def run():
"""====================
test some things
=================="""
D = AntDomain([1000, 1000], pitch=1)
D.set_gaussian(sigma=25)
P = MapPlot(D.Map.X, D.Map.Y, 'blue')
A = Ant(start_pos=[500, 500],
limits=[1000, 1000],
speed=10,
angle=360 * np.random.rand())
i = 0
for loc in 300 + np.random.rand(100, 2) * 600:
i += 1
tic = time.time()
D.local_add_pheromone(loc=loc, Q=1e3)
D.update_pheromone()
# P.draw_contour(D.Map.map)
if i % 5 == 0 or i == 1:
P.draw_contour(D.Map.map)
A.random_step(sigma=10)
P.draw_scatter(A.pos.x, A.pos.y, color='k')
print("Iteration {i} in {s:.4f} msec".format(i=i,
s=(time.time() - tic) *
1e3))
P.hold_until_close()
def epoch(self, pheromoneMatrix):
population = []
for i in range(self.__noAnts):
ant = Ant(self.__problem)
population.append(ant)
for i in range(self.__problem.getNumberOfTasks() - 1):
for ant in population:
ant.update(pheromoneMatrix, self.__alpha, self.__beta,
self.__q0)
t = [1.0 / population[i].fitness() for i in range(len(population))]
for i in range(self.__problem.getNumberOfComputers()):
for j in range(self.__problem.getNumberOfTasks()):
pheromoneMatrix[i][j] = (1 -
self.__rho) * pheromoneMatrix[i][j]
for i in range(len(population)):
for j in range(len(population[i].getPath()) - 1):
x = population[i].getPath()[j]
y = population[i].getPath()[j + 1]
pheromoneMatrix[x][y] = pheromoneMatrix[x][y] + t[i]
fitness = [[population[i].fitness(), i]
for i in range(len(population))]
fitness = min(fitness)
return population[fitness[1]]
def spawnMouseAnts():
global spawnAnts
global pos
if(spawnAnts):
spawnedAnt = Ant()
spawnedAnt.setPos(pos[0], pos[1], map)
antList.append(spawnedAnt)
def create_children(breeders, env, number_of_child, ants_energy, food_value):
# creates children using genes from to selected ants
nextColony = []
breeders_indexes = np.arange(len(breeders))
breeders_indexes_shuffled = np.arange(len(breeders))
np.random.shuffle(breeders_indexes_shuffled)
for i in range(len(breeders) / 2):
# first round of childrean, each pair of randomly selected parents create one of them
# each parent can be selected only once
first_parent_id = breeders_indexes_shuffled[i]
second_parent_id = breeders_indexes_shuffled[
len(breeders_indexes_shuffled) - i - 1]
brain = select_genes(breeders[first_parent_id],
breeders[second_parent_id])
nextColony.append(
Ant(env,
energy=ants_energy,
food_value=food_value,
genetic_inh=brain,
child=1))
for j in range(number_of_child - (len(breeders) / 2)):
# if we need more children, we are going to use again some of the old parents
random_parent = random.choice(breeders_indexes)
brain = select_genes(breeders[random_parent],
breeders[len(breeders) - random_parent - 1])
nextColony.append(
Ant(env,
energy=ants_energy,
food_value=food_value,
genetic_inh=brain,
child=1))
return nextColony
def step(self):
if not self.ant.settled:
try:
self.ant.move()
except Error as e:
raise e
else:
if self.ant.y > self.maxHeight:
self.maxHeight = self.ant.y
if self.checkBridge():
return False
self.addJoints(self.ant)
self.antId = self.antId + 1
self.numAnts += 1
if G.DeterministicAnts:
self.ant = Pyramid(self.antId)
self.oldy = self.y
self.y = self.ant.y
if self.y != self.oldy:
Physics.resetPhysics()
Physics.checkPhysics()
else:
self.ant = Ant(self.antId)
Physics.resetPhysics()
Physics.checkPhysics()
self.updateShaking()
return True
def f(ant: Ant, pheromones: dict) -> Ant:
neighbors = ant.get_neighbors()
