//---------------------------------------------------------------------
///<summary>
/// Run the BDA extension at a particular timestep.
///</summary>
public override void Run()
{
running = true;
PlugIn.ModelCore.UI.WriteLine(" Processing landscape for Biomass Insect events ...");
foreach (IInsect insect in manyInsect)
{
//SiteVars.BiomassRemoved.ActiveSiteValues = 0;
//SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.BiomassRemoved.ActiveSiteValues = 0;
//insect.InitialOutbreakProb.ActiveSiteValues = 0.0;
if (insect.MortalityYear == PlugIn.ModelCore.CurrentTime)
{
Outbreak.Mortality(insect);
}
// Copy the data from current to last
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
insect.LastYearDefoliation[site] = insect.ThisYearDefoliation[site];
}
insect.ActiveOutbreak = false;
PlugIn.ModelCore.NormalDistribution.Mu = 0.0;
PlugIn.ModelCore.NormalDistribution.Sigma = 1.0;
double randomNum = PlugIn.ModelCore.NormalDistribution.NextDouble();
PlugIn.ModelCore.ExponentialDistribution.Lambda = 1 / (insect.MeanDuration); // Mean = 1/lambda
double randomNumE = PlugIn.ModelCore.ExponentialDistribution.NextDouble();
// First, has enough time passed since the last outbreak?
double timeBetweenOutbreaks = insect.MeanTimeBetweenOutbreaks + (insect.StdDevTimeBetweenOutbreaks * randomNum);
double duration = System.Math.Round(randomNumE + 1);
double timeAfterDuration = timeBetweenOutbreaks - duration;
//PlugIn.ModelCore.UI.WriteLine("Calculated time between = {0}. inputMeanTime={1}, inputStdTime={2}.", timeBetweenOutbreaks, insect.MeanTimeBetweenOutbreaks, insect.StdDevTimeBetweenOutbreaks);
//PlugIn.ModelCore.UI.WriteLine("Calculated duration = {0}. inputMeanDura={1}, inputStdDura={2}.", duration, insect.MeanDuration, insect.StdDevDuration);
//PlugIn.ModelCore.UI.WriteLine("Insect Start Time = {0}, Stop Time = {1}.", insect.OutbreakStartYear, insect.OutbreakStopYear);
if (PlugIn.ModelCore.CurrentTime == 1)
{
PlugIn.ModelCore.UI.WriteLine(" Year 1: Setting initial start and stop times.");
insect.OutbreakStartYear = (int)(timeBetweenOutbreaks / 2.0) + 1;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
//PlugIn.ModelCore.UI.WriteLine(" {0} is not active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
}
else if (insect.OutbreakStartYear <= PlugIn.ModelCore.CurrentTime &&
insect.OutbreakStopYear >= PlugIn.ModelCore.CurrentTime)
{
//PlugIn.ModelCore.UI.WriteLine(" An outbreak starts or continues. Start and stop time do not change.");
insect.ActiveOutbreak = true;
//PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
}
if (insect.OutbreakStopYear <= PlugIn.ModelCore.CurrentTime &&
timeAfterDuration > PlugIn.ModelCore.CurrentTime - insect.OutbreakStopYear)
{
//PlugIn.ModelCore.UI.WriteLine(" In between outbreaks, reset start and stop times.");
insect.ActiveOutbreak = true;
//PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
//insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int) timeBetweenOutbreaks;
//insect.OutbreakStopYear = insect.OutbreakStartYear + (int) duration;
}
//PlugIn.ModelCore.UI.WriteLine(" Insect Start Time = {0}, Stop Time = {1}.", insect.OutbreakStartYear, insect.OutbreakStopYear);
if (insect.ActiveOutbreak)
{
// PlugIn.ModelCore.UI.WriteLine(" OutbreakStartYear={0}.", insect.OutbreakStartYear);
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime)
{
// Initialize neighborhoodGrowthReduction with patches
Outbreak.InitializeDefoliationPatches(insect);
}
else
{
insect.NeighborhoodDefoliation.ActiveSiteValues = 0;
}
}
// Now report on the previous year's defoliation, that which has been processed
// through biomass succession.
