void bpbToWig(const isaac::options::BpbToWigOptions &options)
{
isaac::workflow::BpbToWigWorkflow workflow(
options.wigDefaultValue_,
options.sortedReferenceMetadata_,
options.inputFilePath_,
options.outputFormatString_,
options.bitsPerValue_,
options.knownSitesOnly_,
options.bedPrintAllPositions_
);
workflow.run();
}
int main()
{
GaInitialize();
{
Chromosome::GaMatingConfig matingConfiguration(
Chromosome::GaCrossoverSetup( &crossover, &Chromosome::GaCrossoverParams( 0.8f, 2 ), NULL ),
Chromosome::GaMutationSetup( &mutation, &Chromosome::GaMutationParams( 0.03f, false ), NULL ) );
float gridSize[] = { 0.5, 0.5 };
Algorithm::Stubs::GaPAESStub paesStub( WDID_POPULATION, WDID_POPULATION_STATS,
Chromosome::GaInitializatorSetup( &initializator, NULL, &Chromosome::GaInitializatorConfig() ),
Population::GaPopulationFitnessOperationSetup( &populationFitnessOperation, NULL, &Fitness::GaFitnessOperationConfig( &Fitness::Representation::GaMVFitnessParams( 2 ) ) ),
Fitness::GaFitnessComparatorSetup( &fitnessComparator, &Fitness::Comparators::GaSimpleComparatorParams( Fitness::Comparators::GACT_MINIMIZE_ALL ), NULL ),
Population::GaPopulationParams( 33, 1 ),
Chromosome::GaMutationSetup( &mutation, &Chromosome::GaMutationParams( 0.03f, false ), NULL ),
Multiobjective::PAES::GaPAESSelectionParams( PTID_CURRENT_SOLUTION, PTID_CROSSOVER_BUFFER),
Multiobjective::PAES::GaPAESParams( CTID_DOMINANCE, CTID_HYPERBOX, CTID_HYPERBOX_INFO, PTID_HYPERBOX_INFO_BUFFER, PTID_CURRENT_SOLUTION, PTID_CROWDING_STORAGE ),
Common::Grid::GaHyperGrid<Fitness::GaFitness, float, Multiobjective::GaFitnessCoordiantesGetter<float> >( gridSize, 2 ) );
Common::Workflows::GaWorkflow workflow( NULL );
workflow.RemoveConnection( *workflow.GetFirstStep()->GetOutboundConnections().begin(), true );
Common::Workflows::GaWorkflowBarrier* br1 = new Common::Workflows::GaWorkflowBarrier();
paesStub.Connect( workflow.GetFirstStep(), br1 );
Common::Workflows::GaBranchGroup* bg1 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( br1, workflow.GetLastStep(), 0 );
Algorithm::StopCriteria::GaStopCriterionStep* stopStep = new Algorithm::StopCriteria::GaStopCriterionStep(
Algorithm::StopCriteria::GaStopCriterionSetup( &stopCriterion, &Algorithm::StopCriteria::GaGenerationCriterionParams( 1000 ), NULL ),
workflow.GetWorkflowData(), WDID_POPULATION_STATS );
Common::Workflows::GaBranchGroupTransition* bt1 = new Common::Workflows::GaBranchGroupTransition();
bg1->GetBranchGroupFlow()->SetFirstStep( stopStep );
bg1->GetBranchGroupFlow()->ConnectSteps( stopStep, bt1, 0 );
workflow.ConnectSteps( bt1, paesStub.GetStubFlow().GetFirstStep(), 1 );
Common::Workflows::GaDataCache<Population::GaPopulation> population( workflow.GetWorkflowData(), WDID_POPULATION );
population.GetData().GetEventManager().AddEventHandler( Population::GaPopulation::GAPE_NEW_GENERATION, &newGenHandler );
workflow.Start();
workflow.Wait();
}
GaFinalize();
}
int main()
{
GaInitialize();
{
Chromosome::GaMatingConfig matingConfiguration(
Chromosome::GaCrossoverSetup( &crossover, &Chromosome::GaCrossoverParams( 0.8f, 2 ), NULL ),
Chromosome::GaMutationSetup( &mutation, &Chromosome::GaMutationParams( 0.03f, false ), NULL ) );
Algorithm::Stubs::GaSPEAStub speaStub( WDID_POPULATION, WDID_POPULATION_STATS,
Chromosome::GaInitializatorSetup( &initializator, NULL, &Chromosome::GaInitializatorConfig() ),
