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);
}
protected override void Context()
{
base.Context();
sut.PKAnalyses = A.Fake <PopulationSimulationPKAnalyses>();
_pkParameter = A.Fake <QuantityPKParameter>();
A.CallTo(() => _pkParameter.Values).Returns(new[] { 1f, 2, 3 });
A.CallTo(() => sut.PKAnalyses.PKParameterFor("Path", "Cmax")).Returns(_pkParameter);
}
protected override void Context()
{
base.Context();
_pkParameter = new QuantityPKParameter {
QuantityPath = "Path", Name = "toto"
};
A.CallTo(() => _pkParameterRepository.DisplayNameFor(_pkParameter.Name)).Returns("totoDisplay");
}
protected override void Context()
{
base.Context();
_pkParameter = new QuantityPKParameter();
_populationPivotAnalysis = new PopulationPivotAnalysis();
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_field = A.Fake <PopulationAnalysisPKParameterField>();
sut.StartAnalysis(_populationDataCollector, _populationPivotAnalysis);
}
private void validateLength(PopulationSimulation populationSimulation, QuantityPKParameter pkParameter, SimulationPKParametersImport importedPKParameter)
{
if (pkParameter.Count == populationSimulation.NumberOfItems)
{
return;
}
importedPKParameter.AddError(PKSimConstants.Error.NotEnoughPKValuesForParameter(pkParameter.Name, pkParameter.QuantityPath, populationSimulation.NumberOfItems, pkParameter.Count));
}
protected override async Task Context()
{
await base.Context();
_importedPKParameter = A.Fake <QuantityPKParameter>();
_importedPKParameter.QuantityPath = "Quantity";
A.CallTo(() => _importedPKParameter.Count).Returns(10);
A.CallTo(() => _populationSimulation.NumberOfItems).Returns(15);
_importedPKParameters.Add(_importedPKParameter);
}
protected override void Context()
{
base.Context();
_importedPKParameter = A.Fake <QuantityPKParameter>();
_importedPKParameter.QuantityPath = "Quantity";
_availableQuantities[_importedPKParameter.QuantityPath] = new Observer();
A.CallTo(() => _importedPKParameter.Count).Returns(10);
A.CallTo(() => _populationSimulation.NumberOfItems).Returns(15);
_importedPKParameters.Add(_importedPKParameter);
}
private QuantityPKParameterDTO mapFrom(QuantityPKParameter quantityPKParameter, string quantityDisplayPath)
{
return(new QuantityPKParameterDTO
{
DisplayName = _pkParameterRepository.DisplayNameFor(quantityPKParameter.Name),
PKParameter = quantityPKParameter,
QuantityDisplayPath = quantityDisplayPath,
Description = _pkParameterRepository.DescriptionFor(quantityPKParameter.Name)
});
}
private PopulationAnalysisPKParameterField createFieldFrom(QuantityPKParameter pkParameter, string quantityDisplayPath)
{
var quantity = _allQuantities[pkParameter.QuantityPath];
if (quantity == null)
{
return(null);
}
return(_populationAnalysisFieldFactory.CreateFor(pkParameter, quantity.QuantityType, quantityDisplayPath));
}
public PopulationAnalysisPKParameterField CreateFor(QuantityPKParameter pkParameter, QuantityType quantityType, string quantityDisplayPath)
{
return(new PopulationAnalysisPKParameterField
{
Name = new[] { quantityDisplayPath, _pkParameterRepository.DisplayNameFor(pkParameter.Name) }.ToPathString(),
QuantityPath = pkParameter.QuantityPath,
QuantityType = quantityType,
PKParameter = pkParameter.Name,
Dimension = pkParameter.Dimension,
});
}
private void addValues(QuantityPKParameter pkParameter, CsvReader csv)
{
if (!_valuesCache.Contains(pkParameter))
{
_valuesCache.Add(pkParameter, new List <Tuple <int, float> >());
}
var coreUnit = convertValueToCoreValue(pkParameter.Dimension, csv.DoubleAt(VALUE), csv[UNIT]);
