public DataTable SensitivityAnalysisResultsToDataTable(SensitivityAnalysisRunResult sensitivityAnalysisRunResult, IModelCoreSimulation simulation)
{
var dataTable = new DataTable(simulation.Name);
dataTable.AddColumn <string>(Constants.SensitivityAnalysisResults.QUANTITY_PATH);
dataTable.AddColumn <string>(Constants.SensitivityAnalysisResults.PARAMETER);
dataTable.AddColumn <string>(Constants.SensitivityAnalysisResults.PK_PARAMETER);
dataTable.AddColumn <string>(Constants.SensitivityAnalysisResults.VALUE);
dataTable.AddColumn <string>(Constants.SensitivityAnalysisResults.PARAMETER_PATH);
dataTable.BeginLoadData();
foreach (var pkParameterSensitivity in sensitivityAnalysisRunResult.AllPKParameterSensitivities)
{
var row = dataTable.NewRow();
row[Constants.SensitivityAnalysisResults.QUANTITY_PATH] = pkParameterSensitivity.QuantityPath.InQuotes();
row[Constants.SensitivityAnalysisResults.PARAMETER] = pkParameterSensitivity.ParameterName.InQuotes();
row[Constants.SensitivityAnalysisResults.PK_PARAMETER] = pkParameterSensitivity.PKParameterName.InQuotes();
row[Constants.SensitivityAnalysisResults.VALUE] = pkParameterSensitivity.Value.ConvertedTo <string>();
row[Constants.SensitivityAnalysisResults.PARAMETER_PATH] = pkParameterSensitivity.ParameterPath.InQuotes();
dataTable.Rows.Add(row);
}
dataTable.EndLoadData();
return(dataTable);
}
protected override void Context()
{
base.Context();
_runOptions = new SensitivityAnalysisRunOptions();
_allEvents = new List <SensitivityAnalysisEvent>();
A.CallTo(() => _eventPublisher.PublishEvent(A <SensitivityAnalysisStartedEvent> ._))
.Invokes(x => _allEvents.Add(x.GetArgument <SensitivityAnalysisStartedEvent>(0)));
A.CallTo(() => _eventPublisher.PublishEvent(A <SensitivityAnalysisTerminatedEvent> ._))
.Invokes(x => _allEvents.Add(x.GetArgument <SensitivityAnalysisTerminatedEvent>(0)));
A.CallTo(() => _eventPublisher.PublishEvent(A <SensitivityAnalysisResultsUpdatedEvent> ._))
.Invokes(x => _allEvents.Add(x.GetArgument <SensitivityAnalysisResultsUpdatedEvent>(0)));
_variationData = A.Fake <VariationData>();
_dataTable = new DataTable();
A.CallTo(() => _variationData.ToDataTable()).Returns(_dataTable);
A.CallTo(() => _sensitivityAnalysisVariationDataCreator.CreateForRun(_sensitivityAnalysis)).Returns(_variationData);
_populationRunResult = new PopulationRunResults {
Results = new SimulationResults()
};
A.CallTo(() => _populationRunner.RunPopulationAsync(_modelCoreSimulation, _runOptions, _dataTable, null, null)).ReturnsAsync(_populationRunResult);
_sensitivityAnalysisResults = new SensitivityAnalysisRunResult();
A.CallTo(() => _runResultCalculator.CreateFor(_sensitivityAnalysis, _variationData, _populationRunResult.Results, false)).Returns(_sensitivityAnalysisResults);
}
public DataTable MapFrom(SensitivityAnalysis sensitivityAnalysis, SensitivityAnalysisRunResult sensitivityAnalysisRunResult)
{
var dataTable = new DataTable(Captions.SensitivityAnalysis.Results);
dataTable.AddColumns <string>(Captions.SensitivityAnalysis.Output, Captions.SensitivityAnalysis.PKParameterName, Captions.SensitivityAnalysis.ParameterName, Captions.SensitivityAnalysis.ParameterDisplayPath, Captions.SensitivityAnalysis.PKParameterDescription, Captions.SensitivityAnalysis.ParameterPath);
dataTable.AddColumn <double>(Captions.SensitivityAnalysis.Value);
sensitivityAnalysisRunResult.AllPKParameterSensitivities.Each(x => addParameterSensitivity(x, dataTable, sensitivityAnalysis));
return(dataTable);
}
public SensitivityAnalysisRunResult CreateFor(SensitivityAnalysis sensitivityAnalysis, VariationData variationData, SimulationResults simulationResults, bool addOutputParameterSensitivitiesToResult)
{
var sensitivityRunResult = new SensitivityAnalysisRunResult();
addPKAnalysisSensitivities(variationData, simulationResults, sensitivityRunResult, sensitivityAnalysis);
if (addOutputParameterSensitivitiesToResult)
{
addOutputSensitivities(variationData, simulationResults, sensitivityRunResult, sensitivityAnalysis);
}
return(sensitivityRunResult);
}
protected override void Context()
{
base.Context();