Population::GaPopulationFitnessOperationSetup( &populationFitnessOperation, NULL, &Fitness::GaFitnessOperationConfig( &Fitness::Representation::GaMVFitnessParams( 2 ) ) ),
Fitness::GaFitnessComparatorSetup( &fitnessComparator, &Fitness::Comparators::GaSimpleComparatorParams( Fitness::Comparators::GACT_MINIMIZE_ALL ), NULL ),
Population::GaPopulationParams( 64, 0 ),
Chromosome::GaMatingSetup( &mating, NULL, &matingConfiguration ),
Population::GaCouplingSetup(),
Population::SelectionOperations::GaTournamentSelectionParams( 32, PTID_CROSSOVER_BUFFER, -1, 2,
Population::SelectionOperations::GaTournamentSelectionParams::GATST_ROULETTE_WHEEL_SELECTION ),
Multiobjective::SPEA::GaSPEAParams( CTID_DOMINANCE_LIST, CTID_STRENGTH, CTID_DOMINATED, PTID_CLUSTER_STORAGE ) );
Common::Workflows::GaWorkflow workflow( NULL );
workflow.RemoveConnection( *workflow.GetFirstStep()->GetOutboundConnections().begin(), true );
Common::Workflows::GaWorkflowBarrier* br1 = new Common::Workflows::GaWorkflowBarrier();
speaStub.Connect( workflow.GetFirstStep(), br1 );
Common::Workflows::GaBranchGroup* bg1 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( br1, workflow.GetLastStep(), 0 );
Algorithm::StopCriteria::GaStopCriterionStep* stopStep = new Algorithm::StopCriteria::GaStopCriterionStep(
Algorithm::StopCriteria::GaStopCriterionSetup( &stopCriterion, &Algorithm::StopCriteria::GaGenerationCriterionParams( 100 ), NULL ),
workflow.GetWorkflowData(), WDID_POPULATION_STATS );
Common::Workflows::GaBranchGroupTransition* bt1 = new Common::Workflows::GaBranchGroupTransition();
bg1->GetBranchGroupFlow()->SetFirstStep( stopStep );
bg1->GetBranchGroupFlow()->ConnectSteps( stopStep, bt1, 0 );
workflow.ConnectSteps( bt1, speaStub.GetStubFlow().GetFirstStep(), 1 );
Common::Workflows::GaDataCache<Population::GaPopulation> population( workflow.GetWorkflowData(), WDID_POPULATION );
population.GetData().GetEventManager().AddEventHandler( Population::GaPopulation::GAPE_NEW_GENERATION, &newGenHandler );
workflow.Start();
workflow.Wait();
}
GaFinalize();
}
int main(int argc, const char * argv[])
{
try {
init_logger();
parse_options(argc, argv);
Workflow workflow(options);
workflow.run();
}
catch (const std::exception & ex) {
std::cerr << "TealTree failed with exception:" << std::endl;
std::cerr << ex.what() << std::endl;
std::cerr.flush();
destroy_logger();
exit(1);
}
destroy_logger();
return 0;
}
void MainWindow::queueSimulation(const openstudio::path &t_input, const openstudio::path &t_epw)
{
try {
// Build list of jobs to create
std::string jobsstring = toString(ui.cbWorkflow->currentText());
if (jobsstring == "<Custom>")
{
openstudio::path expecteddb = t_input.parent_path() / t_input.stem() / openstudio::toPath("run.db");
if (!boost::filesystem::exists(expecteddb))
{
QMessageBox::critical(this, "Unable to launch job", "Db containing custom workflow for OpenStudio UI created OSM not found at the expected location: " + openstudio::toQString(expecteddb));
} else {
try {
m_runmanager.loadJobs(expecteddb);
statusBar()->showMessage("Job Queued - " + openstudio::toQString(t_input));
} catch (const std::exception &e) {
QMessageBox::critical(this, "Unable to launch job", e.what());
}
}
} else {
// parse the string list with the workflow constructor
openstudio::runmanager::Workflow workflow(jobsstring);
// Build list of tools
openstudio::runmanager::Tools tools;
