protected override void Context()
{
_dataFactory = A.Fake <IDataFactory>();
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new DataRepositoryFromResultsCreator(_dimensionRepository, new ObjectPathFactoryForSpecs(), _dataFactory);
_simulation = new IndividualSimulation().WithName("S");
_simulation.Model = new OSPSuite.Core.Domain.Model();
var root = new Container().WithContainerType(ContainerType.Simulation).WithName(_simulation.Name);
_simulation.Model.Root = root;
var liver = new Container().WithName("LIVER");
liver.Add(new Observer().WithName("C"));
var kidney = new Container().WithName("KIDNEY");
kidney.Add(new Observer().WithName("C"));
root.Add(liver);
root.Add(kidney);
_simulationResults = new SimulationResults();
_simulation.Results = _simulationResults;
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 1f, 2f, 3f }
};
_simulationResults.Time = _timeValues;
_individualResults = new IndividualResults();
_individualResults.Add(new QuantityValues {
QuantityPath = "LIVER|C", Time = _timeValues, Values = new[] { 10f, 20f, 30f }
});
_individualResults.Add(new QuantityValues {
QuantityPath = "KIDNEY|C", Time = _timeValues, Values = new[] { 11f, 22f, 33f }
});
}
protected override void Context()
{
base.Context();
var quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
var quantityValue2 = new QuantityValues {
QuantityPath = "Path1"
};
var individualResults1 = new IndividualResults {
IndividualId = 1
};
individualResults1.Add(quantityValue1);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(quantityValue2);
sut.Time = new QuantityValues {
QuantityPath = "Time"
};
individualResults1.Time = sut.Time;
individualResults2.Time = sut.Time;
sut.AddRange(new[] { individualResults1, individualResults2 });
}
protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path1"
};
_anotherQuantityValue = new QuantityValues {
QuantityPath = "Path2"
};
var individualResults1 = new IndividualResults {
IndividualId = 3
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_anotherQuantityValue);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(_quantityValue2);
sut.Add(individualResults1);
sut.Add(individualResults2);
//reorder results before accessing them
sut.ReorderByIndividualId();
}
protected override void Context()
{
base.Context();
_quantityPath = "Path";
sut.Results = new SimulationResults();
_qv0 = new QuantityValues {
QuantityPath = _quantityPath
};
var indResults0 = new IndividualResults {
_qv0
};
indResults0.IndividualId = 0;
_qv2 = new QuantityValues {
QuantityPath = _quantityPath
};
var indResults2 = new IndividualResults {
_qv2
};
indResults2.IndividualId = 2;
sut.Results.Add(indResults0);
sut.Results.Add(indResults2);
}
private QuantityValues quantityPathFor(IndividualResults individualResult, string path, Cache <QuantityValues, List <float> > cacheQuantitiesValues)
{
var quantity = individualResult.ValuesFor(path);
if (quantity == null)
{
quantity = new QuantityValues {
QuantityPath = path
};
cacheQuantitiesValues.Add(quantity, new List <float>());
individualResult.Add(quantity);
}
return(quantity);
}
private static QuantityValues createArray(string path, IDimension dimension, int numberOfPoints)
{
var quantityValues = new QuantityValues();
quantityValues.ColumnId = ShortGuid.NewGuid();
quantityValues.QuantityPath = path;
var values = new float[numberOfPoints];
for (int i = 0; i < values.Length; i++)
{
values[i] = (float)(_random.NextDouble() * 100);
}
quantityValues.Values = values;
return(quantityValues);
}
protected override void Context()
{
var quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
var quantityValue2 = new QuantityValues {
QuantityPath = "Path2"
};
sut = new IndividualResults();
sut.Time = new QuantityValues {
QuantityPath = "Time"
};
sut.Add(quantityValue1);
sut.Add(quantityValue2);
}
private DataColumn dataColumnFor(QuantityValues quantityValues, Simulation simulation, BaseGrid timeColumn)
{
var quantityAndPath = quantityAndPathFrom(simulation, quantityValues.PathList);
var quantity = quantityAndPath.Item1;
