/*!
* \brief Read an individual bag from a XML file.
* \param inFileName Filename to read individual bag from.
* \param ioSystem Evolutionary system used to read individual.
* \param inBagTag Name of the XML tag containing the list of individuals to read.
* \return True if an individual of the given name was found and read from file.
* false if nothing was found.
*/
bool IndividualBag::readFromFile(std::string inFileName,
System& ioSystem,
std::string inBagTag)
{
Beagle_StackTraceBeginM();
std::ifstream lIFS(inFileName.c_str());
PACC::XML::Document lParser(lIFS, inFileName);
lIFS.close();
PACC::XML::ConstFinder lBagFinder(lParser.getFirstDataTag());
PACC::XML::ConstIterator lIndivTag = lBagFinder.find(std::string("//IndividualBag")+inBagTag);
if(!lIndivTag) return false;
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioSystem.getFactory().getConceptAllocator("Concept"));
Context::Handle lContext =
castHandleT<Context>(lContextAlloc->allocate());
lContext->setSystemHandle(&ioSystem);
Beagle_LogInfoM(
ioSystem.getLogger(),
std::string("Reading an individual bag from file '")+inFileName+
std::string("' that is in-between the XML tags '")+inBagTag+std::string("'")
);
readIndividuals(lIndivTag, *lContext);
return true;
Beagle_StackTraceEndM();
}
/*!
* \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 Push execution context to prepare the execution of the argument.
* \param inNumberArguments Number of arguments of called tree.
* \param ioContext Evolutionary context.
*/
void GP::Argument::pushExecutionContext(unsigned int inNumberArguments, GP::Context& ioContext)
{
Beagle_StackTraceBeginM();
switch(mSharedData->mEvalMode) {
case eCaching: {
Object::Bag::Handle lNewCache = new Object::Bag(inNumberArguments, NULL);
mSharedData->mCaches.push_back(lNewCache);
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
GP::Context::Handle lNewEvalContext =
castHandleT<GP::Context>(lContextAlloc->clone(ioContext));
mSharedData->mEvalContext.push_back(lNewEvalContext);
break;
}
case eJustInTime: {
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
GP::Context::Handle lNewEvalContext =
castHandleT<GP::Context>(lContextAlloc->clone(ioContext));
mSharedData->mEvalContext.push_back(lNewEvalContext);
break;
}
case ePreCompute: {
Object::Bag::Handle lNewCache = new Object::Bag(inNumberArguments, NULL);
lNewCache->resize(inNumberArguments);
for(unsigned int i=0; i<inNumberArguments; ++i) {
Object::Handle lArgI = mSharedData->mTypeAllocator->allocate();
getArgument(i, *lArgI, ioContext);
(*lNewCache)[i] = lArgI;
}
mSharedData->mCaches.push_back(lNewCache);
}
default: {
throw Beagle_InternalExceptionM(std::string("Undefined evaluation mode (")+
uint2str(mSharedData->mEvalMode)+std::string(") for the arguments!"));
}
}
Beagle_StackTraceEndM();
}
/*!
* \brief Read individual from a XML file. If several individuals are in file, read
* first tagged occurence of individual.
* \param inFileName Filename to read individual from.
* \param ioSystem Evolutionary system to read individual.
* \return True if an individual was found and read from file, false if nothing was found.
*/
bool Individual::readFromFile(std::string inFileName, System& ioSystem)
{
Beagle_StackTraceBeginM();
std::ifstream lIFS(inFileName.c_str());
PACC::XML::Document lParser(lIFS, inFileName);
lIFS.close();
PACC::XML::ConstFinder lIndivFinder(lParser.getFirstDataTag());
PACC::XML::ConstIterator lIndivTag = lIndivFinder.find("//Individual");
if(!lIndivTag) return false;
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioSystem.getFactory().getConceptAllocator("Context"));
Context::Handle lContext = castHandleT<Context>(lContextAlloc->allocate());
lContext->setSystemHandle(&ioSystem);
lContext->setIndividualHandle(this);
lContext->setIndividualIndex(0);
readWithContext(lIndivTag, *lContext);
return true;
Beagle_StackTraceEndM();
}
/*!
* \brief Test the fitness of a given individual.
* \param inIndividual Handle to the individual to test.
* \param ioSystem Handle to the system to use to test the individual.
* \par Note:
* This method is provided as a mean to test some individuals after an evolution.
