public void TestSerializationWithRelatedColumnExplicitelyAfter()
{
var baseGrid = new BaseGrid("Bastian", DimensionTime)
{
Values = new float[] { 0F, 3600F, 7200F }
};
var x1 = new DataColumn("Columbus", DimensionLength, baseGrid);
var relColG = new DataColumn("RenateG", DimensionLess, baseGrid);
relColG.DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.GeometricStdDev, " ", new DateTime(2010, 10, 22), "Study1", "Dog", 2.4);
x1.AddRelatedColumn(relColG);
var relColA = new DataColumn("RenateA", DimensionLength, baseGrid);
relColA.DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.ArithmeticStdDev, "cm", new DateTime(2010, 10, 22), "Study1", "Dog", 2.4);
x1.AddRelatedColumn(relColA);
var dr1 = new DataRepository("id")
{
x1, relColG, relColA
};
var dr2 = SerializeAndDeserialize(dr1);
var x2 = dr2.AllButBaseGrid().First(x => x.IsNamed("Columbus"));
AssertForSpecs.AreEqualMcDataColumn(x1, x2);
}
private DataRepository dataForSelectedOntogeny(Unit xUnit, Unit yUnit)
{
var dataRepository = new DataRepository {
Name = PKSimConstants.UI.OntogenyFor(_dto.SelectedOntogeny.DisplayName)
};
var pma = new BaseGrid(PKSimConstants.UI.PostMenstrualAge, _dimensionRepository.AgeInYears)
{
DisplayUnit = xUnit
};
var mean = new DataColumn(dataRepository.Name, _dimensionRepository.Fraction, pma)
{
DisplayUnit = yUnit
};
var std = new DataColumn(PKSimConstants.UI.StandardDeviation, _dimensionRepository.Fraction, pma)
{
DisplayUnit = yUnit
};
mean.DataInfo.AuxiliaryType = AuxiliaryType.GeometricMeanPop;
std.AddRelatedColumn(mean);
dataRepository.Add(mean);
dataRepository.Add(std);
var allOntogenies = _ontogenyRepository.AllValuesFor(_dto.SelectedOntogeny, _dto.SelectedContainer.Name).OrderBy(x => x.PostmenstrualAge).ToList();
pma.Values = values(allOntogenies, x => x.PostmenstrualAge);
mean.Values = values(allOntogenies, x => x.OntogenyFactor);
std.Values = values(allOntogenies, x => x.Deviation);
return(dataRepository);
}
protected override void Context()
{
base.Context();
var path = new List <string>(new[] { "aa", "bb" });
_baseGrid = new BaseGrid("Bastian", DimensionTime)
{
Values = new[] { 0F, 3600F, 7200F }
};
_col1 = new DataColumn("Columbus", DimensionLength, _baseGrid)
{
QuantityInfo = new QuantityInfo("Quain", path, QuantityType.Parameter),
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, "cm", new DateTime(2010, 10, 22), "Study1", "Dog", 2.4),
Values = new[] { 1.0F, 2.1F, -3.4F }
};
_relCol = new DataColumn("Renate", DimensionLength, _baseGrid);
_relCol.DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.ArithmeticStdDev, "cm", new DateTime(2010, 10, 22), "Study1", "Dog", 2.4);
_col2 = new DataColumn("Columbine", DimensionLength, _baseGrid);
_col2.AddRelatedColumn(_relCol);
_col3 = new DataColumn("Colette", DimensionLength, _baseGrid);
_col3.AddRelatedColumn(_relCol);
}
public void TestSerializationWithRelatedColumnExplicitelyBefore()
{
var baseGrid = new BaseGrid("Bastian", DimensionTime)
{
Values = new float[] { 0F, 3600F, 7200F }
};
var x1 = new DataColumn("Columbus", DimensionLength, baseGrid)
{
IsInternal = false
};
var relCol = new DataColumn("Renate", DimensionLess, baseGrid)
{
DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.GeometricStdDev, " ", new DateTime(2010, 10, 22), "Study1", "Dog", 2.4)
};
x1.AddRelatedColumn(relCol);
var dr1 = new DataRepository("id")
{
x1, relCol
};
var dr2 = SerializeAndDeserialize(dr1);
var x2 = dr2.AllButBaseGrid().First(x => x.IsNamed("Columbus"));
AssertForSpecs.AreEqualMcDataColumn(x1, x2);
x2.RelatedColumns.First().Dimension.ShouldNotBeNull();
}
protected override Task Context()
{
_quantityInfoMapper = A.Fake <QuantityInfoMapper>();
_dataInfoMapper = A.Fake <DataInfoMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new DataColumnMapper(_dataInfoMapper, _quantityInfoMapper, _dimensionRepository);
var observedData = DomainHelperForSpecs.ObservedData();
_dataColumn = observedData.ObservationColumns().First();
_baseGrid = observedData.BaseGrid;
