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/**
* Copyright (C) 2010-2018 Gordon Fraser, Andrea Arcuri and EvoSuite
* contributors
*
* This file is part of EvoSuite.
*
* EvoSuite is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3.0 of the License, or
* (at your option) any later version.
*
* EvoSuite 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
* Lesser Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with EvoSuite. If not, see extends GeneticAlgorithm {
private static final long serialVersionUID = -7638497183625040479L;
private static final Logger logger = LoggerFactory.getLogger(SPEA2.class);
private DominanceComparator comparator;
// TODO should we use 'archive' from GeneticAlgorithm class?
private List archive = null;
public SPEA2(ChromosomeFactory factory) {
super(factory);
this.comparator = new DominanceComparator();
}
@SuppressWarnings("unchecked")
@Override
protected void evolve() {
/*
* Reproduction
*/
List offspringPopulation = new ArrayList(Properties.POPULATION);
while (offspringPopulation.size() < Properties.POPULATION) {
// TODO SelectionFunction has to be a BinaryTournamentSelection, i.e.,
// a TournamenteSelection with 2 tournaments
// TODO we might want to use BinaryTournamentSelectionCrowdedComparison
T parent1 = this.selectionFunction.select(this.archive);
T parent2 = this.selectionFunction.select(this.archive);
T offspring1 = (T) parent1.clone();
T offspring2 = (T) parent2.clone();
if (Randomness.nextDouble() <= Properties.CROSSOVER_RATE) {
try {
this.crossoverFunction.crossOver(offspring1, offspring2);
} catch (ConstructionFailedException e) {
logger.error("Crossover failed: " + e.getMessage());
e.printStackTrace();
}
}
if (Randomness.nextDouble() <= Properties.MUTATION_RATE) {
this.notifyMutation(offspring1);
offspring1.mutate();
this.notifyMutation(offspring2);
offspring2.mutate();
}
offspringPopulation.add(offspring1);
offspringPopulation.add(offspring2);
}
/*
* Evaluation
*/
for (T element : offspringPopulation) {
for (final FitnessFunction ff : this.getFitnessFunctions()) {
ff.getFitness(element);
notifyEvaluation(element);
}
}
/*
* Replacement
*/
this.population.clear();
this.population.addAll(offspringPopulation);
this.currentIteration++;
}
@Override
public void initializePopulation() {
this.notifySearchStarted();
this.currentIteration = 0;
// Generate an initial population P0
this.generateInitialPopulation(Properties.POPULATION);
// and create an empty archive of the same size
this.archive = new ArrayList(Properties.POPULATION);
for (T element : this.population) {
for (final FitnessFunction ff : this.getFitnessFunctions()) {
ff.getFitness(element);
notifyEvaluation(element);
}
}
this.updateArchive();
this.writeIndividuals(this.archive);
this.notifyIteration();
}
@Override
public void generateSolution() {
if (this.population.isEmpty()) {
this.initializePopulation();
}
while (!isFinished()) {
this.evolve();
this.updateArchive();
this.notifyIteration();
this.writeIndividuals(this.archive);
}
// replace population object with archive, so that when 'getBestIndividuals()'
// function is called, the correct list of solutions is returned
this.population = this.archive;
this.notifySearchFinished();
}
private void updateArchive() {
List union = new ArrayList(2 * Properties.POPULATION);
union.addAll(population);
union.addAll(this.archive);
this.computeStrength(union);
this.archive = this.environmentalSelection(union);
}
/**
*
* @param population
* @return
*/
protected List environmentalSelection(List union) {
List populationCopy = new ArrayList(union.size());
populationCopy.addAll(union);
// First step is to copy all nondominated individuals, i.e., those
// which have a fitness lower than one, from archive and population
// to the archive of the next generation
List tmpPopulation = new ArrayList(populationCopy.size());
Iterator it = populationCopy.iterator();
while (it.hasNext()) {
T individual = it.next();
if (individual.getDistance() < 1.0) {
tmpPopulation.add(individual);
it.remove();
}
}
// If the nondominated front fits exactly into the archive, the environmental
// selection step is completed
if (tmpPopulation.size() == Properties.POPULATION) {
return tmpPopulation;
}
// If archive is too small, the best dominated individuals in the previous
// archive and population are copied to the new archive
else if (tmpPopulation.size() < Properties.POPULATION) {
Collections.sort(populationCopy, new StrengthFitnessComparator());
int remain = (union.size() < Properties.POPULATION ? union.size() : Properties.POPULATION) - tmpPopulation.size();
for (int i = 0; i < remain; i++) {
tmpPopulation.add(populationCopy.get(i));
}
return tmpPopulation;
}
// when the size of the current nondominated (multi)set exceeds the archive size,
// an archive truncation procedure is invoked which iteratively removes individuals
// from the new front until if fits exactly into the archive. the individual which
// has the minimum distance to another individual is chosen at each stage; if there
// are several individuals with minimum distance the tie is broken by considering the
// second smallest distances and so forth.
