protected override void Context() { _presentationSettingsTask = A.Fake <IPresentationSettingsTask>(); _view = A.Fake <IParameterIdentificationMultipleRunsAnalysisView>(); _chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>(); _curveNamer = A.Fake <ICurveNamer>(); _pathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>(); _chartTemplatingTask = A.Fake <IChartTemplatingTask>(); _dimensionFactory = A.Fake <IDimensionFactory>(); _displayUnitRetriever = A.Fake <IDisplayUnitRetriever>(); _chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>(); _projectRetreiver = A.Fake <IProjectRetriever>(); _chartPresenterContext = A.Fake <ChartPresenterContext>(); A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter); A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer); A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_pathElementsMapper); A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask); A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask); A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory); A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask); A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver); sut = new ParameterIdentificationTimeProfileChartPresenter(_view, _chartPresenterContext, _displayUnitRetriever); _timeProfileAnalysis = new ParameterIdentificationTimeProfileChart(); _outputMapping1 = A.Fake <OutputMapping>(); _outputMapping2 = A.Fake <OutputMapping>(); _observedData1 = DomainHelperForSpecs.ObservedData(); _observedData2 = DomainHelperForSpecs.ObservedData(); A.CallTo(() => _outputMapping1.WeightedObservedData).Returns(new WeightedObservedData(_observedData1)); A.CallTo(() => _outputMapping2.WeightedObservedData).Returns(new WeightedObservedData(_observedData2)); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.AddOutputMapping(_outputMapping1); _parameterIdentification.AddOutputMapping(_outputMapping2); _parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>(); _parameterIdentification.AddResult(_parameterIdentificationRunResult); _optimizationRunResult = new OptimizationRunResult(); _parameterIdentificationRunResult.BestResult = _optimizationRunResult; _parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>(); _parameterIdentification.AddResult(_parameterIdentificationRunResult); _optimizationRunResult2 = new OptimizationRunResult(); _parameterIdentificationRunResult.BestResult = _optimizationRunResult2; }
protected override void Context() { _cloneManager = A.Fake <ICloneManagerForModel>(); _simulationFactory = A.Fake <ICoreSimulationFactory>(); _parameterIdentificationRun = A.Fake <IParameterIdentificationRun>(); _coreUserSettings = A.Fake <ICoreUserSettings>(); _descriptionCreator = A.Fake <ICategorialParameterIdentificationDescriptionCreator>(); _container = A.Fake <Utility.Container.IContainer>(); A.CallTo(() => _container.Resolve <ICoreSimulationFactory>()).Returns(_simulationFactory); _coreUserSettings.MaximumNumberOfCoresToUse = 1; sut = new CategorialParameterIdentificationRunInitializer(_cloneManager, _parameterIdentificationRun, _container, _descriptionCreator, _coreUserSettings); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.Configuration.RunMode = new CategorialParameterIdentificationRunMode(); _simulation = A.Fake <ISimulation>(); _clonedSimulation = A.Fake <ISimulation>(); A.CallTo(() => _simulationFactory.CreateWithCalculationMethodsFrom(_simulation, A <IEnumerable <CalculationMethodWithCompoundName> > ._)).Returns(_clonedSimulation); A.CallTo(() => _cloneManager.Clone(_parameterIdentification)).ReturnsLazily(() => { var pi = new ParameterIdentification(); pi.AddSimulation(_simulation); var identificationParameter = new IdentificationParameter(); identificationParameter.AddLinkedParameter(new ParameterSelection(_simulation, A.Fake <QuantitySelection>())); pi.AddIdentificationParameter(identificationParameter); pi.AddOutputMapping(new OutputMapping { OutputSelection = new SimulationQuantitySelection(_simulation, A.Fake <QuantitySelection>()) }); pi.Configuration.RunMode = new CategorialParameterIdentificationRunMode(); return(pi); }); }
protected override void Context() { _view = A.Fake <IParameterIdentificationSimulationSelectionView>(); _treeNodeFactory = A.Fake <ITreeNodeFactory>(); _applicationController = A.Fake <IApplicationController>(); _lazyLoadTask = A.Fake <ILazyLoadTask>(); _treeNodeContextMenuFactory = A.Fake <ITreeNodeContextMenuFactory>(); _multipleTreeNodeContextMenuFactory = A.Fake <IMultipleTreeNodeContextMenuFactory>(); _dialogCreator = A.Fake <IDialogCreator>(); _parameterIdentificationTask = A.Fake <IParameterIdentificationTask>(); sut = new ParameterIdentificationSimulationSelectionPresenter(_view, _treeNodeFactory, _applicationController, _lazyLoadTask, _treeNodeContextMenuFactory, _multipleTreeNodeContextMenuFactory, _dialogCreator, _parameterIdentificationTask); _parameterIdentification = new ParameterIdentification(); _simulation = A.Fake <ISimulation>().WithId("Id").WithName("S"); _parameterIdentification.AddSimulation(_simulation); _outputMapping = new OutputMapping { OutputSelection = new SimulationQuantitySelection(_simulation, new QuantitySelection("PATH", QuantityType.Drug)) }; _parameterIdentification.AddOutputMapping(_outputMapping); _simulationNode = A.Fake <ITreeNode>(); A.CallTo(() => _treeNodeFactory.CreateFor(_simulation)).Returns(_simulationNode); _simulationSelectionPresenter = A.Fake <ISelectionSimulationPresenter>(); A.CallTo(() => _applicationController.Start <ISelectionSimulationPresenter>()).Returns(_simulationSelectionPresenter); sut.EditParameterIdentification(_parameterIdentification); }