_relatedColumn = new DataColumn("related", DomainHelperForSpecs.NoDimension(), observedData.BaseGrid)
{
Values = new[] { 0f, 0f, 0f },
DataInfo = { Origin = ColumnOrigins.ObservationAuxiliary }
};
_dataColumn.AddRelatedColumn(_relatedColumn);
_quantityInfoSnapshot = new Snapshots.QuantityInfo();
_dataInfoSnapshot = new Snapshots.DataInfo();
A.CallTo(() => _quantityInfoMapper.MapToSnapshot(_dataColumn.QuantityInfo)).Returns(_quantityInfoSnapshot);
A.CallTo(() => _dataInfoMapper.MapToSnapshot(_dataColumn.DataInfo)).Returns(_dataInfoSnapshot);
A.CallTo(() => _dimensionRepository.DimensionByName(_dataColumn.Dimension.Name)).Returns(_dataColumn.Dimension);
A.CallTo(() => _dimensionRepository.DimensionByName(_baseGrid.Dimension.Name)).Returns(_baseGrid.Dimension);
return(Task.FromResult(true));
}
public DataColumn AddErrorColumn(DataColumn column, string name, string errorType)
{
if (!Enum.TryParse(errorType, out AuxiliaryType auxiliaryType))
{
throw new OSPSuiteException(Error.InvalidAuxiliaryType);
}
DataColumn errorColumn;
switch (auxiliaryType)
{
case AuxiliaryType.ArithmeticStdDev:
errorColumn = new DataColumn(name, column.Dimension, column.BaseGrid)
{
DisplayUnit = column.DisplayUnit
};
break;
case AuxiliaryType.GeometricStdDev:
errorColumn = new DataColumn(name, NO_DIMENSION, column.BaseGrid);
break;
default:
throw new OSPSuiteException(Error.InvalidAuxiliaryType);
}
errorColumn.DataInfo.AuxiliaryType = auxiliaryType;
errorColumn.DataInfo.Origin = ColumnOrigins.ObservationAuxiliary;
column.AddRelatedColumn(errorColumn);
//May be null if the method is called for an orphan column... Does not make sense
column.Repository?.Add(errorColumn);
return(errorColumn);
}
protected override void Context()
{
base.Context();
_baseGrid1.Values = new List <float> {
1f, 2f, 3f
};
_col1 = new DataColumn("col1", "col1", _length, _baseGrid1)
{
Values = new[] { 1f, 11f, 111f }
};
_col2 = new DataColumn("col2", "col2", _length, _baseGrid1)
{
Values = new[] { 2f, 22f, 222f }
};
_col3 = new DataColumn("col3", "col3", _length, _baseGrid1)
{
Values = new[] { 3f, 33f, 333f }
};
_col3.DataInfo.AuxiliaryType = AuxiliaryType.ArithmeticStdDev;
_col1.AddRelatedColumn(_col3);
_valuesToAdd = new Cache <string, float>();
sut.Add(_col1);
sut.Add(_col2);
sut.Add(_col3);
}
public DataRepository CreateFor(string confidenceIntervalName, double[] confidenceInterval, OutputMapping outputMapping, OptimizationRunResult runResult)
{
if (confidenceInterval == null)
{
return(new NullDataRepository());
}
var fullOutputPath = outputMapping.FullOutputPath;
var dataRepository = new DataRepository().WithName(fullOutputPath);
var simulationResult = runResult.SimulationResultFor(fullOutputPath);
var simulationBaseGrid = simulationResult.BaseGrid;
var timeGrid = new BaseGrid(simulationBaseGrid.Name, simulationBaseGrid.Dimension)
{
Values = simulationBaseGrid.Values,
DataInfo = simulationBaseGrid.DataInfo.Clone(),
QuantityInfo = simulationBaseGrid.QuantityInfo.Clone(),
};
var outputColumn = new DataColumn(simulationResult.Name, simulationResult.Dimension, timeGrid)
{
Values = simulationResult.Values,
DataInfo = simulationResult.DataInfo.Clone(),
QuantityInfo = simulationResult.QuantityInfo.Clone(),
};
outputColumn.DataInfo.AuxiliaryType = outputMapping.Scaling == Scalings.Linear ? AuxiliaryType.ArithmeticMeanPop : AuxiliaryType.GeometricMeanPop;
var interval = new DataColumn(confidenceIntervalName, simulationResult.Dimension, timeGrid)
{
DisplayUnit = simulationResult.DisplayUnit,
Values = confidenceInterval.ToFloatArray(),
QuantityInfo = simulationResult.QuantityInfo.Clone(),
DataInfo = { Origin = ColumnOrigins.CalculationAuxiliary, MolWeight = outputColumn.DataInfo.MolWeight },
};
outputColumn.IsInternal = true;
interval.AddRelatedColumn(outputColumn);
dataRepository.Add(interval);
return(dataRepository);
}
private IEnumerable <DataColumn> createRepository3DataColumns(IContainer organism, IQuantity q1, BaseGrid baseGrid3)
{
