def generate(self, P): # generate environment and populate with ecosystems #
for i in range(0, P.grid_size): # x coords
self.grid.append([]) # build the rows
for j in range(0, P.grid_size): # y coords
eco = Ecosystem(P, (i, j)) # create an ecosystem at the plot
eco.connect(P.grid_size) # connect the ecosystem to its neighbors
self.grid[i].append(eco) # put ecosystem into environment grid
if( i == 0 and j == 0): # this is the initial founder square with the initial 500 inds
eco.populate(P)
class Game(arcade.Window):
""" Main application class. """
def __init__(self, width, height):
super().__init__(width, height, 'Ecosystem Simulation')
self.sprite_list = None
self.ecosystem = None
arcade.set_background_color(arcade.color.BLACK)
def setup(self):
self.sprite_list = arcade.SpriteList()
self.ecosystem = Ecosystem(int(SCREEN_WIDTH / CELL_WIDTH),
int(SCREEN_HEIGHT / CELL_HEIGHT))
def on_draw(self):
""" Render the screen. """
arcade.start_render()
self.sprite_list.draw()
def update(self, delta_time):
""" All the logic to move, and the game logic goes here. """
self.sprite_list = arcade.SpriteList()
ecosystem_organisms = self.ecosystem.run()
for organism in ecosystem_organisms:
sprite = arcade.Sprite(organism.get_image(), 1)
sprite.center_x = organism.x * CELL_WIDTH + CELL_WIDTH / 2
sprite.center_y = organism.y * CELL_HEIGHT + CELL_HEIGHT / 2
self.sprite_list.append(sprite)
def simulate(i):
genList = ['power', 'velocity', 'intelligence', 'fertility', 'hostility']
numLives = 30
print(f"init start. numlives: {numLives}")
ecosystem = Ecosystem(numLives=numLives,
genList=genList,
MAP_WIDTH=c.MAP_WIDTH,
MAP_HEIGHT=c.MAP_HEIGHT)
print(f"init finished: {i}-----------------------------------------")
while ecosystem.time < 500:
ecosystem.nextEpoch()
# 선택(내부에 evaluation(싸우는거) 포함)
selectedCreatures = ecosystem.selection(ecosystem.lives)
# 교차
crossOveredCreature = ecosystem.crossover(selectedCreatures[0],
selectedCreatures[1])
# 변이
crossOveredCreature = ecosystem.mutation(crossOveredCreature,
c.MUTATION_RATE)
ecosystem.lives.append(crossOveredCreature)
ecosystem.created.append(crossOveredCreature)
ecosystem.time += 1
ecosystem.numLives += 1
# print(f'epoch {ecosystem.time}: numLives: {ecosystem.numLives}')
print(f"simulation finished: {i}---------------------------------------")
'''
print(f"numlives: {ecosystem.numLives}")
print(f"lenoflives: {len(ecosystem.lives)}")
for cr in ecosystem.lives:
print(cr)
'''
return ecosystem.numLives, ecosystem.lives
def generate_data_structure(self, code_directory, output_file):
files = self.get_class_files(code_directory)
self.ecosystem = Ecosystem()
self.parse_files(files)
f = open(output_file, "w")
f.write(self.ecosystem.serialize())
f.close()
return self.ecosystem
def main(argv):
for i in range(len(argv)):
if argv[i] == "-g":
if len(argv)-i == 1: # last argument
graphic_output.graphics_init("f")
else:
graphic_output.graphics_init(argv[i+1])
simMins, width, height = inputCreatures()
ecosystem = Ecosystem(simMins, width, height)
ecosystem.loadCreatures(num_and_what_creatures, creature_funcs, creatures)
ecosystem.startSimulation()
def generate(self,
P): # generate environment and populate with ecosystems #
for i in range(0, P.grid_size): # x coords
self.grid.append([]) # build the rows
for j in range(0, P.grid_size): # y coords
eco = Ecosystem(P, (i, j)) # create an ecosystem at the plot
eco.connect(
P.grid_size) # connect the ecosystem to its neighbors
self.grid[i].append(eco) # put ecosystem into environment grid
if (
i == 0 and j == 0
): # this is the initial founder square with the initial 500 inds
eco.populate(P)
class CodeParser:
def get_directory_files(self, path):
entries = os.listdir(path)
files = []
for entry in entries:
if isfile(join(path, entry)):
files.append(join(path, entry))
elif isdir(join(path, entry)):
files.extend(self.get_directory_files(join(path, entry)))
return files
def get_class_files(self, code_directory):
