Merge pull request #85 from devosoft/parasite-log-injections

Impl, test opt-in injection logging

avida-core/source/main/cAvidaConfig.h

@@ -439,6 +439,7 @@ class cAvidaConfig {
 
   // -------- Parasite options --------
   CONFIG_ADD_GROUP(PARASITE_GROUP, "Parasite config options");
+  CONFIG_ADD_VAR(LOG_PARASITE_INJECTIONS, bool, 0, "Log parasite replications?");
   CONFIG_ADD_VAR(INJECT_METHOD, int, 0, "What should happen to a parasite when it gives birth?\n0 = Leave the parasite thread state untouched.\n1 = Resets the state of the calling thread (for SMT parasites, this must be 1)");
   CONFIG_ADD_VAR(INFECTION_MECHANISM, int, 1, "0: Infection always succeeds. \n1: Infection succeeds if parasite matches at least one host task.\n2: Infection succeeds if parasite does NOT match at least one task.\n3: Parasite tasks must match host tasks exactly (Matching Alleles).");
   CONFIG_ADD_ALIAS(INJECT_IS_TASK_SPECIFIC);

avida-core/source/main/cPopulation.cc

@@ -1270,9 +1270,15 @@ bool cPopulation::ActivateParasite(cOrganism* host, Systematics::UnitPtr parent,
       hw.GetNumThreads() == m_world->GetConfig().MAX_CPU_THREADS.Get()) return false;
 
   //Handle host specific injection
-  if(TestForParasiteInteraction(host, target_organism) == false)
-    return false;
-
+  const bool parasite_interaction = TestForParasiteInteraction(host, target_organism);
+  if (m_world->GetConfig().LOG_PARASITE_INJECTIONS.Get()) {
+    Avida::Output::FilePtr df = Avida::Output::File::StaticWithPath(m_world->GetNewWorld(), "parasite_injection.dat");
+    cString UpdateStr = cStringUtil::Stringf("%d,%d,%d,%d", m_world->GetStats().GetUpdate(), target_organism->GetDemeID(), target_organism->GetCellID(), parasite_interaction);
+    df->WriteRaw(UpdateStr);
+  }
+
+  if(parasite_interaction == false) return false;
+
 
   // Attempt actual parasite injection
   // LZ - use parasige_genotype_list for the GenRepPtr instead IF Config says to

avida-core/tests/parasites_log_injections/config/environment.cfg

@@ -0,0 +1,25 @@
+#for analyze mode, uncomment this line
+#RESOURCE  resECHO:initial=10000000:inflow=40:outflow=0.10
+RESOURCE  resECHO:inflow=40:outflow=0.10
+
+#REACTION  ECHO  echo   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=ECHO
+
+REACTION NOT
+REACTION NAND
+REACTION AND
+REACTION ORN
+REACTION OR
+REACTION ANDN
+REACTION NOR
+REACTION XOR
+REACTION EQU
+
+REACTION  NOT  not   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  NAND nand  process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  AND  and   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  ORN  orn   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  OR   or    process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  ANDN andn  process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  NOR  nor   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  XOR  xor   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT
+REACTION  EQU  equ   process:resource=resECHO:value=0.0:type=pow:frac=0.5:min=1:max=1: requisite:noreaction=EQU:noreaction=XOR:noreaction=NOR:noreaction=ANDN:noreaction=OR:noreaction=ORN:noreaction=AND:noreaction=NAND:noreaction=NOT

avida-core/tests/parasites_log_injections/config/events.cfg

@@ -0,0 +1,57 @@
+##############################################################################
+#
+# This is the setup file for the events system.  From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see:  doc/events.html
+# For other sample event configurations, see:  support/config/
+#
+##############################################################################
+
+# Seed the population with a single organism
+u begin Inject evolved-not.org
+
+u 600 InjectParasite parasite-smt.org ABB 0 400
+#u 0:100:end PrintDepthHistogram
+#u 0:100:end PrintHostDepthHistogram
+#u 0:100:end PrintParasiteDepthHistogram
+
+#u 0:200:end DumpHostTaskGrid
+#u 0:200:end DumpParasiteTaskGrid
+#u 0:100:end PrintMutationRateData
+
+#u 0:100:end PrintPhenotypeData
+#u 0:100:end PrintHostPhenotypeData
+#u 0:100:end PrintParasitePhenotypeData
+
+#u 0:100:end PrintHostTasksData
+u 0:100:end PrintParasiteTasksData
+
+#u 0:100:end PrintParasiteData ParasiteData.dat
+
+# Print all of the standard data files...
+#u 0:100:end PrintAverageData       # Save info about they average genotypes
+#u 0:100:end PrintDominantData      # Save info about most abundant genotypes
+#u 0:100:end PrintStatsData         # Collect satistics about entire pop.
+#u 0:100:end PrintCountData         # Count organisms, genotypes, species, etc.
+#u 0:100:end PrintTasksData         # Save organisms counts for each task.
+#u 0:100:end PrintTimeData          # Track time conversion (generations, etc.)
+#u 0:100:end PrintResourceData      # Track resource abundance.
+
+# A few data files not printed by default
+# u 100:100 PrintDominantGenotype      # Save the most abundant genotypes
+# u 100:100:end PrintErrorData       # Std. Error on averages.
+# u 100:100:end PrintVarianceData    # Variance on averages.
+# u 100:100:end PrintTotalsData      # Total counts over entire run.
+# u 100:100:end PrintTasksExeData    # Num. times tasks have been executed.
+# u 100:100:end PrintTasksQualData   # Task quality information
+
+# Setup the exit time and full population data collection.
+u 600 SavePopulation         # Save current state of population.
+u 900 SavePopulation
+u 900 Exit                        # exit