/*!
* \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 Apply the characteristic operation.
* \param ioDeme Deme to use to write the milestone.
* \param ioContext Context of the evolution.
*/
void RandomShuffleDemeOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::random_shuffle(ioDeme.begin(), ioDeme.end(),
ioContext.getSystem().getRandomizer());
Beagle_StackTraceEndM("void RandomShuffleDemeOp::operate(Deme& ioDeme, Context& ioContext)");
}
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 decimation operation on the deme.
* \param ioDeme Current deme of individuals to decimate.
* \param ioContext Context of the evolution.
*/
void DecimateOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM((mDecimationRatio->getWrappedValue()<=1.0),
mDecimationRatioName,
"The decimation ratio must be less than or equal to 1.0.");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("Applying decimation operation on the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
// Calculate the number of individuals to keep from the deme
unsigned int lMu = 0;
if(mDecimationRatio->getWrappedValue() == -1.0) {
Beagle_AssertM(ioContext.getDemeIndex() < mPopSize->size());
lMu = (*mPopSize)[ioContext.getDemeIndex()];
} else {
lMu = (unsigned int)std::ceil(mDecimationRatio->getWrappedValue()*float(ioDeme.size()));
Beagle_AssertM(ioContext.getDemeIndex() < mPopSize->size());
int lDiffSize = (*mPopSize)[ioContext.getDemeIndex()] - lMu;
if((lDiffSize >= -1) && (lDiffSize <= 1)) lMu = (*mPopSize)[ioContext.getDemeIndex()];
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("Keeping ")+uint2str(lMu)+" of the "+uint2str(ioDeme.size())+
" individuals from the "+uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
// Check that the number of individuals to keep (mu) isn't greater than the deme size
if(lMu > ioDeme.size()) {
std::ostringstream lOSS;
lOSS << "Warning: the actual population size (" << ioDeme.size();
lOSS << ") is less than the desired decimation size (" << lMu;
lOSS << "). Decimation is thus not applied.";
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
lOSS.str()
);
return;
}
// Copy the individuals to be kept into the deme
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
Individual::Bag lSurvivors;
for(unsigned int i=0; i<lMu; ++i) {
lSurvivors.push_back(ioDeme.front());
std::pop_heap(ioDeme.begin(), (ioDeme.end()-i), IsLessPointerPredicate());
}
ioDeme.clear();
ioDeme.insert(ioDeme.begin(), lSurvivors.begin(), lSurvivors.end());
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("There are now ")+uint2str(ioDeme.size())+" individuals in the "+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_StackTraceEndM("void DecimateOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Apply the oversize replacement strategy operation on a deme.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
*/
void OversizeOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(getRootNode());
Beagle_ValidateParameterM
(mOversizeRatio->getWrappedValue() >= 1.0
|| mOversizeRatio->getWrappedValue() == -1.0,
mOversizeRatioName,
"The oversize ratio must be greater than or equal to 1.0, or equal to -1.0.");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("Using oversize replacement strategy to process the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eTrace,
"replacement-strategy", "Beagle::OversizeOp",
(*this)
);
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
// Calculate the increase in size (lambda)
float lRatio = mOversizeRatio->getWrappedValue();
unsigned int lLambda;
if (lRatio == -1.0) {
// Using special ratio of -1.0 ensures deme grows to size specified in 'ec.pop.size'
if (!ioContext.getSystem().getRegister().isRegistered("ec.pop.size")) {
throw Beagle_RunTimeExceptionM(getName()+" requires register variable 'ec.pop.size'");
}
UIntArray::Handle lPopSize = castHandleT<UIntArray>
(ioContext.getSystem().getRegister().getEntry("ec.pop.size"));
unsigned int lSpecifiedDemeSize = (*lPopSize)[ioContext.getDemeIndex()];
unsigned int lCurrentDemeSize = ioDeme.size();
if (lSpecifiedDemeSize < lCurrentDemeSize) {
throw Beagle_RunTimeExceptionM
(std::string("For the ")+uint2ordinal(ioContext.getDemeIndex()+1)+
" deme, the size specified in 'ec.pop.size' ("+uint2str(lSpecifiedDemeSize)+
") is less than the current deme size ("+uint2str(lCurrentDemeSize)+
"). "+getName()+" can only increase the size of the deme. Consider using DecimateOp "+
"if you wish to decrease the size of the deme");
}
lLambda = lSpecifiedDemeSize - lCurrentDemeSize;
} else {
// Using ratio to scale the deme's population
lLambda = (unsigned int)ceil((lRatio-1.0)*float(ioDeme.size()));
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("Population will be increased in size by ")+uint2str(lLambda)+" individuals"
);
// Create the new individuals.