_sensitivityAnalysisRunResult = new SensitivityAnalysisRunResult();
_simulation = A.Fake <IModelCoreSimulation>().WithName("Sim");
var pkParameter = new PKParameterSensitivity
{
QuantityPath = "Liver",
PKParameterName = "AUC",
ParameterName = "P1",
Value = 0.5,
ParameterPath = "ParameterPath"
};
_sensitivityAnalysisRunResult.AddPKParameterSensitivity(pkParameter);
}
public SensitivityAnalysisRunResult CreateFor(SensitivityAnalysis sensitivityAnalysis, VariationData variationData, SimulationResults simulationResults)
{
var sensitivityRunResult = new SensitivityAnalysisRunResult();
var pkAnalyses = _pkAnalysesTask.CalculateFor(sensitivityAnalysis.Simulation, variationData.NumberOfVariations, simulationResults);
foreach (var pkParameter in pkAnalyses.All())
{
sensitivityAnalysis.AllSensitivityParameters.Each((sensitivityParameter, index) =>
{
var pkSensitivity = calculateParameterSensitivity(sensitivityParameter, index, variationData, pkParameter);
if (pkSensitivity != null)
{
sensitivityRunResult.AddPKParameterSensitivity(pkSensitivity);
}
});
}
return(sensitivityRunResult);
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 2, VariationRange = 0.2
};
var containerTask = Api.GetContainerTask();
var liverVolumes = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume");
_sensitivityAnalysis.AddParameters(liverVolumes);
_sensitivityAnalysisRunner = Api.GetSensitivityAnalysisRunner();
_sensitivityAnalysisRunResult = _sensitivityAnalysisRunner.Run(_sensitivityAnalysis);
_allPKParameterSensitivities = _sensitivityAnalysisRunResult.AllPKParameterSensitivities;
}
protected override void Because()
{
_result = sut.CreateFor(_sensitivityAnalysis, _variationData, _simulationResults);
}
private void addPKAnalysisSensitivities(VariationData variationData, SimulationResults simulationResults, SensitivityAnalysisRunResult sensitivityRunResult, SensitivityAnalysis sensitivityAnalysis)
{
var pkAnalyses = _pkAnalysesTask.CalculateFor(sensitivityAnalysis.Simulation, simulationResults);
foreach (var pkParameter in pkAnalyses.All())
{
sensitivityAnalysis.AllSensitivityParameters.Each(sensitivityParameter =>
{
var pkSensitivity = calculatePKParameterSensitivity(sensitivityParameter, variationData, pkParameter);
if (pkSensitivity != null)
{
sensitivityRunResult.AddPKParameterSensitivity(pkSensitivity);
}
});
}
}
private void addOutputSensitivities(VariationData variationData, SimulationResults simulationResults, SensitivityAnalysisRunResult sensitivityRunResult, SensitivityAnalysis sensitivityAnalysis)
{
variationData.AllVariations.Each(variation =>
{
//one variation corresponds to one row in the simulation table (e.g. one IndividualId)
//this is the variation of one parameter compared to the base simulation
var resultsForVariation = simulationResults.ResultsFor(variation.VariationId);
//Retrieve this parameter
var sensitivityParameter = sensitivityAnalysis.SensitivityParameterByName(variation.ParameterName);
var parameterPath = sensitivityParameter.ParameterSelection.Path;
//For all output, we add the sensitivity
resultsForVariation.AllValues.Each(outputValue =>
{
var outputParameterSensitivity = calculateOutputParameterSensitivity(outputValue, variation, parameterPath);
sensitivityRunResult.AddOutputParameterSensitivity(outputParameterSensitivity);
});
});
}
public void ExportResultsToCSV(SensitivityAnalysisRunResult simulationResults, ISimulation simulation, string csvFile)
{
var dataTable = _simulationResultsToDataTableConverter.SensitivityAnalysisResultsToDataTable(simulationResults, simulation);
dataTable.ExportToCSV(csvFile);
}
public SensitivityAnalysisRunResultsImport()
{
SensitivityAnalysisRunResult = new SensitivityAnalysisRunResult();
PKParameterSensitivitiesImportFiles = new List <PKParameterSensitivitiesImportFile>();
}
protected override void Because()
{
_result = sut.CreateFor(_sensitivityAnalysis, _variationData, _simulationResults, addOutputParameterSensitivitiesToResult: false);
}
protected override void Because()
{
sut.ExportResultsToCSV(_sensitivityAnalysisRunResult, _simulation, _csvFile);
_importedResults = sut.ImportResultsFromCSV(_simulation, _csvFile);
}
