public static IDimension FractionDimensionForSpecs()
{
if (_fractionDimension == null)
{
_fractionDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.FRACTION, "");
_fractionDimension.AddUnit(new Unit("%", 1e-2, 0));
}
return(_fractionDimension);
}
public static IDimension MassConcentrationDimensionForSpecs()
{
if (_massConcentrationDimension == null)
{
_massConcentrationDimension = new Dimension(new BaseDimensionRepresentation {
MassExponent = 3, LengthExponent = -1
}, Constants.Dimension.MASS_CONCENTRATION, "µg/l");
_massConcentrationDimension.AddUnit(new Unit("g/l", 1E6, 0));
}
return(_massConcentrationDimension);
}
public static IDimension ConcentrationDimensionForSpecs()
{
if (_concentrationDimension == null)
{
_concentrationDimension = new Dimension(new BaseDimensionRepresentation {
AmountExponent = 3, LengthExponent = -1
}, Constants.Dimension.MOLAR_CONCENTRATION, "µmol/l");
_concentrationDimension.AddUnit(new Unit("mol/l", 1E6, 0));
}
return(_concentrationDimension);
}
public static IDimension TimeDimensionForSpecs()
{
if (_timeDimension == null)
{
_timeDimension = new Dimension(new BaseDimensionRepresentation {
TimeExponent = 1
}, Constants.Dimension.TIME, "min");
_timeDimension.AddUnit(new Unit("h", 60, 0));
}
return(_timeDimension);
}
private static IDimensionFactory generateFactory()
{
var factory = new DimensionFactory();
var amountDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.AMOUNT, "Molar Volume");
amountDimension.AddUnit(new Unit("mol", 1, 0));
var massDimension = new Dimension(new BaseDimensionRepresentation(), DimensionNames.Mass, "g");
massDimension.AddUnit(new Unit("kg", 1000, 0));
massDimension.AddUnit(new Unit("mg", 0.001, 0));
var concentrationDimension = new Dimension(new BaseDimensionRepresentation(), DimensionNames.Concentration, "mol");
factory.AddDimension(massDimension);
factory.AddDimension(concentrationDimension);
factory.AddDimension(amountDimension);
factory.AddDimension(new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.AMOUNT_PER_TIME, "mol/min"));
factory.AddDimension(new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.VOLUME, "l"));
factory.AddDimension(Constants.Dimension.NO_DIMENSION);
var timeDimension = new Dimension(new BaseDimensionRepresentation(), Constants.Dimension.TIME, Constants.Dimension.Units.Minutes);
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Days, 60 * 24, 0));
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Hours, 60, 0));
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Months, 60 * 24 * 30, 0));
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Seconds, 1.0 / 60, 0));
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Weeks, 60 * 24 * 7, 0));
timeDimension.AddUnit(new Unit(Constants.Dimension.Units.Years, 60 * 24 * 365, 0));
factory.AddDimension(timeDimension);
return(factory);
}
/// <summary>
/// Converts a SBML UnitDefinition into a MoBi Unit.