files = self.get_directory_files(code_directory)
return filter(lambda path: path.endswith(".h"), files)
def parse_class_file(self, input_lines, include_path):
current_class = None
current_type = ''
for line in input_lines:
matches = {
'component': re.match(ENGINE_COMPONENT_REGEX, line),
'object': re.match(ENGINE_OBJECT_REGEX, line),
'field': re.match(ENGINE_FIELD_REGEX, line)
}
if matches['component']:
self.ecosystem.add_class_description(copy.copy(current_class))
component_name = matches['component'].group('componentName')
current_class = EngineComponentDescription(component_name, include_path)
elif matches['object']:
self.ecosystem.add_class_description(copy.copy(current_class))
component_name = matches['object'].group('objectName')
current_class = EngineObjectDescription(component_name, include_path)
elif matches['field']:
field_type = matches['field'].group('fieldType')
field_name = matches['field'].group('fieldName')
isArray = False
arrayMatch = re.match(ARRAY_TYPE_REGEX, field_type)
if arrayMatch:
isArray = True
field_type = arrayMatch.group("type")
current_class.add_field(FieldDescription(field_name, field_type, isArray))
self.ecosystem.add_class_description(copy.copy(current_class))
def parse_files(self, files):
for path in files:
f = open(path, "r")
lines = []
for line in f:
lines.append(line)
self.parse_class_file(lines, path)
f.close()
def generate_data_structure(self, code_directory, output_file):
files = self.get_class_files(code_directory)
self.ecosystem = Ecosystem()
self.parse_files(files)
f = open(output_file, "w")
f.write(self.ecosystem.serialize())
f.close()
return self.ecosystem
tls = net.get_trophic_levels()
top, top_preds = net.top_predators()
basal, basal_sps = net.basal()
for u, v in net.edges():
if u in basal_sps and v in top_preds and tls[v] == 3:
net.remove_edge(u, v)
print 'new connectance = ', net.connectance()
else:
net = obtain_interactions_network()
net_to_save = net.copy()
nx.write_graphml(net_to_save, network_file)
ecosystem = Ecosystem(net, drawing=False)
ecosystem.initialise_world(True)
#ecosystem.draw_species_distribution()
out_row = get_out_row(0, net, '', 0, '', '')
out.writerow(out_row)
# iteration_to_reset = (int) (math.ceil(ITERATIONS*NETWORK_RESET))
out_row_eco = get_eco_state_row(0, ecosystem)
out_eco.writerow(out_row_eco)
# print ecosystem.get_groups_counts()
# plot_series = []
# plot_prods = []
# plot_mut_prods = []
def plot(steps):
populations = {
'rabbit': [],
'bee': [],
'fox': [],
'flower': [],
'grass': []
}
genetics_factors = {'rabbit': [], 'fox': []}
ecosystem = Ecosystem(int(SCREEN_WIDTH / CELL_WIDTH),
int(SCREEN_HEIGHT / CELL_HEIGHT))
# Iterate over time
actual_steps = steps
for i in range(steps):
ecosystem_organisms = ecosystem.run()
rabbits = 0
foxes = 0
bees = 0
flowers = 0
grass = 0
rabbit_genetics_factor = 0
fox_genetics_factor = 0
for organism in ecosystem_organisms:
# Observe animal populations
if organism.type == Type.RABBIT:
rabbits += 1
rabbit_genetics_factor += organism.genetics_factor
elif organism.type == Type.FOX:
foxes += 1
fox_genetics_factor += organism.genetics_factor
elif organism.type == Type.BEE:
bees += 1
elif organism.type == Type.FLOWER:
flowers += 1
elif organism.type == Type.GRASS:
grass += 1
populations['rabbit'].append(rabbits)
populations['fox'].append(foxes)
populations['bee'].append(bees)
populations['flower'].append(flowers)
populations['grass'].append(grass)
if not i % 100:
print('Iteration ' + str(i) + ':')
print(' ' + str(foxes) + ' foxes')
print(' ' + str(rabbits) + ' rabbits')
print(' ' + str(bees) + ' bees')
print(' ' + str(flowers) + ' flowers')
if rabbits != 0:
genetics_factors['rabbit'].append(rabbit_genetics_factor / rabbits)
else:
actual_steps = i
break
if foxes != 0:
genetics_factors['fox'].append(fox_genetics_factor / foxes)
else:
actual_steps = i
break
if actual_steps >= 25000:
# Plot the results
plt.plot(populations['rabbit'], label='Rabbits')
plt.plot(populations['fox'], label='Foxes')
