//---------------------------------------------------------------------
///<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++;
}
}
public static void InitializeMetadata(int Timestep,
string statusMapFileName,
string mortalityMapFileName,
string logFileName,
IEnumerable <IAgent> manyAgentParameters,
ICore mCore)
{
ScenarioReplicationMetadata scenRep = new ScenarioReplicationMetadata()
{
//String outputFolder = OutputPath.ReplaceTemplateVars("", FINISH ME LATER);
//FolderName = System.IO.Directory.GetCurrentDirectory().Split("\\".ToCharArray()).Last(),
RasterOutCellArea = PlugIn.ModelCore.CellArea,
TimeMin = PlugIn.ModelCore.StartTime,
TimeMax = PlugIn.ModelCore.EndTime,
//ProjectionFilePath = "Projection.?" //How do we get projections???
};
Extension = new ExtensionMetadata(mCore)
{
Name = PlugIn.ExtensionName,
TimeInterval = Timestep, //change this to PlugIn.TimeStep for other extensions
ScenarioReplicationMetadata = scenRep
};
//---------------------------------------
// table outputs:
//---------------------------------------
if (logFileName != null)
{
System.IO.Directory.CreateDirectory(Path.GetDirectoryName(logFileName));
PlugIn.EventLog = new MetadataTable <EventsLog>(logFileName);
//PlugIn.EventLog = new MetadataTable<EventsLog>("eda-log.csv");
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:
//---------------------------------------
foreach (IAgent activeAgent in manyAgentParameters)
{
string mapTypePath = MapNames.ReplaceTemplateVarsMetadata(statusMapFileName, activeAgent.AgentName);
OutputMetadata mapOut_Status = new OutputMetadata()
{
Type = OutputType.Map,
Name = string.Format(activeAgent.AgentName + " Cell Infection Status "),
FilePath = @mapTypePath,
Map_DataType = MapDataType.Ordinal,
Map_Unit = FieldUnits.Severity_Rank, //based on the metadata library (https://github.com/LANDIS-II-Foundation/Libraries/blob/master/metadata/trunk/src/FieldUnits.cs)
Visualize = true, //it seems like Severity_Rank can have values between 1-5
};
Extension.OutputMetadatas.Add(mapOut_Status);
if (mortalityMapFileName != null)
{
mapTypePath = MapNames.ReplaceTemplateVarsMetadata(mortalityMapFileName, activeAgent.AgentName);
OutputMetadata mapOut_MORT = new OutputMetadata()
{
Type = OutputType.Map,
Name = "Cohort Mortality (Flagged Species)",
FilePath = @mapTypePath,
Map_DataType = MapDataType.Continuous,
Map_Unit = FieldUnits.Count,
Visualize = false,
};
Extension.OutputMetadatas.Add(mapOut_MORT);
}
}
//---------------------------------------
MetadataProvider mp = new MetadataProvider(Extension);
mp.WriteMetadataToXMLFile("Metadata", Extension.Name, Extension.Name);
}