transition_arr = [(ant.solution_path[-1], i) for i in neighbors]
for index in range(len(transition_arr)):
i, j = transition_arr[index]
if i > j:
transition_arr[index] = (j, i)
next_neighbor = None
distances = np.array(list(map(ant.get_distance, transition_arr)))
heuristic = distances**-beta
if np.random.uniform() < q0:
max_pheromone = 0
next_neighbor = np.argmax(
np.array([pheromones[coord]
for coord in transition_arr]) * heuristic)
else:
taos = np.array([pheromones[coord] for coord in transition_arr])
probabilities = ((taos ** alpha)*heuristic) / \
((taos ** alpha)*heuristic).sum()
next_neighbor = np.random.choice(len(transition_arr),
p=probabilities)
ant.add_node(transition_arr[next_neighbor])
return ant
def __init__(self, size=[1000, 1000], pitch=1, n_ants=5):
""" ==================
Do a simulation of an Ant
================== """
self.size = size
self.pitch = pitch
self.Dom = AntDomain(size,
pitch,
food={
'location': [850, 500],
'radius': 50
},
nest={
'location': [150, 500],
'radius': 50
})
self.Dom.set_gaussian(sigma=10)
self.Ant = Ant(
limits=size,
start_pos=[700, 500],
speed=5,
)
self.Ants = [
Ant(limits=size,
start_pos=1000 * np.random.rand(1, 2)[0],
angle=360 * np.random.rand(),
speed=2,
v_max=5,
ant_id=i) for i in range(n_ants)
]
self.Plot = MapPlot(self.Dom.Map.X, self.Dom.Map.Y)
class Sim(object):
def __init__(self):
G.state = np.zeros((G.numBlocksX, G.numBlocksY), dtype=np.int)
G.weight = np.ones((G.numBlocksX, G.numBlocksY))
self.antId = 0
if G.DeterministicAnts:
self.ant = Pyramid(self.antId)
self.y = self.ant.y
self.oldy = self.y
else:
self.ant = Ant(self.antId)
self.numAnts = 1
self.maxHeight = 0
G.jointData = np.zeros((G.numBlocksX * G.numBlocksY * 3))
G.numJoints = 0
G.jointRef = {}
def step(self):
if not self.ant.settled:
try:
self.ant.move()
except Error as e:
raise e
else:
if self.ant.y > self.maxHeight:
self.maxHeight = self.ant.y
if self.checkBridge():
return False
self.addJoints(self.ant)
self.antId = self.antId + 1
self.numAnts += 1
if G.DeterministicAnts:
self.ant = Pyramid(self.antId)
self.oldy = self.y
self.y = self.ant.y
if self.y != self.oldy:
Physics.resetPhysics()
Physics.checkPhysics()
else:
self.ant = Ant(self.antId)
Physics.resetPhysics()
Physics.checkPhysics()
self.updateShaking()
return True
def addJoints(self, ant):
for adjacent in getAdjacent(ant.pos):
if G.state[adjacent]:
Joint(ant.pos, adjacent, -1)
# attach anchor joints
if ant.y == 0:
Joint(ant.pos, (ant.x, ant.y - 1), -1)
Joint(ant.pos, (ant.x - 1, ant.y - 1), -1)
Joint(ant.pos, (ant.x + 1, ant.y - 1), -1)
def getForces(self, (x, y)):
return [f.force() for f in G.jointRef[(x, y)]]
def create_generation(ant: Ant, board: np.ndarray):
print("creating generation")
coords = ant.get_coords()
board_value = board[coords[1], coords[0]]
cell_type = ant.evolve(board_value)
return {"ant": ant, "new_value": cell_type, "coords": coords}
def run(self):
'''
Function to run the rank based Ant Colony Optimization algorithm
'''
best_ant = Ant(0, 0, [])
for i in range(self._n_iterations):
colony = []
for j in range(self._n_ants):
ant = Ant(0, self._distances.shape[0],
copy.deepcopy(self._vehicles))
for x in range(len(ant.vehicles)):
ant.vehicles[x].put_node_path(0, self._occupancies,
self._distances, self._times)
ant.build_path(self._distances, self._times, self._occupancies,
self._pheromone, self._alpha, self._beta)
ant.calculate_distance(self._distances)
