def closeness_neighbors(seed_num, graph=None, graph_json_filename=None, graph_json_str=None):
if graph_json_filename is None and graph_json_str is None and graph is None:
return []
G = None
if graph is not None:
G = graph
elif graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
clse_cent = nx.get_node_attributes(G, "centrality")
if len(clse_cent) == 0:
clse_cent = nx.closeness_centrality(G)
nx.set_node_attributes(G, "centrality", clse_cent)
print "closeness neighbors"
collector = collections.Counter(clse_cent)
clse_cent = collector.most_common(SURROUND_TOP)
nodes = map(lambda (x, y): x, clse_cent)
current_seed = 0
rtn = []
while current_seed < seed_num:
current_node = nodes[current_seed % len(nodes)]
current_neighbors = G.neighbors(current_node)
rtn += random.sample(set(current_neighbors) - set(rtn) - set(nodes), 1)
current_seed += 1
return rtn
def high_degrees_fast(seed_num, graph=None, graph_json_filename=None, graph_json_str=None):
"""
Find the high-degree nodes of the given graph by sorting on the adjacency
list lengths and slicing.
Parameters:
seed_num: Number of nodes to choose.
graph_json_filename: Filename where the adjacency list lives as JSON.
graph_json_str: Graph as an adjacency list string in JSON.
Return: List of 'seed_num' highest degree nodes.
"""
if graph_json_filename is None and graph_json_str is None and graph is None:
return []
G = None
if graph is not None:
G = graph
elif graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
clse_cent = nx.get_node_attributes(G, "centrality")
if len(clse_cent) == 0:
clse_cent = nx.degree_centrality(G)
nx.set_node_attributes(G, "centrality", clse_cent)
print "hi high-degree"
collector = collections.Counter(clse_cent)
clse_cent = collector.most_common(seed_num)
return map(lambda (x, y): x, clse_cent)
def closeness_component(seed_num, graph_json_filename=None, graph_json_str=None):
if graph_json_filename is None and graph_json_str is None:
return []
G = None
if graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
components = list(nx.connected_components(G))
components = filter(lambda x: len(x) > 0.1 * len(G), components)
total_size = sum(map(lambda x: len(x), components))
total_nodes = 0
rtn = []
for comp in components[1:]:
num_nodes = int(float(len(comp)) / total_size * seed_num)
component = G.subgraph(list(comp))
clse_cent = nx.closeness_centrality(component)
collector = collections.Counter(clse_cent)
clse_cent = collector.most_common(num_nodes)
rtn += map(lambda (x, y): x, clse_cent)
total_nodes += num_nodes
num_nodes = seed_num - total_nodes
component = G.subgraph(list(components[0]))
clse_cent = nx.closeness_centrality(component)
collector = collections.Counter(clse_cent)
clse_cent = collector.most_common(num_nodes)
rtn += map(lambda (x, y): x, clse_cent)
return rtn
def __init__(self,
path_to_pb,
files,
scale=0.5,
to_line=False,
prune_method='simple',
outdir=None,
out_suffix=None,
gpu_device='0',
test_orientation=True):
"""
parameter:
path_to_pb: path to trained tensorflow pb file
files: list of image file paths
to_line: approximate line height and write a line map
scale: scale-factor, typically ARU-Net works well on low scales,
which speeds up the inference a lot
prune_method: options=['simple'] TODO: extent
out_dir: output folder
out_suffix: suffix to append to the filename (also decideds file
extension = png if nothing set)
gpu_device: device number as string
test_orientation: test for the orientation. Note: cannot test for
flips / 180 degree orientation :/
"""
self.graph = load_graph(path_to_pb)
self.files = files
self.to_line = to_line
self.scale = scale
self.prune_method = prune_method
self.outdir = outdir
self.out_suffix = out_suffix
self.gpu_device = gpu_device
self.test_orientation = test_orientation
def question1_plot():
"""
plot for question 1
"""
network_graph = load_graph(NETWORK_URL)
n = 1239
p = 0.004
m = 3
er_graph = er(n, 0.004)
upa_graph = upa(n, 3)
graphs = [network_graph, er_graph, upa_graph]
attack_orders = [random_order(graph) for graph in graphs]
resiliences = [compute_resilience(graph, attack_order) for
graph, attack_order in zip(graphs, attack_orders)]
removed_num = range(n + 1)
for resil in resiliences:
plt.plot(removed_num, resil)
