/*!
* \brief Recombine individuals by weighted mean to generate a new individual.
* \param inIndivPool Parents being recombined.
* \param ioContext Evolutionary context.
* \return Children generated by recombination.
*/
Individual::Handle Beagle::ES::RecombinationWeightedOp::recombine(Individual::Bag& inIndivPool,
Context& ioContext)
{
Beagle_StackTraceBeginM();
// Compute recombination weights.
std::vector<double> lWeights(inIndivPool.size());
for(unsigned int i=0; i<lWeights.size(); ++i) {
lWeights[i] = std::log(double(lWeights.size()+1));
lWeights[i] -= std::log(double(i+1));
}
// Recombine parents to generate new individual.
const Factory& lFactory = ioContext.getSystem().getFactory();
Individual::Alloc::Handle lIndivAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
Genotype::Alloc::Handle lGenotypeAlloc =
castHandleT<Genotype::Alloc>(lFactory.getConceptAllocator("Genotype"));
Individual::Handle lChildIndiv = castHandleT<Individual>(lIndivAlloc->allocate());
std::vector< std::vector<double> > lCountGenoSum;
for(unsigned int i=0; i<inIndivPool.size(); ++i) {
const unsigned int lPoolISize = inIndivPool[i]->size();
const unsigned int lChildSize = lChildIndiv->size();
if(lPoolISize > lChildSize) {
lCountGenoSum.resize(lPoolISize);
lChildIndiv->resize(lPoolISize);
for(unsigned int j=lChildSize; j<lPoolISize; ++j) {
(*lChildIndiv)[j] = castHandleT<Genotype>(lGenotypeAlloc->allocate());
}
}
for(unsigned int j=0; j<lPoolISize; ++j) {
FltVec::FloatVector::Handle lChildGenoJ = castHandleT<FltVec::FloatVector>((*lChildIndiv)[j]);
FltVec::FloatVector::Handle lPoolIGenoJ = castHandleT<FltVec::FloatVector>((*inIndivPool[i])[j]);
const unsigned int lPoolIGenoJSize = lPoolIGenoJ->size();
if(lPoolIGenoJSize > lChildGenoJ->size()) {
lChildGenoJ->resize(lPoolIGenoJSize,0.0);
lCountGenoSum[j].resize(lPoolIGenoJSize,0);
}
for(unsigned int k=0; k<lPoolIGenoJSize; ++k) {
(*lChildGenoJ)[k] += (lWeights[i] * (*lPoolIGenoJ)[k]);
lCountGenoSum[j][k] += lWeights[i];
}
}
}
for(unsigned int i=0; i<lChildIndiv->size(); ++i) {
FltVec::FloatVector::Handle lChildGenoI = castHandleT<FltVec::FloatVector>((*lChildIndiv)[i]);
for(unsigned int j=0; j<lChildGenoI->size(); ++j) {
(*lChildGenoI)[j] /= lCountGenoSum[i][j];
}
}
Beagle_LogDebugM(ioContext.getSystem().getLogger(), *lChildIndiv);
return lChildIndiv;
Beagle_StackTraceEndM();
}
/*!
* \brief Select inN first individuals.
* \param inN Number of individuals to select.
* \param ioPool Pool from which the individuals are choosen.
* \param ioContext Evolutionary context.
* \param outSelections Vector of unsigned ints that say how often an individual was selected.
*
* The output of this method is via outSelection. It produces a
* vector the same size as ioPool, where each index says how many
* times an individual was selected. If this is not the desired
* output, consider using the method convertToList().
*/
void SelectFirstOp::selectNIndividuals(unsigned int inN,
Individual::Bag& ioPool,
Context& ioContext,
std::vector<unsigned int>& outSelections)
{
Beagle_StackTraceBeginM();
const unsigned int lDivNP = inN / ioPool.size();
const unsigned int lModNP = inN % ioPool.size();
outSelections.resize(ioPool.size());
for(unsigned int i=0; i<ioPool.size(); ++i) {
outSelections[i] = (i<lModNP) ? lDivNP+1 : lDivNP;
}
Beagle_StackTraceEndM("void SelectFirstOp::selectNIndividuals(unsigned int,Individual::Bag&,Context&,std::vector<unsigned int>&)");
}
/*!
