def batch_analysis(n_vents):
# Genera n vent casualmente
vent_list = []
# Seleziona tra le simulazioni salvate
for sim in os.listdir(("sparse/")):
if "sparse_sim_c" in sim:
vent_list.append(sim[13:-4])
vent_list = random.sample(vent_list, n_vents)
metrics_matrix = []
print("Vent to analyze:", vent_list)
for vent in vent_list:
propagation = Propagation()
# Esecuzione algoritmo
sparse_matrix = propagation.trivector(vent)
# Esportazione in ASCII e calcolo metriche
metrics_list = metrics.compute(vent, "trivector", sparse_matrix)
metrics_matrix.append(metrics_list)
print("vent:", vent, " analyzed")
dataframe = pd.DataFrame(metrics_matrix,
columns=[
"PPV", "PPVF", "TPR", "TPRF", "F1", "F1F",
"THREAT", "THREATF"
])
print(dataframe)
print("\n")
print(dataframe.describe())
def realsim_cmd(id_vent: int, real_class: str, neighbor_method: str,
radius: int):
id_vent = str(id_vent - 1)
propagation = Propagation()
id_vents = [id_vent]
neighbor = ""
# Se la classe è 0 allora bisogna fare Unify
if real_class == "0":
if neighbor_method != None:
if neighbor_method == "moore" or neighbor_method == "neumann":
id_vents = utility.get_neighborhood(id_vent, neighbor_method,
radius)
neighbor = "_" + neighbor_method + str(radius)
else:
print(
"You must specify a valid neighbor method: moore / neumann."
)
return None
sparse_matrix_c, sparse_matrix_d = propagation.real(
id_vents, real_class, neighbor)
# Esportazione in ASCII Grid
for i in range(len(id_vents)):
id_vents[i] = int(id_vents[i]) + 1
mc.ascii_creator(id_vents, "ucsim" + neighbor, sparse_matrix_c)
mc.ascii_creator(id_vents, "udsim" + neighbor, sparse_matrix_d)
return
else:
if len(id_vents) > 1:
raise ValueError("multiple vents not supported for class != 0")
sparse_matrix = propagation.real(id_vents, real_class, neighbor)
# Esportazione in ASCII Grid
mc.ascii_creator([str(id_vent + 1)], neighbor + real_class,
sparse_matrix)
return
def get_ppv_list(G, vent_list):
p = Propagation()
p.set_Graph(G)
ppv_list = []
for vent in vent_list:
sparse_matrix = p.trivector([vent])
ppv = compute([vent], "", sparse_matrix, G)[0]
ppv_list.append(ppv)
return ppv_list
def get_tpr_list(G, vent_list):
p = Propagation()
p.set_Graph(G)
tpr_list = []
for vent in vent_list:
sparse_matrix = p.trivector([vent])
tpr = compute([vent], "", sparse_matrix, G)[2]
tpr_list.append(tpr)
return tpr_list
def trivector_cmd(id_vent: str,
neighbor_method: str,
radius: int,
threshold: float,
graph: str,
header=False):
propagation = Propagation()
# Setta i parametri
if os.path.isfile("graph_gexf/" + graph):
propagation.set_Graph(utility.load_graph(graph))
else:
print("Graph doesn't exist, default are loaded")
propagation.set_trivector(threshold)
id_vents = []
propagation_method = "trivector"
neighbor = ""
if neighbor_method != None:
if neighbor_method == "moore" or neighbor_method == "neumann":
id_vents = utility.get_neighborhood(id_vent, neighbor_method,
radius)
neighbor += "_" + neighbor_method + str(radius)
else:
print("You must specify a valid neighbor method: moore / neumann.")