ant.objectve_function(self._distance_cost)
colony.append(ant)
n_bests_ants = self.find_n_bests_ants(colony)
if n_bests_ants[0].of_value < best_ant.of_value:
best_ant = n_bests_ants[0]
self.update_pheromone(best_ant, n_bests_ants)
#print("Iteration: %d Best OF: %f" %(i + 1, best_ant.of_value))
return best_ant
def pheromone_update(self, ant: Ant):
""" Pheromone update method to be potentially used after each batch of ants
:param self: Reference to the graph
:param ant: The ant during the update
"""
# Update the pheromone levels for each edge the ant took
value = self.get_path_value(ant.get_tour())
for n1, n2 in ant.get_tour():
self.edges[n1, n2]['pheromone'] = (1 - self.global_evaporation_rate) * self.edges[n1, n2]['pheromone'] + \
self.global_evaporation_rate * value
def init_tiles_ants(self):
self.screen_size = self.screen.get_size()[0]
self.tile_size = self.screen_size // cfg.N_TILES
if isinstance(self.init_tiles, str) and self.init_tiles == 'random':
self.tiles = np.random.randint(0, 2, (cfg.N_TILES, cfg.N_TILES))
elif self.init_tiles is not None:
self.tiles = self.init_tiles
else:
self.tiles = np.zeros((cfg.N_TILES, cfg.N_TILES))
self.ant = Ant(self.ant_init_pos, self.ant_init_direction)
self.total_step = 0
def __init__(self, data, alpha=0.2, label=None, mask=None, option=None):
self.mask = mask
self.option = option
self.al = alpha
self.nest_counter = 1
if label is None:
self.ants = set([Ant(datum) for datum in data.tolist()])
else:
self.ants = set([
Ant(datum, true_label=label[i])
for i, datum in enumerate(data.tolist())
])
def make_ants(G, pos, num_steps, anthill_data):
ants = []
for ant_num in range(1, int(anthill_data['ants']) + 1):
ant = Ant(ant_num)
ant.set_node_path(anthill_data)
ant.set_location(pos, anthill_data)
ant.set_journey(pos, num_steps, anthill_data)
ant.color = ant_colors[ant_num % 11]
ants.append(ant)
return (ants)
class LangtonsAnt:
def __init__(
self, initial_state: List[List[bool]], start_position: List[int]
) -> None:
self._grid = Grid(initial_state)
self._ant = Ant(start_position[0], start_position[1])
def next(self) -> bool:
current_ant_position_x, current_ant_position_y = self._ant.position
if self._grid.get_color(current_ant_position_x, current_ant_position_y):
self._grid.change_color(current_ant_position_x, current_ant_position_y)
self._ant.turn(TurnDirection.RIGHT)
self._ant.move()
else:
self._grid.change_color(current_ant_position_x, current_ant_position_y)
self._ant.turn(TurnDirection.LEFT)
self._ant.move()
return self.validate_move()
@property
def state(self):
return self._grid.state
@property
def ant_position(self):
return self._ant.position
def validate_move(self) -> bool:
current_ant_position_x, current_ant_position_y = self._ant.position
return self._grid.validate_point(current_ant_position_x, current_ant_position_y)
def validate(self) -> bool:
return self._grid.validate()
def populate_world(self):
first_ant = Ant(world=self,
n_nodes=self.n_nodes,
alpha=self.alpha,
beta=self.beta)
ant = first_ant
for i in range(self.n_ants - 1):
ant.next = Ant(world=self,
n_nodes=self.n_nodes,
alpha=self.alpha,
beta=self.beta)
ant = ant.next
self.first_ant = first_ant
def __init__(self, parameters, instance):
self.instance = instance
self.ants = [Ant(instance) for i in range(parameters.n_ants)]
self.best_so_far_ant = Ant(instance)
self.restart_best_ant = Ant(instance)
self.prob_of_selection = [0 for i in range(parameters.nn_ants + 1)]
