public DistributedParameterValue[] DistributionsFor(OriginData batchOriginData, IEnumerable <MoleculeOntogeny> moleculeOntogenies)
{
var originData = _originDataMapper.MapFrom(batchOriginData);
var individual = _individualFactory.CreateAndOptimizeFor(originData);
return(individual.GetAllChildren <IDistributedParameter>().Select(distributedParameterValueFrom).ToArray());
}
public ParameterValue[] CreateIndividual(OriginData batchOriginData, IEnumerable <MoleculeOntogeny> moleculeOntogenies)
{
var originData = _originDataMapper.MapFrom(batchOriginData);
var individual = _individualFactory.CreateAndOptimizeFor(originData);
var individualProperties = _individualPropertiesMapper.MapFrom(individual);
var allIndividualParameters = individualProperties.ParameterValues.ToList();
allIndividualParameters.AddRange(_ontogenyFactorsRetriever.FactorsFor(originData, moleculeOntogenies));
return(allIndividualParameters.ToArray());
}
protected override void Context()
{
base.Context();
_batchOriginData = new OriginData();
_batchOriginData.Species = CoreConstants.Species.Human;
_batchOriginData.Population = CoreConstants.Population.ICRP;
_batchOriginData.Age = 30;
_batchOriginData.Weight = 75;
_batchOriginData.Height = 17.5;
_batchOriginData.Gender = CoreConstants.Gender.Male;
}
protected override void Context()
{
_speciesRepository = A.Fake <ISpeciesRepository>();
_originDataTask = A.Fake <IOriginDataTask>();
_individualModelTask = A.Fake <IIndividualModelTask>();
_male = new Gender().WithName(CoreConstants.Gender.Male);
_female = new Gender().WithName(CoreConstants.Gender.Female);
_human = new Species().WithName(CoreConstants.Species.Human);
_icrp = new SpeciesPopulation {
IsHeightDependent = true, IsAgeDependent = true
}.WithName(CoreConstants.Population.ICRP);
_anotherPop = new SpeciesPopulation().WithName("Another Pop");
_cmForHuman = new CalculationMethod();
_cmForHuman.AddSpecies(_human.Name);
_icrp.AddGender(_male);
_human.AddPopulation(_icrp);
_category = new CalculationMethodCategory();
_category.Add(_cmForHuman);
A.CallTo(() => _speciesRepository.All()).Returns(new[] { _human });
A.CallTo(() => _originDataTask.AllCalculationMethodCategoryFor(_human)).Returns(new[] { _category });
_batchOriginData = new OriginData();
sut = new OriginDataMapper(_speciesRepository, _originDataTask, _individualModelTask);
}
public Model.OriginData MapFrom(BatchOriginData batchOriginData)
{
var originData = new Model.OriginData();
var species = _speciesRepository.FindByName(batchOriginData.Species);
if (species == null)
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindSpecies(batchOriginData.Species, _speciesRepository.AllNames()));
}
originData.Species = species;
var population = species.PopulationByName(batchOriginData.Population);
if (population == null)
{
if (string.IsNullOrEmpty(batchOriginData.Population) && species.Populations.Count() == 1)
{
population = species.Populations.ElementAt(0);
}
else
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindPopulationForSpecies(batchOriginData.Population, batchOriginData.Species, species.Populations.AllNames()));
}
}
originData.SpeciesPopulation = population;
var gender = population.GenderByName(batchOriginData.Gender);
if (gender == null)
{
if (string.IsNullOrEmpty(batchOriginData.Gender))
{
gender = population.Genders.ElementAt(0);
}
else
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindGenderForPopulation(batchOriginData.Gender, batchOriginData.Population, population.Genders.AllNames()));
}
}
originData.Gender = gender;
//this is not defined in matlab yet
originData.SubPopulation = _originDataTask.DefaultSubPopulationFor(species);
if (originData.SpeciesPopulation.IsAgeDependent)
{
originData.Age = batchOriginData.Age;
var meanAgeParameter = _individualModelTask.MeanAgeFor(originData);
originData.Age = valueFrom(batchOriginData.Age, meanAgeParameter.Value);
originData.AgeUnit = meanAgeParameter.Dimension.BaseUnit.Name;
originData.GestationalAge = valueFrom(batchOriginData.GestationalAge, CoreConstants.NOT_PRETERM_GESTATIONAL_AGE_IN_WEEKS);
originData.GestationalAgeUnit = CoreConstants.Units.Weeks;
}
var calculationMethodCategoryForSpecies = _originDataTask.AllCalculationMethodCategoryFor(species);
foreach (var category in calculationMethodCategoryForSpecies)
{
string selectedCalculationMethod = batchOriginData.CalculationMethodFor(category.Name);
if (string.IsNullOrEmpty(selectedCalculationMethod))
{
originData.AddCalculationMethod(category.DefaultItemForSpecies(species));
}
else
{
var calculationMethod = category.AllItems().FindByName(selectedCalculationMethod);
if (calculationMethod == null)
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindCalculationMethodInCategory(selectedCalculationMethod, category.Name, category.AllItems().AllNames()));
}
if (calculationMethod.AllSpecies.Contains(species.Name))
{
originData.AddCalculationMethod(calculationMethod);
}
else
{
throw new PKSimException(PKSimConstants.Error.CalculationMethodIsNotDefinedForSpecies(selectedCalculationMethod, category.Name, species.Name));
}
}
}
var meanWeightParameter = _individualModelTask.MeanWeightFor(originData);
originData.Weight = valueFrom(batchOriginData.Weight, meanWeightParameter.Value).Value;
originData.WeightUnit = meanWeightParameter.Dimension.BaseUnit.Name;
if (originData.SpeciesPopulation.IsHeightDependent)
{
var meanHeightParameter = _individualModelTask.MeanHeightFor(originData);
originData.Height = valueFrom(batchOriginData.Height, meanHeightParameter.Value);
originData.HeightUnit = meanHeightParameter.Dimension.BaseUnit.Name;
}
return(originData);
}