ConfigOptions co = m_runmanager.getConfigOptions();
tools.append(co.getTools());
workflow.add(tools);
workflow.setInputFiles(t_input, t_epw);
openstudio::runmanager::Job job = workflow.create(getOutDir(t_input, workflow, jobsstring, co.getSimpleName()));
m_runmanager.enqueue(job, false);
statusBar()->showMessage("Job Queued - " + openstudio::toQString(job.description()));
}
} catch (const std::exception &e) {
QMessageBox::critical(this, "Unable to launch job", e.what());
}
}
int main()
{
GaInitialize();
{
int values[ Problems::TNG::TNG_NUMBER_COUNT ];
values[ 0 ] = GaGlobalRandomIntegerGenerator->Generate( 1, 9 );
values[ 1 ] = GaGlobalRandomIntegerGenerator->Generate( 1, 9 );
values[ 2 ] = GaGlobalRandomIntegerGenerator->Generate( 1, 9 );
values[ 3 ] = GaGlobalRandomIntegerGenerator->Generate( 1, 9 );
values[ 4 ] = ( 10 + GaGlobalRandomIntegerGenerator->Generate( 0, 2 ) * 5 );
values[ 5 ] = ( 25 + GaGlobalRandomIntegerGenerator->Generate( 0, 3 ) * 25 );
int target = ( GaGlobalRandomIntegerGenerator->Generate( 100, 999 ) );
Chromosome::GaMatingConfig matingConfiguration(
Chromosome::GaCrossoverSetup( &crossover, &Chromosome::GaCrossoverPointParams( 0.8f, 2, 1 ), NULL ),
Chromosome::GaMutationSetup( &mutation, &Chromosome::GaMutationSizeParams( 0.3f, true, 2L ), NULL ) );
Chromosome::GaInitializatorSetup initializatorSetup( &initializator, NULL, &Chromosome::GaInitializatorConfig(
&Problems::TNG::TngConfigBlock( values, target, &Chromosome::Representation::GaBinaryChromosomeParams() ) ) );
Fitness::GaFitnessComparatorSetup fitnessComparatorSetup( &fitnessComparator, &Fitness::Comparators::GaSimpleComparatorParams( Fitness::Comparators::GACT_MAXIMIZE_ALL ), NULL );
Algorithm::Stubs::GaSimpleGAStub::GaStatTrackersCollection trackers;
trackers[ Population::GaPopulationSizeTracker::TRACKER_ID ] = &sizeTracker;
trackers[ Population::GaRawFitnessTracker::TRACKER_ID ] = &rawTracker;
trackers[ Population::GaScaledFitnessTracker::TRACKER_ID ] = &scaledTracker;
Population::GaSelectionSetup selectionSetup( &selection, &Population::SelectionOperations::GaDuplicatesSelectionParams( 8, 1, 2 ),
&Population::GaCouplingConfig( Chromosome::GaMatingSetup( &mating, NULL, &matingConfiguration ) ) );
Population::GaReplacementSetup replacementSetup( &replacement, &Population::ReplacementOperations::GaRandomReplacementParams( 8, 4, 3 ),
&Population::GaReplacementConfig( Chromosome::GaChromosomeComparatorSetup( &chromosomeComparator, NULL, NULL ) ) );
Population::GaScalingSetup scalingSetup( &scaling, &Population::ScalingOperations::GaScalingFactorParams( 2.0f )/*&Population::ScalingOperations::GaShareFitnessParams( 0.2f, 1.0f, 4 )*/,
&Population::ScalingOperations::GaShareFitnessScalingConfig( NULL, Chromosome::GaChromosomeComparatorSetup( &chromosomeComparator, NULL, NULL ) ) );
/*
Population::GaPopulation* population = new Population::GaPopulation( Population::GaPopulationParams( 32, 0, Population::GaPopulationParams::GAPFO_FILL_ON_INIT ),
Chromosome::GaInitializatorSetup( &initializator, NULL, &Chromosome::GaInitializatorConfig(
&Problems::TNG::TngConfigBlock( values, target, &Chromosome::Representation::GaBinaryChromosomeParams() ) ) ),
Population::GaPopulationFitnessOperationSetup( &populationFitnessOperation, NULL, &Fitness::GaFitnessOperationConfig() ),
fitnessComparatorSetup );
*/
Algorithm::Stubs::GaSimpleGAStub simpleGA( WDID_POPULATION, WDID_POPULATION_STATS,
