Updated Implementation Framework

Updated to cover changes made by Dan to Master regarding general design changes

Also added remove_two_worst survivor selection method

src/EasyGA.py

@@ -3,25 +3,29 @@ import random
 from initialization import Population as create_population
 from initialization import Chromosome as create_chromosome
 from initialization import Gene as create_gene
-# Import example classes
+# Structure Methods
 from fitness_function import Fitness_Examples
-from initialization import Initialization_Types
-from termination_point import Termination_Types
-from selection import Selection_Types
-from crossover import Crossover_Types
-from mutation import Mutation_Types
+from initialization import Initialization_Methods
+from termination_point import Termination_Methods
+# Population Methods
+from selection import Selection_Methods
+# Manipulation Methods
+from mutation import Mutation_Methods
+from crossover import Crossover_Methods
 
 class GA:
     def __init__(self):
         """Initialize the GA."""
         # Initilization variables
         self.chromosome_length = 10
-        self.population_size = 150
+        self.population_size = 100
         self.chromosome_impl = None
         self.gene_impl = None
         self.population = None
         # Termination varibles
         self.current_generation = 0
+        self.generation_goal = 50
+
         self.current_fitness = 0
         self.generation_goal = 100
         self.fitness_goal = 3
@@ -32,19 +36,52 @@ class GA:
         self.update_fitness = True
 
         # Defualt EastGA implimentation structure
-        self.initialization_impl = Initialization_Types().random_initialization
+        self.initialization_impl = Initialization_Methods().random_initialization
         self.fitness_function_impl = Fitness_Examples().is_it_5
-        self.mutation_impl = Mutation_Types().per_gene_mutation
-        self.parent_selection_impl = Selection_Types().Parent_Selection().Tournament().with_replacement
-        self.survivor_selection_impl = Selection_Types().Survivor_Selection().repeated_crossover
-        self.crossover_impl = Crossover_Types().single_point_crossover
-        self.termination_impl = Termination_Types().generation_based
+        # Selects which chromosomes should be automaticly moved to the next population
+        self.survivor_selection_impl = Selection_Methods().Survivor_Selection().remove_two_worst
+        # Methods for accomplishing parent-selection -> Crossover -> Mutation
+        self.parent_selection_impl = Selection_Methods().Parent_Selection().Tournament().with_replacement
+        self.crossover_impl = Crossover_Methods().single_point_crossover
+        self.mutation_impl = Mutation_Methods().per_gene_mutation
+        # The type of termination to impliment
+        self.termination_impl = Termination_Methods().generation_based
+
+    def evolve_generation(self, number_of_generations = 1, consider_termination = True):
+        """Evolves the ga the specified number of generations."""
+        while(number_of_generations > 0 and (consider_termination == False or self.termination_impl(self))):
+            # If its the first generation then initialize the population
+            if self.current_generation == 0:
+                self.initialize_population()
+                self.set_all_fitness(self.population.chromosome_list)
+            
+            self.parent_selection_impl(self)
+            next_population = self.crossover_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.set_all_fitness(self.population.chromosome_list)
+
+            number_of_generations -= 1
+            self.current_generation += 1
+
+    def evolve(self):
+        """Runs the ga until the termination point has been satisfied."""
+        # While the termination point hasnt been reached keep running
+        while(self.active()):
+            self.evolve_generation()
+
+    def active(self):
+        """Returns if the ga should terminate base on the termination implimented"""
+        # Send termination_impl the whole ga class
+        return self.termination_impl(self)
 
     def initialize_population(self):
         """Initialize the population using the initialization
          implimentation that is currently set"""
         self.population = self.initialization_impl(self)
-        
+
     def set_all_fitness(self,chromosome_set):
         """Will get and set the fitness of each chromosome in the population.
         If update_fitness is set then all fitness values are updated.
@@ -69,7 +106,7 @@ class GA:
             # If its the first generation then initialize the population
             if self.current_generation == 0:
                 self.initialize_population()
-                self.set_all_fitness(self.population.chromosomes)
+                self.set_all_fitness(self.population.chromosome_list)
             
             self.parent_selection_impl(self)
             next_population = self.crossover_impl(self)
@@ -77,7 +114,7 @@ class GA:
             next_population.set_all_chromosomes(self.mutation_impl(self, next_population.get_all_chromosomes()))
 
             self.population = next_population
-            self.set_all_fitness(self.population.chromosomes)
+            self.set_all_fitness(self.population.chromosome_list)
 
             number_of_generations -= 1
             self.current_generation += 1

src/crossover/__init__.py

@@ -1,2 +1,2 @@
 # FROM (. means local) file_name IMPORT function_name
-from .crossover_types import Crossover_Types
+from .crossover_methods import Crossover_Methods

src/crossover/crossover_methods.py

@@ -2,7 +2,7 @@ import random
 from initialization.chromosome_structure.chromosome import Chromosome
 from initialization.population_structure.population import Population
 
-class Crossover_Types:
+class Crossover_Methods:
     """ Crossover explination goes here.
 
