public static void InitializeMetadata(int Timestep, string SpeciesMapFileName, IEnumerable <IModelDefinition> modelDefs, ICore mCore, string LogFileName, string SpeciesLogFileNames)
{
ScenarioReplicationMetadata scenRep = new ScenarioReplicationMetadata()
{
RasterOutCellArea = PlugIn.ModelCore.CellArea,
TimeMin = PlugIn.ModelCore.StartTime,
TimeMax = PlugIn.ModelCore.EndTime //,
//ProjectionFilePath = "Projection.?"
};
Extension = new ExtensionMetadata(mCore)
{
Name = PlugIn.PlugInName,
TimeInterval = Timestep,
ScenarioReplicationMetadata = scenRep
};
//---------------------------------------
// table outputs:
//---------------------------------------
if (LogFileName != null)
{
System.IO.Directory.CreateDirectory(Path.GetDirectoryName(LogFileName));
PlugIn.habitatLog = new MetadataTable <SpeciesHabitatLog>(LogFileName);
OutputMetadata tblOut_events = new OutputMetadata()
{
Type = OutputType.Table,
Name = "SppHabitatLog",
FilePath = PlugIn.habitatLog.FilePath,
Visualize = true,
};
tblOut_events.RetriveFields(typeof(SpeciesHabitatLog));
Extension.OutputMetadatas.Add(tblOut_events);
}
if (SpeciesLogFileNames != null)
{
PlugIn.sppLogs = new MetadataTable <IndividualSpeciesHabitatLog> [50];
int selectModelCount = 0;
foreach (ModelDefinition sppModel in modelDefs)
{
string sppLogPath = BirdHabitat.SpeciesLogFileNames.ReplaceTemplateVars(SpeciesLogFileNames, sppModel.Name);
System.IO.Directory.CreateDirectory(Path.GetDirectoryName(sppLogPath));
PlugIn.sppLogs[selectModelCount] = new MetadataTable <IndividualSpeciesHabitatLog>(sppLogPath);
selectModelCount++;
OutputMetadata tblOut_events = new OutputMetadata()
{
Type = OutputType.Table,
Name = ("SpeciesLog_" + sppModel.Name),
FilePath = sppLogPath,
Visualize = true,
};
tblOut_events.RetriveFields(typeof(IndividualSpeciesHabitatLog));
Extension.OutputMetadatas.Add(tblOut_events);
}
}
//---------------------------------------
// map outputs:
//---------------------------------------
foreach (ModelDefinition sppModel in modelDefs)
{
string sppMapPath = SpeciesMapFileNames.ReplaceTemplateVars(SpeciesMapFileName, sppModel.Name);
OutputMetadata mapOut_Birds = new OutputMetadata()
{
Type = OutputType.Map,
Name = ("Species Habitat Map: " + sppModel.Name),
//sppModel.Name,
FilePath = @sppMapPath,
Map_DataType = MapDataType.Continuous,
Map_Unit = "Index of Abundance",
Visualize = true,
};
Extension.OutputMetadatas.Add(mapOut_Birds);
}
//---------------------------------------
MetadataProvider mp = new MetadataProvider(Extension);
mp.WriteMetadataToXMLFile("Metadata", Extension.Name, Extension.Name);
}
//---------------------------------------------------------------------
/// <summary>
/// Runs the component for a particular timestep.
/// </summary>
/// <param name="currentTime">
/// The current model timestep.
