//---------------------------------------------------------------------
public static void ReadMap(string path, int agentIndex)
{
IInputRaster <BytePixel> map;
try
{
map = PlugIn.ModelCore.OpenRaster <BytePixel>(path);
}
catch (FileNotFoundException)
{
string mesg = string.Format("Error: The file {0} does not exist", path);
throw new System.ApplicationException(mesg);
}
if (map.Dimensions != PlugIn.ModelCore.Landscape.Dimensions)
{
string mesg = string.Format("Error: The input map {0} does not have the same dimension (row, column) as the ecoregions map", path);
throw new System.ApplicationException(mesg);
}
using (map)
{
BytePixel pixel = map.BufferPixel;
foreach (Site site in PlugIn.ModelCore.Landscape.AllSites)
{
map.ReadBufferPixel();
byte mapCode = pixel.MapCode.Value;
if (mapCode > 1)
{
string mesg = string.Format("Error: The input map {0} must have 0-1 values, where 0 = susceptible, 1 = infected", path);
throw new System.ApplicationException(mesg);
}
if (site.IsActive)
{
SiteVars.InfStatus[site][agentIndex] = mapCode;
if (mapCode == 0)
{
SiteVars.PSusceptible[site][agentIndex] = 1;
SiteVars.PInfected[site][agentIndex] = mapCode;
}
else
{
SiteVars.PSusceptible[site][agentIndex] = 0;
SiteVars.PInfected[site][agentIndex] = mapCode;
}
}
}
}
}
//---------------------------------------------------------------------
///<summary>
/// Run the EDA extension at a particular timestep.
///</summary>
public override void Run()
{
ModelCore.UI.WriteLine(" Processing landscape for EDA events ...");
if (!reinitialized)
{
InitializePhase2();
}
int eventCount = 0;
int agentIndex = 0;
foreach (IAgent activeAgent in manyAgentParameters)
{
Epidemic.Initialize(activeAgent);
if (activeAgent.DispersalType == DispersalType.STATIC)
{
ModelCore.UI.WriteLine(" Simulating spread of epidemic...");
Epidemic currentEpic = Epidemic.Simulate(activeAgent, ModelCore.CurrentTime, agentIndex);
if (currentEpic != null)
{
LogEvent(ModelCore.CurrentTime, currentEpic, activeAgent);
//----- Write Infection Status maps (SUSCEPTIBLE (0), INFECTED (cryptic-non symptomatic) (1), DISEASED (symptomatic) (2) --------
string path = MapNames.ReplaceTemplateVars(statusMapName, activeAgent.AgentName, ModelCore.CurrentTime);
modelCore.UI.WriteLine(" Writing infection status map to {0} ...", path);
using (IOutputRaster <BytePixel> outputRaster = modelCore.CreateRaster <BytePixel>(path, modelCore.Landscape.Dimensions))
{
BytePixel pixel = outputRaster.BufferPixel;
foreach (Site site in ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (byte)(SiteVars.InfStatus[site][agentIndex] + 1);
}
else
{
//Inactive site
pixel.MapCode.Value = 0;
}
outputRaster.WriteBufferPixel();
}
}
if (!(mortMapNames == null))
{
//----- Write Cohort Mortality Maps (number dead cohorts for selected species) --------
string path2 = MapNames.ReplaceTemplateVars(mortMapNames, activeAgent.AgentName, ModelCore.CurrentTime);
modelCore.UI.WriteLine(" Writing cohort mortality map to {0} ...", path2);
using (IOutputRaster <ShortPixel> outputRaster = modelCore.CreateRaster <ShortPixel>(path2, modelCore.Landscape.Dimensions))
{
ShortPixel pixel = outputRaster.BufferPixel;
foreach (Site site in ModelCore.Landscape.AllSites)
{
if (site.IsActive)
{
pixel.MapCode.Value = (short)(SiteVars.NumberMortSppKilled[site][agentIndex]);
}
else
{
//Inactive site
pixel.MapCode.Value = -999; //should work with "short" type
}
outputRaster.WriteBufferPixel();
}
}
}
eventCount++;
}
}
else if (activeAgent.DispersalType == DispersalType.DYNAMIC)
{
/*****************TODO*******************/
Console.WriteLine("Dynamic dispersal type has not been implemented yet!!");
}
agentIndex++;
}
}
