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);
}
protected override void Context()
{
base.Context();
_numberOfVariations = 5;
_pkParameter1 = new QuantityPKParameter {
QuantityPath = "Output1", Name = "AUC"
};
_pkParameter1.SetNumberOfIndividuals(_numberOfVariations);
_pkParameter1.SetValue(0, 10);
_pkParameter1.SetValue(1, 11);
_pkParameter1.SetValue(2, 12);
_pkParameter1.SetValue(4, _defaultPK1Value);
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Output2", Name = "Cmax"
};
_pkParameter2.SetNumberOfIndividuals(_numberOfVariations);
_pkParameter2.SetValue(0, 20);
_pkParameter2.SetValue(1, 21);
_pkParameter2.SetValue(2, 22);
_pkParameter2.SetValue(3, 23);
_pkParameter2.SetValue(4, _defaultPK2Value);
_sensitivityParameter1 = A.Fake <SensitivityParameter>().WithName("SP1");
A.CallTo(() => _sensitivityParameter1.DefaultValue).Returns(10);
_sensitivityParameter2 = A.Fake <SensitivityParameter>().WithName("SP2");
A.CallTo(() => _sensitivityParameter2.DefaultValue).Returns(20);
_sensitivityParameter3 = A.Fake <SensitivityParameter>().WithName("SP3");
A.CallTo(() => _sensitivityParameter3.DefaultValue).Returns(0);
A.CallTo(() => _sensitivityParameter3.VariationRangeValue).Returns(0.8);
_pkAnalyses.AddPKAnalysis(_pkParameter1);
_pkAnalyses.AddPKAnalysis(_pkParameter2);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter2);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter3);
var pv11 = new ParameterVariation {
ParameterName = _sensitivityParameter1.Name, VariationId = 0, Variation = new[] { 15d, 200d, 300d }
};
var pv12 = new ParameterVariation {
ParameterName = _sensitivityParameter1.Name, VariationId = 1, Variation = new[] { 20d, 200d, 300d }
};
var pv21 = new ParameterVariation {
ParameterName = _sensitivityParameter2.Name, VariationId = 2, Variation = new[] { 100d, 21d, 300d }
};
var pv22 = new ParameterVariation {
ParameterName = _sensitivityParameter2.Name, VariationId = 3, Variation = new[] { 100d, 31d, 300d }
};
_variationData.DefaultValues = new[] { 100d, 200d, 300d };
_variationData.AddVariation(pv11);
_variationData.AddVariation(pv12);
_variationData.AddVariation(pv21);
_variationData.AddVariation(pv22);
}
public void TestSerialization()
{
var x1 = new QuantityPKParameter
{
Name = "C_max",
Dimension = DimensionMassConcentration,
QuantityPath = "A|B|C"
};
x1.SetValue(1, 5.0f);
x1.SetValue(2, 4.0f);
x1.SetValue(8, 2.0f);
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualQuantity(x2, x1);
}
private QuantityPKParameter createPKAnalyses(string path)
{
var pk = new QuantityPKParameter {
QuantityPath = path
};
pk.Name = "AUC";
for (int i = 0; i < _numberOfIndividuals; i++)
{
pk.SetValue(i, (float)_random.NextDouble() * 100);
}
return(pk);
}
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));
}
}
}
protected override void Context()
{
base.Context();
_pkParameter1 = new QuantityPKParameter {
QuantityPath = "Output1", Name = "AUC"
};
_pkParameter1.SetValue(0, 10);
_pkParameter1.SetValue(1, 11);
_pkParameter1.SetValue(2, 12);
_pkParameter1.SetValue(4, _defaultPK1Value);
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Output2", Name = "Cmax"
};
_pkParameter2.SetValue(0, 20);
_pkParameter2.SetValue(1, 21);
_pkParameter2.SetValue(2, 22);
_pkParameter2.SetValue(3, 23);
_pkParameter2.SetValue(4, _defaultPK2Value);
_pkAnalyses.AddPKAnalysis(_pkParameter1);
_pkAnalyses.AddPKAnalysis(_pkParameter2);
_sensitivityParameter1 = A.Fake <SensitivityParameter>().WithName("SP1");
A.CallTo(() => _sensitivityParameter1.DefaultValue).Returns(10);
A.CallTo(() => _sensitivityParameter1.ParameterSelection.Path).Returns("SP1-PATH");
_sensitivityParameter2 = A.Fake <SensitivityParameter>().WithName("SP2");
A.CallTo(() => _sensitivityParameter2.DefaultValue).Returns(20);
A.CallTo(() => _sensitivityParameter2.ParameterSelection.Path).Returns("SP2-PATH");
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter2);
var pv11 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 0, variation: new[] { 15d, 200d, 300d });
var pv12 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 1, variation: new[] { 20d, 200d, 300d });
var pv21 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 2, variation: new[] { 100d, 21d, 300d });
var pv22 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 3, variation: new[] { 100d, 31d, 300d });
_variationData.DefaultValues = new[] { 100d, 200d, 300d };
_variationData.AddVariation(pv11);
_variationData.AddVariation(pv12);
_variationData.AddVariation(pv21);
_variationData.AddVariation(pv22);
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 1, 2, 3, 4, 5f }
};
_resV11 = new IndividualResults {
IndividualId = 0, Time = _timeValues
};
_resV11.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 111.1f, 211.1f, 311.1f, 411.1f, 511.1f }
});
_resV11.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 111.2f, 211.2f, 311.2f, 411.2f, 511.2f }
});
_resV11.UpdateQuantityTimeReference();
_resV12 = new IndividualResults {
IndividualId = 1, Time = _timeValues
};
_resV12.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 112.1f, 212.1f, 312.1f, 412.1f, 512.1f }
});
_resV12.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 112.2f, 212.2f, 312.2f, 412.2f, 512.2f }
});
_resV12.UpdateQuantityTimeReference();
_resV21 = new IndividualResults {
IndividualId = 2, Time = _timeValues
};
_resV21.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 121.1f, 221.1f, 321.1f, 421.1f, 521.1f }
});
_resV21.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 121.2f, 221.2f, 321.2f, 421.2f, 521.2f }
});
_resV21.UpdateQuantityTimeReference();
_resV22 = new IndividualResults {
IndividualId = 3, Time = _timeValues
};
_resV22.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 122.1f, 222.1f, 322.1f, 422.1f, 522.1f }
});
_resV22.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 122.2f, 222.2f, 322.2f, 422.2f, 522.2f }
});
_resV22.UpdateQuantityTimeReference();
_simulationResults.Add(_resV11);
_simulationResults.Add(_resV12);
_simulationResults.Add(_resV21);
_simulationResults.Add(_resV22);
}
