[Avida-SVN] r2644 - in development/source: actions analyze cpu main
connel42 at myxo.css.msu.edu
connel42 at myxo.css.msu.edu
Fri Jun 13 07:34:24 PDT 2008
Author: connel42
Date: 2008-06-13 10:34:23 -0400 (Fri, 13 Jun 2008)
New Revision: 2644
Added:
development/source/main/cOrgMovementPredicate.h
Modified:
development/source/actions/EnvironmentActions.cc
development/source/actions/PopulationActions.cc
development/source/analyze/cAnalyzeJobQueue.cc
development/source/cpu/cHardwareCPU.cc
development/source/cpu/cHardwareCPU.h
development/source/cpu/cTestCPUInterface.h
development/source/main/cAvidaConfig.h
development/source/main/cDeme.cc
development/source/main/cDeme.h
development/source/main/cDemeCellEvent.cc
development/source/main/cDemeCellEvent.h
development/source/main/cOrgInterface.h
development/source/main/cOrgMessagePredicate.h
development/source/main/cOrganism.cc
development/source/main/cOrganism.h
development/source/main/cPopulation.cc
development/source/main/cPopulation.h
development/source/main/cPopulationCell.cc
development/source/main/cPopulationInterface.h
development/source/main/cStats.cc
development/source/main/cStats.h
development/source/main/cTaskContext.h
development/source/main/cTaskLib.cc
development/source/main/cTaskLib.h
Log:
* added deme movement and message replication predicates
* added some movement tasks
* added a few fields to organism to facilitate movement tasks
Modified: development/source/actions/EnvironmentActions.cc
===================================================================
--- development/source/actions/EnvironmentActions.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/actions/EnvironmentActions.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -726,15 +726,19 @@
}
};
+
class cActionDelayedDemeEvent : public cAction
{
private:
int m_x1, m_y1, m_x2, m_y2; // bounding box of event in deme
int m_delay; // deme age when event occurs
int m_duration; // length of event; subverted when deme is reset
+ bool m_static_pos;
+ int m_time_to_live; // update when event no longer exists
+ int m_id;
public:
- cActionDelayedDemeEvent(cWorld* world, const cString& args) : cAction(world, args), m_x1(-1), m_y1(-1), m_x2(-1), m_y2(-1), m_delay(-1), m_duration(-1)
+ cActionDelayedDemeEvent(cWorld* world, const cString& args) : cAction(world, args), m_x1(-1), m_y1(-1), m_x2(-1), m_y2(-1), m_delay(-1), m_duration(-1), m_static_pos(1), m_time_to_live(-1), m_id(-1)
{
cString largs(args);
if (largs.GetSize()) m_x1 = largs.PopWord().AsInt();
@@ -743,16 +747,19 @@
if (largs.GetSize()) m_y2 = largs.PopWord().AsInt();
if (largs.GetSize()) m_delay = largs.PopWord().AsInt();
if (largs.GetSize()) m_duration = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_static_pos = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_time_to_live = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_id = largs.PopWord().AsInt();
}
- static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion>"; }
+ static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <int static_position> <int time_to_live> <event ID>"; }
void Process(cAvidaContext& ctx)
{
cPopulation& pop = m_world->GetPopulation();
int numDemes = pop.GetNumDemes();
for(int i = 0; i < numDemes; i++) {
- pop.GetDeme(i).SetCellEvent(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration);
+ pop.GetDeme(i).SetCellEvent(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration, m_static_pos, m_time_to_live, m_id);
}
}
};
Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/actions/PopulationActions.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -565,6 +565,7 @@
m_world->GetPopulation().Inject(genome,
m_world->GetPopulation().GetDeme(i).GetCellID(0),
m_merit, m_lineage_label, m_neutral_metric);
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
}
} else {
for(int i=0; i<m_world->GetPopulation().GetNumDemes(); ++i) {
@@ -573,12 +574,167 @@
m_world->GetPopulation().Inject(genome,
m_world->GetPopulation().GetDeme(i).GetCellID(0),
m_merit, m_lineage_label, m_neutral_metric);
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
+
}
}
}
};
+/*! Injects one or more organisms into all demes in the population at a specified cell.
+ * Note: This gets the genotype from the germline, so germline use is required
+ * Note: one organism is inserted each time this is called, and it will stop
+ * when the given number of organisms has been injected.
+
+ Parameters:
+ - number of orgs (int): number of organisms to inject into each deme - default 1
+ - nest cell (int): relative cell id into which organism is injected - default 0
+ - merit (double): The initial merit of the organism. If set to -1, this is ignored - default -1
+ - lineage label (integer): An integer that marks all descendants of this organism - default 0
+ - neutral metric (double): A double value that randomly drifts over time - default 0
+
+*/
+
+class cActionInjectDemesFromNest : public cAction
+{
+private:
+ int m_num_orgs;
+ int m_nest_cellid;
+ double m_merit;
+ int m_lineage_label;
+ double m_neutral_metric;
+
+public:
+ cActionInjectDemesFromNest(cWorld* world, const cString& args):
+ cAction(world, args),
+ m_num_orgs(1),
+ m_nest_cellid(0),
+ m_merit(-1),
+ m_lineage_label(0),
+ m_neutral_metric(0)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_num_orgs = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_nest_cellid = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_merit = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_lineage_label = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_neutral_metric = largs.PopWord().AsDouble();
+ } //End cActionInjectDemesFromNest constructor
+
+ static const cString GetDescription() { return "Arguments: [int num_orgs=1] [int nest_cellid=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ for(int i=0; i<m_world->GetPopulation().GetNumDemes(); ++i) {
+
+ // The first deme will have initially had one organism injected. If this
+ // is the first injection and energy is used, increment the injected
+ // count (the initial injection wasn't counted) and skip the first deme
+ // so that the energies don't get messed up.
+ if( (i==0) && (m_world->GetConfig().ENERGY_ENABLED.Get() == 1) &&
+ (m_world->GetPopulation().GetDeme(i).GetInjectedCount() == 0) ) {
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
+ continue;
+ }
+
+ if(m_world->GetPopulation().GetDeme(i).GetInjectedCount() < m_num_orgs) {
+ m_world->GetPopulation().Inject(m_world->GetPopulation().GetDeme(i).GetGermline().GetLatest(),
+ m_world->GetPopulation().GetDeme(i).GetCellID(m_nest_cellid),
+ m_merit, m_lineage_label, m_neutral_metric);
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
+ }
+
+ } //End iterating through demes
+
+ } //End Process()
+
+}; //End cActionInjectDemesFromNest
+
+
+
+/*! Injects one or more organisms into all demes in a randomly-chosen cell.
+ * Note: This gets the genotype from the germline, so germline use is required
+ * Note: one organism is inserted each time this is called, and it will stop
+ * when the given number of organisms has been injected.
+
+ Parameters:
+ - number of orgs (int): number of organisms to inject into each deme - default 1
+ - merit (double): The initial merit of the organism. If set to -1, this is ignored - default -1
+ - lineage label (integer): An integer that marks all descendants of this organism - default 0
+ - neutral metric (double): A double value that randomly drifts over time - default 0
+
+*/
+
+class cActionInjectDemesRandom : public cAction
+{
+private:
+ int m_num_orgs;
+ double m_merit;
+ int m_lineage_label;
+ double m_neutral_metric;
+
+public:
+ cActionInjectDemesRandom(cWorld* world, const cString& args):
+ cAction(world, args),
+ m_num_orgs(1),
+ m_merit(-1),
+ m_lineage_label(0),
+ m_neutral_metric(0)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_num_orgs = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_merit = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_lineage_label = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_neutral_metric = largs.PopWord().AsDouble();
+ } //End cActionInjectDemesRandom constructor
+
+ static const cString GetDescription() { return "Arguments: [int num_orgs=1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ int target_cell, target_cellr;
+ int deme_size;
+
+ for(int i=0; i<m_world->GetPopulation().GetNumDemes(); ++i) {
+
+ // The first deme will have initially had one organism injected. If this
+ // is the first injection and energy is used, increment the injected
+ // count (the initial injection wasn't counted) and skip the first deme
+ // so that the energies don't get messed up.
+ if( (i==0) && (m_world->GetConfig().ENERGY_ENABLED.Get() == 1) &&
+ (m_world->GetPopulation().GetDeme(i).GetInjectedCount() == 0) ) {
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
+ continue;
+ }
+
+ target_cell = -1;
+ target_cellr = -1;
+ deme_size = m_world->GetPopulation().GetDeme(i).GetSize();
+
+ // Find a random, unoccupied cell to use. Assumes one exists.
+ do {
+ target_cellr = m_world->GetRandom().GetInt(0, deme_size-1);
+ target_cell = m_world->GetPopulation().GetDeme(i).GetCellID(target_cellr);
+ } while (m_world->GetPopulation().GetCell(target_cell).IsOccupied());
+
+ assert(target_cell > -1);
+ assert(target_cell < m_world->GetPopulation().GetSize());
+
+ if(m_world->GetPopulation().GetDeme(i).GetInjectedCount() < m_num_orgs) {
+ m_world->GetPopulation().Inject(m_world->GetPopulation().GetDeme(i).GetGermline().GetLatest(), target_cell, m_merit,
+ m_lineage_label, m_neutral_metric);
+ m_world->GetPopulation().GetDeme(i).IncInjectedCount();
+ }
+
+ } //End iterating through demes
+
+ } //End Process()
+
+}; //End cActionInjectDemesRandom
+
+
+
/*
Randomly removes a certain proportion of the population.
@@ -1111,6 +1267,7 @@
'corners' - ...demes with upper left and lower right corners filled.
'deme-age' - ...demes that are a certain age
'birth-count' ...demes that have had a certain number of births.
+ 'sat-mov-pred' - ...demes whose movement predicate was previously satisfied
*/
class cActionReplicateDemes : public cAction
@@ -1129,6 +1286,7 @@
else if (in_trigger == "corners") m_rep_trigger = 2;
else if (in_trigger == "deme-age") m_rep_trigger = 3;
else if (in_trigger == "birth-count") m_rep_trigger = 4;
+ else if (in_trigger == "sat-mov-pred") m_rep_trigger = 5;
else {
cString err("Unknown replication trigger '");
err += in_trigger;
@@ -1680,7 +1838,78 @@
}
};
+/*
+ Added predicate to all demes that is satisified when an organism reaches the center of an event
+*/
+class cActionPred_DemeEventMoveCenter : public cAction
+{
+private:
+ int m_times;
+public:
+ cActionPred_DemeEventMoveCenter(cWorld* world, const cString& args) : cAction(world, args), m_times(1) {
+ cString largs(args);
+ if (largs.GetSize()) m_times = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: [int times=1]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ m_world->GetPopulation().AddDemePred("EventMovedIntoCenter", m_times);
+ }
+};
+
+
+/*
+ Added predicate to all demes that is satisified when an organism reaches a target cell
+ modified cActionPred_DemeEventMoveCenter
+*/
+class cActionPred_DemeEventMoveBetweenTargets : public cAction
+{
+private:
+ int m_times;
+
+public:
+ cActionPred_DemeEventMoveBetweenTargets(cWorld* world, const cString& args) : cAction(world, args), m_times(1) {
+ cString largs(args);
+ if (largs.GetSize()) m_times = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: [int times=1]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ m_world->GetPopulation().AddDemePred("EventMovedBetweenTargets", m_times);
+ }
+};
+
+
+/*
+ Added predicate to all demes that is satisified when a number of organisms
+ reach a target cell
+*/
+class cActionPred_DemeEventEventNUniqueIndividualsMovedIntoTarget : public cAction
+{
+private:
+ int m_numorgs;
+
+public:
+ cActionPred_DemeEventEventNUniqueIndividualsMovedIntoTarget(cWorld* world, const cString& args) : cAction(world, args), m_numorgs(1) {
+ cString largs(args);
+ if (largs.GetSize()) m_numorgs = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: [int numorgs=1]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ m_world->GetPopulation().AddDemePred("EventNUniqueIndividualsMovedIntoTarget", m_numorgs);
+ }
+};
+
+
+
void RegisterPopulationActions(cActionLibrary* action_lib)
{
action_lib->Register<cActionInject>("Inject");
@@ -1691,6 +1920,8 @@
action_lib->Register<cActionInjectSequence>("InjectSequence");
action_lib->Register<cActionInjectSequenceWithDivMutRate>("InjectSequenceWDivMutRate");
action_lib->Register<cActionInjectDemes>("InjectDemes");
+ action_lib->Register<cActionInjectDemesFromNest>("InjectDemesFromNest");
+ action_lib->Register<cActionInjectDemesRandom>("InjectDemesRandom");
action_lib->Register<cActionInjectParasite>("InjectParasite");
action_lib->Register<cActionInjectParasitePair>("InjectParasitePair");
@@ -1756,4 +1987,8 @@
action_lib->Register<cActionConnectCells>("connect_cells");
action_lib->Register<cActionDisconnectCells>("disconnect_cells");
action_lib->Register<cActionSwapCells>("swap_cells");
+
+ action_lib->Register<cActionPred_DemeEventMoveCenter>("Pred_DemeEventMoveCenter");
+ action_lib->Register<cActionPred_DemeEventMoveBetweenTargets>("Pred_DemeEventMoveBetweenTargets");
+ action_lib->Register<cActionPred_DemeEventEventNUniqueIndividualsMovedIntoTarget>("Pred_DemeEventNUniqueIndividualsMovedIntoTarget");
}
Modified: development/source/analyze/cAnalyzeJobQueue.cc
===================================================================
--- development/source/analyze/cAnalyzeJobQueue.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/analyze/cAnalyzeJobQueue.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -134,4 +134,5 @@
ctx.SetRandom(GetRandom(job->GetID()));
job->Run(ctx);
delete job;
-}
\ No newline at end of file
+}
+
Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/cpu/cHardwareCPU.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -394,6 +394,31 @@
// Placebo instructions
tInstLibEntry<tMethod>("skip", &cHardwareCPU::Inst_Skip),
+ // @BDC additions for pheromones
+ tInstLibEntry<tMethod>("phero-on", &cHardwareCPU::Inst_PheroOn),
+ tInstLibEntry<tMethod>("phero-off", &cHardwareCPU::Inst_PheroOff),
+ tInstLibEntry<tMethod>("pherotoggle", &cHardwareCPU::Inst_PheroToggle),
+ tInstLibEntry<tMethod>("sense-target", &cHardwareCPU::Inst_SenseTarget),
+ tInstLibEntry<tMethod>("sense-target-faced", &cHardwareCPU::Inst_SenseTargetFaced),
+ tInstLibEntry<tMethod>("sensef", &cHardwareCPU::Inst_SenseLog2Facing),
+ tInstLibEntry<tMethod>("sensef-unit", &cHardwareCPU::Inst_SenseUnitFacing),
+ tInstLibEntry<tMethod>("sensef-m100", &cHardwareCPU::Inst_SenseMult100Facing),
+ tInstLibEntry<tMethod>("sense-pheromone", &cHardwareCPU::Inst_SensePheromone),
+ tInstLibEntry<tMethod>("sense-pheromone-faced", &cHardwareCPU::Inst_SensePheromoneFaced),
+ tInstLibEntry<tMethod>("exploit", &cHardwareCPU::Inst_Exploit),
+ tInstLibEntry<tMethod>("exploit-forward5", &cHardwareCPU::Inst_ExploitForward5),
+ tInstLibEntry<tMethod>("exploit-forward3", &cHardwareCPU::Inst_ExploitForward3),
+ tInstLibEntry<tMethod>("explore", &cHardwareCPU::Inst_Explore),
+ tInstLibEntry<tMethod>("movetarget", &cHardwareCPU::Inst_MoveTarget),
+ tInstLibEntry<tMethod>("movetarget-forward5", &cHardwareCPU::Inst_MoveTargetForward5),
+ tInstLibEntry<tMethod>("movetarget-forward3", &cHardwareCPU::Inst_MoveTargetForward3),
+ tInstLibEntry<tMethod>("supermove", &cHardwareCPU::Inst_SuperMove),
+ tInstLibEntry<tMethod>("if-target", &cHardwareCPU::Inst_IfTarget),
+ tInstLibEntry<tMethod>("if-not-target", &cHardwareCPU::Inst_IfNotTarget),
+ tInstLibEntry<tMethod>("if-pheromone", &cHardwareCPU::Inst_IfPheromone),
+ tInstLibEntry<tMethod>("if-not-pheromone", &cHardwareCPU::Inst_IfNotPheromone),
+ tInstLibEntry<tMethod>("drop-pheromone", &cHardwareCPU::Inst_DropPheromone),
+
// Must always be the last instruction in the array
tInstLibEntry<tMethod>("NULL", &cHardwareCPU::Inst_Nop, 0, "True no-operation instruction: does nothing"),
};
@@ -552,8 +577,7 @@
organism->SetRunning(false);
return false;
}
-
-
+
cPhenotype& phenotype = organism->GetPhenotype();
// First instruction - check whether we should be starting at a promoter, when enabled.