*/
Fitness::Handle Beagle::MPI::EvaluationOp::test(Individual::Handle inIndividual, System::Handle ioSystem)
{
Beagle_LogInfoM(
ioSystem->getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
std::string("Testing the following individual: ")+inIndividual->serialize()
);
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioSystem->getContextAllocatorHandle());
Context::Handle lContext = castHandleT<Context>(lContextAlloc->allocate());
lContext->setSystemHandle(ioSystem);
lContext->setIndividualHandle(inIndividual);
Fitness::Handle lFitness = evaluate(*inIndividual, *lContext);
Beagle_LogInfoM(
ioSystem->getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
std::string("New fitness of the individual: ")+lFitness->serialize()
);
return lFitness;
}
/*!
* \brief Evaluate the fitness of the given individual.
* \param inIndividual Current individual to evaluate.
* \param ioContext Evolutionary context.
* \return Handle to the fitness value of the individual.
*
* This method evaluates only a single individual. For this
* operator, it is much better to group individuals into a bag and
* pass the bag to evaluate(Individual::Bag& ioIndividuals, Context::Bag& ioContexts).
*/
Fitness::Handle EvaluationMultipleOp::evaluate(Individual& inIndividual, Context& ioContext)
{
Beagle_StackTraceBeginM();
// Create a bag for the individual
Individual::Bag lIndividuals;
lIndividuals.resize(1);
Beagle_AssertM(inIndividual == ioContext.getIndividual());
lIndividuals[0] = ioContext.getIndividualHandle();
// Create a context for the individual
Context::Bag lContexts;
lContexts.resize(1);
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
lContexts[0] = castHandleT<Context>(lContextAlloc->clone(ioContext));
// Call evalutate()
Fitness::Bag::Handle lFitnessBag = evaluateIndividuals(lIndividuals,lContexts);
// Return fitness
Beagle_AssertM( !lFitnessBag->empty() );
return lFitnessBag->at(0);
Beagle_StackTraceEndM();
}
/*!
* \brief Read a primitive super set from a XML subtree.
* \param inIter XML iterator used to read the super set from.
* \param ioSystem Evolutionary system.
* \throw Beagle::IOException If size atribute not present.
*/
void GP::PrimitiveSuperSet::readWithSystem(PACC::XML::ConstIterator inIter, Beagle::System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="GP-PrimitiveSuperSet"))
throw Beagle_IOExceptionNodeM(*inIter, "tag <GP-PrimitiveSuperSet> expected!");
const Factory& lFactory = ioSystem.getFactory();
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(lFactory.getConceptAllocator("Context"));
GP::Context::Handle lGPContext =
castHandleT<GP::Context>(lContextAlloc->allocate());
lGPContext->setSystemHandle(System::Handle(&ioSystem));
GP::PrimitiveSet::Alloc::Handle lPrimitSetsAlloc =
castHandleT<GP::PrimitiveSet::Alloc>(lFactory.getConceptAllocator("GP-PrimitiveSet"));
mPrimitSets.clear();
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if((lChild->getType()==PACC::XML::eData) && (lChild->getValue()=="GP-PrimitiveSet")) {
GP::PrimitiveSet::Handle lPrimitSet =
castHandleT<GP::PrimitiveSet>(lPrimitSetsAlloc->allocate());
lPrimitSet->readWithContext(lChild, *lGPContext);
mPrimitSets.push_back(lPrimitSet);
}
}
Beagle_StackTraceEndM("void GP::PrimitiveSuperSet::readWithSystem(PACC::XML::ConstIterator inIter, Beagle::System& ioSystem)");
}
/*!
* \brief Add individuals to the bag such that the total equals getIndisPerGroup().
* \param ioIndividuals Bag of individuals to evaluate.
* \param ioContexts Bag of evolutionary context.
* \return The number of individuals added to the bag.
*
* The new individuals are chosen from the current deme.