double sumDefoliation = 0.0;
int numSites0_33 = 0;
int numSites33_66 = 0;
int numSites66_100 = 0;
int numInitialSites = 0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
sumDefoliation += insect.LastYearDefoliation[site];
if (insect.LastYearDefoliation[site] > 0.0 && insect.LastYearDefoliation[site] <= 0.33)
{
numSites0_33++;
}
else if (insect.LastYearDefoliation[site] > 0.33 && insect.LastYearDefoliation[site] <= 0.66)
{
numSites33_66++;
}
else if (insect.LastYearDefoliation[site] > 0.66 && insect.LastYearDefoliation[site] <= 1.0)
{
numSites66_100++;
}
else if (insect.LastYearDefoliation[site] > 1.0)
{
PlugIn.ModelCore.UI.WriteLine("Defoliation exceeds 1.0");
}
if (insect.Disturbed[site] && insect.InitialOutbreakProb[site] > 0)
{
numInitialSites++;
}
}
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime)
{
insect.InitialSites = numInitialSites;
}
double meanDefoliation = 0.0;
if (numSites0_33 + numSites33_66 + numSites66_100 > 0)
{
meanDefoliation = sumDefoliation / (double)(numSites0_33 + numSites33_66 + numSites66_100);
}
//PlugIn.ModelCore.UI.WriteLine(" sumDefoliation={0}, numSites={1}.", sumDefoliation, numSites0_33 + numSites33_66 + numSites66_100);
int totalBioRemoved = 0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//totalBioRemoved += SiteVars.BiomassRemoved[site];
totalBioRemoved += insect.BiomassRemoved[site];
}
//PlugIn.ModelCore.UI.WriteLine(" totalBioRemoved={0}.", totalBioRemoved);
// ONly add to log & output maps during outbreak
if ((insect.ActiveOutbreak && insect.OutbreakStartYear < PlugIn.ModelCore.CurrentTime) || (meanDefoliation > 0) || (insect.LastBioRemoved > 0))
{
if (insect.ActiveOutbreak)
{
log.Write("{0},{1},{2},{3},{4:0.00},{5},{6},{7},{8},{9}",
PlugIn.ModelCore.CurrentTime - 1, //0
insect.Name, //1
insect.OutbreakStartYear, //2
insect.OutbreakStopYear, //3
meanDefoliation, //4
numSites0_33, //5
numSites33_66, //6
numSites66_100, //7
insect.InitialSites, //8
insect.LastBioRemoved //9
);
}
else
{
log.Write("{0},{1},{2},{3},{4:0.00},{5},{6},{7},{8},{9}",
PlugIn.ModelCore.CurrentTime - 1, //0
insect.Name, //1
insect.LastStartYear, //2
insect.LastStopYear, //3
meanDefoliation, //4
numSites0_33, //5
numSites33_66, //6
numSites66_100, //7
insect.InitialSites, //8
insect.LastBioRemoved //9
);
}
//foreach (IEcoregion ecoregion in Ecoregions.Dataset)
// log.Write(",{0}", 1);
log.WriteLine("");
//----- Write Insect GrowthReduction maps --------
string path = MapNames.ReplaceTemplateVars(mapNameTemplate, insect.Name, PlugIn.ModelCore.CurrentTime - 1);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(insect.LastYearDefoliation[site] * 100.0);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
//----- Write Initial Patch maps --------
string path2 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("InitialPatchMap-" + insect.Name), PlugIn.ModelCore.CurrentTime - 1);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path2, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
if (insect.Disturbed[site])
{
pixel.MapCode.Value = (short)(insect.InitialOutbreakProb[site] * 100);
}
else
{
pixel.MapCode.Value = 0;
}
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
//----- Write Biomass Reduction maps --------
string path3 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("BiomassRemoved-" + insect.Name), PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path3, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(insect.BiomassRemoved[site] / 100); // convert to Mg/ha
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
}
insect.ThisYearDefoliation.ActiveSiteValues = 0.0; //reset this year to 0 for all sites
insect.LastBioRemoved = totalBioRemoved;
if (insect.OutbreakStopYear <= PlugIn.ModelCore.CurrentTime &&
timeAfterDuration > PlugIn.ModelCore.CurrentTime - insect.OutbreakStopYear)
{
insect.LastStartYear = insect.OutbreakStartYear;
insect.LastStopYear = insect.OutbreakStopYear;
insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int)timeBetweenOutbreaks;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration;
//PlugIn.ModelCore.UI.WriteLine(" Insect Start Time = {0}, Stop Time = {1}.", insect.OutbreakStartYear, insect.OutbreakStopYear);
}
}
}
//---------------------------------------------------------------------
///<summary>
/// Run Biomass Insects extension at a particular timestep.