@@ -3919,11 +3943,16 @@
// Get population
cPopulation& pop = m_world->GetPopulation();
-
+ cDeme &deme = pop.GetDeme(pop.GetCell(organism->GetCellID()).GetDemeID());
+
// Get stepsize. Currently, all moves are one cell regardless of stepsize.
// This could be changed in the future.
const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
-
+
+ // Pheromone stuff
+ double pher_amount = 0;
+ int drop_mode = -1;
+
// Code
if (0 < stepsize) {
// Current cell
@@ -3932,12 +3961,70 @@
if (-1 == fromcellID) return false;
// Destination cell
destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
// Actually perform the move using SwapCells
- //cout << "SwapCells: " << fromcellID << " to " << destcellID << endl;
pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
// Swap inputs and facings between cells using helper function
pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ // updates movement predicates
+ m_world->GetStats().Move(*organism);
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ // Old CellData-based version
+ //const int newval = pop.GetCell(destcellID).GetCellData() + 1;
+ //pop.GetCell(destcellID).SetCellData(newval);
+
+ } //End laying pheromone
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().MOVETARGET_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,5", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+
+ // check tasks. general movement tasks are not yet supported.
+ //organism->DoOutput(ctx);
+
+ // Brian movement
+ organism->Move(ctx);
+
return true;
} else {
return false;
@@ -4798,3 +4885,1455 @@
IP().Advance();
return true;
}
+
+// @BDC Pheromone-related instructions
+bool cHardwareCPU::Inst_PheroOn(cAvidaContext& ctx)
+{
+ organism->SetPheromone(true);
+ return true;
+} //End Inst_PheroOn()
+
+bool cHardwareCPU::Inst_PheroOff(cAvidaContext& ctx)
+{
+ organism->SetPheromone(false);
+ return true;
+} //End Inst_PheroOff()
+
+bool cHardwareCPU::Inst_PheroToggle(cAvidaContext& ctx)
+{
+ organism->TogglePheromone();
+ return true;
+} //End Inst_PheroToggle()
+
+// BDC: same as DoSense, but uses senses from cell that org is facing
+bool cHardwareCPU::DoSenseFacing(cAvidaContext& ctx, int conversion_method, double base)
+{
+ cPopulationCell& mycell = m_world->GetPopulation().GetCell(organism->GetCellID());
+
+ int faced_id = mycell.GetCellFaced().GetID();
+
+ // Returns the amount of a resource or resources
+ // specified by modifying NOPs into register BX
+ const tArray<double> & res_count = m_world->GetPopulation().GetCellResources(faced_id);
+
+ // Arbitrarily set to BX since the conditional instructions use this directly.
+ int reg_to_set = REG_BX;
+
+ // There are no resources, return
+ if (res_count.GetSize() == 0) return false;
+
+ // Only recalculate logs if these values have changed
+ static int last_num_resources = 0;
+ static int max_label_length = 0;
+ int num_nops = GetInstSet().GetNumNops();
+
+ if ((last_num_resources != res_count.GetSize()))
+ {
+ max_label_length = (int) ceil(log((double)res_count.GetSize())/log((double)num_nops));
+ last_num_resources = res_count.GetSize();
+ }
+
+ // Convert modifying NOPs to the index of the resource.
+ // If there are fewer than the number of NOPs required
+ // to uniquely specify a resource, then add together
+ // a subset of resources (motivation: regulation can evolve
+ // to be more specific if there is an advantage)
+
+ // Find the maximum number of NOPs needed to specify this number of resources
+ // Note: It's a bit wasteful to recalculate this every time and organisms will
+ // definitely be confused if the number of resources changes during a run
+ // because their mapping to resources will be disrupted
+
+ // Attempt to read a label with this maximum length
+ ReadLabel(max_label_length);
+
+ // Find the length of the label that we actually obtained (max is max_reg_needed)
+ int real_label_length = GetLabel().GetSize();
+
+ // Start and end labels to define the start and end indices of
+ // resources that we need to add together
+ cCodeLabel start_label = cCodeLabel(GetLabel());
+ cCodeLabel end_label = cCodeLabel(GetLabel());
+
+ for (int i = 0; i < max_label_length - real_label_length; i++)
+ {
+ start_label.AddNop(0);
+ end_label.AddNop(num_nops-1);
+ }
+
+ int start_index = start_label.AsInt(num_nops);
+ int end_index = end_label.AsInt(num_nops);
+
+ // If the label refers to ONLY resources that
+ // do not exist, then the operation fails
+ if (start_index >= res_count.GetSize()) return false;
+
+ // Otherwise sum all valid resources that it might refer to
+ // (this will only be ONE if the label was of the maximum length).
+ int resource_result = 0;
+ double dresource_result = 0;
+ for (int i = start_index; i <= end_index; i++)
+ {
+ // if it's a valid resource
+ if (i < res_count.GetSize())
+ {
+ if (conversion_method == 0) // Log
+ {
+ // for log, add together and then take log
+ dresource_result += (double) res_count[i];
+ }
+ else if (conversion_method == 1) // Addition of multiplied resource amount
+ {
+ int add_amount = (int) (res_count[i] * base);
+ // Do some range checking to make sure we don't overflow
+ resource_result = (INT_MAX - resource_result <= add_amount) ? INT_MAX : resource_result + add_amount;
+ }
+ }
+ }
+
+ // Take the log after adding resource amounts together! This way a zero can be assigned to INT_MIN
+ if (conversion_method == 0) // Log2
+ {
+ // You really shouldn't be using the log method if you can get to zero resources
+ if(dresource_result == 0.0)
+ {
+ resource_result = INT_MIN;
+ }
+ else
+ {
+ resource_result = (int)(log(dresource_result)/log(base));
+ }
+ }
+
+ //Dump this value into an arbitrary register: BX
+ GetRegister(reg_to_set) = resource_result;
+
+ //We have to convert this to a different index that includes all degenerate labels possible: shortest to longest
+ int sensed_index = 0;
+ int on = 1;
+ for (int i = 0; i < real_label_length; i++)
+ {
+ sensed_index += on;
+ on *= num_nops;
+ }
+ sensed_index+= GetLabel().AsInt(num_nops);
+ organism->GetPhenotype().IncSenseCount(sensed_index);
+
+ return true;
+
+ // Note that we are converting <double> resources to <int> register values
+} //End DoSenseFacing()
+
+bool cHardwareCPU::Inst_SenseLog2Facing(cAvidaContext& ctx)
+{
+ return DoSenseFacing(ctx, 0, 2);
+}
+
+bool cHardwareCPU::Inst_SenseUnitFacing(cAvidaContext& ctx)
+{
+ return DoSenseFacing(ctx, 1, 1);
+}
+
+bool cHardwareCPU::Inst_SenseMult100Facing(cAvidaContext& ctx)
+{
+ return DoSenseFacing(ctx, 1, 100);
+}
+
+// Sense if the organism is on a target -- put 1 in reg is so, 0 otherwise
+bool cHardwareCPU::Inst_SenseTarget(cAvidaContext& ctx) {
+ int reg_to_set = FindModifiedRegister(REG_CX);
+ int cell_data = m_world->GetPopulation().GetCell(organism->GetCellID()).GetCellData();
+ int val = 0;
+
+ if(cell_data > 0) {
+ val = 1;
+ }
+
+ GetRegister(reg_to_set) = val;
+ return true;
+} //End Inst_SenseTarget()
+
+// Sense if the cell faced is a target -- put 1 in reg is so, 0 otherwise
+bool cHardwareCPU::Inst_SenseTargetFaced(cAvidaContext& ctx) {
+ int reg_to_set = FindModifiedRegister(REG_CX);
+
+ cPopulation& pop = m_world->GetPopulation();
+ cPopulationCell& mycell = pop.GetCell(organism->GetCellID());
+
+ int cell_data = mycell.GetCellFaced().GetCellData(); //absolute id of faced cell
+ int val = 0;
+
+ if(cell_data > 0) {
+ val = 1;
+ }
+
+ GetRegister(reg_to_set) = val;
+ return true;
+} //End Inst_SenseTargetFaced()
+
+// DoSensePheromone -- modified version of DoSense to only sense from
+// pheromone resource in given cell
+bool cHardwareCPU::DoSensePheromone(cAvidaContext& ctx, int cellid)
+{
+ int reg_to_set = FindModifiedRegister(REG_BX);
+
+ cPopulation& pop = m_world->GetPopulation();
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+ double pher_amount = 0;
+
+ if(deme_resource_count.GetSize() == 0) return false;
+
+ for (int i = 0; i < deme_resource_count.GetSize(); i++) {
+ if(strncmp(deme_resource_count.GetResName(i), "pheromone", 9) == 0) {
+ pher_amount += cell_resources[i];
+ }
+ }
+
+ GetRegister(reg_to_set) = (int)round(pher_amount);
+
+ return true;
+
+} //End DoSensePheromone()
+
+bool cHardwareCPU::Inst_SensePheromone(cAvidaContext& ctx)
+{
+ int cellid = organism->GetCellID(); //absolute id of current cell
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ return DoSensePheromone(ctx, cellid);
+} //End Inst_SensePheromone()
+
+bool cHardwareCPU::Inst_SensePheromoneFaced(cAvidaContext& ctx)
+{
+ int cellid = organism->GetCellID(); //absolute id of current cell
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulation& pop = m_world->GetPopulation();
+ cPopulationCell& mycell = pop.GetCell(cellid);
+
+ int fcellid = mycell.GetCellFaced().GetID(); //absolute id of faced cell
+
+ return DoSensePheromone(ctx, fcellid);
+} //End Inst_SensePheromoneFacing()
+
+bool cHardwareCPU::Inst_Exploit(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+ double phero_amount = 0;
+ double max_pheromone = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+ //tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+ tArray<double> cell_resources;
+
+ int fromcellID, destcellID;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0; // this is used in the logging
+ int drop_mode = -1;
+
+ if( (m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get() >= 0) &&
+ (m_world->GetRandom().P(m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get())) ) {
+ num_rotations = ctx.GetRandom().GetUInt(organism->GetNeighborhoodSize());
+ } else {
+ // Find which neighbor has the strongest pheromone
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ phero_amount = 0;
+ cell_resources = deme_resource_count.GetCellResources(deme.GetRelativeCellID(mycell.GetCellFaced().GetID()));
+
+ for (int j = 0; j < deme_resource_count.GetSize(); j++) {
+ if(strncmp(deme_resource_count.GetResName(j), "pheromone", 9) == 0) {
+ phero_amount += cell_resources[j];
+ }
+ }
+
+ if(phero_amount > max_pheromone) {
+ num_rotations = i;
+ max_pheromone = phero_amount;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+ }
+
+ // Rotate until we face the neighbor with the strongest pheromone.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().EXPLOIT_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,3", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} //End Inst_Exploit()
+
+
+
+// Sense neighboring cells, and rotate and move to the neighbor with the
+// strongest pheromone. If there is no winner, just move forward.
+// This instruction doesn't sense the three cells behind the organism,
+// i.e. the one directly behind, and behind and to the left and right.
+bool cHardwareCPU::Inst_ExploitForward5(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+ double phero_amount = 0;
+ double max_pheromone = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+ //tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+ tArray<double> cell_resources;
+
+ int fromcellID, destcellID;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0; // this is used in the logging.
+ int drop_mode = -1;
+
+
+ if( (m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get() >= 0) &&
+ (m_world->GetRandom().P(m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get())) ) {
+ num_rotations = ctx.GetRandom().GetUInt(organism->GetNeighborhoodSize());
+ } else {
+ // Find which neighbor has the strongest pheromone
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ // Skip the cells in the back
+ if(i == 3 || i == 4 || i == 5) {
+ mycell.ConnectionList().CircNext();
+ continue;
+ }
+
+ phero_amount = 0;
+ cell_resources = deme_resource_count.GetCellResources(deme.GetRelativeCellID(mycell.GetCellFaced().GetID()));
+
+ for (int j = 0; j < deme_resource_count.GetSize(); j++) {
+ if(strncmp(deme_resource_count.GetResName(j), "pheromone", 9) == 0) {
+ phero_amount += cell_resources[j];
+ }
+ }
+
+ if(phero_amount > max_pheromone) {
+ num_rotations = i;
+ max_pheromone = phero_amount;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+ }
+
+ // Rotate until we face the neighbor with the strongest pheromone.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().EXPLOIT_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,7", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} //End Inst_ExploitForward5()
+
+
+// Sense neighboring cells, and rotate and move to the neighbor with the
+// strongest pheromone. If there is no winner, just move forward.
