public static void InitializeMetadata(int Timestep, string MapFileName, string eventLogName)
{
ScenarioReplicationMetadata scenRep = new ScenarioReplicationMetadata()
{
RasterOutCellArea = PlugIn.ModelCore.CellArea,
TimeMin = PlugIn.ModelCore.StartTime,
TimeMax = PlugIn.ModelCore.EndTime,
};
Extension = new ExtensionMetadata(PlugIn.ModelCore)
//Extension = new ExtensionMetadata()
{
Name = PlugIn.ExtensionName,
TimeInterval = Timestep,
ScenarioReplicationMetadata = scenRep
};
//---------------------------------------
// table outputs:
//---------------------------------------
CreateDirectory(eventLogName);
PlugIn.eventLog = new MetadataTable <EventsLog>(eventLogName);
//PlugIn.eventLog = new MetadataTable<EventsLog>("Harvest-event-log.csv");
//PlugIn.summaryLog = new MetadataTable<SummaryLog>("Harvest-summary-log.csv");
PlugIn.ModelCore.UI.WriteLine(" Generating event table...");
OutputMetadata tblOut_events = new OutputMetadata()
{
Type = OutputType.Table,
Name = "EventLog",
FilePath = PlugIn.eventLog.FilePath,
Visualize = false,
};
tblOut_events.RetriveFields(typeof(EventsLog));
Extension.OutputMetadatas.Add(tblOut_events);
//---------------------------------------
// map outputs:
//---------------------------------------
//OutputMetadata mapOut_BiomassRemoved = new OutputMetadata()
//{
// Type = OutputType.Map,
// Name = "biomass removed",
// FilePath = @HarvestMapName,
// Map_DataType = MapDataType.Continuous,
// Map_Unit = FieldUnits.Mg_ha,
// Visualize = true,
//};
//Extension.OutputMetadatas.Add(mapOut_BiomassRemoved);
OutputMetadata mapOut_biomassRemoved = new OutputMetadata()
{
Type = OutputType.Map,
Name = "BiomassRemoved",
FilePath = MapNames.ReplaceTemplateVars(MapFileName, Timestep),
Map_DataType = MapDataType.Continuous,
Visualize = true,
//Map_Unit = "categorical",
};
Extension.OutputMetadatas.Add(mapOut_biomassRemoved);
//---------------------------------------
MetadataProvider mp = new MetadataProvider(Extension);
mp.WriteMetadataToXMLFile("Metadata", Extension.Name, Extension.Name);
}
//---------------------------------------------------------------------
///<summary>
/// Run the plug-in at a particular timestep.
///</summary>
public override void Run()
{
modelCore.UI.WriteLine(" Processing Drought Disturbance ...");
double totalRemoved = 0;
int totalKilled = 0;
double dy_sum = 0;
int siteCount = 0;
double[] removedSpp = new double[PlugIn.ModelCore.Species.Count];
int[] killedSpp = new int[PlugIn.ModelCore.Species.Count];
double[] extraRemovedSpp = new double[PlugIn.ModelCore.Species.Count];
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
removedSpp[species.Index] = 0;
killedSpp[species.Index] = 0;
extraRemovedSpp[species.Index] = 0;
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double siteBioRemoved = 0;
double dy = SiteVars.DroughtYears[site];
if (dy > dy_max)
{
dy = dy_max;
}
dy_sum += dy;
siteCount += 1;
if (dy > dy_min)
{
// Sort Cohorts be decreasing age
List <ICohort> cohortList = new List <ICohort>();
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
{
foreach (ICohort cohort in speciesCohorts)
{
cohortList.Add(cohort);
}
}
cohortList = cohortList.OrderByDescending(x => x.Age).ToList();
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
double bioRemovedSpp = removedSpp[species.Index];
int cohortKilledSpp = killedSpp[species.Index];
double extraBioRemovedSpp = extraRemovedSpp[species.Index];
// Calculate 95% CI of intercept and slope
double int_max = parameters.Drought_Y[species] + (1.96 * parameters.Drought_YSE[species]);
double int_min = parameters.Drought_Y[species] - (1.96 * parameters.Drought_YSE[species]);
double slope_max = parameters.Drought_B[species] + (1.96 * parameters.Drought_BSE[species]);
double slope_min = parameters.Drought_B[species] - (1.96 * parameters.Drought_BSE[species]);
// Calculate upper and lower CI predicted values
double maxPropMort = int_max + slope_max * dy;
double minPropMort = int_min + slope_min * dy;
double rangePropMort = maxPropMort - minPropMort;
int bioRemoved = 0;
int cohortsKilled = 0;
int extraRemoved = 0;
int woodyRemoved = 0;
int nonWoodyRemoved = 0;
if (rangePropMort > 0)
{
double Tbiomass = 0;
double propLongev = 0;
int oldestCohortBio = 0;
//foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
//{
//foreach (ICohort cohort in speciesCohorts)
foreach (ICohort cohort in cohortList)
{
if (cohort.Species == species)
{
Tbiomass += cohort.Biomass;
if (((double)cohort.Age / (double)cohort.Species.Longevity) > propLongev)
{
propLongev = (double)cohort.Age / (double)cohort.Species.Longevity;
oldestCohortBio = cohort.Biomass;
}
}
}
//}
if (Tbiomass > 0)
{
