Ejemplo n.º 1
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();
}
/*!
 *  \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)");
}
Ejemplo n.º 4
0
/*!
 *  \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 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();
}