//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
//PlugIn.ModelCore.UI.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
PartialDisturbance.ReduceCohortBiomass(site);
if (insect.BiomassRemoved[site] > 0)
{
//PlugIn.ModelCore.UI.WriteLine(" Biomass removed at {0}/{1}: {2}.", site.Location.Row, site.Location.Column, SiteVars.BiomassRemoved[site]);
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime;
}
}
}
//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
//PlugIn.ModelCore.Log.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
PartialDisturbance.ReduceCohortBiomass(site);
if (SiteVars.BiomassRemoved[site] > 0)
{
//PlugIn.ModelCore.Log.WriteLine(" Biomass removed at {0}/{1}: {2}.", site.Location.Row, site.Location.Column, SiteVars.BiomassRemoved[site]);
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime;
}
}
}
//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
UI.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, Model.Core.CurrentTime);
foreach (ActiveSite site in Model.Core.Landscape)
{
PartialDisturbance.ReduceCohortBiomass(site);
if (SiteVars.BiomassRemoved[site] > 0)
{
SiteVars.TimeOfLastEvent[site] = Model.Core.CurrentTime;
}
}
}
//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
// PlugIn.ModelCore.UI.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//Try zeroing out biomass removed here @ start of each defoliation mortality year. Remove if doesn't work.
if (SiteVars.BiomassRemoved[site] > 0)
SiteVars.BiomassRemoved[site] = 0;
PartialDisturbance.ReduceCohortBiomass(site);
if (SiteVars.BiomassRemoved[site] > 0)
{
// PlugIn.ModelCore.UI.WriteLine(" Biomass removed at {0}/{1}: {2}.", site.Location.Row, site.Location.Column, SiteVars.BiomassRemoved[site]);
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime;
SiteVars.InsectName[site] = insect.Name;
}
}
}
//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
UI.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, Model.Core.CurrentTime);
foreach (ActiveSite site in Model.Core.Landscape)
{
//Try zeroing out biomass removed here @ start of each defoliation mortality year. Remove if doesn't work.
if (SiteVars.BiomassRemoved[site] > 0)
SiteVars.BiomassRemoved[site] = 0;
PartialDisturbance.ReduceCohortBiomass(site);
if (SiteVars.BiomassRemoved[site] > 0)
{
SiteVars.TimeOfLastEvent[site] = Model.Core.CurrentTime;
//SiteVars.WoodyDebris[site].AddMass(SiteVars.BiomassRemoved[site], 0.1);
}
}
}
//---------------------------------------------------------------------
///<summary>
// Go through all active sites and damage them. Mortality should occur the year FOLLOWING an active year.
///</summary>
public static void Mortality(IInsect insect)
{
// PlugIn.ModelCore.UI.WriteLine(" {0} mortality. StartYear={1}, StopYear={2}, CurrentYear={3}.", insect.Name, insect.OutbreakStartYear, insect.OutbreakStopYear, PlugIn.ModelCore.CurrentTime);
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//Try zeroing out biomass removed here @ start of each defoliation mortality year. Remove if doesn't work.
if (SiteVars.BiomassRemoved[site] > 0)
{
SiteVars.BiomassRemoved[site] = 0;
}
//PlugIn.ModelCore.UI.WriteLine(" Reducing cohort biomass for {0}...", insect.Name);
PartialDisturbance.ReduceCohortBiomass(site);
//PartialDisturbance.AddPartialMortalityToWoodyDebris(site);
if (SiteVars.BiomassRemoved[site] > 0)
{
// PlugIn.ModelCore.UI.WriteLine(" Biomass removed at {0}/{1}: {2}.", site.Location.Row, site.Location.Column, SiteVars.BiomassRemoved[site]);
SiteVars.TimeOfLastEvent[site] = PlugIn.ModelCore.CurrentTime;
}
}
}
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
PlugIn.ModelCore.UI.WriteLine(" Initializing Defoliation Patches... ");
SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
insect.NeighborhoodDefoliation.ActiveSiteValues = 0.0;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
foreach (ISpeciesCohorts speciesCohorts in SiteVars.Cohorts[site])
//foreach (ISpeciesCohorts speciesCohorts in (Landis.Library.BiomassCohorts.ISpeciesCohorts) SiteVars.Cohorts[site]) // Rob's suggestion. Raised an error...