* \brief Apply the operation on a deme in the given context.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
*/
void GenerationalOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(getRootNode());
Beagle_NonNullPointerAssertM(mElitismKeepSize);
Beagle_ValidateParameterM(mElitismKeepSize->getWrappedValue() <= ioDeme.size(),
"ec.elite.keepsize",
"The elistism keepsize must be less than the deme size!");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Processing using generational replacement strategy the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
Beagle_LogTraceM(ioContext.getSystem().getLogger(), (*this));
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
Individual::Bag lOffsprings;
const Factory& lFactory = ioContext.getSystem().getFactory();
if(mElitismKeepSize->getWrappedValue() > 0) {
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
for(unsigned int i=0; i<mElitismKeepSize->getWrappedValue(); ++i) {
std::string lIndividualType = ioDeme[0]->getType();
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getAllocator(lIndividualType));
Individual::Handle lEliteIndiv = castHandleT<Individual>(lIndividualAlloc->allocate());
lEliteIndiv->copy(*ioDeme[0], ioContext.getSystem());
lOffsprings.push_back(lEliteIndiv);
if(lHistory != NULL) {
HistoryID::Handle lHID = castHandleT<HistoryID>(ioDeme[0]->getMember("HistoryID"));
std::vector<HistoryID> lParent;
if(lHID != NULL) lParent.push_back(*lHID);
lHistory->allocateNewID(*lEliteIndiv);
lHistory->trace(ioContext, lParent, lEliteIndiv, getName(), "elitism");
}
std::pop_heap(ioDeme.begin(), (ioDeme.end()-i), IsLessPointerPredicate());
}
}
for(unsigned int i=mElitismKeepSize->getWrappedValue(); i<ioDeme.size(); ++i) {
unsigned int lIndexBreeder = lRoulette.select(ioContext.getSystem().getRandomizer());
BreederNode::Handle lSelectedBreeder=getRootNode();
for(unsigned int j=0; j<lIndexBreeder; ++j)
lSelectedBreeder=lSelectedBreeder->getNextSibling();
Beagle_NonNullPointerAssertM(lSelectedBreeder);
Beagle_NonNullPointerAssertM(lSelectedBreeder->getBreederOp());
Individual::Handle lBredIndiv =
lSelectedBreeder->getBreederOp()->breed(ioDeme, lSelectedBreeder->getFirstChild(), ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
lOffsprings.push_back(lBredIndiv);
}
for(unsigned int j=0; j<lOffsprings.size(); ++j) ioDeme[j] = lOffsprings[j];
Beagle_StackTraceEndM();
}
/*!
* \brief Select an individual using the tournament selection method.
* \param ioPool Individual pool to use for selection.
* \param ioContext Context of the evolution.
* \return Index of the choosen individual in the pool.
*/
unsigned int SelectTournamentOp::selectOneIndividual(Individual::Bag& ioPool, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mNumberParticipants->getWrappedValue() > 0,
"ec.sel.tournsize", ">0");
unsigned int lChoosenIndividual =
ioContext.getSystem().getRandomizer().rollInteger(0,((unsigned int)ioPool.size())-1);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("Starting by choosing the ")+
uint2ordinal(lChoosenIndividual+1)+" individual"
);
for(unsigned int j=1; j<mNumberParticipants->getWrappedValue(); j++) {
unsigned int lTriedIndividual =
ioContext.getSystem().getRandomizer().rollInteger(0,((unsigned int)ioPool.size())-1);
if(ioPool[lChoosenIndividual]->isLess(*ioPool[lTriedIndividual])) {
lChoosenIndividual = lTriedIndividual;
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("Trying the ")+uint2ordinal(lTriedIndividual+1)+
" individual -> choosing it"
);
} else {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("Trying the ")+uint2ordinal(lTriedIndividual+1)+
" individual -> the previously choosen one is better"
);
}
}
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Selecting the " << uint2ordinal(lChoosenIndividual+1) << " individual"
);
Beagle_LogDebugM(ioContext.getSystem().getLogger(), *ioPool[lChoosenIndividual]);
return lChoosenIndividual;
Beagle_StackTraceEndM();
}
/*!
