/*!
* \brief Interpret the GP individual.
* \param outResult Datum containing the result of the interpretation.
* \param ioContext GP evolutionary context.
* \throw Beagle::ObjectException When individual or tree are empty.
* \throw Beagle::AssertException When context is not correctly set.
* \throw Beagle::GP::MaxNodesExecutionException If number of nodes execution is more than allowed.
* \throw Beagle::GP::MaxTimeExecutionException If elapsed execution time is more than allowed.
*/
void GP::Individual::run(GP::Datum& outResult, GP::Context& ioContext)
{
Beagle_StackTraceBeginM();
if(&ioContext.getIndividual() != this) {
std::ostringstream lOSS;
lOSS << "In GP::Individual::run(): For the given context, ";
lOSS << "getIndividual() did not return the same individual as was passed to this (run) ";
lOSS << "method. Consider setting the context's individual to be the same by using the ";
lOSS << "method Context::setIndividualHandle().";
throw Beagle_RunTimeExceptionM(lOSS.str());
}
if(empty()) throw Beagle_ObjectExceptionM("Could not interpret, individual has no trees!");
if((*this)[0]->empty()) throw Beagle_ObjectExceptionM("Could not interpret, 1st tree is empty!");
Tree::Handle lOldTreeHandle = ioContext.getGenotypeHandle();
unsigned int lOldTreeIndex = ioContext.getGenotypeIndex();
ioContext.setGenotypeIndex(0);
ioContext.setGenotypeHandle((*this)[0]);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Running the ")+uint2ordinal(ioContext.getIndividualIndex()+1)+
std::string(" individual")
);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("The individual is: ")
);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
(*this)
);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("Executing the first tree root node '")+
(*(*this)[0])[0].mPrimitive->getName()+"'"
);
ioContext.setNodesExecutionCount(0);
ioContext.incrementNodesExecuted();
ioContext.getExecutionTimer().reset();
ioContext.pushCallStack(0);
(*(*this)[0])[0].mPrimitive->execute(outResult, ioContext);
ioContext.popCallStack();
ioContext.checkExecutionTime();
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
std::string("Result of executing the ")+uint2ordinal(ioContext.getIndividualIndex()+1)+
std::string(" individual: ")+outResult.serialize()
);
ioContext.setGenotypeIndex(lOldTreeIndex);
ioContext.setGenotypeHandle(lOldTreeHandle);
Beagle_StackTraceEndM();
}
/*!
* \brief Validate the GP individual.
* \param ioContext Evolutionary context.
* \return True if the GP individual is valid, false if not.
*/
bool GP::Individual::validate(GP::Context& ioContext)
{
Beagle_StackTraceBeginM();
bool lResult = true;
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
std::string("Validating ")+uint2ordinal(ioContext.getIndividualIndex()+1)+
std::string(" individual")
);
// Store original values.
GP::Tree::Handle lOldTreeHandle = ioContext.getGenotypeHandle();
unsigned int lOldTreeIndex = ioContext.getGenotypeIndex();
// Loop through each of the trees in the individual
for (unsigned int i=0; i<size(); i++) {
GP::Tree::Handle lTree = (*this)[i];
if (lTree == NULL) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Skipping ")+uint2ordinal(i+1)+std::string(" tree because it's NULL-valued")
);
continue;
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Validating ")+uint2ordinal(i+1)+std::string(" tree")
);
// Store the new values
ioContext.setGenotypeHandle(lTree);
ioContext.setGenotypeIndex(i);
lTree->setContextToNode(0, ioContext);
if(!lTree->validateSubTree(0, ioContext)) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Validation of ")+uint2ordinal(i+1)+std::string(" tree failed.")
);
lResult = false;
break;
}
}
if(lResult) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Individual passed validation testing.")
);
}
// Restore the original values.
ioContext.setGenotypeHandle(lOldTreeHandle);
ioContext.setGenotypeIndex(lOldTreeIndex);
return lResult;
Beagle_StackTraceEndM();
}
/*!
* \brief Evaluate the individual fitness.
* \param inIndividual Individual to evaluate.
* \param ioContext Evolutionary context.
* \return Handle to the fitness measure.
*/
Fitness::Handle SharedLibEvalOp::evaluate(GP::Individual& inIndividual, GP::Context& ioContext)
{
Beagle_StackTraceBeginM();
std::ostringstream lOSS;
lOSS << "Evaluating individual " << ioContext.getIndividualIndex() << ", deme ";
lOSS << ioContext.getDemeIndex() << ", generation " << ioContext.getGeneration();
Beagle_LogDebugM(ioContext.getSystem().getLogger(), "evaluate", "Beagle::GP::SpamebaseEvalOp", lOSS.str());
GP::PrimitiveSuperSet::Handle lPrimitiveSuperSet=
castHandleT<GP::PrimitiveSuperSet>(ioContext.getSystem().getComponent("GP-PrimitiveSuperSet"));
GP::PrimitiveSet::Handle lPrimitiveSet= (*lPrimitiveSuperSet)[0];
// Get a handle on the shared library used for evaluation.
