/*!
 *  \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 SAES::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) {
			SAES::PairVector::Handle lChildGenoJ = castHandleT<SAES::PairVector>((*lChildIndiv)[j]);
			SAES::PairVector::Handle lPoolIGenoJ = castHandleT<SAES::PairVector>((*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 += (lWeights[i] * (*lPoolIGenoJ)[k].mValue);
				(*lChildGenoJ)[k].mStrategy += (lWeights[i] * (*lPoolIGenoJ)[k].mStrategy);
				lCountGenoSum[j][k] += lWeights[i];
			}

		}
	}
	for(unsigned int i=0; i<lChildIndiv->size(); ++i) {
		SAES::PairVector::Handle lChildGenoI = castHandleT<SAES::PairVector>((*lChildIndiv)[i]);
		for(unsigned int j=0; j<lChildGenoI->size(); ++j) {
			(*lChildGenoI)[j].mValue /= lCountGenoSum[i][j];
			(*lChildGenoI)[j].mStrategy /= lCountGenoSum[i][j];
		}
	}

	Beagle_LogDebugM(ioContext.getSystem().getLogger(), *lChildIndiv);
	
	return lChildIndiv;
	Beagle_StackTraceEndM();
}
Example #2
0
/*!
 *  \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();
}
Example #3
0
/*!
 *  \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();
}
Example #4
0
/*!
 *  \brief Read individuals of a bag.
 *  \param inIter XML iterator to read the individuals from.
 *  \param ioContext Evolutionary context.
 */
void IndividualBag::readIndividuals(PACC::XML::ConstIterator inIter, Context& ioContext)
{
	Beagle_StackTraceBeginM();

	clear();
	Individual::Handle lPrevIndivHandle = ioContext.getIndividualHandle();
	unsigned int lPrevIndivIndex = ioContext.getIndividualIndex();

	for(PACC::XML::ConstIterator lIter=inIter; lIter; ++lIter) {
		if(lIter->getType() != PACC::XML::eData) continue;
		if(lIter->getValue() == "NullHandle") {
			push_back(NULL);
			continue;
		} else if(lIter->getValue() != "Individual") continue;

		Individual::Alloc::Handle lIndivAlloc = NULL;
		std::string lIndivTypeName = lIter->getAttribute("type");
		const Factory& lFactory = ioContext.getSystem().getFactory();
		if(lIndivTypeName.empty()) {
			lIndivAlloc =
			    castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
		} else {
			lIndivAlloc =
			    castHandleT<Individual::Alloc>(lFactory.getAllocator(lIndivTypeName));
		}
		Individual::Handle lReadIndiv = castHandleT<Individual>(lIndivAlloc->allocate());
		const unsigned int lBackIndex = size();
		push_back(lReadIndiv);
		ioContext.setIndividualHandle(lReadIndiv);
		ioContext.setIndividualIndex(lBackIndex);
		lReadIndiv->readWithContext(lIter, ioContext);
	}

	ioContext.setIndividualIndex(lPrevIndivIndex);
	ioContext.setIndividualHandle(lPrevIndivHandle);

	Beagle_StackTraceEndM();
}
Example #5
0
/*!
 *  \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 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 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)");
}
Example #8
0
/*!
 *  \brief Send a receive a deme.
 *
 *  A deme here is more a sub-deme since it only has a portion of
 *  the total individuals of a deme.
 *  \throw Beagle_InternalExceptionM Bad application name received
 */
void Master::EvalClient::sendAndReceiveDeme()
{
	Beagle_StackTraceBeginM();

	Beagle::String::Handle lAppName=
	    castHandleT<Beagle::String>(mContext->getSystem().getRegister().getEntry("db.app.name"));

	const Factory& lFactory = mContext->getSystem().getFactory();
	Individual::Alloc::Handle lIndividualAlloc =
		castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));

	std::ostringstream lOSS;
	lOSS << setprecision(10);

	if(mDemeStored) {
		double lTimeEval = mTimeStart.getValue()/(double)mDeme->size();
		std::ostringstream lOSSTime;
		lOSSTime << lTimeEval;

