protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter(min: 10, max: 20, startValue: 30));
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
}
protected override void Context()
{
sut = DomainHelperForSpecs.IdentificationParameter(min: 0, max: 1, startValue: 0.5);
_parameterSelection = A.Fake <ParameterSelection>();
_parameter = new Parameter();
A.CallTo(() => _parameterSelection.Parameter).Returns(_parameter);
A.CallTo(() => _parameterSelection.IsValid).Returns(true);
sut.AddLinkedParameter(_parameterSelection);
}
protected override void PerformExtraInitializationSteps()
{
_parameter3 = A.Fake <IParameter>();
_parameter3.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameter3.Value = 100;
_parameterSelection3 = ParameterSelectionFor(_parameter3, "ParameterPath3");
_fixedIdentificationParameter = DomainHelperForSpecs.IdentificationParameter("Fixed IdParam", min: 0, max: 200, startValue: 60, isFixed: true);
_fixedIdentificationParameter.AddLinkedParameter(_parameterSelection3);
_parameterIdentification.AddIdentificationParameter(_fixedIdentificationParameter);
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
A.CallTo(() => outputMapping.IsValid).Returns(false);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
outputMapping.Output.Dimension = DomainHelperForSpecs.FractionDimensionForSpecs();
}
protected override void Context()
{
sut = DomainHelperForSpecs.IdentificationParameter(min: 0.1, max: 10, startValue: 1.5);
_parameterSelection = A.Fake <ParameterSelection>();
_parameter = new Parameter();
A.CallTo(() => _parameterSelection.Parameter).Returns(_parameter);
A.CallTo(() => _parameterSelection.IsValid).Returns(true);
sut.UseAsFactor = true;
sut.AddLinkedParameter(_parameterSelection);
_parameter.Value = 100;
_parameter.MinValue = 1;
_parameter.MaxValue = 1000;
_parameter.MaxIsAllowed = true;
}
protected override void Context()
{
base.Context();
_optimizedParameterValue = new OptimizedParameterValue("PARAM", 10, 20, 0, 0, Scalings.Linear);
_parameterIdentification = new ParameterIdentification();
_identificationParameter = DomainHelperForSpecs.IdentificationParameter("PARAM", 0.1, 100, 20);
_identificationParameter.Scaling = Scalings.Log;
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
var runResult = new ParameterIdentificationRunResult();
runResult.BestResult.AddValue(_optimizedParameterValue);
_parameterIdentification.AddResult(runResult);
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.RunMode = new MultipleParameterIdentificationRunMode {
NumberOfRuns = 3
};
A.CallTo(() => _cloneManager.Clone(_parameterIdentification)).ReturnsLazily(x =>
{
var clone = new ParameterIdentification();
var ip = DomainHelperForSpecs.IdentificationParameter(min: 10, max: 20, startValue: 15).WithName("PARA1");
clone.AddIdentificationParameter(ip);
var fixedIp = DomainHelperForSpecs.IdentificationParameter(min: 20, max: 40, startValue: 30, isFixed: true).WithName("PARA2");
clone.AddIdentificationParameter(fixedIp);
return(clone);
});
sut.Initialize(_parameterIdentification, 2, new RandomGenerator());
}
protected override void Context()
{
base.Context();
var parameter = new Parameter
{
Dimension = DomainHelperForSpecs.TimeDimensionForSpecs(),
Value = 80,
MinValue = 20,
MinIsAllowed = true,
MaxValue = 120,
MaxIsAllowed = true
};
parameter.DisplayUnit = parameter.Dimension.Unit("h");
A.CallTo(() => _parameterSelection.Parameter).Returns(parameter);
A.CallTo(() => _parameterSelection.IsValid).Returns(true);
sut = DomainHelperForSpecs.IdentificationParameter(min: 20, max: 120, startValue: 60);
sut.AddLinkedParameter(_parameterSelection);
sut.MaxValueParameter.Value = 200;
}
protected override void Context()
{
base.Context();
_dimension = A.Fake <IDimension>();
_parameterSelection = A.Fake <ParameterSelection>();
A.CallTo(() => _parameterSelection.FullQuantityPath).Returns("P1");
A.CallTo(() => _parameterSelection.Dimension).Returns(_dimension);
_runResult.JacobianMatrix = new JacobianMatrix(new [] { _parameterSelection.FullQuantityPath });
_identificationParameter = DomainHelperForSpecs.IdentificationParameter("IP1");
_confidenceIntervals = new Cache <string, double>();
_confidenceIntervals.Add(_identificationParameter.Name, 5);
A.CallTo(_confidenceIntervalCalculator).WithReturnType <ICache <string, double> >().Returns(_confidenceIntervals);
A.CallTo(() => _runResult.BestResult.Values).Returns(new [] { new OptimizedParameterValue(_identificationParameter.Name, 10, 20) });
A.CallTo(() => _parameterIdentification.IdentificationParameterByName(_identificationParameter.Name)).Returns(_identificationParameter);
_identificationParameter.AddLinkedParameter(_parameterSelection);
A.CallTo(() => _dimension.BaseUnitValueToUnitValue(_identificationParameter.StartValueParameter.DisplayUnit, 5)).Returns(50);
A.CallTo(() => _dimension.BaseUnitValueToUnitValue(_identificationParameter.StartValueParameter.DisplayUnit, 10)).Returns(100);
}
protected override void Context()
{
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_residualCalculatorFactory = A.Fake <IResidualCalculatorFactory>();
_timeGridUpdater = A.Fake <ITimeGridUpdater>();