///</summary>
public override void Run()
{
running = true;
PlugIn.ModelCore.UI.WriteLine(" Processing landscape for Biomass Insect events ...");
SiteVars.SiteDefoliation.ActiveSiteValues = 0;
foreach (IInsect insect in manyInsect)
{
//SiteVars.BiomassRemoved.ActiveSiteValues = 0;
//SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
if (insect.MortalityYear == PlugIn.ModelCore.CurrentTime)
{
Outbreak.Mortality(insect);
}
if (insect.MortalityYear != PlugIn.ModelCore.CurrentTime)
{
insect.LastBioRemoved = 0;
}
// Copy the data from current to last
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double thisYearDefol = insect.ThisYearDefoliation[site];
insect.LastYearDefoliation[site] = thisYearDefol;
SiteVars.SiteDefoliation[site] += (int)Math.Round(thisYearDefol * 100);
if (thisYearDefol > 0)
{
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime - 1;
SiteVars.InsectName[site] = insect.Name;
}
}
insect.ThisYearDefoliation.ActiveSiteValues = 0.0;
insect.ActiveOutbreak = false;
insect.SingleOutbreakYear = false;
//PlugIn.ModelCore.NormalDistribution.Mu = 0.0;
//PlugIn.ModelCore.NormalDistribution.Sigma = 1.0;
//double randomNum = PlugIn.ModelCore.NormalDistribution.NextDouble();
//randomNum = PlugIn.ModelCore.NormalDistribution.NextDouble();
double randomNum = Distribution.GenerateRandomNum(DistributionType.Normal, 0.0, 1.0);
DistributionType distDuration = insect.DurationDistribution;
double randomNumE = Distribution.GenerateRandomNum(distDuration, insect.DurationParameter1, insect.DurationParameter2);
// First, has enough time passed since the last outbreak? This is calculated each year,
// but only used in last year of an outbreak to generate next outbreak characteristics.
double timeBetweenOutbreaks = insect.MeanTimeBetweenOutbreaks + (insect.StdDevTimeBetweenOutbreaks * randomNum);
double duration = System.Math.Round(randomNumE);
if (distDuration == DistributionType.Exponential || distDuration == DistributionType.Normal)
{
duration = System.Math.Max(duration + 1, 1); // Duration cannot be less than 1. Added to allow Normal distribution parameters.
}
else
{
duration = System.Math.Max(duration, 1); // Duration cannot be less than 1.
}
// Apply optional maximum - if not used maxDur = Inf
if (duration > insect.MaxDuration)
{
duration = insect.MaxDuration;
}
double timeAfterDuration = timeBetweenOutbreaks - duration;
// Users can parameterize model to have overlapping outbreaks, but then patches will not initialize correctly.
// Do below to prevent overlapping outbreaks of same insect. This will affect the realized distribution of time between outbreaks somewhat.
while (timeAfterDuration <= 1.0)
{
PlugIn.ModelCore.UI.WriteLine("CAUTION: Time Between Outbreaks TOO SMALL (< 1), you may need to adjust timing parameters: {0}.", timeAfterDuration);
timeBetweenOutbreaks = timeBetweenOutbreaks + 1;
timeAfterDuration = timeBetweenOutbreaks - duration;
}
//PlugIn.ModelCore.UI.WriteLine("Calculated time between = {0:0.00}. inputMeanTime={1:0.00}, inputStdTime={2:0.00}., timeAftDur={3:0.00}.", timeBetweenOutbreaks, insect.MeanTimeBetweenOutbreaks, insect.StdDevTimeBetweenOutbreaks, timeAfterDuration);
// The logic below determines whether an outbreak is active. And sets a new outbreak duration and timeBetweenOutbreaks
// for the next outbreak if is the last year of an outbreak.
