Several Changes

Crossover/Mutation:
- Split into individual and population subclasses.
- Added sequential population crossover selection.
- Renamed and reimplemented mutation methods.

EasyGA:
- Improved make_obj methods for the chromosomes and populations to take arguments.

Initialization:
- Improved to shorter code.
- Fixed repeated error messages

Chromosome:
- Changed get/set_genes to get/set_gene_list.

src/EasyGA.py

@@ -49,14 +49,19 @@ class GA:
         # Default EasyGA implimentation structure
         self.initialization_impl   = Initialization_Methods.random_initialization
         self.fitness_function_impl = Fitness_Examples.index_dependent_values
+        self.make_population       = create_population
+        self.make_chromosome       = create_chromosome
+        self.make_gene             = create_gene
 
         # Selects which chromosomes should be automaticly moved to the next population
         self.survivor_selection_impl = Survivor_Selection.fill_in_best
 
         # Methods for accomplishing parent-selection -> Crossover -> Mutation
         self.parent_selection_impl     = Parent_Selection.Tournament.with_replacement
-        self.crossover_impl = Crossover_Methods.single_point_crossover
+        self.crossover_individual_impl = Crossover_Methods.Individual.single_point_crossover
-        self.mutation_impl = Mutation_Methods.per_gene_mutation
+        self.crossover_population_impl = Crossover_Methods.Population.random_selection
+        self.mutation_individual_impl  = Mutation_Methods.Individual.single_gene
+        self.mutation_population_impl  = Mutation_Methods.Population.random_selection
 
         # The type of termination to impliment
         self.termination_impl = Termination_Methods.generation_based
@@ -72,11 +77,10 @@ class GA:
                 self.population.set_all_chromosomes(self.sort_by_best_fitness(self.population.get_all_chromosomes()))
             else:
                 self.parent_selection_impl(self)
-                next_population = self.crossover_impl(self)
+                next_population = self.crossover_population_impl(self)
                 next_population = self.survivor_selection_impl(self, next_population)
-                next_population.set_all_chromosomes(self.mutation_impl(self, next_population.get_all_chromosomes()))
-
                 self.population = next_population
+                self.mutation_population_impl(self)
                 self.set_all_fitness(self.population.chromosome_list)
                 self.population.set_all_chromosomes(self.sort_by_best_fitness(self.population.get_all_chromosomes()))
 
@@ -100,7 +104,8 @@ class GA:
 
     def initialize_population(self):
         """Initialize the population using the initialization
-         implimentation that is currently set"""
+        implimentation that is currently set
+        """
         self.population = self.initialization_impl(self)
 
 
@@ -132,18 +137,3 @@ class GA:
         chromosome_set = chromosome_set_temp
 
         return chromosome_set
-
-
-    def make_gene(self,value):
-        """Let's the user create a gene."""
-        return create_gene(value)
-
-
-    def make_chromosome(self):
-        """Let's the user create a chromosome."""
-        return create_chromosome()
-
-
-    def make_population(self):
-        """Let's the user create a population."""
-        return create_population()

src/crossover/crossover_methods.py

@@ -3,29 +3,34 @@ from initialization.chromosome_structure.chromosome import Chromosome
 from initialization.population_structure.population import Population
 
 class Crossover_Methods:
-    def single_point_crossover(ga):
-        """Single point crossover is when a "point" is selected and the genetic
-        make up of the two parent chromosomes are swapped at that point"""
 
-        crossover_pool = ga.population.mating_pool
+    class Population:
+        """Methods for selecting chromosomes to crossover"""
 
-        """The structure of GA requires that the crossover method return a population strictly with offspring chromosomes"""
+        def sequential_selection(ga):
-        new_population = Population()
+            """Select sequential pairs from the mating pool"""
-        for i in range(len(crossover_pool)):
-            if i + 1 < len(crossover_pool):
-                new_gene_set = []
-                parent_one = crossover_pool[i].get_genes()
-                parent_two = crossover_pool[i+1].get_genes()
-                #halfway_point = int(ga.chromosome_length/2)
-                split_point = random.randint(0,ga.chromosome_length)
-                new_gene_set.extend(parent_one[0:split_point])
-                new_gene_set.extend(parent_two[split_point:])
-                new_chromosome = Chromosome(new_gene_set)
-                new_population.add_chromosome(new_chromosome)
 