* \brief Select best individual of a pool of individuals.
* \param ioPool Pool of individuals to use for selection.
* \param ioContext Evolutionary context.
*/
unsigned int SelectBestOp::selectIndividual(Individual::Bag& ioPool, Context& ioContext)
{
Beagle_StackTraceBeginM();
unsigned int lBestIndex = 0;
for(unsigned int i=1; i<ioPool.size(); ++i) {
if(ioPool[lBestIndex]->isLess(*ioPool[i])) {
lBestIndex = i;
}
}
return lBestIndex;
Beagle_StackTraceEndM("unsigned int SelectBestOp::selectIndividual(Individual::Bag&,Context&)");
}
/*!
* \brief Evaluate niche count of an individual over a pool of individuals.
* \param inEvalIndividual Individual for which we need to evaluate crowding distance.
* \param inIndividualPool Pool of individuals to evaluate distance on.
* \return Niche count value.
*/
float NPGA2Op::evalNicheCount(const Individual& inEvalIndividual,
const Individual::Bag& inIndividualPool) const
{
Beagle_StackTraceBeginM();
double lNicheCount = 0.;
const Fitness::Handle lEvalFitness = inEvalIndividual.getFitness();
for(unsigned int i=0; i<inIndividualPool.size(); ++i) {
float lDistance = lEvalFitness->getDistance(*inIndividualPool[i]->getFitness());
if(lDistance < mNicheRadius->getWrappedValue()) {
lNicheCount += (1.0 - (lDistance / mNicheRadius->getWrappedValue()));
}
}
return lNicheCount;
Beagle_StackTraceEndM();
}
/*!
* \brief Add individuals to the bag such that the total equals getIndisPerGroup().
* \param ioIndividuals Bag of individuals to evaluate.
* \param ioContexts Bag of evolutionary context.
* \return The number of individuals added to the bag.
*
* The new individuals are chosen from the current deme.
*/
unsigned int EvaluationMultipleOp::enlargeGroup(Individual::Bag& ioIndividuals,
Context::Bag& ioContexts)
{
Beagle_StackTraceBeginM();
Context& lContext = castObjectT<Context&>(*(ioContexts[0]));
// Calculate the number of individuals to add
unsigned int lNumToAdd = mIndisPerGroup - ioIndividuals.size();
Beagle_LogVerboseM(
lContext.getSystem().getLogger(),
std::string("Adding ")+uint2str(lNumToAdd)+std::string(" individuals to the group (for padding)")
);
// Resize the bags
unsigned int lIndisCounter = ioIndividuals.size();
ioIndividuals.resize(mIndisPerGroup);
ioContexts.resize(mIndisPerGroup);
// Loop through all the individuals in the deme
Deme& lDeme = lContext.getDeme();
std::vector<unsigned int> lSelectableIndis;
lSelectableIndis.resize(lDeme.size());
unsigned int lSelectableIndisCounter = 0;
for (unsigned int i=0; i<lDeme.size(); i++) {
// Loop through all the individuals in the bag
bool lAdd = true;
for(unsigned int j=0; j<ioIndividuals.size(); j++) {
if(lDeme[i] == ioIndividuals[j]) {
lAdd = false;
break;
}
}
// If the individual is not already in the bag, add it as an option
if(lAdd) {
lSelectableIndis[lSelectableIndisCounter] = i;
lSelectableIndisCounter++;
}
}
// Check there are sufficient individuals to choose
if(lSelectableIndis.size() < lNumToAdd) {
throw Beagle_RunTimeExceptionM("There are insufficient individuals in the deme to perform evaluation");
}
// Add individuals
for(unsigned int i=0; i<lNumToAdd; i++) {
unsigned int lIndex =
lContext.getSystem().getRandomizer().rollInteger(0,lSelectableIndisCounter-1);
unsigned int lIndiIndex = lSelectableIndis[lIndex];
Beagle_LogVerboseM(
lContext.getSystem().getLogger(),
std::string("Adding ")+uint2ordinal(lIndiIndex+1)+
std::string(" individual to the group (for padding)")
);
Beagle_AssertM(lIndiIndex < lDeme.size());
ioIndividuals[lIndisCounter] = lDeme[ lIndiIndex ];
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(lContext.getSystem().getFactory().getConceptAllocator("Context"));
ioContexts[lIndisCounter] = castHandleT<Context>(lContextAlloc->clone(*(ioContexts[0])));
ioContexts[lIndisCounter]->setIndividualHandle( ioIndividuals[lIndisCounter] );
ioContexts[lIndisCounter]->setIndividualIndex( lIndiIndex );
lIndisCounter++;
}
Beagle_AssertM( lIndisCounter==ioIndividuals.size() );
return lNumToAdd;
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the evaluation process on the invalid individuals of the deme.
