//---------------------------------------------------------------------
private void LogEvent(int currentTime,
Epidemic CurrentEvent,
int ROS)
{
log.Write("{0},{1},{2},{3},{4:0.0}",
currentTime,
ROS,
CurrentEvent.CohortsKilled,
CurrentEvent.TotalSitesDamaged,
CurrentEvent.MeanSeverity);
//foreach (IEcoregion ecoregion in Model.Ecoregions)
//{
//if(ecoregion.Active)
//log.Write(",{0}", CurrentEvent.SitesInEvent[ecoregion.Index]);
//}
log.WriteLine("");
}
//---------------------------------------------------------------------
///<summary>
///Simulate an Epidemic - This is the controlling function that calls the
///subsequent function. The basic logic of an epidemic resides here.
///</summary>
public static Epidemic Simulate(IAgent agent,
int currentTime,
int timestep,
int ROS)
{
Epidemic CurrentEpidemic = new Epidemic(agent);
UI.WriteLine(" New BDA Epidemic Activated: {0}.", agent.AgentName);
SiteResources.SiteResourceDominance(agent, ROS);
SiteResources.SiteResourceDominanceModifier(agent);
if (agent.Dispersal)
{
//Asynchronous - Simulate Agent Dispersal
// Calculate Site Vulnerability without considering the Neighborhood
// If neither disturbance modifiers nor ecoregion modifiers are active,
// Vulnerability will equal SiteReourceDominance.
SiteResources.SiteVulnerability(agent, ROS, false);
Epicenters.NewEpicenters(agent, timestep);
}
else
{
//Synchronous: assume that all Active sites can potentially be
//disturbed without regard to initial locations.
foreach (ActiveSite site in Model.Core.Landscape)
{
agent.OutbreakZone[site] = Zone.Newzone;
}
}
//Consider the Neighborhood if requested:
if (agent.NeighborFlag)
{
SiteResources.NeighborResourceDominance(agent);
}
//Recalculate Site Vulnerability considering neighbors if necessary:
SiteResources.SiteVulnerability(agent, ROS, agent.NeighborFlag);
CurrentEpidemic.DisturbSites(agent);
return(CurrentEpidemic);
}
//---------------------------------------------------------------------
///<summary>
///Simulate an Epidemic - This is the controlling function that calls the
///subsequent function. The basic logic of an epidemic resides here.
///</summary>
public static Epidemic Simulate(IAgent agent,
int currentTime,
int timestep,
int ROS)
{
Epidemic CurrentEpidemic = new Epidemic(agent);
UI.WriteLine(" New BDA Epidemic Activated: {0}.", agent.AgentName);
SiteResources.SiteResourceDominance(agent, ROS);
SiteResources.SiteResourceDominanceModifier(agent);
if(agent.Dispersal) {
//Asynchronous - Simulate Agent Dispersal
// Calculate Site Vulnerability without considering the Neighborhood
// If neither disturbance modifiers nor ecoregion modifiers are active,
// Vulnerability will equal SiteReourceDominance.
SiteResources.SiteVulnerability(agent, ROS, false);
Epicenters.NewEpicenters(agent, timestep);
} else
{
//Synchronous: assume that all Active sites can potentially be
//disturbed without regard to initial locations.
foreach (ActiveSite site in Model.Core.Landscape)
agent.OutbreakZone[site] = Zone.Newzone;
}
//Consider the Neighborhood if requested:
if (agent.NeighborFlag)
SiteResources.NeighborResourceDominance(agent);
//Recalculate Site Vulnerability considering neighbors if necessary:
SiteResources.SiteVulnerability(agent, ROS, agent.NeighborFlag);
CurrentEpidemic.DisturbSites(agent);
return CurrentEpidemic;
}
//---------------------------------------------------------------------
private void LogEvent(int currentTime,
Epidemic CurrentEvent,
int ROS)
{
log.Write("{0},{1},{2},{3},{4:0.0}",
currentTime,
ROS,
CurrentEvent.CohortsKilled,
CurrentEvent.TotalSitesDamaged,
CurrentEvent.MeanSeverity);
//foreach (IEcoregion ecoregion in Model.Ecoregions)
//{
//if(ecoregion.Active)
//log.Write(",{0}", CurrentEvent.SitesInEvent[ecoregion.Index]);
//}
log.WriteLine("");
}
//---------------------------------------------------------------------
///<summary>
/// Run the BDA extension at a particular timestep.
