/** {@inheritDoc} */
@Override
public void absorb(Niche algorithm) {
for (PopulationBasedAlgorithm pba : algorithm.getPopulations()) {
RadiusVisitor radiusVisitor = new RadiusVisitor();
pba.accept(radiusVisitor);
double radius = radiusVisitor.getResult().doubleValue();
Topology<? extends Entity> mainSwarmTopology = algorithm.getMainSwarm().getTopology();
for (int i = 0; i < mainSwarmTopology.size(); i++) {
Entity entity = mainSwarmTopology.get(i);
double distance =
distanceMeasure.distance(
entity.getCandidateSolution(),
Topologies.getBestEntity(pba.getTopology()).getCandidateSolution());
if (distance <= radius) {
Particle p = (Particle) entity;
p.setVelocityProvider(new GCVelocityProvider());
p.setNeighbourhoodBest((Particle) Topologies.getBestEntity(pba.getTopology()));
Topology<Particle> topology = (Topology<Particle>) pba.getTopology();
topology.add(p);
algorithm.getMainSwarm().getTopology().remove(entity);
}
}
}
}
/**
* Just reevaluate the {@link Entity entities} inside the topology. An entity's implementation
* should handle updating anything else that is necessary, e.g. a {@link StandardParticle}'s
* <code>personal best position</code> in the case of {@link PSO}.
*
* <p>{@inheritDoc}
*/
@Override
public void performReaction(E algorithm) {
Topology<? extends Entity> entities = algorithm.getTopology();
int reevaluateCount = (int) Math.floor(reevaluationRatio * entities.size());
reevaluate(entities, reevaluateCount);
}
@Override
public Topology<Particle> f(PSO pso) {
Topology<Particle> newTopology = pso.getTopology().getClone();
newTopology.clear();
for (Particle p : pso.getTopology()) {
newTopology.add(function.f(p));
}
return newTopology;
}
/**
* Respond to environment change by re-evaluating each particle's position, personal best and
* neighbourhood best, and reinitializing the positions of a specified percentage of particles.
*
* @param algorithm PSO algorithm that has to respond to environment change
*/
@Override
public void respond(E algorithm) {
Topology<? extends Entity> topology = algorithm.getTopology();
// Reevaluate current position. Update personal best (done by reevaluate()).
Iterator<? extends Entity> iterator = topology.iterator();
int reinitCounter = 0;
int keepCounter = 0;
int populationSize = algorithm.getTopology().size();
while (iterator.hasNext()) {
DynamicParticle current = (DynamicParticle) iterator.next();
ZeroTransformation zt = new ZeroTransformation();
// makes sure the charged particles are randomly positionned accross the topology
if (reinitCounter < Math.floor(populationSize * reinitialisationRatio)
&& randomiser.nextDouble() < reinitialisationRatio
&& current != (algorithm).getTopology().getBestEntity()) {
current.getPosition().randomize(this.randomiser);
current
.getProperties()
.put(EntityType.Particle.VELOCITY, Vectors.transform(current.getVelocity(), zt));
current
.getProperties()
.put(EntityType.Particle.BEST_POSITION, current.getPosition().getClone());
++reinitCounter;
} // if
else if (keepCounter > Math.floor(populationSize * (1.0 - reinitialisationRatio))
&& current != (algorithm).getTopology().getBestEntity()) {
current.getPosition().randomize(this.randomiser);
current
.getProperties()
.put(EntityType.Particle.VELOCITY, Vectors.transform(current.getVelocity(), zt));
current
.getProperties()
.put(EntityType.Particle.BEST_POSITION, current.getPosition().getClone());
++reinitCounter;
} // else if
else {
++keepCounter;
} // else
}
// Re-evaluate:
reevaluateParticles(algorithm); // super class method
}
/**
* Get a list of individuals that are suitable to be used within the recombination arithmetic
* operator.
*
* @param topology The {@see net.sourceforge.cilib.entity.Topology Topology} containing the
* entites.
* @return A list of unique entities.