plt.plot(populations['bee'], label='Bees')
plt.plot(populations['flower'], label='Flowers')
plt.plot(populations['grass'], label='Grass')
plt.xlabel('Time')
plt.legend(loc='upper right')
plt.ylabel('Population amount')
plt.show()
plt.plot(genetics_factors['rabbit'], label='Rabbits')
plt.plot(genetics_factors['fox'], label='Foxes')
plt.xlabel('Time')
plt.legend(loc='upper right')
plt.ylabel('Genetics factor')
plt.show()
return True, actual_steps
else:
return False, actual_steps
def setup(self):
self.sprite_list = arcade.SpriteList()
self.ecosystem = Ecosystem(int(SCREEN_WIDTH / CELL_WIDTH),
int(SCREEN_HEIGHT / CELL_HEIGHT))
def main():
args= parse_args()
file = args.file
target_string = args.target
charset = args.charset
random_crossover = args.random_crossover
tournament_size = args.tournament_size
population_size = args.population_size
if not file and not target_string:
print 'ERROR: Must pass either a file containing a target string or a target string'
sys.exit(1)
if file:
with open(file) as f:
target_string = f.readline()
for char in target_string:
if char not in charset:
print 'ERROR: Characters does not contain all characters in target string'
sys.exit(1)
# set ideal target
target_individual = Individual(list(target_string))
# set ecosystem
ecosystem = Ecosystem(charset, target_individual, tournament_size)
ecosystem.set_random_current_population(population_size)
# evolve ecosystem until the fittest individual matches the target
while ecosystem.get_current_fittest() != target_individual:
ecosystem.print_results()
ecosystem.evolve()
ecosystem.print_results()
# print success message
ecosystem.print_success()
def build_ecosystem(ecosystem_type, directional):
if ecosystem_type == '2_competitive':
scenarios = [
CompetitiveScenario(agent_colors=['red', 'yellow'],
directional=directional)
]
populations = create_populations(2)
assigned_pops = [populations]
elif ecosystem_type == '2_cooperative':
scenarios = [
CooperativeScenario(agent_colors=['green', 'blue'],
directional=directional)
]
populations = create_populations(2)
assigned_pops = [populations]
elif ecosystem_type == '3_mixed':
scenarios = [
CompetitiveScenario(agent_colors=['red', 'yellow'],
directional=directional),
CooperativeScenario(agent_colors=['yellow', 'blue'],
directional=directional)
]
populations = create_populations(3)
assigned_pops = [populations[0:2], populations[1:3]]
elif ecosystem_type == '3_competitive':
scenarios = [
CompetitiveScenario(agent_colors=['red', 'orange'],
directional=directional),
CompetitiveScenario(agent_colors=['orange', 'yellow'],
directional=directional)
]
populations = create_populations(3)
assigned_pops = [populations[0:2], populations[1:3]]
elif ecosystem_type == '4_mixed':
scenarios = [
CooperativeScenario(agent_colors=['green', 'yellow'],
directional=directional),
CompetitiveScenario(agent_colors=['yellow', 'orange'],
directional=directional),
CooperativeScenario(agent_colors=['orange', 'blue'],
directional=directional)
]
populations = create_populations(4)
assigned_pops = [populations[0:2], populations[1:3], populations[2:4]]
elif ecosystem_type == '2_spread':
scenarios = [SimpleSpreadScenario(num_agents=2)]
populations = create_populations(2)
assigned_pops = [populations]
else:
raise RuntimeError("Invalid ecosystem type {}".format(ecosystem_type))
environments = []
for scenario in scenarios:
world = scenario.make_world()
if directional:
env = DirectionalMultiAgentEnv(world,
scenario.reset_world,
scenario.reward,
scenario.observation_organism,
done_callback=scenario.done)
else:
env = MultiAgentEnv(world,
scenario.reset_world,
scenario.reward,
scenario.observation,
done_callback=scenario.done)
environments.append(env)
ecosystem = Ecosystem(environments, populations, assigned_pops)
return ecosystem
tls = net.get_trophic_levels()
top, top_preds = net.top_predators()
basal, basal_sps = net.basal()
for u,v in net.edges():
if u in basal_sps and v in top_preds and tls[v] == 3:
