public static void AddRawThinned(ref Culture culture, int skip = 0, bool isFirstDeriv = false, CalibrationFunction calibrationFunction = null)
{
var raw = culture.GrowthMeasurements.GetMeasurements(DataType.Raw);
var thinRaw = new List <GrowthMeasurement>();
for (int i = 0; i < raw.Count; i += skip + 1)
{
var measurement = raw[i];
thinRaw.Add(measurement);
}
culture.GrowthMeasurements.SetMeasurements(thinRaw, DataType.RawThinned);
var processesThinned = Modules.ReProccessedDatapoints(thinRaw, BlankValue, calibrationFunction);
if (isFirstDeriv)
{
var firstDeriv = Modules.CalculateFirstDerivative(processesThinned, FirstDerivWindow);
culture.GrowthMeasurements.SetMeasurements(firstDeriv, DataType.FirstDerivative);
}
culture.GrowthMeasurements.SetMeasurements(processesThinned, DataType.ProcessedThinned);
if (Modules.NoGrowth(processesThinned))
{
return;
}
var metaDataThinned = new GrowthVariableMetaData();
var macroLagData = Modules.GetLag(processesThinned);
metaDataThinned.Lag = macroLagData.InterceptStretchs;
var macroYieldData = Modules.GetYield(processesThinned);
metaDataThinned.Yield = macroYieldData.YieldAnchors;
var macroRateData = Modules.GetGT(processesThinned);
metaDataThinned.Rate = macroRateData.RateSlopeAnchors;
culture.GrowthMeasurements.SetMetaData(DataType.ProcessedThinned, metaDataThinned);
}
public static void ReProcess(Culture culture)
{
var raw = culture.GrowthMeasurements.GetMeasurements(DataType.Raw);
var thinRaw = culture.GrowthMeasurements.GetMeasurements(DataType.RawThinned);
if (thinRaw != null)
{
var processesThinned = Modules.ProccessedDatapoints(thinRaw, BlankValue, TrueODCalibartionFunction);
culture.GrowthMeasurements.SetMeasurements(processesThinned, DataType.ProcessedThinned);
if (!Modules.NoGrowth(processesThinned))
{
var metaDataThinned = new GrowthVariableMetaData();
var macroLagData = Modules.GetLag(processesThinned);
metaDataThinned.Lag = macroLagData.InterceptStretchs;
var macroYieldData = Modules.GetYield(processesThinned);
metaDataThinned.Yield = macroYieldData.YieldAnchors;
var macroRateData = Modules.GetGT(processesThinned);
metaDataThinned.Rate = macroRateData.RateSlopeAnchors;
culture.GrowthMeasurements.SetMetaData(DataType.ProcessedThinned, metaDataThinned);
}
}
var smooth = Modules.ProccessedDatapoints(raw, BlankValue, TrueODCalibartionFunction);
culture.GrowthMeasurements.SetMeasurements(smooth, DataType.Processed);
var firstDeriv = Modules.CalculateFirstDerivative(smooth, FirstDerivWindow);
culture.GrowthMeasurements.SetMeasurements(firstDeriv, DataType.FirstDerivative);
culture.GrowthMeasurements.SetMeasurements(Modules.ConvertBioScreenTimeToHrs(raw), DataType.Raw);
double lag;
double yield;
double gt;
var metaData = new GrowthVariableMetaData();
var processed = culture.GrowthMeasurements.GetMeasurements(DataType.Processed);
if (Modules.NoGrowth(processed))
{
lag = 48;
yield = double.NaN;
gt = double.NaN;
}
else
{
var macroLagData = Modules.GetLag(processed);
lag = macroLagData.Lag;
metaData.Lag = macroLagData.InterceptStretchs;
var macroYieldData = Modules.GetYield(processed);
yield = macroYieldData.Yield;
metaData.Yield = macroYieldData.YieldAnchors;
var macroRateData = Modules.GetGT(processed);
gt = macroRateData.GT;
metaData.Rate = macroRateData.RateSlopeAnchors;
}
culture.Lag = lag;
culture.Rate = gt;
culture.Yield = yield;
culture.GrowthMeasurements.SetMetaData(DataType.Processed, metaData);
}
private static void ExtractTraits(Culture culture, RateTraitExtractionMethod rateTraitExtractionMethod)
{
const bool getRawMetada = false;
double lag;
double yield;
double gt;
var qIdx = new QualityIndex();
var processed = culture.GrowthMeasurements.GetMeasurements(DataType.Processed);
if (Modules.NoGrowth(processed))
{
lag = 48;
yield = double.NaN;
gt = double.NaN;
}
else
{
var metaData = new GrowthVariableMetaData();
var macroLagData = Modules.GetLag(processed);
lag = macroLagData.Lag;
metaData.Lag = macroLagData.InterceptStretchs;
var macroYieldData = Modules.GetYield(processed);
yield = macroYieldData.Yield;
metaData.Yield = macroYieldData.YieldAnchors;
//var macroRateData = Modules.GetGtSim(processed);
MacroRateData macroRateData;
switch (rateTraitExtractionMethod)
{
case RateTraitExtractionMethod.Default:
macroRateData = Modules.GetGT(processed);
break;
case RateTraitExtractionMethod.LinearRegression:
macroRateData = Modules.GetGTLinearRegression(processed);
break;
default:
throw new ArgumentOutOfRangeException(nameof(rateTraitExtractionMethod), rateTraitExtractionMethod, null);
}
gt = macroRateData.GT;
metaData.Rate = macroRateData.RateSlopeAnchors;
qIdx = Modules.GetQualityIndex(culture, DataType.Raw);
culture.GrowthMeasurements.SetMetaData(DataType.Processed, metaData);
if (getRawMetada)
{
var raw = culture.GrowthMeasurements.GetMeasurements(DataType.Raw);
var rawMetaData = new GrowthVariableMetaData();
var rawMacroLagData = Modules.GetLag(raw);
rawMetaData.Lag = rawMacroLagData.InterceptStretchs;
var rawMacroYieldData = Modules.GetYield(raw);
rawMetaData.Yield = rawMacroYieldData.YieldAnchors;
var rawMacroRateData = Modules.GetGT(raw);
rawMetaData.Rate = rawMacroRateData.RateSlopeAnchors;
culture.GrowthMeasurements.SetMetaData(DataType.Raw, rawMetaData);
}
}
culture.Lag = lag;
culture.Rate = gt;
culture.Yield = yield;
culture.QualityIndex = qIdx;
}