     Points - Defined as sections between the chromosomes genetic makeup

src/fitness_function/__init__.py

@@ -1,2 +1,2 @@
 # FROM (. means local) file_name IMPORT class name
-from .examples import Fitness_Examples
+from .fitness_examples import Fitness_Examples

src/fitness_function/fitness_examples.py

@@ -1,13 +1,12 @@
 class Fitness_Examples:
     """Fitness function examples used"""
-    
     def is_it_5(self, chromosome):
         """A very simple case test function - If the chromosomes gene value is a 5 add one
          to the chromosomes overall fitness value."""
         # Overall fitness value
         fitness = 0
         # For each gene in the chromosome
-        for gene in chromosome.genes:
+        for gene in chromosome.gene_list:
             # Check if its value = 5
             if(gene.value == 5):
                 # If its value is 5 then add one to

src/fitness_function/test_examples.py

@@ -0,0 +1,12 @@
+class test_fitness_funciton:
+    def get_fitness(self, chromosome):
+        # For every gene in chromosome
+        for i in range(len(chromosome.genes)):
+            # If the gene has a five then add one to the fitness
+            # Example -> Chromosome = [5],[2],[2],[5],[5] then fitness = 3
+            if (chromosome.genes[i].get_value == 5):
+                # Add to the genes fitness
+                chromosome.genes[i].fitness += 1
+                # Add to the chromosomes fitness
+                chromosome.fitness += 1
+        return chromosome.fitness

src/initialization/__init__.py

@@ -1,5 +1,5 @@
 # FROM (. means local) file_name IMPORT function_name
-from .initialization_types import Initialization_Types
+from .initialization_methods import Initialization_Methods
 from .population_structure.population import Population
 from .chromosome_structure.chromosome import Chromosome
 from .gene_structure.gene import Gene

src/initialization/chromosome_structure/chromosome.py

@@ -2,37 +2,37 @@ class Chromosome:
 
     def __init__(self, genes = None):
         if genes is None:
-            self.genes = []
+            self.gene_list = []
         else:
-            self.genes = genes
+            self.gene_list = genes
         self.fitness = None
         self.selected = False
 
     def add_gene(self, gene, index = -1):
         if index == -1:
-            index = len(self.genes)
-        self.genes.insert(index, gene)
+            index = len(self.gene_list)
+        self.gene_list.insert(index, gene)
 
     def remove_gene(self, index):
-        del self.genes[index]
+        del self.gene_list[index]
 
     def get_genes(self):
-        return self.genes
+        return self.gene_list
 
     def get_fitness(self):
         return self.fitness
 
     def set_gene(self, gene, index):
-        self.genes[index] = gene
+        self.gene_list[index] = gene
 
     def set_genes(self, genes):
-        self.genes = genes
+        self.gene_list = genes
 
     def set_fitness(self, fitness):
         self.fitness = fitness
 
     def __repr__(self):
         output_str = ''
-        for gene in self.genes:
+        for gene in self.gene_list:
             output_str += gene.__repr__()
         return output_str

src/initialization/gene_function/gene_random.py

@@ -1,22 +0,0 @@
-# Imported library
-import random
-
-def check_values(low,high):
-    #Check to make sure its not less then zero
-    assert low > 0 , "The random gene low can not be less then zero"
-    # Check to make sure the high value is not
-    # lower than or equal to low and not 0.
-    assert high > low, "High value can not be smaller then low value"
-    assert high != 0, "High value can not be zero"
-
-def random_gene(gene_input, gene_input_type, gene_index):
-    created_gene = None
-
-    if gene_input_type[gene_index] == "range":
-        created_gene = random.randint(gene_input[gene_index][0], gene_input[gene_index][1])
-    elif gene_input_type[gene_index] == "domain":
-        created_gene = random.choice(gene_input[gene_index])
-    elif gene_input_type[gene_index] == "float-range":
-        created_gene = random.uniform(gene_input[gene_index][0], gene_input[gene_index][1])
-
-    return created_gene

src/initialization/initialization_methods.py

@@ -3,12 +3,12 @@ from .population_structure.population import Population as create_population
 from .chromosome_structure.chromosome import Chromosome as create_chromosome
 from .gene_structure.gene import Gene as create_gene
 