* \param ioDeme Deme to process.
* \param ioContext Context of the evolution.
*/
void EvaluationMultipleOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Evaluating the fitness of the individuals in the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
Beagle_AssertM( ioDeme.size()!=0 );
// Prepare stats
prepareStats(ioDeme,ioContext);
// Generate a vector of indicies into the population
std::vector<unsigned int> lEvalVector;
for(unsigned int i=0; i<ioDeme.size(); i++) {
if((ioDeme[i]->getFitness() == NULL) ||
(ioDeme[i]->getFitness()->isValid() == false)) {
lEvalVector.push_back(i);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Added " << uint2ordinal(i+1) << " individual for evaluation."
);
}
}
std::random_shuffle(lEvalVector.begin(), lEvalVector.end(),
ioContext.getSystem().getRandomizer());
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"There are " << lEvalVector.size() << " individuals to be evaluated."
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
while ( !lEvalVector.empty() ) {
// Put individuals and context into bags.
Individual::Bag lIndividuals;
Context::Bag lContexts;
lIndividuals.resize( mIndisPerGroup );
lContexts.resize( mIndisPerGroup );
unsigned int lIndiCounter =0;
for (unsigned int i=0; i<mIndisPerGroup; i++) {
// Set individual
lIndividuals[i] = ioDeme[lEvalVector.back()];
lIndiCounter++;
// Set context
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext = castHandleT<Context>(lContextAlloc->clone(ioContext));
lContext->setIndividualIndex( lEvalVector.back() );
lContext->setIndividualHandle( ioDeme[lEvalVector.back()] );
lContexts[i] = lContext;
// Remove this index from the evaluation vector
lEvalVector.pop_back();
if(lEvalVector.empty()) {
lIndividuals.resize( lIndiCounter );
lContexts.resize( lIndiCounter );
break;
}
}
// Evaluate individuals
std::ostringstream lOSS;
lOSS << "Evaluating the fitness of the ";
for(unsigned int i=0; i<lIndiCounter; i++) {
// Add to message
if (i==lIndiCounter-1) lOSS << " and ";
lOSS << uint2ordinal(lContexts[i]->getIndividualIndex()+1);
if (i<lIndiCounter-2) lOSS << ", ";
}
lOSS << " individuals";
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
lOSS.str()
);
Fitness::Bag::Handle lFitnessBag = evaluateIndividuals(lIndividuals, lContexts);
// Assign fitnesses
for (unsigned int i=0; i<lIndiCounter; i++) {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Considering fitness of the " << uint2ordinal(lContexts[i]->getIndividualIndex()+1) << " individual"
);
Beagle_AssertM( i < lFitnessBag->size() );
Fitness::Handle lFitness = lFitnessBag->at(i);
Beagle_NonNullPointerAssertM( lFitness );
lIndividuals[i]->setFitness( lFitness );
lIndividuals[i]->getFitness()->setValid();
if(lHistory != NULL) {
lHistory->allocateID(*lIndividuals[i]);
lHistory->trace(ioContext, std::vector<HistoryID>(), lIndividuals[i], getName(), "evaluation");
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
*lIndividuals[i]->getFitness()
);
}
// Update stats
updateStats(lIndividuals.size(),ioContext);
}
updateHallOfFameWithDeme(ioDeme,ioContext);
Beagle_StackTraceEndM();
}
/*!