/// </param>
public override void Run()
{
// Calculate Local Variables
foreach (IMapDefinition map in mapDefs)
{
List <IForestType> forestTypes = map.ForestTypes;
foreach (Site site in modelCore.Landscape.AllSites)
{
int mapCode = 0;
if (site.IsActive)
{
mapCode = CalcForestType(forestTypes, site);
}
else
{
mapCode = 0;
}
SiteVars.LocalVars[site][map.Name] = mapCode;
}
}
// Calculate Derived Variables
foreach (IVariableDefinition var in varDefs)
{
foreach (Site site in modelCore.Landscape.AllSites)
{
SiteVars.DerivedVars[site][var.Name] = 0;
}
List <string> variables = var.Variables;
List <string> operators = var.Operators;
// Parse variable name into mapDef and fortype
for (int i = 0; i < variables.Count; i++)
{
string fullVar = variables[i];
// string[] varSplit = Regex.Split(fullVar, "\\[.*?\\]");
string[] varSplit = fullVar.Split(new char[] { '[', ']' }, StringSplitOptions.RemoveEmptyEntries);
string mapName = varSplit[0];
string varName = varSplit[1];
int mapCode = 0;
foreach (IMapDefinition map in mapDefs)
{
if (map.Name == mapName)
{
int forTypeCnt = 1;
foreach (IForestType forestType in map.ForestTypes)
{
if (forestType.Name == varName)
{
mapCode = forTypeCnt;
}
forTypeCnt++;
}
}
}
foreach (Site site in modelCore.Landscape.AllSites)
{
if (SiteVars.LocalVars[site][mapName] == mapCode)
{
SiteVars.DerivedVars[site][var.Name] = 1;
}
}
}
}
// Calculate Neighborhood Variables
foreach (INeighborVariableDefinition neighborVar in neighborVarDefs)
{
//Parse LocalVar
string fullVar = neighborVar.LocalVariable;
//string[] varSplit = Regex.Split(fullVar, "[]");
string[] varSplit = fullVar.Split(new char[] { '[', ']' }, StringSplitOptions.RemoveEmptyEntries);
string varName = "";
int mapCode = 0;
string mapName = "";
if (varSplit.Length > 1)
{
mapName = varSplit[0];
varName = varSplit[1];
foreach (IMapDefinition map in mapDefs)
{
if (map.Name == mapName)
{
int forTypeCnt = 1;
foreach (IForestType forestType in map.ForestTypes)
{
if (forestType.Name == varName)
{
mapCode = forTypeCnt;
}
forTypeCnt++;
}
}
}
}
else
{
varName = fullVar;
}
// Calculate neighborhood
double CellLength = PlugIn.ModelCore.CellLength;
PlugIn.ModelCore.UI.WriteLine("Creating Dispersal Neighborhood List.");
List <RelativeLocation> neighborhood = new List <RelativeLocation>();
int neighborRadius = neighborVar.NeighborRadius;
int numCellRadius = (int)(neighborRadius / CellLength);
PlugIn.ModelCore.UI.WriteLine("NeighborRadius={0}, CellLength={1}, numCellRadius={2}",
neighborRadius, CellLength, numCellRadius);
double centroidDistance = 0;
double cellLength = CellLength;
for (int row = (numCellRadius * -1); row <= numCellRadius; row++)
{
for (int col = (numCellRadius * -1); col <= numCellRadius; col++)
{
centroidDistance = DistanceFromCenter(row, col);
//PlugIn.ModelCore.Log.WriteLine("Centroid Distance = {0}.", centroidDistance);
if (centroidDistance <= neighborRadius)
{
neighborhood.Add(new RelativeLocation(row, col));
}
}
}
// Calculate neighborhood value (% area of forest types)
foreach (Site site in modelCore.Landscape.AllSites)
{
int totalNeighborCells = 0;
int targetNeighborCells = 0;
foreach (RelativeLocation relativeLoc in neighborhood)
{
Site neighbor = site.GetNeighbor(relativeLoc);
if (neighbor != null && neighbor.IsActive)
{
if (mapName == "")
{
if (SiteVars.DerivedVars[neighbor][varName] > 0)
{
targetNeighborCells++;
}
}
else if (SiteVars.LocalVars[neighbor][mapName] == mapCode)
{
targetNeighborCells++;
}
totalNeighborCells++;
}
}
double pctValue = 100.0 * (double)targetNeighborCells / (double)totalNeighborCells;
// Calculate transformation
double transformValue = pctValue;
if (neighborVar.Transform.Equals("log10", StringComparison.OrdinalIgnoreCase))
//if (neighborVar.Transform == "log10")
{
transformValue = Math.Log10(pctValue + 1);
}
else if (neighborVar.Transform.Equals("ln", StringComparison.OrdinalIgnoreCase))
//else if (neighborVar.Transform == "ln")
{
