/**
* @throws Exception
* @author Klaus Meffert
*/
public void testGetPopulationSize_0() throws Exception {
Configuration conf = new Configuration();
assertEquals(0, conf.getPopulationSize());
final int SIZE = 22;
conf.setPopulationSize(SIZE);
assertEquals(SIZE, conf.getPopulationSize());
}
/**
* @throws Exception
* @author Klaus Meffert
*/
public void testGetter_0() throws Exception {
Configuration conf = new Configuration();
Genotype.setStaticConfiguration(conf);
assertEquals(false, conf.isLocked());
FitnessFunction fitFunc = new StaticFitnessFunction(2);
conf.setFitnessFunction(fitFunc);
Gene gene = new BooleanGene(conf);
Chromosome sample = new Chromosome(conf, gene, 55);
conf.setSampleChromosome(sample);
NaturalSelector natSel = new WeightedRouletteSelector();
conf.addNaturalSelector(natSel, false);
RandomGenerator randGen = new StockRandomGenerator();
conf.setRandomGenerator(randGen);
IEventManager evMan = new EventManager();
conf.setEventManager(evMan);
GeneticOperator mutOp = new MutationOperator(conf);
conf.addGeneticOperator(mutOp);
GeneticOperator croOp = new CrossoverOperator(conf);
conf.addGeneticOperator(croOp);
conf.setPopulationSize(7);
assertEquals(fitFunc, conf.getFitnessFunction());
assertEquals(natSel, conf.getNaturalSelectors(false).get(0));
assertEquals(randGen, conf.getRandomGenerator());
assertEquals(sample, conf.getSampleChromosome());
assertEquals(evMan, conf.getEventManager());
assertEquals(7, conf.getPopulationSize());
assertEquals(2, conf.getGeneticOperators().size());
assertEquals(mutOp, conf.getGeneticOperators().get(0));
assertEquals(croOp, conf.getGeneticOperators().get(1));
}
/**
* The reproduce method will be invoked on each of the reproduction operators referenced by the
* current Configuration object during the evolution phase. Operators are given an opportunity to
* run in the order they are added to the Configuration. Iterates over species and determines each
* one's number of offspring based on fitness, then passes control to subclass <code>
* reproduce( final Configuration config,
* final List parents, int numOffspring, List offspring )</code> method to perform specific
* reproduction.
*
* @param config The current active genetic configuration.
* @param parentSpecies <code>List</code> contains <code>Species</code> objects containing parent
* chromosomes from which to produce offspring.
* @param offspring <code>List</code> contains offspring <code>ChromosomeMaterial</code> objects;
* this method adds new offspring to this list
* @throws InvalidConfigurationException
* @see ReproductionOperator#reproduce(Configuration, List, int, List)
*/
public final void reproduce(
final Configuration config,
final List<Species> parentSpecies,
List<ChromosomeMaterial> offspring)
throws InvalidConfigurationException {
// Calculate total fitness and number of elites
int totalEliteCount = 0;
// double totalSpeciesFitnessTemp = 0;
final double[] speciesNewSizeProportional = new double[parentSpecies.size()];
int si = 0;
for (Species species : parentSpecies) {
// totalSpeciesFitnessTemp += species.getAverageFitnessValue();
totalEliteCount += species.getEliteCount();
speciesNewSizeProportional[si++] = species.getAverageFitnessValue();
}
ArrayUtil.normaliseSum(speciesNewSizeProportional);
final int targetNewOffspringCount =
(int) Math.round((config.getPopulationSize() - totalEliteCount) * getSlice());
// final double totalSpeciesFitness = totalSpeciesFitnessTemp;
// Make sure species don't drastically increase in size (in some cases an oscillation can
// develop in the size
// of a species where the species size increases massively and then decreases massively in
// alternate
// generations, for a reason too long to explain here).
si = 0;
for (Species species : parentSpecies) {
int newSpeciesSize =
(int) Math.round(speciesNewSizeProportional[si] * targetNewOffspringCount);
if (newSpeciesSize > 1.5 * species.size()) {
// Reduce new size.
speciesNewSizeProportional[si] /= newSpeciesSize / (species.size() * 1.45);
}
si++;
}
// Allow for adjustments just made for proportional sizes.