# Ensure that we do not run over the last element in the random wheel.
self.prob_of_selection[parameters.nn_ants] = math.inf
self.pheromone = [[None for i in range(instance.n)]
for i in range(instance.n)]
self.total = [[None for i in range(instance.n)]
for i in range(instance.n)]
self.nn_tour = None
self.compute_nn_tour()
def put_ants(self):
points = range(1,self.points+1)
position = 0
for tower in self.__towers:
ant = Ant()
ant.position = position
ant.set_coverage(copy(points))
ant.possible_towers = copy(self.__towers)
ant.route = []
ant.set_actual_tower(tower)
self.__ants.append(ant)
position += 1
def update(self, data):
map(lambda tile, pheromones: tile.update(**pheromones), self.tiles,
data['board'])
for tile in self.tiles:
rect, color = tile.render()
pygame.draw.rect(self.screen, color, rect)
for ant_repr in data['ants']:
if ant_repr['id'] in self.ants:
ant = self.ants[ant_repr['id']]
ant.position = ant_repr['position']
else:
ant = Ant(**ant_repr)
self.ants[ant_repr['id']] = ant
pos = map(lambda coord: coord * TILE_SIZE + TILE_SIZE / 2,
ant.position)
ant_color = YELLOW if ant.carries_food else GREEN
pygame.draw.circle(self.screen, ant_color, pos, TILE_SIZE / 5)
# Place colony
pygame.draw.rect(self.screen, GREEN, self.colony)
# Place food
food_pos = self.food['position']
pile = [[
food_pos[0] * TILE_SIZE + TILE_SIZE / 2, food_pos[1] * TILE_SIZE
], [food_pos[0] * TILE_SIZE, (food_pos[1] + 1) * TILE_SIZE],
[(food_pos[0] + 1) * TILE_SIZE, (food_pos[1] + 1) * TILE_SIZE]]
pygame.draw.polygon(self.screen, YELLOW, pile)
pygame.display.flip()
def __init__(self):
self.area = Area()
self.ant_num = 20
self.ant_list = []
self.add_number = 0
for i in range(self.ant_num):
self.ant_list.append(Ant(self.area.area))
def Start_find_food(self):
# while True:
ant_x_list = []
ant_y_list = []
dispatch = False
mydispatch = False
direction = 0
if self.add_number > 0:
self.ant_list.append(Ant(self.area.area))
self.add_number = self.add_number - 1
self.ant_num = self.ant_num + 1
for i in range(self.ant_num):
dispatch = self.ant_list[i].walking()
if len(self.ant_list[i].previous_location_list) > 2000:
self.ant_list[i].previous_location_lis = []
if dispatch == True:
mydispatch = True
ant_x_list.append(self.ant_list[i].location[0])
ant_y_list.append(self.ant_list[i].location[1])
# if self.ant_list[i].direction_x==self.ant_list[i].driection_y and self.ant_list[i].direction_x:
# direction=direction+1
# print(direction)
pass
print(len(self.ant_list[19].previous_location_list))
if mydispatch == True:
if self.ant_num < 50:
self.add_number = 5
return ant_x_list, ant_y_list
def reconnaissance(self, iterations=1):
maze = self.maze
if self.do_reconnaissance < 1:
return maze
print 'performing reconnaissance with %d ants for %d steps in %d iterations' % (
self.ant_count, self.do_reconnaissance, iterations)
disabled = set()
start_time = time.time()
for iteration in range(iterations):
ants = []
for i in range(self.ant_count):
ants.append(Ant(maze, maze.start))
results = self.pool.map_async(
ant_loop_apply,
itertools.izip(ants, [self.do_reconnaissance] *
self.ant_count)).get(999999)
for ant in results:
for disable in ant.disable_positions:
maze.disable_at(disable)
disabled.add(disable)
print 'Reconnaissance done, %d cells disabled in %0.2fs' % (
len(disabled), time.time() - start_time)
return maze
def ant_colony_opt(matrix, n_ants=10, max_iterations=23000):