transformValue = Math.Log(pctValue + 1);
}
// Write Site Variable
SiteVars.NeighborVars[site][neighborVar.Name] = (float)transformValue;
}
}
// Calculate Climate Variables
foreach (IClimateVariableDefinition climateVar in climateVarDefs)
{
Dictionary <IEcoregion, Dictionary <string, double> > ecoClimateVars = new Dictionary <IEcoregion, Dictionary <string, double> >();
string varName = climateVar.Name;
string climateLibVar = climateVar.ClimateLibVariable;
string climateYear = climateVar.Year;
int minMonth = climateVar.MinMonth;
int maxMonth = climateVar.MaxMonth;
string transform = climateVar.Transform;
int currentYear = PlugIn.ModelCore.CurrentTime;
int actualYear = currentYear;
int firstActiveEco = 0;
foreach (IEcoregion ecoregion in modelCore.Ecoregions)
{
if (ecoregion.Active)
{
firstActiveEco = ecoregion.Index;
break;
}
}
if (Climate.Future_MonthlyData != null)
{
AnnualClimate_Monthly AnnualWeather = Climate.Future_MonthlyData[Climate.Future_MonthlyData.Keys.Min()][firstActiveEco];
int maxSpinUpYear = Climate.Spinup_MonthlyData.Keys.Max();
if (PlugIn.ModelCore.CurrentTime > 0)
{
currentYear = (PlugIn.ModelCore.CurrentTime - 1) + Climate.Future_MonthlyData.Keys.Min();
if (climateYear == "prev")
{
if (Climate.Future_MonthlyData.ContainsKey(currentYear - 1))
{
AnnualWeather = Climate.Future_MonthlyData[currentYear - 1][firstActiveEco];
}
else
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear][firstActiveEco];
}
}
else
{
AnnualWeather = Climate.Future_MonthlyData[currentYear][firstActiveEco];
}
}
if (PlugIn.ModelCore.CurrentTime == 0)
{
if (climateYear == "prev")
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear - 1][firstActiveEco];
}
else
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear][firstActiveEco];
}
}
actualYear = AnnualWeather.Year;
}
else
{
if (climateYear == "prev")
{
actualYear = currentYear - 1;
}
}
if (climateVar.SourceName == "Library")
{
foreach (IEcoregion ecoregion in modelCore.Ecoregions)
{
if (ecoregion.Active)
{
if (!ecoClimateVars.ContainsKey(ecoregion))
{
ecoClimateVars.Add(ecoregion, new Dictionary <string, double>());
}
AnnualClimate_Monthly AnnualWeather = Climate.Future_MonthlyData[Climate.Future_MonthlyData.Keys.Min()][ecoregion.Index];
int maxSpinUpYear = Climate.Spinup_MonthlyData.Keys.Max();
if (PlugIn.ModelCore.CurrentTime == 0)
{
if (climateYear == "prev")
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear - 1][ecoregion.Index];
}
else
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear][ecoregion.Index];
}
}
else if (climateYear == "prev")
{
if (!Climate.Future_MonthlyData.ContainsKey(currentYear - 1))
{
AnnualWeather = Climate.Spinup_MonthlyData[maxSpinUpYear][ecoregion.Index];
}
else
{
AnnualWeather = Climate.Future_MonthlyData[currentYear - 1][ecoregion.Index];
}
}
else
{
AnnualWeather = Climate.Future_MonthlyData[currentYear][ecoregion.Index];
}
double monthTotal = 0;
int monthCount = 0;
double varValue = 0;
var monthRange = Enumerable.Range(minMonth, (maxMonth - minMonth) + 1);
foreach (int monthIndex in monthRange)
{
//if (climateVar.ClimateLibVariable == "PDSI")
//{
//double monthPDSI = PDSI_Calculator.PDSI_Monthly[monthIndex-1];
// varValue = monthPDSI;
//}
if (climateVar.ClimateLibVariable.Equals("precip", StringComparison.OrdinalIgnoreCase))
//if (climateVar.ClimateLibVariable == "Precip")
{
double monthPrecip = AnnualWeather.MonthlyPrecip[monthIndex - 1];
varValue = monthPrecip * 10.0; //Convert cm to mm
}
else if (climateVar.ClimateLibVariable.Equals("temp", StringComparison.OrdinalIgnoreCase))
//else if (climateVar.ClimateLibVariable == "Temp")
{
double monthTemp = AnnualWeather.MonthlyTemp[monthIndex - 1];
varValue = monthTemp;
}
else
{
string mesg = string.Format("Climate variable {0} is {1}; expected 'precip' or 'temp'.", climateVar.Name, climateVar.ClimateLibVariable);
throw new System.ApplicationException(mesg);
}
monthTotal += varValue;
monthCount++;
}
double avgValue = monthTotal / (double)monthCount;