* \brief Evaluate the fitness of the given bag of individuals.
* \param ioIndividuals Bag of individuals to evaluate.
* \param ioContexts Bag of evolutionary context.
* \return Handle to a bag of fitness values, one for each individual.
*/
Fitness::Bag::Handle EvaluationMultipleOp::evaluateIndividuals(Individual::Bag& ioIndividuals,
Context::Bag& ioContexts)
{
Beagle_StackTraceBeginM();
Beagle_AssertM(ioIndividuals.size()==ioContexts.size());
Beagle_AssertM(ioIndividuals.size()!=0);
Context& lContext = castObjectT<Context&>(*(ioContexts[0]));
// Check if sufficient individuals are in the bag
Beagle_AssertM( ioIndividuals.size() <= mIndisPerGroup );
unsigned int lNumToIgnore = 0;
if (ioIndividuals.size() != mIndisPerGroup) {
lNumToIgnore = enlargeGroup(ioIndividuals, ioContexts);
}
// Create bag of null-fitnesses
Fitness::Bag::Handle lFitnessBagAll = new Fitness::Bag;
lFitnessBagAll->resize( ioIndividuals.size() );
Beagle_NonNullPointerAssertM( lFitnessBagAll );
// Set up cases
if (mCases == NULL) setupCases(ioIndividuals.size(),lContext);
Case::Bag::Handle lCases = pruneIgnorableCases(lNumToIgnore);
// Call evaluateCase for each case
for (unsigned int i=0; i<lCases->size(); i++) {
Beagle_LogVerboseM(
lContext.getSystem().getLogger(),
std::string("Evaluating the ")+uint2ordinal(i+1)+std::string(" case")
);
Case& lCase = *(lCases->at(i));
Beagle_AssertM( lCase.mIndices.size() == mIndisPerCase );
// Setup bags of individuals and contexts
Individual::Bag lIndividuals;
Context::Bag lContexts;
lIndividuals.resize( mIndisPerCase );
lContexts.resize( mIndisPerCase );
for (unsigned int j=0; j<mIndisPerCase; j++) {
unsigned int lIndex = lCase.mIndices[j];
lIndividuals[j] = ioIndividuals[ lIndex ];
lContexts[j] = ioContexts[ lIndex ];
}
// Log individual's details
std::ostringstream lOSS;
for (unsigned int j=0; j<lIndividuals.size(); j++) {
if (j!=0) lOSS << ", ";
lOSS << uint2ordinal(lContexts[j]->getIndividualIndex()+1);
}
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
uint2ordinal(i+1) << " case: " << lOSS.str()
);
// Call evalutateCase()
Fitness::Bag::Handle lFitnessBagCase =
evaluateCase(lIndividuals, lContexts);
// Log resulting fitnesses
Beagle_NonNullPointerAssertM( lFitnessBagCase );
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Evaluation of the case is complete. The fitnesses are as follows:"
);
for (unsigned int j=0; j<mIndisPerCase; j++) {
Beagle_NonNullPointerAssertM( lFitnessBagCase->at(j) );
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
std::string("Fitness of the ")+
uint2ordinal(ioContexts[lCase.mIndices[j]]->getIndividualIndex()+1)+
std::string(" individual")
);
Beagle_LogDebugM(lContext.getSystem().getLogger(), *(*lFitnessBagCase)[j]);
// Need to assign fitness values from case to lFitnessBagAll
unsigned int lIndex = lCase.mIndices[j];
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Setting fitness for lFitnessBagAll at index " << uint2str(lIndex)
);
Beagle_AssertM(lIndex < lFitnessBagAll->size());
if (lFitnessBagAll->at(lIndex)==NULL) {
(*lFitnessBagAll)[lIndex] = lFitnessBagCase->at(j);
} else {
combineFitnesses(lFitnessBagAll->at(lIndex),
lFitnessBagCase->at(j) );
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Fitness of the " << uint2ordinal(ioContexts[lIndex]->getIndividualIndex()+1) <<
" individual has been combined to"
);
Beagle_LogDebugM(lContext.getSystem().getLogger(), *(*lFitnessBagAll)[lIndex]);
}
}
}
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Evaluation of all cases is complete. Fitnesses are as follows:"
);
for (unsigned int i=0;
i<ioIndividuals.size();
i++) {
if (i>=mIndisPerGroup-lNumToIgnore) {
// Nullify ignorable individuals' fitness scores
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Ignoring fitness of the " << uint2ordinal(ioContexts[i]->getIndividualIndex()+1) << " individual"
);
(*lFitnessBagAll)[i] = NULL;
continue;
}
Beagle_NonNullPointerAssertM( lFitnessBagAll->at(i) );
Beagle_LogDebugM(
lContext.getSystem().getLogger(),
"Fitness of the " << uint2ordinal(ioContexts[i]->getIndividualIndex()+1) << " individual"
);
Beagle_LogDebugM(lContext.getSystem().getLogger(), *(*lFitnessBagAll)[i]);
}
return lFitnessBagAll;
Beagle_StackTraceEndM();
}
/*!