-        return new_population
+            mating_pool = ga.population.mating_pool
+            return Population([ga.crossover_individual_impl(mating_pool[index], mating_pool[index+1]) for index in range(len(mating_pool)-1)])
 
-    def multi_point_crossover(ga, number_of_points = 2):
+
-        """Multi point crossover is when a specific number (More then one) of
+        def random_selection(ga):
-        "points" are created to merge the genetic makup of the chromosomes."""
+            """Select random pairs from the mating pool"""
+
+            mating_pool = ga.population.mating_pool
+            return Population([ga.crossover_individual_impl(random.choice(mating_pool), random.choice(mating_pool)) for n in mating_pool])
+
+
+    class Individual:
+        """Methods for crossing parents"""
+
+        def single_point_crossover(parent_one, parent_two):
+            """Cross two parents by swapping genes at one random point"""
+
+            index = random.randint(0, parent_one.size()-1)
+            return Chromosome(parent_one.get_gene_list()[:index] + parent_two.get_gene_list()[index:])
+
+
+        def multi_point_crossover(parent_one, parent_two):
+            """Cross two parents by swapping genes at multiple points"""
             pass

src/initialization/chromosome_structure/chromosome.py

@@ -27,7 +27,7 @@ class Chromosome:
         del self.gene_list[index]
 
 
-    def get_genes(self):
+    def get_gene_list(self):
         return self.gene_list
 
 
@@ -40,7 +40,7 @@ class Chromosome:
         self.gene_list[index] = gene
 
 
-    def set_genes(self, genes):
+    def set_gene_list(self, genes):
         self.gene_list = genes
 
 

src/initialization/initialization_methods.py

@@ -7,27 +7,26 @@ class Initialization_Methods:
     """Initialization examples that are used as defaults and examples"""
 
     def random_initialization(ga):
-        """Takes the initialization inputs and choregraphs them to output the type of population with the given parameters."""
+        """Takes the initialization inputs and returns a population with the given parameters."""
 
-        # Create the population object
-        population = create_population()
-
-        # Fill the population with chromosomes
-        for i in range(ga.population_size):
-            chromosome = create_chromosome()
-            #Fill the Chromosome with genes
-            for j in range(ga.chromosome_length):
         # Using the chromosome_impl to set every index inside of the chromosome
         if ga.chromosome_impl != None:
-                    # Each chromosome location is specified with its own function
+            return create_population([
-                    chromosome.add_gene(create_gene(ga.chromosome_impl(j)))
+                       create_chromosome([
-                    # Will break if chromosome_length != len(lists) in domain
+                           create_gene(ga.chromosome_impl(j))
+                       for j in range(ga.chromosome_length)])
+                   for i in range(ga.population_size)])
+
+        # Using the gene_impl to set every gene to be the same
         elif ga.gene_impl != None:
             function = ga.gene_impl[0]
-                    chromosome.add_gene(create_gene(function(*ga.gene_impl[1:])))
+            return create_population([
+                       create_chromosome([
+                           create_gene(function(*ga.gene_impl[1:]))
+                       for j in range(ga.chromosome_length)])
+                   for i in range(ga.population_size)])
+
+        # Exit because no gene creation method specified
         else:
-                    #Exit because either were not specified
             print("You did not specify any initialization constraints.")
-                    break
+            return None
-            population.add_chromosome(chromosome)
-        return population

src/mutation/mutation_methods.py

@@ -2,45 +2,62 @@ import random
 
 class Mutation_Methods:
 
-    def __init__(self):
+    class Population:
-        pass
+        """Methods for selecting chromosomes to mutate"""
 