_valuesCache[pkParameter].Add(new Tuple <int, float>(csv.IntAt(INDIVIDUAL_ID), coreUnit.ToFloat()));
}
protected override void Context()
{
base.Context();
_importedPKParameter = A.Fake <QuantityPKParameter>();
_existingPKParameter = A.Fake <QuantityPKParameter>();
_importedPKParameter.QuantityPath = "Quantity";
_availableQuantities[_importedPKParameter.QuantityPath] = new Observer();
A.CallTo(() => _importedPKParameter.Id).Returns("IMPORTED PARAMETER");
A.CallTo(() => _importedPKParameter.ToString()).Returns(_importedPKParameter.Id);
_importedPKParameters.Add(_importedPKParameter);
A.CallTo(() => _pkAnalyses.PKParameterBy(_importedPKParameter.Id)).Returns(_existingPKParameter);
}
protected override async Task Context()
{
await base.Context();
_importedPKParameter = A.Fake <QuantityPKParameter>();
_existingPKParameter = A.Fake <QuantityPKParameter>();
_importedPKParameter.QuantityPath = "Quantity";
A.CallTo(() => _importedPKParameter.Id).Returns("IMPORTED PARAMETER");
A.CallTo(() => _importedPKParameter.ToString()).Returns(_importedPKParameter.Id);
_importedPKParameters.Add(_importedPKParameter);
A.CallTo(() => _pkAnalyses.PKParameterBy(_importedPKParameter.Id)).Returns(_existingPKParameter);
}
protected override void Context()
{
base.Context();
_context = A.Fake <IExecutionContext>();
_pkParameter1 = A.Fake <QuantityPKParameter>();
A.CallTo(() => _pkParameter1.Id).Returns("Id1");
_pkParameter2 = A.Fake <QuantityPKParameter>();
A.CallTo(() => _pkParameter2.Id).Returns("Id2");
_pkParameters.Add(_pkParameter1);
_pkParameters.Add(_pkParameter2);
_pkAnalysis = new PopulationSimulationPKAnalyses();
_populationSimulation.PKAnalyses = _pkAnalysis;
}
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);
}
protected override void Context()
{
base.Context();
_population = A.Fake <IPopulationDataCollector>();
_pkParameter = new QuantityPKParameter {
Dimension = A.Fake <IDimension>(), Name = "toto", QuantityPath = "A|B|C"
};
A.CallTo(() => _pkParameterRepository.DisplayNameFor(_pkParameter.Name)).Returns("totoDisplay");
_settings = new DistributionSettings();
_displayUnit = A.Fake <Unit>();
_data = new ContinuousDistributionData(AxisCountMode.Count, 10);
A.CallTo(() => _displayUnitRetriever.PreferredUnitFor(_pkParameter.Dimension)).Returns(_displayUnit);
A.CallTo(() => _distributionDataCreator.CreateFor(_population, _settings, _pkParameter, _pkParameter.Dimension, _displayUnit)).Returns(_data);
}
protected override void Context()
{
base.Context();
_displayUnit = A.Fake <Unit>();
_mergedDimension = A.Fake <IDimension>();
_pkParameterDimension = A.Fake <IDimension>();
_pkParameter = new QuantityPKParameter().WithName("AUC").WithDimension(_pkParameterDimension);
_pkParameterField = new PopulationAnalysisPKParameterField().WithDimension(_pkParameterDimension);
_pkParameterField.DisplayUnit = _displayUnit;
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <NumericFieldContext> ._))
.Invokes(x => _numericFieldContect = x.GetArgument <NumericFieldContext>(0))
.Returns(_mergedDimension);
}
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);
}
protected override void Context()
{
base.Context();
_populationSimulation = A.Fake <PopulationSimulation>();
_pkParameter1 = new QuantityPKParameter();
_pkParameter2 = new QuantityPKParameter();
_pkAnalyses = new List <QuantityPKParameter> {
_pkParameter1, _pkParameter2
};
_importSimulationResultsPresenter = A.Fake <IImportSimulationPKAnalysesPresenter>();
A.CallTo(() => _applicationController.Start <IImportSimulationPKAnalysesPresenter>()).Returns(_importSimulationResultsPresenter);
