def get_organism(self):
"""
:return: The organism information as Organism object.
"""
if self.organism:
organism = Organism(self.organism['ScientificName'])
organism.load_entry(self.organism)
return organism
def __init__(self, startingEnergy, senseOfSmell, smellRatio, endurance):
'''Creates a new critter with the specified energy level, sense of smell (as a radius), and smell strength.'''
self.__type__ = "Critter"
#Initialize all the parameters contained in the Organism superclass
Organism.__init__(self, startingEnergy, int(startingEnergy/smellRatio), METABOLISM)
#Set sense of smell radius, hunger and mating thresholds, and energy-to-smell ratio
self.smellRatio = smellRatio
self.sense = senseOfSmell
self.hungerThreshold = HUNGER_THRESHOLD
self.matingThreshold = HUNGER_THRESHOLD + endurance
#Sets self.hungry based on energy
self.hungry = True
self.checkHunger()
def spawn_organisms(self, number):
"""
number: amount of such organisms to add
"""
for _ in range(number):
# want to randomly configure these components
self.organisms.append(Organism(self))
return
def convert_to_object(data, type):
"""
This function creates either a Gene or Organism object and adds extra information from NCBI (if possible).
:param data: A gene or species name.
:param type: The type of the data, this could be Gene or Organism.
:return: An Organism of Gene object (depending on the input type).
"""
if data is not None:
if type == "Gene":
gen = Gene(data)
gen = gather_extra_data(gen, data, "gene")
return gen
if type == "Species":
organism = Organism(data)
organism = gather_extra_data(organism, data, "taxonomy")
return organism
return None
def evolution(gen_size, num_of_gens, num_of_parents, num_of_bests, epochs, to_print):
start_time = time.time()
cur_gen = []
prev_gen = []
n_gen = 0
best_org_fit = 0
best_org_weights = []
# initializing generation 0
for i in range(0, gen_size):
cur_gen.append(Organism())
# start evolution
while n_gen < num_of_gens:
n_gen += 1
prev_gen.clear()
# compute fitness for each organism on current generation
for org in cur_gen:
org.forward_propagation(X_train, Y_train)
prev_gen.append(org)
cur_gen.clear()
prev_gen = sorted(prev_gen, key=lambda x: x.fitness)
prev_gen.reverse()
# save the fitness of the best organism of current generation
cur_best_fit = prev_gen[0].fitness
# save the fitness and weights of the best organism until now
if cur_best_fit > best_org_fit:
best_org_fit = cur_best_fit
best_org_weights.clear()
for layer in prev_gen[0].layers:
best_org_weights.append(layer.get_weights()[0])
if to_print:
print('Generation: %1.f' % n_gen, '\tBest Fitness: %.4f' % cur_best_fit)
# crossover current generation
cur_gen = crossover(gen_size, prev_gen, num_of_bests, num_of_parents)
best_organism = Organism(best_org_weights)
best_organism.compile_train(epochs, X_train, Y_train, to_print)
# test
Y_hat = best_organism.predict(X_test)
Y_hat = Y_hat.argmax(axis=1)
end_time = time.time()
return accuracy_score(Y_test, Y_hat), end_time - start_time
def dynamic_crossover(nn1, nn2=None, nn3=None):
nn1_weights = []
nn2_weights = []
nn3_weights = []
child_weights = []
for layer in nn1.layers:
nn1_weights.append(layer.get_weights()[0])
if nn2 is not None:
for layer in nn2.layers:
nn2_weights.append(layer.get_weights()[0])
if nn3 is not None:
for layer in nn3.layers:
nn3_weights.append(layer.get_weights()[0])
for i in range(0, len(nn1_weights)):
net_len = np.shape(nn1_weights[i])[1] - 1
if nn2 is not None:
split1 = random.randint(0, net_len)
if nn3:
split2 = random.randint(split1, net_len)
else:
split2 = net_len
for j in range(split1, split2):
nn1_weights[i][:, j] = nn2_weights[i][:, j]
for j in range(split2, net_len):
nn1_weights[i][:, j] = nn3_weights[i][:, j]
child_weights.append(nn1_weights[i])
mutation(child_weights)
child = Organism(child_weights)
return child
def __init__(self):
#create the map that defines this Universe
self.map = Map("simple.map")
#self.map = Map("medium.map")
print "Initializing map and first generation...\n"
print str(self.map)
self.pickleFile = open('pickles.txt', 'w')
self.pickler = Pickler(self.pickleFile, 0)
#generate first set of parents
self.parents = [
Organism(NUM_STATES, MEMORY_SIZE, NUM_VALUES)
for i in range(ORIGINAL_POOL_SIZE)
]
for i in range(ORIGINAL_POOL_SIZE):
self.parents[i].birthday = 0
#for each generation,
for i in range(NUM_GENERATIONS):
self.currentGeneration = i + 1
self.testParents()
self.selectParents()
self.nextGeneration()
## Create simpy env and start pygame
env = simpy.RealtimeEnvironment(initial_time=0, factor=0.1, strict=False)
pygame.init()
print("Starting simulation")
ecosystem = Ecosystem()
size = width, height = 1000, 800
screen = pygame.display.set_mode(size)
display = pygame.display
image = pygame.image
event = pygame.event
for org in range(START_NUM_OF_ORGANISMS):
new_org = Organism("O-" + str(org), ecosystem, env)
ecosystem.add_being(new_org)
for food in range(NUM_OF_FOOD):
new_food = Food("F-" + str(food), ecosystem, env)
ecosystem.add_being(new_food)
Emerge = World(ecosystem, env, screen, display, image, event)
##TODO: Attempt to minimilize code by combining this part with above when initializing the organisms/food
for being in ecosystem.all_beings():
env.process(being.run())
env.process(Emerge.run())
env.run(until=100)
def __init__(self, s, i, a, w, t):
Organism.__init__(self, s, i, a, w, t)
def Kill(self, s):
Organism.Kill(self, self.string + " has been slain by " + s)
def __init__(self, world, position, power):
Organism.__init__(self, world, position, power, 0)
def __init__(self, s, a, w, p, t):
Organism.__init__(self, s, 0, a, w, t)
self.__probability = p
def Kill(self, s):
Organism.Kill(self, self.string + " has been eaten by " + s)
def loseEnergy(self):
'''Decreases the critter's energy based on its metabolic rate, returns the amount of energy lost, and updates whether or not it is hungry.'''
#Superclass method!
Organism.loseEnergy(self)
self.checkHunger()
self.updateSmell()
def loseEnergy(self):
'''Decreases the fruit's energy by its decay rate, returns the amount of energy lost in case the World needs to refer to it.'''
return Organism.loseEnergy(self)
self.updateEnergy()
def __init__(self, startingEnergy):
'''Creates a new Fruit with the specified amount of energy.'''
self.__type__ = "Fruit"
Organism.__init__(self, startingEnergy, startingEnergy, DECAY_RATE)