protected override Task Context()
{
_advancedParameterMapper = A.Fake <AdvancedParameterMapper>();
_randomPopulationFactory = A.Fake <IRandomPopulationFactory>();
_randomPopulationSettingsMapper = A.Fake <RandomPopulationSettingsMapper>();
sut = new PopulationMapper(_advancedParameterMapper, _randomPopulationSettingsMapper, _randomPopulationFactory);
_advancedParameters = new AdvancedParameterCollection();
_advancedParameter = new AdvancedParameter
{
DistributedParameter = DomainHelperForSpecs.NormalDistributedParameter()
};
_advancedParameters.AddAdvancedParameter(_advancedParameter);
_advancedParameterSnapshot = new Snapshots.AdvancedParameter();
A.CallTo(() => _advancedParameterMapper.MapToSnapshot(_advancedParameter)).Returns(_advancedParameterSnapshot);
_population = CreateRandomPopulation();
_settingsSnapshot = new PopulationSettings();
A.CallTo(() => _randomPopulationSettingsMapper.MapToSnapshot(_population.Settings)).Returns(_settingsSnapshot);
return(Task.FromResult(true));
}
public RandomPopulationSettings MapFrom(PopulationSettings batchPopulationSettings)
{
var originData = originDataFrom(batchPopulationSettings);
var individual = _individualFactory.CreateStandardFor(originData);
var populationSettings = _individualToPopulationSettingsMapper.MapFrom(individual);
populationSettings.NumberOfIndividuals = batchPopulationSettings.NumberOfIndividuals;
setRange(populationSettings, CoreConstants.Parameter.AGE, batchPopulationSettings.MinAge, batchPopulationSettings.MaxAge);
setRange(populationSettings, CoreConstants.Parameter.MEAN_HEIGHT, batchPopulationSettings.MinHeight, batchPopulationSettings.MaxHeight);
setRange(populationSettings, CoreConstants.Parameter.MEAN_WEIGHT, batchPopulationSettings.MinWeight, batchPopulationSettings.MaxWeight);
setRange(populationSettings, CoreConstants.Parameter.BMI, batchPopulationSettings.MinBMI, batchPopulationSettings.MaxBMI);
if (populationSettings.ContainsParameterRangeFor(CoreConstants.Parameter.GESTATIONAL_AGE))
{
setRange(populationSettings, CoreConstants.Parameter.GESTATIONAL_AGE, batchPopulationSettings.MinGestationalAge, batchPopulationSettings.MaxGestationalAge);
}
//in case of multiple gender, adjust the ration according to the feamales proportion
if (individual.AvailableGenders().Count() > 1)
{
populationSettings.GenderRatio(_genderRepository.Female).Ratio = batchPopulationSettings.ProportionOfFemales;
populationSettings.GenderRatio(_genderRepository.Male).Ratio = 100 - batchPopulationSettings.ProportionOfFemales;
}
return(populationSettings);
}
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 IParameterValueCache CreatePopulation(PopulationSettings matlabPopulationSettings, IEnumerable <string> moleculeNames)
{
var populationSettings = _populationSettingsMapper.MapFrom(matlabPopulationSettings);
var population = _randomPopulationFactory.CreateFor(populationSettings, new CancellationToken()).Result;
return(population.IndividualPropertiesCache);
}
protected override void Context()
{
base.Context();
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.ICRP,
};
originData.AddCalculationMethods("SurfaceAreaPlsInt_VAR1");
_settings = new PopulationSettings
{
Individual = new Individual
{
OriginData = originData
},
Age = new ParameterRange
{
Min = 0,
Max = 80,
Unit = "year(s)",
},
Weight = new ParameterRange
{
Min = 70,
Unit = "kg",
},
NumberOfIndividuals = 10,
ProportionOfFemales = 70
};
_moleculeOntogenies = new [] { new MoleculeOntogeny("CYP3A4", "CYP3A4"), new MoleculeOntogeny("CYP2D6", "CYP2D6") };
}
private Model.OriginData originDataFrom(PopulationSettings batchPopulationSettings)
{
//create default individual based on given data
var batchOriginData = new OriginData
{
Species = batchPopulationSettings.Species,
Population = batchPopulationSettings.Population
};
batchPopulationSettings.AllCalculationMethods.KeyValues.Each(kv => batchOriginData.AddCalculationMethod(kv.Key, kv.Value));
return(_originDataMapper.MapFrom(batchOriginData));
}
protected override void Context()
{
base.Context();
_settings = new PopulationSettings
{
Species = CoreConstants.Species.Human,
Population = CoreConstants.Population.ICRP,
MinAge = 0,
MaxAge = 80,
MinWeight = 70,
NumberOfIndividuals = 10,
ProportionOfFemales = 70
};
_settings.AddCalculationMethod("SurfaceAreaPlsInt", "SurfaceAreaPlsInt_VAR1");
}
public GeneticSimulator(PopulationSettings populationSettings, ScoreSettings scoreSettings, GameSettings gameSettings)
{
var gameFactory = CreateGameFactory(gameSettings, scoreSettings, UpdateGameBoardAsync);
var offspringGameFactory = CreateGameFactory(gameSettings, scoreSettings, null);
_populationFitnessFunction = new SnakeGameFitnessFunction(gameFactory);
_offspringFitnessFunction = new SnakeGameFitnessFunction(offspringGameFactory);
_population = new Population
(
populationSettings,
new PointBasedCrossoverOperator(),
new SoftmaxSelectionOperator(),
new MutationOperator(),
() => (Individual)gameFactory.CreatePlayer()
);
_population.GenerationCompleted += OnGenerationFinished;
_tokenSource = new CancellationTokenSource();
}
protected override void Context()
{
base.Context();
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.PRETERM,
};
originData.AddCalculationMethods("SurfaceAreaPlsInt_VAR1");
_settings = new PopulationSettings
{
Individual = new Individual
{
OriginData = originData
},
Age = new ParameterRange
{
Min = 0,
Max = 80,
Unit = "year(s)",
},
Weight = new ParameterRange
{
Min = 70,
Unit = "kg",
},
GestationalAge = new ParameterRange
{
Min = 30,
Max = 35,
Unit = "week(s)",
},
NumberOfIndividuals = 10,
ProportionOfFemales = 70
};
}