* \brief Select inN best individuals.
* \param inN Number of individuals to select.
* \param ioPool Pool from which the individuals are choosen.
* \param ioContext Evolutionary context.
* \param outSelections Vector of unsigned ints that say how often an individual was selected.
*
* The output of this method is via outSelection. It produces a
* vector the same size as ioPool, where each index says how many
* times an individual was selected. If this is not the desired
* output, consider using the method convertToList().
*/
void SelectBestOp::selectNIndividuals(unsigned int inN,
Individual::Bag& ioPool,
Context& ioContext,
std::vector<unsigned int>& outSelections)
{
Beagle_StackTraceBeginM();
// Check that we're not selecting all the individuals
if((inN%ioPool.size()) == 0) {
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
std::string("Warning! Selecting the best ")+uint2str(inN)+" individuals from a pool size of "+
uint2str(ioPool.size())+" (during SelectBestOp) means that every individual will be selected "+
uint2str(inN/ioPool.size())+" times, thus applying no selective pressure."
);
}
// Copy the pool, pairing indices and handles to individuals
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
"Copying pool's individuals and pairing them to their indices"
);
typedef std::vector< std::pair< unsigned int, Individual::Handle > > lTempPoolType;
lTempPoolType lTempPool;
lTempPool.resize(ioPool.size());
unsigned int lIndex = 0;
for(lTempPoolType::iterator lItr=lTempPool.begin(); lItr!=lTempPool.end(); ++lItr) {
lItr->first = lIndex;
lItr->second = ioPool[lIndex++];
}
Beagle_AssertM(ioPool.size() == lTempPool.size());
// Sort population
if(inN > ioPool.size()) {
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
std::string("Warning sorting entire copy of pool because number to select (")+uint2str(inN)+
") is greater than size of pool ("+uint2str(ioPool.size())+")"
);
std::sort(lTempPool.begin(),lTempPool.end(), TempPoolPredicate());
} else {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
std::string("Partial sorting top ")+uint2str(inN)+" individuals in copy of pool"
);
std::partial_sort(lTempPool.begin(), lTempPool.begin()+inN, lTempPool.end(), TempPoolPredicate());
}
// Write to the selection table
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
"Writing selection table"
);
outSelections.clear();
outSelections.resize(lTempPool.size());
for (unsigned int i=0; i<inN; i++) {
unsigned int lSelection = lTempPool[i%lTempPool.size()].first;
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"selection", "Beagle::SelectBestOp",
std::string("Selecting ")+uint2ordinal(i+1)+" best ("+uint2ordinal(lSelection+1)+" individual)"
);
++(outSelections[lSelection]);
}
Beagle_StackTraceEndM("void SelectBestOp::selectNIndividuals(unsigned int,Individual::Bag&,Context&,std::vector<unsigned int>&)");
}
/*!
* \brief Do fast non-dominated sort and evaluate Pareto fronts of data up to given size.
* \param outParetoFronts Pareto fronts from the fast ND sort.
* \param inSortStop Number of individuals on the Pareto fronts needed to stop the sort.
* \param inIndividualPool Pool of individuals to get next Pareto front of.
