protected override void Context()
{
base.Context();
_sourceParameterSelection = A.Fake <SensitivityParameter>();
_parameterSelection = A.Fake <ParameterSelection>();
_sourceParameterSelection.ParameterSelection = _parameterSelection;
}
protected override void Context()
{
_sensitivityAnalysisParametersView = A.Fake <ISensitivityAnalysisParametersView>();
_sensitivityParameterFactory = A.Fake <ISensitivityParameterFactory>();
_sensitivityParameterToSensitivityParameterDTOMapper = A.Fake <ISensitivityParameterToSensitivityParameterDTOMapper>();
_sensitivityAnalysisSetNMaxPresenter = A.Fake <ISensitivityAnalysisSetValuePresenter>();
_sensitivityAnalysisSetRangePresenter = A.Fake <ISensitivityAnalysisSetValuePresenter>();
_sensitivityAnalysisTask = A.Fake <ISensitivityAnalysisTask>();
sut = new SensitivityAnalysisParametersPresenter(_sensitivityAnalysisParametersView, _sensitivityParameterFactory,
_sensitivityParameterToSensitivityParameterDTOMapper, _sensitivityAnalysisSetNMaxPresenter,
_sensitivityAnalysisSetRangePresenter, _sensitivityAnalysisTask);
_sensitivityAnalysis = new SensitivityAnalysis();
_parameterDTO = A.Fake <IParameterDTO>();
A.CallTo(() => _parameterDTO.Value).Returns(4.0);
_selectedSensitivityParameter = A.Fake <SensitivityParameter>();
_unSelectedSensitivityParameter = A.Fake <SensitivityParameter>();
_sensitivityAnalysis.AddSensitivityParameter(_selectedSensitivityParameter);
_sensitivityAnalysis.AddSensitivityParameter(_unSelectedSensitivityParameter);
A.CallTo(() => _selectedSensitivityParameter.NumberOfStepsParameter).Returns(new Parameter());
A.CallTo(() => _selectedSensitivityParameter.VariationRangeParameter).Returns(new Parameter());
A.CallTo(() => _unSelectedSensitivityParameter.NumberOfStepsParameter).Returns(new Parameter());
A.CallTo(() => _unSelectedSensitivityParameter.VariationRangeParameter).Returns(new Parameter());
_sensitivityParameterDTO = new SensitivityParameterDTO(_selectedSensitivityParameter);
A.CallTo(() => _sensitivityAnalysisParametersView.SelectedParameters()).Returns(new[] { _sensitivityParameterDTO });
A.CallTo(() => _sensitivityParameterToSensitivityParameterDTOMapper.MapFrom(_selectedSensitivityParameter)).Returns(_sensitivityParameterDTO);
A.CallTo(() => _sensitivityParameterToSensitivityParameterDTOMapper.MapFrom(_unSelectedSensitivityParameter)).Returns(new SensitivityParameterDTO(_unSelectedSensitivityParameter));
}
private PKParameterSensitivity calculateParameterSensitivity(SensitivityParameter sensitivityParameter, int sensitivityParameterIndex, VariationData variationData, QuantityPKParameter pkParameter)
{
var defaultParameterValue = sensitivityParameter.DefaultValue;
var defaultPKValue = pkParameter.Values[variationData.DefaultVariationId];
var allVariations = variationData.VariationsFor(sensitivityParameter.Name);
if (float.IsNaN(defaultPKValue) || defaultPKValue == 0 || defaultParameterValue == 0 || !allVariations.Any())
{
return(null);
}
var sensitivity = new PKParameterSensitivity
{
ParameterName = sensitivityParameter.Name,
PKParameterName = pkParameter.Name,
QuantityPath = pkParameter.QuantityPath,
Value = double.NaN
};
var delta = (from variation in allVariations
let deltaP = difference(variation.Variation[sensitivityParameterIndex], defaultParameterValue)
let deltaPK = difference(pkParameter.Values[variation.VariationId], defaultPKValue)
select deltaPK / deltaP).Sum();
sensitivity.Value = delta * defaultParameterValue / defaultPKValue / allVariations.Count;
if (Math.Abs(sensitivity.Value) < Constants.SENSITIVITY_THRESHOLD)
{
sensitivity.Value = 0.0;
}
return(sensitivity);
}
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);