{
foreach (ICohort cohort in speciesCohorts)
{
suscIndexSum += cohort.Biomass * (insect.SppTable[cohort.Species.Index].Susceptibility);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if (suscIndexSum <= 0 || sumBio <= 0)
{
SiteVars.InitialOutbreakProb[site] = 0.0;
continue;
}
int suscIndex = (int)Math.Round(suscIndexSum / sumBio) - 1;
if (suscIndex > 2.0 || suscIndex < 0)
{
PlugIn.ModelCore.UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, suscIndex, suscIndexSum, sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors and draw initial defoliation from the most intense neighborhood distribution:
DistributionType dist = insect.SusceptibleTable[suscIndex].Distribution_80.Name;
// PlugIn.ModelCore.UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[suscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[suscIndex].Distribution_80.Value2;
double probability = Distribution.GenerateRandomNum(dist, value1, value2);
if (probability > 1.0 || probability < 0)
{
PlugIn.ModelCore.UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
// Try cleaning up defoliation patterns so areas outside main patches are less defoliated
// How about using Brian's patch shape calibrator here instead. Divide probability by susIndex * PSC, to tie initial patch probs. more closely to host abundance...
//SiteVars.InitialOutbreakProb[site] = probability;
SiteVars.InitialOutbreakProb[site] = probability / ((double)suscIndex + 1);
// PlugIn.ModelCore.UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//get a random site from the stand
double randomNum = PlugIn.ModelCore.GenerateUniform();
double randomNum2 = PlugIn.ModelCore.GenerateUniform();
//Create random variability in outbreak area within a simulation so outbreaks are more variable.
double initialAreaCalibratorRandomNum = (randomNum2 - 0.5) * insect.InitialPatchOutbreakSensitivity / 2;
//Start spreading!
if (randomNum < SiteVars.InitialOutbreakProb[site] * (insect.InitialPatchOutbreakSensitivity + initialAreaCalibratorRandomNum))
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue <ActiveSite> sitesToConsider = new Queue <ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
// PlugIn.ModelCore.UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliation is given a value.
// The value is used in Defoliate.DefoliateCohort()
insect.NeighborhoodDefoliation[currentSite] = SiteVars.InitialOutbreakProb[currentSite];
areaSelected += PlugIn.ModelCore.CellArea;
//insect.Disturbed[currentSite] = true;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
//double maxNeighborProb = 0.0;
//Site maxNeighbor = currentSite;
//bool foundNewNeighbor = false;
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null &&
neighbor.IsActive &&
!sitesToConsider.Contains((ActiveSite)neighbor) &&
!insect.Disturbed[neighbor])
{
insect.Disturbed[currentSite] = true;
randomNum = PlugIn.ModelCore.GenerateUniform();
/*if (SiteVars.InitialOutbreakProb[neighbor] > maxNeighborProb)
* {
* maxNeighbor = currentSite.GetNeighbor(loc);
* maxNeighborProb = SiteVars.InitialOutbreakProb[neighbor];
* foundNewNeighbor = true;
* }*/
//check if it's a valid neighbor:
if (SiteVars.InitialOutbreakProb[neighbor] > randomNum)
{
sitesToConsider.Enqueue((ActiveSite)neighbor);
}
}
}
//if(foundNewNeighbor)
// sitesToConsider.Enqueue((ActiveSite) maxNeighbor);
}
// PlugIn.ModelCore.UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
}
}
}
//---------------------------------------------------------------------
// Outbreak Constructor
public Outbreak(IInsect insect)
{
this.outbreakParms = insect;
}
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
UI.WriteLine(" Initializing Defoliation Patches... ");
SiteVars.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
cohorts = Model.Core.SuccessionCohorts as ILandscapeCohorts;
foreach(ActiveSite site in Model.Core.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
foreach(ISpecies species in Model.Core.Species)
{
ISpeciesCohorts speciesCohorts = cohorts[site][species];
if(speciesCohorts == null)
continue;
foreach (ICohort cohort in speciesCohorts)
{
suscIndexSum += cohort.Biomass * (insect.SppTable[cohort.Species.Index].Susceptibility);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if(suscIndexSum <= 0 || sumBio <=0)
{
SiteVars.InitialOutbreakProb[site] = 0.0;
continue;
}
int suscIndex = (int) Math.Round(suscIndexSum /sumBio) - 1;