* \param ioContext Evolutionary context.
*/
void EMO::NSGA2Op::sortFastND(NSGA2Op::Fronts& outParetoFronts,
unsigned int inSortStop,
const Individual::Bag& inIndividualPool,
Context& ioContext) const
{
Beagle_StackTraceBeginM();
outParetoFronts.clear();
if(inSortStop == 0) return;
outParetoFronts.resize(1);
unsigned int lParetoSorted = 0;
// N: Number of dominating individuals
std::vector<unsigned int> lN(inIndividualPool.size(), 0);
// S: Set of dominated individuals
Fronts lS(inIndividualPool.size());
// First pass to get first Pareto front and domination sets
for(unsigned int i=0; i<inIndividualPool.size(); ++i) {
Fitness::Handle lFitI = inIndividualPool[i]->getFitness();
for(unsigned int j=(i+1); j<inIndividualPool.size(); ++j) {
Fitness::Handle lFitJ = inIndividualPool[j]->getFitness();
if(lFitJ->isDominated(*lFitI)) {
lS[i].push_back(j); // Add index j to dominated set of i
++lN[j]; // Increment domination counter of j
} else if(lFitI->isDominated(*lFitJ)) {
lS[j].push_back(i); // Add index i to dominated set of j
++lN[i]; // Increment domination counter of i
}
}
if(lN[i] == 0) { // If i is non-dominated
outParetoFronts.back().push_back(i);
++lParetoSorted;
}
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
uint2ordinal(1)+std::string(" Pareto front consists of ")+
uint2str(outParetoFronts.back().size())+" individuals"
);
// Continue ranking until individual pool is empty or stop criterion reach
while((lParetoSorted < inIndividualPool.size()) && (lParetoSorted < inSortStop)) {
unsigned int lIndexLastFront = outParetoFronts.size() - 1;
outParetoFronts.resize(outParetoFronts.size() + 1);
for(unsigned int k=0; k<outParetoFronts[lIndexLastFront].size(); ++k) {
unsigned int lIndexPk = outParetoFronts[lIndexLastFront][k];
for(unsigned int l=0; l<lS[lIndexPk].size(); ++l) {
unsigned int lIndexSl = lS[lIndexPk][l];
if(--lN[lIndexSl] == 0) {
outParetoFronts.back().push_back(lIndexSl);
++lParetoSorted;
}
}
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
uint2ordinal(outParetoFronts.size())+std::string(" Pareto front consists of ")+
uint2str(outParetoFronts.back().size())+" individuals"
);
}
Beagle_StackTraceEndM();
}
/*!
* \brief Recombine individuals by averaging to generate a new individual.
* \param inIndivPool Parents being recombined.
* \param ioContext Evolutionary context.
* \return Children generated by recombination.
*/
Individual::Handle Beagle::GA::RecombinationESVecOp::recombine(Individual::Bag& inIndivPool,
Context& ioContext)
{
Beagle_StackTraceBeginM();
// Recombine parents to generate new individual.