double transformValue = avgValue;
if (transform.Equals("log10", StringComparison.OrdinalIgnoreCase))
//if (transform == "Log10")
{
transformValue = Math.Log10(avgValue + 1);
}
else if (transform.Equals("ln", StringComparison.OrdinalIgnoreCase))
//else if (transform == "ln")
{
transformValue = Math.Log(avgValue + 1);
}
if (!ecoClimateVars[ecoregion].ContainsKey(varName))
{
ecoClimateVars[ecoregion].Add(varName, 0.0);
}
ecoClimateVars[ecoregion][varName] = transformValue;
}
}
foreach (Site site in modelCore.Landscape.AllSites)
{
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
double climateValue = 0;
if (ecoregion != null)
{
climateValue = ecoClimateVars[ecoregion][varName];
}
// Write Site Variable
SiteVars.ClimateVars[site][varName] = (float)climateValue;
}
}
else
{
double monthTotal = 0;
int monthCount = 0;
double varValue = 0;
var monthRange = Enumerable.Range(minMonth, (maxMonth - minMonth) + 1);
foreach (int monthIndex in monthRange)
{
string selectString = "Year = '" + actualYear + "' AND Month = '" + monthIndex + "'";
DataRow[] rows = parameters.ClimateDataTable.Select(selectString);
if (rows.Length == 0)
{
string mesg = string.Format("Climate data is empty. No record exists for variable {0} in year {1}.", climateVar.Name, actualYear);
if (actualYear == 0)
{
mesg = mesg + " Note that if using the options Monthly_AverageAllYears or Daily_AverageAllYears you should provide average values for climate variables listed as Year 0.";
}
throw new System.ApplicationException(mesg);
}
foreach (DataRow row in rows)
{
varValue = Convert.ToDouble(row[climateVar.ClimateLibVariable]);
}
monthTotal += varValue;
monthCount++;
}
double avgValue = monthTotal / (double)monthCount;
double transformValue = avgValue;
if (transform.Equals("log10", StringComparison.OrdinalIgnoreCase))
//if (transform == "Log10")
{
transformValue = Math.Log10(avgValue + 1);
}
else if (transform.Equals("ln", StringComparison.OrdinalIgnoreCase))
//else if (transform == "ln")
{
transformValue = Math.Log(avgValue + 1);
}
foreach (Site site in modelCore.Landscape.AllSites)
{
SiteVars.ClimateVars[site][varName] = (float)transformValue;
}
}
}
Dictionary <string, float>[] ecoregionAvgValues = new Dictionary <string, float> [ModelCore.Ecoregions.Count];
Dictionary <string, float> landscapeAvgValues = new Dictionary <string, float>();
int[] activeSiteCount = new int[ModelCore.Ecoregions.Count];
foreach (IEcoregion ecoregion in ModelCore.Ecoregions)
{
ecoregionAvgValues[ecoregion.Index] = new Dictionary <string, float>();
activeSiteCount[ecoregion.Index] = 0;
}
foreach (ActiveSite site in ModelCore.Landscape)
{
IEcoregion ecoregion = ModelCore.Ecoregion[site];
activeSiteCount[ecoregion.Index]++;
}
// Calculate Species Models
foreach (IModelDefinition model in modelDefs)
{
float [] ecoregionSum = new float[ModelCore.Ecoregions.Count];
float landscapeSum = 0;
foreach (Site site in modelCore.Landscape.AllSites)
{
IEcoregion ecoregion = ModelCore.Ecoregion[site];
double modelPredict = 0;
int paramIndex = 0;
foreach (string parameter in model.Parameters)
{
string paramType = model.ParamTypes[paramIndex];
double paramValue = model.Values[paramIndex];
if (paramType.Equals("int", StringComparison.OrdinalIgnoreCase))
//if (paramType == "int")
{
modelPredict += paramValue;
}
else if (paramType.Equals("neighbor", StringComparison.OrdinalIgnoreCase))
//else if (paramType == "neighbor")
{
double modelValue = SiteVars.NeighborVars[site][parameter] * paramValue;
modelPredict += modelValue;
}
else if (paramType.Equals("climate", StringComparison.OrdinalIgnoreCase))
//else if (paramType == "climate")
{
double modelValue = SiteVars.ClimateVars[site][parameter] * paramValue;
modelPredict += modelValue;
}
else if (paramType.Equals("biomass", StringComparison.OrdinalIgnoreCase))
//else if (paramType =="biomass")
{
double modelValue = Util.ComputeBiomass(SiteVars.Cohorts[site]) * paramValue;
