public IParameterValueCache CreatePopulation(PopulationSettings matlabPopulationSettings, IEnumerable <MoleculeOntogeny> moleculeOntogenies)
{
var populationSettings = _populationSettingsMapper.MapFrom(matlabPopulationSettings);
var population = _randomPopulationFactory.CreateFor(populationSettings, new CancellationToken()).Result;
foreach (var moleculeOntogeny in moleculeOntogenies)
{
var allOntogeniesForSpecies = _ontogenyRepository.AllFor(matlabPopulationSettings.Individual.OriginData.Species).ToList();
if (!allOntogeniesForSpecies.Any())
{
continue;
}
var ontogeny = allOntogeniesForSpecies.FindByName(moleculeOntogeny.Ontogeny);
if (ontogeny == null)
{
continue;
}
var molecule = _individualEnzymeFactory.CreateEmpty().WithName(moleculeOntogeny.Molecule);
molecule.Ontogeny = ontogeny;
population.AddMolecule(molecule);
}
_ontogenyVariabilityUpdater.UpdateAllOntogenies(population);
return(population.IndividualPropertiesCache);
}
public CreatePopulationResults CreatePopulation(PopulationCharacteristics populationCharacteristics)
{
var populationSettings = _populationSettingsMapper.MapToModel(populationCharacteristics, new SnapshotContext()).Result;
validate(populationSettings);
var population = _randomPopulationFactory.CreateFor(populationSettings, new CancellationToken(), seed: populationCharacteristics.Seed).Result;
foreach (var moleculeOntogeny in populationCharacteristics.MoleculeOntogenies)
{
var allOntogeniesForSpecies = _ontogenyRepository.AllFor(populationCharacteristics.Individual.OriginData.Species);
if (!allOntogeniesForSpecies.Any())
{
continue;
}
var ontogeny = allOntogeniesForSpecies.FindByName(moleculeOntogeny.Ontogeny);
if (ontogeny == null)
{
continue;
}
var molecule = _individualEnzymeFactory.CreateEmpty().WithName(moleculeOntogeny.Molecule);
molecule.Ontogeny = ontogeny;
population.AddMolecule(molecule);
}
_ontogenyVariabilityUpdater.UpdateAllOntogenies(population);
return(new CreatePopulationResults(population.IndividualValuesCache, population.Seed));
}
private void addUserDefinedVariabilityAndOntogenyForMolecules(RandomPopulation randomPopulation)
{
_moleculeParameterVariabilityCreator.AddVariabilityTo(randomPopulation);
_moleculeOntogenyVariabilityUpdater.UpdateAllOntogenies(randomPopulation);
}
public Task <RandomPopulation> CreateFor(RandomPopulationSettings populationSettings, CancellationToken cancellationToken, int?seed = null, bool addMoleculeParametersVariability = true)
{
return(Task.Run(() =>
{
using (var progressUpdater = _progressManager.Create())
{
var randomPopulation = createPopulationFor(populationSettings, seed);
fllUpGenderQueueBasedOn(populationSettings);
progressUpdater.Initialize(populationSettings.NumberOfIndividuals, PKSimConstants.UI.CreatingPopulation);
//the base individual is used to retrieve the default values.
var baseIndividual = populationSettings.BaseIndividual;
//current individual defined as a clone of the based individual. The current individual will be the one varying
var currentIndividual = _cloner.Clone(populationSettings.BaseIndividual);
//cache containing all parameters changed by the create individual from the current individual. This will be used just as reference to the current parameters
var allChangedByCreatedIndividualParameters = getAllCreateIndividualParametersFrom(currentIndividual);
//all distributed parameters. This will be used to update the distribution for the current individual
var allDistributedParameters = getAllDistributedParametersFrom(currentIndividual);
var allBaseDistributedParameters = getAllDistributedParametersFrom(baseIndividual);
//all individual parameters. Just an optimization to avoid call GetAllChildren for each individual
var allIndividualParameters = currentIndividual.GetAllChildren <IParameter>().ToList();
int maxTotalIterations = populationSettings.NumberOfIndividuals * _maxIterations;
uint numberOfTry = 0;
var currentGender = _genderQueue.Dequeue();
do
{
cancellationToken.ThrowIfCancellationRequested();
numberOfTry++;
//could not create one item in max Iteration try=>exit
if (numberOfTry > _maxIterations && randomPopulation.NumberOfItems == 0)
{
throw new CannotCreatePopulationWithConstraintsException(_reportGenerator.StringReportFor(populationSettings));
}
//create a new individual based on population settings defined by the user
updateCurrentIndividualFromSettings(populationSettings, currentIndividual, allDistributedParameters, allBaseDistributedParameters, currentGender, randomPopulation.RandomGenerator);
bool success = tryRandomize(currentIndividual, populationSettings, allIndividualParameters, randomPopulation.RandomGenerator);
if (!success)
{
continue;
}
randomPopulation.AddIndividualValues(_individualValuesMapper.MapFrom(currentIndividual, allChangedByCreatedIndividualParameters));
currentGender = _genderQueue.Dequeue();
progressUpdater.IncrementProgress(PKSimConstants.UI.CreatingIndividualInPopulation(randomPopulation.NumberOfItems, populationSettings.NumberOfIndividuals));
} while (randomPopulation.NumberOfItems < populationSettings.NumberOfIndividuals && numberOfTry < maxTotalIterations);
if (numberOfTry >= maxTotalIterations)
{
throw new CannotCreatePopulationWithConstraintsException(_reportGenerator.StringReportFor(populationSettings));
}
if (addMoleculeParametersVariability)
{
_moleculeParameterVariabilityCreator.AddVariabilityTo(randomPopulation);
}
_moleculeOntogenyVariabilityUpdater.UpdateAllOntogenies(randomPopulation);
randomPopulation.IsLoaded = true;
return randomPopulation;
}
}, cancellationToken));
}