best_pheromone_matrix = np.ones(shape=(9, 9, 9)) / 9
ants = [Ant(matrix.copy(), best_pheromone_matrix) for _ in range(n_ants)]
print(ants[0].fitness())
best_fitness = float('inf')
best_ant = None
history = []
for _ in tqdm(range(max_iterations)):
for i, ant in enumerate(ants):
ant.solve_sudoku(epsilon_greedy=0.05)
fitness = ant.fitness()
if fitness < best_fitness:
best_ant = copy.deepcopy(ant)
best_fitness = fitness
tqdm.write(str(best_fitness))
for i in range(9):
for j in range(9):
best_pheromone_matrix[i][j][best_ant.current_solution[i, j] -
1] += 0.0005
best_pheromone_matrix[i][j] /= np.sum(
best_pheromone_matrix[i][j])
history.append(best_fitness)
if best_fitness == 0:
# We found the solution, just stop
break
return best_ant.current_solution, history
def __init__(self,
graph,
num_ants,
alpha=1.0,
beta=5.0,
iterations=10,
evaporation=0.5):
self.graph = graph
self.locationsLength = len(graph.locations)
self.num_ants = num_ants
self.alpha = alpha # importância do feromônio
self.beta = beta # importância da informação heurística
self.iterations = iterations # quantidade de iterações
self.evaporation = evaporation # taxa de evaporação
self.ants = [] # lista de ants
locations = self.graph.getLocationsList()
# cria as ants colocando cada uma em uma location diferente
for _ in range(self.num_ants):
location_ant = random.choice(locations)
locations.remove(location_ant)
self.ants.append(Ant(location=location_ant))
if not locations:
locations = [
location for location in range(1, self.locationsLength + 1)
]
# reestrutura location como set
locations = self.graph.locations
for key_edge in self.graph.edges:
# pheromone = 1.0 / (self.locationsLength * cost)
self.graph.setPheromoneEdge(key_edge[0], key_edge[1], 0.1)
def thread_body(queue):
pixels = NeoPixel(DATA_PIN, N_PIXELS, brightness=BRIGHTNESS,
auto_write=False)
updates = {'RAINBOW': Rainbow(pixels),
'ANT': Ant(pixels),
'OCD': Ocd(pixels),
'FLASH': Flash(pixels),
'IMPLODE': Implode(pixels),
'ERROR': Error(pixels),
'QUIT': Quit(pixels)}
assert set(updates.keys()) == MODES
mode = "OCD"
while True:
try:
new_mode = queue.get_nowait()
assert new_mode in MODES, "unknown mode %s" % mode
if new_mode != mode:
updates[new_mode].setup()
mode = new_mode
except:
pass
sleep = updates[mode].exec_update()
if mode == "QUIT":
break
time.sleep(sleep)
def perform_tours(self, instance):
"""
Initialises ants within colony and makes the ants perform their tours around the tsp instance
"""
# Create n ants with each one starting on a random node where n is the amount of nodes
node_range = len(instance.nodes) - 1
self.ants = [
Ant(instance, random.randint(0, node_range))
for _ in range(node_range)
]
# Make each ant perform a tour around the instance
for ant in self.ants:
ant.perform_tour(instance)
# Update pheromones locally
self.local_update_pheromones(instance, ant.nodes_traversed())
distance = ant.get_distance(instance)
# Initialise the minimum distance as infinity if None
if not (self.min_distance):
self.min_distance = float('inf')
# Update the colonys minimum distance and shortest path if the ant has found a shorter distance
if self.min_distance > distance:
self.min_distance = distance
self.shortest_path = ant.path[:]
def ant_algorithm(self):
for i in range(self.max_iter):
ants = list(Ant(self.graph) for j in range(self.ants_num))
for k in range(self.ants_num):
while not len(ants[k].att_to_visit) == 0:
next_index = self.select_next_attraction(ants[k])
if not ants[k].check_condition(next_index):
next_index = self.select_next_attraction(ants[k])
if not ants[k].check_condition(next_index):
next_index = 0
ants[k].visit_attraction(next_index)
ants[k].visit_attraction(0)
paths_distance = np.array(
[ant.total_travel_distance for ant in ants])
best_index = np.argmin(paths_distance)
if self.best_path is None or paths_distance[
best_index] < self.best_path_distance:
self.best_path = ants[int(best_index)].travel_path
self.best_path_distance = paths_distance[best_index]
self.best_vehicle_num = self.best_path.count(0) - 1
self.graph.update_pheromones(self.best_path,
self.best_path_distance)
print('Iteration ' + str(i))
print('Best path distance is ' +
str(round(self.best_path_distance, 3)) +
', number of vehicle is ' + str(self.best_vehicle_num))
def create_ants(self):
self.reset()
ants = []
for i in range(0, self.num_ants):
ant = Ant(i, random.randint(0, self.graph.num_nodes - 1), self)
ants.append(ant)
return ants
def create_new_ant():
sensing_area = random.randint(1, 10)
p_repeat = random.random()
p_target = random.random()
p_pheromone = random.random()
new_ant = Ant(sensing_area, p_repeat, p_target, p_pheromone, get_id = get_ant_id)
return new_ant
def setup(self):
if settings.DRAW_BASE:
self.create_base()
for _ in range(settings.NUM_WALLS):
self.create_wall()
for _ in range(settings.NUM_FOOD_BLOBS):
self.create_food_blob(settings.FOOD_BLOB_SIZE)
self.colony = Colony()
for _ in range(settings.NUM_ANTS):
ant = Ant(settings.SCREEN_WIDTH / 2,
0,
self,
self.colony,
scale=settings.SCALE)
self.ant_list.append(ant)
arcade.set_background_color(settings.FIELD_COLOR)
if self.generation_callback:
self.generation_callback(self.generation, self)
def main(commands: dict, ordered_colours: list):
"""
The main function responsible for running and simulating the ant's movements
"""
ant = Ant(commands, ordered_colours)
board = Board(ant)
run = True
clock = pygame.time.Clock()
rows, cols = ROWS, COLS
while run:
clock.tick(FPS)
for event in pygame.event.get():
if event.type == pygame.QUIT:
pygame.quit()
exit()
board.draw_board(rows, cols, WIN)
board.draw_ant(rows, WIN)
board.update_ant_dir()
board.update_ant_pos()
if board.check_edge():
rows, cols = (rows * 3), (cols * 3)
board.increase_board()
pygame.display.update()
def test_completable_path():
num_nodes = 8
delta_mat = [[0,1,1,1,1,1,1,1],[1,0,1,1,1,1,1,1],[1,1,0,1,1,1,1,1],[1,1,1,0,1,1,1,1],[1,1,1,1,0,1,1,1],[1,1,1,1,1,0,1,1],[1,1,1,1,1,1,0,1],[1,1,1,1,1,1,1,0]]
num_ants = 1
num_iterations = 10
colors1 = "RRRRBBBB"
graph1 = AntGraph(num_nodes,delta_mat,colors1)
colony1 = AntColony(graph1,num_ants,num_iterations)
ant1 = Ant(1, 1, colony1)
print "testing reds_left initialization: " + str(ant1.reds_left)
#Visited: 1,2,3
ant1.currNode = 3
ant1.last_3_colors = ("R","R","R")
self.reds_left = 1
def new_ant(self):
"""
Creates new ant and adds it to the Node's ant list.
Parameters:
None
Returns:
None
"""
ant = Ant(self.num, random.randint(0, self.net_size - 2))
if ant.dest >= self.num:
ant.dest += 1
ant.prev = self.num
self.ants.append(ant)
def spawnBlueAnts():
global spawnBlueAnts
global pos
if(spawnBAnts):
spawnedBlueAnt = Ant()
spawnedBlueAnt.setPos(pos[0], pos[1], map)
spawnedBlueAnt.setFaction("blue")
spawnedBlueAnt.setColor()
antList.append(spawnedBlueAnt)
def spawnGreenAnts():