modelPredict += modelValue;
}
else
{
string mesg = string.Format("For model {0}, parameter {1} has parameter type {2}; expected 'int', 'neighbor','climate' or 'biomass'.", model.Name, parameter, paramType);
throw new System.ApplicationException(mesg);
}
paramIndex++;
}
// Back-transform model prediction
float finalPredict = (float)Math.Exp(modelPredict);
// Write Site Variable
SiteVars.SpeciesModels[site][model.Name] = (float)finalPredict;
if (site.IsActive)
{
ecoregionSum[ecoregion.Index] += finalPredict;
landscapeSum += finalPredict;
}
}
foreach (IEcoregion ecoregion in ModelCore.Ecoregions)
{
//ecoregionAvgValues[ecoregion.Index].Add(model.Name, 0);
ecoregionAvgValues[ecoregion.Index][model.Name] = ecoregionSum[ecoregion.Index] / activeSiteCount[ecoregion.Index];
}
landscapeAvgValues[model.Name] = landscapeSum / ModelCore.Landscape.ActiveSiteCount;
}
foreach (IModelDefinition model in modelDefs)
{
habitatLog.Write("{0},", ModelCore.CurrentTime);
habitatLog.Write("{0},", model.Name);
habitatLog.Write("{0}", landscapeAvgValues[model.Name]);
foreach (IEcoregion ecoregion in ModelCore.Ecoregions)
{
habitatLog.Write(",{0}", ecoregionAvgValues[ecoregion.Index][model.Name]);
}
habitatLog.WriteLine("");
}
/*
* foreach (IModelDefinition model in modelDefs)
* {
* foreach (IEcoregion ecoregion in ModelCore.Ecoregions)
* {
* habitatLog.Clear();
* SpeciesHabitatLog shl = new SpeciesHabitatLog();
* shl.Time = ModelCore.CurrentTime;
* shl.Ecoregion = ecoregion.Name;
* shl.EcoregionIndex = ecoregion.Index;
* shl.NumSites = activeSiteCount[ecoregion.Index];
* //shl.SppHabitat[ecoregion.Index][model.Name] = avgHabitat[ecoregion.Index][;
* }
* }
* */
// Ouput Maps
if (!(parameters.LocalVarMapFileNames == null))
{
//----- Write LocalVar maps --------
foreach (MapDefinition localVar in parameters.ReclassMaps)
{
string localVarPath = MapFileNames.ReplaceTemplateVars(parameters.LocalVarMapFileNames, localVar.Name, PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <BytePixel> outputRaster = modelCore.CreateRaster <BytePixel>(localVarPath, modelCore.Landscape.Dimensions))
{
BytePixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (byte)(SiteVars.LocalVars[site][localVar.Name] + 1);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
}
if (!(parameters.NeighborMapFileNames == null))
{
//----- Write LocalVar maps --------
foreach (NeighborVariableDefinition neighborVar in parameters.NeighborVars)
{
string neighborVarPath = NeighborMapFileNames.ReplaceTemplateVars(parameters.NeighborMapFileNames, neighborVar.Name, PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(neighborVarPath, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(System.Math.Round(SiteVars.NeighborVars[site][neighborVar.Name] * 100.0));
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
}
if (!(parameters.ClimateMapFileNames == null))
{
//----- Write LocalVar maps --------
foreach (ClimateVariableDefinition climateVar in parameters.ClimateVars)
{
string climateVarPath = ClimateMapFileNames.ReplaceTemplateVars(parameters.ClimateMapFileNames, climateVar.Name, PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(climateVarPath, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(System.Math.Round(SiteVars.ClimateVars[site][climateVar.Name] * 100.0));
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
}
if (!(parameters.SpeciesMapFileNames == null))
{
//----- Write Species Model maps --------
foreach (ModelDefinition sppModel in parameters.Models)
{
string sppModelPath = SpeciesMapFileNames.ReplaceTemplateVars(parameters.SpeciesMapFileNames, sppModel.Name, PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(sppModelPath, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)System.Math.Round(SiteVars.SpeciesModels[site][sppModel.Name] * 100.0);
//pixel.MapCode.Value = (short)System.Math.Round(SiteVars.SpeciesModels[site][sppModel.Name]);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
}
}