// The very first outbreak is set first.
if (PlugIn.ModelCore.CurrentTime == 1)
{
PlugIn.ModelCore.UI.WriteLine(" Year 1: Setting initial start and stop times.");
double randomNum1 = PlugIn.ModelCore.GenerateUniform();
//insect.OutbreakStartYear = (int) (timeBetweenOutbreaks / 2.0) + 1;
insect.OutbreakStartYear = Math.Max(2, (int)(randomNum1 * timeBetweenOutbreaks + 1)); // New, try making 1st start year more random. 1st outbreak has to occur > year1 to for InitializeDefoliationPatches to work properly.
insect.OutbreakStartYear = Math.Max(insect.OutbreakStartYear, insect.StartYear); // BRM - optional start year (first outbreak can't be before StartYear)
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
// PlugIn.ModelCore.UI.WriteLine(" {0} is not active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
}
else if (insect.OutbreakStartYear <= PlugIn.ModelCore.CurrentTime &&
insect.OutbreakStopYear > PlugIn.ModelCore.CurrentTime) // first year of a multiyear outbreak
{
// PlugIn.ModelCore.UI.WriteLine(" An outbreak starts or continues. Start and stop time do not change.");
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
}
//Special case for single year outbreak.
else if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime &&
insect.OutbreakStopYear == PlugIn.ModelCore.CurrentTime)
{
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
if (insect.OutbreakStartYear == insect.OutbreakStopYear) // shouldn't need this. JRF
{
insect.SingleOutbreakYear = true;
}
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int)timeBetweenOutbreaks;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
}
else if (insect.OutbreakStopYear <= PlugIn.ModelCore.CurrentTime &&
timeAfterDuration > PlugIn.ModelCore.CurrentTime - insect.OutbreakStopYear)
{
// PlugIn.ModelCore.UI.WriteLine(" In between outbreaks, reset start and stop times.");
insect.ActiveOutbreak = true;
PlugIn.ModelCore.UI.WriteLine(" {0} is active. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
insect.MortalityYear = PlugIn.ModelCore.CurrentTime + 1;
insect.LastStartYear = insect.OutbreakStartYear; // Added here for Brian's log file.
insect.LastStopYear = insect.OutbreakStopYear; // Added here for Brian's log file.
insect.OutbreakStartYear = PlugIn.ModelCore.CurrentTime + (int)timeBetweenOutbreaks;
insect.OutbreakStopYear = insect.OutbreakStartYear + (int)duration - 1;
}
PlugIn.ModelCore.UI.WriteLine(" Insect Start Time = {0}, Stop Time = {1}.", insect.OutbreakStartYear, insect.OutbreakStopYear);
// Now that logic determining when an outbreak will be active is done, tell model what to do when outbreak is occurring.
if (insect.ActiveOutbreak)
{
// PlugIn.ModelCore.UI.WriteLine(" OutbreakStartYear={0}.", insect.OutbreakStartYear);
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime || insect.SingleOutbreakYear)
{
// Initialize neighborhoodGrowthReduction with patches
Outbreak.InitializeDefoliationPatches(insect);
}
else
{
insect.NeighborhoodDefoliation.ActiveSiteValues = 0;
}
}
// Now report on the previous year's defoliation, that which has been processed
// through biomass succession. Calculations for logfile.
double sumDefoliation = 0.0;
double meanDefoliation = 0.0;
int numSites0_33 = 0;
int numSites33_66 = 0;
int numSites66_100 = 0;
int numInitialSites = 0;
int numSitesActive = 0; // Just get a sum of all active sites to calculate mean defoliation accurately for log file.