legend_text = ['Computer Network', 'ER Graph, p = %.3f' % (p),
'UPA Graph, m = %d' % (m)]
plt.legend(legend_text, loc="upper right")
plt.xlabel('the number of nodes removed')
plt.ylabel('the size of the largest connect component')
plt.title('Graph resiliences')
plt.show()
def __init__(self, network):
self.graph_path = network
self.graph = load_graph(network)
self.free_flow_speed = 100
self.congestion_speed = 20
self.init_travel_time()
self.traveller_state_dict = {}
self.car_logger = CarLogger()
self.planner_logger = PlannerLogger()
self.event_logger = EventLogger()
def __init__(self, network):
self.graph = load_graph(network)
self.events = [
"road_works_start", "road_works_start", "road_works_start",
"road_works_start", "road_works_end"
]
# self.events = ["road_works_start", "road_works_start", "road_works_start", "road_works_start",
# "road_works_end", "spawn_random_agents", "spawn_random"]
self.event_factors = [round(i * 0.1, 2) for i in range(2, 10)]
self.event_times = [i for i in range(3, 10)]
self.num_agents = [i for i in range(1, 6)]
self.agent_counter = 1
self.construction_sites = set()
def eigenvector_centrality(seed_num, graph=None, graph_json_filename=None, graph_json_str=None):
if graph_json_filename is None and graph_json_str is None and graph is None:
return []
G = None
if graph is not None:
G = graph
elif graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
clse_cent = nx.get_node_attributes(G, "centrality")
if len(clse_cent) == 0:
clse_cent = nx.eigenvector_centrality(G)
nx.set_node_attributes(G, "centrality", clse_cent)
print "hi eigen-vector"
collector = collections.Counter(clse_cent)
clse_cent = collector.most_common(seed_num)
return map(lambda (x, y): x, clse_cent)
def cut_control(seed_num, graph_json_filename=None, graph_json_str=None):
"""
Randomly choose 'seed_num' number of cut-vertices from the given graph.
If there are fewer cut vertices than 'seed_num' then choose the vertices
adjacent to cut vertices .
Parameters:
seed_num: Number of nodes to choose.
graph_json_filename: Filename where the adjacency list lives as JSON.
graph_json_str: Graph as an adjacency list string in JSON.
Return: List of the chosen nodes.
"""
if graph_json_filename is None and graph_json_str is None:
return []
G = None
if graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
iters_since_change = 0
cut_vertices = list(set(nx.articulation_points(G)))
while (len(cut_vertices) < seed_num):
rand_node = cut_vertices[rand.randint(0, len(cut_vertices) - 1)]
adj_node_lst = G.neighbors(rand_node)
rand_adj_node = adj_node_lst[rand.randint(0, len(adj_node_lst) - 1)]
if (rand_adj_node not in cut_vertices):
iters_since_change = 0
cut_vertices.append(rand_adj_node)
else:
iters_since_change = iters_since_change + 1
if (iters_since_change > 10):
break
return cut_vertices[0:seed_num]
def plot_titles_graph():
graph = util.load_graph(cfg.paths['titles-refs-graph'])
hist = util.load_csv_hist(cfg.paths['titles-refs-hist'])
fig, ax, mapping = plot_graph(graph,
hist,
relabel=RELABEL_TITLES,
max_n_nodes=MAX_N_TITLE_NODES)
fig.set_size_inches(get_savefig_size(MAX_N_TITLE_NODES), forward=False)
fig.savefig(cfg.paths['titles-graph-plot'], dpi=333)
print('saved titles graph plot to "{}"'.format(
cfg.paths['titles-graph-plot']))
if mapping is not None:
util.save_json(cfg.paths['titles-graph-plot-mapping'], mapping)
print('saved titles graph plot mapping to "{}"'.format(
cfg.paths['titles-graph-plot-mapping']))
def plot_authors_graph():
graph = util.load_graph(cfg.paths['authors-refs-graph'])
hist = get_def_dict(util.load_csv_hist(cfg.paths['authors-refs-hist']),
int)
fig, ax, mapping = plot_graph(graph,
hist,
relabel=RELABEL_AUTHORS,
max_n_nodes=MAX_N_AUTHOR_NODES)
fig.set_size_inches(get_savefig_size(MAX_N_AUTHOR_NODES), forward=False)
fig.savefig(cfg.paths['authors-graph-plot'], dpi=333)
print('saved authors graph plot to "{}"'.format(
cfg.paths['authors-graph-plot']))
if mapping is not None:
util.save_json(cfg.paths['authors-graph-plot-mapping'], mapping)
print('saved authors graph plot mapping to "{}"'.format(
cfg.paths['authors-graph-plot-mapping']))
def __init__(self, args: argparse.Namespace) -> None:
"""Creates a SampleStack object.