return None
else:
id_vents = [id_vent]
# Esecuzione algoritmo
sparse_matrix = propagation.trivector(id_vents)
# Esportazione in ASCII e calcolo metriche
G = propagation.get_Graph()
utility.visualize_and_metrics(id_vents, propagation_method, neighbor,
sparse_matrix, G, header)
def __init__(self, id_nodes: list, edges: list, real_vect: list, max_age = 5):
# Id node
self.id_nodes = id_nodes
# Lista dei pesi degli archi
self.edges = np.array(edges)
# Real vector
self.real_vect = real_vect
# Valore di fitness della soluzione
self.fitness = 0
# Età massima della soluzione
self.max_age = max_age
# Vita della soluzione
self.age = np.random.randint(0, (2 * max_age) / 3)
self.propagation = Propagation()
def analyse(self, threshold, window=100):
prop = Propagation(self.signals, threshold, window)
self.spikes = prop.getspikes()
temp = self.spikes[0]
self.spikes[0] = self.spikes[1]
self.spikes[1] = temp
self.spikes[0] = numpy.array(self.spikes[0])
self.spikes[1] = numpy.array(self.spikes[1])
print str(len(self.spikes[0]))
self.peaks[0] = findpeaks(self.spikes[0])
self.peaks[1] = findpeaks(self.spikes[1])
times = getspeeds(self.peaks[0], self.peaks[1])
self.times = [
x * window / self.signals[0].sampling_rate.magnitude for x in times
]
print self.times
return self.times
def cut_cmd(id_vent, list_edges: list, neighbor_method, radius):
edges_to_cut = []
for edges in list_edges:
edges_to_cut.append(edges.split(','))
propagation = Propagation()
id_vents = []
propagation_method = "trivector"
neighbor = ""
if neighbor_method != None:
if neighbor_method == "moore" or neighbor_method == "neumann":
id_vents = utility.get_neighborhood(id_vent, neighbor_method,
radius)
neighbor += "_" + neighbor_method + str(radius)
else:
print("You must specify a valid neighbor method: moore / neumann.")
return None
else:
id_vents = [id_vent]
propagation.cut_edges(edges_to_cut)
# Esportazione in ASCII e calcolo metriche
sparse_matrix = propagation.trivector(id_vents)
G = propagation.get_Graph()
utility.visualize_and_metrics(id_vents, propagation_method, neighbor,
sparse_matrix, G, False)
mc.ascii_barrier(id_vent, propagation_method + neighbor, edges_to_cut)
def parameter_analysis(id_vent):
print("Vent to analyze:", id_vent)
metrics_matrix = []
parameter_list = [0.001, 0.0001, 0.01]
# Algoritmo eseguito con i parametri di default
for parameter in parameter_list:
propagation = Propagation()
# Setta i parametri
propagation.set_trivector(parameter)
# Esecuzione algoritmo
sparse_matrix = propagation.trivector(id_vent)
# Esportazione in ASCII e calcolo metriche
metrics_list = metrics.compute(id_vent, "trivector", sparse_matrix)
metrics_matrix.append(metrics_list)
dataframe = pd.DataFrame(metrics_matrix,
columns=[
"PPV", "PPVF", "TPR", "TPRF", "F1", "F1F",
"THREAT", "THREATF"
])
print(dataframe)
print("\n")
def immunological_train_cmd(id_vent: int, size: int, step: int,
population_len: int, rho: int, epochs: int):
# Lista vents/nodes del sottografo
id_nodes, id_vents = utility.get_node_vent_chessboard(id_vent, size, step)
print("Calcolo chessboard terminato!")
# Creazione del vettore dei real vect
real_vect_list = []
for vent in id_vents:
real_vect_list.append(
np.load("Data/real_vectors/" + str(vent) + ".npy"))
# Creazione del vettore dei trivector
p = Propagation()
tri_vect_list = []
for node in id_nodes:
tri_vect_list.append(p.trivector_train(node))
# Real vect e tri vect unificati
real_vect = np.zeros(5820)
tri_vect = np.zeros(5820)
for i in range(5820):
for vect in tri_vect_list:
if vect[i] > 0:
tri_vect[i] = 1
break
for vect in real_vect_list:
if vect[i] > 0:
real_vect[i] = 1
break
# Creazione del sottografo
SG = ga.get_trivector_subgraph(tri_vect, real_vect)
print("Init immunological Algorithm")
# Algoritmo immunologico
imm = Immunological_algorithm(id_vents, id_nodes, SG.edges, population_len,
rho)
imm.start(epochs)
def autocut_cmd(id_vent: str, distance: int, neighbor_method: str, radius: int,
dimension: int, mode: str):
propagation = Propagation()
id_vents = []
propagation_method = "trivector"
neighbor = ""
if neighbor_method != None:
if neighbor_method == "moore" or neighbor_method == "neumann":
id_vents = utility.get_neighborhood(id_vent, neighbor_method,
radius)
neighbor += "_" + neighbor_method + str(radius)
else:
print("You must specify a valid neighbor method: moore / neumann.")