ArrayUtil.normaliseSum(speciesNewSizeProportional);
si = 0;
for (Species species : parentSpecies) {
species.newProportionalSize = speciesNewSizeProportional[si++];
}
if (targetNewOffspringCount > 0) {
if (parentSpecies.isEmpty()) {
throw new IllegalStateException("no parent species from which to produce offspring");
}
final List<ChromosomeMaterial> newOffspring =
Collections.synchronizedList(new ArrayList<ChromosomeMaterial>(targetNewOffspringCount));
// Reproduce from each species relative to its percentage of total fitness
Parallel.foreach(
parentSpecies,
0,
new Parallel.Operation<Species>() {
public void perform(Species species) {
if (!species.isEmpty()) {
double percentFitness =
species.getAverageFitnessValue() / species.newProportionalSize;
int numSpecieOffspring =
(int) Math.round(species.newProportionalSize * targetNewOffspringCount)
- species.getEliteCount();
// Always create at least one offspring with the clone operator, or any operator if
// it has more than 50% of the slice.
// (Otherwise there's no point hanging on to a species).
if (numSpecieOffspring <= 0
&& (getSlice() > 0.5 || getClass().equals(CloneReproductionOperator.class)))
numSpecieOffspring = 1;
if (numSpecieOffspring > 0)
try {
reproduce(config, species.getChromosomes(), numSpecieOffspring, newOffspring);
} catch (InvalidConfigurationException e) {
e.printStackTrace();
}
}
}
});
// Remove random offspring if we have too many.
while (newOffspring.size() > targetNewOffspringCount) {
Collections.shuffle(newOffspring, config.getRandomGenerator());
newOffspring.remove(newOffspring.size() - 1);
}
for (ChromosomeMaterial c : newOffspring) {
// Mutate if it has the same parents, otherwise according to probability.
boolean mutate =
c.getSecondaryParentId() != null
&& c.getPrimaryParentId().equals(c.getSecondaryParentId());
mutate |= mutateProbability > config.getRandomGenerator().nextDouble();
c.setShouldMutate(mutate);
}
// Add clones of random offspring if we don't have enough.
while (newOffspring.size() > 0 && newOffspring.size() < targetNewOffspringCount) {
int idx = config.getRandomGenerator().nextInt(newOffspring.size());
ChromosomeMaterial clonee = (ChromosomeMaterial) newOffspring.get(idx);
ChromosomeMaterial c = clonee.clone(null);
// Clones should always be mutated.
c.setShouldMutate(true);
newOffspring.add(c);
}
offspring.addAll(newOffspring);
}
}
public static void main(String[] args) {
Funid funid = new Funid();
int executionTimes = 10;
System.out.println("Start");
// Map<String, List<GeneticApplication>> applicationMap = new
// HashMap<String, List<GeneticApplication>>();
// List<GeneticApplication> applications;
List<Configuration> configurations = Configuration.getBasicsConfigurations();
try {
for (Configuration config : configurations) {
System.out.println(config.toString());
System.out.println("Algo 1");
System.out.println("Execucao;Melhor;Gen. Enc.;Med. P. Ini; Med. P. Fin.;Razao;Tempo");
for (int i = 0; i < executionTimes; i++) {
funid.setPopulationSize(config.getPopulationSize());
System.out.print((i + 1) + ";");
GeneticParameters params =
new GeneticParameters(
config.getCrossoverRate(),
config.getMutationRate(),
config.getPopulationSize(),
config.getMaxGeneration(),
MAXIMIZE,
new Elitism(),
new OnePointCrosserOver(),
new RoulleteSelector(MAXIMIZE),
new InversionMutator(),
funid);
new GeneticApplication(funid.getInitialPopulation()).setParams(params).execute();
}
System.out.println(config.toString());
System.out.println("Algo 2");
System.out.println("Execucao;Melhor;Gen. Enc.;Med. P. Ini; Med. P. Fin.;Razao;Tempo");
for (int i = 0; i < executionTimes; i++) {
System.out.print((i + 1) + ";");
GeneticParameters params =
new GeneticParameters(
config.getCrossoverRate(),
config.getMutationRate(),
config.getPopulationSize(),
config.getMaxGeneration(),
MAXIMIZE,
new Generational(),
new TwoPointsCrosserOver(),
new RoulleteSelector(MAXIMIZE),
new InversionMutator(),
funid);
new GeneticApplication(funid.getInitialPopulation()).setParams(params).execute();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Evolves the population of chromosomes within a genotype. This will execute all of the genetic
* operators added to the present active configuration and then invoke the natural selector to
* choose which chromosomes will be included in the next generation population.