// ONly calculate for log file when outbreak or mortality is active <- Modified, JRF, add to log file each year.
if (insect.ActiveOutbreak || insect.SingleOutbreakYear || (insect.LastStopYear + 1 >= PlugIn.ModelCore.CurrentTime) || (insect.LastBioRemoved > 0))
{
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
sumDefoliation += insect.LastYearDefoliation[site];
if (insect.LastYearDefoliation[site] > 0.0 && insect.LastYearDefoliation[site] <= 0.33)
{
numSites0_33++;
}
if (insect.LastYearDefoliation[site] > 0.33 && insect.LastYearDefoliation[site] <= 0.66)
{
numSites33_66++;
}
if (insect.LastYearDefoliation[site] > 0.66 && insect.LastYearDefoliation[site] <= 1.0)
{
numSites66_100++;
}
if (insect.Disturbed[site] && SiteVars.InitialOutbreakProb[site] > 0)
{
numInitialSites++;
}
numSitesActive++;
}
if (insect.OutbreakStartYear == PlugIn.ModelCore.CurrentTime)
{
insect.InitialSites = numInitialSites;
}
if (numSites0_33 + numSites33_66 + numSites66_100 > 0)
{
meanDefoliation = sumDefoliation / (double)numSitesActive;
}
//PlugIn.ModelCore.UI.WriteLine(" sumDefoliation={0}, numSites={1}.", sumDefoliation, numSites0_33 + numSites33_66 + numSites66_100);
}
int totalBioRemoved = 0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
totalBioRemoved += SiteVars.BiomassRemoved[site]; // kg across all defoliated sites
}
insect.LastBioRemoved = totalBioRemoved; //Assign variables for the logfile
// PlugIn.ModelCore.UI.WriteLine(" totalBioRemoved={0}.", totalBioRemoved);
// ONly add to log & output maps during outbreak <- Modified, JRF, add to log file each year.
//if ((insect.ActiveOutbreak && insect.OutbreakStartYear < PlugIn.ModelCore.CurrentTime) || (meanDefoliation > 0) || (insect.LastBioRemoved > 0))
//{
/* Old code for log file
* if (meanDefoliation > 0)
* {
*
* log.Write("{0},{1},{2},{3},{4:0.0000},{5},{6},{7},{8},{9}",
* PlugIn.ModelCore.CurrentTime-1, //0
* insect.Name, //1
* insect.LastStartYear, //2
* insect.LastStopYear, //3
* meanDefoliation, //4
* numSites0_33, //5
* numSites33_66, //6
* numSites66_100, //7
* insect.InitialSites, //8
* insect.LastBioRemoved //9
* );
* }
*
* else
* {
* log.Write("{0},{1},{2},{3},{4:0.0000},{5},{6},{7},{8},{9}",
* PlugIn.ModelCore.CurrentTime - 1, //0
* insect.Name, //1
* 0, //2
* 0, //3
* meanDefoliation, //4
* numSites0_33, //5
* numSites33_66, //6
* numSites66_100, //7
* 0, //8
* insect.LastBioRemoved //9
* );
* }
*
*
* //foreach (IEcoregion ecoregion in Ecoregions.Dataset)
* // log.Write(",{0}", 1);
*
* log.WriteLine("");
*/
eventLog.Clear();
EventsLog el = new EventsLog();
el.Time = PlugIn.ModelCore.CurrentTime - 1;
el.InsectName = insect.Name;
el.MeanDefoliation = meanDefoliation;
el.NumSitesDefoliated0_33 = numSites0_33;
el.NumSitesDefoliated33_66 = numSites33_66;
el.NumSitesDefoliated66_100 = numSites66_100;
el.NumOutbreakInitialSites = insect.InitialSites;
el.MortalityBiomass = insect.LastBioRemoved;
if (insect.ActiveOutbreak)
{
el.StartYear = insect.OutbreakStartYear;
el.StopYear = insect.OutbreakStopYear;
}
else
{
el.StartYear = insect.LastStartYear;
el.StopYear = insect.LastStopYear;
}
eventLog.AddObject(el);
eventLog.WriteToFile();
//----- Write Insect Defoliation/GrowthReduction maps --------
string path = MapNames.ReplaceTemplateVars(mapNameTemplate, insect.Name, PlugIn.ModelCore.CurrentTime - 1);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(insect.LastYearDefoliation[site] * 100.0);
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
//----- Write Initial Patch maps --------
string path2 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("InitialPatchMap" + insect.Name), PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path2, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
if (insect.Disturbed[site])
{
pixel.MapCode.Value = (short)(SiteVars.InitialOutbreakProb[site] * 100);
}
else
{
pixel.MapCode.Value = 0;
}
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
//Zero out the InitialOutbreakProb after output maps are written.