return None
else:
id_vents = [id_vent]
# Esecuzione algoritmo prima di tagliare
no_cutted_sparse = propagation.trivector(id_vents)
G = propagation.get_Graph()
# Decommentare se si vuole stampare le metriche del trivector senza taglio
# utility.visualize_and_metrics(id_vents, propagation_method, no_cutted_sparse, G, False)
# selezione degli archi da tagliare
list_edges = ga.get_edges_to_cut(G, id_vents, distance, dimension, mode)
propagation.set_Graph(utility.load_graph())
# taglio archi selezionati
propagation.cut_edges(list_edges)
# esecuzione trivector dopo il taglio degli archi
cutted_sparse = propagation.trivector(id_vents)
G = propagation.get_Graph()
utility.visualize_and_metrics(id_vents, propagation_method, neighbor,
cutted_sparse, G, False)
mc.ascii_barrier(id_vent, propagation_method + neighbor, list_edges)
def eruption_cmd(id_vent, volume, n_days, threshold, header=False):
propagation = Propagation()
# Setta i parametri
propagation.set_eruption(volume, n_days, threshold)
# Esecuzione algoritmo
sparse_matrix = propagation.eruption([id_vent])
# Esportazione in ASCII e calcolo metriche
G = propagation.get_Graph()
utility.visualize_and_metrics([id_vent], "eruption", "", sparse_matrix, G,
header)
def montecarlo_cmd(id_vent, n_epochs, second_chance, header=False):
if id_vent == 0:
return
propagation = Propagation()
# Setta i parametri
propagation.set_montecarlo(n_epochs, second_chance)
# Esecuzione algoritmo
sparse_matrix = propagation.montecarlo([id_vent])
# Esportazione in ASCII e calcolo metriche
G = propagation.get_Graph()
utility.visualize_and_metrics([id_vent], "montecarlo", "", sparse_matrix,
G, header)
class Immunological_solution:
def __init__(self, id_nodes: list, edges: list, real_vect: list, max_age = 5):
# Id node
self.id_nodes = id_nodes
# Lista dei pesi degli archi
self.edges = np.array(edges)
# Real vector
self.real_vect = real_vect
# Valore di fitness della soluzione
self.fitness = 0
# Età massima della soluzione
self.max_age = max_age
# Vita della soluzione
self.age = np.random.randint(0, (2 * max_age) / 3)
self.propagation = Propagation()
def __fbeta_score(self, tri_vect, idx: int):
tp, fp, tn, fn = 0, 0, 0, 0
for i in range(0, len(self.real_vect[idx])):
if tri_vect[i] > 0 and self.real_vect[idx][i] == 1: # tp
tp += 1
if tri_vect[i] > 0 and self.real_vect[idx][i] == 0: # fp
fp += 1
if tri_vect[i] == 0 and self.real_vect[idx][i] == 0: # tn
tn += 1
if tri_vect[i] == 0 and self.real_vect[idx][i] == 1: # fn
fn += 1
ppv = tp / (tp + fp)
tpr = tp / (tp + fn)
