public void should_return_the_expected_path_values()
{
var sut = new PopulationSimulationPKAnalyses();
sut.AddPKAnalysis(createPKAnalyses("Path1"));
sut.AddPKAnalysis(createPKAnalyses("Path2"));
sut.AllQuantityPaths.ShouldOnlyContain("Path1", "Path2");
}
protected override void Context()
{
base.Context();
_quantityPKParameter1 = new QuantityPKParameter {
QuantityPath = "Path1", Name = "AUC"
};
_quantityPKParameter2 = new QuantityPKParameter {
QuantityPath = "Path1", Name = "C_max"
};
_pop_pk = new PopulationSimulationPKAnalyses();
_pop_pk.AddPKAnalysis(_quantityPKParameter1);
_pop_pk.AddPKAnalysis(_quantityPKParameter2);
}
private void addPKParametersForOutput(ISimulation simulation, int numberOfIndividuals, SimulationResults runResults, Action <int> performIndividualScalingAction,
QuantitySelection selectedQuantity, PopulationSimulationPKAnalyses popAnalyses, string moleculeName,
PKCalculationOptions pkCalculationOptions, IReadOnlyList <PKCalculationOptionsFactory.ApplicationParameters> allApplicationParameters)
{
var availablePKParameters = _pkParameterRepository.All().Where(p => PKParameterCanBeUsed(p, pkCalculationOptions)).ToList();
//create pk parameter for each quantities
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = new QuantityPKParameter {
Name = pkParameter.Name, QuantityPath = selectedQuantity.Path, Dimension = pkParameter.Dimension
};
quantityPKParameter.SetNumberOfIndividuals(numberOfIndividuals);
popAnalyses.AddPKAnalysis(quantityPKParameter);
}
//add the values for each individual
foreach (var individualResult in runResults.AllIndividualResults)
{
performIndividualScalingAction(individualResult.IndividualId);
_pkCalculationOptionsFactory.UpdateAppliedDose(simulation, moleculeName, pkCalculationOptions, allApplicationParameters);
var values = individualResult.ValuesFor(selectedQuantity.Path);
var pkValues = _pkValuesCalculator.CalculatePK(individualResult.Time.Values, values.Values, pkCalculationOptions);
foreach (var pkParameter in availablePKParameters)
{
var quantityPKParameter = popAnalyses.PKParameterFor(selectedQuantity.Path, pkParameter.Name);
quantityPKParameter.SetValue(individualResult.IndividualId, pkValues.ValueOrDefaultFor(pkParameter.Name));
}
}
}
protected override void Context()
{
base.Context();
var pKAnalyses = new PopulationSimulationPKAnalyses();
_populationSimulation = new PopulationSimulation {
PKAnalyses = pKAnalyses
};
var pkParameter = new QuantityPKParameter {
QuantityPath = "Liver", Name = "P"
};
var dimension = A.Fake <IDimension>();
var unit = A.Fake <Unit>();
A.CallTo(() => unit.Name).Returns("UNIT");
A.CallTo(() => _displayUnitRetriever.PreferredUnitFor(pkParameter, null)).Returns(unit);
pkParameter.Dimension = dimension;
pkParameter.SetNumberOfIndividuals(2);
pkParameter.SetValue(0, 10);
pkParameter.SetValue(1, 11);
A.CallTo(() => dimension.BaseUnitValueToUnitValue(unit, 10)).Returns(100.10);
A.CallTo(() => dimension.BaseUnitValueToUnitValue(unit, 11)).Returns(110.20);
pKAnalyses.AddPKAnalysis(pkParameter);
}
protected override void Context()
{
base.Context();
_pkAnalysis = new PopulationSimulationPKAnalyses();
_populationSimulation = A.Fake <IModelCoreSimulation>();
var quantityPKParameter = new QuantityPKParameter {
QuantityPath = "Liver", Name = "P"
};
var pkParameter = new PKParameter {
DisplayUnit = "UNIT", Name = "P"
};
A.CallTo(() => _pkParameterRepository.FindByName(quantityPKParameter.Name)).Returns(pkParameter);
var mergedDimension = A.Fake <IDimension>();
quantityPKParameter.SetValue(0, 10);
quantityPKParameter.SetValue(1, 11);
A.CallTo(() => _dimensionFactory.MergedDimensionFor(A <QuantityPKParameterContext> ._))