*/
unsigned int EvaluationMultipleOp::enlargeGroup(Individual::Bag& ioIndividuals,
Context::Bag& ioContexts)
{
Beagle_StackTraceBeginM();
Context& lContext = castObjectT<Context&>(*(ioContexts[0]));
// Calculate the number of individuals to add
unsigned int lNumToAdd = mIndisPerGroup - ioIndividuals.size();
Beagle_LogVerboseM(
lContext.getSystem().getLogger(),
std::string("Adding ")+uint2str(lNumToAdd)+std::string(" individuals to the group (for padding)")
);
// Resize the bags
unsigned int lIndisCounter = ioIndividuals.size();
ioIndividuals.resize(mIndisPerGroup);
ioContexts.resize(mIndisPerGroup);
// Loop through all the individuals in the deme
Deme& lDeme = lContext.getDeme();
std::vector<unsigned int> lSelectableIndis;
lSelectableIndis.resize(lDeme.size());
unsigned int lSelectableIndisCounter = 0;
for (unsigned int i=0; i<lDeme.size(); i++) {
// Loop through all the individuals in the bag
bool lAdd = true;
for(unsigned int j=0; j<ioIndividuals.size(); j++) {
if(lDeme[i] == ioIndividuals[j]) {
lAdd = false;
break;
}
}
// If the individual is not already in the bag, add it as an option
if(lAdd) {
lSelectableIndis[lSelectableIndisCounter] = i;
lSelectableIndisCounter++;
}
}
// Check there are sufficient individuals to choose
if(lSelectableIndis.size() < lNumToAdd) {
throw Beagle_RunTimeExceptionM("There are insufficient individuals in the deme to perform evaluation");
}
// Add individuals
for(unsigned int i=0; i<lNumToAdd; i++) {
unsigned int lIndex =
lContext.getSystem().getRandomizer().rollInteger(0,lSelectableIndisCounter-1);
unsigned int lIndiIndex = lSelectableIndis[lIndex];
Beagle_LogVerboseM(
lContext.getSystem().getLogger(),
std::string("Adding ")+uint2ordinal(lIndiIndex+1)+
std::string(" individual to the group (for padding)")
);
Beagle_AssertM(lIndiIndex < lDeme.size());
ioIndividuals[lIndisCounter] = lDeme[ lIndiIndex ];
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(lContext.getSystem().getFactory().getConceptAllocator("Context"));
ioContexts[lIndisCounter] = castHandleT<Context>(lContextAlloc->clone(*(ioContexts[0])));
ioContexts[lIndisCounter]->setIndividualHandle( ioIndividuals[lIndisCounter] );
ioContexts[lIndisCounter]->setIndividualIndex( lIndiIndex );
lIndisCounter++;
}
Beagle_AssertM( lIndisCounter==ioIndividuals.size() );
return lNumToAdd;
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the evaluation process on the invalid individuals of the deme.
* \param ioDeme Deme to process.
* \param ioContext Context of the evolution.
*/
void EvaluationMultipleOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Evaluating the fitness of the individuals in the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
Beagle_AssertM( ioDeme.size()!=0 );
// Prepare stats
prepareStats(ioDeme,ioContext);
// Generate a vector of indicies into the population
std::vector<unsigned int> lEvalVector;
for(unsigned int i=0; i<ioDeme.size(); i++) {
if((ioDeme[i]->getFitness() == NULL) ||
(ioDeme[i]->getFitness()->isValid() == false)) {
lEvalVector.push_back(i);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Added " << uint2ordinal(i+1) << " individual for evaluation."
);
}
}
std::random_shuffle(lEvalVector.begin(), lEvalVector.end(),
ioContext.getSystem().getRandomizer());
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"There are " << lEvalVector.size() << " individuals to be evaluated."
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
while ( !lEvalVector.empty() ) {
// Put individuals and context into bags.