initializatorSetup,
Population::GaPopulationFitnessOperationSetup( &populationFitnessOperation, NULL, &Fitness::GaFitnessOperationConfig() ),
fitnessComparatorSetup,
Population::GaPopulationParams( 32, 0, Population::GaPopulationParams::GAPFO_FILL_ON_INIT ),
trackers,
Chromosome::GaMatingSetup(),
selectionSetup,
Population::GaCouplingSetup(),
replacementSetup,
scalingSetup,
Population::GaFitnessComparatorSortingCriteria( fitnessComparatorSetup, Population::GaChromosomeStorage::GAFT_RAW ) );
/*
Common::Workflows::GaWorkflow workflow( NULL );
Common::Workflows::GaDataStorage* storage = workflow.GetWorkflowData();
storage->AddData( new Common::Workflows::GaDataEntry<Population::GaPopulation>( 1, population ), Common::Workflows::GADSL_WORKFLOW );
storage->AddData( new Common::Workflows::GaDataEntry<Statistics::GaStatistics>( 2, Common::Memory::GaAutoPtr<Statistics::GaStatistics>( &population->GetStatistics(),
Common::Memory::GaNoDeletionPolicy<Statistics::GaStatistics>::GetInstance() ) ), Common::Workflows::GADSL_WORKFLOW );
storage->AddData( new Common::Workflows::GaDataEntry<Population::GaChromosomeGroup>( 3, new Population::GaChromosomeGroup( false ) ), Common::Workflows::GADSL_WORKFLOW );
Common::Workflows::GaWorkflowBarrier* br1 = new Common::Workflows::GaWorkflowBarrier();
Common::Workflows::GaWorkflowBarrier* br2 = new Common::Workflows::GaWorkflowBarrier();
Common::Workflows::GaBranchGroup* bg1 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( workflow.GetFirstStep(), br1, 0 );
Common::Workflows::GaBranchGroup* bg2 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( br1, br2, 0 );
Common::Workflows::GaBranchGroup* bg3 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( br2, workflow.GetLastStep(), 0 );
Common::Workflows::GaFlowStep* initStep =
new Common::Workflows::GaSimpleMethodExecStep<Population::GaPopulation, Common::Workflows::GaMethodExecIgnoreBranch<Population::GaPopulation> >(
&Population::GaPopulation::Initialize, storage, 1 );
bg1->GetBranchGroupFlow()->SetFirstStep( initStep );
Common::Workflows::GaFlowStep* sortStep = new Population::GaSortPopulationStep<Population::GaFitnessSortingCriteria>( storage, 1, Population::GaFitnessSortingCriteria( population ) );
Common::Workflows::GaFlowStep* scalingStep = new Population::GaScalingStep(
Population::GaScalingSetup( &scaling, &Population::ScalingOperations::GaScalingFactorParams( 2.0f ), //&Population::ScalingOperations::GaShareFitnessParams( 0.2f, 1.0f, 4 ),
&Population::ScalingOperations::GaShareFitnessScalingConfig( NULL, Chromosome::GaChromosomeComparatorSetup( &chromosomeComparator, NULL, NULL ) ) ), storage, 1 );
Chromosome::GaMatingConfig matingConfiguration(
Chromosome::GaCrossoverSetup( &crossover, &Chromosome::GaCrossoverPointParams( 0.8f, 2, 1 ), NULL ),
Chromosome::GaMutationSetup( &mutation, &Chromosome::GaMutationSizeParams( 0.3f, true, 2L ), NULL ) );
Common::Workflows::GaFlowStep* selectionStep = new Population::GaSelectionStep(
Population::GaSelectionSetup( &selection, &Population::SelectionOperations::GaDuplicatesSelectionParams( 8, 1, 2 ),
&Population::GaCouplingConfig( Chromosome::GaMatingSetup( &mating, NULL, &matingConfiguration ) ) ), storage, 1, storage, 3 );
Common::Workflows::GaFlowStep* replacementStep = new Population::GaReplacementStep(
