/// <summary>
/// Creates a empty Data Table for the Stochastic Parameter Control based on the user inputs gathered
/// from the General Options control parameter.
/// </summary>
/// <param name="objNT">Object representing the Stochastic Parameter</param>
/// <param name="genOpt">Paramters from the General Options Control</param>
/// <param name="fleetDependent">Is this Stochastic Parameter dependent on the
/// nubmber of fleets? Default is false.</param>
public void CreateStochasticParameterFallbackDataTable(Nmfs.Agepro.CoreLib.AgeproStochasticAgeTable objNT,
Nmfs.Agepro.CoreLib.AgeproGeneral genOpt,
StochasticAgeFleetDependency fleetDependent = StochasticAgeFleetDependency.independent)
{
this.numFleets = Convert.ToInt32(genOpt.numFleets);
this.seqYears = Array.ConvertAll(genOpt.SeqYears(), element => element.ToString());
this.readInputFileState = true;
//Reset Tables if they were used before
if (this.stochasticAgeTable != null)
{
this.stochasticAgeTable.Reset();
this.stochasticCV.Reset();
}
if (this.timeVarying == true)
{
this.stochasticAgeTable = CreateFallbackAgeDataTable(genOpt.NumAges(),
genOpt.SeqYears().Count(), this.numFleets);
}
else
{
if (fleetDependent == StochasticAgeFleetDependency.dependent)
{
this.stochasticAgeTable = CreateFallbackAgeDataTable(genOpt.NumAges(), 1, this.numFleets);
this.stochasticCV = CreateFallbackAgeDataTable(genOpt.NumAges(), 1, this.numFleets);
}
else
{
this.stochasticAgeTable = CreateFallbackAgeDataTable(genOpt.NumAges(), 1, 1);
this.stochasticCV = CreateFallbackAgeDataTable(genOpt.NumAges(), 1, 1);
}
}
objNT.byAgeData = this.stochasticAgeTable;
objNT.byAgeCV = this.stochasticCV;
this.readInputFileState = false;
}
public string ReadRetroAdjustmentFactorsTable(StreamReader sr, AgeproGeneral General)
{
string line = sr.ReadLine();
string[] rafLine = line.Split(" ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
DataTable rafTable = new DataTable("Retro Adjustment Factors");
_ = rafTable.Columns.Add(); //set column without name
//Throw warning/error if 'rafLine' length doesn't match number of Ages
if (rafLine.Length != General.NumAges())
{
throw new InvalidAgeproParameterException("Number of retro adjustment factors does not match number of ages");
}
for (int i = 0; i < General.NumAges(); i++)
{
_ = rafTable.Rows.Add(rafLine[i]);
}
RetroAdjust = rafTable;
return(line);
}
/// <summary>
/// Reads in the AGERPRO Input file values by line
/// </summary>
/// <param name="sr">SreamReader Object</param>
private void ReadInputFileLineValues(StreamReader sr)
{
string line;
_ = CheckINPVersion(sr);
while (!sr.EndOfStream)
{
line = sr.ReadLine();
//Case ID
if (line.Equals("[CASEID]"))
{
CaseID = sr.ReadLine();
}
//General
else if (line.Equals("[GENERAL]"))
{
_ = General.ReadGeneralModelParameters(sr);
}
else if (line.Equals("[RECRUIT]"))
{
//Read Recruit Data
Recruitment.ObservationYears = General.SeqYears();
Recruitment.ReadRecruitmentData(sr, General.NumYears(), General.NumRecModels);
}
else if (line.Equals("[STOCK_WEIGHT]"))
{
Jan1StockWeight.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges());
}
else if (line.Equals("[SSB_WEIGHT]"))
{
SSBWeight.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges());
}
else if (line.Equals("[MEAN_WEIGHT]"))
{
MeanWeight.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges());
}
else if (line.Equals("[CATCH_WEIGHT]"))
{
CatchWeight.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges(), General.NumFleets);
}
else if (line.Equals("[DISC_WEIGHT]"))
{
DiscardWeight.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges(), General.NumFleets);
}
else if (line.Equals("[NATMORT]"))
{
NaturalMortality.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges());
}
else if (line.Equals("[MATURITY]"))
{
BiologicalMaturity.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges());
}
else if (line.Equals("[FISHERY]"))
{
Fishery.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges(), General.NumFleets);
}
else if (line.Equals("[DISCARD]"))
{
DiscardFraction.ReadStochasticAgeData(sr, General.NumYears(), General.NumAges(), General.NumFleets);
}
else if (line.Equals("[BIOLOGICAL]"))
{
BiologicalTSpawn.ReadBiologicalData(sr, General.SeqYears());
}
else if (line.Equals("[BOOTSTRAP]"))
{
Bootstrap.ReadBootstrapData(sr);
}
else if (line.Equals("[HARVEST]"))
{
HarvestScenario.ReadHarvestTable(sr, General.NumYears(), General.NumFleets);
}
else if (line.Equals("[REBUILD]"))
{
Rebuild.ObsYears = General.SeqYears();
Rebuild.ReadCalculationDataLines(sr);
HarvestScenario.AnalysisType = HarvestScenarioAnalysis.Rebuilder;
}
else if (line.Equals("[REFPOINT]"))
{
Options.EnableRefpoint = true;
_ = Refpoint.ReadRefpointLines(sr);
}
else if (line.Equals("[BOUNDS]"))
{
Options.EnableBounds = true;
_ = Bounds.ReadBounds(sr);
}
else if (line.Equals("[RETROADJUST]"))
{
Options.EnableRetroAdjustmentFactors = true;
_ = RetroAdjustments.ReadRetroAdjustmentFactorsTable(sr, General);
}
else if (line.Equals("[OPTIONS]"))
{
_ = Options.ReadAgeproOptions(sr);
}
else if (line.Equals("[SCALE]"))
{
Options.EnableScaleFactors = true;
_ = Scale.ReadScaleFactors(sr);
}
else if (line.Equals("[PERC]"))
{
Options.EnablePercentileReport = true;
ReportPercentile.Percentile = Convert.ToDouble(sr.ReadLine());
}
else if (line.Equals("[PSTAR]"))
{
PStar.ObsYears = General.SeqYears();
PStar.ReadCalculationDataLines(sr);
HarvestScenario.AnalysisType = HarvestScenarioAnalysis.PStar;
}
}
}