-class Initialization_Types:
+class Initialization_Methods:
     """Initialization examples that are used as defaults and examples"""
-
+    
     def random_initialization(self, ga):
-        """Takes the initialization inputs and choregraphs them to output the type of population
-        with the given parameters."""
+        """Takes the initialization inputs and choregraphs them to output the type of population with the given parameters."""
+
         # Create the population object
         population = create_population()
 

src/initialization/population_structure/population.py

@@ -3,9 +3,9 @@ class Population:
     # fitness = Empty; population = [chromosome, chromosome, etc.]
     def __init__(self, chromosomes = None):
         if chromosomes is None:
-          self.chromosomes = []
+          self.chromosome_list = []
         else:
-          self.chromosomes = chromosomes
+          self.chromosome_list = chromosomes
         self.fitness = None
 
     def get_closet_fitness(self,value):
@@ -14,46 +14,38 @@ class Population:
 
     def add_chromosome(self, chromosome, index = -1):
         if index == -1:
-            index = len(self.chromosomes)
-        self.chromosomes.insert(index, chromosome)
+            index = len(self.chromosome_list)
+        self.chromosome_list.insert(index, chromosome)
 
     def remove_chromosome(self, index):
-        del self.chromosomes[index]
+        del self.chromosome_list[index]
 
     def get_all_chromosomes(self):
         """returns all chromosomes in the population"""
-        return self.chromosomes
+        return self.chromosome_list
 
     def get_fitness(self):
         return self.fitness
 
     def set_all_chromosomes(self, chromosomes):
-        self.chromosomes = chromosomes
+        self.chromosome_list = chromosomes
 
     def set_chromosome(self, chromosome, index = -1):
         if index == -1:
             index = len(self.chromosomes)-1
-        self.chromosomes[index] = chromosome
+        self.chromosome_list[index] = chromosome
 
     def set_fitness(self, fitness):
         self.fitness = fitness
 
     def __repr__(self):
         for index in range(len(self.chromosomes)):
-            return f'{self.chromosomes[index]}'
+            return f'{self.chromosome_list[index]}'
 
     def print_all(self):
         # Ex .Current population
         #     Chromosome 1 - [gene][gene][gene][.etc] /  Chromosome fitness - #
         print("Current population:")
-        for index in range(len(self.chromosomes)):
-            print(f'Chromosome - {index} {self.chromosomes[index]}', end = "")
-            print(f' / Fitness = {self.chromosomes[index].fitness}')
-
-    def generate_first_chromosomes(self, chromosome_count, chromosome_length, gene_lower_bound, gene_upper_bound):
-        #Creating the chromosomes with Genes of random size
-        for x in range(chromosome_count):
-            chromosome = Chromosome(chromosome_length)
-            for y in range(chromosome_length):
-                chromosome.gene_set[y] = Gene(random.randint(gene_lower_bound[y], gene_upper_bound[y]))
-            self.chromosome_set.append(chromosome)
+        for index in range(len(self.chromosome_list)):
+            print(f'Chromosome - {index} {self.chromosome_list[index]}', end = "")
+            print(f' / Fitness = {self.chromosome_list[index].fitness}')

src/initialization/random_initialization.py

@@ -1,31 +0,0 @@
-# Import the data structure
-from .population_structure.population import population as create_population
-from .chromosome_structure.chromosome import chromosome as create_chromosome
-from .gene_structure.gene import gene as create_gene
-from .gene_function.gene_random import random_gene as random_gene
-
-def random_initialization(chromosome_length,population_size,gene_function,gene_input,gene_input_type):
-
-    if gene_function == random_gene:
-        # Create the population object
-        population = create_population()
-        # Fill the population with chromosomes
-        for i in range(population_size):
-            chromosome = create_chromosome()
-            #Fill the Chromosome with genes
-            for j in range(chromosome_length):
-                chromosome.add_gene(create_gene(gene_function(gene_input, gene_input_type, j)))
-            population.add_chromosome(chromosome)
-        return population
-
-    else: #For user input gene-function, don't do anything with gene_input parameter
-        # Create the population object
-        population = create_population()
-        # Fill the population with chromosomes
-        for i in range(population_size):
-            chromosome = create_chromosome()
-            #Fill the Chromosome with genes
-            for j in range(chromosome_length):
-                chromosome.add_gene(create_gene(gene_function()))
-            population.add_chromosome(chromosome)
-        return population

src/mutation/__init__.py

@@ -1,2 +1,2 @@
 # FROM (. means local) file_name IMPORT function_name
-from .mutation_types import Mutation_Types
+from .mutation_methods import Mutation_Methods

src/mutation/mutation_methods.py

@@ -1,6 +1,6 @@
 import random
 
-class Mutation_Types:
+class Mutation_Methods:
     
     def __init__(self):
         pass

src/run_testing.py

@@ -5,8 +5,7 @@ import random
 # Create the Genetic algorithm
 ga = EasyGA.GA()
 