public void AddOutputMapping() { var newOutputMapping = new OutputMapping(); _parameterIdentification.AddOutputMapping(newOutputMapping); _allOutputMappingDTOs.Add(mapFrom(newOutputMapping)); OnStatusChanged(); }
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() { base.Context(); _parameterIdentification = new ParameterIdentification(); var outputMapping = A.Fake <OutputMapping>(); ConfigureOutputMapping(outputMapping); _parameterIdentification.AddOutputMapping(outputMapping); _parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX"); }
protected override void Context() { base.Context(); _project = A.Fake <IProject>(); _parameterIdentification = new ParameterIdentification(); A.CallTo(() => _executionContext.Project).Returns(_project); A.CallTo(() => _project.AllParameterIdentifications).Returns(new List <ParameterIdentification> { _parameterIdentification }); _simulation = A.Fake <ISimulation>(); _sensitivityAnalysis = new SensitivityAnalysis { Simulation = _simulation, IsLoaded = true }; _sensitivityAnalysis.AddSensitivityParameter(new SensitivityParameter()); A.CallTo(() => _project.AllSensitivityAnalyses).Returns(new List <SensitivityAnalysis> { _sensitivityAnalysis }); _secondSimulation = A.Fake <ISimulation>(); _parameterIdentification.AddSimulation(_simulation); _parameterIdentification.AddSimulation(_secondSimulation); _outputMapping = new OutputMapping { OutputSelection = new ParameterSelection(_simulation, "a|path") }; _secondOutputMapping = new OutputMapping { OutputSelection = new ParameterSelection(_secondSimulation, "a|path") }; _identificationParameter = new IdentificationParameter(); _linkedParameter = new ParameterSelection(_simulation, "a|path"); _secondLinkedParameter = new ParameterSelection(_secondSimulation, "a|path"); _identificationParameter.AddLinkedParameter(_linkedParameter); _identificationParameter.AddLinkedParameter(_secondLinkedParameter); _parameterIdentification.AddIdentificationParameter(_identificationParameter); _parameterIdentification.AddOutputMapping(_outputMapping); _parameterIdentification.AddOutputMapping(_secondOutputMapping); _parameterIdentification.IsLoaded = true; }
protected override void Context() { base.Context(); _parameterIdentification = new ParameterIdentification(); _parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter()); var outputMapping = A.Fake <OutputMapping>(); ConfigureOutputMapping(outputMapping); _parameterIdentification.AddOutputMapping(outputMapping); outputMapping.Scaling = Scalings.Log; var outputMapping2 = A.Fake <OutputMapping>(); ConfigureOutputMapping(outputMapping2); _parameterIdentification.AddOutputMapping(outputMapping2); outputMapping2.Scaling = Scalings.Linear; A.CallTo(() => outputMapping2.Output).Returns(outputMapping.Output); _parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX"); }
protected override void Context() { base.Context(); _sourceParameterIdentification = new ParameterIdentification(); _identificationParameter = new IdentificationParameter(); _cloneOfIdentificationParameter = new IdentificationParameter(); _sourceParameterIdentification.AddSimulation(_simulation); _sourceParameterIdentification.AddOutputMapping(_outputMapping); _sourceParameterIdentification.AddIdentificationParameter(_identificationParameter); _cloneManager = A.Fake <ICloneManager>(); A.CallTo(() => _cloneManager.Clone(_identificationParameter)).Returns(_cloneOfIdentificationParameter); }
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() { base.Context(); _dataRepository = A.Fake <DataRepository>(); _parameterIdentification = new ParameterIdentification(); _parameterIdentifications = new List <ParameterIdentification> { _parameterIdentification, new ParameterIdentification() }; A.CallTo(() => _executionContext.Project.AllParameterIdentifications).Returns(_parameterIdentifications); _parameterIdentification.AddOutputMapping(new OutputMapping { WeightedObservedData = new WeightedObservedData(_dataRepository) }); }
protected override void Context() { base.Context(); _parameterIdentification = new ParameterIdentification(); var outputMapping = A.Fake <OutputMapping>(); ConfigureOutputMapping(outputMapping); outputMapping.WeightedObservedData = null; A.CallTo(() => outputMapping.IsValid).Returns(true); _parameterIdentification.AddOutputMapping(outputMapping); _parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX"); _parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter()); }