*/
public static List<Entity> getRandomParentEntities(Topology<? extends Entity> topology) {
List<Entity> parents = new ArrayList<Entity>(3);
ProbabilityDistributionFuction randomNumber = new UniformDistribution();
int count = 0;
while (count < 3) {
int random = randomNumber.getRandomProvider().nextInt(topology.size());
Entity parent = topology.get(random);
if (!parents.contains(parent)) {
parents.add(parent);
count++;
}
}
return parents;
}
/**
* This is an Synchronous strategy:
*
* <ol>
* <li>For all particles:
* <ol>
* <li>Update the particle velocity
* <li>Update the particle position
* </ol>
* <li>For all particles:
* <ol>
* <li>Calculate the particle fitness
* <li>For all particles in the current particle's neighbourhood:
* <ol>
* <li>Update the neighbourhood best
* </ol>
* </ol>
* </ol>
*
* @see
* net.sourceforge.cilib.PSO.IterationStrategy#performIteration(net.sourceforge.cilib.PSO.PSO)
* @param pso The {@link PSO} to have an iteration applied.
*/
@Override
public void performIteration(PSO pso) {
Topology<Particle> topology = pso.getTopology();
for (Particle current : topology) {
current.updateVelocity();
current.updatePosition(); // TODO: replace with visitor (will simplify particle interface)
boundaryConstraint.enforce(current);
}
Problem problem = AbstractAlgorithm.getAlgorithmList().get(0).getOptimisationProblem();
for (Particle current : topology) {
current.calculateFitness();
for (Particle other : topology.neighbourhood(current)) {
Particle p1 = current.getNeighbourhoodBest().getClone();
Particle p2 = other.getNeighbourhoodBest().getClone();
OptimisationSolution s1 =
new OptimisationSolution(
p1.getCandidateSolution().getClone(),
problem.getFitness(p1.getCandidateSolution().getClone()));
OptimisationSolution s2 =
new OptimisationSolution(
p2.getCandidateSolution().getClone(),
problem.getFitness(p2.getCandidateSolution().getClone()));
MOFitness fitness1 = (MOFitness) s1.getFitness();
MOFitness fitness2 = (MOFitness) s2.getFitness();
// System.out.println("fitness1 = ");
// for (int i=0; i < fitness1.getDimension(); i++)
// System.out.println(fitness1.getFitness(i).getValue());
//
// System.out.println("fitness2 = ");
// for (int i=0; i < fitness2.getDimension(); i++)
// System.out.println(fitness2.getFitness(i).getValue());
if (fitness1.compareTo(fitness2) > 0) {
other.setNeighbourhoodBest(current);
}
}
}
}
/**
* Perform an iteration of the DE algorithm defined as the DE/x/y/z implementation but including a
* parameter adaptation step.
*
* @param ec The {@linkplain EC} on which to perform this iteration.
*/
@Override
public void performIteration(EC ec) {
Topology<SaDEIndividual> topology = (Topology<SaDEIndividual>) ec.getTopology();
for (int i = 0; i < topology.size(); i++) {
SaDEIndividual current = topology.get(i);
current.calculateFitness();
// Create the trial vector by applying mutation
SaDEIndividual targetEntity =
(SaDEIndividual) targetVectorSelectionStrategy.on(topology).exclude(current).select();
// Create the trial vector / entity
SaDEIndividual trialEntity =
(SaDEIndividual)
current.getTrialVectorCreationStrategy().create(targetEntity, current, topology);
// Create the offspring by applying cross-over
List<SaDEIndividual> offspring =
(List<SaDEIndividual>)
current
.getCrossoverStrategy()
.crossover(Arrays.asList(current, trialEntity)); // Order is VERY important here!!
// Replace the parent (current) if the offspring is better
SaDEIndividual offspringEntity = offspring.get(0);
boundaryConstraint.enforce(offspringEntity);
offspringEntity.calculateFitness();
if (offspringEntity.getFitness().compareTo(current.getFitness())
> 0) { // the trial vector is better than the parent
topology.set(i, offspringEntity); // Replace the parent with the offspring individual
}
topology.get(i).updateParameters();
}
}
@Override
public void visit(Topology<? extends Entity> topology) {
double maxDistance = 0.0;
Iterator<? extends Entity> k1 = topology.iterator();
while (k1.hasNext()) {
Entity p1 = (Entity) k1.next();
if (p1 instanceof ChargedParticle && ((ChargedParticle) p1).getCharge() != 0) continue;
Vector position1 = (Vector) p1.getCandidateSolution();
Iterator<? extends Entity> k2 = topology.iterator();
while (k2.hasNext()) {
Entity p2 = (Entity) k2.next();
if (p2 instanceof ChargedParticle && ((ChargedParticle) p2).getCharge() != 0) continue;
Vector position2 = (Vector) p2.getCandidateSolution();
double actualDistance = distanceMeasure.distance(position1, position2);
if (actualDistance > maxDistance) maxDistance = actualDistance;
}
}
// result = maxDistance;
distance = maxDistance;
}
/*
* Performs an iteration of the standard co-operative algorithm.
