protected override void Context()
{
_randomGenerator = new RandomGenerator();
sut = new PKSimDistributedParameter().WithName("P");
_minValue = 5;
_maxValue = 10;
sut.Info.MinValue = _minValue;
sut.Info.MaxValue = _maxValue;
_pathFactory = new ObjectPathFactoryForSpecs();
_minimumParameter = new PKSimParameter {
Name = Constants.Distribution.MINIMUM
}.WithFormula(new ExplicitFormula("0"));
_maximumParameter = new PKSimParameter {
Name = Constants.Distribution.MAXIMUM
}.WithFormula(new ExplicitFormula("1"));
_percentileParameter = new PKSimParameter {
Name = Constants.Distribution.PERCENTILE
}.WithFormula(new ExplicitFormula("0.5"));
sut.Add(_minimumParameter);
sut.Add(_maximumParameter);
sut.Add(_percentileParameter);
_distributedFormula = new UniformDistributionFormula();
_distributedFormula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _minimumParameter).WithAlias(Constants.Distribution.MINIMUM));
_distributedFormula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _maximumParameter).WithAlias(Constants.Distribution.MAXIMUM));
sut.Formula = _distributedFormula;
}
private void addEffectiveSurfaceAreaParameter(ISpatialStructure spatialStructure)
{
var organism = getOrganism(spatialStructure);
if (organism == null)
{
return;
}
var lumen = organism.EntityAt <IContainer>("Lumen");
if (lumen == null)
{
return;
}
var variabilityFactor = lumen.EntityAt <IParameter>(EFFECTIVE_SURFACE_AREA_VARIABILITY_FACTOR);
var area = _dimensionFactory.Dimension("Area");
foreach (var containerWithSurfaceArea in organism.GetAllChildren <IContainer>(c => c.ContainsName(EFFECTIVE_SURFACE_AREA_ENHANCEMENT_FACTOR)))
{
var effectiveSurfaceArea = _objectBaseFactory.Create <IParameter>()
.WithName(EFFECTIVE_SURFACE_AREA)
.WithDimension(area)
.WithGroup("GI_ANATOMY_AREA")
.WithDescription("Effective surface area of GI segment");
var geometricSurfaceArea = containerWithSurfaceArea.EntityAt <IParameter>(GEOMETRIC_SURFACE_AREA);
if (geometricSurfaceArea == null)
{
continue;
}
var effectiveSurfaceAreaEnahncementFactor = containerWithSurfaceArea.EntityAt <IParameter>(EFFECTIVE_SURFACE_AREA_ENHANCEMENT_FACTOR);
containerWithSurfaceArea.Add(effectiveSurfaceArea);
var formula = spatialStructure.FormulaCache.FindByName("PARAM_EffectiveSurfaceArea") as ExplicitFormula;
if (formula == null)
{
formula = _formulaTask.CreateNewFormula <ExplicitFormula>(area).WithName("PARAM_EffectiveSurfaceArea");
formula.AddObjectPath(_objectPathFactory.CreateRelativeFormulaUsablePath(effectiveSurfaceArea, variabilityFactor).WithAlias("AeffVariabilityFactor"));
formula.AddObjectPath(_objectPathFactory.CreateRelativeFormulaUsablePath(effectiveSurfaceArea, geometricSurfaceArea).WithAlias("Ageom"));
formula.AddObjectPath(_objectPathFactory.CreateRelativeFormulaUsablePath(effectiveSurfaceArea, effectiveSurfaceAreaEnahncementFactor).WithAlias("AeffFactor"));
formula.FormulaString = "Ageom * AeffFactor * AeffVariabilityFactor";
spatialStructure.AddFormula(formula);
}
effectiveSurfaceArea.Formula = formula;
}
}
protected override void Context()
{
var organism = new Container().WithName("Organism");
_objectPathFactory = new ObjectPathFactory(new AliasCreator());
_fuParameter = new Parameter().WithName("fu").WithValue(0.5);
organism.Add(_fuParameter);
var liver = new Container().WithName("Liver").WithParentContainer(organism);
var liverVolume = new Parameter().WithName("Volume").WithValue(10).WithParentContainer(liver);
var f_vas_liver = new Parameter().WithName("f_vas").WithValue(0.1);
liver.Add(f_vas_liver);
var kidney = new Container().WithName("Kidney").WithParentContainer(organism);
var kidneyVolume = new Parameter().WithName("Volume").WithValue(20).WithParentContainer(kidney);
kidney.Add(new Parameter().WithName("f_vas").WithValue(0.2));
sut = new SumFormula();
sut.Criteria = Create.Criteria(x => x.With("Volume"));
sut.Variable = "V";
sut.FormulaString = "fu * V_#i * f_vas_#i";
sut.AddObjectPath(_objectPathFactory.CreateRelativeFormulaUsablePath(liverVolume, f_vas_liver).WithAlias("f_vas_#i"));
sut.AddObjectPath(_objectPathFactory.CreateAbsoluteFormulaUsablePath(_fuParameter).WithAlias("fu"));
sut.Dimension = new Dimension(new BaseDimensionRepresentation(), "dim1", "unit1");
_allFormulaUsable = organism.GetAllChildren <IFormulaUsable>().ToEntityDescriptorMapList();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).Returns(new ExplicitFormula());
}
protected override void Context()
{
sut = new PKSimDistributedParameter();
_pathFactory = new ObjectPathFactoryForSpecs();
_meanParameter = new PKSimParameter {
Name = Constants.Distribution.MEAN
}.WithFormula(new ExplicitFormula("10"));
_stdParameter = new PKSimParameter {
Name = Constants.Distribution.DEVIATION
}.WithFormula(new ExplicitFormula("10"));
_percentileParameter = new PKSimParameter {
Name = Constants.Distribution.PERCENTILE
}.WithFormula(new ExplicitFormula("0.5"));
sut.Add(_meanParameter);
sut.Add(_stdParameter);
sut.Add(_percentileParameter);
sut.Formula = new NormalDistributionFormula();
sut.Formula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _meanParameter));
sut.Formula.AddObjectPath(_pathFactory.CreateRelativeFormulaUsablePath(sut, _stdParameter));
}
private void addObjectPathToDistributionFormula(IDistributionFormula distribution,
IDistributedParameter distributedParameter,
IParameter usedParameter,
string alias)
{
var usedParameterPath = _objectPathFactory.CreateRelativeFormulaUsablePath(distributedParameter, usedParameter);
usedParameterPath.Alias = alias;
usedParameterPath.Dimension = usedParameter.Dimension;
distribution.AddObjectPath(usedParameterPath);
}
private IFormulaUsablePath createRelativePathBase(IFormulaUsable formulaUsable, IEntity refObject)
{
if (refObject == null)
{
return(null);
}
if (formulaUsable.IsAtMolecule() && formulaUsable.RootContainer.Equals(formulaUsable.ParentContainer))
{
return(CreateFormulaUsablePathFrom(new[] { formulaUsable.ParentContainer.Name, formulaUsable.Name }, formulaUsable));
}
return(_objectPathFactory.CreateRelativeFormulaUsablePath(refObject, formulaUsable));
}