		PACC::XML::Streamer lStreamer(lOSS, 0);
		lStreamer.openTag("SG");
		lStreamer.insertAttribute("id", Beagle::uint2str(mDemeID));
		lStreamer.insertAttribute("app", lAppName->getWrappedValue());
		lStreamer.insertAttribute("gen", Beagle::uint2str(mGeneration));
		lStreamer.insertAttribute("tf", lOSSTime.str());

		// Send evaluated scores
		for(unsigned int i=0; i<mDeme->size(); ++i) {
			lStreamer.openTag("J"); //Job
			lStreamer.insertAttribute("id", Beagle::uint2str(mIndivID[i])); //job id
			lStreamer.openTag("Sc"); //Score
			lStreamer.insertAttribute("eval", "no"); //evaluation
			(*mDeme)[i]->getFitness()->write(lStreamer, false);
			lStreamer.closeTag();
			lStreamer.closeTag();
		}

		lStreamer.closeTag();
	}

	std::string lDemeSerialized = lOSS.str();

	DAGS::SubGroup lSubGroupDAGS;
	std::vector< std::pair<std::string,DAGS::Job> > lJobs;
	std::vector<std::string> lDontParseVector;
	lDontParseVector.push_back("Dt");  //Data
	lDontParseVector.push_back("Sc");  //Score
	lDontParseVector.push_back("Env"); //Environment
	doNotParseXMLTags(lDontParseVector);

	mDemeStored = false;
	while(true) {
		int lErrorNbr = getJobs(lDemeSerialized, lSubGroupDAGS, lJobs, lAppName->getWrappedValue());
		if(lErrorNbr == DAGS::Client::NoError) break;
		if(lErrorNbr < -17) logError(getErrorMessage());
		lDemeSerialized = std::string("");
		PACC::Threading::Thread::sleep(1);
	}

	mTimeStart.reset();

	std::string lObtAppName = lSubGroupDAGS.getAppName();
	if(lObtAppName != lAppName->getWrappedValue()) {
		std::string lMessage = "Bad application name received (desired: '";
		lMessage += lAppName->getWrappedValue();
		lMessage += "', obtained: '";
		lMessage += lObtAppName;
		lMessage += "').";
		throw Beagle_InternalExceptionM(lMessage);
	}

	mDemeID = (unsigned int)(lSubGroupDAGS.getGroupId());
	mGeneration = (unsigned int)lSubGroupDAGS.getGeneration();

	if(mEnvManager != NULL) {
		std::string lEnvironment = lSubGroupDAGS.getEnvironment();
		std::istringstream lEnvIS(lEnvironment);
		PACC::XML::Document lParserEnv;
		lParserEnv.parse(lEnvIS, "environmnent");
		PACC::XML::Iterator lEnvNode(lParserEnv.getFirstRoot());
		if(lEnvNode) {
			mEnvManager->readEnvironment(lEnvNode, *mDeme, *mContext);
		}
	}

	// Get jobs individual
	mIndivID.clear();
	const unsigned int lOldDemeSize = mDeme->size();
	mDeme->resize(lJobs.size());
	for(unsigned int i=lOldDemeSize; i<lJobs.size(); ++i) {
		(*mDeme)[i] = castHandleT<Individual>(lIndividualAlloc->allocate());
	}
	
	for(unsigned int i=0; i<mDeme->size(); ++i) {
		mIndivID.push_back(lJobs[i].second.getId());
		std::ostringstream lOSS;
		lOSS << "<Individual>" << lJobs[i].second.getData() << "</Individual>";
		std::istringstream lGenoIS(lOSS.str());
		PACC::XML::Document lParser;
		lParser.parse(lGenoIS);
		PACC::XML::Iterator lRootNode(lParser.getFirstRoot());
		(*mDeme)[i]->readWithContext(lRootNode, *mContext);
		(*mDeme)[i]->setFitness(NULL);
	}

	mDemeStored = true;