net.remove_edge(u,v)
print 'new connectance = ', net.connectance()
if not READ_FILE_NETWORK:
net_to_save = net.copy()
nx.write_graphml(net_to_save, network_file)
##################################################################################################################
ecosystem = Ecosystem(net, drawing=False)
ecosystem.initialise_world(True)
out_row = get_out_row(0, net, '', 0, '', '')
out.writerow(out_row)
out_row_eco = get_eco_state_row(0, ecosystem)
out_eco.writerow(out_row_eco)
series_counts = dict()
if SPATIAL_VARIATION:
centroids_counts = dict()
areas_counts = dict()
##this structure holds the numbers of immigration, birth and dead of individuals
##for each species during the last ITERATIONS_TO_RECORD iterations
def simulate2(i):
genList = ['power', 'velocity', 'intelligence', 'fertility', 'hostility']
numLives = 30
print(f"init start. numlives: {numLives}")
ecosystem = Ecosystem(numLives=numLives,
genList=genList,
MAP_WIDTH=c.MAP_WIDTH,
MAP_HEIGHT=c.MAP_HEIGHT)
print(f"init finished: {i}-----------------------------------------")
data = list()
powerData = list()
veloData = list()
intelData = list()
fertilData = list()
hostilData = list()
numLivesData = list()
epochtime = 500
while ecosystem.time < epochtime:
ecosystem.nextEpoch()
# 선택(내부에 evaluation(싸우는거) 포함)
selectedCreatures = ecosystem.selection(ecosystem.lives)
# 교차
crossOveredCreature = ecosystem.crossover(selectedCreatures[0],
selectedCreatures[1])
# 변이
crossOveredCreature = ecosystem.mutation(crossOveredCreature,
c.MUTATION_RATE)
ecosystem.lives.append(crossOveredCreature)
ecosystem.created.append(crossOveredCreature)
ecosystem.time += 1
ecosystem.numLives += 1
# print(f'epoch {ecosystem.time}: numLives: {ecosystem.numLives}')
avgDict = {
'power': 0,
'velocity': 0,
'intelligence': 0,
'fertility': 0,
'hostility': 0,
}
if not ecosystem.numLives:
data.append((0, avgDict))
print("numLives is 0")
continue
if ecosystem.numLives < 0:
# data.append((0, avgDict))
print("numLives < 0")
continue
for creature in ecosystem.lives:
infos = creature.getInfo()
for geneName in avgDict.keys():
avgDict[geneName] += infos[geneName]
for geneName in avgDict.keys():
avgDict[geneName] /= ecosystem.numLives
data.append((ecosystem.numLives, avgDict))
print(f"simulation finished: {i}---------------------------------------")
for numLives, d in data:
powerData.append(d['power'])
veloData.append(d['velocity'])
intelData.append(d['intelligence'])
fertilData.append(d['fertility'])
hostilData.append(d['hostility'])
numLivesData.append(numLives)
f, axes = plt.subplots(2, 3)
xrange = np.arange(epochtime)
axes[0][0].set_title("power")
axes[0][0].plot(xrange, powerData)
axes[0][1].set_title("velocity")
axes[0][1].plot(xrange, veloData)
axes[0][2].set_title("intelligence")
axes[0][2].plot(xrange, intelData)
axes[1][0].set_title("fertility")
axes[1][0].plot(xrange, fertilData)
axes[1][1].set_title("hostility")
axes[1][1].plot(xrange, hostilData)
axes[1][2].set_title("numLives")
axes[1][2].plot(xrange, numLivesData)
plt.show()
return ecosystem.numLives, ecosystem.lives
def main():
setup_logger()
logger.debug('DEBUG')
print " *"*30, "\nWe start NOW!" # ***
# all_gene_names = extract_all_gene_names(my_example_of_ecosystem_settings)
# all_strings = extract_all_strings(
# my_example_of_ecosystem_settings,
# exceptions = No_effect_directives + All_action_names)
# print 'ALL GENES:', all_gene_names
# print 'ALL STRINGS:', all_strings
# print 'DIFFERENCE:', [
# item
# for item in all_strings
# if not item in all_gene_names and \
# not item in All_allowed_directives_in_expression]
enable_graphics = True
make_sleeps = False
time_lapse = 4
Total_time = 5000
ecosystem = Ecosystem(my_example_of_ecosystem_settings,
elements_to_store)
ecosystem.minimum_population_allowed = 200
""" *********************** TRIAL ZONE ****************************
ecosystem.evolve()
org = ecosystem.get_random_organisms(1)[0]
print_dictionary(