if (quantity == null)
{
return(null);
}
var dimension = quantity.Dimension ?? _dimensionRepository.MolarConcentration;
var column = createDataColumn(dataColumnIdFrom(quantityValues), quantity.Name, quantityAndPath.Item2, quantity, dimension, timeColumn, simulation);
column.Values = quantityValues.Values;
return(column);
}
protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1"
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path2"
};
var individualResults1 = new IndividualResults {
IndividualId = 1
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_quantityValue2);
sut.Add(individualResults1);
}
private void setSeriesValues(CurveData <TimeProfileXValue, TimeProfileYValue> series, DataRow row)
{
var statisticalAggregation = row[STATISTICAL_AGGREGATION].DowncastTo <StatisticalAggregation>();
var timeAndAllValues = (Tuple <QuantityValues, FloatMatrix>)row[TIME_AND_VALUES];
QuantityValues time = timeAndAllValues.Item1;
FloatMatrix allValues = timeAndAllValues.Item2;
var results = getResultsFor(statisticalAggregation, allValues);
for (int i = 0; i < time.Length; i++)
{
var yValue = results[i];
if (yValue.IsValid)
{
series.Add(new TimeProfileXValue(time[i]), yValue);
}
}
}
public static PivotResult CreateOutputResults(PopulationPivotAnalysis analysis, PopulationAnalysisCovariateField genderField, PopulationAnalysisOutputField outputField1,
PopulationAnalysisOutputField outputField2,
ObservedDataCollection observedDataCollection = null)
{
var populationSimulation = A.Fake <IPopulationDataCollector>();
var pivotResultCreator = new PivotResultCreator(new Pivoter(), new PopulationAnalysisFlatTableCreator());
//simulation with 4 time points
var time = new QuantityValues {
Values = new float[] { 1, 2, 3, 4 }
};
var output11 = createValues(time, 10, 20, 30, 40);
var output12 = createValues(time, 100, 200, 300, 400);
var output13 = createValues(time, 1000, 2000, 3000, 4000);
var output21 = createValues(time, 50, 60, 70, 80);
var output22 = createValues(time, 500, 600, 700, 800);
var output23 = createValues(time, 5000, 6000, 7000, 8000);
A.CallTo(() => populationSimulation.NumberOfItems).Returns(3);
A.CallTo(() => populationSimulation.AllCovariateValuesFor(CoreConstants.Covariates.GENDER)).Returns(new List <string> {
"Male", "Female", "Male"
});
A.CallTo(() => populationSimulation.AllOutputValuesFor(outputField1.QuantityPath)).Returns(new List <QuantityValues> {
output11, output12, output13
});
A.CallTo(() => populationSimulation.AllOutputValuesFor(outputField2.QuantityPath)).Returns(new List <QuantityValues> {
output21, output22, output23
});
A.CallTo(() => populationSimulation.AllSimulationNames).Returns(new List <string> {
"Sim", "Sim", "Sim"
});
if (observedDataCollection == null)
{
observedDataCollection = new ObservedDataCollection();
}
return(pivotResultCreator.Create(analysis, populationSimulation, observedDataCollection, AggregationFunctions.QuantityAggregation));
}
protected override void Context()
{
base.Context();
_quantityValue1 = new QuantityValues {
QuantityPath = "Path1", Values = new [] { 1f, 2f, 3f }
};
_quantityValue2 = new QuantityValues {
QuantityPath = "Path1", Values = new[] { 4f, 5f, 6f }
};
_anotherQuantityValue = new QuantityValues {
QuantityPath = "Path2", Values = new[] { 7f, 8f, 9f }
};
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 10f, 20f, 30f }
};
var individualResults1 = new IndividualResults {
IndividualId = 3
};
individualResults1.Add(_quantityValue1);
individualResults1.Add(_anotherQuantityValue);
var individualResults2 = new IndividualResults {
IndividualId = 2
};
individualResults2.Add(_quantityValue2);
sut.Add(individualResults1);
sut.Add(individualResults2);
sut.Time = _timeValues;
//reorder results before accessing them
sut.ReorderByIndividualId();
}
public void should_return_true_for_a_null_reference()
{
QuantityValues qv = null;
qv.IsNull().ShouldBeTrue();
}
public void should_return_false_otherwise()
{
QuantityValues qv = new QuantityValues();
qv.IsNull().ShouldBeFalse();
}
private static QuantityValues createValues(QuantityValues time, params float[] values)