double predictPctMort = (minPropMort + (rangePropMort * propLongev));
double backTransPctMort = predictPctMort;
double backTrans0 = 0;
if (parameters.BackTransform == "EXP")
{
// Back-transform - EXP()
backTransPctMort = Math.Exp(predictPctMort);
if (parameters.IntCorrect == "Y")
{
backTrans0 = Math.Exp(parameters.Drought_Y[species]);
}
}
else if (parameters.BackTransform == "SQUARE")
{
//Back-transform - Square
backTransPctMort = Math.Pow(predictPctMort, 2);
if (parameters.IntCorrect == "Y")
{
backTrans0 = Math.Pow(parameters.Drought_Y[species], 2);
}
}
// Account for timestep
double actualPctMort = (backTransPctMort - backTrans0) * Timestep;
//double actualPctMort = predictPctMort * Timestep;
actualPctMort = Math.Min(actualPctMort, 100);
//Convert to proportion
double actualPropMort = actualPctMort / 100.0;
// Calculate biomass removed
bioRemoved = (int)Math.Round(Tbiomass * actualPropMort);
/*
* // Drought kills oldest cohort 50% of time
* if (bioRemoved < oldestCohortBio)
* {
* int oldBioDiff = oldestCohortBio - bioRemoved;
* if (PlugIn.ModelCore.GenerateUniform() > 0.5)
* bioRemoved += oldBioDiff;
* else
* {
* bioRemoved -= oldBioDiff;
* if (bioRemoved < 0)
* bioRemoved = 0;
* }
* }
*/
int remainBioRem = bioRemoved;
//Remove biomass from cohorts, starting with the oldest
//foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
//{
//foreach (ICohort cohort in speciesCohorts)
foreach (ICohort cohort in cohortList)
{
if (cohort.Species == species)
{
if (remainBioRem > 0)
{
int nonWoody = cohort.ComputeNonWoodyBiomass(site);
int woody = (cohort.Biomass - nonWoody);
if (cohort.Biomass > remainBioRem)
{
if ((remainBioRem / cohort.Biomass) > 0.9)
{
extraRemoved = (cohort.Biomass - remainBioRem);
remainBioRem = cohort.Biomass;
cohortsKilled++;
}
else
{
double nonWoodRatio = (double)nonWoody / (double)woody;
nonWoody = (int)Math.Round(remainBioRem * nonWoodRatio);
woody = remainBioRem - nonWoody;
}
PartialDisturbance.RecordBiomassReduction(cohort, remainBioRem);
remainBioRem = 0;
woodyRemoved += woody;
nonWoodyRemoved += nonWoody;
}
else
{
remainBioRem = remainBioRem - cohort.Biomass;
PartialDisturbance.RecordBiomassReduction(cohort, cohort.Biomass);
cohortsKilled++;
woodyRemoved += woody;
nonWoodyRemoved += nonWoody;
}
}
}
}
}
//}
}
siteBioRemoved += bioRemoved;
bioRemovedSpp += bioRemoved;
Landis.Extension.Succession.Biomass.ForestFloor.AddWoody(woodyRemoved, species, site);
Landis.Extension.Succession.Biomass.ForestFloor.AddLitter(nonWoodyRemoved, species, site);
cohortKilledSpp += cohortsKilled;
extraBioRemovedSpp += extraRemoved;
removedSpp[species.Index] = bioRemovedSpp;
killedSpp[species.Index] = cohortKilledSpp;
extraRemovedSpp[species.Index] = extraBioRemovedSpp;
totalKilled += cohortsKilled;
}
PartialDisturbance.ReduceCohortBiomass(site);
}
SiteVars.DroughtBioRemoved[site] = (ushort)siteBioRemoved;
totalRemoved += siteBioRemoved;
}
double avg_dy = dy_sum / siteCount;
int i = 0;
eventLog.Clear();
EventsLog el = new EventsLog();
el.Time = ModelCore.CurrentTime;
el.AverageDrought = avg_dy;
el.BiomassRemoved = new double[PlugIn.ModelCore.Species.Count];
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
el.BiomassRemoved[i] = removedSpp[species.Index];
i = i + 1;
}
i = 0;
el.TotalBiomassRemoved = totalRemoved;
el.CohortsKilledSpecies = new int[PlugIn.ModelCore.Species.Count];
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
el.CohortsKilledSpecies[i] = killedSpp[species.Index];
i = i + 1;
}
i = 0;
el.TotalCohortsKilled = totalKilled;
el.ExtraRemoved = new double[PlugIn.ModelCore.Species.Count];
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
el.ExtraRemoved[i] = extraRemovedSpp[species.Index];
i = i + 1;
}
eventLog.AddObject(el);
eventLog.WriteToFile();
// Write Biomass Removed map
string path = MapNames.ReplaceTemplateVars(mapNameTemplate, modelCore.CurrentTime);
modelCore.UI.WriteLine(" Writing Drought Biomass Removed map to {0} ...", path);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in modelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(SiteVars.DroughtBioRemoved[site]);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
// Modify establishment
if (avg_dy >= dy_min)
{
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
double drought_Mod = 1.0;
if (parameters.Drought_Sens[species] == 2)
{
drought_Mod = 0.5;
}
else if (parameters.Drought_Sens[species] == 3)
{
drought_Mod = 0.0;
}
if (drought_Mod < 1)
{
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
Landis.Extension.Succession.Biomass.SpeciesData.EstablishModifier[species, ecoregion] *= drought_Mod;
}
}
}
}
else
{
modelCore.UI.WriteLine(" Drought does not exceed threshold this timestep ...");
}
}