if (suscIndex > 2.0 || suscIndex < 0)
{
UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, suscIndex,suscIndexSum,sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors whatsoever:
DistributionType dist = insect.SusceptibleTable[suscIndex].Distribution_80.Name;
//UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[suscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[suscIndex].Distribution_80.Value2;
double probability = Distribution.GenerateRandomNum(dist, value1, value2);
if(probability > 1.0 || probability < 0)
{
UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
SiteVars.InitialOutbreakProb[site] = probability;
//UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach(ActiveSite site in Model.Core.Landscape)
{
//get a random site from the stand
double randomNum = Landis.Util.Random.GenerateUniform();
if(randomNum < SiteVars.InitialOutbreakProb[site] * insect.InitialAreaCalibrator)
//Start spreading!
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue<ActiveSite> sitesToConsider = new Queue<ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
//UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliaiton is given a value.
// The value is used in Defoliate.DefoliateCohort()
SiteVars.NeighborhoodDefoliation[currentSite] = SiteVars.InitialOutbreakProb[currentSite];
areaSelected += Model.Core.CellArea;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null
&& neighbor.IsActive
&& !sitesToConsider.Contains((ActiveSite) neighbor)
&& !insect.Disturbed[neighbor])
{
insect.Disturbed[currentSite] = true;
randomNum = Landis.Util.Random.GenerateUniform();
//UI.WriteLine("That darn Queue! randomnum={0}, prob={1}.", randomNum, SiteVars.InitialOutbreakProb[neighbor]);
//check if it's a valid neighbor:
if (SiteVars.InitialOutbreakProb[neighbor] > randomNum)
{
sitesToConsider.Enqueue((ActiveSite) neighbor);
}
}
}
} //endwhile
//UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
} //endif
} //endfor
} //endfunc
//---------------------------------------------------------------------
// Outbreak Constructor
public Outbreak(IInsect insect)
{
this.outbreakParms = insect;
}
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
PlugIn.ModelCore.UI.WriteLine(" Initializing Defoliation Patches... ");
insect.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
foreach(ActiveSite site in PlugIn.ModelCore.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
double protectBiomass = 0.0;
Landis.Library.BiomassCohorts.ISiteCohorts siteCohorts = SiteVars.Cohorts[site];
foreach (ISpeciesCohorts speciesCohorts in siteCohorts)
{
foreach (ICohort cohort in speciesCohorts)
{
int sppSuscIndex = insect.Susceptibility[cohort.Species];
if (sppSuscIndex == 4)
{
protectBiomass += cohort.Biomass;
sppSuscIndex = 3;
}
suscIndexSum += cohort.Biomass * (sppSuscIndex);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if(suscIndexSum <= 0 || sumBio <=0)
{
insect.InitialOutbreakProb[site] = 0.0;
continue;
}
int siteSuscIndex = (int) Math.Round(suscIndexSum /sumBio) - 1;
double protectProp = protectBiomass / sumBio;
if (siteSuscIndex > 2.0 || siteSuscIndex < 0)
{
PlugIn.ModelCore.UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, siteSuscIndex,suscIndexSum,sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors whatsoever:
DistributionType dist = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Name;
//PlugIn.ModelCore.UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value2;
double probability = Distribution.GenerateRandomNum(dist, value1, value2);
// Account for protective effect of Susc Class 4
if (protectProp > 0)
{
double slope = 1.0;
double protectReduce = 1- (protectProp * slope);
if (protectReduce > 1)
protectReduce = 1;
if (protectReduce < 0)
protectReduce = 0;
probability = probability * protectReduce;
}
if(probability > 1.0 || probability < 0)
{
PlugIn.ModelCore.UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
insect.InitialOutbreakProb[site] = probability; // This probability reflects the protective effects
//PlugIn.ModelCore.UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach(ActiveSite site in PlugIn.ModelCore.Landscape)
{
//get a random site from the stand
double randomNum = PlugIn.ModelCore.GenerateUniform();
double randomNum2 = PlugIn.ModelCore.GenerateUniform();
//Create random variability in outbreak area within a simulation so outbreaks are more variable.
