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(); }