Individual::Bag lIndividuals;
Context::Bag lContexts;
lIndividuals.resize( mIndisPerGroup );
lContexts.resize( mIndisPerGroup );
unsigned int lIndiCounter =0;
for (unsigned int i=0; i<mIndisPerGroup; i++) {
// Set individual
lIndividuals[i] = ioDeme[lEvalVector.back()];
lIndiCounter++;
// Set context
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext = castHandleT<Context>(lContextAlloc->clone(ioContext));
lContext->setIndividualIndex( lEvalVector.back() );
lContext->setIndividualHandle( ioDeme[lEvalVector.back()] );
lContexts[i] = lContext;
// Remove this index from the evaluation vector
lEvalVector.pop_back();
if(lEvalVector.empty()) {
lIndividuals.resize( lIndiCounter );
lContexts.resize( lIndiCounter );
break;
}
}
// Evaluate individuals
std::ostringstream lOSS;
lOSS << "Evaluating the fitness of the ";
for(unsigned int i=0; i<lIndiCounter; i++) {
// Add to message
if (i==lIndiCounter-1) lOSS << " and ";
lOSS << uint2ordinal(lContexts[i]->getIndividualIndex()+1);
if (i<lIndiCounter-2) lOSS << ", ";
}
lOSS << " individuals";
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
lOSS.str()
);
Fitness::Bag::Handle lFitnessBag = evaluateIndividuals(lIndividuals, lContexts);
// Assign fitnesses
for (unsigned int i=0; i<lIndiCounter; i++) {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Considering fitness of the " << uint2ordinal(lContexts[i]->getIndividualIndex()+1) << " individual"
);
Beagle_AssertM( i < lFitnessBag->size() );
Fitness::Handle lFitness = lFitnessBag->at(i);
Beagle_NonNullPointerAssertM( lFitness );
lIndividuals[i]->setFitness( lFitness );
lIndividuals[i]->getFitness()->setValid();
if(lHistory != NULL) {
lHistory->allocateID(*lIndividuals[i]);
lHistory->trace(ioContext, std::vector<HistoryID>(), lIndividuals[i], getName(), "evaluation");
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
*lIndividuals[i]->getFitness()
);
}
// Update stats
updateStats(lIndividuals.size(),ioContext);
}
updateHallOfFameWithDeme(ioDeme,ioContext);
Beagle_StackTraceEndM();
}
/*!
* \brief Swap subtree mutate a GP individual.
* \param ioIndividual GP individual to swap subtree mutate.
* \param ioContext Context of the evolution.
*/
bool GP::MutationSwapSubtreeOp::mutate(Beagle::Individual& ioIndividual, Beagle::Context& ioContext)
{
Beagle_StackTraceBeginM();
// Initial parameters checks.
Beagle_AssertM(ioIndividual.size() > 0);
Beagle_ValidateParameterM(mNumberAttempts->getWrappedValue()>0, "gp.try", ">0");
// Cast method arguments.
GP::Individual& lGPIndiv = castObjectT<GP::Individual&>(ioIndividual);
GP::Context& lContext1 = castObjectT<GP::Context&>(ioContext);
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
GP::Context::Handle lContextHdl2 = castHandleT<GP::Context>(lContextAlloc->clone(lContext1));
const Factory& lFactory = ioContext.getSystem().getFactory();
GP::Tree::Alloc::Handle lTreeAlloc =
castHandleT<GP::Tree::Alloc>(lFactory.getConceptAllocator("Genotype"));
// Get parameters in local values, with the total number of nodes of the mutated individual.
bool lMatingDone = false;
float lDistrProba = mDistributionProba->getWrappedValue();
unsigned int lMaxTreeDepth = mMaxTreeDepth->getWrappedValue();
GP::Tree::Handle lOldTreeHandle1 = lContext1.getGenotypeHandle();
unsigned int lOldTreeIndex1 = lContext1.getGenotypeIndex();
unsigned int lSizeIndiv = 0;
for(unsigned int i=0; i<lGPIndiv.size(); ++i) lSizeIndiv += lGPIndiv[i]->size();
// Some outputs.
Beagle_LogDebugM(
lContext1.getSystem().getLogger(),
"mutation",
"Beagle::GP::MutationSwapSubtreeOp",
"Individual tried for swap subtree mutation (before)"
);
Beagle_LogObjectDebugM(
lContext1.getSystem().getLogger(),
"mutation",
"Beagle::GP::MutationSwapSubtreeOp",
lGPIndiv
);
// Mutation loop. Try the given number of attempts to mutation the individual.
for(unsigned int lAttempt=0; lAttempt < mNumberAttempts->getWrappedValue(); lAttempt++) {
// Calculate the number of nodes in the individual
unsigned int lNbNodes = 0;
for(unsigned int i=0; i<lGPIndiv.size(); i++) lNbNodes += lGPIndiv[i]->size();
if(lNbNodes == 0) return false;
// Choose a node of the individual to mutate.
unsigned int lNode1 = lContext1.getSystem().getRandomizer().rollInteger(0, lNbNodes-1);
// Get the tree in which the choosen node is. Change the global node index to the tree's index.
unsigned int lChoosenTree = 0;
for(; lChoosenTree<lGPIndiv.size(); ++lChoosenTree) {
if(lNode1 < lGPIndiv[lChoosenTree]->size()) break;
Beagle_AssertM(lNode1 >= lGPIndiv[lChoosenTree]->size());
lNode1 -= lGPIndiv[lChoosenTree]->size();
}
Beagle_AssertM(lChoosenTree < lGPIndiv.size());
// Cannot do anything with an tree of size <= 1.
if(lGPIndiv[lChoosenTree]->size() <= 1) continue;
// Some outputs.