double initialAreaCalibratorRandomNum = (randomNum2 - 0.5) * insect.InitialPatchOutbreakSensitivity / 2;
//Start spreading!
if (randomNum < insect.InitialOutbreakProb[site] * (insect.InitialPatchOutbreakSensitivity + initialAreaCalibratorRandomNum))
//if(randomNum < SiteVars.InitialOutbreakProb[site] * insect.InitialPatchOutbreakSensitivity)
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue<ActiveSite> sitesToConsider = new Queue<ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
//PlugIn.ModelCore.UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliaiton is given a value.
// The value is used in Defoliate.DefoliateCohort()
insect.NeighborhoodDefoliation[currentSite] = insect.InitialOutbreakProb[currentSite];
areaSelected += PlugIn.ModelCore.CellArea;
insect.Disturbed[currentSite] = true;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
//double maxNeighborProb = 0.0;
//Site maxNeighbor = currentSite;
//bool foundNewNeighbor = false;
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null
&& neighbor.IsActive
&& !sitesToConsider.Contains((ActiveSite) neighbor)
&& !insect.Disturbed[neighbor])
{
//insect.Disturbed[currentSite] = true;
randomNum = PlugIn.ModelCore.GenerateUniform();
/*if (SiteVars.InitialOutbreakProb[neighbor] > maxNeighborProb)
{
maxNeighbor = currentSite.GetNeighbor(loc);
maxNeighborProb = SiteVars.InitialOutbreakProb[neighbor];
foundNewNeighbor = true;
}*/
//check if it's a valid neighbor:
if (insect.InitialOutbreakProb[neighbor] * insect.InitialPatchShapeCalibrator > randomNum)
{
sitesToConsider.Enqueue((ActiveSite) neighbor);
}
}
}
//if(foundNewNeighbor)
// sitesToConsider.Enqueue((ActiveSite) maxNeighbor);
}
//PlugIn.ModelCore.UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
}
}
}
protected override IInputParameters Parse()
{
InputVar <string> landisData = new InputVar <string>("LandisData");
ReadVar(landisData);
if (landisData.Value.Actual != PlugIn.ExtensionName)
{
throw new InputValueException(landisData.Value.String, "The value is not \"{0}\"", PlugIn.ExtensionName);
}
InputParameters parameters = new InputParameters();
InputVar <int> timestep = new InputVar <int>("Timestep");
ReadVar(timestep);
parameters.Timestep = timestep.Value;
//----------------------------------------------------------
// Read in Map and Log file names.
InputVar <string> mapNames = new InputVar <string>("MapNames");
ReadVar(mapNames);
parameters.MapNamesTemplate = mapNames.Value;
InputVar <string> logFile = new InputVar <string>("LogFile");
ReadVar(logFile);
parameters.LogFileName = logFile.Value;
//----------------------------------------------------------
// Last, read in Insect File names,
// then parse the data in those files into insect parameters.