evaluate_functions_of_a_dictionary(
org['offers to sell'], org
)
)
f_set = {'-': ('nutrient A reserve',
'minimum nutrient A reserve for procreating')}
f = ecosystem.function_maker.read_function_settings(
'#organism',
f_set)
print_organism(org, 'nutrient A reserve',
'minimum nutrient A reserve for procreating')
print_organism(org, 'nutrient A surplus')
print f(org)
print org['value in next cycle']['nutrient A surplus'](org)
exit()
f_set = {'curve from 0 to 1': 'photosynthesis capacity'}
f = ecosystem.function_maker.read_function_settings(
'output function #organism #input',
f_set)
for org in ecosystem.organisms_list:
print f(org, 5)
exit()
f_set = {'extract #biotope sunlight (percentage)': (
'normalized location x',
'normalized location y',
0.8
)}
f_2_set = {
'#biotope sunlight': (
'normalized location x',
'normalized location y'
)
}
org = choice(ecosystem.organisms_list)
print_dictionary(org)
f = ecosystem.function_maker.read_function_settings('#organism', f_set)
f_2 = ecosystem.function_maker.read_function_settings('#organism', f_2_set)
print f(org), f_2(org)
for i in range(10):
org.act()
print_dictionary(org)
# f_set = ecosystem.settings['constraints']['can procreate']
# f_set = {'cost': 'procreate'}
f_set = 'time'
f = ecosystem.function_maker.read_function_settings('#organism', f_set)
# print f(ecosystem)
for org in ecosystem.organisms_list:
print f(org)
exit()
*********************** (TRIAL ZONE) ************************** """
if enable_graphics:
gui = GUI(ecosystem)
# Loop
print "LOOPING:"
while ((len(ecosystem.organisms_list) > 0) and
(ecosystem.time < Total_time)):
# Print ecosystem status:
if ecosystem.time % time_lapse == 0:
print_ecosystem_status(ecosystem)
# organism1, organism2 = ecosystem.get_random_organisms(
# number_of_random_organisms = 2)
if flag_store_data:
ecosystem.data_storer.store_data()
# Evolve:
ecosystem.evolve()
if enable_graphics:
gui.handle_events()
gui.draw_ecosystem()
if make_sleeps:
sleep(1.0) # To remove
if ecosystem.population() < ecosystem.minimum_population_allowed:
n = ecosystem.minimum_population_allowed - ecosystem.population()
ecosystem.create_new_organisms(n)
print n, "organisms created",
print "Time:", ecosystem.time, "Number of organisms:", \
len(ecosystem.organisms_list) # ***
if enable_graphics:
gui.delete()
tls = net.get_trophic_levels()
top, top_preds = net.top_predators()
basal, basal_sps = net.basal()
for u,v in net.edges():
if u in basal_sps and v in top_preds and tls[v] == 3:
net.remove_edge(u,v)
print 'new connectance = ', net.connectance()
if not READ_FILE_NETWORK:
net_to_save = net.copy()
nx.write_graphml(net_to_save, network_file)
##############################################
ecosystem = Ecosystem(net, drawing=False)
ecosystem.initialise_world(True)
# here it works out the inital populations
series_counts = dict()
dict_stats = get_eco_state_row(0, ecosystem)
series_counts[0] = ecosystem.populations
# we don't this to store data, just for its keys
cumulative_sps_stats = dict.fromkeys(net.nodes(), None)
##############################################
for i in range(1, ITERATIONS+1):
print i
ecosystem.update_world()
tls = net.get_trophic_levels()
top, top_preds = net.top_predators()
basal, basal_sps = net.basal()
for u, v in net.edges():
if u in basal_sps and v in top_preds and tls[v] == 3:
net.remove_edge(u, v)
print "new connectance = ", net.connectance()
else:
net = obtain_interactions_network()
net_to_save = net.copy()
nx.write_graphml(net_to_save, network_file)
ecosystem = Ecosystem(net, drawing=False)
ecosystem.initialise_world(True)
# here it works out the inital populations
series_counts = dict()
dict_stats = get_eco_state_row(0, ecosystem)
series_counts[0] = ecosystem.populations
# we don't this to store data, just for its keys!
cumulative_sps_stats = dict.fromkeys(net.nodes(), None)
for i in range(1, ITERATIONS + 1):
print i
ecosystem.update_world()
# dict_stats = get_eco_state_row(ITERATIONS, ecosystem)