+// This instruction doesn't sense the three cells behind the organism,
+// or the ones to the sides.
+bool cHardwareCPU::Inst_ExploitForward3(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+ double phero_amount = 0;
+ double max_pheromone = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+ //tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+ tArray<double> cell_resources;
+
+ int fromcellID, destcellID;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0; // this is used in the logging.
+ int drop_mode = -1;
+
+ if( (m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get() >= 0) &&
+ (m_world->GetRandom().P(m_world->GetConfig().EXPLOIT_EXPLORE_PROB.Get())) ) {
+ num_rotations = ctx.GetRandom().GetUInt(organism->GetNeighborhoodSize());
+ } else {
+ // Find which neighbor has the strongest pheromone
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ // Skip the cells in the back
+ if(i == 2 || i == 3 || i == 4 || i == 5 || i == 6) {
+ mycell.ConnectionList().CircNext();
+ continue;
+ }
+
+ phero_amount = 0;
+ cell_resources = deme_resource_count.GetCellResources(deme.GetRelativeCellID(mycell.GetCellFaced().GetID()));
+
+ for (int j = 0; j < deme_resource_count.GetSize(); j++) {
+ if(strncmp(deme_resource_count.GetResName(j), "pheromone", 9) == 0) {
+ phero_amount += cell_resources[j];
+ }
+ }
+
+ if(phero_amount > max_pheromone) {
+ num_rotations = i;
+ max_pheromone = phero_amount;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+ }
+
+ // Rotate until we face the neighbor with the strongest pheromone.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().EXPLOIT_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,9", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} //End Inst_ExploitForward3()
+
+bool cHardwareCPU::Inst_Explore(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+
+ int fromcellID, destcellID;
+ int cell_data;
+
+ // Pheromone drop stuff
+ double pher_amount = 0;
+ int drop_mode = -1;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Rotate randomly. Code taken from tumble.
+ const int num_neighbors = organism->GetNeighborhoodSize();
+ for(unsigned int i = 0; i < ctx.GetRandom().GetUInt(num_neighbors); i++) {
+ organism->Rotate(1); // Rotate doesn't rotate N times, just once.
+ }
+
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+ // If organism is dropping pheromones, mark the cells appropriately
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().EXPLORE_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,2", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} // End Inst_Explore()
+
+// This command should move the organism to the neighbor cell that is a
+// target. If more than one target exists, it moves towards the last-seen
+// one. If no target exists, the organism moves forward in its original
+// facing.
+bool cHardwareCPU::Inst_MoveTarget(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+
+ int fromcellID, destcellID;
+ int cell_data;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0; // this is used in logging
+ int drop_mode = -1;
+
+int smc = mycell.ConnectionList().GetSize();
+ //SingleProcess shows decent-looking cellids until the end. maybe this is a deme replication problem (probably)
+ cPopulationCell faced = mycell.GetCellFaced();
+
+ // Find if any neighbor is a target
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+ cell_data = mycell.GetCellFaced().GetCellData();
+
+ if(cell_data > 0) {
+ num_rotations = i;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+
+ assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+
+ // Rotate until we face the neighbor with a target.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().MOVETARGET_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,1", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} // End Inst_MoveTarget()
+
+
+
+// This command should move the organism to the neighbor cell that is a
+// target. If more than one target exists, it moves towards the last-seen
+// one. If no target exists, the organism moves forward in its original
+// facing. This version ignores the neighbors beind the organism, i.e.
+// the cells directly behind and behind and to the left and right.
+bool cHardwareCPU::Inst_MoveTargetForward5(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+
+ int fromcellID, destcellID;
+ int cell_data;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0;
+ int drop_mode = -1;
+
+ cPopulationCell faced = mycell.GetCellFaced();
+
+ // Find if any neighbor is a target
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ // Skip the cells behind
+ if(i == 3 || i == 4 || i == 5) {
+ mycell.ConnectionList().CircNext();
+ continue;
+ }
+
+ cell_data = mycell.GetCellFaced().GetCellData();
+
+ if(cell_data > 0) {
+ num_rotations = i;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+
+ assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+
+ // Rotate until we face the neighbor with a target.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().MOVETARGET_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,6", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} // End Inst_MoveTargetForward5()
+
+
+// This command should move the organism to the neighbor cell that is a
+// target. If more than one target exists, it moves towards the last-seen
+// one. If no target exists, the organism moves forward in its original
+// facing. This version ignores the neighbors beind and to the side of
+// the organism
+bool cHardwareCPU::Inst_MoveTargetForward3(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+
+ int fromcellID, destcellID;
+ int cell_data;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0;
+ int drop_mode = -1;
+
+ cPopulationCell faced = mycell.GetCellFaced();
+
+ // Find if any neighbor is a target
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ // Skip the cells behind
+ if(i==2 || i == 3 || i == 4 || i == 5 || i == 6) {
+ mycell.ConnectionList().CircNext();
+ continue;
+ }
+
+ cell_data = mycell.GetCellFaced().GetCellData();
+
+ if(cell_data > 0) {
+ num_rotations = i;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+
+ assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+
+ // Rotate until we face the neighbor with a target.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().MOVETARGET_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,8", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} // End Inst_MoveTargetForward3()
+
+bool cHardwareCPU::Inst_SuperMove(cAvidaContext& ctx)
+{
+ int num_rotations = 0;
+ float phero_amount = 0;
+ float max_pheromone = 0;
+
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulationCell& mycell = pop.GetCell(cellid);
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+
+ int fromcellID, destcellID;
+ int cell_data;
+
+ // Get stepsize. Currently, all moves are one cell regardless of stepsize.
+ // This could be changed in the future.
+ const int stepsize = m_world->GetConfig().BIOMIMETIC_MOVEMENT_STEP.Get();
+
+ // Pheromone drop stuff
+ double pher_amount = 0;
+ int drop_mode = -1;
+
+ // Set num_rotations to a random number for explore -- lowest priority
+ const int num_neighbors = organism->GetNeighborhoodSize();
+ num_rotations = ctx.GetRandom().GetUInt(num_neighbors);
+
+
+ // Find the neighbor with highest pheromone -- medium priority
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+
+ phero_amount = 0;
+ cell_resources = deme_resource_count.GetCellResources(deme.GetRelativeCellID(mycell.GetCellFaced().GetID()));
+
+ for (int j = 0; j < deme_resource_count.GetSize(); j++) {
+ if(strncmp(deme_resource_count.GetResName(j), "pheromone", 9) == 0) {
+ phero_amount += cell_resources[j];
+ }
+ }
+
+ if(phero_amount > max_pheromone) {
+ num_rotations = i;
+ max_pheromone = phero_amount;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Find if any neighbor is a target -- highest priority
+ for(int i = 0; i < mycell.ConnectionList().GetSize(); i++) {
+ cell_data = mycell.GetCellFaced().GetCellData();
+
+ if(cell_data > 0) {
+ num_rotations = i;
+ }
+
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Rotate until we face the neighbor with a target.
+ // If there was no winner, just move forward.
+ for(int i = 0; i < num_rotations; i++) {
+ mycell.ConnectionList().CircNext();
+ }
+
+ // Move to the faced cell
+ if(stepsize > 0) {
+ fromcellID = organism->GetCellID();
+
+ if(fromcellID == -1) {
+ return false;
+ }
+
+ destcellID = pop.GetCell(fromcellID).GetCellFaced().GetID();
+
+ /*********************/
+ // TEMP. Remove once movement tasks are implemented.
+ if(pop.GetCell(fromcellID).GetCellData() < pop.GetCell(destcellID).GetCellData()) { // move up gradient
+ organism->SetGradientMovement(1.0);
+ } else if(pop.GetCell(fromcellID).GetCellData() == pop.GetCell(destcellID).GetCellData()) {
+ organism->SetGradientMovement(0.0);
+ } else { // move down gradient
+ organism->SetGradientMovement(-1.0);
+ }
+ /*********************/
+
+ pop.SwapCells(pop.GetCell(fromcellID),pop.GetCell(destcellID));
+ pop.MoveOrganisms(ctx, pop.GetCell(fromcellID), pop.GetCell(destcellID));
+
+ m_world->GetStats().Move(*organism);
+
+ // If organism is dropping pheromones, mark the appropriate cell(s)
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ }
+ else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+
+ } //End laying pheromone
+
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().MOVETARGET_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("movelog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_srcid = deme.GetRelativeCellID(fromcellID);
+ int rel_destid = deme.GetRelativeCellID(destcellID);
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%d,%f,%d,4", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_srcid, rel_destid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ organism->Move(ctx);
+
+ return true;
+ } else {
+ return false;
+ }
+
+ return true;
+
+} // End Inst_SuperMove()
+
+bool cHardwareCPU::Inst_IfTarget(cAvidaContext& ctx)
+{
+ int cell_data = m_world->GetPopulation().GetCell(organism->GetCellID()).GetCellData();
+
+ if(cell_data == -1) {
+ IP().Advance();
+ }
+
+ return true;
+} //End Inst_IfTarget()
+
+
+bool cHardwareCPU::Inst_IfNotTarget(cAvidaContext& ctx)
+{
+ int cell_data = m_world->GetPopulation().GetCell(organism->GetCellID()).GetCellData();
+
+ if(cell_data > 0) {
+ IP().Advance();
+ }
+
+ return true;
+} //End Inst_IfNotTarget()
+
+
+bool cHardwareCPU::Inst_IfPheromone(cAvidaContext& ctx)
+{
+ int cellid = organism->GetCellID(); //absolute id of current cell
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulation& pop = m_world->GetPopulation();
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+
+ if(deme_resource_count.GetSize() == 0) return false;
+
+ double pher_amount = 0;
+
+ for (int i = 0; i < deme_resource_count.GetSize(); i++) {
+ if(strncmp(deme_resource_count.GetResName(i), "pheromone", 9) == 0) {
+ pher_amount += cell_resources[i];
+ }
+ }
+
+ if(pher_amount == 0) {
+ IP().Advance();
+ }
+
+ return true;
+
+} //End Inst_IfPheromone()
+
+
+bool cHardwareCPU::Inst_IfNotPheromone(cAvidaContext& ctx)
+{
+ int cellid = organism->GetCellID(); //absolute id of current cell
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cPopulation& pop = m_world->GetPopulation();
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+ int relative_cell_id = deme.GetRelativeCellID(cellid);
+
+ cResourceCount deme_resource_count = deme.GetDemeResourceCount();
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+
+ if(deme_resource_count.GetSize() == 0) return false;
+
+ double pher_amount = 0;
+
+ for (int i = 0; i < deme_resource_count.GetSize(); i++) {
+ if(strncmp(deme_resource_count.GetResName(i), "pheromone", 9) == 0) {
+ pher_amount += cell_resources[i];
+ }
+ }
+
+ if(pher_amount > 0) {
+ IP().Advance();
+ }
+
+ return true;
+
+} //End Inst_IfNotPheromone()
+
+
+bool cHardwareCPU::Inst_DropPheromone(cAvidaContext& ctx)
+{
+ cPopulation& pop = m_world->GetPopulation();
+ int cellid = organism->GetCellID();
+
+ if(cellid == -1) {
+ return true;
+ }
+
+ cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
+
+ // If organism is dropping pheromones, mark the appropriate cell
+ // Note: right now, we're ignoring the organism's pheromone status and always
+ // dropping if pheromones are enabled
+ if(m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) {
+
+ const double pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ //const int drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ // We can't use the different drop modes, because we only know the cell
+ // that the organism is currently in.
+ /*
+ if(drop_mode == 0) {
+ deme.AddPheromone(fromcellID, pher_amount/2);
+ deme.AddPheromone(destcellID, pher_amount/2);
+ } else if(drop_mode == 1) {
+ deme.AddPheromone(fromcellID, pher_amount);
+ } else if(drop_mode == 2) {
+ deme.AddPheromone(destcellID, pher_amount);
+ }
+ */
+ deme.AddPheromone(cellid, pher_amount);
+
+ // Write some logging information if LOG_PHEROMONE is set. This is done
+ // out here so that non-pheromone moves are recorded.
