void LogIndividualDataOp::operate(Deme& ioDeme, Context& ioContext) {
Beagle_StackTraceBeginM();
if(mNumberIndividualPerDem->getWrappedValue() <= 0) {
return;
}
// Temporary buffer of individuals.
Individual::Bag lTempPop;
if(ioContext.getGeneration() != mGenerationCalculated) {
mGenerationCalculated = ioContext.getGeneration();
mNbDemesCalculated = 0;
}
if(++mNbDemesCalculated == mPopSize->size() && mOnlyVivarium->getWrappedValue()) {
//Make heap of all individual in the vivarium
for( unsigned int i = 0; i < ioContext.getVivarium().size(); ++i) {
lTempPop.insert(lTempPop.end(), ioContext.getVivarium()[i]->begin(), ioContext.getVivarium()[i]->end());
}
} else if(mOnlyVivarium->getWrappedValue()){
return;
} else {
//Process only this deme
// Insert pointer of all the individuals of the deme in the buffer.
lTempPop.insert(lTempPop.end(), ioDeme.begin(), ioDeme.end());
}
// Make the buffer a STL heap with the fittest individual on the top.
std::make_heap(lTempPop.begin(), lTempPop.end(), IsLessPointerPredicate());
for(unsigned int i = 0; i < mNumberIndividualPerDem->getWrappedValue(); ++i) {
Individual::Handle lIndividual = NULL;
if( !mKeepData->getWrappedValue() ) {
//Strip the simulation data of the individual
lIndividual = castHandleT<Individual>(ioDeme.getTypeAlloc()->cloneData(*lTempPop[0]));
LogFitness::Handle lFitness = castHandleT<LogFitness>(lIndividual->getFitness());
lFitness->clearData();
} else {
lIndividual = lTempPop[0];
}
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eStats,
"history", "Beagle::LogIndividualDataOp",
*lIndividual
);
// STL heap pop of the best individual of the temporary buffer.
std::pop_heap(lTempPop.begin(), lTempPop.end(), IsLessPointerPredicate());
lTempPop.pop_back();
}
Beagle_StackTraceEndM("void LogIndividualDataOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Apply the fitness invalidation operation on a breeding pool, returning a bred individual.
* \param inBreedingPool Breeding pool to use for the breeding operation.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the breeding operation.
* \return Invalidated bred individual.
*/
Individual::Handle InvalidateFitnessOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(inChild);
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
Individual::Handle lBredIndividual =
inChild->getBreederOp()->breed(inBreedingPool, inChild->getFirstChild(), ioContext);
if((lBredIndividual->getFitness()!=NULL) && (lBredIndividual->getFitness()->isValid())) {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Invalidating the fitness of the following bred individual"
);
Beagle_LogDebugM(ioContext.getSystem().getLogger(), *lBredIndividual);
lBredIndividual->getFitness()->setInvalid();
}
return lBredIndividual;
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 adaptation operation on a breeding pool.
* \param inBreedingPool Breeding pool to give to the underlying breeding tree.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the mutation operation.
* \return Mutated individual.
*/
Individual::Handle ES::AdaptOneFifthRuleOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(inChild);
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
Individual::Handle lIndiv =
inChild->getBreederOp()->breed(inBreedingPool, inChild->getFirstChild(), ioContext);
// Look whether the mutation is successful.
Fitness::Handle lFitParent = inBreedingPool[ioContext.getIndividualIndex()]->getFitness();
Fitness::Handle lFitChild = lIndiv->getFitness();
if(lFitChild != NULL) {
// Check whether the mutation is successful or not.
const bool lSuccessful = (*lFitChild) > (*lFitParent);
if(lSuccessful) {
++mSuccessCount->getWrappedValue();
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Successful mutation"
);
} else {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"The mutation is not successful"
);
}
++mMutationsCount->getWrappedValue();
// Adapt the sigma if the necessary number of observed mutations is reached.