*
* @param a_pop the population to evolve
* @param a_conf the configuration to use for evolution
* @return evolved population
* @author Klaus Meffert
* @since 3.2
*/
public Population evolve(Population a_pop, Configuration a_conf) {
Population pop = a_pop;
int originalPopSize = a_conf.getPopulationSize();
boolean monitorActive = a_conf.getMonitor() != null;
IChromosome fittest = null;
// If first generation: Set age to one to allow genetic operations,
// see CrossoverOperator for an illustration.
// ----------------------------------------------------------------
if (a_conf.getGenerationNr() == 0) {
int size = pop.size();
for (int i = 0; i < size; i++) {
IChromosome chrom = pop.getChromosome(i);
chrom.increaseAge();
}
} else {
// Select fittest chromosome in case it should be preserved and we are
// not in the very first generation.
// -------------------------------------------------------------------
if (a_conf.isPreserveFittestIndividual()) {
/** @todo utilize jobs. In pop do also utilize jobs, especially for fitness computation */
fittest = pop.determineFittestChromosome(0, pop.size() - 1);
}
}
if (a_conf.getGenerationNr() > 0) {
// Adjust population size to configured size (if wanted).
// Theoretically, this should be done at the end of this method.
// But for optimization issues it is not. If it is the last call to
// evolve() then the resulting population possibly contains more
// chromosomes than the wanted number. But this is no bad thing as
// more alternatives mean better chances having a fit candidate.
// If it is not the last call to evolve() then the next call will
// ensure the correct population size by calling keepPopSizeConstant.
// ------------------------------------------------------------------
keepPopSizeConstant(pop, a_conf);
}
// Ensure fitness value of all chromosomes is udpated.
// ---------------------------------------------------
if (monitorActive) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_BEFORE_UPDATE_CHROMOSOMES1,
a_conf.getGenerationNr(),
new Object[] {pop});
}
updateChromosomes(pop, a_conf);
if (monitorActive) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_AFTER_UPDATE_CHROMOSOMES1,
a_conf.getGenerationNr(),
new Object[] {pop});
}
// Apply certain NaturalSelectors before GeneticOperators will be executed.
// ------------------------------------------------------------------------
pop = applyNaturalSelectors(a_conf, pop, true);
// Execute all of the Genetic Operators.
// -------------------------------------
applyGeneticOperators(a_conf, pop);
// Reset fitness value of genetically operated chromosomes.
// Normally, this should not be necessary as the Chromosome class
// initializes each newly created chromosome with
// FitnessFunction.NO_FITNESS_VALUE. But who knows which Chromosome
// implementation is used...
// ----------------------------------------------------------------
int currentPopSize = pop.size();
for (int i = originalPopSize; i < currentPopSize; i++) {
IChromosome chrom = pop.getChromosome(i);
chrom.setFitnessValueDirectly(FitnessFunction.NO_FITNESS_VALUE);
// Mark chromosome as new-born.
// ----------------------------
chrom.resetAge();
// Mark chromosome as being operated on.
// -------------------------------------
chrom.increaseOperatedOn();
}
// Increase age of all chromosomes which are not modified by genetic
// operations.
// -----------------------------------------------------------------
int size = Math.min(originalPopSize, currentPopSize);
for (int i = 0; i < size; i++) {
IChromosome chrom = pop.getChromosome(i);
chrom.increaseAge();
// Mark chromosome as not being operated on.
// -----------------------------------------
chrom.resetOperatedOn();
}
// If a bulk fitness function has been provided, call it.
// ------------------------------------------------------
BulkFitnessFunction bulkFunction = a_conf.getBulkFitnessFunction();
if (bulkFunction != null) {
if (monitorActive) {
// Monitor that bulk fitness will be called for evaluation.
// --------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_BEFORE_BULK_EVAL,
a_conf.getGenerationNr(),
new Object[] {bulkFunction, pop});
}
/** @todo utilize jobs: bulk fitness function is not so important for a prototype! */
bulkFunction.evaluate(pop);
if (monitorActive) {
// Monitor that bulk fitness has been called for evaluation.
// ---------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_AFTER_BULK_EVAL,
a_conf.getGenerationNr(),
new Object[] {bulkFunction, pop});
}
}
// Ensure fitness value of all chromosomes is udpated.
