protected override void Context()
{
base.Context();
_popSim1 = new PopulationSimulation {
IsLoaded = true
}.WithId("PopSim1");
_popSim2 = new PopulationSimulation {
IsLoaded = true
}.WithId("PopSim2");
_objectBaseRepository = IoC.Resolve <IWithIdRepository>();
_objectBaseRepository.Register(_popSim1);
_objectBaseRepository.Register(_popSim2);
_populationSimulationComparison = new PopulationSimulationComparison();
_populationSimulationComparison.AddSimulation(_popSim1);
_populationSimulationComparison.AddSimulation(_popSim2);
_populationSimulationComparison.ReferenceSimulation = _popSim1;
_groupingItem = new GroupingItem {
Color = Color.Black, Label = "Reference", Symbol = Symbols.Circle
};
_populationSimulationComparison.ReferenceGroupingItem = _groupingItem;
_populationSimulationComparison.SelectedDistributions.Add(new ParameterDistributionSettings {
ParameterPath = "P1", Settings = new DistributionSettings {
AxisCountMode = AxisCountMode.Percent
}
});
}
public override void GlobalContext()
{
base.GlobalContext();
_idRepository = IoC.Resolve <IWithIdRepository>();
var baseGrid = new BaseGrid("base", Constants.Dimension.NO_DIMENSION);
_dataColumn = new DataColumn("Col", Constants.Dimension.NO_DIMENSION, baseGrid);
_dataColumn.DataInfo.Origin = ColumnOrigins.Observation;
_dataRepository = new DataRepository();
_dataRepository.Add(_dataColumn);
_idRepository.Register(_dataRepository);
}
public override void GlobalContext()
{
base.GlobalContext();
_withIdRepository = IoC.Resolve <IWithIdRepository>();
_simulation = new IndividualSimulation().WithId("Sim");
_simulation.IsLoaded = true;
_withIdRepository.Register(_simulation);
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Ind", PKSimBuildingBlockType.Individual)
{
BuildingBlock = DomainHelperForSpecs.CreateIndividual()
});
_transporter = new IndividualTransporter().WithName("Trans");
_enzyme = new IndividualEnzyme().WithName("Enz");
_simulation.Individual.AddMolecule(_transporter);
_simulation.Individual.AddMolecule(_enzyme);
}
private void register <TObject>(TObject objectToRegister) where TObject : IWithId
{
_withIdRepository.Register(objectToRegister);
}
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();
}
public void Visit(IObjectBase objToVisit)
{
_withIdRepository.Register(objToVisit);
}