.WhenArgumentsMatch(x => x.Get <QuantityPKParameterContext>(0).QuantityPKParameter == quantityPKParameter)
.Returns(mergedDimension);
var unit = A.Fake <Unit>();
A.CallTo(() => unit.Name).Returns(pkParameter.DisplayUnit);
A.CallTo(() => mergedDimension.UnitOrDefault(pkParameter.DisplayUnit)).Returns(unit);
A.CallTo(() => mergedDimension.BaseUnitValueToUnitValue(unit, 10)).Returns(100.10f);
A.CallTo(() => mergedDimension.BaseUnitValueToUnitValue(unit, 11)).Returns(110.20f);
_pkAnalysis.AddPKAnalysis(quantityPKParameter);
}
public void TestSerializationPopulationSimulationPKAnalyses()
{
var x1 = new PopulationSimulationPKAnalyses();
x1.AddPKAnalysis(createPKAnalyses("Path1"));
x1.AddPKAnalysis(createPKAnalyses("Path2"));
x1.AddPKAnalysis(createPKAnalyses("Path3"));
x1.AddPKAnalysis(createPKAnalyses("Path4"));
x1.AddPKAnalysis(createPKAnalyses("Path5"));
var x2 = SerializeAndDeserialize(x1);
x2.ShouldNotBeNull();
x2.All().Count().ShouldBeEqualTo(5);
x2.PKParameterFor("Path1", "AUC").Count.ShouldBeEqualTo(_numberOfIndividuals);
}
public PopulationSimulationPKAnalyses ImportPKAnalysesFromCSV(string fileName, IModelCoreSimulation simulation)
{
var pkSimulationImport = _simulationPKParametersImportTask.ImportPKParameters(fileName, simulation, CancellationToken.None).Result;
pkSimulationImport.ThrowOnError();
_logger.Log(pkSimulationImport);
var simulationPKAnalyses = new PopulationSimulationPKAnalyses();
pkSimulationImport.PKParameters.Each(x => simulationPKAnalyses.AddPKAnalysis(x));
return(simulationPKAnalyses);
}
public void Visit(PopulationSimulationPKAnalyses populationSimulationPKAnalyses)
{
var allQuantityPKAnalysis = populationSimulationPKAnalyses.All().ToList();
populationSimulationPKAnalyses.Clear();
allQuantityPKAnalysis.Each(x =>
{
x.Name = ConvertPKParameterName(x.Name);
populationSimulationPKAnalyses.AddPKAnalysis(x);
});
_converted = true;
}
private void addPKParametersForOutput(
IModelCoreSimulation simulation,
SimulationResults simulationResults,
Action <int> performIndividualScalingAction,
QuantitySelection selectedQuantity,
PopulationSimulationPKAnalyses popAnalyses,
string moleculeName,
PKCalculationOptions pkCalculationOptions,
IReadOnlyList <ApplicationParameters> allApplicationParameters)
{
var allPKParameters = _pkParameterRepository.All().Where(p => PKParameterCanBeUsed(p, pkCalculationOptions)).ToList();
var allUserDefinedPKParameters = allPKParameters.OfType <UserDefinedPKParameter>().ToList();
//create pk parameter for each pk parameters (predefined and dynamic)
foreach (var pkParameter in allPKParameters)
{
var quantityPKParameter = new QuantityPKParameter {
Name = pkParameter.Name, QuantityPath = selectedQuantity.Path, Dimension = pkParameter.Dimension
};
popAnalyses.AddPKAnalysis(quantityPKParameter);
}
//add the values for each individual
foreach (var individualResult in simulationResults.AllIndividualResults)
{
performIndividualScalingAction(individualResult.IndividualId);
_pkCalculationOptionsFactory.UpdateTotalDrugMassPerBodyWeight(simulation, moleculeName, pkCalculationOptions, allApplicationParameters);
var values = individualResult.QuantityValuesFor(selectedQuantity.Path);
//This can happen is the results do not match the simulation
if (values == null)
{
continue;
}
var pkValues = _pkValuesCalculator.CalculatePK(individualResult.Time.Values, values.Values, pkCalculationOptions, allUserDefinedPKParameters);
foreach (var quantityPKParameter in popAnalyses.AllPKParametersFor(selectedQuantity.Path))
{
quantityPKParameter.SetValue(individualResult.IndividualId, pkValues.ValueOrDefaultFor(quantityPKParameter.Name));
}
}
}