Parameters
---------
args : argparse.Namespace
the command-line arguments provided by the user
"""
# Load graph
# Create stack of samples
# Use List as stack
self.t_load_start = timeit.default_timer()
self.full_graph, self.true_block_assignment = load_graph(args)
self.t_load_end = timeit.default_timer()
self.stack = list() # type: List[Tuple[Graph, Sample]]
self.create_sample_stack(args)
self.t_sample_end = timeit.default_timer()
def __init__(self, network, num_routes, agent_type, start_node=None, destination_node=None, max_speed=100, ):
self.num_routes = num_routes
self.route_count = 0
self.agent_type = agent_type
self.graph = load_graph(network)
self.init_state = True
self.max_speed = max_speed
self.current_speed = max_speed
self.travelled_edge_distance = 0
self.current_edge_distance = 0
self.next_node = None
self.final_edge = False
if start_node is not None and destination_node is not None:
self.current_node = start_node
self.destination_node = destination_node
else:
self.current_node = self.choose_start_node()
self.destination_node = self.choose_destination_node()
if self.agent_type == "local":
self.route = self.get_route()
self.node_count = 0
self.set_next_node()
def sccf_helper(seed_num, graph=None, graph_json_filename=None, graph_json_str=None):
# parse the graph
G = None
if graph is not None:
G = graph
elif graph_json_filename is not None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
# initialize queue for subgraphs
# try to get about 2 nodes in each cluster
node_per_cluster = 2
max_depth = int(math.ceil(np.log2(seed_num / node_per_cluster))) + 1
cluster_queue = Queue.Queue()
cluster_queue.put(G)
# divide graph into 2**max_depth clusters
while (cluster_queue.qsize() < 2**max_depth ):
G_curr = cluster_queue.get()
# work only on the largest connected component
G_curr_c = max(nx.connected_component_subgraphs(G_curr), key=len)
if (G_curr_c.size() < 2 * node_per_cluster):
# put it back if cluster is too small
cluster_queue.put(G_curr_c)
continue
# get fiedler vector
fiedler_vector = nx.fiedler_vector(G_curr_c, normalized=True, tol=1e-01)
node_list_sub_1 = []
node_list_sub_2 = []
node_list = G_curr_c.nodes()
# split positive and negative terms in fielder vector
for i in range(len(fiedler_vector)):
if (fiedler_vector[i] >= 0):
node_list_sub_1.append(node_list[i])
else:
node_list_sub_2.append(node_list[i])
# seperate the graph into two subgraphs
if (len(node_list_sub_1) >= node_per_cluster):
# ignore clusters too small
G_sub_1 = G_curr_c.subgraph(node_list_sub_1)
cluster_queue.put(G_sub_1)
if (len(node_list_sub_2) >= node_per_cluster):
# ignore clusters too small
G_sub_2 = G_curr_c.subgraph(node_list_sub_2)
cluster_queue.put(G_sub_2)
# get node_per_cluster highest degree nodes from each cluster
candidate_nodes = []
candidate_neighbors = {}
while not (cluster_queue.empty()):
G_curr = cluster_queue.get()
# measure used to pick node with in clusters
degree_dict = nx.closeness_centrality(G_curr)
node_keys = sorted(degree_dict, key=degree_dict.get,
reverse=True)[:node_per_cluster]
for i in node_keys:
# append i and a neighbor of i
if (i not in candidate_nodes):
candidate_nodes.append(i)
candidate_neighbors[i] = list(nx.all_neighbors(G, i))
# return candidate nodes and neighbors
return candidate_nodes, candidate_neighbors
def __init__(self, path_to_pb, scale=0.33, mode='L'):
self.graph = load_graph(path_to_pb)
self.scale = scale
self.mode = mode
def tf_classify():
# TODO: python -m scripts.label_image --graph=tf_files/retrained_graph.pb --image=test/aurelia.jpeg
import socket
print("In tf_classify handler from {}".format(socket.getfqdn()))
file_name = "models/mobilenet/example/3475870145_685a19116d.jpg"
file_name = "https://www.eopugetsound.org/sites/default/files/styles/magazinewidth_592px/public/topical_article/images/moon_jellyfish.jpg?itok=Esreg6zX"
# Get payload
payload = request.get_json(silent=True, force=True)
if payload == None:
if request.get_data() != None:
payload = json.loads(request.get_data())
if payload != None:
if payload.get("nlp").get("entities").get("url"):
file_name = payload.get("nlp").get("entities").get("url")[0].get(
"raw")
# Load model file
model_file = "models/mobilenet/retrained_graph.pb"
label_file = "models/mobilenet/retrained_labels.txt"
input_height = 224
input_width = 224
input_mean = 128
input_std = 128
input_layer = "input"
output_layer = "final_result"
graph = util.load_graph(model_file)
t = util.read_tensor_from_image_file(file_name,
input_height=input_height,
input_width=input_width,
input_mean=input_mean,
input_std=input_std)
input_name = "import/" + input_layer
output_name = "import/" + output_layer
input_operation = graph.get_operation_by_name(input_name)
output_operation = graph.get_operation_by_name(output_name)
with tf.Session(graph=graph) as sess:
start = time.time()
results = sess.run(output_operation.outputs[0],
{input_operation.outputs[0]: t})
end = time.time()
results = np.squeeze(results)
top_k = results.argsort()[-5:][::-1]
labels = util.load_labels(label_file)
print('\nEvaluation time (1-image): {:.3f}s\n'.format(end - start))
template = "{} (score={:0.5f})"
print(top_k)
for i in top_k:
print(template.format(labels[i], results[i]))
# I really don't know, my best guess is []
if results[0] < 0.1:
response = "I really don't know, my best guess is that this looks like a " + labels[
top_k[0]]
else:
response = 'I think this is a ' + labels[top_k[0]]
response = 'I think this is a ' + labels[top_k[0]]
return jsonify(
status=200,
replies=[{
'type': 'text',
'content': response
}],
conversation={'memory': {
'plankton': labels[top_k[0]]
}})
else:
adj_matrix = np.random.choice([0, 1], size=(n, n),
p=[0.8, 0.2]).astype(np.float64)
np.save(source[:-4], adj_matrix)
e = np.ones(adj_matrix.shape[0])
adj_matrix = add_random(adj_matrix, e=e)
A = scale_rows(adj_matrix)
r = page_rank(A, e=np.ones(adj_matrix.shape[0]))
print("\nresult for small test. r:\n", np.round(r, 4))
print("checking SNAP...")
for filename in ["p2p-Gnutella08.txt", "Wiki-Vote.txt"]:
print(filename)
adjacency_matrix = load_graph(filename)
n = adjacency_matrix.shape[0]
for e_val in [
1, 0.5, 0
]: # different values of d are equivalent to changing values in e
e = np.full(n, fill_value=e_val, dtype=np.float32)
print(f"d*e values = [{e_val}/{adjacency_matrix.shape[0]}, ...]")
adj_matrix = add_random(adjacency_matrix, e=e)
A = scale_rows(adj_matrix)
r = page_rank(A, e=e, delta=1e-8)
print(f"r min ={np.min(r)}, r max = {np.max(r)}\n")
print("e[i]=0 except e[0]=1")
e = np.zeros(n, dtype=np.float32)
e[0] = 1
import random
import matplotlib.pyplot as plt
import statistics
import time
from util import load_graph
from PopGenerator import PopGenerator
from GA import GA
random.seed()
instance = './data/kroa100.tsp'
graph = load_graph(instance)
m = 2
max_iters = 1000
experiments_count = 3
evaluators_conf = (GA.get_min_by_fitness, GA.get_min_by_penalty,
GA.get_min_by_DEB, GA.get_min_by_hierarchy)
breaks_generator_conf = (PopGenerator.generate_breaks_rules, PopGenerator.generate_breaks_fully_random,
PopGenerator.generate_breaks_fully_random, PopGenerator.generate_breaks_fully_random)
names_conf = ('Constrained generation', 'Penalization function',
"Deb's rules", "Stochastic hierarchy")
print(instance+' '+str(m))
for i_conf in range(0, len(evaluators_conf)):
print(names_conf[i_conf]+'\n')
experiments_list = []
evaluator = evaluators_conf[i_conf]
generator = PopGenerator(graph, breaks_generator_conf[i_conf])
def spectrum_cluster(seed_num, graph_json_filename=None, graph_json_str=None):
"""
Identifies clusters in the network using laplacian spectrum, and loops over
each cluster to pick the node with largest degree until seed_num nodes were
chosen.
Parameters:
seed_num: Number of nodes to choose.
graph_json_filename: Filename where the adjacency list lives as JSON.
graph_json_str: Graph as an adjacency list string in JSON.
Return: List of the chosen nodes.