Population::GaReplacementSetup( &replacement, &Population::ReplacementOperations::GaRandomReplacementParams( 8, 4, 3 ),
&Population::GaReplacementConfig( Chromosome::GaChromosomeComparatorSetup( &chromosomeComparator, NULL, NULL ) ) ),
storage, 3, storage, 1 );
Common::Workflows::GaFlowStep* nextGenStep = new Common::Workflows::GaSimpleMethodExecStep<Population::GaPopulation>( &Population::GaPopulation::NextGeneration, storage, 1 );
Common::Workflows::GaBranchGroupFlow* flow2 = bg2->GetBranchGroupFlow();
flow2->SetFirstStep( sortStep );
flow2->ConnectSteps( sortStep, scalingStep, 0 );
flow2->ConnectSteps( scalingStep, nextGenStep, 0 );
flow2->ConnectSteps( selectionStep, replacementStep, 0 );
flow2->ConnectSteps( replacementStep, sortStep, 0 );
Fitness::Representation::GaSVFitness<float> targetFitness( 1.0f, Common::Memory::GaSmartPtr<const Fitness::GaFitnessParams>::NullPtr );
Algorithm::StopCriteria::GaStopCriterionStep* stopStep = new Algorithm::StopCriteria::GaStopCriterionStep(
Algorithm::StopCriteria::GaStopCriterionSetup( &stopCriterion,
&Algorithm::StopCriteria::GaStatsCriterionParams<Fitness::GaFitness>(
Population::GADV_BEST_FITNESS, targetFitness, Algorithm::StopCriteria::GAST_STOP_IF_EQUAL_TO,
Algorithm::StopCriteria::GaStatsCriterionComparator<Fitness::GaFitness>( fitnessComparatorSetup ) ), NULL ), storage, 2 );
Common::Workflows::GaBranchGroupTransition* bt32 = new Common::Workflows::GaBranchGroupTransition();
Common::Workflows::GaBranchGroupFlow* flow3 = bg3->GetBranchGroupFlow();
flow3->SetFirstStep( stopStep );
flow3->ConnectSteps( stopStep, bt32, 0 );
workflow.ConnectSteps( bt32, selectionStep, 1 );
population->GetEventManager().AddEventHandler( Population::GaPopulation::GAPE_NEW_GENERATION, &newGenHandler );
workflow.Start();
workflow.Wait();
*/
Common::Workflows::GaWorkflow workflow( NULL );
workflow.RemoveConnection( *workflow.GetFirstStep()->GetOutboundConnections().begin(), true );
Common::Workflows::GaWorkflowBarrier* br1 = new Common::Workflows::GaWorkflowBarrier();
simpleGA.Connect( workflow.GetFirstStep(), br1 );
Common::Workflows::GaBranchGroup* bg1 = (Common::Workflows::GaBranchGroup*)workflow.ConnectSteps( br1, workflow.GetLastStep(), 0 );
Fitness::Representation::GaSVFitness<float> targetFitness( 1.0f, Common::Memory::GaSmartPtr<const Fitness::GaFitnessParams>::NullPtr );
Algorithm::StopCriteria::GaStopCriterionStep* stopStep = new Algorithm::StopCriteria::GaStopCriterionStep(
Algorithm::StopCriteria::GaStopCriterionSetup( &stopCriterion,
&Algorithm::StopCriteria::GaStatsCriterionParams<Fitness::GaFitness>(
Population::GADV_BEST_FITNESS, targetFitness, Algorithm::StopCriteria::GAST_STOP_IF_EQUAL_TO,
Algorithm::StopCriteria::GaStatsCriterionComparator<Fitness::GaFitness>( fitnessComparatorSetup ) ), NULL ), workflow.GetWorkflowData(), WDID_POPULATION_STATS );
Common::Workflows::GaBranchGroupTransition* bt1 = new Common::Workflows::GaBranchGroupTransition();
bg1->GetBranchGroupFlow()->SetFirstStep( stopStep );
bg1->GetBranchGroupFlow()->ConnectSteps( stopStep, bt1, 0 );
workflow.ConnectSteps( bt1, simpleGA.GetStubFlow().GetFirstStep(), 1 );
Common::Workflows::GaDataCache<Population::GaPopulation> population( workflow.GetWorkflowData(), WDID_POPULATION );
population.GetData().GetEventManager().AddEventHandler( Population::GaPopulation::GAPE_NEW_GENERATION, &newGenHandler );
workflow.Start();
workflow.Wait();
}
GaFinalize();
return 0;
}