+ if( (m_world->GetConfig().LOG_PHEROMONE.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().PHEROMONE_LOG_START.Get()) ) {
+ cString tmpfilename = cStringUtil::Stringf("drop-pheromone-log.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int rel_cellid = deme.GetRelativeCellID(cellid);
+ double pher_amount;
+ const int drop_mode = m_world->GetConfig().PHEROMONE_DROP_MODE.Get();
+
+ // By columns: update ID, org ID, source cell (relative), destination cell (relative), amount dropped, drop mode
+ if( (m_world->GetConfig().PHEROMONE_ENABLED.Get() == 1) &&
+ (organism->GetPheromoneStatus() == true) ) {
+ pher_amount = m_world->GetConfig().PHEROMONE_AMOUNT.Get();
+ } else {
+ pher_amount = 0;
+ }
+
+ cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d,%f,%d", m_world->GetStats().GetUpdate(), organism->GetID(), deme.GetDemeID(), rel_cellid, pher_amount, drop_mode);
+ df.WriteRaw(UpdateStr);
+ }
+
+ } //End laying pheromone
+
+ return true;
+
+} //End Inst_DropPheromone()
+
Modified: development/source/cpu/cHardwareCPU.h
===================================================================
--- development/source/cpu/cHardwareCPU.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/cpu/cHardwareCPU.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -603,6 +603,34 @@
//// Placebo ////
bool Inst_Skip(cAvidaContext& ctx);
+
+ // @BDC Additions for pheromones
+ bool Inst_PheroOn(cAvidaContext& ctx);
+ bool Inst_PheroOff(cAvidaContext& ctx);
+ bool Inst_PheroToggle(cAvidaContext& ctx);
+ bool DoSenseFacing(cAvidaContext& ctx, int conversion_method, double base);
+ bool Inst_SenseLog2Facing(cAvidaContext& ctx);
+ bool Inst_SenseUnitFacing(cAvidaContext& ctx);
+ bool Inst_SenseMult100Facing(cAvidaContext& ctx);
+ bool Inst_SenseTarget(cAvidaContext& ctx);
+ bool Inst_SenseTargetFaced(cAvidaContext& ctx);
+ bool DoSensePheromone(cAvidaContext& ctx, int cellid);
+ bool Inst_SensePheromone(cAvidaContext& ctx);
+ bool Inst_SensePheromoneFaced(cAvidaContext& ctx);
+ bool Inst_Exploit(cAvidaContext& ctx);
+ bool Inst_ExploitForward5(cAvidaContext& ctx);
+ bool Inst_ExploitForward3(cAvidaContext& ctx);
+ bool Inst_Explore(cAvidaContext& ctx);
+ bool Inst_MoveTarget(cAvidaContext& ctx);
+ bool Inst_MoveTargetForward5(cAvidaContext& ctx);
+ bool Inst_MoveTargetForward3(cAvidaContext& ctx);
+ bool Inst_SuperMove(cAvidaContext& ctx);
+ bool Inst_IfTarget(cAvidaContext& ctx);
+ bool Inst_IfNotTarget(cAvidaContext& ctx);
+ bool Inst_IfPheromone(cAvidaContext& ctx);
+ bool Inst_IfNotPheromone(cAvidaContext& ctx);
+ bool Inst_DropPheromone(cAvidaContext& ctx);
+
};
Modified: development/source/cpu/cTestCPUInterface.h
===================================================================
--- development/source/cpu/cTestCPUInterface.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/cpu/cTestCPUInterface.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -50,6 +50,13 @@
void SetCellID(int in_id) { ; }
void SetDemeID(int in_id) { ; }
+ int GetPrevSeenCellID() { return 0; }
+ int GetPrevTaskCellID() { return 0; }
+ void AddReachedTaskCell() { }
+ int GetNumTaskCellsReached() { return 0; }
+ void SetPrevSeenCellID(int in_id) { ; }
+ void SetPrevTaskCellID(int in_id) { ; }
+
bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome);
cOrganism* GetNeighbor();
int GetNumNeighbors();
Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cAvidaConfig.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -274,7 +274,7 @@
CONFIG_ADD_VAR(ANALYZE_MODE, int, 0, "0 = Disabled\n1 = Enabled\n2 = Interactive");
CONFIG_ADD_VAR(VIEW_MODE, int, 1, "Initial viewer screen");
CONFIG_ADD_VAR(CLONE_FILE, cString, "-", "Clone file to load");
- CONFIG_ADD_VAR(VERBOSITY, int, 1, "0 = No output at all\n1=Normal output\n2 = Verbose output, detailing progress\n3 = High level of details, as available\n4 = Print Debug Information, as applicable");
+ CONFIG_ADD_VAR(VERBOSITY, int, 1, "0 = No output at all\n1 = Normal output\n2 = Verbose output, detailing progress\n3 = High level of details, as available\n4 = Print Debug Information, as applicable");
CONFIG_ADD_GROUP(ARCH_GROUP, "Architecture Variables");
CONFIG_ADD_VAR(WORLD_X, int, 60, "Width of the Avida world");
@@ -321,6 +321,7 @@
CONFIG_ADD_VAR(DEMES_DEFAULT_GERMLINE_PROPENSITY, double, 0.0, "Default germline propensity of organisms in deme.\nFor use with DEMES_DIVIDE_METHOD 2.");
CONFIG_ADD_VAR(DEMES_FOUNDER_GERMLINE_PROPENSITY, double, -1.0, "Default germline propensity of founder organisms in deme.\nFor use with DEMES_DIVIDE_METHOD 2.\n <0 = OFF");
CONFIG_ADD_VAR(DEMES_PREFER_EMPTY, int, 0, "Give empty demes preference as targets of deme replication?");
+ CONFIG_ADD_VAR(MAX_DEME_BIRTHS, int, 500, "The maximum number of births within a deme to be\nused for birth-based replication (default=500).");
CONFIG_ADD_GROUP(REPRODUCTION_GROUP, "Birth and Death");
CONFIG_ADD_VAR(BIRTH_METHOD, int, 0, "Which organism should be replaced on birth?\n0 = Random organism in neighborhood\n1 = Oldest in neighborhood\n2 = Largest Age/Merit in neighborhood\n3 = None (use only empty cells in neighborhood)\n4 = Random from population (Mass Action)\n5 = Oldest in entire population\n6 = Random within deme\n7 = Organism faced by parent\n8 = Next grid cell (id+1)\n9 = Largest energy used in entire population\n10 = Largest energy used in neighborhood");
@@ -527,6 +528,20 @@
CONFIG_ADD_VAR(BIOMIMETIC_MOVEMENT_FACTOR, double, 1.0, "Scale merit bonus due to movement (m<1.0 applies a cost)");
CONFIG_ADD_VAR(BIOMIMETIC_EVAL_ON_MOVEMENT, int, 0, "Force task evaluation on each movement step");
CONFIG_ADD_VAR(BIOMIMETIC_K, int, 0, "Carrying capacity in number of organisms");
+
+ // BDC: Additions for pheromones
+ CONFIG_ADD_GROUP(PHEROMONE_GROUP, "Pheromone Settings");
+ CONFIG_ADD_VAR(PHEROMONE_ENABLED, bool, 0, "Enable pheromone usage. 0/1 (off/on)");
+ CONFIG_ADD_VAR(PHEROMONE_AMOUNT, double, 1.0, "Amount of pheromone to add per drop");
+ CONFIG_ADD_VAR(PHEROMONE_DROP_MODE, int, 0, "Where to drop pheromone\n0 = Half amount at src, half at dest\n1 = All at source\n2 = All at dest");
+ CONFIG_ADD_VAR(EXPLOIT_EXPLORE_PROB, double, 0.00, "Probability of random exploration\ninstead of pheromone trail following");
+ CONFIG_ADD_VAR(LOG_PHEROMONE, bool, 0, "Log pheromone drops. 0/1 (off/on)");
+ CONFIG_ADD_VAR(PHEROMONE_LOG_START, int, 0, "Update at which to start logging pheromone drops");
+ CONFIG_ADD_VAR(EXPLOIT_LOG_START, int, 0, "Update at which to start logging exploit moves");
+ CONFIG_ADD_VAR(EXPLORE_LOG_START, int, 0, "Update at which to start logging explore moves");
+ CONFIG_ADD_VAR(MOVETARGET_LOG_START, int, 0, "Update at which to start logging movetarget moves");
+ CONFIG_ADD_VAR(LOG_INJECT, bool, 0, "Log injection of organisms. 0/1 (off/on)");
+ CONFIG_ADD_VAR(INJECT_LOG_START, int, 0, "Update at which to start logging injection of\norganisms");
CONFIG_ADD_CUSTOM_FORMAT(INST_SET_NEW, "Instruction Set Definition");
CONFIG_ADD_FORMAT_VAR(INST, "Instruction entry in the instruction set");
Modified: development/source/main/cDeme.cc
===================================================================
--- development/source/main/cDeme.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cDeme.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -31,6 +31,8 @@
#include "cPopulationCell.h"
#include "cResource.h"
#include "cWorld.h"
+#include "cOrgMessagePredicate.h"
+#include "cOrgMovementPredicate.h"
void cDeme::Setup(int id, const tArray<int> & in_cells, int in_width, cWorld* world)
{
@@ -94,8 +96,9 @@
{
assert(cell_ids.GetSize()>0);
assert(GetWidth() > 0);
- cellid -= cell_ids[0];
- return std::make_pair(cellid % GetWidth(), cellid / GetWidth());
+// cellid -= cell_ids[0];
+// return std::make_pair(cellid % GetWidth(), cellid / GetWidth());
+ return std::make_pair(cellid % GetWidth(), ( cellid % cell_ids.GetSize() ) / GetWidth());
}
cPopulationCell& cDeme::GetCell(int pos)
@@ -104,14 +107,23 @@
}
void cDeme::ProcessUpdate() {
- for(int i = 0; i < cell_events.GetSize(); i++) {
+ for(int i = 0; i < cell_events.Size(); i++) {
cDemeCellEvent& event = cell_events[i];
if(event.GetDelay() == _age) {
event.ActivateEvent(m_world); //start event
int eventCell = event.GetNextEventCellID();
while(eventCell != -1) {
// place event ID in cells' data
- m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventID());
+ if(event.IsDecayed()) {
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventIDDecay(GetCellPosition(eventCell)));
+ } else {
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventID());
+ }
+
+ // record activation of each cell in stats
+ std::pair<int, int> pos = GetCellPosition(eventCell);
+ m_world->GetStats().IncEventCount(pos.first, pos.second);
+
eventCell = event.GetNextEventCellID();
}
} else if(event.GetDelay()+event.GetDuration() == _age) {
@@ -158,11 +170,22 @@
time_used = 0;
cur_birth_count = 0;
cur_normalized_time_used = 0;
+ injected_count = 0;
cur_task_exe_count.SetAll(0);
cur_reaction_count.SetAll(0);
if(resetResources) deme_resource_count.ReinitializeResources();
+
+ //reset remaining message predicates
+ for(int i = 0; i < message_pred_list.Size(); i++) {
+ (*message_pred_list[i]).Reset();
+ }
+ //reset remaining message predicates
+ for(int i = 0; i < movement_pred_list.Size(); i++) {
+ (*movement_pred_list[i]).Reset();
+ }
+
}
@@ -354,11 +377,23 @@
deme_resource_count.ModifyCell(cell_resources, relative_cell_id);
}
-void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration) {
- cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width);
- cell_events.Push(demeEvent);
+void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live, int ID) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_pos, time_to_live, this);
+ if(ID != -1)
+ demeEvent.SetEventID(ID);
+ cell_events.Add(demeEvent);
}
+void cDeme::SetCellEventGradient(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_pos, time_to_live, this);
+ demeEvent.DecayEventIDFromCenter();
+ cell_events.Add(demeEvent);
+}
+
+int cDeme::GetNumEvents() {
+ return cell_events.Size();
+}
+
double cDeme::CalculateTotalEnergy() {
assert(m_world->GetConfig().ENERGY_ENABLED.Get());
@@ -423,3 +458,151 @@
}
+bool cDeme::MsgPredSatisfiedPreviously() {
+ for(int i = 0; i < message_pred_list.Size(); i++) {
+ if(message_pred_list[i]->PreviouslySatisfied()) {
+ message_pred_list[i]->UpdateStats(m_world->GetStats());
+ return true;
+ }
+ }
+ return false;
+}
+
+bool cDeme::MovPredSatisfiedPreviously() {
+ for(int i = 0; i < movement_pred_list.Size(); i++) {
+ if(movement_pred_list[i]->PreviouslySatisfied()) {
+ movement_pred_list[i]->UpdateStats(m_world->GetStats());
+ return true;
+ }
+ }
+ return false;
+}
+
+int cDeme::GetNumMessagePredicates() {
+ return message_pred_list.Size();
+}
+
+int cDeme::GetNumMovementPredicates() {
+ return movement_pred_list.Size();
+}
+
+cOrgMessagePredicate* cDeme::GetMsgPredicate(int i) {
+ assert(i < message_pred_list.Size());
+ return message_pred_list[i];
+}
+
+cOrgMovementPredicate* cDeme::GetMovPredicate(int i) {
+ assert(i < movement_pred_list.Size());
+ return movement_pred_list[i];
+}
+
+void cDeme::AddEventReceivedCenterPred(int times) {
+ if(cell_events.Size() == 0) {
+ cerr<<"Error: An EventReceivedCenterPred cannot be created until a CellEvent is added.\n";
+ exit(1);
+ }
+ for(int i = 0; i < cell_events.Size(); i++) {
+ if(!cell_events[i].IsDead()) {
+ int sink_cell = GetCellID(GetSize()/2);
+ cOrgMessagePred_EventReceivedCenter* pred = new cOrgMessagePred_EventReceivedCenter(&cell_events[i], sink_cell, times);
+ m_world->GetStats().AddMessagePredicate(pred);
+ message_pred_list.Add(pred);
+ }
+ }
+}
+
+void cDeme::AddEventReceivedLeftSidePred(int times) {
+ if(cell_events.Size() == 0) {
+ cerr<<"Error: An EventReceivedLeftSidePred cannot be created until a CellEvent is added.\n";
+ exit(1);
+ }
+ for(int i = 0; i < cell_events.Size(); i++) {
+ if(!cell_events[i].IsDead()) {
+ cOrgMessagePred_EventReceivedLeftSide* pred = new cOrgMessagePred_EventReceivedLeftSide(&cell_events[i], m_world->GetPopulation(), times);
+ m_world->GetStats().AddMessagePredicate(pred);
+ message_pred_list.Add(pred);
+ }
+ }
+}
+
+void cDeme::AddEventMoveCenterPred(int times) {
+ if(cell_events.Size() == 0) {
+ cerr<<"Error: An EventMovedIntoCenter cannot be created until a CellEvent is added.\n";
+ exit(1);
+ }
+ for(int i = 0; i < cell_events.Size(); i++) {
+ if(!cell_events[i].IsDead()) {
+ cOrgMovementPred_EventMovedIntoCenter* pred = new cOrgMovementPred_EventMovedIntoCenter(&cell_events[i], m_world->GetPopulation(), times);
+ m_world->GetStats().AddMovementPredicate(pred);
+ movement_pred_list.Add(pred);
+ }
+ }
+}
+
+
+void cDeme::AddEventMoveBetweenTargetsPred(int times) {
+ if(cell_events.Size() == 0) {
+ cerr<<"Error: An EventMoveBetweenTargets cannot be created until at least one CellEvent is added.\n";
+ exit(1);
+ }
+
+ tVector<cDemeCellEvent *> alive_events;
+
+ for(int i = 0; i < cell_events.Size(); i++) {
+ if(!cell_events[i].IsDead()) {
+ alive_events.Add(&cell_events[i]);
+ }
+ }
+
+ cOrgMovementPred_EventMovedBetweenTargets* pred = new cOrgMovementPred_EventMovedBetweenTargets(alive_events, m_world->GetPopulation(), times);
+ m_world->GetStats().AddMovementPredicate(pred);
+ movement_pred_list.Add(pred);
+}
+
+
+void cDeme::AddEventEventNUniqueIndividualsMovedIntoTargetPred(int times) {
+ if(cell_events.Size() == 0) {
+ cerr<<"Error: An EventMovedIntoCenter cannot be created until a CellEvent is added.\n";
+ exit(1);
+ }
+ for(int i = 0; i < cell_events.Size(); i++) {
+ if(!cell_events[i].IsDead()) {
+ cOrgMovementPred_EventNUniqueIndividualsMovedIntoTarget* pred = new cOrgMovementPred_EventNUniqueIndividualsMovedIntoTarget(&cell_events[i], m_world->GetPopulation(), times);
+ m_world->GetStats().AddMovementPredicate(pred);
+ movement_pred_list.Add(pred);
+ }
+ }
+}
+
+void cDeme::AddPheromone(int absolute_cell_id, double value)
+{
+ assert(cell_ids[0] <= absolute_cell_id);
+ assert(absolute_cell_id <= cell_ids[cell_ids.GetSize()-1]);
+
+ cPopulation& pop = m_world->GetPopulation();
+
+ int relative_cell_id = GetRelativeCellID(absolute_cell_id);
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+
+ for (int i = 0; i < deme_resource_count.GetSize(); i++) {
+ if(strcmp(deme_resource_count.GetResName(i), "pheromone") == 0) {
+ // There should only be one "pheromone" resource, so no need to divvy value up
+ cell_resources[i] = value;
+ }
+ else {
+ cell_resources[i] = 0;
+ }
+ }
+
+//It appears that ModifyCell adds the amount of resources specified in the cell_resources array, so I'm just
+//settign the element to the value I want to add instead of setting the element to the current value plus the amount to add
+// Ask Ben why he does it differently in GiveBackCellEnergy()
+
+ deme_resource_count.ModifyCell(cell_resources, relative_cell_id);
+
+ // CellData-based version
+ //const int newval = pop.GetCell(absolute_cell_id).GetCellData() + (int) round(value);
+ //pop.GetCell(absolute_cell_id).SetCellData(newval);
+
+} //End AddPheromone()
+
Modified: development/source/main/cDeme.h
===================================================================
--- development/source/main/cDeme.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cDeme.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -29,6 +29,7 @@
#include "cPhenotype.h"
#include "cMerit.h"
#include "tArray.h"
+#include "tVector.h"
#include "cResourceCount.h"
#include "cStringList.h"
@@ -37,6 +38,8 @@
class cPopulationCell;
class cGenotype;
class cOrganism;
+class cOrgMovementPredicate;
+class cOrgMessagePredicate;
/*! Demes are groups of cells in the population that are somehow bound together
as a unit. The deme object is used from within cPopulation to manage these
@@ -55,6 +58,7 @@
int last_birth_count;
int cur_org_count; //!< Number of organisms are currently in this deme.
