public Individual CreateAndOptimizeFor(OriginData originData, int?seed = null)
{
var individual = CreateStandardFor(originData);
if (seed.HasValue)
{
individual.Seed = seed.Value;
}
//this creates a healthy individual
_createIndividualAlgorithm.Optimize(individual);
//Apply disease states if required
var diseaseStateImplementation = _diseaseStateImplementationFactory.CreateFor(individual);
diseaseStateImplementation.ApplyTo(individual);
validate(individual);
return(individual);
}
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);
var diseaseStateImplementation = _diseaseStateImplementationFactory.CreateFor(populationSettings.BaseIndividual);
//the base individual is used to retrieve the default values.
var baseIndividual = diseaseStateImplementation.CreateBaseIndividualForPopulation(populationSettings.BaseIndividual);
//current individual defined as a clone of the based individual. The current individual will be the one varying
var currentIndividual = _cloner.Clone(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 allCurrentIndividualParameters = currentIndividual.GetAllChildren <IParameter>();
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, baseIndividual, currentIndividual, allDistributedParameters, allBaseDistributedParameters, currentGender, randomPopulation.RandomGenerator);
var success = tryRandomize(currentIndividual, populationSettings, allCurrentIndividualParameters, randomPopulation.RandomGenerator);
if (!success)
{
continue;
}
success = diseaseStateImplementation.ApplyForPopulationTo(currentIndividual);
if (!success)
{
continue;
}
randomPopulation.AddIndividualValues(_individualValuesMapper.MapFrom(currentIndividual, allChangedByCreatedIndividualParameters));
diseaseStateImplementation.ResetParametersAfterPopulationIteration(currentIndividual);
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));
}
private void updateMoleculeParametersForDiseaseState(ISimulationSubject simulationSubject, IndividualMolecule moleculeInIndividual)
{
var diseaseStateImplementation = _diseaseStateImplementationFactory.CreateFor(simulationSubject.Individual);
diseaseStateImplementation.ApplyTo(moleculeInIndividual);
}