// ---------------------------------------------------
if (monitorActive) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_BEFORE_UPDATE_CHROMOSOMES2,
a_conf.getGenerationNr(),
new Object[] {pop});
}
updateChromosomes(pop, a_conf);
if (monitorActive) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_AFTER_UPDATE_CHROMOSOMES2,
a_conf.getGenerationNr(),
new Object[] {pop});
}
// Apply certain NaturalSelectors after GeneticOperators have been applied.
// ------------------------------------------------------------------------
pop = applyNaturalSelectors(a_conf, pop, false);
// Fill up population randomly if size dropped below specified percentage
// of original size.
// ----------------------------------------------------------------------
if (a_conf.getMinimumPopSizePercent() > 0) {
int sizeWanted = a_conf.getPopulationSize();
int popSize;
int minSize = (int) Math.round(sizeWanted * (double) a_conf.getMinimumPopSizePercent() / 100);
popSize = pop.size();
if (popSize < minSize) {
IChromosome newChrom;
IChromosome sampleChrom = a_conf.getSampleChromosome();
Class sampleChromClass = sampleChrom.getClass();
IInitializer chromIniter =
a_conf.getJGAPFactory().getInitializerFor(sampleChrom, sampleChromClass);
while (pop.size() < minSize) {
try {
/**
* @todo utilize jobs as initialization may be time-consuming as invalid combinations
* may have to be filtered out
*/
newChrom = (IChromosome) chromIniter.perform(sampleChrom, sampleChromClass, null);
if (monitorActive) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_BEFORE_ADD_CHROMOSOME,
a_conf.getGenerationNr(),
new Object[] {pop, newChrom});
}
pop.addChromosome(newChrom);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
}
}
IChromosome newFittest = reAddFittest(pop, fittest);
if (monitorActive && newFittest != null) {
// Monitor that fitness value of chromosomes is being updated.
// -----------------------------------------------------------
a_conf
.getMonitor()
.event(
IEvolutionMonitor.MONITOR_EVENT_READD_FITTEST,
a_conf.getGenerationNr(),
new Object[] {pop, fittest});
}
// Increase number of generations.
// -------------------------------
a_conf.incrementGenerationNr();
// Fire an event to indicate we've performed an evolution.
// -------------------------------------------------------
m_lastPop = pop;
m_lastConf = a_conf;
a_conf
.getEventManager()
.fireGeneticEvent(new GeneticEvent(GeneticEvent.GENOTYPE_EVOLVED_EVENT, this));
return pop;
}
/**
* @throws Exception
* @author Klaus Meffert
* @since 2.6
*/
public void testToString_1() throws Exception {
Configuration conf = new ConfigurationForTesting();
conf.getGeneticOperators().clear();
conf.getNaturalSelectors(false).clear();
conf.getNaturalSelectors(true).clear();
privateAccessor.setField(conf, "m_eventManager", null);
String s = trimString(conf.toString());
String eventmgr = conf.S_NONE;
String genops = conf.S_NONE;
// natural selectors (pre)
String natselsPre = conf.S_NONE;
// natural selectors (post)
String natselsPost = conf.S_NONE;
assertEquals(
trimString(
conf.S_CONFIGURATION
+ ":"
+ conf.S_CONFIGURATION_NAME
+ ":"
+ conf.getName()
+ " "
+ conf.S_POPULATION_SIZE
+ ":"
+ conf.getPopulationSize()
+ " "
+ conf.S_MINPOPSIZE
+ ":"
+ conf.getMinimumPopSizePercent()
+ " "
+ conf.S_CHROMOSOME_SIZE
+ ":"
+ conf.getChromosomeSize()
+ " "
+ conf.S_SAMPLE_CHROM
+ ":"
+ conf.S_SIZE
+ ":"