// TODO: Open shared lib only once per generation!
this->mTimer.reset();
if (this->mSharedLibHandle)
{
dlclose(this->mSharedLibHandle);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(), "evaluate", "Beagle::GP::SpamebaseEvalOp",
"Closed previously opened shared lib.");
}
if (!ioContext.getSystem().getRegister().isRegistered("icu.compiler.lib-path"))
{
throw Beagle_RunTimeExceptionM("Parameter icu.compiler.lib-path not found in registry; make sure to apply SharedLibCompilerOp before applying SharedLibEvalOp.");
}
std::string lLibName= castHandleT<String>(ioContext.getSystem().getRegister()["icu.compiler.lib-path"])->getWrappedValue();
this->mSharedLibHandle= dlopen((const char*)lLibName.c_str(), RTLD_LAZY);
if (!this->mSharedLibHandle)
{
throw Beagle_RunTimeExceptionM("Cannot open shared library "+ lLibName+ ": "+ dlerror()+ ".");
}
dlerror();
// Draw a sample from the data set to construct the training set.
this->mTimer.reset();
// Get a handle on D, S, and L.
DataSetBinaryClassification::Handle lDataSet= castHandleT<DataSetBinaryClassification>(ioContext.getSystem().getComponent("DataSet"));
std::vector<unsigned int>* lIndexesPositives= lDataSet->getIndexesPositives();
std::vector<unsigned int>* lIndexesNegatives= lDataSet->getIndexesNegatives();
int lNrSamplesPositive= castHandleT<Int>(ioContext.getSystem().getRegister()["icu.trainingset.size-pos"])->getWrappedValue();
int lNrSamplesNegative= castHandleT<Int>(ioContext.getSystem().getRegister()["icu.trainingset.size-neg"])->getWrappedValue();
// Shuffle both negative and positive indexes.
std::random_shuffle(lIndexesPositives->begin(), lIndexesPositives->end(), ioContext.getSystem().getRandomizer());
std::random_shuffle(lIndexesNegatives->begin(), lIndexesNegatives->end(), ioContext.getSystem().getRandomizer());
// Nr of columns in each row in the dataset.
int lNrColumns= castHandleT<Int>(ioContext.getSystem().getRegister()["icu.dataset.columns"])->getWrappedValue();
double lTimeInit= this->mTimer.getValue();
this->mTimer.reset();
// Evaluate sampled test cases
unsigned int lTruePositives = 0;
unsigned int lTrueNegatives = 0;
unsigned int lFalsePositives= 0;
unsigned int lFalseNegatives= 0;
int (*apply_individual)(float[])= 0;
float lValues[lNrColumns];
std::vector<unsigned int>::iterator lLastIndex= lIndexesPositives->begin()+ lNrSamplesPositive;
// Positives.
for(std::vector<unsigned int>::const_iterator lIndex=lIndexesPositives->begin(); lIndex!=lLastIndex; ++lIndex)
{
const Beagle::Vector& lData = (*lDataSet)[*lIndex].second;
std::ostringstream lFunctionName;
lFunctionName << "apply_individual_";
lFunctionName << ioContext.getGeneration() << "_" << ioContext.getDemeIndex() << "_" << ioContext.getIndividualIndex();
apply_individual= (int(*)(float*))dlsym(this->mSharedLibHandle, lFunctionName.str().c_str());
char* lError= 0;
if ((lError = dlerror()) != NULL) {
throw Beagle_RunTimeExceptionM("Error loading function "+ lFunctionName.str()+ ": "+ lError+ ".");
}
for(unsigned int j=0; j<lData.size(); ++j) {
lValues[j]= Float(lData[j]);
}
bool lResult= apply_individual(lValues);
(lResult == 1) ? lTruePositives++ : lFalseNegatives++;
}
// Negatives.
lLastIndex= lIndexesNegatives->begin()+ lNrSamplesNegative;
for(std::vector<unsigned int>::const_iterator lIndex=lIndexesNegatives->begin(); lIndex!=lLastIndex; ++lIndex)
{
const Beagle::Vector& lData = (*lDataSet)[*lIndex].second;
std::ostringstream lFunctionName;
lFunctionName << "apply_individual_";
lFunctionName << ioContext.getGeneration() << "_" << ioContext.getDemeIndex() << "_" << ioContext.getIndividualIndex();
apply_individual= (int(*)(float*))dlsym(this->mSharedLibHandle, lFunctionName.str().c_str());
char* lError= 0;
if ((lError = dlerror()) != NULL) {
throw Beagle_RunTimeExceptionM("Error loading function "+ lFunctionName.str()+ ": "+ lError+ ".");
}
for(unsigned int j=0; j<lData.size(); ++j) {
lValues[j]= Float(lData[j]);
}
bool lResult= apply_individual(lValues);
(lResult == 0) ? lTrueNegatives++ : lFalsePositives++;
}
double lTimeEvaluate= this->mTimer.getValue();
{
using namespace std;
ostringstream lOSS;
lOSS << "g" << ioContext.getGeneration();
lOSS << " d" << ioContext.getDemeIndex();
lOSS << " i" << ioContext.getIndividualIndex() << ", ";
lOSS << "TP|FP|FN|TN = ";
lOSS.width(7);
lOSS << right << lTruePositives << "|";
lOSS.width(7);
lOSS << right << lFalsePositives << "|";
lOSS.width(7);
lOSS << right << lFalseNegatives << "|";
lOSS.width(7);
lOSS << right << lTrueNegatives;
Beagle_LogDetailedM(ioContext.getSystem().getLogger(), "evaluate", "Beagle::GP::SharedLibEvalOp", lOSS.str());
}
GP::FitnessMCC* fitness= new GP::FitnessMCC(lTruePositives, lFalsePositives, lTrueNegatives, lFalseNegatives);
return fitness;
Beagle_StackTraceEndM("SharedLibEvalOp::evaluate(GP::Individual& inIndividual, GP::Context& ioContext)");
}