}
private string parameterFullPathFor(SensitivityParameter sensitivityParameter)
{
if (sensitivityParameter?.Parameter == null)
{
return(string.Empty);
}
return(_entityPathResolver.FullPathFor(sensitivityParameter.Parameter));
}
private string parameterDisplayPathFor(SensitivityParameter sensitivityParameter)
{
if (sensitivityParameter?.Parameter == null)
{
return(string.Empty);
}
return(_quantityDisplayPathMapper.DisplayPathAsStringFor(sensitivityParameter.Parameter, addSimulationName: true));
}
public void EditSensitivityAnalysis(SensitivityAnalysis sensitivityAnalysis)
{
_sensitivityAnalysis = sensitivityAnalysis;
_sensitivityParameterForUpdates = _sensitivityParameterFactory.EmptySensitivityParameter();
_sensitivityAnalysisSetNMaxPresenter.Edit(_sensitivityParameterForUpdates.NumberOfStepsParameter);
_sensitivityAnalysisSetRangePresenter.Edit(_sensitivityParameterForUpdates.VariationRangeParameter);
updateView();
}
protected override void Context()
{
base.Context();
_newSimulation = A.Fake <ISimulation>();
var sensitivityParameter = new SensitivityParameter {
ParameterSelection = new ParameterSelection(_oldSimulation, A.Fake <QuantitySelection>())
};
sut.AddSensitivityParameter(sensitivityParameter);
}
public SensitivityParameterDTO MapFrom(SensitivityParameter sensitivityParameter)
{
var sensitivityParameterDTO = new SensitivityParameterDTO(sensitivityParameter);
sensitivityParameterDTO.NumberOfStepsParameter = _parameterMapper.MapFrom(sensitivityParameter.NumberOfStepsParameter, sensitivityParameterDTO, x => x.NumberOfSteps, x => x.NumberOfStepsParameter);
sensitivityParameterDTO.VariationRangeParameter = _parameterMapper.MapFrom(sensitivityParameter.VariationRangeParameter, sensitivityParameterDTO, x => x.VariationRange, x => x.VariationRangeParameter);
sensitivityParameterDTO.DisplayPath = sensitivityParameter.Parameter != null?_quantityDisplayPathMapper.DisplayPathAsStringFor(sensitivityParameter.Parameter, addSimulationName : true) : sensitivityParameter.ParameterSelection.Path;
return(sensitivityParameterDTO);
}
protected override void Context()
{
_simulation = A.Fake <ISimulation>();
A.CallTo(() => _simulation.OutputSelections.HasSelection).Returns(true);
_sensitivityAnalysis = new SensitivityAnalysis {
Simulation = _simulation
};
sut = new SensitivityAnalysisValidator();
_sensitivityParameter = DomainHelperForSpecs.SensitivityParameter();
_sensitivityParameter.ParameterSelection = A.Fake <ParameterSelection>();
}
protected override void Context()
{
base.Context();
_sensitivityAnalysis = new SensitivityAnalysis();
_sensitivityParameter = new SensitivityParameter().WithName("OLD_NAME");
_parameterSensitivity1 = new PKParameterSensitivity {
ParameterName = _sensitivityParameter.Name
};
_parameterSensitivity2 = new PKParameterSensitivity {
ParameterName = "Another name"
};
_sensitivityAnalysis.Results = new SensitivityAnalysisRunResult();
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_parameterSensitivity1);
_sensitivityAnalysis.Results.AddPKParameterSensitivity(_parameterSensitivity2);
}
public override void GlobalContext()
{
base.GlobalContext();
_sim1 = new IndividualSimulation
{
Id = "Sim1",
Name = "Sim1",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim1.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
var objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <IWorkspace>();
_project = IoC.Resolve <PKSimProject>();
workspace.Project = _project;
objectBaseRepository.Register(_sim1);
_project.AddBuildingBlock(_sim1);
_sensitivityAnalysis = new SensitivityAnalysis
{
Name = "SA",
Simulation = _sim1
};
