[Avida-SVN] r3553 - development/source/actions

[beckma24 at myxo.css.msu.edu]

Author: beckma24
Date: 2009-12-15 10:40:55 -0500 (Tue, 15 Dec 2009)
New Revision: 3553

Modified:
   development/source/actions/PopulationActions.cc
Log:
Added event KillWithinRadiusBelowResourceThresholdTestAll

Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc	2009-12-11 19:55:58 UTC (rev 3552)
+++ development/source/actions/PopulationActions.cc	2009-12-15 15:40:55 UTC (rev 3553)
@@ -4105,7 +4105,103 @@
     } //End Process()
   };
 
+/*
+ Kill organisms within a given radius of a randomly-chosen cell if the level
+ of the given resource in the chosen cells are below the given threshold.  Currently
+ only works for toruses and bounded grids.
+ 
+ Parameters:
+ - The number of kill radii to use (default: 0)
+ - The radius of the kill zone (default: 0)
+ - The name of the resource
+ - The amount of resource below which to execute the kill (default: 0)
+ - The fraction of orgs in the region to kill (1=all, 0.5 leave half) (default: 1) -- useful for controlling density with biofilms
+ */
 
+class cActionKillWithinRadiusBelowResourceThresholdTestAll : public cAction {
+private:
+	int m_numradii;
+	int m_radius;
+	cString m_resname;
+	double m_threshold;
+	double m_kill_density;
+public:
+	cActionKillWithinRadiusBelowResourceThresholdTestAll(cWorld* world, const cString& args) : cAction(world, args), m_numradii(0), m_radius(0), m_threshold(0.0), m_kill_density(1.0)
+	{
+		cString largs(args);
+		if (largs.GetSize()) m_numradii = largs.PopWord().AsInt();
+		if (largs.GetSize()) m_radius = largs.PopWord().AsInt();
+		if (largs.GetSize()) m_resname = largs.PopWord();
+		if (largs.GetSize()) m_threshold = largs.PopWord().AsDouble();
+		if (largs.GetSize()) m_kill_density = largs.PopWord().AsDouble();
+	}
+	
+	static const cString GetDescription() { return "Arguments: [int numradii=0, int radius=0, string resource name, double threshold=0, double killdensity=1]"; }
+	
+	void Process(cAvidaContext& ctx)
+	{
+		const int world_x = m_world->GetPopulation().GetWorldX();
+		const int world_y = m_world->GetPopulation().GetWorldY();
+		const int geometry = m_world->GetConfig().WORLD_GEOMETRY.Get();
+		
+		assert(m_numradii >= 0);
+		assert(m_radius >= 0);
+		assert(m_radius <= world_x);
+		assert(m_radius <= world_y);
+		assert(m_threshold >= 0.0);
+		assert(m_kill_density >= 0.0);
+		assert(m_kill_density <= 1.0);
+		assert(geometry == nGeometry::GRID || geometry == nGeometry::TORUS);
+		
+		cPopulation& pop = m_world->GetPopulation();
+		int res_id = m_world->GetPopulation().GetResourceCount().GetResourceCountID(m_resname);
+		
+		assert(res_id != -1);
+		
+		for (int i = 0; i < m_numradii; i++) {
+			
+			int target_cell = m_world->GetRandom().GetInt(0, pop.GetSize()-1);
+			const int current_row = target_cell / world_x;
+			const int current_col = target_cell % world_x;
+			
+			for(int row = current_row - m_radius; row <= current_row + m_radius; row++) {
+				
+				if( ((row < 0) || (row >= world_y)) && (geometry == nGeometry::GRID) ) continue;
+				
+				for(int col = current_col - m_radius; col <= current_col + m_radius; col++) {
+					if( ((col < 0) || (col >= world_x)) && (geometry == nGeometry::GRID) ) continue;
+					
+					int row_adj = 0;
+					int col_adj = 0;
+					
+					if(geometry == nGeometry::TORUS) {
+						row_adj = (row + world_y) % world_y;
+						col_adj = (col + world_x) % world_x;
+					} else if(geometry == nGeometry::GRID) {
+						row_adj = row;
+						col_adj = col;
+					}
+					
+					int current_cell = (world_x * row_adj) + col_adj;
+					cPopulationCell& cell = pop.GetCell(current_cell);
+					m_world->GetStats().IncNumCellsScannedAtKill();
+					
+					double level = pop.GetResourceCount().GetSpatialResource(res_id).GetAmount(current_cell);
+					
+					if(level < m_threshold) {
+						if( (cell.IsOccupied()) && (ctx.GetRandom().P(m_kill_density)) ) {
+							pop.KillOrganism(cell);
+							m_world->GetStats().IncNumOrgsKilled();
+						} else {
+							m_world->GetStats().IncNumUnoccupiedCellAttemptedToKill();
+						}
+					}
+				}
+			}
+		}
+	}
+};
+
 /*
  Kill a percentage of organisms in all demes
  
@@ -4419,6 +4515,7 @@
   action_lib->Register<cActionKillNBelowResourceThreshold>("KillNBelowResourceThreshold");
   action_lib->Register<cActionKillNAboveResourceThreshold>("KillNAboveResourceThreshold");
   action_lib->Register<cActionKillWithinRadiusBelowResourceThreshold>("KillWithinRadiusBelowResourceThreshold");
+	action_lib->Register<cActionKillWithinRadiusBelowResourceThresholdTestAll>("KillWithinRadiusBelowResourceThresholdTestAll");
 	
 	action_lib->Register<cActionDiffuseHGTGenomeFragments>("DiffuseHGTGenomeFragments");