if(lSuccessful && (mMutationsCount->getWrappedValue()>=mAdaptationPeriod->getWrappedValue())) {
const double lSuccessRate = double(mSuccessCount->getWrappedValue()) /
double(mMutationsCount->getWrappedValue());
if(lSuccessRate > 0.2) {
for(unsigned int i=0; i<mMutateGaussSigma->size(); ++i) {
(*mMutateGaussSigma)[i] /= mSigmaAdaptFactor->getWrappedValue();
}
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
string("Increasing the sigma value by a factor ")+
dbl2str(1./mSigmaAdaptFactor->getWrappedValue())
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
string("Sigma value after the increase: ")+mMutateGaussSigma->serialize()
);
} else if(lSuccessRate < 0.2) {
for(unsigned int i=0; i<mMutateGaussSigma->size(); ++i) {
(*mMutateGaussSigma)[i] *= mSigmaAdaptFactor->getWrappedValue();
}
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
string("Reducing the sigma value by a factor ")+
dbl2str(mSigmaAdaptFactor->getWrappedValue())
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
string("Sigma value after the reduction: ")+mMutateGaussSigma->serialize()
);
} else {
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"Sigma value unchanged"
);
}
}
}
return lIndiv;
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 evaluation operation on a breeding pool, returning a evaluated bred individual.
* \param inBreedingPool Breeding pool to use for the breeding operation.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the breeding operation.
* \return Evaluated bred individual.
*/
Individual::Handle Beagle::MPI::EvaluationOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_NonNullPointerAssertM(inChild);
Deme& lDeme = *ioContext.getDemeHandle();
if(lDeme.getStats()->isValid()) {
ioContext.setProcessedDeme(0);
if((ioContext.getGeneration()!=0) && (lDeme.getStats()->existItem("total-processed"))) {
ioContext.setTotalProcessedDeme((unsigned int)lDeme.getStats()->getItem("total-processed"));
}
else ioContext.setTotalProcessedDeme(0);
lDeme.getStats()->setInvalid();
if(ioContext.getDemeIndex()==0) {
Stats& lVivaStats = *ioContext.getVivarium().getStats();
ioContext.setProcessedVivarium(0);
if((ioContext.getGeneration()!=0) && (lVivaStats.existItem("total-processed"))) {
ioContext.setTotalProcessedVivarium((unsigned int)lVivaStats.getItem("total-processed"));
}
else ioContext.setTotalProcessedVivarium(0);
lVivaStats.setInvalid();
}
}
Beagle_NonNullPointerAssertM(inChild);
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
Individual::Handle lBredIndividual =
inChild->getBreederOp()->breed(inBreedingPool, inChild->getFirstChild(), ioContext);
if((lBredIndividual->getFitness()==NULL) || (lBredIndividual->getFitness()->isValid()==false)) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
"Evaluating the fitness of a new bred individual"
);
individualEvaluation(*lBredIndividual, ioContext);
// lBredIndividual->setFitness(evaluate(*lBredIndividual, ioContext));
// lBredIndividual->getFitness()->setValid();
ioContext.setProcessedDeme(ioContext.getProcessedDeme()+1);
ioContext.setTotalProcessedDeme(ioContext.getTotalProcessedDeme()+1);
ioContext.setProcessedVivarium(ioContext.getProcessedVivarium()+1);
ioContext.setTotalProcessedVivarium(ioContext.getTotalProcessedVivarium()+1);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
std::string("The individual fitness value is: ")+
lBredIndividual->getFitness()->serialize()
);
if(mDemeHOFSize->getWrappedValue() > 0) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
"Updating the deme hall-of-fame"
);
lDeme.getHallOfFame().updateWithIndividual(mDemeHOFSize->getWrappedValue(),
*lBredIndividual, ioContext);
}
if(mVivaHOFSize->getWrappedValue() > 0) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
"Updating the vivarium hall-of-fame"
);
ioContext.getVivarium().getHallOfFame().updateWithIndividual(mVivaHOFSize->getWrappedValue(),
*lBredIndividual, ioContext);
}
}
return lBredIndividual;
}