const Factory& lFactory = ioContext.getSystem().getFactory();
Individual::Alloc::Handle lIndivAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
Genotype::Alloc::Handle lGenotypeAlloc =
castHandleT<Genotype::Alloc>(lFactory.getConceptAllocator("Genotype"));
Individual::Handle lChildIndiv = castHandleT<Individual>(lIndivAlloc->allocate());
std::vector< std::vector<unsigned int> > lCountGenoSum;
for(unsigned int i=0; i<inIndivPool.size(); ++i) {
const unsigned int lPoolISize = inIndivPool[i]->size();
const unsigned int lChildSize = lChildIndiv->size();
if(lPoolISize > lChildSize) {
lCountGenoSum.resize(lPoolISize);
lChildIndiv->resize(lPoolISize);
for(unsigned int j=lChildSize; j<lPoolISize; ++j) {
(*lChildIndiv)[j] = castHandleT<Genotype>(lGenotypeAlloc->allocate());
}
}
for(unsigned int j=0; j<lPoolISize; ++j) {
GA::ESVector::Handle lChildGenoJ = castHandleT<GA::ESVector>((*lChildIndiv)[j]);
GA::ESVector::Handle lPoolIGenoJ = castHandleT<GA::ESVector>((*inIndivPool[i])[j]);
const unsigned int lPoolIGenoJSize = lPoolIGenoJ->size();
if(lPoolIGenoJSize > lChildGenoJ->size()) {
lChildGenoJ->resize(lPoolIGenoJSize,0.0);
lCountGenoSum[j].resize(lPoolIGenoJSize,0);
}
for(unsigned int k=0; k<lPoolIGenoJSize; ++k) {
(*lChildGenoJ)[k].mValue += (*lPoolIGenoJ)[k].mValue;
(*lChildGenoJ)[k].mStrategy += (*lPoolIGenoJ)[k].mStrategy;
++lCountGenoSum[j][k];
}
}
}
for(unsigned int i=0; i<lChildIndiv->size(); ++i) {
GA::ESVector::Handle lChildGenoI = castHandleT<GA::ESVector>((*lChildIndiv)[i]);
for(unsigned int j=0; j<lChildGenoI->size(); ++j) {
(*lChildGenoI)[j].mValue /= double(lCountGenoSum[i][j]);
(*lChildGenoI)[j].mStrategy /= double(lCountGenoSum[i][j]);
}
}
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"crossover", "Beagle::GA::RecombinationESVecOp",
"Individual generated by recombination"
);
Beagle_LogObjectDebugM(
ioContext.getSystem().getLogger(),
"crossover", "Beagle::GA::RecombinationESVecOp",
*lChildIndiv
);
return lChildIndiv;
Beagle_StackTraceEndM("Individual::Handle Beagle::GA::RecombinationESVecOp::recombine(Individual::Bag& inIndivPool,Context& ioContext)");
}
/*!
* \brief Apply the recombination operation on a breeding pool, returning a recombined individual.
* \param inBreedingPool Breeding pool to use for the recombination operation.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the recombination operation.
* \return Recombined individual.
*/
Individual::Handle RecombinationOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
// Generate parents for recombination.
Individual::Bag::Handle lParents = new Individual::Bag;
if(inChild == NULL) {
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? inBreedingPool.size() :
minOf<unsigned int>(inBreedingPool.size(), mNumberRecomb->getWrappedValue());
if(lNbGenerated == inBreedingPool.size()) (*lParents) = inBreedingPool;
else {
std::vector<unsigned int> lIndices(inBreedingPool.size());
for(unsigned int i=0; i<lIndices.size(); ++i) lIndices[i] = i;
std::random_shuffle(lIndices.begin(), lIndices.end(),
ioContext.getSystem().getRandomizer());
for(unsigned int i=0; i<lNbGenerated; ++i) {
lParents->push_back(inBreedingPool[lIndices[i]]);
}
}
} else {
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? inBreedingPool.size() :
minOf<unsigned int>(inBreedingPool.size(), mNumberRecomb->getWrappedValue());
for(unsigned int i=0; i<lNbGenerated; ++i) {
Individual::Handle lIndiv = inChild->getBreederOp()->breed(inBreedingPool,
inChild->getFirstChild(),
ioContext);
lParents->push_back(lIndiv);
}
}
// Log parents selected for recombination.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Recombining ")+uint2str(lParents->size())+std::string(" individuals together")
);
// Do recombination operation on parent and get the resulting child.
Individual::Handle lChildIndiv = recombine(*lParents, ioContext);
if(lChildIndiv->getFitness() != NULL) {
lChildIndiv->getFitness()->setInvalid();
}
// Log information to history, if it is used.
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
if(lHistory != NULL) {
std::vector<HistoryID> lParentNames;
for(unsigned int i=0; i<lParents->size(); ++i) {
HistoryID::Handle lHID = castHandleT<HistoryID>(lParents->at(i)->getMember("HistoryID"));
if(lHID != NULL) lParentNames.push_back(*lHID);
}
lHistory->incrementHistoryVar(*lChildIndiv);
lHistory->trace(ioContext, lParentNames, lChildIndiv, getName(), "recombination");
}
return lChildIndiv;
Beagle_StackTraceEndM();
}