private void addOutputMapping(IQuantity output, string outputPath, DataRepository observedData, ISimulation simulation, ParameterIdentification parameterIdentification) { if (parameterIdentification.UsesObservedData(observedData)) { return; } parameterIdentification.AddOutputMapping(new OutputMapping { OutputSelection = new SimulationQuantitySelection(simulation, new QuantitySelection(outputPath, output.QuantityType)), WeightedObservedData = new WeightedObservedData(observedData), Scaling = DefaultScalingFor(output) }); }
protected override void Context() { _eventPublisher = A.Fake <IEventPublisher>(); _view = A.Fake <IParameterIdentificationWeightedObservedDataCollectorView>(); _applicationController = A.Fake <IApplicationController>(); sut = new ParameterIdentificationWeightedObservedDataCollectorPresenter(_view, _applicationController, _eventPublisher); _parameterIdentification = new ParameterIdentification(); _weightedObservedData = new WeightedObservedData(DomainHelperForSpecs.ObservedData()); _outputMapping = new OutputMapping { WeightedObservedData = _weightedObservedData }; _parameterIdentification.AddOutputMapping(_outputMapping); _presenter = A.Fake <IParameterIdentificationWeightedObservedDataPresenter>(); A.CallTo(() => _applicationController.Start <IParameterIdentificationWeightedObservedDataPresenter>()).Returns(_presenter); }
protected override void Context() { base.Context(); _simulation = new IndividualSimulation(); _usedObservedData = new UsedObservedData { Id = "dataRepositoryId", Simulation = _simulation }; _dataRepository = new DataRepository(_usedObservedData.Id); _simulation.AddUsedObservedData(_usedObservedData); _parameterIdentification = new ParameterIdentification(); _project.AddObservedData(_dataRepository); _project.AddParameterIdentification(_parameterIdentification); var outputMapping = A.Fake <OutputMapping>(); A.CallTo(() => outputMapping.UsesObservedData(_dataRepository)).Returns(true); A.CallTo(() => outputMapping.UsesSimulation(_simulation)).Returns(false); _parameterIdentification.AddOutputMapping(outputMapping); }
protected override void Context() { base.Context(); _outputPath = "Liver|Cell|Drug"; _simulation = A.Fake <ISimulation>().WithId("Sim"); _parameterIdentification = new ParameterIdentification(); _output1 = A.Fake <IQuantity>(); var allOutputs = new PathCacheForSpecs <IQuantity> { { _outputPath, _output1 } }; A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation)).Returns(allOutputs); _observedData1 = DomainHelperForSpecs.ObservedData("OBS1"); _observedData2 = DomainHelperForSpecs.ObservedData("OBS2"); _observedData3 = DomainHelperForSpecs.ObservedData("OBS3"); A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation)).Returns(new[] { _observedData1, _observedData2 }); var simulationQuantitySelection = A.Fake <SimulationQuantitySelection>(); A.CallTo(() => simulationQuantitySelection.Path).Returns(_outputPath); _parameterIdentification.AddOutputMapping(new OutputMapping { WeightedObservedData = new WeightedObservedData(_observedData2), OutputSelection = simulationQuantitySelection }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.MOLECULE, Value = "Drug" }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.ORGAN, Value = "Liver" }); _observedData1.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.COMPARTMENT, Value = "Cell" }); _observedData3.ExtendedProperties.Add(new ExtendedProperty <string> { Name = ObservedData.ORGAN, Value = "Kidney" }); }
protected override void Context() { base.Context(); _simulation = A.Fake <ISimulation>(); _project = A.Fake <IProject>(); _parameterIdentification = new ParameterIdentification(); A.CallTo(() => _executionContext.Project).Returns(_project); A.CallTo(() => _project.AllParameterIdentifications).Returns(new[] { _parameterIdentification }); _parameterIdentification.AddSimulation(_simulation); _initialObjectPath = new ObjectPath("oldName", "path"); var parameterIdentificationRunResult = new ParameterIdentificationRunResult { BestResult = new OptimizationRunResult() }; _simulationDataRepository = DomainHelperForSpecs.SimulationDataRepositoryFor("oldName"); _observationDataRepository = DomainHelperForSpecs.ObservedData(); _observationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath); _simulationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath); parameterIdentificationRunResult.BestResult.AddResult(_simulationDataRepository); _residualsResult = new ResidualsResult(); _residualsResult.AddOutputResiduals(_initialObjectPath.PathAsString, _observationDataRepository, new List <Residual> { new Residual(0, 1, 1) }); parameterIdentificationRunResult.BestResult.ResidualsResult = _residualsResult; _parameterIdentification.AddResult(parameterIdentificationRunResult); var outputMapping = new OutputMapping { WeightedObservedData = new WeightedObservedData(_observationDataRepository), OutputSelection = new ParameterSelection(_simulation, _initialObjectPath.PathAsString) }; _parameterIdentification.AddOutputMapping(outputMapping); }
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); }