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
std::string("Trying a swap subtree mutation of the ")+uint2ordinal(lChoosenTree+1)+
std::string(" tree")
);
// Make two clones of the choosen tree.
GP::Tree::Handle lTreeClone1 = castHandleT<GP::Tree>(lTreeAlloc->clone(*lGPIndiv[lChoosenTree]));
GP::Tree::Handle lTreeClone2 = castHandleT<GP::Tree>(lTreeAlloc->clone(*lGPIndiv[lChoosenTree]));
// Now we decide whether the swap subtree mutation is internal or external.
bool lMutationType = lContext1.getSystem().getRandomizer().rollUniform(0.0, 1.0) < lDistrProba;
// Cannot do an internal mutation when there is only one branch in the tree.
if(lTreeClone1->size() == (*lTreeClone1)[0].mPrimitive->getNumberArguments()+1)
lMutationType = false;
// This is special case, a linear tree. Cannot do an external mutation.
if(lTreeClone1->size() == (*lTreeClone1)[1].mSubTreeSize+1) {
if(lTreeClone1->size()==2) continue; // Cannot do anything here with the tree.
lMutationType = true;
}
// lMutationType is true -> internal mutation
if(lMutationType) {
// If the selected node is a terminal, or a branch with a subtree made only of terminals,
// choose another node in the same tree.
while((*lTreeClone1)[lNode1].mSubTreeSize ==
((*lTreeClone1)[lNode1].mPrimitive->getNumberArguments()+1)) {
lNode1 = lContext1.getSystem().getRandomizer().rollInteger(0, lTreeClone1->size()-1);
}
// Choosing the second node, a branch in lNode1's subtree.
unsigned int lSubTreeSizeN1 = (*lTreeClone1)[lNode1].mSubTreeSize;
unsigned int lN2OffN1 =
lContext1.getSystem().getRandomizer().rollInteger(1, lSubTreeSizeN1-1);
unsigned int lNode2 = lNode1 + lN2OffN1;
while((*lTreeClone1)[lNode2].mPrimitive->getNumberArguments() == 0) {
lN2OffN1 = lContext1.getSystem().getRandomizer().rollInteger(1, lSubTreeSizeN1-1);
lNode2 = lNode1 + lN2OffN1;
}
// Choosing the third node, any node in lNode2's subtree.
unsigned int lSubTreeSizeN2 = (*lTreeClone1)[lNode2].mSubTreeSize;
unsigned int lN3OffN2 =
lContext1.getSystem().getRandomizer().rollInteger(1, lSubTreeSizeN2-1);
// Ok, now we can exchange the subtrees.
// New value of lNode1 and lNode2 for the second exchange.
unsigned int lNode3Exch2 = lNode1 + lN3OffN2;
unsigned int lNode1Exch2 = lNode2;
// New value of lNode1 and lNode2 for the third exchange.
unsigned int lNode2Exch3 = lNode1 + lN3OffN2 + lN2OffN1;
unsigned int lNode3Exch3 = lNode2;
// First exchange.
lTreeClone1->setContextToNode(lNode1, lContext1);
lTreeClone2->setContextToNode(lNode2, *lContextHdl2);
exchangeSubTrees(*lTreeClone1, lNode1, lContext1,
*lTreeClone2, lNode2, *lContextHdl2);
// Second exchange.
lTreeClone1->setContextToNode(lNode3Exch2, lContext1);
lTreeClone2->setContextToNode(lNode1Exch2, *lContextHdl2);
exchangeSubTrees(*lTreeClone1, lNode3Exch2, lContext1,
*lTreeClone2, lNode1Exch2, *lContextHdl2);
// Third exchange.
lTreeClone1->setContextToNode(lNode2Exch3, lContext1);
lTreeClone2->setContextToNode(lNode3Exch3, *lContextHdl2);
exchangeSubTrees(*lTreeClone1, lNode2Exch3, lContext1,
*lTreeClone2, lNode3Exch3, *lContextHdl2);
// Checking if the tree depth is respected. If not, start again.
if(lTreeClone1->getTreeDepth() > lMaxTreeDepth) {
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
"Tree maximum depth exceeded. GP swap subtree mutation invalid."