-    def random_mutation(ga, chromosome_set = None):
+        def random_selection(ga):
-        """Will take the input population and randomly reset entire chromosomes based on the GA's mutation rate"""
+            """Selects random chromosomes"""
 
-        """Defaulting to the GA's current population if no input is explicitly given"""
+            # Loop through the population
-        if chromosome_set == None:
+            for index in range(ga.population.size()):
-            chromosome_set = ga.population.get_all_chromosomes()
 
-        chromosome_mutate_num = int(len(chromosome_set)*ga.mutation_rate)
+                # Randomly apply mutations
-        temp_population = ga.initialization_impl(ga)
+                if random.uniform(0, 1) < ga.mutation_rate:
+                    ga.population.set_chromosome(ga.mutation_individual_impl(ga, ga.population.get_all_chromosomes()[index]), index)
 
-        """While more chromosomes need to be mutated, grab a random chromosome and re-initialize it entirely"""
-        while chromosome_mutate_num > 0:
-            chromosome_set[random.randint(0,ga.population_size-1)] = temp_population.get_all_chromosomes()[chromosome_mutate_num]
-            chromosome_mutate_num -= 1
 
-        return chromosome_set
+    class Individual:
+        """Methods for mutating a single chromosome"""
 
-    def per_gene_mutation(ga, chromosome_set = None, gene_mutate_count = 1):
+        def whole_chromosome(ga, chromosome):
-        """Will iterate through all chromosomes, and if its selected, will randomly replace one of its genes based on initialization values"""
+            """Makes a completely random chromosome"""
 
-        gene_mutate_count_static = int(gene_mutate_count)
+            # Using the chromosome_impl to set every index inside of the chromosome
+            if ga.chromosome_impl != None:
+                return ga.make_chromosome([
+                           ga.make_gene(ga.chromosome_impl(j))
+                       for j in range(chromosome.size())])
 
-        if chromosome_set == None:
+            # Using the gene_impl
-            chromosome_set = ga.population.get_all_chromosomes()
+            elif ga.gene_impl != None:
+                function = ga.gene_impl[0]
+                return ga.make_chromosome([
+                           ga.make_gene(function(*ga.gene_impl[1:]))
+                       for j in range(chromosome.size())])
 
-        for i in range(len(chromosome_set)):
+            # Exit because no gene creation method specified
-            random_num = random.uniform(0,1)
+            else:
+                print("You did not specify any initialization constraints.")
+                return None
 
-            """If a chromosome was selected to be mutated"""
-            if (random_num <= ga.mutation_rate):
-                while gene_mutate_count > 0:
-                    dummy_population = ga.initialization_impl(ga) #Really inefficient, but works for now
-                    random_index = random.randint(0, ga.chromosome_length-1)
-                    """Replaces a random gene in the actual chromosome with a gene from a newly initialized chromosome"""
-                    chromosome_set[i].get_genes()[random_index] = dummy_population.get_all_chromosomes()[random.randint(0,ga.population_size-1)].get_genes()[random_index]
-                    gene_mutate_count -= 1
-            gene_mutate_count = int(gene_mutate_count_static)
 
-        return chromosome_set
+        def single_gene(ga, chromosome):
+            """Makes a completely random chromosome"""
+            chromosome.set_fitness(None)
+
+            # Using the chromosome_impl
+            if ga.chromosome_impl != None:
+                index = random.randint(0, chromosome.size()-1)
+                chromosome.set_gene(ga.make_gene(ga.chromosome_impl(index)), index)
+
+            # Using the gene_impl
+            elif ga.gene_impl != None:
+                function = ga.gene_impl[0]
+                index = random.randint(0, chromosome.size()-1)
+                chromosome.set_gene(ga.make_gene(function(*ga.gene_impl[1:])), index)
+
+            # Exit because no gene creation method specified
+            else:
+                print("You did not specify any initialization constraints.")
+
+            return chromosome