public ParameterValue[] CreateIndividual(OriginData matlabOriginData, IEnumerable <MoleculeOntogeny> moleculeOntogenies)
{
var originData = originDataFrom(matlabOriginData);
var individual = _individualFactory.CreateAndOptimizeFor(originData);
var individualProperties = _individualPropertiesMapper.MapFrom(individual);
var allIndividualParameters = individualProperties.ParameterValues.ToList();
allIndividualParameters.AddRange(_ontogenyFactorsRetriever.FactorsFor(originData, moleculeOntogenies));
return(allIndividualParameters.ToArray());
}
public Individual CreateBaseIndividualForPopulation(Individual originalIndividual)
{
//we need to create a new individual WITHOUT CKD and set all percentiles as in the original individuals. Other parameters, value wil be taken as is
var originData = originalIndividual.OriginData.Clone();
//remove the disease state to create a healthy Individual
originData.DiseaseState = null;
var healthyIndividual = _individualFactory.CreateAndOptimizeFor(originData, originalIndividual.Seed);
var allCKDParameters = parametersChangedByCKDAlgorithmAsList(healthyIndividual);
//Make sure we update the flags that might not be set coming from the database
allCKDParameters.Each(x => x.IsChangedByCreateIndividual = true);
//do not update parameters changed by CKD algorithm or that are not visible
var allHealthyParameters = _containerTask.CacheAllChildrenSatisfying <IParameter>(healthyIndividual, x => !allCKDParameters.Contains(x) && x.Visible);
var allOriginalParameters = _containerTask.CacheAllChildren <IParameter>(originalIndividual);
_parameterSetUpdater.UpdateValues(allOriginalParameters, allHealthyParameters);
//we have a healthy individuals based on the CKD individual where all changes were all manual changes were accounted for
//we now need to add the disease state contributions from the original individual
originData.DiseaseState = originalIndividual.OriginData.DiseaseState;
originalIndividual.OriginData.DiseaseStateParameters.Each(x => originData.AddDiseaseStateParameter(x.Clone()));
return(healthyIndividual);
}
private Individual createIndividual()
{
var originData = new OriginData
{
Species = CoreConstants.Species.HUMAN,
Population = CoreConstants.Population.ICRP,
Age = new Parameter
{
Value = 30,
Unit = "year(s)",
},
Weight = new Parameter
{
Value = 75,
Unit = "kg",
},
Height = new Parameter
{
Value = 175,
Unit = "cm",
},
Gender = CoreConstants.Gender.MALE
};
var modelOriginData = _originDataMapper.MapToModel(originData, new SnapshotContext()).Result;
var individual = _individualFactory.CreateAndOptimizeFor(modelOriginData);
return(individual);
}
public Model.Individual MapFrom(Individual batchIndividual)
{
var batchOriginData = new OriginData
{
Species = batchIndividual.Species,
Population = batchIndividual.Population,
Gender = batchIndividual.Gender,
Age = batchIndividual.Age.GetValueOrDefault(double.NaN),
Height = batchIndividual.Height.GetValueOrDefault(double.NaN),
Weight = batchIndividual.Weight.GetValueOrDefault(double.NaN),
GestationalAge = batchIndividual.GestationalAge.GetValueOrDefault(double.NaN),
};
var originData = _originDataMapper.MapFrom(batchOriginData);
var individual = _individualFactory.CreateAndOptimizeFor(originData, batchIndividual.Seed).WithName("Individual");
batchIndividual.Enzymes.Each(enzyme => addMoleculeTo <IndividualEnzyme>(individual, enzyme));
batchIndividual.OtherProteins.Each(otherProtein => addMoleculeTo <IndividualOtherProtein>(individual, otherProtein));
batchIndividual.Transporters.Each(transporter =>
{
var individualTransporter = addMoleculeTo <IndividualTransporter>(individual, transporter);
individualTransporter.TransportType = EnumHelper.ParseValue <TransportType>(transporter.TransportType);
_batchLogger.AddDebug($"Transport type for transporter '{individualTransporter.Name}' is {individualTransporter.TransportType}");
});
return(individual);
}
private void updateLiverStructure(Individual individual)
{
var templateIndividual = _individualFactory.CreateAndOptimizeFor(individual.OriginData);
var originalLiver = liverIn(individual);
var newLiver = _cloner.Clone(liverIn(templateIndividual));
individual.Organism.RemoveChild(originalLiver);
individual.Organism.Add(newLiver);
updateContainerParameterValues(originalLiver, newLiver);
addMissingNeighborhoods(individual, templateIndividual);
removeOldNeighbhorhoods(individual);
}
public override async Task <ModelIndividual> MapToModel(SnapshotIndividual individualSnapshot)
{
var originData = await _originDataMapper.MapToModel(individualSnapshot.OriginData);
var individual = _individualFactory.CreateAndOptimizeFor(originData, individualSnapshot.Seed);
MapSnapshotPropertiesToModel(individualSnapshot, individual);
await updateIndividualParameters(individualSnapshot, individual);
var molecules = await _moleculeMapper.MapToModels(individualSnapshot.Molecules, individual);
molecules?.Each(individual.AddMolecule);
return(individual);
}
public override async Task <ModelIndividual> MapToModel(SnapshotIndividual individualSnapshot, SnapshotContext snapshotContext)
{
var originData = await _originDataMapper.MapToModel(individualSnapshot.OriginData, snapshotContext);
var individual = _individualFactory.CreateAndOptimizeFor(originData, individualSnapshot.Seed);
MapSnapshotPropertiesToModel(individualSnapshot, individual);
await updateIndividualParameters(individualSnapshot, individual, snapshotContext);
if (snapshotContext.IsV10FormatOrEarlier)
{
await convertMoleculesToExpressionProfiles(individualSnapshot, snapshotContext);
}
individualSnapshot.ExpressionProfiles?.Each(x =>
{
var expressionProfile = snapshotContext.Project.BuildingBlockByName <Model.ExpressionProfile>(x);
_moleculeExpressionTask.AddExpressionProfile(individual, expressionProfile);
});
individual.Icon = individual.Species.Icon;
return(individual);
}
public PKSim.Core.Model.Individual MapFrom(IndividualSettingsDTO individualSettingsDTO)
{
return(_individualFactory.CreateAndOptimizeFor(_mapper.MapFrom(individualSettingsDTO)));
}
public Individual MapFrom(IndividualSettingsDTO individualSettingsDTO)
{
return(_individualFactory.CreateAndOptimizeFor(_originDataMapper.MapFrom(individualSettingsDTO)));
}