{
return(new QuantityValues {
Values = values, Time = time
});
}
public NullQuantityValues()
{
Time = new QuantityValues();
}
protected override void Context()
{
base.Context();
_pkParameter1 = new QuantityPKParameter {
QuantityPath = "Output1", Name = "AUC"
};
_pkParameter1.SetValue(0, 10);
_pkParameter1.SetValue(1, 11);
_pkParameter1.SetValue(2, 12);
_pkParameter1.SetValue(4, _defaultPK1Value);
_pkParameter2 = new QuantityPKParameter {
QuantityPath = "Output2", Name = "Cmax"
};
_pkParameter2.SetValue(0, 20);
_pkParameter2.SetValue(1, 21);
_pkParameter2.SetValue(2, 22);
_pkParameter2.SetValue(3, 23);
_pkParameter2.SetValue(4, _defaultPK2Value);
_pkAnalyses.AddPKAnalysis(_pkParameter1);
_pkAnalyses.AddPKAnalysis(_pkParameter2);
_sensitivityParameter1 = A.Fake <SensitivityParameter>().WithName("SP1");
A.CallTo(() => _sensitivityParameter1.DefaultValue).Returns(10);
A.CallTo(() => _sensitivityParameter1.ParameterSelection.Path).Returns("SP1-PATH");
_sensitivityParameter2 = A.Fake <SensitivityParameter>().WithName("SP2");
A.CallTo(() => _sensitivityParameter2.DefaultValue).Returns(20);
A.CallTo(() => _sensitivityParameter2.ParameterSelection.Path).Returns("SP2-PATH");
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter2);
var pv11 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 0, variation: new[] { 15d, 200d, 300d });
var pv12 = new ParameterVariation(parameterName: _sensitivityParameter1.Name, parameterIndex: 0, variationId: 1, variation: new[] { 20d, 200d, 300d });
var pv21 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 2, variation: new[] { 100d, 21d, 300d });
var pv22 = new ParameterVariation(parameterName: _sensitivityParameter2.Name, parameterIndex: 1, variationId: 3, variation: new[] { 100d, 31d, 300d });
_variationData.DefaultValues = new[] { 100d, 200d, 300d };
_variationData.AddVariation(pv11);
_variationData.AddVariation(pv12);
_variationData.AddVariation(pv21);
_variationData.AddVariation(pv22);
_timeValues = new QuantityValues {
QuantityPath = "Time", Values = new[] { 1, 2, 3, 4, 5f }
};
_resV11 = new IndividualResults {
IndividualId = 0, Time = _timeValues
};
_resV11.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 111.1f, 211.1f, 311.1f, 411.1f, 511.1f }
});
_resV11.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 111.2f, 211.2f, 311.2f, 411.2f, 511.2f }
});
_resV11.UpdateQuantityTimeReference();
_resV12 = new IndividualResults {
IndividualId = 1, Time = _timeValues
};
_resV12.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 112.1f, 212.1f, 312.1f, 412.1f, 512.1f }
});
_resV12.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 112.2f, 212.2f, 312.2f, 412.2f, 512.2f }
});
_resV12.UpdateQuantityTimeReference();
_resV21 = new IndividualResults {
IndividualId = 2, Time = _timeValues
};
_resV21.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 121.1f, 221.1f, 321.1f, 421.1f, 521.1f }
});
_resV21.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 121.2f, 221.2f, 321.2f, 421.2f, 521.2f }
});
_resV21.UpdateQuantityTimeReference();
_resV22 = new IndividualResults {
IndividualId = 3, Time = _timeValues
};
_resV22.Add(new QuantityValues {
QuantityPath = "Output1", Values = new[] { 122.1f, 222.1f, 322.1f, 422.1f, 522.1f }
});
_resV22.Add(new QuantityValues {
QuantityPath = "Output2", Values = new[] { 122.2f, 222.2f, 322.2f, 422.2f, 522.2f }
});
_resV22.UpdateQuantityTimeReference();
_simulationResults.Add(_resV11);
_simulationResults.Add(_resV12);
_simulationResults.Add(_resV21);
_simulationResults.Add(_resV22);
}
private string dataColumnIdFrom(QuantityValues quantityValues)
{
return(quantityValues.ColumnId ?? ShortGuid.NewGuid());
}
private OutputParameterSensitivity calculateOutputParameterSensitivity(QuantityValues outputValue, ParameterVariation variationData, string parameterPath)
{
return(new OutputParameterSensitivity(variationData.ParameterName, parameterPath, variationData.ParameterValue, outputValue.QuantityPath, outputValue.Values, outputValue.Time.Values));
}