int last_org_count;
+ int injected_count; //<! Number of organisms that have been injected into this deme
int _age; //!< Age of this deme, in updates.
int generation; //!< Generation of this deme
@@ -88,7 +92,7 @@
cResourceCount deme_resource_count; //!< Resources available to the deme
tArray<int> energy_res_ids; //!< IDs of energy resources
- tArray<cDemeCellEvent> cell_events;
+ tVector<cDemeCellEvent> cell_events;
int m_germline_genotype_id; // Genotype id of germline (if in use)
tArray<int> m_founder_genotype_ids; // List of genotype ids used to found deme.
@@ -97,10 +101,13 @@
cMerit _current_merit; //!< Deme merit applied to all organisms living in this deme.
cMerit _next_merit; //!< Deme merit that will be inherited upon deme replication.
+
+ tVector<cOrgMessagePredicate*> message_pred_list; // Message Predicates
+ tVector<cOrgMovementPredicate*> movement_pred_list; // Movement Predicates
public:
cDeme() : _id(0), width(0), cur_birth_count(0), last_birth_count(0), cur_org_count(0), last_org_count(0),
- _age(0), generation(0), total_org_energy(0.0),
+ injected_count(0), _age(0), generation(0), total_org_energy(0.0),
time_used(0), gestation_time(0), cur_normalized_time_used(0.0), last_normalized_time_used(0.0),
avg_founder_generation(0.0), generations_per_lifetime(0.0),
deme_resource_count(0), m_germline_genotype_id(0) { ; }
@@ -112,6 +119,7 @@
int GetSize() const { return cell_ids.GetSize(); }
int GetCellID(int pos) const { return cell_ids[pos]; }
int GetCellID(int x, int y) const;
+ int GetDemeID() const { return _id; }
//! Returns an (x,y) pair for the position of the passed-in cell ID.
std::pair<int, int> GetCellPosition(int cellid) const;
cPopulationCell& GetCell(int pos);
@@ -138,6 +146,9 @@
int GetGeneration() const { return generation; }
+ int GetInjectedCount() const { return injected_count; }
+ void IncInjectedCount() { injected_count++; }
+
bool IsEmpty() const { return cur_org_count == 0; }
bool IsFull() const { return cur_org_count == cell_ids.GetSize(); }
@@ -194,7 +205,9 @@
void Update(double time_step) { deme_resource_count.Update(time_step); }
int GetRelativeCellID(int absolute_cell_id) { return absolute_cell_id % GetSize(); } //!< assumes all demes are the same size
- void SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration);
+ void SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live, int ID = -1);
+ void SetCellEventGradient(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live);
+ int GetNumEvents();
double CalculateTotalEnergy();
@@ -217,6 +230,26 @@
// --- Germline management --- //
void ReplaceGermline(cGenotype& _in_genotype);
int GetGermlineGenotypeID() { return m_germline_genotype_id; }
+
+ // --- Message/Movement predicates --- //
+ bool MsgPredSatisfiedPreviously();
+ bool MovPredSatisfiedPreviously();
+ int GetNumMessagePredicates();
+ int GetNumMovementPredicates();
+ cOrgMessagePredicate* GetMsgPredicate(int i);
+ cOrgMovementPredicate* GetMovPredicate(int i);
+
+ void AddEventReceivedCenterPred(int times);
+ void AddEventReceivedLeftSidePred(int times);
+ void AddEventMoveCenterPred(int times);
+ void AddEventMoveBetweenTargetsPred(int times);
+ void AddEventMigrateToTargetsPred(int times);
+ void AddEventEventNUniqueIndividualsMovedIntoTargetPred(int times);
+
+ // --- Pheromones --- //
+ void AddPheromone(int absolute_cell_id, double value);
+
+
};
#endif
Modified: development/source/main/cDemeCellEvent.cc
===================================================================
--- development/source/main/cDemeCellEvent.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cDemeCellEvent.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -1,30 +1,48 @@
#include "cDemeCellEvent.h"
+#include "cDeme.h"
#include "cWorld.h"
-cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width) :
- m_delay(delay)
- , m_duration(duration)
- , m_iter(0)
- , m_active(false)
+cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, int time_to_live, cDeme* deme) :
+m_delay(delay)
+, m_duration(duration)
+, m_iter(0)
+, m_deme_width(deme_width)
+, m_deme_height(deme_height)
+, m_time_to_live(time_to_live)
+, m_use_gradient(false)
+, m_active(false)
+, m_static_pos(static_pos)
+, m_dead (false)
+, m_id_set(false)
+, m_deme(deme)
{
assert(x1 <= x2);
assert(y1 <= y2);
- assert(y1 < width && y2 < width);
+ assert(y1 < deme_width && y2 < deme_width);
assert(delay >= 0);
assert(duration >= 0);
m_event_cells.ResizeClear((x2-x1+1) * (y2-y1+1));
+ int i = 0;
- int i = 0;
- for(int j = y1; j <= y2; j++) {
- for(int k = x1; k <= x2; k++) {
- m_event_cells[i] = j*width+k;
- i++;
+ if(m_static_pos) {
+ for(int j = y1; j <= y2; j++) {
+ for(int k = x1; k <= x2; k++) {
+ m_event_cells[i] = j*m_deme_width+k;
+ i++;
+ }
}
+ pair<int, int> centerBottomleft = make_pair((int)floor(((x2-x1)/2.0)), (int)floor(((y2-y1)/2.0)));
+ pair<int, int> centerTopRight = make_pair((int)ceil(((x2-x1)/2.0)), (int)ceil(((y2-y1)/2.0)));
+ center = make_pair(centerBottomleft, centerTopRight);
+ } else {
+ //non-static event position
+ m_event_width = x2-x1;
+ m_event_height = y2-y1;
}
}
int cDemeCellEvent::GetNextEventCellID() {
- if(m_active && m_iter < m_event_cells.GetSize()) {
+ if(!m_dead && m_active && m_iter < m_event_cells.GetSize()) {
return m_event_cells[m_iter++];
}
m_iter = 0;
@@ -32,10 +50,110 @@
}
void cDemeCellEvent::ActivateEvent(cWorld* m_world) {
- m_eventID = m_world->GetRandom().GetInt(0x7FFFFFFF);
+
+ if(m_dead) {
+ return;
+ }
+
+ if(!m_id_set)
+ m_eventID = m_world->GetRandom().GetInt(0x7FFFFFFF);
+ if(!m_static_pos) {
+ //non-static event position
+ int rand_x1 = m_world->GetRandom().GetInt(m_deme_width-m_event_width);
+ int rand_y1 = m_world->GetRandom().GetInt(m_deme_height-m_event_height);
+ int i = 0;
+ for(int j = rand_y1; j <= rand_y1+m_event_height; j++) {
+ for(int k = rand_x1; k <= rand_x1+m_event_width; k++) {
+ m_event_cells[i] = j*m_deme_width+k;
+ i++;
+ }
+ }
+ pair<int, int> centerBottomleft = make_pair((int)floor((m_event_width/2.0)), (int)floor((m_event_height/2.0)));
+ pair<int, int> centerTopRight = make_pair((int)ceil((m_event_width/2.0)), (int)ceil((m_event_height/2.0)));
+ center = make_pair(centerBottomleft, centerTopRight);
+ }
m_active = true;
}
+int cDemeCellEvent::GetDelay() {
+ if(m_dead){
+ return 0;
+ }
+ return m_delay;
+}
+
+int cDemeCellEvent::GetDuration() {
+ if(m_dead){
+ return 0;
+ }
+ return m_duration;
+}
+
+int cDemeCellEvent::GetEventID() {
+ if(m_dead){
+ return -1;
+ }
+ return m_eventID;
+}
+
+int cDemeCellEvent::GetEventIDDecay(pair<int, int> pos) {
+ if(m_dead){
+ return -1;
+ }
+
+ double maxd = sqrt(pow(m_deme_width-1.0 ,2) + pow(m_deme_height-1.0 ,2));//cdistance(1,1,wx,wy);
+ double top = ceil(maxd);
+ pair<double, double> centerPoint = GetCenter(); // # dx.dy -- coordinates of peak value
+ double cdistance = sqrt(pow(pos.first-centerPoint.first ,2) + pow(pos.second-centerPoint.second ,2));
+
+ // return decayed value
+ int decayed_value = (int)floor(linmap(cdistance,0.0,top,top*1.414,1.0));
+ return decayed_value;
+}
+
+std::pair<double, double> cDemeCellEvent::GetCenter() const {
+ return make_pair((center.first.first+center.second.first)/2.0, (center.first.second+center.second.second)/2.0);
+}
+
+bool cDemeCellEvent::InCenter(pair<int, int> pos) const {
+ if((center.first <= pos) && (pos <= center.second)) {
+ return true;
+ }
+ return false;
+}
+
+bool cDemeCellEvent::OnEventCell(int demeRelative_cell_ID) const {
+ for(int i = 0; i < m_event_cells.GetSize(); i++) {
+ if(m_event_cells[i] == demeRelative_cell_ID)
+ return true;
+ }
+ return false;
+}
+
+int cDemeCellEvent::GetTimeToLive() {
+ if(m_dead){
+ return 0;
+ }
+ return m_time_to_live;
+}
+
+bool cDemeCellEvent::IsActive() {
+ if(m_dead){
+ return false;
+ }
+ return m_active;
+}
+
void cDemeCellEvent::DeactivateEvent() {
m_active = false;
}
+
+double cDemeCellEvent::linmap(const double dp, const double ds, const double de, const double rs, const double re) const {
+ double rp;
+ if (0.0 == (de - ds)) { // Domain has zero length; exception should be taken
+ rp = 0.0;
+ } else {
+ rp = (dp - ds) * ((re - rs) / (de - ds)) + rs;
+ }
+ return rp;
+}
Modified: development/source/main/cDemeCellEvent.h
===================================================================
--- development/source/main/cDemeCellEvent.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cDemeCellEvent.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -1,24 +1,48 @@
#ifndef cDemeCellEvent_h
#define cDemeCellEvent_h
+#include <utility>
#include "tArray.h"
+
+class cDeme;
class cWorld;
class cDemeCellEvent {
private:
tArray<int> m_event_cells;
- int m_delay, m_duration, m_eventID, m_iter;
- bool m_active;
+ int m_eventID;
+ int m_delay, m_duration, m_iter, m_deme_width, m_deme_height;
+ int m_event_width, m_event_height, m_time_to_live;
+ bool m_use_gradient, m_active, m_static_pos, m_dead, m_id_set;
+ std::pair<std::pair<int, int>, std::pair<int, int> > center;
+ cDeme* m_deme;
+ std::pair<double, double> GetCenter() const;
+
public:
- cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0); }
- cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width);
+ cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0, 0, true, 0, NULL); m_id_set = false;}
+ cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, int time_to_live, cDeme* deme);
int GetNextEventCellID();
- int GetDelay() { return m_delay; }
- int GetDuration() { return m_duration; }
- int GetEventID() { return m_eventID; }
+ int GetDelay();
+ cDeme* GetDeme() const { return m_deme; }
+ int GetDuration();
+ int GetEventID();
+ int GetEventIDDecay(std::pair<int, int> pos);
+ int GetTimeToLive();
+ bool IsActive();
+ bool IsDead() const { return m_dead; }
+ bool IsDecayed() { return m_use_gradient; }
+ bool InCenter(std::pair<int, int> pos) const;
+ bool OnEventCell(int demeRelative_cell_ID) const;
+
+ void SetEventID(int ID) { m_eventID = ID; m_id_set = true;}
+ void DecayEventIDFromCenter() { m_use_gradient = true; }
void ActivateEvent(cWorld* m_world);
void DeactivateEvent();
+ void Terminate() { m_dead = true; }
+
+ // gradient generators
+ double linmap(const double dp, const double ds, const double de, const double rs, const double re) const;
};
#endif
Modified: development/source/main/cOrgInterface.h
===================================================================
--- development/source/main/cOrgInterface.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cOrgInterface.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -60,6 +60,13 @@
virtual void SetCellID(int in_id) = 0;
virtual void SetDemeID(int in_id) = 0;
+ virtual int GetPrevSeenCellID() = 0;
+ virtual int GetPrevTaskCellID() = 0;
+ virtual int GetNumTaskCellsReached() = 0;
+ virtual void AddReachedTaskCell() = 0;
+ virtual void SetPrevSeenCellID(int in_id) = 0;
+ virtual void SetPrevTaskCellID(int in_id) = 0;
+
virtual bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome) = 0;
virtual cOrganism* GetNeighbor() = 0;
virtual int GetNumNeighbors() = 0;
Modified: development/source/main/cOrgMessagePredicate.h
===================================================================
--- development/source/main/cOrgMessagePredicate.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cOrgMessagePredicate.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -42,6 +42,10 @@
virtual bool operator()(const cOrgMessage& msg) = 0;
virtual void Print(std::ostream& out) { }
virtual void Reset() { }
+ virtual bool PreviouslySatisfied() = 0;
+ virtual cString GetName() = 0;
+ virtual void UpdateStats(cStats& stats) {}
+ virtual cDemeCellEvent* GetEvent() { return NULL; }
};
@@ -127,4 +131,186 @@
};
+/*! A predicate that returns true if a demeCellEvent has been received but the base station
+*/
+struct cOrgMessagePred_EventReceivedCenter : public cOrgMessagePredicate {
+ cOrgMessagePred_EventReceivedCenter(cDemeCellEvent* event, int base_station, int times) :
+ m_base_station(base_station)
+ , m_event_received(false)
+ , m_stats_updated(false)
+ , m_event(event)
+ , m_total_times(times)
+ , m_current_times(0) { }
+
+ ~cOrgMessagePred_EventReceivedCenter() { }
+
+ virtual bool operator()(const cOrgMessage& msg) {
+ int deme_id = msg.GetSender()->GetOrgInterface().GetDemeID();
+
+ if(deme_id != m_event->GetDeme()->GetDemeID() || m_event->IsDead()) {
+ return false;
+ }
+
+ unsigned int eventID = m_event->GetEventID();
+
+ if(m_event->IsActive() && eventID != 0 &&
+ (eventID == msg.GetData() ||
+ eventID == msg.GetLabel())) {
+ m_cell_ids.insert(msg.GetSender()->GetCellID());
+
+ if(m_base_station == msg.GetReceiver()->GetCellID()) {
+ m_current_times++;
+ if(m_current_times >= m_total_times) {
+ m_event_received = true;
+ }
+ }
+ }
+ return m_event_received;
+ }
+
+ //need to print update!!!