global spawnGreenAnts
global pos
if(spawnGAnts):
spawnedGreenAnt = Ant()
spawnedGreenAnt.setPos(pos[0], pos[1], map)
spawnedGreenAnt.setFaction("green")
spawnedGreenAnt.setColor()
antList.append(spawnedGreenAnt)
def spawnRedAnts():
global spawnRedAnts
global pos
if(spawnRAnts):
spawnedRedAnt = Ant()
spawnedRedAnt.setPos(pos[0], pos[1], map)
spawnedRedAnt.setFaction("red")
spawnedRedAnt.setColor()
antList.append(spawnedRedAnt)
def test_valid_color():
num_nodes = 6
delta_mat = [[0,1,1,1,1,1],[1,0,1,1,1,1],[1,1,0,1,1,1],[1,1,1,0,1,1],[1,1,1,1,0,1],[1,1,1,1,1,0]]
num_ants = 1
num_iterations = 10
colors1 = "RRRRRR"
colors2 = "RRRBBB"
colors3 = "BBBBBB"
graph1 = AntGraph(num_nodes,delta_mat,colors1)
colony1 = AntColony(graph1,num_ants,num_iterations)
ant1 = Ant(1, 1, colony1)
ant1.last_3_colors = ("R","R","R")
print "False: " + str(ant1.valid_color(1))
ant1.last_3_colors = ("B","B","B")
print "True: " + str(ant1.valid_color(1))
ant1.last_3_colors = ("R","R","B")
print "True: " + str(ant1.valid_color(1))
graph2 = AntGraph(num_nodes,delta_mat,colors2)
colony2 = AntColony(graph2,num_ants,num_iterations)
ant2 = Ant(1, 1, colony2)
ant2.last_3_colors = ("R","R","R")
print "True: " + str(ant2.valid_color(3))
print "False: " + str(ant2.valid_color(1))
graph3 = AntGraph(num_nodes,delta_mat,colors3)
colony3 = AntColony(graph3,num_ants,num_iterations)
ant3 = Ant(1, 1, colony3)
ant3.last_3_colors = ("R","R","R")
print "True: " + str(ant3.valid_color(1))
ant3.last_3_colors = ("B","B","B")
print "False: " + str(ant3.valid_color(1))
ant3.last_3_colors = ("B","R","B")
print "True: " + str(ant3.valid_color(1))
def updatePhermone(): if randint(0, 10) >= 0: count = 0 for i in antGrid.storedInformation: sPhermoneLevel = antGrid.storedInformation[count][1] if sPhermoneLevel > 5: antGrid.storedInformation[count][1] = sPhermoneLevel - 1 count += 1 backlog = len(antGrid.storedIndex) if backlog > 40000: antGrid.storedIndex.pop(0) antGrid.storedInformation.pop(0) ant = Ant(DEFAULT_COORDINATES) antGrid = Grid(ant.GRID_WIDTH, ant.GRID_HEIGHT) screen = pygame.display.set_mode((ant.GRID_WIDTH, ant.GRID_HEIGHT)) running = True herd = [Ant(DEFAULT_COORDINATES) for i in range(0, NUMBER_ANTS)] iterations = 1 # for debugging purposes while running: displayAnts() updatePhermone() for ant in herd:
def spawn_worker(cont):
own = cont.owner
worker = Ant(bge.logic.getCurrentScene().addObject("Ant"))
worker.worldPosition.xy = own.worldPosition.xy
bge.logic.sendMessage("GUI")
worker.target = own.worldPosition + Vector((0, -3, 0))
def __init__(self, position):
Ant.__init__(self, position)
self.path = []
self.index = 0
self.target = None
def spawn_test_ants():
redLocation = [100, 100]
greenLocation = [120, 120]
redAnt = Ant()
redAnt.setFaction("red")
redAnt.setColor()
redAnt.health = 25
redAnt.setPos(redLocation[0], redLocation[1], map)
antList.append(redAnt)
greenAnt = Ant()
greenAnt.setFaction("green")
greenAnt.setColor()
greenAnt.health = 100
greenAnt.setPos(greenLocation[0], greenLocation[1], map)
antList.append(greenAnt)
def __init__(self, position):
Ant.__init__(self, position)
self.path = []
self.index = 0
def gwas(start_snp, end_snp, individuals, ants_number, update_times, factor, threshold):
"""
individuals: sum of cases and control.
factor: 0<factor<1 user-adjustable distribution.if factor is near 1,snps with high scores are only slightly
more likely to be selected.