"""
# parse the graph
G = None
if graph_json_str is None:
G = util.load_graph(graph_json_filename=graph_json_filename)
else:
G = util.load_graph(graph_json_str=graph_json_str)
# initialize queue for subgraphs
# try to get about 2 nodes in each cluster
node_per_cluster = 2
max_depth = int(math.ceil(np.log2(seed_num / node_per_cluster))) + 1
cluster_queue = Queue.Queue()
cluster_queue.put(G)
# divide graph into 2**max_depth clusters
while (cluster_queue.qsize() < 2**max_depth ):
G_curr = cluster_queue.get()
# work only on the largest connected component
G_curr_c = max(nx.connected_component_subgraphs(G_curr), key=len)
if (G_curr_c.size() < 2 * node_per_cluster):
# put it back if cluster is too small
cluster_queue.put(G_curr_c)
continue
# get fiedler vector
fiedler_vector = nx.fiedler_vector(G_curr_c, normalized=True, tol=1e-04)
node_list_sub_1 = []
node_list_sub_2 = []
node_list = G_curr_c.nodes()
# split positive and negative terms in fielder vector
for i in range(len(fiedler_vector)):
if (fiedler_vector[i] >= 0):
node_list_sub_1.append(node_list[i])
else:
node_list_sub_2.append(node_list[i])
# seperate the graph into two subgraphs
if (len(node_list_sub_1) >= node_per_cluster):
# ignore clusters too small
G_sub_1 = G_curr_c.subgraph(node_list_sub_1)
cluster_queue.put(G_sub_1)
if (len(node_list_sub_2) >= node_per_cluster):
# ignore clusters too small
G_sub_2 = G_curr_c.subgraph(node_list_sub_2)
cluster_queue.put(G_sub_2)
# get node_per_cluster highest degree nodes from each cluster
candidate_nodes = []
while not (cluster_queue.empty()):
G_curr = cluster_queue.get()
# measure used to pick node with in clusters
degree_dict = nx.degree(G_curr)
node_keys = sorted(degree_dict, key=degree_dict.get,
reverse=True)[:node_per_cluster]
for i in node_keys:
candidate_nodes.append(i)
# randomly pick seed_num nodes from candidate_nodes
rtn = list(np.random.choice(candidate_nodes, replace=False, size=seed_num))
return rtn
# -----------------------------
x_test, y_test = util.get_data("test")
# np.random.seed(0)
# sample_index = np.random.randint(len(y_test), size=sample_size)
sample_index = np.arange(len(y_test))
x_test_sample = x_test[sample_index]
y_test_sample = y_test[sample_index]
# print("x_sample:{}, y_sample:{}".format(x_test_sample.shape, y_test_sample.shape))
init_end_time = time.time()
print("loading data takes {:6.4f} ms".format(
(init_end_time - init_time) * 1000))
print("predicting cases:")
graph = util.load_graph(frozen_model)
if not __debug__:
print('\n'.join(map(str, [op.name for op in graph.get_operations()])))
session = tf.Session(graph=graph)
begin_time = time.time()
X, Y = util.get_tensor_by_op_name(graph, ["input", "label"])
output, accuracy, cost = util.get_tensor_by_op_name(
graph, ["output", "accuracy", "cost"])
label_prob = session.run(output,
feed_dict={
X: x_test_sample,
Y: y_test_sample
})
end_time = time.time()
else:
# cluster间
nx.draw_networkx_edges(G,
pos,
edgelist=edgelist,
width=3,
alpha=0.8,
edge_color=colors[index])
# 可视化label
nx.draw_networkx_labels(G, pos, labels, font_size=12)
plt.axis('off')
plt.show()
if __name__ == '__main__':
# 加载网络并可视化
G = util.load_graph("network/test.txt")
pos = nx.spring_layout(G)
nx.draw(G, pos, with_labels=True, font_weight='bold')
plt.show()
# GN算法
algo = GN(G)
partition = algo.execute()
print(partition)
# 可视化结果
showCommunity(algo._G_cloned, partition, pos)
# End of parse_arguments()
if __name__ == "__main__":
args = parse_arguments()
t_start = timeit.default_timer()
if args.sample_type != "none":
samplestack = SampleStack(args)
sampled_graph, sampled_graph_partition, vertex_mapping, block_mapping, evaluation = samplestack.unstack(
args)
full_graph, full_graph_partition, evaluation = samplestack.extrapolate_sample_partition(
sampled_graph_partition, vertex_mapping, args, evaluation)
else:
graph, true_block_assignment = load_graph(args)
t_load = timeit.default_timer()
t_sample = timeit.default_timer()
print("Performing stochastic block partitioning")
evaluation = Evaluation(args, graph)
# Please refer to the graph-tool documentation under graph-tool.inference for details on the input parameters
partition = minimize_blockmodel_dl(graph,
shrink_args={'parallel': True},
verbose=args.verbose,
mcmc_equilibrate_args={
'verbose': args.verbose,
'epsilon': 1e-4
})
t_partition = timeit.default_timer()
t_end = timeit.default_timer()