+ virtual void Print(std::ostream& out) {
+ if(m_event->IsDead()) {
+ return;
+ }
+
+ out << m_event->GetEventID() << " [ ";
+ for(std::set<int>::iterator i=m_cell_ids.begin(); i!=m_cell_ids.end(); i++) {
+ out << *i << " ";
+ }
+ out << "]\n";
+
+ m_cell_ids.clear();
+ }
+
+ virtual void Reset() {
+ m_event_received = false;
+ m_stats_updated = false;
+ m_current_times = 0;
+ }
+
+ virtual bool PreviouslySatisfied() {
+ return m_event_received;
+ }
+
+ virtual cString GetName() {
+ return "EventReceivedCenter";
+ }
+
+ virtual void UpdateStats(cStats& stats) {
+ if(m_event_received && !m_stats_updated) {
+ int eventCell = m_event->GetNextEventCellID();
+ while(eventCell != -1) {
+ stats.IncPredSat(eventCell);
+ eventCell = m_event->GetNextEventCellID();
+ }
+ m_stats_updated = true;
+ }
+ }
+
+ cDemeCellEvent* GetEvent() { return m_event; }
+
+ int m_base_station;
+ bool m_event_received;
+ bool m_stats_updated;
+ cDemeCellEvent* m_event;
+ std::set<int> m_cell_ids;
+ int m_total_times;
+ int m_current_times;
+};
+
+/*! A predicate that returns true if a demeCellEvent has been received but the base station
+*/
+struct cOrgMessagePred_EventReceivedLeftSide : public cOrgMessagePredicate {
+ cOrgMessagePred_EventReceivedLeftSide(cDemeCellEvent* event, cPopulation& population, int times) :
+ pop(population)
+ , m_event_received(false)
+ , m_stats_updated(false)
+ , m_event(event)
+ , m_total_times(times)
+ , m_current_times(0){ }
+
+ ~cOrgMessagePred_EventReceivedLeftSide() { }
+
+ virtual bool operator()(const cOrgMessage& msg) {
+ int deme_id = msg.GetSender()->GetOrgInterface().GetDemeID();
+
+ if(deme_id != m_event->GetDeme()->GetDemeID() || m_event->IsDead()) {
+ return false;
+ }
+
+ if(m_event->IsActive() &&
+ ((unsigned int)m_event->GetEventID() == msg.GetData() ||
+ (unsigned int)m_event->GetEventID() == msg.GetLabel())) {
+ m_cell_ids.insert(msg.GetSender()->GetCellID());
+
+ // find receiver coordinates
+ cOrganism* receiver = msg.GetReceiver();
+ int absolute_cell_ID = receiver->GetCellID();
+ int deme_id = receiver->GetOrgInterface().GetDemeID();
+ std::pair<int, int> pos = pop.GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+
+ // does receiver have x cordinate of zero
+ if(pos.first == 0) {
+ m_current_times++;
+ if(m_current_times >= m_total_times) {
+ m_event_received = true;
+ }
+ }
+ }
+ return m_event_received;
+ }
+
+ virtual void Print(std::ostream& out) {
+ if(m_event->IsDead()) {
+ return;
+ }
+
+ out << m_event->GetEventID() << " [ ";
+ for(std::set<int>::iterator i=m_cell_ids.begin(); i!=m_cell_ids.end(); i++) {
+ out << *i << " ";
+ }
+ out << "]\n";
+
+ m_cell_ids.clear();
+ }
+
+ virtual void Reset() {
+ m_event_received = false;
+ m_stats_updated = false;
+ m_current_times = 0;
+ m_cell_ids.clear();
+ }
+
+ virtual bool PreviouslySatisfied() {
+ return m_event_received;
+ }
+
+ virtual cString GetName() {
+ return "EventReceivedLeftSide";
+ }
+
+ virtual void UpdateStats(cStats& stats) {
+ if(m_event_received && !m_stats_updated) {
+ int eventCell = m_event->GetNextEventCellID();
+ while(eventCell != -1) {
+ stats.IncPredSat(eventCell);
+ eventCell = m_event->GetNextEventCellID();
+ }
+ m_stats_updated = true;
+ }
+ }
+
+ cDemeCellEvent* GetEvent() { return m_event; }
+
+ cPopulation& pop;
+ bool m_event_received;
+ bool m_stats_updated;
+ cDemeCellEvent* m_event;
+ std::set<int> m_cell_ids;
+ int m_total_times;
+ int m_current_times;
+};
+
+
#endif
Added: development/source/main/cOrgMovementPredicate.h
===================================================================
--- development/source/main/cOrgMovementPredicate.h (rev 0)
+++ development/source/main/cOrgMovementPredicate.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -0,0 +1,375 @@
+/*
+ * cOrgMovementPredicate.h
+ * Avida
+ *
+ * Created by Benjamin Beckmann on 11/6/07.
+ * Copyright 2007 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+/*
+ * cOrgMessagePredicate.h
+ * Avida
+ *
+ * Copyright 2005-2006 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; version 2
+ * of the License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ *
+ */
+#ifndef cOrgMovementPredicate_h
+#define cOrgMovementPredicate_h
+
+#include <iostream>
+#include <functional>
+#include <set>
+
+#include "cDemeCellEvent.h"
+#include "cOrganism.h"
+#include "cPopulation.h"
+#include "cStats.h"
+
+
+/*! \brief An STL-compatible predicate on cOrgMessages. The intent here is to
+provide a straightforward way to track arbitrary messages *wherever* they appear
+in the population. The most utility can be had from message predicates if they're
+installed into cStats (since every message goes through cStats). */
+struct cOrgMovementPredicate : public std::unary_function<cOrganism, bool>
+{
+ virtual ~cOrgMovementPredicate() { }
+ virtual bool operator()(cOrganism& org) = 0;
+ virtual void Print(std::ostream& out) { }
+ virtual void Reset() { }
+ virtual bool PreviouslySatisfied() = 0;
+ virtual cString GetName() = 0;
+ virtual void UpdateStats(cStats& stats) {}
+ virtual cDemeCellEvent* GetEvent(int i) { return NULL; }
+ virtual int GetNumEvents() { return 1; }
+};
+
+/*! A predicate that returns true if an organism has made it to the center of the gradient event
+*/
+struct cOrgMovementPred_EventMovedIntoCenter : public cOrgMovementPredicate {
+ cOrgMovementPred_EventMovedIntoCenter(cDemeCellEvent* event, cPopulation& population, int times) :
+ pop(population)
+ , m_event_received(false)
+ , m_stats_updated(false)
+ , m_event(event)
+ , m_total_times(times)
+ , m_current_times(0){ }
+
+ ~cOrgMovementPred_EventMovedIntoCenter() { }
+
+ virtual bool operator()(cOrganism& org) {
+ int deme_id = org.GetOrgInterface().GetDemeID();
+
+ if(deme_id != m_event->GetDeme()->GetDemeID() || m_event->IsDead()) {
+ return false;
+ }
+
+ if(m_event->IsActive()) {
+ // find organism coordinates
+ int absolute_cell_ID = org.GetCellID();
+ std::pair<int, int> pos = pop.GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+
+ // does receiver have x cordinate of zero
+ if(m_event->InCenter(pos)) {
+ m_current_times++;
+ if(m_current_times >= m_total_times) {
+ m_event_received = true;
+ }
+ }
+ }
+ return m_event_received;
+ }
+
+ virtual void Print(std::ostream& out) {
+ if(m_event->IsDead()) {
+ return;
+ }
+ // WHAT TO PRINT
+ }
+
+ virtual void Reset() {
+ m_event_received = false;
+ m_stats_updated = false;
+ m_current_times = 0;
+ }
+
+ virtual bool PreviouslySatisfied() {
+ return m_event_received;
+ }
+
+ virtual cString GetName() {
+ return "EventMovedIntoCenter";
+ }
+
+ virtual void UpdateStats(cStats& stats) {
+ if(m_event_received && !m_stats_updated) {
+/* int eventCell = m_event->GetNextEventCellID();
+ while(eventCell != -1) {
+ stats.IncPredSat(eventCell);
+ eventCell = m_event->GetNextEventCellID();
+ }*/
+ m_stats_updated = true;
+ }
+ }
+
+ cDemeCellEvent* GetEvent(int i) { return m_event; }
+
+ cPopulation& pop;
+ bool m_event_received;
+ bool m_stats_updated;
+ cDemeCellEvent* m_event;
+ int m_total_times;
+ int m_current_times;
+};
+
+
+
+/*! A predicate that returns true if an organism has made it to a target cell.
+ * Modified from cOrgMovementPred_EventMovedIntoCenter
+*/
+struct cOrgMovementPred_EventMovedBetweenTargets : public cOrgMovementPredicate {
+ cOrgMovementPred_EventMovedBetweenTargets(tVector<cDemeCellEvent *> events, cPopulation& population, unsigned int times) :
+ pop(population)
+ , m_event_received(false)
+ , m_stats_updated(false)
+ , m_events(events)
+ , m_total_orgs(1) // TODO: eventually, want to make this a parameter. problem is cPopulation::AddDemePred takes only 1 arg
+ , m_total_times(times) {
+
+ m_event_success.clear();
+ for(int i = 0; i < m_events.Size(); i++) {
+ set<int> p;
+ p.clear();
+ m_event_success.push_back(p);
+ }
+ m_successful_orgs.clear();
+ } //End constructor
+
+ ~cOrgMovementPred_EventMovedBetweenTargets() { }
+
+ virtual bool operator()(cOrganism& org) {
+ int deme_id = org.GetOrgInterface().GetDemeID();
+ set<int>::iterator it;
+ int other_event; // Index of the other event
+
+ m_event_received = false;
+
+ for(int i = 0; i < m_events.Size(); i++) {
+ cDemeCellEvent *event = m_events[i];
+ other_event = (i+1) % 2;
+
+ if( (event->IsDead() == false) && (event->IsActive()) &&
+ (deme_id == event->GetDeme()->GetDemeID()) ) {
+
+ int absolute_cell_ID = org.GetCellID();
+ int relative_cell_ID = pop.GetDeme(deme_id).GetRelativeCellID(absolute_cell_ID);
+
+
+ if(event->OnEventCell(relative_cell_ID)) {
+
+ int org_id = -1;
+ org_id = ((cOrganism&) org).GetID();
+
+ m_event_success[i].insert(org_id);
+
+ it = m_event_success[other_event].find(org_id);
+
+ if(it != m_event_success[other_event].end())
+ {
+ // See how many times this org has gone back and forth. If it has
+ // done it enough times, it is considered successful
+ unsigned int num_backforth = (int) floor(org.GetNumTaskCellsReached()/2);
+
+ if(num_backforth >= m_total_times) {
+ m_successful_orgs.insert(org_id);
+
+ //---- do some logging ----------------------------------------------------------------------
+ ofstream predlog;
+ predlog.open("data/predlog.dat", ios::app);
+ predlog << "Organism " << org_id << " in deme " << deme_id ;
+ predlog << " has touched both targets " << num_backforth << " times. " << m_successful_orgs.size();
+ predlog << " orgs have done this out of " << m_total_orgs << endl;
+
+ set<int>::iterator it;
+ for(unsigned int q = 0; q < m_event_success.size(); q++) {
+ predlog << "ORGS FOR EVENT " << q;
+ for ( it=m_event_success[q].begin() ; it != m_event_success[q].end(); it++ )
+ predlog << " " << *it;
+ predlog << endl;
+ }
+
+ predlog.close();
+ //---- end of logging -----------------------------------------------------------------------
+
+ // If enough organisms have touched both targets, predicate is satisfied.