_sensitivityParameter1 = DomainHelperForSpecs.SensitivityParameter(range: 0.5d, steps: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_sensitivityParameter1.ParameterSelection = _parameterSelection1;
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_deserializedSensitivityAnalysis = SerializeAndDeserialize(_sensitivityAnalysis);
}
protected override void Context()
{
_oldSimulation = A.Fake <ISimulation>();
_sensitivityAnalysis = new SensitivityAnalysis {
Simulation = _oldSimulation
};
_newSimulation = A.Fake <ISimulation>();
_simulationQuantitySelectionFinder = A.Fake <ISimulationQuantitySelectionFinder>();
sut = new SensitivityAnalysisSimulationSwapCorrector(_simulationQuantitySelectionFinder);
_validSensitivityParameter = new SensitivityParameter {
ParameterSelection = new ParameterSelection(_oldSimulation, "valid")
};
_sensitivityAnalysis.AddSensitivityParameter(_validSensitivityParameter);
_invalidSensitivityParameter = new SensitivityParameter {
ParameterSelection = new ParameterSelection(_oldSimulation, "invalid")
};
_sensitivityAnalysis.AddSensitivityParameter(_invalidSensitivityParameter);
A.CallTo(() => _simulationQuantitySelectionFinder.SimulationHasSelection(_invalidSensitivityParameter.ParameterSelection, _newSimulation)).Returns(false);
A.CallTo(() => _simulationQuantitySelectionFinder.SimulationHasSelection(_validSensitivityParameter.ParameterSelection, _newSimulation)).Returns(true);
}
protected override void ActionForMissingSensitivityParameterPaths(SensitivityAnalysis sensitivityAnalysis, ISimulation newSimulation, SensitivityParameter sensitivityParameter)
{
sensitivityAnalysis.RemoveSensitivityParameter(sensitivityParameter);
}
protected abstract void ActionForMissingSensitivityParameterPaths(SensitivityAnalysis sensitivityAnalysis, ISimulation newSimulation, SensitivityParameter sensitivityParameter);
protected override void Because()
{
_result = sut.CreateFor(_parameterSelection, _sensitivityAnalysis);
}
protected override void ActionForMissingSensitivityParameterPaths(SensitivityAnalysis sensitivityAnalysis, ISimulation newSimulation, SensitivityParameter sensitivityParameter)
{
_validationResult.AddMessage(
NotificationType.Warning,
sensitivityAnalysis,
Error.SensitivityAnalysis.SimulationDoesNotHaveParameterPath(newSimulation.Name, sensitivityParameter.ParameterSelection.Path));
}
private static void setNumberOfSteps(IParameterDTO parameterDTO, SensitivityParameter sensitivityParameter)
{
setParameterValues(parameterDTO, sensitivityParameter.NumberOfStepsParameter);
}
private void addParametersTo(SensitivityParameter sensitivityParameter)
{
sensitivityParameter.Add(createParameter(Constants.Parameters.VARIATION_RANGE, _dimensionFactory.Dimension(Constants.Dimension.FRACTION), defaultValue: 0.1, min: 0, minAllowed: false));
sensitivityParameter.Add(createParameter(Constants.Parameters.NUMBER_OF_STEPS, Constants.Dimension.NO_DIMENSION, defaultValue: 2, min: 1, max: 10));
}
public void UpdateSensitivityParameterName(SensitivityAnalysis sensitivityAnalysis, SensitivityParameter sensitivityParameter, string newName)
{
var oldName = sensitivityParameter.Name;
sensitivityParameter.Name = newName;
if (!sensitivityAnalysis.HasResults)
{
return;
}
sensitivityAnalysis.Results.UpdateSensitivityParameterName(oldName, newName);
_executionContext.PublishEvent(new SensitivityAnalysisResultsUpdatedEvent(sensitivityAnalysis));
}
private static void setRange(IParameterDTO parameterDTO, SensitivityParameter sensitivityParameter)
{
setParameterValues(parameterDTO, sensitivityParameter.VariationRangeParameter);
}
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);
}