///</summary>
public override void Run()
{
UI.WriteLine("Processing landscape for BDA events ...");
//SiteVars.Epidemic.SiteValues = null;
int eventCount = 0;
foreach (IAgent activeAgent in manyAgentParameters)
{
activeAgent.TimeSinceLastEpidemic += Timestep;
//UI.WriteLine("TimeSince={0}, TimeToNext={1}", activeAgent.TimeSinceLastEpidemic, activeAgent.TimeToNextEpidemic);
//(activeAgent.TimeSinceLastEpidemic+ activeAgent.TimeToNextEpidemic));
int ROS = RegionalOutbreakStatus(activeAgent, Timestep);
if (ROS > 0)
{
Epidemic.Initialize(activeAgent);
Epidemic currentEpic = Epidemic.Simulate(activeAgent,
Model.Core.CurrentTime,
Timestep,
ROS);
//activeAgent.TimeSinceLastEpidemic = activeAgent.TimeSinceLastEpidemic + Timestep;
if (currentEpic != null)
{
LogEvent(Model.Core.CurrentTime, currentEpic, ROS);
//----- Write BDA severity maps --------
IOutputRaster <SeverityPixel> map = CreateMap(Model.Core.CurrentTime, activeAgent.AgentName);
using (map) {
SeverityPixel pixel = new SeverityPixel();
foreach (Site site in Model.Core.Landscape.AllSites)
{
if (site.IsActive)
{
if (SiteVars.Disturbed[site])
{
pixel.Band0 = (byte)(activeAgent.Severity[site] + 1);
}
else
{
pixel.Band0 = 1;
}
}
else
{
// Inactive site
pixel.Band0 = 0;
}
map.WritePixel(pixel);
}
}
if (!(srdMapNames == ""))
{
//----- Write BDA SRD maps --------
IOutputRaster <UShortPixel> srdmap = CreateSRDMap(Model.Core.CurrentTime, activeAgent.AgentName);
using (srdmap)
{
UShortPixel pixel = new UShortPixel();
foreach (Site site in Model.Core.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.Band0 = (ushort)System.Math.Round(SiteVars.SiteResourceDom[site] * 100.00);
}
else
{
// Inactive site
pixel.Band0 = 0;
}
srdmap.WritePixel(pixel);
}
}
}
if (!(nrdMapNames == ""))
{
//----- Write BDA NRD maps --------
IOutputRaster <UShortPixel> nrdmap = CreateNRDMap(Model.Core.CurrentTime, activeAgent.AgentName);
using (nrdmap)
{
UShortPixel pixel = new UShortPixel();
foreach (Site site in Model.Core.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.Band0 = (ushort)System.Math.Round(SiteVars.NeighborResourceDom[site] * 100.00);
}
else
{
// Inactive site
pixel.Band0 = 0;
}
nrdmap.WritePixel(pixel);
}
}
}
//----- Write Site Vulnerability or OutbreakZone maps --------
//----- USED FOR LANDSCAPE TESTING -----------
/*IOutputRaster<UShortPixel> dmap = CreateUShortMap(Model.Core.CurrentTimestep, activeAgent.AgentName);
* using (dmap) {
* UShortPixel pixel = new UShortPixel();
* foreach (Site site in Model.Core.Landscape.AllSites) {
* if (site.IsActive) {
* //pixel.Band0 = (ushort) (activeAgent.OutbreakZone[site]);
* pixel.Band0 = (ushort) (SiteVars.Vulnerability[site] * 100);
* }
* else {
* // Inactive site
* pixel.Band0 = 0;
* }
* dmap.WritePixel(pixel);
* }
* }*/
/*IOutputRaster<UShortPixel> nmap = CreateUShortMap2(Model.Core.CurrentTimestep, activeAgent.AgentName);
* using (nmap) {
* UShortPixel pixel = new UShortPixel();
* foreach (Site site in Model.Landscape.AllSites) {
* if (site.IsActive) {
* //pixel.Band0 = (ushort) (activeAgent.OutbreakZone[site]);
* pixel.Band0 = (ushort) System.Math.Round(SiteVars.NeighborResourceDom[site] * 100.00);
* }
* else {
* // Inactive site
* pixel.Band0 = 0;
* }
* nmap.WritePixel(pixel);
* }
* }*/
eventCount++;
}
}
}
}