Individual::Bag lOffsprings;
for(unsigned int i=0; i<lLambda; ++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);
}
// Add the new individuals into the deme.
ioDeme.insert(ioDeme.end(), lOffsprings.begin(), lOffsprings.end());
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("There are now ")+uint2str(ioDeme.size())+" individuals in the "+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_StackTraceEndM("void OversizeOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Generate children from the breeder tree.
* \param ioDeme Deme to generate children from.
* \param ioContext Evolutionary context.
* \param lNbChildren Number of children to generate.
* \param inN Dimensionality of the problem.
* \param ioCMAValues CMA values to use to generate new individual.
* \param inSelectionWeights Selection weights used to generate children.
*/
void CMA::MuWCommaLambdaCMAFltVecOp::generateChildren(Deme& ioDeme,
Context& ioContext,
unsigned int inNbChildren,
unsigned int inN,
CMAValues& ioCMAValues,
const Vector& inSelectionWeights) const
{
Beagle_StackTraceBeginM();
// Check parameters and log some information
Beagle_NonNullPointerAssertM(mElitismKeepSize);
Beagle_ValidateParameterM(mLMRatio->getWrappedValue() >= 1.0,
mLMRatioName,
"The LM ratio must be higher or equal to 1.0.");
Beagle_ValidateParameterM(mElitismKeepSize->getWrappedValue() <= ioDeme.size(),
"ec.elite.keepsize",
"The elistism keepsize must be less than the deme size!");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Using CMA-ES (mu_w,lambda) replacement strategy to process the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogTraceM(ioContext.getSystem().getLogger(), (*this));
const Factory& lFactory = ioContext.getSystem().getFactory();
// Create weighted mean individual.
std::sort(ioDeme.begin(), ioDeme.end(), IsMorePointerPredicate());
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
Individual::Handle lMeanInd = castHandleT<Individual>(lIndividualAlloc->allocate());
Genotype::Alloc::Handle lGenotypeAlloc =
castHandleT<Genotype::Alloc>(lFactory.getConceptAllocator("Genotype"));
FltVec::FloatVector::Handle lMeanFloatVec =
castHandleT<FltVec::FloatVector>(lGenotypeAlloc->allocate());
lMeanFloatVec->resize(inN);
lMeanInd->push_back(lMeanFloatVec);
for(unsigned int i=0; i<inN; ++i) (*lMeanFloatVec)[i] = 0.0;
if(ioDeme.size()==1) {
Beagle_AssertM(ioDeme[0]->size() == 1);
FltVec::FloatVector::Handle lInd = castHandleT<FltVec::FloatVector>((*ioDeme[0])[0]);
(*lMeanFloatVec) = *lInd;
} else {
for(unsigned int i=0; i<ioDeme.size(); ++i) {
Beagle_AssertM(ioDeme[i]->size()==1);
FltVec::FloatVector::Handle lVecI = castHandleT<FltVec::FloatVector>((*ioDeme[i])[0]);
Beagle_AssertM(lVecI->size()==inN);
for(unsigned int j=0; j<inN; ++j) (*lMeanFloatVec)[j] += (inSelectionWeights[i] * (*lVecI)[j]);
}
}
ioCMAValues.mXmean.resize(inN);
for(unsigned int i=0; i<inN; ++i) ioCMAValues.mXmean[i] = (*lMeanFloatVec)[i];
// Generate lambda children with breeder tree, first build breeder roulette
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
// Keep best individuals if elitism is used
const unsigned int lElitismKS=mElitismKeepSize->getWrappedValue();
if(lElitismKS > 0) {
Individual::Bag lBestInd;
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
for(unsigned int i=0; i<lElitismKS; ++i) {
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(*ioDeme[0]);
lHistory->trace(ioContext, lParent, ioDeme[0], getName(), "elitism");
}
lBestInd.push_back(ioDeme[0]);
std::pop_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
ioDeme.pop_back();
}
ioDeme.clear();
ioDeme.insert(ioDeme.end(), lBestInd.begin(), lBestInd.end());
} else ioDeme.clear();
// Generate the children
Individual::Bag lBagWithMeanInd;
lBagWithMeanInd.push_back(lMeanInd);
for(unsigned int i=0; i<inNbChildren; ++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(lBagWithMeanInd,
lSelectedBreeder->getFirstChild(),
ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
ioDeme.push_back(lBredIndiv);
}
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the CMA-ES (Mu_W+Lambda) replacement strategy operation on a deme.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
* \throw Beagle::ValidationException If a parameter is missing or have a bad value.
