/// <summary>
/// Initializes the extension with a data file.
/// </summary>
public override void Initialize()
{
reinitialized = false;
//initialize metadata
MetadataHandler.InitializeMetadata(parameters.Timestep,
parameters.StatusMapNames,
parameters.MortMapNames,
parameters.LogFileName,
parameters.ManyAgentParameters,
ModelCore);
//get input params map names
Timestep = parameters.Timestep;
statusMapName = parameters.StatusMapNames;
mortMapNames = parameters.MortMapNames;
//initialize site variables:
int numAgents = parameters.ManyAgentParameters.Count();
SiteVars.Initialize(modelCore, numAgents);
//Dispersal probdisp = new Dispersal();
manyAgentParameters = parameters.ManyAgentParameters;
int agentIndex = 0;
//Initialize non-library climate data
loadedClimateData = ClimateData.ReadClimateData(manyAgentParameters);
foreach (IAgent activeAgent in manyAgentParameters)
{
if (activeAgent == null)
{
ModelCore.UI.WriteLine("Agent Parameters NOT loading correctly.");
}
//read initial infection map and initialize cell status for each agent
EpidemicRegions.ReadMap(activeAgent.InitEpiMap, agentIndex);
agentIndex++;
//initialize and populate dictionary with dispersal probabilities for current agent
//probdisp.Initialize(activeAgent);
Dispersal.Initialize(activeAgent);
//Initialize climate data to calculate historic average for normalization
ClimateVariableDefinition.CalculateHistoricClimateVariables(activeAgent);
}
}
//---------------------------------------------------------------------
public static ExternalClimateData ReadClimateData(IEnumerable <IAgent> manyAgentParameters)
{
ExternalClimateData climateData = new ExternalClimateData();
climateData.ExternalData = new Dictionary <string, ExternalClimateYear>();
List <string> fileList = new List <string>();
foreach (IAgent agent in manyAgentParameters)
{
foreach (IClimateVariableDefinition climateVar in agent.ClimateVars)
{
if (!(climateVar.SourceName.Equals("Library", StringComparison.OrdinalIgnoreCase)))
{
fileList.Add(climateVar.SourceName);
//climateData.ExternalData.Add(climateVar.SourceName, null);
}
}
}
// Remove duplicate filenames from list
List <string> filteredList = fileList.Distinct().ToList();
foreach (string filename in filteredList)
{
//Read climate table
DataTable weatherTable = ReadWeatherFile(filename);
string[] columnNames = weatherTable.Columns.Cast <DataColumn>()
.Select(x => x.ColumnName)
.ToArray();
List <int> yearList = new List <int>();
DataTable uniqueYears = weatherTable.DefaultView.ToTable(true, "Year");
foreach (DataRow dr in uniqueYears.Rows)
{
int year = (int)dr["Year"];
yearList.Add(year);
}
List <int> ecoList = new List <int>();
DataTable uniqueEco = weatherTable.DefaultView.ToTable(true, "EcoregionIndex");
foreach (DataRow dr in uniqueEco.Rows)
{
int eco = (int)dr["EcoregionIndex"];
ecoList.Add(eco);
}
ExternalClimateYear yearValues = new ExternalClimateYear();
yearValues.YearClimate = new Dictionary <int, ExternalClimateEcoregion>();
foreach (int year in yearList)
{
ExternalClimateEcoregion ecoregionValues = new ExternalClimateEcoregion();
ecoregionValues.EcoregionClimate = new Dictionary <int, ExternalClimateVariableValues>();
foreach (int eco in ecoList)
{
ExternalClimateVariableValues externalValues = new ExternalClimateVariableValues();
externalValues.ClimateVariableValues = new Dictionary <string, double[]>();
foreach (string columnName in columnNames)
{
// Check for Year and EcoregionIndex variables
// All else store as climate variables (if numeric)
//FIXME - N/A if restricted to Climate Library
bool numericField = true;
if (columnName != "Year" && columnName != "EcoregionIndex")
{
List <double> varList = new List <double>();
foreach (DataRow dr in weatherTable.Rows)
{
double value;
if (!double.TryParse(dr[columnName].ToString(), out value))
{
numericField = false;
break;
}
varList.Add(value);
}
if (numericField)
{
double[] varArray = varList.ToArray <double>();
externalValues.ClimateVariableValues.Add(columnName, varArray);
}
}
}
ecoregionValues.EcoregionClimate.Add(eco, externalValues);
}
yearValues.YearClimate.Add(year, ecoregionValues);
}
climateData.ExternalData.Add(filename, yearValues);
}
return(climateData);
}
