionInComponent(ids) / denominator;
     }
 
     @Override
     Double computeCoupling(MetricRepository mR, long[] ids1, long[] ids2) {
-        return mR.computeCouplingBetweenComponents(ids1, ids2);
+        return mR.computeCouplingBetweenComponents(ids1, ids2) / ((ids1.length + ids2.length) * (ids1.length + ids2.length - 1) / 2);
+    }
+
+    @Override
+    Double computeMQ(Map<Long, Set<Long>> decomposition) {
+        return ModularizationQualityCalculator.computeCouplingBasedMQ(decomposition);
     }
 
     @Override

diff --git a/...om/buchmais/sarf/classification/criterion/cohesion/LongObjectiveSimilarityChromosome.java b/...om/buchmais/sarf/classification/criterion/cohesion/LongObjectiveSimilarityChromosome.java
@@ -1,10 +1,14 @@
 package com.buchmais.sarf.classification.criterion.cohesion;
 
+import com.buchmais.sarf.benchmark.ModularizationQualityCalculator;
 import com.buchmais.sarf.repository.MetricRepository;
 import org.jenetics.LongGene;
 import org.jenetics.util.ISeq;
 import org.jenetics.util.LongRange;
 
+import java.util.Map;
+import java.util.Set;
+
 /**
  * @author Stephan Pirnbaum
  */
@@ -30,7 +34,12 @@ Double computeCohesion(MetricRepository mR, long[] ids) {
 
     @Override
     Double computeCoupling(MetricRepository mR, long[] ids1, long[] ids2) {
-        return mR.computeSimilarityCouplingBetweenComponents(ids1, ids2);
+        return mR.computeSimilarityCouplingBetweenComponents(ids1, ids2) / ((ids1.length + ids2.length) * (ids1.length + ids2.length - 1) / 2);
+    }
+
+    @Override
+    Double computeMQ(Map<Long, Set<Long>> decomposition) {
+        return ModularizationQualityCalculator.computeSimilarityBasedMQ(decomposition);
     }
 
     @Override

diff --git a/src/main/java/com/buchmais/sarf/classification/criterion/cohesion/Partitioner.java b/src/main/java/com/buchmais/sarf/classification/criterion/cohesion/Partitioner.java
@@ -33,15 +33,15 @@ public static Map<Long, Set<Long>> partition(long[] ids, Map<Long, Set<Long>> in
         Genotype<LongGene> genotype = createGenotype(initialPartitioning, similarityBased);
         final Engine<LongGene, Double> engine = Engine
                 .builder(Partitioner::computeFitnessValue, genotype)
-                .offspringFraction(0.7)
+                .offspringFraction(0.5)
                 .survivorsSelector(new ParetoFrontierSelector())
                 .offspringSelector(new ParetoFrontierSelector())
                 .populationSize(100)
                 .alterers(
                         new MultiPointCrossover<>(1),
                         similarityBased ?
-                                new SimilarityMutator(0.004 * Math.log10(ids.length) / Math.log10(2)) :
-                                new CouplingMutator(0.004 * Math.log10(ids.length) / Math.log10(2)),
+                                new SimilarityMutator(0.008 * Math.log10(ids.length) / Math.log10(2)) :
+                                new CouplingMutator(0.008 * Math.log10(ids.length) / Math.log10(2)),
                         new GaussianMutator<>(0.004 * Math.log10(ids.length) / Math.log10(2)))
                 .executor(Runnable::run)
                 .build();
@@ -94,7 +94,7 @@ private static Genotype<LongGene> createGenotype(Map<Long, Set<Long>> initialPar
 
     static Double computeFitnessValue(final Genotype<LongGene> prospect) {
         LongObjectiveChromosome chromosome = (LongObjectiveChromosome) prospect.getChromosome();
-        return chromosome.getCohesionObjective() + chromosome.getCouplingObjective() + chromosome.getComponentCountObjective() + chromosome.getComponentRangeObjective() + chromosome.getComponentSizeObjective();
+        return chromosome.getMQ();
     }
 
     private static void update(final EvolutionResult<LongGene, Double> result) {

diff --git a/src/main/java/com/buchmais/sarf/repository/MetricRepository.java b/src/main/java/com/buchmais/sarf/repository/MetricRepository.java
@@ -303,7 +303,7 @@ Long countInvokesStatic(@Parameter("t1") Long t1,
             "WHERE" +
             "  ID(e1) IN {ids1} AND ID(e2) IN {ids2} " +
             "RETURN" +
-            "  toFloat(SUM(c.coupling) / COUNT(c))")
+            "  toFloat(SUM(c.coupling))")
     Double computeCouplingBetweenComponents(@Parameter("ids1") long[] ids1, @Parameter("ids2") long[] ids2);
 
     @ResultOf
@@ -339,7 +339,7 @@ Long countInvokesStatic(@Parameter("t1") Long t1,
             "WHERE" +
             "  ID(e1) IN {ids1} AND ID(e2) IN {ids2} " +
             "RETURN" +
-            "  toFloat(SUM(s.similarity)/(COUNT(s) + 0.00000001))")
+            "  toFloat(SUM(s.similarity))")
     Double computeSimilarityCouplingBetweenComponents(@Parameter("ids1") long[] ids1, @Parameter("ids2") long[] ids2);
 
     @ResultOf

diff --git a/src/main/resources/benchmark3.xml b/src/main/resources/benchmark3.xml
@@ -1,4 +1,5 @@
-<Configuration iteration="1">
+<Configuration iteration="1"
+    decomposition="flat" optimization="similarity">
     <Component shape="Component" name="1">
         <Rules>
             <Name rule="IndexController" weight="100"/>

diff --git a/src/main/resources/configuration_3.xml b/src/main/resources/configuration_3.xml
@@ -1,4 +1,5 @@
-<Configuration iteration="1">
+<Configuration iteration="1"
+    decomposition="deep">
     <Component shape="Layer" name="DataLayer">
         <Rules>
             <!--Dependency rule="javax\.persistence.*" weight="50"/>