List <DataColumn> columns = new List <DataColumn>();
var arterialBlood = organism.GetSingleChildByName <IContainer>("ArterialBlood");
var q2 = arterialBlood.GetSingleChildByName <IQuantity>("Q");
var dc1A = new DataColumn("Spec1", q1.Dimension, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, q1.Dimension.DefaultUnitName, "Patient A", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q1),
Values = new[] { 1.5F, 0.8F, Single.PositiveInfinity }
};
columns.Add(dc1A);
var dc2AStdDevA = new DataColumn("Spec2DevA", q2.Dimension, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.ArithmeticStdDev, q2.Dimension.DefaultUnitName, "Patient A", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 0.6F, 0.2F, 0.8F }
};
var dc2A = new DataColumn("Spec2", q2.Dimension, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, q2.Dimension.DefaultUnitName, "Patient A", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 2.3F, 0.8F, 0.4F }
};
dc2A.AddRelatedColumn(dc2AStdDevA);
columns.Add(dc2A);
var dc1B = new DataColumn("Spec1", q1.Dimension, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, q1.Dimension.DefaultUnitName, "Patient B", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q1),
Values = new[] { 1.6F, 1.1F, 3.9F }
};
columns.Add(dc1B);
var dimless = _dimensionFactory.Dimension("Dimensionless");
var dc2BStdDevG = new DataColumn("Spec2DevG", dimless, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.ObservationAuxiliary, AuxiliaryType.GeometricStdDev, dimless.DefaultUnitName, "Patient B", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 0.1F, 0.1F, 0.15F }
};
var dc2B = new DataColumn("Spec2", q2.Dimension, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, q2.Dimension.DefaultUnitName, "Patient B", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 2.1F, 0.4F, 3.3F }
};
dc2B.AddRelatedColumn(dc2BStdDevG);
columns.Add(dc2B);
var length = _dimensionFactory.Dimension("Length");
var dc3L1 = new DataColumn("Length1", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, length.DefaultUnitName, "Patient A", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q1),
Values = new[] { 1.1F, 1.8F, 1.4F }
};
columns.Add(dc3L1);
var dc3L2 = new DataColumn("Length2", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, length.DefaultUnitName, "Patient A", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q1),
Values = new[] { 2.1F, 2.8F, 2.4F }
};
columns.Add(dc3L2);
var dc0 = new DataColumn("ValuesWith0", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Observation, AuxiliaryType.Undefined, length.DefaultUnitName, "Patient A", 320)
{
LLOQ = 1000
},
QuantityInfo = Helper.CreateQuantityInfo(q1),
Values = new[] { 0F, 0F, 1F }
};
columns.Add(dc0);
var dcX1ArithMeanPop = new DataColumn("X1_ArithMeanPop", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.ArithmeticMeanPop, length.DefaultUnitName, "Patient A", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 2.3F, 0.8F, 3.4F }
};
columns.Add(dcX1ArithMeanPop);
var dcX1ArithMeanStdDev = new DataColumn("X1_ArithMeanStdDev", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.Undefined, length.DefaultUnitName, "Patient A", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 0.4F, 0.2F, 0.3F }
};
dcX1ArithMeanStdDev.AddRelatedColumn(dcX1ArithMeanPop);
columns.Add(dcX1ArithMeanStdDev);
var dcX1GeomMeanPop = new DataColumn("X1_GeomMeanPop", length, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.GeometricMeanPop, length.DefaultUnitName, "Patient A", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 2.3F, 0.8F, 3.4F }
};
columns.Add(dcX1GeomMeanPop);
var dcX1GeomMeanStdDev = new DataColumn("X1_GeomMeanStdDev", dimless, baseGrid3)
{
DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.Undefined, dimless.DefaultUnitName, "Patient A", 320),
QuantityInfo = Helper.CreateQuantityInfo(q2),
Values = new[] { 0.4F, 0.2F, 0.3F }
};
dcX1GeomMeanStdDev.AddRelatedColumn(dcX1GeomMeanPop);
columns.Add(dcX1GeomMeanStdDev);
return(columns);
}