A.CallTo(() => _importSimulationResultsPresenter.ImportPKAnalyses(_populationSimulation)).Returns(_pkAnalyses);
A.CallTo(() => _buildingBlockTask.AddCommandToHistory(A <IPKSimCommand> ._))
.Invokes(x => _command = x.GetArgument <IPKSimCommand>(0));
}
private QuantityPKParameter retrieveOrCreatePKParameterFor(CsvReader csv)
{
var parameterName = csv[PARAMETER_NAME];
var quantityPath = csv[QUANTITY_PATH];
var id = QuantityPKParameter.CreateId(quantityPath, parameterName);
if (!_importedPK.Contains(id))
{
var dimension = findDimensionFor(csv[UNIT]);
var pkParameter = new QuantityPKParameter {
Name = parameterName, QuantityPath = quantityPath, Dimension = dimension
};
_importedPK.Add(pkParameter);
}
return(_importedPK[id]);
}
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 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 = "Path1", Name = "AUC"
};
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Path2", Name = "AUC"
};
_pkParameter3 = new QuantityPKParameter {
QuantityPath = "Path1", Name = "CMax"
};
_pkParameter4 = new QuantityPKParameter {
QuantityPath = "Path1", Name = "TMax"
};
sut.AddPKAnalysis(_pkParameter1);
sut.AddPKAnalysis(_pkParameter2);
sut.AddPKAnalysis(_pkParameter3);
sut.AddPKAnalysis(_pkParameter4);
}
public void Plot(IPopulationDataCollector populationDataCollector, QuantityPKParameter pkParameter, DistributionSettings settings = null, IDimension dimension = null, Unit displayUnit = null)
{
var displayUnitToUse = displayUnit ?? _displayUnitRetriever.PreferredUnitFor(pkParameter.Dimension);
plot(populationDataCollector, pkParameter, _distributionDataCreator.CreateFor, updatePlotOptionsDefaultsFor, settings, dimension, displayUnitToUse);
}
public ContinuousDistributionData CreateFor(IPopulationDataCollector populationDataCollector, DistributionSettings settings, QuantityPKParameter parameter, IDimension dimension, Unit displayUnit)
{
var allValues = populationDataCollector.AllPKParameterValuesFor(parameter.QuantityPath, parameter.Name);
return(CreateFor(populationDataCollector, settings, allValues, dimension, displayUnit));
}
private string getTitleFor(QuantityPKParameter pkParameter, Unit displayUnit)
{
var parameterDisplayName = _pkParameterRepository.DisplayNameFor(pkParameter.Name);
return(Constants.NameWithUnitFor(parameterDisplayName, displayUnit));
}
private void updatePlotOptionsDefaultsFor(QuantityPKParameter parameter, DistributionSettings settings, Unit displayUnit)
{
updatePlotOptionsDefaultsFor(getTitleFor(parameter, displayUnit), settings, parameter.QuantityPath);
}
public void Plot(IPopulationDataCollector populationDataCollector, QuantityPKParameter pkParameter, PopulationAnalysisPKParameterField pkParameterField)
{
plotContinousData(populationDataCollector, pkParameter, pkParameterField, x => x.Plot);
}
private void warnIfParameterAlreadyExists(PopulationSimulationPKAnalyses pkAnalyses, QuantityPKParameter pkParameter, SimulationPKParametersImport importedPKParameter)
{
if (pkAnalyses.IsNull())
{
return;
}
if (pkAnalyses.PKParameterBy(pkParameter.Id) == null)
{
return;
}
importedPKParameter.AddWarning(PKSimConstants.Warning.PKParameterAlreadyExistsAndWillBeOverwritten(pkParameter.Name, pkParameter.QuantityPath));
}
private void verifyThatQuantityExistsInSimulation(PathCache <IQuantity> allQuantities, QuantityPKParameter pkParameter, SimulationPKParametersImport importedPKParameter)
{
if (allQuantities.Contains(pkParameter.QuantityPath))
{
return;
}
importedPKParameter.AddError(PKSimConstants.Error.CouldNotFindQuantityWithPath(pkParameter.QuantityPath));
}
