Changeset 1060 for framspy/FramsticksEvolution.py

Timestamp:

01/24/21 13:29:42 (3 years ago)

Author:

Maciej Komosinski

Message:

"Vectorized" mutation for better performance due to decreased time of communication py<->frams (mutate many genotypes in one call)

File:

• framspy/FramsticksEvolution.py (modified) (4 diffs)

framspy/FramsticksEvolution.py

@@ -14 +14 @@
 
 def frams_evaluate(frams_cli, individual):
-        genotype = individual[0]  # [0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
+        genotype = individual[0]  # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
         data = frams_cli.evaluate([genotype])
         # print("Evaluated '%s'" % genotype, 'evaluation is:', data)
@@ -22 +22 @@
                 default_evaluation_data = evaluation_data[""]
                 fitness = [default_evaluation_data[crit] for crit in OPTIMIZATION_CRITERIA]
-        except (KeyError, TypeError) as e:  # the evaluation may have failed for invalid genotypes (or some other reason)
-                fitness = [-1] * len(OPTIMIZATION_CRITERIA)
+        except (KeyError, TypeError) as e:  # the evaluation may have failed for an invalid genotype (such as X[@][@] with "Don't simulate genotypes with warnings" option) or for some other reason
+                fitness = [-1] * len(OPTIMIZATION_CRITERIA)  # fitness of -1 is intended to discourage further propagation of this genotype via selection ("this one is very poor")
                 print("Error '%s': could not evaluate genotype '%s', returning fitness %s" % (str(e), genotype, fitness))
         return fitness
@@ -29 +29 @@
 
 def frams_crossover(frams_cli, individual1, individual2):
-        geno1 = individual1[0]  # [0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
-        geno2 = individual2[0]  # [0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
+        geno1 = individual1[0]  # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
+        geno2 = individual2[0]  # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
         individual1[0] = frams_cli.crossOver(geno1, geno2)
         individual2[0] = frams_cli.crossOver(geno1, geno2)
@@ -37 +37 @@
 
 def frams_mutate(frams_cli, individual):
-        individual[0] = frams_cli.mutate(individual[0])
+        individual[0] = frams_cli.mutate([individual[0]])[0]  # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str.
         return individual,