/*!
* \brief Apply the crossover operation on a breeding pool, returning a mated individual.
* \param inBreedingPool Breeding pool to use for the crossover operation.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the crossover operation.
* \return Mated individual.
*/
Individual::Handle CrossoverOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext2 = castHandleT<Context>(lContextAlloc->clone(ioContext));
Beagle_NonNullPointerAssertM(inChild);
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
Individual::Handle lIndiv1 = inChild->getBreederOp()->breed(inBreedingPool,
inChild->getFirstChild(),
ioContext);
Beagle_NonNullPointerAssertM(inChild->getNextSibling());
Beagle_NonNullPointerAssertM(inChild->getNextSibling()->getBreederOp());
Individual::Handle lIndiv2 =
inChild->getNextSibling()->getBreederOp()->breed(inBreedingPool,
inChild->getNextSibling()->getFirstChild(),
*lContext2);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Mating the ")+uint2ordinal(ioContext.getIndividualIndex()+1)+
std::string(" individual with the ")+uint2ordinal(lContext2->getIndividualIndex()+1)+
" individual"
);
if((lIndiv1 != NULL) && (lIndiv2 != NULL)) {
bool lMated = mate(*lIndiv1, ioContext, *lIndiv2, *lContext2);
if(lMated) {
if(lIndiv1->getFitness() != NULL) lIndiv1->getFitness()->setInvalid();
if(lIndiv2->getFitness() != NULL) lIndiv2->getFitness()->setInvalid();
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
if(lHistory != NULL) {
std::vector<HistoryID> lParents;
HistoryID::Handle lHID1 = castHandleT<HistoryID>(lIndiv1->getMember("HistoryID"));
if(lHID1 != NULL) lParents.push_back(*lHID1);
HistoryID::Handle lHID2 = castHandleT<HistoryID>(lIndiv2->getMember("HistoryID"));
if(lHID2 != NULL) lParents.push_back(*lHID2);
lHistory->incrementHistoryVar(*lIndiv1);
lHistory->trace(ioContext, lParents, lIndiv1, getName(), "crossover");
}
}
}
return lIndiv1;
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the breeding operation on a breeding pool, returning a bred individual.
* \param inBreedingPool
* \param inChild
* \param ioContext Evolutionary context of the breeding operation.
* \return Bred individual.
*/
Individual::Handle InitializationOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
const Factory& lFactory = ioContext.getSystem().getFactory();
Individual::Alloc::Handle lIndivAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
Individual::Handle lNewIndiv = castHandleT<Individual>(lIndivAlloc->allocate());
initIndividual(*lNewIndiv, ioContext);
if(lNewIndiv->getFitness() != NULL) lNewIndiv->getFitness()->setInvalid();
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
if(lHistory != NULL) {
lHistory->incrementHistoryVar(*lNewIndiv);
lHistory->trace(ioContext, std::vector<HistoryID>(), lNewIndiv, getName(), "initialization");
}
ioContext.setIndividualHandle(lNewIndiv);
return lNewIndiv;
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the initialization operation on the deme.
* \param ioDeme Current deme of individuals to initialize.
* \param ioContext Context of the evolution.
*/
void InitializationOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
#ifndef BEAGLE_NDEBUG
if(ioContext.getVivariumHandle()!=NULL) {
Beagle_AssertM(mPopSize->size() == ioContext.getVivarium().size());
}
#endif // BEAGLE_NDEBUG
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Initializing the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
if(!ioDeme.empty()) {
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
std::string("Warning! Applying '")+getName()+"' will overwrite the "+
uint2str(ioDeme.size())+" individual(s) currently in the deme with newly initialized "+
"individuals. If this is not what you desire consider using OversizeOp instead."