+ conf.getSampleChromosome().size()
+ " "
+ conf.S_TOSTRING
+ ":"
+ conf.getSampleChromosome().toString()
+ " "
+ conf.S_RANDOM_GENERATOR
+ ":"
+ conf.getRandomGenerator().getClass().getName()
+ " "
+ conf.S_EVENT_MANAGER
+ ":"
+ eventmgr
+ " "
+ conf.S_CONFIGURATION_HANDLER
+ ":"
+ conf.getConfigurationHandler().getName()
+ " "
+ conf.S_FITNESS_FUNCTION
+ ":"
+ conf.getFitnessFunction().getClass().getName()
+ " "
+ conf.S_FITNESS_EVALUATOR
+ ":"
+ conf.getFitnessEvaluator().getClass().getName()
+ " "
+ conf.S_GENETIC_OPERATORS
+ ":"
+ genops
+ " "
+ conf.S_NATURAL_SELECTORS
+ "("
+ conf.S_PRE
+ ")"
+ ":"
+ natselsPre
+ " "
+ conf.S_NATURAL_SELECTORS
+ "("
+ conf.S_POST
+ ")"
+ ":"
+ natselsPost
+ " "
// + conf.S_POPCONSTANT_SELECTOR + ":"
// + "null" + " "
),
s);
}
/**
* @throws Exception
* @author Klaus Meffert
* @since 2.4
*/
public void testToString_0() throws Exception {
Configuration conf = new ConfigurationForTesting();
conf.addGeneticOperator(new MutationOperator(conf));
conf.addNaturalSelector(new WeightedRouletteSelector(conf), true);
conf.addNaturalSelector(new WeightedRouletteSelector(conf), false);
conf.addNaturalSelector(new BestChromosomesSelector(conf), false);
String s = trimString(conf.toString());
String eventmgr =
conf.getEventManager() != null ? conf.getEventManager().getClass().getName() : conf.S_NONE;
String genops = "";
if (conf.getGeneticOperators().size() < 1) {
genops = conf.S_NONE;
} else {
for (int i = 0; i < conf.getGeneticOperators().size(); i++) {
if (i > 0) {
genops += "; ";
}
genops += conf.getGeneticOperators().get(i).getClass().getName();
;
}
}
// natural selectors (pre)
String natselsPre = "";
int natsize = conf.getNaturalSelectors(true).size();
if (natsize < 1) {
natselsPre = conf.S_NONE;
} else {
for (int i = 0; i < natsize; i++) {
if (i > 0) {
natselsPre += "; ";
}
natselsPre += " " + conf.getNaturalSelectors(true).get(i).getClass().getName();
}
}
// natural selectors (post)
String natselsPost = "";
natsize = conf.getNaturalSelectors(false).size();
if (natsize < 1) {
natselsPost = conf.S_NONE;
} else {
for (int i = 0; i < natsize; i++) {
if (i > 0) {
natselsPost += "; ";
}
natselsPost += " " + conf.getNaturalSelectors(false).get(i).getClass().getName();
}
}
assertEquals(
trimString(
conf.S_CONFIGURATION
+ ":"
+ conf.S_CONFIGURATION_NAME
+ ":"
+ conf.getName()
+ " "
+ conf.S_POPULATION_SIZE
+ ":"
+ conf.getPopulationSize()
+ " "
+ conf.S_MINPOPSIZE
+ ":"
+ conf.getMinimumPopSizePercent()
+ " "
+ conf.S_CHROMOSOME_SIZE
+ ":"
+ conf.getChromosomeSize()
+ " "
+ conf.S_SAMPLE_CHROM
+ ":"
+ conf.S_SIZE
+ ":"
+ conf.getSampleChromosome().size()
+ " "
+ conf.S_TOSTRING
+ ":"
+ conf.getSampleChromosome().toString()
+ " "
+ conf.S_RANDOM_GENERATOR
+ ":"
+ conf.getRandomGenerator().getClass().getName()
+ " "
+ conf.S_EVENT_MANAGER
+ ":"
+ eventmgr
+ " "
+ conf.S_CONFIGURATION_HANDLER
+ ":"
+ conf.getConfigurationHandler().getName()
+ " "
+ conf.S_FITNESS_FUNCTION
+ ":"
+ conf.getFitnessFunction().getClass().getName()
+ " "
+ conf.S_FITNESS_EVALUATOR
+ ":"
+ conf.getFitnessEvaluator().getClass().getName()
+ " "
+ conf.S_GENETIC_OPERATORS
+ ":"
+ genops
+ " "
+ conf.S_NATURAL_SELECTORS
+ "("
+ conf.S_PRE
+ ")"
+ ":"
+ natselsPre
+ " "
+ conf.S_NATURAL_SELECTORS
+ "("
+ conf.S_POST
+ ")"
+ ":"
+ natselsPost
+ " "
// + conf.S_POPCONSTANT_SELECTOR + ":"
// + "null" + " "
),
s);
}