double[][] distance = this.euclideanDistanceMatrix(tmpPopulation);
List>> distanceList = new LinkedList>>();
for (int i = 0; i < tmpPopulation.size(); i++) {
List> distanceNodeList = new LinkedList>();
for (int j = 0; j < tmpPopulation.size(); j++) {
if (i != j) {
distanceNodeList.add(Pair.of(j, distance[i][j]));
}
}
// sort by distance so that later we can just get the first element, i.e.,
// the one with the smallest distance
Collections.sort(distanceNodeList, new Comparator>() {
@Override
public int compare(Pair pair1, Pair pair2) {
if (pair1.getRight() < pair2.getRight()) {
return -1;
} else if (pair1.getRight() > pair2.getRight()) {
return 1;
} else {
return 0;
}
}
});
distanceList.add(distanceNodeList);
}
while (tmpPopulation.size() > Properties.POPULATION) {
double minDistance = Double.POSITIVE_INFINITY;
int minimumIndex = -1;
for (int i = 0; i < distanceList.size(); i++) {
List> distances = distanceList.get(i);
Pair point = distances.get(0);
// as this list is sorted, we just need to get the first element of it.
if (point.getRight() < minDistance) {
minDistance = point.getRight();
minimumIndex = i;
} else if (point.getRight() == minDistance) {
// as there is a tie, the th smallest distances as to to be searched for
// find the k-th smallest distance that is not equal to the one just
// selected. i.e., go through all distances and skip the ones that
// are equal.
for (int k = 0; k < distances.size(); k++) {
double kdist1 = distances.get(k).getRight();
double kdist2 = distanceList.get(minimumIndex).get(k).getRight();
if (kdist1 == kdist2) {
continue;
} else if (kdist1 < kdist2) {
minimumIndex = i;
}
break;
}
}
}
assert minimumIndex != -1;
// remove the solution with the smallest distance
tmpPopulation.remove(minimumIndex);
distanceList.remove(minimumIndex);
// remove from the neighbours' list of neighbours, the one we just removed
for (List> distances : distanceList) {
ListIterator> iterator = distances.listIterator();
while (iterator.hasNext()) {
if (iterator.next().getLeft() == minimumIndex) {
iterator.remove();
// TODO can we break the loop? is there any chance that 'distances'
// has repeated elements?!
}
}
}
}
return tmpPopulation;
}
/**
*
* @param solutions
*/
protected void computeStrength(List solution) {
// count the number of individuals each solution dominates
int[] strength = new int[solution.size()];
for (int i = 0; i < solution.size() - 1; i++) {
for (int j = i + 1; j < solution.size(); j++) {
int comparison = this.comparator.compare(solution.get(i), solution.get(j));
if (comparison < 0) {
strength[i]++;
} else if (comparison > 0) {
strength[j]++;
}
}
}
// the raw fitness is the sum of the dominance counts (strength)
// of all dominated solutions
double[] rawFitness = new double[solution.size()];
for (int i = 0; i < solution.size() - 1; i++) {
for (int j = i + 1; j < solution.size(); j++) {
int comparison = this.comparator.compare(solution.get(i), solution.get(j));
if (comparison > 0) {
rawFitness[i] += strength[j];
} else if (comparison < 0) {
rawFitness[j] += strength[i];
}
}
}
// Add the distance to the k-th individual. In the reference paper of SPEA2,
// k = sqrt(population.size()), but a value of k = 1 is recommended. See
// http://www.tik.ee.ethz.ch/pisa/selectors/spea2/spea2_documentation.txt
double[][] distance = this.euclideanDistanceMatrix(solution);
int k = 1;
for (int i = 0; i < distance.length; i++) {
Arrays.sort(distance[i]);
double kDistance = 1.0 / (distance[i][k] + 2.0);
// TODO for now let's use 'distance' field, however the right
// name should be 'strength' or 'fitness-strength'
solution.get(i).setDistance(rawFitness[i] + kDistance);
}
}
/**
* Returns a matrix with the euclidean distance between each pair of solutions in the population.
*
* @param solution
* @return
*/
protected double[][] euclideanDistanceMatrix(List solution) {
double[][] distance = new double[solution.size()][solution.size()];
for (int i = 0; i < solution.size(); i++) {
distance[i][i] = 0.0;
for (int j = i + 1; j < solution.size(); j++) {
distance[i][j] = this.distanceBetweenObjectives(solution.get(i), solution.get(j));
distance[j][i] = distance[i][j];
}
}
return distance;
}
/**
* Returns the euclidean distance between a pair of solutions in the objective space.
*
* @param t1
* @param t2
* @return
*/
protected double distanceBetweenObjectives(T t1, T t2) {
double distance = 0.0;
// perform euclidean distance
for (FitnessFunction ff : t1.getFitnessValues().keySet()) {
double diff = t1.getFitness(ff) - t2.getFitness(ff);
distance += Math.pow(diff, 2.0);
}
return Math.sqrt(distance);
}
}
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