);
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Resizing the deme from ")+
uint2str(ioDeme.size())+" to "+
uint2str((*mPopSize)[ioContext.getDemeIndex()])+" individuals"
);
const Factory& lFactory = ioContext.getSystem().getFactory();
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
ioDeme.clear();
const unsigned int lDemeSize = (*mPopSize)[ioContext.getDemeIndex()];
for(unsigned int i=0; i<lDemeSize; ++i) {
ioDeme.push_back(lIndividualAlloc->allocate());
}
unsigned int lSeededIndividuals = 0;
if(mSeedsFile->getWrappedValue().empty() == false) {
Beagle_LogInfoM(
ioContext.getSystem().getLogger(),
std::string("Reading seeds file '")+mSeedsFile->getWrappedValue()+
std::string("' to initialize the ")+uint2ordinal(ioContext.getDemeIndex()+1)+
std::string(" deme")
);
lSeededIndividuals = readSeeds(mSeedsFile->getWrappedValue(), ioDeme, ioContext);
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
uint2str(lSeededIndividuals)+std::string(" individuals read to seed the deme")
);
}
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
for(unsigned int i=lSeededIndividuals; i<ioDeme.size(); ++i) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Initializing the ")+uint2ordinal(i+1)+" individual"
);
ioContext.setIndividualHandle(ioDeme[i]);
ioContext.setIndividualIndex(i);
initIndividual(*ioDeme[i], ioContext);
if(ioDeme[i]->getFitness() != NULL) {
ioDeme[i]->getFitness()->setInvalid();
}
if(lHistory != NULL) {
lHistory->incrementHistoryVar(*ioDeme[i]);
lHistory->trace(ioContext, std::vector<HistoryID>(), ioDeme[i], getName(), "initialization");
}
}
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the crossover operation on the deme.
* \param ioDeme Current deme of individuals to mate.
* \param ioContext Context of the evolution.
*/
void CrossoverOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mMatingProba->getWrappedValue()>=0.0, mMatingProbaName, "<0");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Mating individuals of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Mating individuals with probability ")+
dbl2str(mMatingProba->getWrappedValue())
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
std::vector<unsigned int> lMateVector;
for(unsigned int i=0; i<ioDeme.size(); i++) {
if(ioContext.getSystem().getRandomizer().rollUniform() <= mMatingProba->getWrappedValue()) {
lMateVector.push_back(i);
}
}
std::random_shuffle(lMateVector.begin(), lMateVector.end(),
ioContext.getSystem().getRandomizer());
if((lMateVector.size() % 2) != 0) lMateVector.pop_back();
int j = 0;
int lSize = lMateVector.size();
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
static OpenMP::Handle lOpenMP = castHandleT<OpenMP>(ioContext.getSystem().getComponent("OpenMP"));
const Factory& lFactory = ioContext.getSystem().getFactory();
const std::string& lContextName = lFactory.getConceptTypeName("Context");
Context::Alloc::Handle lContextAlloc = castHandleT<Context::Alloc>(lFactory.getAllocator(lContextName));
Context::Bag lContexts(lOpenMP->getMaxNumThreads());
Context::Bag lContexts2(lOpenMP->getMaxNumThreads());
for(unsigned int i = 0; i < lOpenMP->getMaxNumThreads(); ++i) {
lContexts[i] = castHandleT<Context>(lContextAlloc->clone(ioContext));
lContexts2[i] = castHandleT<Context>(lContextAlloc->clone(ioContext));
}
#if defined(BEAGLE_USE_OMP_NR)
#pragma omp parallel for shared(lSize, lMateVector, lHistory, lContexts, lContexts2) private(j) schedule(dynamic)
#elif defined(BEAGLE_USE_OMP_R)
const int lChunkSize = std::max((int)(lSize / lOpenMP->getMaxNumThreads()), 1);
#pragma omp parallel for shared(lSize, lMateVector, lHistory, lContexts, lContexts2) private(j) schedule(static, lChunkSize)
#endif
#else
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext2 = castHandleT<Context>(lContextAlloc->clone(ioContext));
#endif
for(j=0; j<lSize; j+=2) {
unsigned int lFirstMate = lMateVector[j];
unsigned int lSecondMate = lMateVector[j+1];
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
lContexts[lOpenMP->getThreadNum()]->setIndividualIndex(lFirstMate);
lContexts[lOpenMP->getThreadNum()]->setIndividualHandle(ioDeme[lFirstMate]);
lContexts2[lOpenMP->getThreadNum()]->setIndividualIndex(lSecondMate);
lContexts2[lOpenMP->getThreadNum()]->setIndividualHandle(ioDeme[lSecondMate]);