+ if(m_successful_orgs.size() >= m_total_orgs) {
+ m_event_received = true;
+ return m_event_received;
+ }
+ }
+
+
+ } //End if this organism has gone to the other target as well
+
+ } //End if org is in event area
+
+ } //End if this event matches the predicate
+
+ } //End going through events
+
+ return m_event_received;
+
+ } //End operator()
+
+ virtual void Print(std::ostream& out) {
+ // WHAT TO PRINT
+ }
+
+ virtual void Reset() {
+ m_event_received = false;
+ m_stats_updated = false;
+
+ m_event_success.clear();
+ for(int i = 0; i < m_events.Size(); i++) {
+ set<int> p;
+ p.clear();
+ m_event_success.push_back(p);
+ }
+ m_successful_orgs.clear();
+ }
+
+ virtual bool PreviouslySatisfied() {
+ return m_event_received;
+ }
+
+ virtual cString GetName() {
+ return "EventMovedBetweenTargets";
+ }
+
+ virtual void UpdateStats(cStats& stats) {
+ if(m_event_received && !m_stats_updated) {
+/* int eventCell = m_event->GetNextEventCellID();
+ while(eventCell != -1) {
+ stats.IncPredSat(eventCell);
+ eventCell = m_event->GetNextEventCellID();
+ }*/
+ m_stats_updated = true;
+ }
+ }
+
+ cDemeCellEvent * GetEvent(int i) {
+ return m_events[i];
+ }
+
+ virtual int GetNumEvents() {
+ return m_events.Size();
+ }
+
+ cPopulation& pop;
+ bool m_event_received;
+ bool m_stats_updated;
+ tVector<cDemeCellEvent *> m_events;
+ unsigned int m_total_times;
+ unsigned int m_total_orgs;
+
+ vector< set<int> > m_event_success;
+ set<int> m_successful_orgs;
+};
+
+
+
+
+/*! A predicate that returns true if the appropriate number of organisms touch
+ * target cells
+*/
+
+struct cOrgMovementPred_EventNUniqueIndividualsMovedIntoTarget : public cOrgMovementPredicate {
+ cOrgMovementPred_EventNUniqueIndividualsMovedIntoTarget(cDemeCellEvent* event, cPopulation& population, unsigned int unique_individuals) :
+ pop(population)
+ , m_satisfied(false)
+ , m_stats_updated(false)
+ , m_event(event)
+ , m_total_individuals(unique_individuals) {
+ unique_org_ids.clear();
+ }
+
+ virtual bool operator()(cOrganism& org) {
+ int deme_id = org.GetOrgInterface().GetDemeID();
+
+ if(deme_id != m_event->GetDeme()->GetDemeID() || m_event->IsDead()) {
+ return false;
+ }
+
+ if(m_event->IsActive()) {
+ int absolute_cell_ID = org.GetCellID();
+ int relative_cell_ID = pop.GetDeme(deme_id).GetRelativeCellID(absolute_cell_ID);
+
+ // is the organism in an event cell
+ if(m_event->OnEventCell(relative_cell_ID)) {
+ unique_org_ids.insert(org.GetID());
+
+ // have enough unique organisms visited the event cells?
+ if(unique_org_ids.size() >= m_total_individuals) {
+ m_satisfied = true;
+ }
+ }
+ }
+ return m_satisfied;
+ }
+
+ virtual void Print(std::ostream& out) {
+ if(m_event->IsDead()) {
+ return;
+ }
+ // WHAT TO PRINT
+ }
+
+ virtual void Reset() {
+ m_satisfied = false;
+ m_stats_updated = false;
+ unique_org_ids.clear();
+ }
+
+ virtual bool PreviouslySatisfied() {
+ return m_satisfied;
+ }
+
+ virtual cString GetName() {
+ return "EventNUniqueIndividualsMovedIntoTarget";
+ }
+
+ virtual void UpdateStats(cStats& stats) {
+ if(m_satisfied && !m_stats_updated) {
+ m_stats_updated = true;
+ }
+ }
+
+ virtual cDemeCellEvent* GetEvent(int i) {
+ return m_event;
+ }
+
+ cPopulation& pop;
+ bool m_satisfied;
+ bool m_stats_updated;
+ cDemeCellEvent* m_event;
+ unsigned int m_total_individuals;
+ set<int> unique_org_ids;
+};
+
+#endif
Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cOrganism.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -72,6 +72,7 @@
, m_is_dead(false)
, m_net(NULL)
, m_msg(0)
+ , m_pher_drop(false)
{
// Initialization of structures...
m_hardware = m_world->GetHardwareManager().Create(this);
@@ -664,3 +665,11 @@
return 0;
}
+
+// Brian Movement
+void cOrganism::Move(cAvidaContext& ctx)
+{
+ assert(m_interface);
+ DoOutput(ctx);
+} //End cOrganism::Move()
+
Modified: development/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cOrganism.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -118,11 +118,14 @@
bool m_sent_active; // Has this org sent a number?
int m_test_receive_pos; // In a test CPU, what message to receive next?
+ double m_gradient_movement; // TEMP. Remove once movement tasks are implemented.
+ bool m_pher_drop; // Is the organism dropping pheromone?
+
int m_max_executed; // Max number of instruction executed before death.
bool m_is_running; // Does this organism have the CPU?
bool m_is_sleeping; // Is this organisms sleeping?
bool m_is_dead; // Is this organism dead?
-
+
class cNetSupport
{
public:
@@ -185,6 +188,10 @@
bool IsDead() { return m_is_dead; }
+ bool GetPheromoneStatus() { return m_pher_drop; }
+ void TogglePheromone() { m_pher_drop = (m_pher_drop == true) ? false : true; }
+ void SetPheromone(bool newval) { m_pher_drop = newval; }
+
// -------- cOrgInterface Methods --------
cHardwareBase& GetHardware() { return *m_hardware; }
cOrganism* GetNeighbor() { return m_interface->GetNeighbor(); }
@@ -211,6 +218,13 @@
tListNode<tListNode<cSaleItem> >* AddSoldItem(tListNode<cSaleItem>* node) { return m_sold_items.PushRear(node); }
tList<tListNode<cSaleItem> >* GetSoldItems() { return &m_sold_items; }
void UpdateMerit(double new_merit) { m_interface->UpdateMerit(new_merit); }
+
+ int GetPrevSeenCellID() const { return m_interface->GetPrevSeenCellID(); }
+ int GetPrevTaskCellID() const { return m_interface->GetPrevTaskCellID(); }
+ void SetPrevSeenCellID(int id) const { m_interface->SetPrevSeenCellID(id); }
+ void SetPrevTaskCellID(int id) const { m_interface->SetPrevTaskCellID(id); }
+ int GetNumTaskCellsReached() const { m_interface->GetNumTaskCellsReached(); }
+ void AddReachedTaskCell() { m_interface->AddReachedTaskCell(); }
// -------- Input and Output Methods --------
@@ -348,6 +362,21 @@
//! Called to check for (and initialize) messaging support within this organism.
inline void InitMessaging() { if(!m_msg) m_msg = new cMessagingSupport(); }
// -------- End of messaging support --------
+
+ // -------- Movement TEMP --------
+public:
+ double GetGradientMovement() const {
+ return m_gradient_movement;
+ }
+
+ void SetGradientMovement(const double value) {
+ m_gradient_movement = value;
+ }
+
+ // -------- BDC Movement ---------
+public:
+ void Move(cAvidaContext& ctx);
+
};
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cPopulation.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -1180,6 +1180,7 @@
2: 'corners' - ...demes with upper left and lower right corners filled.
3: 'deme-age' - ...demes who have reached their maximum age
4: 'birth-count' ...demes that have had a certain number of births.
+5: 'sat-mov-pred'...demes whose movement predicate was previously satisfied
*/
@@ -1224,6 +1225,10 @@
if(source_deme.GetBirthCount() < m_world->GetConfig().DEMES_MAX_BIRTHS.Get()) continue;
break;
}
+ case 5: {
+ if(!(source_deme.MovPredSatisfiedPreviously())) continue;
+ break;
+ }
default: {
cerr << "ERROR: Invalid replication trigger " << rep_trigger
<< " in cPopulation::ReplicateDemes()" << endl;
@@ -2402,6 +2407,33 @@
InjectClone( cell2_id, *(cell_array[cell1_id].GetOrganism()) );
}
+void cPopulation::AddDemePred(cString type, int times) {
+ if(type == "EventReceivedCenter") {
+ for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
+ deme_array[deme_id].AddEventReceivedCenterPred(times);
+ }
+ } else if(type == "EventReceivedLeftSide") {
+ for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
+ deme_array[deme_id].AddEventReceivedLeftSidePred(times);
+ }
+ } else if(type == "EventMovedIntoCenter") {
+ for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
+ deme_array[deme_id].AddEventMoveCenterPred(times);
+ }
+ } else if(type == "EventMovedBetweenTargets") {
+ for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
+ deme_array[deme_id].AddEventMoveBetweenTargetsPred(times);
+ }
+ } else if(type == "EventNUniqueIndividualsMovedIntoTarget") {
+ for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
+ deme_array[deme_id].AddEventEventNUniqueIndividualsMovedIntoTargetPred(times);
+ }
+ } else {
+ cout << "Unknown Predicate\n";
+ exit(1);
+ }
+}
+
void cPopulation::CheckImplicitDemeRepro(cDeme& deme) {
if (GetNumDemes() <= 1) return;
@@ -4230,6 +4262,25 @@
// Activate the organism in the population...
ActivateOrganism(ctx, new_organism, cell_array[cell_id]);
+
+ // Log the injection of this organism if LOG_INJECT is set to 1 and
+ // the current update number is >= INJECT_LOG_START
+ if ( (m_world->GetConfig().LOG_INJECT.Get() == 1) &&
+ (m_world->GetStats().GetUpdate() >= m_world->GetConfig().INJECT_LOG_START.Get()) ){
+
+ cString tmpfilename = cStringUtil::Stringf("injectlog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int update = m_world->GetStats().GetUpdate();
+ int orgid = new_organism->GetID();
+ int deme_id = m_world->GetPopulation().GetCell(cell_id).GetDemeID();
+ int facing = new_organism->GetFacing();
+ const char *orgname = (const char *)new_genotype->GetName();
+
+ cString UpdateStr = cStringUtil::Stringf("%d %d %d %d %d %s", update, orgid, cell_id, deme_id, facing, orgname);
+ df.WriteRaw(UpdateStr);
+ }
+
}
Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cPopulation.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -221,6 +221,7 @@
void ResetDemes();
void CopyDeme(int deme1_id, int deme2_id);
void SpawnDeme(int deme1_id, int deme2_id=-1);
+ void AddDemePred(cString type, int times);
void CheckImplicitDemeRepro(cDeme& deme);
Modified: development/source/main/cPopulationCell.cc
===================================================================
--- development/source/main/cPopulationCell.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cPopulationCell.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -185,6 +185,11 @@
// Adjust the organism's attributes to match this cell.
m_organism->GetOrgInterface().SetCellID(m_cell_id);
m_organism->GetOrgInterface().SetDemeID(m_deme_id);
+
+ // If this organism is new, set the previously-seen cell id
+ if(m_organism->GetOrgInterface().GetPrevSeenCellID() == -1) {
+ m_organism->GetOrgInterface().SetPrevSeenCellID(m_cell_id);
+ }
if(m_world->GetConfig().ENERGY_ENABLED.Get() == 1 && m_world->GetConfig().FRAC_ENERGY_TRANSFER.Get() > 0.0) {
// uptake all the cells energy
Modified: development/source/main/cPopulationInterface.h
===================================================================
--- development/source/main/cPopulationInterface.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cPopulationInterface.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -48,6 +48,10 @@
int m_cell_id;
int m_deme_id;
+ int m_prevseen_cell_id; // Previously-seen cell's ID
+ int m_prev_task_cell; // Cell ID of previous task
+ int m_num_task_cells; // Number of task cells seen
+
cPopulationInterface(); // @not_implemented
cPopulationInterface(const cPopulationInterface&); // @not_implemented
cPopulationInterface operator=(const cPopulationInterface&); // @not_implemented
@@ -62,6 +66,13 @@
void SetCellID(int in_id) { m_cell_id = in_id; }
void SetDemeID(int in_id) { m_deme_id = in_id; }
+ int GetPrevSeenCellID() { return m_prevseen_cell_id; }
+ int GetPrevTaskCellID() { return m_prev_task_cell; }
+ int GetNumTaskCellsReached() { return m_num_task_cells; }
+ void AddReachedTaskCell() { m_num_task_cells++; }
+ void SetPrevSeenCellID(int in_id) { m_prevseen_cell_id = in_id; }
+ void SetPrevTaskCellID(int in_id) { m_prev_task_cell = in_id; }
+
bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome);
cOrganism* GetNeighbor();
int GetNumNeighbors();
Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cStats.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -38,6 +38,7 @@
#include "tDataEntry.h"
#include "cOrgMessage.h"
#include "cOrgMessagePredicate.h"
+#include "cOrgMovementPredicate.h"
#include "cReaction.h"
#include "functions.h"
@@ -229,6 +230,17 @@
numAsleep.Resize(m_world->GetConfig().NUM_DEMES.Get());
numAsleep.SetAll(0);
+ if(m_world->GetConfig().NUM_DEMES.Get() == 0) {
+ relative_pos_event_count.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get());
+ relative_pos_pred_sat.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get());
+ } else {
+ relative_pos_event_count.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get() / m_world->GetConfig().NUM_DEMES.Get());
+ relative_pos_pred_sat.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get() / m_world->GetConfig().NUM_DEMES.Get());
+ }
+
+ relative_pos_event_count.SetAll(0);
+ relative_pos_pred_sat.SetAll(0);
+
SetupPrintDatabase();
}
@@ -1196,7 +1208,50 @@
m_message_predicates.push_back(predicate);
}
+void cStats::RemoveMessagePredicate(cOrgMessagePredicate* predicate)
+{
+ for(message_pred_ptr_list::iterator iter = m_message_predicates.begin(); iter != m_message_predicates.end(); iter++) {
+ if((*iter) == predicate) {
+ m_message_predicates.erase(iter);
+ return;
+ }
+ }
+}
+
+/*! This method adds a movement predicate to the list of all movement predicates. Each predicate
+ * in the list is evaluated for every organism movement.
+ *
+ * NOTE: cStats does NOT own the predicate pointer! (It DOES NOT delete them!)
+ * */
+void cStats::AddMovementPredicate(cOrgMovementPredicate* predicate)
+{
+ m_movement_predicates.push_back(predicate);
+}
+
+/*! This method is called whenever an organism moves.*/
+void cStats::Move(cOrganism& org) {
+ // Check to see if this message matches any of our predicates.