-#def random_parent_selection(population):
-    #while ()
+
 
 ga.gene_impl = [random.randrange,1,100]
 

src/selection/__init__.py

@@ -1,2 +1,2 @@
 # FROM (. means local) file_name IMPORT function_name
-from .selection_types import Selection_Types
+from .selection_methods import Selection_Methods

src/selection/selection_methods.py

@@ -4,7 +4,7 @@ from initialization.gene_structure.gene import Gene as create_gene
 from initialization.population_structure.population import Population
 from initialization.chromosome_structure.chromosome import Chromosome
 
-class Selection_Types:
+class Selection_Methods:
     """Selection is the process by which chromosomes are selected for crossover and eventually, influence the next generation of chromosomes."""
     def __init__(self):
         pass
@@ -68,8 +68,8 @@ class Selection_Types:
                                 break
 
     class Survivor_Selection:
-        def repeated_crossover(self, ga, next_population):
-            while len(next_population.chromosomes) < ga.population_size:
+        def repeated_crossover(self, ga, next_population): #Might be cheating? I don't know honestly - RG
+            while len(next_population.get_all_chromosomes()) < ga.population_size:
                 crossover_pool = []
                 for i in range(ga.population_size):
                     if ga.population.get_all_chromosomes()[i].selected:
@@ -90,10 +90,31 @@ class Selection_Types:
                 
                 for i in range(len(chromosome_list)):
                     next_population.add_chromosome(chromosome_list[i])
-                    if len(next_population.chromosomes) >= ga.population_size:
+                    if len(next_population.get_all_chromosomes()) >= ga.population_size:
                         break
             return next_population
     
+        def remove_two_worst(self, ga, next_population):
+
+            #Bubble sorting by highest fitness
+            temp_population = ga.population
+            not_sorted_check = 0
+            while (not_sorted_check != len(temp_population.get_all_chromosomes())):
+                not_sorted_check = 0
+                for i in range(len(temp_population.get_all_chromosomes())):
+                    if ((i + 1 < len(temp_population.get_all_chromosomes())) and (temp_population.get_all_chromosomes()[i + 1].fitness > temp_population.get_all_chromosomes()[i].fitness)):
+                        temp = temp_population.get_all_chromosomes()[i]
+                        temp_population.get_all_chromosomes()[i] = ga.population.get_all_chromosomes()[i + 1]
+                        temp_population.get_all_chromosomes()[i + 1] = temp
+                    else:
+                        not_sorted_check += 1
+
+            iterator = 0
+            while len(next_population.get_all_chromosomes()) < ga.population_size:
+                next_population.add_chromosome(temp_population.get_all_chromosomes()[iterator])
+                iterator += 1
+            return next_population
+
     def roulette_selection(self, ga):
         """Roulette selection works based off of how strong the fitness is of the
         chromosomes in the population. The stronger the fitness the higher the probability

src/termination_point/__init__.py

@@ -1,2 +1,2 @@
 # FROM (. means local) file_name IMPORT class name
-from .termination_types import Termination_Types
+from .termination_methods import Termination_Methods

src/termination_point/termination_methods.py

@@ -1,16 +1,16 @@
-class Termination_Types:
+class Termination_Methods:
     """Example functions that can be used to terminate the the algorithms loop"""
 
     def fitness_based(self, ga):
         """Fitness based approach to terminate when the goal fitness has been reached"""
-        continue_status = True
+        status = True
         if(ga.current_fitness > ga.fitness_goal):
-            continue_status = False
-        return continue_status
+            status = False
+        return status
 
     def generation_based(self, ga):
         """Generation based approach to terminate when the goal generation has been reached"""
-        continue_status = True
-        if(ga.current_generation > ga.generation_goal-1):
-            continue_status = False
-        return continue_status
+        status = True
+        if(ga.current_generation > ga.generation_goal):
+            status = False
+        return status