	Beagle_StackTraceEndM();
}
Example #9
0
/*!
 *  \brief Apply NPGA2 multiobjective selection operator.
 *  \param ioDeme Deme on which selection operator is applied.
 *  \param ioContext Evolutionary context.
 */
void NPGA2Op::operate(Deme& ioDeme, Context& ioContext)
{
	Beagle_StackTraceBeginM();
	if(ioDeme.size() == 0) return;

	Beagle_LogTraceM(
	    ioContext.getSystem().getLogger(),
	    std::string("Applying NPGA2 multiobjective selection on the ")+
	    uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
	);

	std::vector<bool> lAlreadySelectedIndiv(ioDeme.size(), false);
	Individual::Bag   lSelectedIndividual;
	const Factory&    lFactory = ioContext.getSystem().getFactory();

	// Generate new generation by selection
	for(unsigned int i=0; i<ioDeme.size(); ++i) {

		// First participant
		unsigned int lFirstParticipant =
		    ioContext.getSystem().getRandomizer().rollInteger(0, ioDeme.size()-1);
		std::vector<unsigned int> lNDParticipants(1, lFirstParticipant);

		// Following participants to tournament
		for(unsigned int j=1; j<mNumberParticipants->getWrappedValue(); ++j) {
			unsigned int lParticipant =
			    ioContext.getSystem().getRandomizer().rollInteger(0, ioDeme.size()-1);
			// Test if participant is dominated or dominate other participants
			bool lIsDominated = false;
			Fitness::Handle lPartFitness = ioDeme[lParticipant]->getFitness();
			for(unsigned int k=0; k<lNDParticipants.size(); ++k) {
				Fitness::Handle lFitnessNDk = ioDeme[lNDParticipants[k]]->getFitness();
				if(lPartFitness->isDominated(*lFitnessNDk)) {
					lIsDominated = true;
				} else if(lFitnessNDk->isDominated(*lPartFitness)) {
					lNDParticipants.erase(lNDParticipants.begin()+k);
				}
			}
			if(lIsDominated==false) lNDParticipants.push_back(lParticipant);
		}

		// Test if there is a tie. If so evaluate niche count.
		Beagle_AssertM(lNDParticipants.size() != 0);
		unsigned int lWinner = lNDParticipants[0];
		if(lNDParticipants.size() > 1) {
			float lLowestNicheCount = evalNicheCount(*ioDeme[lNDParticipants[0]], lSelectedIndividual);
			for(unsigned int j=1; j<lNDParticipants.size(); ++j) {
				float lNicheCount = evalNicheCount(*ioDeme[lNDParticipants[j]], lSelectedIndividual);
				if(lNicheCount < lLowestNicheCount) {
					lLowestNicheCount = lNicheCount;
					lWinner = lNDParticipants[j];
				}
			}
		}

		// Put winner in selected individual bag
		if(lAlreadySelectedIndiv[lWinner]) {
			std::string lIndividualType = ioDeme[lWinner]->getType();
			Individual::Alloc::Handle lIndividualAlloc =
				castHandleT<Individual::Alloc>(lFactory.getAllocator(lIndividualType));
			Individual::Handle lIndividual = castHandleT<Individual>(lIndividualAlloc->allocate());
			lIndividual->copy(*ioDeme[lWinner], ioContext.getSystem());
			lSelectedIndividual.push_back(lIndividual);
			Beagle_LogVerboseM(
			    ioContext.getSystem().getLogger(),
			    uint2ordinal(lWinner+1)+" individual selected again in NPGA2 selection process"
			);
		} else {
			lSelectedIndividual.push_back(ioDeme[lWinner]);
			lAlreadySelectedIndiv[lWinner] = true;
			Beagle_LogVerboseM(
			    ioContext.getSystem().getLogger(),
			    uint2ordinal(lWinner+1)+" individual selected in NPGA2 selection process"
			);
		}
	}

	// Copy selected individuals into deme
	for(unsigned int j=0; j<ioDeme.size(); ++j) ioDeme[j] = lSelectedIndividual[j];
	Beagle_StackTraceEndM();
}