* \throw Beagle::AssertException If an invalid condition appears.
*/
void CMA::MuWCommaLambdaCMAFltVecOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
// Get real popsize and size of float vectors from register.
UIntArray::Handle lPopSize;
if(ioContext.getSystem().getRegister().isRegistered("ec.pop.size")) {
lPopSize = castHandleT<UIntArray>(ioContext.getSystem().getRegister()["ec.pop.size"]);
} else {
std::ostringstream lOSS;
lOSS << "Population size parameter 'ec.pop.size' is not found in register!";
throw ValidationException(lOSS.str());
}
const unsigned int lDemeSize = (*lPopSize)[ioContext.getDemeIndex()];
UInt::Handle lFloatVectorSize;
if(ioContext.getSystem().getRegister().isRegistered("ga.init.vectorsize")) {
lFloatVectorSize = castHandleT<UInt>(ioContext.getSystem().getRegister()["ga.init.vectorsize"]);
} else {
std::ostringstream lOSS;
lOSS << "GA::MuWCommaLambdaCMAFltVecOp must be used in fixed-lenght float vector ";
lOSS << "individuals. Parameter 'ga.init.vectorsize' is not in register, ";
lOSS << "while it is needed to set initial size of the different CMA-ES matrices ";
lOSS << "and vectors.";
throw ValidationException(lOSS.str());
}
const unsigned int lN=lFloatVectorSize->getWrappedValue();
// Get the appropriate CMA values from the CMA holder component.
CMA::CMAValues& lValues = getCMAValues(ioContext.getDemeIndex(),lN,ioContext);
// Compute weights and effective mu
Vector lWeight;
double lMuEff = 0.0;
lMuEff = generateSelectionWeights(lDemeSize, lWeight);
if(ioDeme.size() == 1) lMuEff = 1.;
// If the replacement strategy possess a breeder tree
if(getRootNode()!=NULL) {
// Generate new children.
const unsigned int lLambda =
(unsigned int)std::ceil(mLMRatio->getWrappedValue()*double(lDemeSize));
generateChildren(ioDeme, ioContext, lLambda, lN, lValues, lWeight);
// Check if all individuals have known fitness.
for(unsigned int i=0; i<ioDeme.size(); ++i) {
// If there is one invalid fitness, we should exit.
// Evaluation will be taken elsewhere (we hope), and actual operator will be recalled.
if((ioDeme[i]->getFitness()==NULL) || (ioDeme[i]->getFitness()->isValid()==false)) return;
}
}
// Keep mu best children
Beagle_AssertM(ioDeme.size() > lDemeSize);
std::sort(ioDeme.begin(), ioDeme.end(), IsMorePointerPredicate());
ioDeme.resize(lDemeSize);
// Update CMA-ES values.
updateValues(ioDeme, ioContext, lN, lMuEff, lWeight, lValues);
Beagle_StackTraceEndM();
}