threshold <-> P-Value: 26.12<->0.001；20.09<->0.01；15.51<->.0.05
"""
snps_number = end_snp - start_snp + 1
dict_pair = Prepare.dict_pair(start_snp, end_snp)
print('dict_pair done')
n = 0
for order in range(1, 101):
dict_prob = Prepare.dict_prob1(start_snp, end_snp + 1)
print('dict_prob done')
label, data_set = Prepare.data_matrix(order, individuals, snps_number)
dict_weka = Prepare.load_weka_ranking(order)
snps_sequence = Prepare.snps_sequence1(start_snp, end_snp)
snps_scores = [0] * snps_number
# Rank dict on weight,return a list of tuples
list_weka = sorted(dict_weka.items(), key=lambda weka: weka[1], reverse=True)
rank = Prepare.scaling_rank(factor, snps_number)
for snp_weight_tuple, new_weight in zip(list_weka, rank):
# allocate scaling rank weight to corresponding snp
snps_scores[snp_weight_tuple[0] - start_snp] = new_weight
selected_pairs = {}
for x in range(update_times):
list_k1_threshold = [] # 存储chi2_statistics > 阈值的pair在dict_prob[first_snp]中的索引位置
list_k2_threshold = [] # 存储chi2_statistics > 阈值的pair在dict_prob[second_snp]中的索引位置
list_chi2_statistics = [] # 存储chi2_statistics > 阈值的pair的卡方值，在update的时候使用
list_k1 = [] # 存储chi2_statistics < 阈值的pair在dict_prob[first_snp]中的索引位置
list_k2 = [] # 存储chi2_statistics < 阈值的pair在dict_prob[second_snp]中的索引位置
list_first_snp_threshold = [] # 存储chi2_statistics > 阈值的first_snp
list_second_snp_threshold = [] # 存储chi2_statistics > 阈值的second_snp
list_first_snp = [] # 存储chi2_statistics < 阈值的first_snp
list_second_snp = [] # 存储chi2_statistics < 阈值的second_snp
for y in range(ants_number):
first_snp = Ant.ant_first_snp(snps_sequence, snps_scores)
second_snp = Ant.ant_second_snp(first_snp, dict_pair, dict_prob)
# print(first_snp, second_snp)
if second_snp > first_snp:
k1 = second_snp - start_snp - 1
k2 = first_snp - start_snp
else:
k1 = second_snp - start_snp
k2 = first_snp - start_snp - 1
case_row, control_row = ChiSquareTest.chi2_table(data_set, label, first_snp, second_snp, individuals)
sum_colum, A2_NcNr, chi2_statistics = ChiSquareTest.chi2_test(case_row, control_row, individuals)
if chi2_statistics > threshold:
list_k1_threshold.append(k1)
list_k2_threshold.append(k2)
list_chi2_statistics.append(chi2_statistics)
list_first_snp_threshold.append(first_snp)
list_second_snp_threshold.append(second_snp)
else:
list_k1.append(k1)
list_k2.append(k2)
list_first_snp.append(first_snp)
list_second_snp.append(second_snp)
# 更新条件概率和snps_scores.
# 除以 10 的目的是将卡方值转换到和weight同样的量级.snps_score_original[x]引入expert information
for m, i, j in zip(list_first_snp_threshold, list_k1_threshold, list_chi2_statistics):
dict_prob[m][i] += (int(j) / 10)
for m, i, j in zip(list_second_snp_threshold, list_k2_threshold, list_chi2_statistics):
dict_prob[m][i] += (int(j) / 10)
for m, i in zip(list_first_snp, list_k1):
dict_prob[m][i] = 0
for m, i in zip(list_second_snp, list_k2):
dict_prob[m][i] = 0
for first, second, i in zip(list_first_snp_threshold, list_second_snp_threshold, list_k1_threshold):
selected_pairs[(first, second)] = dict_prob[first][i]
print(selected_pairs)
result = sorted(selected_pairs.items(), key=lambda x: x[1], reverse=True)
for x in result[0:20]:
if x[0] == (999, 988) or x[0] == (998, 999):
n += 1
break
f = open('result_conProb-H0.1-{ants}_{updates}-fac={factor}.txt'.format(
ants=ants_number, updates=update_times, factor=factor), 'a')
f.writelines('\n')
f.writelines(str(x[0]) + '\t' + str(x[1]) + '\n' for x in result[0:20])
f.writelines('----------------------------------')
f.close()
f = open('result_conProb-H0.1-{ants}_{updates}-fac={factor}.txt'.format(
ants=ants_number, updates=update_times, factor=factor), 'a')
f.writelines('\nThe pow of this ACO algorithm is ' + str(n) + '%')
f.close()
def __checkPoint__(self, point):
fake_ant = Ant('fake')
fake_ant.picture = self.picture
fake_ant.point = point
return not self.__isAntIntersectAnything(fake_ant)
def __init__(self, position):
Ant.__init__(self, position)
def step(self, start_node_name):
ant = Ant(self.graph, start_node_name)
distance = ant.run()
if distance < self.best_distance:
ant.pheromonize()
self.best_distance = distance