);
continue;
}
lGPIndiv[lChoosenTree] = lTreeClone1;
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
"GP swap subtree mutation valid"
);
lMatingDone = true;
break; // The swap subtree mutation is valid.
}
// lMutationType is false -> external mutation
else {
// Deterniming the minimal node index to use.
unsigned int lMinNodeIndex = 0;
for(; lTreeClone1->size() == ((*lTreeClone1)[lMinNodeIndex].mSubTreeSize+lMinNodeIndex);
++lMinNodeIndex) {
if(lMinNodeIndex == (lTreeClone1->size()-1)) continue; // Can't do anything with linear tree.
}
// Change lNode1 if less than minimum node index.
if(lNode1 < lMinNodeIndex)
lNode1 = lContext1.getSystem().getRandomizer().rollInteger(lMinNodeIndex,
lTreeClone1->size()-1);
// Choosing second swap subtree mutation point.
std::vector<unsigned int> lValidN2;
for(unsigned int i=lMinNodeIndex; i<lTreeClone1->size(); ++i) {
if((i>=lNode1) && (i<lNode1+(*lTreeClone1)[lNode1].mSubTreeSize)) continue;
else if((lNode1>=i) && (lNode1<(i+(*lTreeClone1)[i].mSubTreeSize))) continue;
else lValidN2.push_back(i);
}
unsigned int lNode2 =
lValidN2[lContext1.getSystem().getRandomizer().rollInteger(0, lValidN2.size()-1)];
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
std::string("Trying an external swap subtree mutation of the ")+uint2ordinal(lNode1+1)+
std::string(" node with the subtree to the ")+uint2ordinal(lNode2+1)+
std::string(" node")
);
// Ok, now we can exchange the subtrees.
// New value of lNode1 and lNode2 for the second exchange.
unsigned int lNode1Exch2 = lNode1;
unsigned int lNode2Exch2 = lNode2;
if(lNode1 < lNode2) {
lNode2Exch2 += (*lTreeClone1)[lNode2].mSubTreeSize;
lNode2Exch2 -= (*lTreeClone1)[lNode1].mSubTreeSize;
} else {
lNode1Exch2 += (*lTreeClone1)[lNode1].mSubTreeSize;
lNode1Exch2 -= (*lTreeClone1)[lNode2].mSubTreeSize;
}
// First exchange.
lTreeClone1->setContextToNode(lNode1, lContext1);
lTreeClone2->setContextToNode(lNode2, *lContextHdl2);
exchangeSubTrees(*lTreeClone1, lNode1, lContext1,
*lTreeClone2, lNode2, *lContextHdl2);
// Second exchange.
lTreeClone1->setContextToNode(lNode2Exch2, lContext1);
lTreeClone2->setContextToNode(lNode1Exch2, *lContextHdl2);
exchangeSubTrees(*lTreeClone1, lNode2Exch2, lContext1,
*lTreeClone2, lNode1Exch2, *lContextHdl2);
// Checking if the tree depth is respected. If not, start again.
if(lTreeClone1->getTreeDepth() > lMaxTreeDepth) {
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
"Tree maximum depth exceeded. GP swap subtree mutation invalid."
);
continue;
}
lGPIndiv[lChoosenTree] = lTreeClone1;
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
"GP swap subtree mutation valid"
);
lMatingDone = true;
break; // The swap subtree mutation is valid.
}
}
// Replace the contexts.
lContext1.setGenotypeHandle(lOldTreeHandle1);
lContext1.setGenotypeIndex(lOldTreeIndex1);
if(lMatingDone) {
Beagle_LogDebugM(
lContext1.getSystem().getLogger(),
"mutation",
"Beagle::GP::MutationSwapSubtreeOp",
"Individual after swap subtree mutation"
);
Beagle_LogObjectDebugM(
lContext1.getSystem().getLogger(),
"mutation",
"Beagle::GP::MutationSwapSubtreeOp",
lGPIndiv
);
} else {
Beagle_LogVerboseM(
lContext1.getSystem().getLogger(),
"mutation", "Beagle::GP::MutationSwapSubtreeOp",
"No GP swap subtree mutation done"
);
}
return lMatingDone;
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();
}