InputVar <string> insectFileName = new InputVar <string>("InsectInputFiles");
ReadVar(insectFileName);
List <IInsect> insectParameterList = new List <IInsect>();
InsectParser insectParser = new InsectParser();
IInsect insectParameters = Landis.Data.Load <IInsect>(insectFileName.Value, insectParser);
insectParameterList.Add(insectParameters);
// Check that insectParameters for first insect loaded correctly...
if (insectParameters == null)
{
PlugIn.ModelCore.UI.WriteLine(" Biomass Insect: Insect Parameters NOT loading correctly.");
}
else
{
PlugIn.ModelCore.UI.WriteLine("Name of Insect = {0}", insectParameters.Name);
}
while (!AtEndOfInput)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(insectFileName, currentLine);
insectParameters = Landis.Data.Load <IInsect>(insectFileName.Value, insectParser);
insectParameterList.Add(insectParameters);
// Try moving below loop here because right now it only lists the last insect in ManyInsect...
//foreach (IInsect activeInsect in insectParameterList)
//{
// Check that insectParameters for 2+ insects loaded correctly...
if (insectParameters == null)
{
PlugIn.ModelCore.UI.WriteLine(" Biomass Insect: Insect Parameters NOT loading correctly.");
}
else
{
PlugIn.ModelCore.UI.WriteLine("Name of Insect = {0}", insectParameters.Name);
}
//}
GetNextLine();
}
/*foreach(IInsect activeInsect in insectParameterList)
* {
* if(insectParameters == null)
* PlugIn.ModelCore.UI.WriteLine(" Biomass Insect: Insect Parameters NOT loading correctly.");
* else
* PlugIn.ModelCore.UI.WriteLine("Name of Insect = {0}", insectParameters.Name);
*
* }*/
parameters.ManyInsect = insectParameterList;
return(parameters);
}
//---------------------------------------------------------------------
// Initialize landscape with patches of defoliation during the first year
public static void InitializeDefoliationPatches(IInsect insect)
{
PlugIn.ModelCore.UI.WriteLine(" Initializing Defoliation Patches... ");
insect.InitialOutbreakProb.ActiveSiteValues = 0.0;
insect.Disturbed.ActiveSiteValues = false;
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
double suscIndexSum = 0.0;
double sumBio = 0.0;
double protectBiomass = 0.0;
Landis.Library.BiomassCohorts.ISiteCohorts siteCohorts = SiteVars.Cohorts[site];
foreach (ISpeciesCohorts speciesCohorts in siteCohorts)
{
foreach (ICohort cohort in speciesCohorts)
{
int sppSuscIndex = insect.Susceptibility[cohort.Species];
if (sppSuscIndex == 4)
{
protectBiomass += cohort.Biomass;
sppSuscIndex = 3;
}
suscIndexSum += cohort.Biomass * (sppSuscIndex);
sumBio += cohort.Biomass;
}
}
// If no biomass, no chance of defoliation, go to the next site.
if (suscIndexSum <= 0 || sumBio <= 0)
{
insect.InitialOutbreakProb[site] = 0.0;
continue;
}
int siteSuscIndex = (int)Math.Round(suscIndexSum / sumBio) - 1;
double protectProp = protectBiomass / sumBio;
if (siteSuscIndex > 2.0 || siteSuscIndex < 0)
{
PlugIn.ModelCore.UI.WriteLine("SuscIndex < 0 || > 2. Site R/C={0}/{1},suscIndex={2},suscIndexSum={3},sumBio={4}.", site.Location.Row, site.Location.Column, siteSuscIndex, suscIndexSum, sumBio);
throw new ApplicationException("Error: SuscIndex is not between 2.0 and 0.0");
}
// Assume that there are no neighbors whatsoever:
DistributionType dist = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Name;
//PlugIn.ModelCore.UI.WriteLine("suscIndex={0},suscIndexSum={1},cohortBiomass={2}.", suscIndex,suscIndexSum,sumBio);
double value1 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value1;
double value2 = insect.SusceptibleTable[siteSuscIndex].Distribution_80.Value2;
double probability = Distribution.GenerateRandomNum(dist, value1, value2);
// Account for protective effect of Susc Class 4
if (protectProp > 0)
{
double slope = 1.0;
double protectReduce = 1 - (protectProp * slope);
if (protectReduce > 1)
{
protectReduce = 1;
}
if (protectReduce < 0)
{
protectReduce = 0;
}
probability = probability * protectReduce;
}
if (probability > 1.0 || probability < 0)
{
PlugIn.ModelCore.UI.WriteLine("Initial Defoliation Probility < 0 || > 1. Site R/C={0}/{1}.", site.Location.Row, site.Location.Column);
throw new ApplicationException("Error: Probability is not between 1.0 and 0.0");
}
insect.InitialOutbreakProb[site] = probability; // This probability reflects the protective effects
//PlugIn.ModelCore.UI.WriteLine("Susceptiblity index={0}. Outbreak Probability={1:0.00}. R/C={2}/{3}.", suscIndex, probability, site.Location.Row, site.Location.Column);
}
foreach (ActiveSite site in PlugIn.ModelCore.Landscape)
{
//get a random site from the stand
double randomNum = PlugIn.ModelCore.GenerateUniform();
double randomNum2 = PlugIn.ModelCore.GenerateUniform();
//Create random variability in outbreak area within a simulation so outbreaks are more variable.