* It holds a context particle, adapts the swarms to hold the context particle
* with the appropriate dimension difference,updates the personal and global
* bests and then updates the particles.
*/
@Override
public void performIteration(CooperativePSO algorithm) {
int populationIndex = 0;
table = new StandardDataTable();
DataClusteringPSO pso;
Topology newTopology;
ClusterParticle particleWithContext;
for (PopulationBasedAlgorithm currentAlgorithm : algorithm.getPopulations()) {
table =
((SinglePopulationDataClusteringIterationStrategy)
((DataClusteringPSO) currentAlgorithm).getIterationStrategy())
.getDataset();
if (!contextinitialised) {
initialiseContextParticle(algorithm);
}
pso = ((DataClusteringPSO) currentAlgorithm);
newTopology = ((DataClusteringPSO) currentAlgorithm).getTopology().getClone();
newTopology.clear();
for (ClusterParticle particle : ((DataClusteringPSO) currentAlgorithm).getTopology()) {
clearDataPatterns(contextParticle);
assignDataPatternsToParticle(
(CentroidHolder) contextParticle.getCandidateSolution(), table);
contextParticle.calculateFitness();
particleWithContext = new ClusterParticle();
particleWithContext.setCandidateSolution(contextParticle.getCandidateSolution().getClone());
particleWithContext
.getProperties()
.put(EntityType.Particle.BEST_POSITION, particle.getBestPosition().getClone());
particleWithContext
.getProperties()
.put(EntityType.Particle.BEST_FITNESS, particle.getBestFitness().getClone());
particleWithContext
.getProperties()
.put(EntityType.Particle.VELOCITY, particle.getVelocity().getClone());
particleWithContext.setNeighbourhoodBest(particle.getNeighbourhoodBest());
((CentroidHolder) particleWithContext.getCandidateSolution())
.set(
populationIndex,
((CentroidHolder) particle.getCandidateSolution()).get(populationIndex));
particleWithContext
.getProperties()
.put(
EntityType.Particle.Count.PBEST_STAGNATION_COUNTER,
particle
.getProperties()
.get(EntityType.Particle.Count.PBEST_STAGNATION_COUNTER)
.getClone());
particleWithContext.setCentroidInitialisationStrategy(
particle.getCentroidInitialisationStrategyCandidate().getClone());
clearDataPatterns(particleWithContext);
assignDataPatternsToParticle(
(CentroidHolder) particleWithContext.getCandidateSolution(), table);
particleWithContext.calculateFitness();
if (particleWithContext.getFitness().compareTo(particleWithContext.getBestFitness()) > 0) {
particle.getProperties().put(EntityType.Particle.BEST_POSITION, particle.getPosition());
particle.getProperties().put(EntityType.Particle.BEST_FITNESS, particle.getFitness());
particleWithContext
.getProperties()
.put(EntityType.Particle.BEST_POSITION, particle.getPosition());
particleWithContext
.getProperties()
.put(EntityType.Particle.BEST_FITNESS, particle.getFitness());
}
if (particleWithContext.getBestFitness().compareTo(contextParticle.getFitness()) > 0) {
((CentroidHolder) contextParticle.getCandidateSolution())
.set(
populationIndex,
((CentroidHolder) particle.getCandidateSolution()).get(populationIndex));
}
if (contextParticle.getFitness().compareTo(contextParticle.getBestFitness()) > 0) {
contextParticle
.getProperties()
.put(EntityType.Particle.BEST_POSITION, contextParticle.getPosition())
.getClone();
contextParticle
.getProperties()
.put(EntityType.Particle.BEST_FITNESS, contextParticle.getFitness())
.getClone();
}
newTopology.add(particleWithContext);
}
if (elitist) {
contextParticle
.getProperties()
.put(EntityType.CANDIDATE_SOLUTION, contextParticle.getBestPosition().getClone());
contextParticle
.getProperties()
.put(EntityType.FITNESS, contextParticle.getBestFitness().getClone());
}
pso.setTopology(newTopology);
pso.performIteration();
populationIndex++;
}
}