protected IChromosome reAddFittest(Population a_pop, IChromosome a_fittest) {
// Determine if all-time fittest chromosome is in the population.
// --------------------------------------------------------------
if (a_fittest != null && !a_pop.contains(a_fittest)) {
// Re-add fittest chromosome to current population.
// ------------------------------------------------
a_pop.addChromosome(a_fittest);
return a_fittest;
}
return null;
}
/**
* @param a_pop the population to verify
* @return true if all chromosomes in the populationa are unique
* @author Klaus Meffert
* @since 3.3.1
*/
public static boolean uniqueChromosomes(Population a_pop) {
// Check that all chromosomes are unique
for (int i = 0; i < a_pop.size() - 1; i++) {
IChromosome c = a_pop.getChromosome(i);
for (int j = i + 1; j < a_pop.size(); j++) {
IChromosome c2 = a_pop.getChromosome(j);
if (c == c2) {
return false;
}
}
}
return true;
}
protected void updateChromosomes(Population a_pop, Configuration a_conf) {
int currentPopSize = a_pop.size();
// Ensure all chromosomes are updated.
// -----------------------------------
BulkFitnessFunction bulkFunction = a_conf.getBulkFitnessFunction();
boolean bulkFitFunc = (bulkFunction != null);
if (!bulkFitFunc) {
for (int i = 0; i < currentPopSize; i++) {
IChromosome chrom = a_pop.getChromosome(i);
chrom.getFitnessValue();
}
}
}
/**
* Cares that population size is kept constant and does not exceed the desired size.
*
* @param a_pop Population
* @param a_conf Configuration
*/
protected void keepPopSizeConstant(Population a_pop, Configuration a_conf) {
if (a_conf.isKeepPopulationSizeConstant()) {
try {
a_pop.keepPopSizeConstant();
} catch (InvalidConfigurationException iex) {
throw new RuntimeException(iex);
}
}
}
/**
* 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;
}