double initialAreaCalibratorRandomNum = (randomNum2 - 0.5) * insect.InitialPatchOutbreakSensitivity / 2;
//Start spreading!
if (randomNum < insect.InitialOutbreakProb[site] * (insect.InitialPatchOutbreakSensitivity + initialAreaCalibratorRandomNum))
//if(randomNum < SiteVars.InitialOutbreakProb[site] * insect.InitialPatchOutbreakSensitivity)
{
//start with this site (if it's active)
ActiveSite currentSite = site;
//queue to hold sites to defoliate
Queue <ActiveSite> sitesToConsider = new Queue <ActiveSite>();
//put initial site on queue
sitesToConsider.Enqueue(currentSite);
DistributionType dist = insect.InitialPatchDistr;
double targetArea = Distribution.GenerateRandomNum(dist, insect.InitialPatchValue1, insect.InitialPatchValue2);
//PlugIn.ModelCore.UI.WriteLine(" Target Patch Area={0:0.0}.", targetArea);
double areaSelected = 0.0;
//loop through stand, defoliating patches of size target area
while (sitesToConsider.Count > 0 && areaSelected < targetArea)
{
currentSite = sitesToConsider.Dequeue();
// Because this is the first year, neighborhood defoliaiton is given a value.
// The value is used in Defoliate.DefoliateCohort()
insect.NeighborhoodDefoliation[currentSite] = insect.InitialOutbreakProb[currentSite];
areaSelected += PlugIn.ModelCore.CellArea;
insect.Disturbed[currentSite] = true;
//Next, add site's neighbors to the list of
//sites to consider.
//loop through the site's neighbors enqueueing all the good ones.
//double maxNeighborProb = 0.0;
//Site maxNeighbor = currentSite;
//bool foundNewNeighbor = false;
foreach (RelativeLocation loc in all_neighbor_locations)
{
Site neighbor = currentSite.GetNeighbor(loc);
//get a neighbor site (if it's non-null and active)
if (neighbor != null &&
neighbor.IsActive &&
!sitesToConsider.Contains((ActiveSite)neighbor) &&
!insect.Disturbed[neighbor])
{
//insect.Disturbed[currentSite] = true;
randomNum = PlugIn.ModelCore.GenerateUniform();
/*if (SiteVars.InitialOutbreakProb[neighbor] > maxNeighborProb)
* {
* maxNeighbor = currentSite.GetNeighbor(loc);
* maxNeighborProb = SiteVars.InitialOutbreakProb[neighbor];
* foundNewNeighbor = true;
* }*/
//check if it's a valid neighbor:
if (insect.InitialOutbreakProb[neighbor] * insect.InitialPatchShapeCalibrator > randomNum)
{
sitesToConsider.Enqueue((ActiveSite)neighbor);
}
}
}
//if(foundNewNeighbor)
// sitesToConsider.Enqueue((ActiveSite) maxNeighbor);
}
//PlugIn.ModelCore.UI.WriteLine(" Initial Patch Area Selected={0:0.0}.", areaSelected);
}
}
}