+ for(movement_pred_ptr_list::iterator i=m_movement_predicates.begin();
+ i!=m_movement_predicates.end(); ++i) {
+ (**i)(org); // Predicate is responsible for tracking info about movement.
+ }
+}
+
+// deme predicate stats
+void cStats::IncEventCount(int x, int y) {
+ relative_pos_event_count.ElementAt(x,y)++;
+}
+
+void cStats::IncPredSat(int cell_id) {
+ cPopulation& pop = m_world->GetPopulation();
+ int deme_id = pop.GetCell(cell_id).GetDemeID();
+ std::pair<int, int> pos = pop.GetDeme(deme_id).GetCellPosition(cell_id);
+ relative_pos_pred_sat.ElementAt(pos.first, pos.second)++;
+}
+
+
+
/*! This method prints information contained within all active message predicates.
about specific messages that are being tracked.
@@ -1224,7 +1279,33 @@
df.Endl();
}
+void cStats::PrintPredSatFracDump(const cString& filename) {
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteComment( "Displays the fraction of events detected in cell since last print.\n" );
+ df.FlushComments();
+ cString UpdateStr = cStringUtil::Stringf( "%07i", GetUpdate() ) + " = [ ...";
+ df.WriteRaw(UpdateStr);
+ int rows = relative_pos_pred_sat.GetNumRows();
+ int cols = relative_pos_pred_sat.GetNumCols();
+ for (int x = 0; x < rows; x++) {
+ for (int y = 0; y < cols; y++) {
+ double data;
+ if(relative_pos_event_count.ElementAt(x,y) == 0) {
+ data = 0.0;
+ } else {
+ data = (double) relative_pos_pred_sat.ElementAt(x,y) / (double) relative_pos_event_count.ElementAt(x,y);
+ }
+ df.WriteBlockElement(data, x*cols+y, cols);
+ }
+ }
+ df.WriteRaw("];");
+ df.Endl();
+
+ relative_pos_pred_sat.SetAll(0);
+ relative_pos_event_count.SetAll(0);
+}
+
void cStats::DemePreReplication(cDeme& source_deme, cDeme& target_deme)
{
++m_deme_num_repls;
Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cStats.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -53,6 +53,9 @@
#ifndef tDataManager_h
#include "tDataManager.h"
#endif
+#ifndef tMatrix_h
+#include "tMatrix.h"
+#endif
#ifndef nGeometry_h
#include "nGeometry.h"
#endif
@@ -67,8 +70,10 @@
class cGenotype;
class cInjectGenotype;
class cWorld;
+class cOrganism;
class cOrgMessage;
class cOrgMessagePredicate;
+class cOrgMovementPredicate;
class cDeme;
class cGermline;
@@ -279,6 +284,10 @@
cDoubleSum sum_deme_generations_per_lifetime;
int m_num_occupied_demes;
+ // deme predicate stats
+ tMatrix<int> relative_pos_event_count;
+ tMatrix<int> relative_pos_pred_sat;
+
// Speculative Execution Stats
int m_spec_total;
int m_spec_num;
@@ -688,6 +697,14 @@
// @WRE: Added event for printing visit counts
void PrintCellVisitsData(const cString& filename);
+ // deme predicate stats
+ void IncEventCount(int x, int y);
+ void IncPredSat(int cell_id);
+ void PrintPredSatFracDump(const cString& filename);
+
+ void addOrgLocations(std::vector<std::pair<int, int> >);
+ void PrintDemeRepOrgLocation(const cString& filename);
+
// -------- Messaging support --------
public:
//! Type for a list of pointers to message predicates.
@@ -697,6 +714,8 @@
void SentMessage(const cOrgMessage& msg);
//! Adds a predicate that will be evaluated for each message.
void AddMessagePredicate(cOrgMessagePredicate* predicate);
+ //! Removes a predicate.
+ void RemoveMessagePredicate(cOrgMessagePredicate* predicate);
//! Prints information regarding messages that "passed" their predicate.
void PrintPredicatedMessages(const cString& filename);
@@ -707,6 +726,17 @@
message_pred_ptr_list m_message_predicates;
// -------- End messaging support --------
+
+ // -------- Movement support -------------
+public:
+ //! Type for a list of pointers to movement predicates.
+ typedef std::vector<cOrgMovementPredicate*> movement_pred_ptr_list;
+ void Move(cOrganism& org);
+ void AddMovementPredicate(cOrgMovementPredicate* predicate);
+protected:
+ movement_pred_ptr_list m_movement_predicates;
+ // -------- End movement support --------
+
// -------- Deme replication support --------
public:
Modified: development/source/main/cTaskContext.h
===================================================================
--- development/source/main/cTaskContext.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cTaskContext.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -118,6 +118,7 @@
return ret;
}
inline void AddTaskState(cTaskState* value) { m_task_states->Add(m_task_entry, value); }
+ inline cOrgInterface* GetOrgInterface() { return m_interface; }
};
Modified: development/source/main/cTaskLib.cc
===================================================================
--- development/source/main/cTaskLib.cc 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cTaskLib.cc 2008-06-13 14:34:23 UTC (rev 2644)
@@ -30,6 +30,10 @@
#include "cEnvReqs.h"
#include "tHashTable.h"
#include "cTaskState.h"
+#include "cPopulation.h"
+#include "cPopulationCell.h"
+#include "cOrgMessagePredicate.h"
+#include "cOrgMovementPredicate.h"
#include "platform.h"
@@ -384,8 +388,30 @@
else if (name == "net_receive")
NewTask(name, "Successfully Received Network Message", &cTaskLib::Task_NetReceive);
+ // Movement Tasks
+ if (name == "move_up_gradient")
+ NewTask(name, "Move up gradient", &cTaskLib::Task_MoveUpGradient);
+ else if (name == "move_neutral_gradient")
+ NewTask(name, "Move neutral gradient", &cTaskLib::Task_MoveNeutralGradient);
+ else if (name == "move_down_gradient")
+ NewTask(name, "Move down gradient", &cTaskLib::Task_MoveDownGradient);
+ else if (name == "move_not_up_gradient")
+ NewTask(name, "Move not up gradient", &cTaskLib::Task_MoveNotUpGradient);
+ else if (name == "move_to_right_side")
+ NewTask(name, "Move to right side", &cTaskLib::Task_MoveToRightSide);
+ else if (name == "move_to_left_side")
+ NewTask(name, "Move to left side", &cTaskLib::Task_MoveToLeftSide);
+ // BDC Movement Tasks
+ else if (name == "move")
+ NewTask(name, "Successfully Moved", &cTaskLib::Task_Move);
+ else if (name == "movetotarget")
+ NewTask(name, "Move to a target area", &cTaskLib::Task_MoveToTarget);
+ else if (name == "movetoevent")
+ NewTask(name, "Move to a target area", &cTaskLib::Task_MoveToMovementEvent);
+ else if (name == "movebetweenevent")
+ NewTask(name, "Move to a target area", &cTaskLib::Task_MoveBetweenMovementEvent);
+
-
// Make sure we have actually found a task
if (task_array.GetSize() == start_size) {
if (errors != NULL && errors->GetSize() == 0) {
@@ -2834,3 +2860,150 @@
if (ctx.NetIsValid()) return 1.0;
return 0.0;
}
+
+//TODO: add movement tasks here
+
+double cTaskLib::Task_MoveUpGradient(cTaskContext& ctx) const {
+ if(ctx.GetOrganism()->GetGradientMovement() == 1.0)
+ return 1.0;
+ return 0.0;
+}
+
+double cTaskLib::Task_MoveNeutralGradient(cTaskContext& ctx) const {
+ if(ctx.GetOrganism()->GetGradientMovement() == 0.0)
+ return 1.0;
+ return 0.0;
+}
+
+double cTaskLib::Task_MoveDownGradient(cTaskContext& ctx) const {
+ if(ctx.GetOrganism()->GetGradientMovement() == -1.0)
+ return 1.0;
+ return 0.0;
+}
+
+double cTaskLib::Task_MoveNotUpGradient(cTaskContext& ctx) const {
+ if(Task_MoveUpGradient(ctx))
+ return 0.0;
+ return 1.0;
+}
+
+double cTaskLib::Task_MoveToRightSide(cTaskContext& ctx) const {
+ cDeme& deme = m_world->GetPopulation().GetDeme(ctx.GetOrgInterface()->GetDemeID());
+ std::pair<int, int> location = deme.GetCellPosition(ctx.GetOrgInterface()->GetCellID());
+
+ if(location.first == m_world->GetConfig().WORLD_X.Get()-1)
+ return 1.0;
+ return 0.0;
+}
+
+double cTaskLib::Task_MoveToLeftSide(cTaskContext& ctx) const {
+ cDeme& deme = m_world->GetPopulation().GetDeme(ctx.GetOrgInterface()->GetDemeID());
+ std::pair<int, int> location = deme.GetCellPosition(ctx.GetOrgInterface()->GetCellID());
+
+ if(location.first == 0)
+ return 1.0;
+ return 0.0;
+}
+
+double cTaskLib::Task_Move(cTaskContext& ctx) const
+{
+ if(ctx.GetOrganism()->GetCellID() != ctx.GetOrganism()->GetPrevSeenCellID()) {
+ ctx.GetOrganism()->SetPrevSeenCellID(ctx.GetOrganism()->GetCellID());
+ return 1.0;
+ }
+
+ return 0.0;
+
+} //End cTaskLib::Task_Move()
+
+double cTaskLib::Task_MoveToTarget(cTaskContext& ctx) const
+//Note - a generic version of this is now at - Task_MoveToMovementEvent
+{
+ cOrgInterface* iface = ctx.GetOrgInterface();
+ cDeme& deme = m_world->GetPopulation().GetDeme(ctx.GetOrgInterface()->GetDemeID());
+ int celldata = m_world->GetPopulation().GetCell(iface->GetCellID()).GetCellData();
+
+ int current_cell = deme.GetRelativeCellID(iface->GetCellID());
+ int prev_target = deme.GetRelativeCellID(iface->GetPrevTaskCellID());
+
+ // If the organism is currently on a target cell, see which target cell it previously
+ // visited. Since we want them to move back and forth, only reward if we are on
+ // a different target cell.
+
+ if(celldata > 1)
+ {
+ if (current_cell == prev_target) {
+ // At some point, we may want to return a fraction
+ return 0;
+ } else {
+ iface->AddReachedTaskCell();
+ iface->SetPrevTaskCellID(current_cell);
+ return 1.0;
+ }
+ }
+
+ return 0;
+
+} //End cTaskLib::TaskMoveToTarget()
+
+double cTaskLib::Task_MoveToMovementEvent(cTaskContext& ctx) const {
+ cDeme& deme = m_world->GetPopulation().GetDeme(ctx.GetOrgInterface()->GetDemeID());
+ int cell_data = m_world->GetPopulation().GetCell(ctx.GetOrgInterface()->GetCellID()).GetCellData();
+ cOrgInterface* iface = ctx.GetOrgInterface();
+
+ if(cell_data <= 0)
+ return 0.0;
+
+ for(int i = 0; i < deme.GetNumMovementPredicates(); i++) {
+ if(deme.GetMovPredicate(i)->GetEvent(0)->GetEventID() == cell_data) {
+ iface->AddReachedTaskCell();
+ iface->SetPrevTaskCellID(cell_data);
+ return 1.0;
+ }
+ }
+ return 0.0;
+}
+
+
+double cTaskLib::Task_MoveBetweenMovementEvent(cTaskContext& ctx) const {
+ cDeme& deme = m_world->GetPopulation().GetDeme(ctx.GetOrgInterface()->GetDemeID());
+ int cell_data = m_world->GetPopulation().GetCell(ctx.GetOrgInterface()->GetCellID()).GetCellData();
+ cOrgInterface* iface = ctx.GetOrgInterface();
+ int prev_target = deme.GetRelativeCellID(iface->GetPrevTaskCellID());
+
+ int cellid = ctx.GetOrgInterface()->GetCellID();
+
+ // NOTE: as of now, orgs aren't rewarded if they touch a target more than
+ // once in a row. Could be useful in the future to have fractional reward
+ // or something.
+ if( (cell_data <= 0) || (cell_data == prev_target) )
+ return 0.0;
+
+ for(int i = 0; i < deme.GetNumMovementPredicates(); i++) {
+ // NOTE: having problems with calling the GetNumEvents function for some reason. FIXME
+ //int num_events = deme.GetMovPredicate(i)->GetNumEvents;
+ int num_events = 2;
+
+ if(num_events == 1) {
+ if( (deme.GetMovPredicate(i)->GetEvent(0)->IsActive()) &&
+ (deme.GetMovPredicate(i)->GetEvent(0)->GetEventID() == cell_data) ) {
+ iface->AddReachedTaskCell();
+ iface->SetPrevTaskCellID(cell_data);
+ return 1.0;
+ }
+ } else {
+ for(int j = 0; j < num_events; j++) {
+ cDemeCellEvent *event = deme.GetMovPredicate(i)->GetEvent(j);
+ if( (event != NULL) && (event->IsActive()) &&
+ (event->GetEventID() == cell_data) ) {
+ iface->AddReachedTaskCell();
+ iface->SetPrevTaskCellID(cell_data);
+ return 1.0;
+ }
+ }
+ }
+
+ }
+ return 0.0;
+}
+
Modified: development/source/main/cTaskLib.h
===================================================================
--- development/source/main/cTaskLib.h 2008-06-11 19:37:26 UTC (rev 2643)
+++ development/source/main/cTaskLib.h 2008-06-13 14:34:23 UTC (rev 2644)
@@ -278,6 +278,21 @@
// Network Tasks
double Task_NetSend(cTaskContext& ctx) const;
double Task_NetReceive(cTaskContext& ctx) const;
+
+ // Movement tasks (temp, rely on hack)
+ double Task_MoveUpGradient(cTaskContext& ctx) const;
+ double Task_MoveNeutralGradient(cTaskContext& ctx) const;
+ double Task_MoveDownGradient(cTaskContext& ctx) const;
+ double Task_MoveNotUpGradient(cTaskContext& ctx) const;
+ double Task_MoveToRightSide(cTaskContext& ctx) const;
+ double Task_MoveToLeftSide(cTaskContext& ctx) const;
+
+ // BDC Movement tasks
+ double Task_Move(cTaskContext& ctx) const;
+ double Task_MoveToTarget(cTaskContext& ctx) const;
+ double Task_MoveToMovementEvent(cTaskContext& ctx) const;
+ double Task_MoveBetweenMovementEvent(cTaskContext& ctx) const;
+
};
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