SiteVars.InitialOutbreakProb[site] = 0;
}
}
//----- Write Biomass Reduction maps --------
string path3 = MapNames.ReplaceTemplateVars(mapNameTemplate, ("BiomassRemoved" + insect.Name), PlugIn.ModelCore.CurrentTime);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path3, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
if (SiteVars.BiomassRemoved[site] > 0)
{
pixel.MapCode.Value = Math.Max((short)1, (short)(SiteVars.BiomassRemoved[site] / 100)); // convert to Mg/ha
}
else
{
pixel.MapCode.Value = 0;
}
}
else
{
// Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
//Zero out the BiomassRemoved after the last insect mortality event in a given year.
SiteVars.BiomassRemoved[site] = 0;
}
}
//}
//insect.ThisYearDefoliation.ActiveSiteValues = 0.0; //reset this year to 0 for all sites, this was already done at the top of loop to initialize defoliation patchs, Outbreak.cs
}
}
public static void InitializeMetadata(int Timestep,
string MapFileName,
string logFileName,
IEnumerable <IInsect> insects,
ICore mCore)
{
ScenarioReplicationMetadata scenRep = new ScenarioReplicationMetadata()
{
RasterOutCellArea = PlugIn.ModelCore.CellArea,
TimeMin = PlugIn.ModelCore.StartTime,
TimeMax = PlugIn.ModelCore.EndTime,
};
Extension = new ExtensionMetadata(mCore)
{
Name = PlugIn.ExtensionName,
TimeInterval = 1, //Timestep, //change this to PlugIn.TimeStep for other extensions
ScenarioReplicationMetadata = scenRep
};
//---------------------------------------
// table outputs:
//---------------------------------------
PlugIn.eventLog = new MetadataTable <EventsLog>("insects-log.csv");
OutputMetadata tblOut_events = new OutputMetadata()
{
Type = OutputType.Table,
Name = "EventsLog",
FilePath = PlugIn.eventLog.FilePath,
Visualize = false,
};
tblOut_events.RetriveFields(typeof(EventsLog));
Extension.OutputMetadatas.Add(tblOut_events);
//---------------------------------------
// map outputs:
//---------------------------------------
foreach (IInsect insect in insects)
{
string mapPath = MapNames.ReplaceTemplateVarsMetadata(MapFileName, insect.Name);
OutputMetadata mapOut_GrowthReduction = new OutputMetadata()
{
Type = OutputType.Map,
Name = "Growth Reduction",
FilePath = @mapPath,
Map_DataType = MapDataType.Continuous,
Map_Unit = FieldUnits.Percentage,
Visualize = false,
};
Extension.OutputMetadatas.Add(mapOut_GrowthReduction);
mapPath = MapNames.ReplaceTemplateVarsMetadata(MapFileName, ("InitialPatchMap-" + insect.Name));
OutputMetadata mapOut_InitialPatchProb = new OutputMetadata()
{
Type = OutputType.Map,
Name = "Initial Outbreak Probabilities",
FilePath = @mapPath,
Map_DataType = MapDataType.Continuous,
Map_Unit = FieldUnits.Percentage,
Visualize = false,
};
Extension.OutputMetadatas.Add(mapOut_InitialPatchProb);
mapPath = MapNames.ReplaceTemplateVarsMetadata(MapFileName, ("BiomassRemoved-" + insect.Name));
OutputMetadata mapOut_BiomassRemoved = new OutputMetadata()
{
Type = OutputType.Map,
Name = System.String.Format(insect.Name + " Biomass Mortality"),
FilePath = @mapPath,
Map_DataType = MapDataType.Continuous,
Map_Unit = FieldUnits.Mg_ha,
Visualize = true,
};
Extension.OutputMetadatas.Add(mapOut_BiomassRemoved);
}
//---------------------------------------
MetadataProvider mp = new MetadataProvider(Extension);
mp.WriteMetadataToXMLFile("Metadata", Extension.Name, Extension.Name);
}