/// </summary>
public IDimension ConvertUnit(UnitDefinition unitDefinition)
{
var sbmlUnit = unitDefinition.getId();
var dimension = _moBiDimensionFactory.TryGetDimensionCaseInsensitive(sbmlUnit);
if (dimension != Constants.Dimension.NO_DIMENSION)
{
_sbmlInformation.MobiDimension[sbmlUnit] = dimension;
return dimension;
}
var newFactor = 1.0;
var unitsList = new List<Unit>();
var brList = new List<BaseDimensionRepresentation>();
for (long i = 0; i < unitDefinition.getNumUnits(); i++)
{
var mobiUnit = SBMLBaseUnitToMoBi(unitDefinition.getUnit(i));
if (mobiUnit == null) continue;
var unitDimension = _moBiDimensionFactory.DimensionForUnit(mobiUnit.Name);
var unitBr = unitDimension.BaseRepresentation;
unitBr = SetExponents(unitDefinition, unitBr, i);
brList.Add(unitBr);
if (Math.Abs(newFactor) < 0.0001)
{
newFactor = unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
else
{
newFactor = newFactor * unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
unitsList.Add(mobiUnit);
}
var baseDimensionRepresentation = CreateBaseDimRepresentationExponents(brList);
IDimension newDim = new Dimension(baseDimensionRepresentation, String.Format("SBML_{0}",unitDefinition.getId()), String.Format("SBML_{0}_BaseUnit",unitDefinition.getId()));
var newBaseUnit = newDim.BaseUnit;
newBaseUnit.Visible = false;
var newUnit = new Unit(unitDefinition.getId(), newFactor, 0);
newDim.AddUnit(newUnit);
newDim.DefaultUnit = newUnit;
_sbmlInformation.MobiDimension[sbmlUnit] = newDim;
if (_moBiDimensionFactory.Dimensions.All(dim => dim.Name != newDim.Name))
_moBiDimensionFactory.AddDimension(newDim);
return newDim;
}
protected override void Context()
{
base.Context();
_similarDimension = new Dimension(new BaseDimensionRepresentation(), "XXX", "1/mol");
_similarDimension.AddUnit("mol", 10, 0);
_tables = new DataTableProvider(numberOfRowsToImport: 1).ImportTables();
_startValuesBuildingBlock.Add(new ParameterStartValue
{
ContainerPath = ContainerPathFromDataTableRow(_tables, 0),
Name = "ParameterName",
Dimension = _similarDimension,
DisplayUnit = _similarDimension.DefaultUnit
});
}
private void addDummyDimension(KeyValuePair <string, string> dimensions)
{
var newDimension = _dimensionFactory.Dimension(dimensions.Value);
var dummyDimension = new Dimension(new BaseDimensionRepresentation(), dimensions.Key, newDimension.BaseUnit.Name);
foreach (var unit in newDimension.Units)
{
if (unit == newDimension.BaseUnit)
{
continue;
}
dummyDimension.AddUnit(unit.Name, unit.Factor, unit.Offset);
}
_dummyDimensionsForConversion.Add(dummyDimension);
}
protected override void Context()
{
base.Context();
var dimension = new Dimension(new BaseDimensionRepresentation {
TimeExponent = 1
}, "Time", "min");
dimension.AddUnit("h", 60, 0);
sut.StartTimeParameter = new ParameterDTO(DomainHelperForSpecs.ConstantParameterWithValue(20).WithDimension(dimension));
sut.StartTimeParameter.Parameter.DisplayUnit = dimension.Unit("min");
sut.EndTimeParameter = new ParameterDTO(DomainHelperForSpecs.ConstantParameterWithValue(120).WithDimension(dimension));
sut.EndTimeParameter.Parameter.DisplayUnit = dimension.Unit("h");
}
protected override void Context()
{
base.Context();
_dataRepository = new DataRepository();
_timeDimension = new Dimension(new BaseDimensionRepresentation {
TimeExponent = 1
}, "Time", "min");
_hourUnit = _timeDimension.AddUnit("h", 60, 0);
_concentrationDimension = new Dimension(new BaseDimensionRepresentation {
MassExponent = 1
}, "Conc", "mg/l");
_gramPerLiterUnit = _concentrationDimension.AddUnit("g/l", 1000, 0);
_time = new BaseGrid("Time", _timeDimension);
_conc = new DataColumn("Conc", _concentrationDimension, _time);
_dataRepository.Add(_conc);
A.CallTo(() => _displayUnitRetriever.PreferredUnitFor(_conc)).Returns(_gramPerLiterUnit);
A.CallTo(() => _displayUnitRetriever.PreferredUnitFor(_time)).Returns(_hourUnit);
}
protected override void Context()
{
base.Context();
var dimension = new Dimension(new BaseDimensionRepresentation(), "none", "l/f");
_newUnit = new Unit("kl/f", 1000, 0);
dimension.AddUnit(_newUnit);
_pkSimParameter = new PKSimParameter {
Dimension = dimension
};
_allPKanalysis.First().PKAnalysis.Add(_pkSimParameter);
_settings = new DefaultPresentationSettings();
A.CallTo(() => _presenterSettingsTask.PresentationSettingsFor <DefaultPresentationSettings>(A <IPresenterWithSettings> ._, A <IWithId> ._)).Returns(_settings);
_settings.SetSetting(_pkSimParameter.Name, "kl/f");
A.CallTo(() => _populationDataCollector.Name).Returns("TOTO");
sut.LoadSettingsForSubject(A.Fake <IWithId>());
}