# beta grande!
beta = 3
fbeta_score = (1 + beta**2) * ppv * tpr / ((beta**2 * ppv) + tpr)
return fbeta_score
def __update_weights(self, edges_dict: dict):
# Prendere il grafo
G = self.propagation.get_Graph()
# Aggiornare i pesi
i = 0
for u, v in edges_dict:
G.edges[u, v]['prop_weight'] = float(self.edges[i])
i += 1
# Settare il grafo
self.propagation.set_Graph(G)
def compute_fitness(self, edges_dict: dict):
# Aggiornare i pesi
self.__update_weights(edges_dict)
# Trivector
fit_list = []
for i in range(len(self.id_nodes)):
tri_vect = self.propagation.trivector_train(self.id_nodes[i])
# f_beta score
fit_list.append(self.__fbeta_score(tri_vect, i))
self.fitness = np.mean(fit_list)
def hypermutation(self, rho):
alpha = math.exp(-rho * self.fitness)
number_of_mutation = math.floor((alpha * len(self.edges)))
std = (1 - self.fitness) / 5
for _ in range(number_of_mutation):
r = np.random.randint(0, len(self.edges)-1)
w = np.random.normal(self.edges[r], std)
if w < 0:
w = 0
if w > 1:
w = 1
self.edges[r] = w
def increment_age(self):
self.age += 1
def set_random_age(self):
self.age = np.random.randint(0, (2 * self.max_age) / 3)
def set_fitness(self, fitness):
self.fitness = fitness
def test_active_error(G, test_seeds, gold_infect_list):
propagation = Propagation(G, beta, max_infect_rate)
test_infect_list = propagation.infect_by_rate(test_seeds, 0)
res = active_error(G, gold_infect_list, test_infect_list)
return res
def run_propagation(G, seed_num):
propagation = Propagation(G, beta, max_infect_rate)
seeds = propagation.choice_seeds(seed_num)
infected_list = propagation.infect_by_rate(seeds, 0)
#infected_list = propagation.infect_by_step(seeds, 0) ;
return [seeds, infected_list]
num) + ".abf"
print("Loading " + fileName)
try:
r = neo.io.AxonIO(fileName)
bl = r.read_block(lazy=False, cascade=True)
except IOError:
break
signals = [None] * 2
signals[0] = bl.segments[0].analogsignals[0]
signals[1] = bl.segments[0].analogsignals[15]
t = numpy.linspace(1, signals[0].sampling_rate.magnitude,
len(signals[0]))
print("Data loaded")
prop = Propagation(signals)
spikes = prop.getspikes()
#peaks1 = find_peaks_cwt(spikes[0],numpy.arange(11,12))
#peaks2 = find_peaks_cwt(spikes[1], numpy.arange(11,12))
spikes1 = array(spikes[0])
spikes2 = array(spikes[1])
xs = numpy.linspace(1,
signals[0].sampling_rate.magnitude,
num=len(spikes1))
peaks1 = findpeaks(spikes[0])
peaks2 = findpeaks(spikes[1])
print "Length of peaks1: " + str(len(peaks1))
print "Length of peaks2: " + str(len(peaks2))
def test(id_vent, distance=4):
propagation = Propagation()
propagation.trivector([id_vent])
G = propagation.get_Graph()
# Conversione vent
id_node = conversion.get_node_from_idvent(int(id_vent))
# Estrazione sottografo
for i in range(len(G.nodes)):
if G.nodes[str(i)]['current_flow'] == 0:
G.remove_node(str(i))
# Cambio pesi
for u, v, data in G.edges(data=True):
if data['trasmittance'] == 0:
G.edges[u, v]['trasmittance'] = math.inf
else:
G.edges[u, v]['trasmittance'] = -math.log(data['trasmittance'])
# Lista nodi città
city_nodes = []
for n in G.nodes:
if G.nodes[n]['priority'] > 0:
city_nodes.append(n)
# Shortest paths
shortest_paths = {}
for n in city_nodes:
shortest_paths[n] = nx.shortest_path(G,
id_node,
n,
weight='trasmittance')
cutted_edges = {}
for n in shortest_paths:
path = shortest_paths[n]
for i in range(distance, len(path) - distance):
edge_id = (path[i - 1], path[i])
if edge_id not in cutted_edges:
propagation.set_Graph(utility.load_graph())
propagation.cut_edges([[path[i - 1], path[i]]])
sparse_matrix = propagation.trivector([id_vent])
G = propagation.get_Graph()
risk = metrics.compute([id_vent], 'trivector', sparse_matrix,
G)[-1]
cutted_edges[edge_id] = risk
print(edge_id, risk)
min_risk = min(cutted_edges, key=cutted_edges.get)
print(min_risk)