_simModelBatchFactory = A.Fake <ISimModelBatchFactory>();
_optimizationAlgorithmMapper = A.Fake <IParameterIdentificationAlgorithmToOptmizationAlgorithmMapper>();
_outputSelectionUpdater = A.Fake <IOutputSelectionUpdater>();
_coreUserSettings = A.Fake <ICoreUserSettings>();
_jacobianMatrixCalculator = A.Fake <IJacobianMatrixCalculator>();
_coreUserSettings.MaximumNumberOfCoresToUse = 2;
sut = new ParameterIdentificationRun(_residualCalculatorFactory, _timeGridUpdater, _simModelBatchFactory, _modelCoreSimulationMapper,
_optimizationAlgorithmMapper, _outputSelectionUpdater, _coreUserSettings, _jacobianMatrixCalculator);
_simulation = A.Fake <ISimulation>();
_parameter1 = A.Fake <IParameter>();
_parameter1.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameter1.Value = 15;
_parameter2 = A.Fake <IParameter>();
_parameter2.Value = 35;
_parameter2.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.LLOQMode = LLOQModes.OnlyObservedData;
_parameterIdentification.Configuration.RemoveLLOQMode = RemoveLLOQModes.NoTrailing;
_parameterIdentification.AddSimulation(_simulation);
_parameterSelection1 = ParameterSelectionFor(_parameter1, "ParameterPath1");
_parameterSelection2 = ParameterSelectionFor(_parameter2, "ParameterPath2");
_identificationParameter = DomainHelperForSpecs.IdentificationParameter("IdParam", min: 10, max: 20, startValue: 15);
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_modelCoreSimulation = A.Fake <IModelCoreSimulation>();
A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_simulation, true)).Returns(_modelCoreSimulation);
_outputMapping = A.Fake <OutputMapping>();
A.CallTo(() => _outputMapping.UsesSimulation(_simulation)).Returns(true);
A.CallTo(() => _outputMapping.WeightedObservedData.ObservedData).Returns(DomainHelperForSpecs.ObservedData());
_parameterIdentification.AddOutputMapping(_outputMapping);
_simModelBatch = A.Fake <ISimModelBatch>();
A.CallTo(() => _simModelBatchFactory.Create()).Returns(_simModelBatch);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_residualCalculator = A.Fake <IResidualCalculator>();
A.CallTo(_residualCalculatorFactory).WithReturnType <IResidualCalculator>().Returns(_residualCalculator);
_algorithm = A.Fake <IOptimizationAlgorithm>();
A.CallTo(() => _optimizationAlgorithmMapper.MapFrom(_parameterIdentification.AlgorithmProperties)).Returns(_algorithm);
_cancellationTokenSource = new CancellationTokenSource();
_cancellationToken = _cancellationTokenSource.Token;
_runInitializer = A.Fake <IParameterIdentifcationRunInitializer>();
A.CallTo(() => _runInitializer.InitializeRun()).ReturnsAsync(_parameterIdentification);
PerformExtraInitializationSteps();
sut.InitializeWith(_runInitializer);
}
protected override void Context()
{
sut = DomainHelperForSpecs.IdentificationParameter(min: 5, max: 20, startValue: 10);
}
private IdentificationParameter createIdentificationParameter(string name, double value, double min, double max)
{
return(DomainHelperForSpecs.IdentificationParameter(name, min, max, value));
}
protected override void Context()
{
base.Context();
sut = DomainHelperForSpecs.IdentificationParameter(min: 20, max: 120, startValue: 60);
}
public override void GlobalContext()
{
base.GlobalContext();
_observedData = DomainHelperForSpecs.ObservedData();
_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"));
_sim2 = new IndividualSimulation
{
Id = "Sim2",
Name = "Sim2",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim2.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <ICoreWorkspace>();
_project = IoC.Resolve <PKSimProject>();
workspace.Project = _project;
_objectBaseRepository.Register(_sim1);
_objectBaseRepository.Register(_sim2);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_sim1);
_project.AddBuildingBlock(_sim2);
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_sim1);
_parameterIdentification.AddSimulation(_sim2);
_outputMapping = new OutputMapping
{
WeightedObservedData = new WeightedObservedData(_observedData),
OutputSelection = new SimulationQuantitySelection(_sim1, new QuantitySelection("A|B", QuantityType.Metabolite)),
Weight = 5,
Scaling = Scalings.Log
};
_outputMapping.WeightedObservedData.Weights[1] = 10;
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = DomainHelperForSpecs.IdentificationParameter(min: 1, max: 10, startValue: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_parameterSelection2 = new ParameterSelection(_sim2, new QuantitySelection("Liver|P", QuantityType.Parameter));
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_identificationParameter.Scaling = Scalings.Linear;
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("AA");
_parameterIdentification.AlgorithmProperties.Add(new ExtendedProperty <double> {
Name = "Toto", Value = 5
});
_runResult = new ParameterIdentificationRunResult();
_parameterIdentification.AddResult(_runResult);
_parameterIdentification.AddAnalysis(new ParameterIdentificationPredictedVsObservedChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationTimeProfileChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualHistogram());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualVsTimeChart());
GlobalBecause();
}