#else
ioContext.setIndividualIndex(lFirstMate);
ioContext.setIndividualHandle(ioDeme[lFirstMate]);
lContext2->setIndividualIndex(lSecondMate);
lContext2->setIndividualHandle(ioDeme[lSecondMate]);
#endif
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Mating the ")+uint2ordinal(lFirstMate+1)+
std::string(" individual with the ")+uint2ordinal(lSecondMate+1)+" individual"
);
std::vector<HistoryID> lParents;
if(lHistory != NULL) {
#pragma omp critical (Beagle_History)
{
HistoryID::Handle lHID1 = castHandleT<HistoryID>(ioDeme[lFirstMate]->getMember("HistoryID"));
if(lHID1 != NULL) lParents.push_back(*lHID1);
HistoryID::Handle lHID2 = castHandleT<HistoryID>(ioDeme[lSecondMate]->getMember("HistoryID"));
if(lHID2 != NULL) lParents.push_back(*lHID2);
}
}
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
bool lMated = mate(*ioDeme[lFirstMate], *(lContexts[lOpenMP->getThreadNum()]), *ioDeme[lSecondMate], *(lContexts2[lOpenMP->getThreadNum()]));
#else
bool lMated = mate(*ioDeme[lFirstMate], ioContext, *ioDeme[lSecondMate], *lContext2);
#endif
if(lMated) {
if(ioDeme[lFirstMate]->getFitness() != NULL) {
ioDeme[lFirstMate]->getFitness()->setInvalid();
}
if(ioDeme[lSecondMate]->getFitness() != NULL) {
ioDeme[lSecondMate]->getFitness()->setInvalid();
}
if(lHistory != NULL) {
#pragma omp critical (Beagle_History)
{
lHistory->incrementHistoryVar(*ioDeme[lFirstMate]);
#if defined(BEAGLE_USE_OMP_R) || defined(BEAGLE_USE_OMP_NR)
lHistory->trace(*lContexts[lOpenMP->getThreadNum()], lParents, ioDeme[lFirstMate], getName(), "crossover");
#else
lHistory->trace(ioContext, lParents, ioDeme[lFirstMate], getName(), "crossover");
#endif
lHistory->incrementHistoryVar(*ioDeme[lSecondMate]);
#if defined(BEAGLE_USE_OMP_R) || defined(BEAGLE_USE_OMP_NR)
lHistory->trace(*lContexts[lOpenMP->getThreadNum()], lParents, ioDeme[lSecondMate], getName(), "crossover");
#else
lHistory->trace(ioContext, lParents, ioDeme[lSecondMate], getName(), "crossover");
#endif
}
}
}
}
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
Beagle_StackTraceEndM();
}
/*!
* \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();
}
/*!
* \brief Apply the recombination operation on the deme.
* \param ioDeme Current deme of individuals to recombine.
* \param ioContext Context of the evolution.
*/
void RecombinationOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mRecombProba->getWrappedValue()>=0.0, mRecombProbaName, "<0");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals with probability ")+
dbl2str(mRecombProba->getWrappedValue())
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Bag lRecombinedIndiv(ioDeme.size());
for(unsigned int i=0; i<lRecombinedIndiv.size(); ++i) {
if(ioContext.getSystem().getRandomizer().rollUniform() <= mRecombProba->getWrappedValue()) {
Individual::Bag::Handle lParents = new Individual::Bag;
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? ioDeme.size() :
minOf<unsigned int>(ioDeme.size(), mNumberRecomb->getWrappedValue());
if(lNbGenerated == ioDeme.size()) (*lParents) = ioDeme;
else {
std::vector<unsigned int> lIndices(ioDeme.size());
for(unsigned int j=0; j<lIndices.size(); ++j) lIndices[j] = j;
std::random_shuffle(lIndices.begin(), lIndices.end(),
ioContext.getSystem().getRandomizer());
for(unsigned int j=0; j<lNbGenerated; ++j) {
lParents->push_back(ioDeme[lIndices[j]]);
}
}
lRecombinedIndiv[i] = recombine(*lParents, ioContext);
if(lRecombinedIndiv[i]->getFitness() != NULL) {
lRecombinedIndiv[i]->getFitness()->setInvalid();
}
// Log and update history.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("The ")+uint2ordinal(i+1)+
std::string(" individual as been replaced by recombination")
);
if(lHistory != NULL) {
std::vector<HistoryID> lParentNames;
for(unsigned int j=0; j<lParents->size(); ++j) {
HistoryID::Handle lHID = castHandleT<HistoryID>(lParents->at(j)->getMember("HistoryID"));
if(lHID != NULL) lParentNames.push_back(*lHID);
}
lHistory->incrementHistoryVar(*lRecombinedIndiv[i]);
lHistory->trace(ioContext, lParentNames, lRecombinedIndiv[i], getName(), "recombination");
}
}
}
for(unsigned int i=0; i<ioDeme.size(); ++i) {
if(lRecombinedIndiv[i] != NULL) ioDeme[i] = lRecombinedIndiv[i];
}
Beagle_StackTraceEndM();
}
