def test_loc_eff_bin():
x = load_sample(thres=.4)
leff = bct.efficiency_bin(x, local=True)
y = bct.binarize(x)
leff2 = bct.efficiency_bin(y, local=True)
print(np.sum(leff), np.sum(leff2), 105.5111)
assert np.allclose(np.sum(leff), 105.5111, atol=0.1)
assert np.allclose(np.sum(leff2), 105.5111, atol=0.1)
def test_glob_eff_bin():
x = load_sample(thres=.4)
geff = bct.efficiency_bin(x)
y = bct.binarize(x)
geff2 = bct.efficiency_bin(y)
print(geff, geff2, 0.6999)
assert np.allclose(geff, 0.6999, atol=1e-4)
assert np.allclose(geff2, 0.6999, atol=1e-4)
def calculate_path_and_efficiency_bin(G):
"""
Return the following network metrics for your graph. Uses brain connectivity tool-box.
Input:
G (np.array): binarized matrix, symmetric
Outputs:
Eglob: Global efficiency
average_Elocal: mean Local Efficiency
char_path: Average shortest path length
clustering: Average Clustering coefficient
"""
if not np.allclose(G, G.T):
raise bct.BCTParamError('Not undirected')
average_shortest_path, Eglob, _, _, _ = bct.charpath(bct.distance_bin(G))
average_clustering = np.mean(abs(bct.clustering_coef_bu(G)))
average_Elocal = np.mean(bct.efficiency_bin(G, 1))
return Eglob, average_Elocal, average_clustering, average_shortest_path
10 34
14 34
15 34
16 34
19 34
20 34
21 34
23 34
24 34
27 34
28 34
29 34
30 34
31 34
32 34
33 34
""".strip()
arr = np.zeros((34, 34), dtype=np.uint8)
for row in s.split('\n'):
first, second = row.split(' ')
arr[int(first) - 1, int(second) - 1] += 1
arr = bct.binarize(arr + arr.T)
np.random.seed(1991)
eff = bct.efficiency_bin(arr)
mod = bct.modularity_und(arr)
rand = bct.randmio_und_connected(arr, 5)
return np.where(CIJ[i] > 0)[0]
def min_hop_count(CIJ):
mhc = bct.distance_bin(CIJ)
mhc[mhc == 0] = np.Inf
return mhc
def network_of_neighbours(CIJ, i):
neighbours = np.where(CIJ[i] > 0)[0]
return CIJ[neighbours][:, neighbours]
N = int(sys.argv[1])
k = int(sys.argv[2])
p = float(sys.argv[3])
net = NetworkWattsStrogatz(N, k, p)
print("BrainConnectivityToolbox...\n")
print("\tEff[Global] = " + str(bct.efficiency_bin(net)))
print("\tEff[Local] = " + str(bct.efficiency_bin(net, local=True)))
print("\n\nHomebrew...\n")
print("\tEff[Global] = " + str(global_eff(net)))
print("\tEff[Local] = " + str(local_eff(net)))
PlotConnectivity(net)
def threshold_global_cost_efficiency(mtx, iterations):
""" Threshold a graph based on the Global Efficiency - Cost formula.
.. [Basset2009] Bassett, D. S., Bullmore, E. T., Meyer-Lindenberg, A., Apud, J. A., Weinberger, D. R., & Coppola, R. (2009). Cognitive fitness of cost-efficient brain functional networks. Proceedings of the National Academy of Sciences, 106(28), 11747-11752.
Parameters
----------
mtx : array-like, shape(N, N)
Symmetric, weighted and undirected connectivity matrix.
iterations : int
Number of steps, as a resolution when search for optima.
Returns
-------
binary_mtx : array-like, shape(N, N)
A binary mask matrix.
threshold : float
The threshold that maximizes the global cost efficiency.
global_cost_eff_max : float
Global cost efficiency.
efficiency : float
Global efficiency.
cost_max : float
Cost of the network at the maximum global cost efficiency
"""
binary_mtx = np.zeros_like(mtx, dtype=np.int32)
step = 1.0 / iterations
thresholds = np.arange(0, 1 + step, step)
N, _ = np.shape(mtx)
num_connections = (N * (N - 1)) / 2.0
global_cost_eff = np.zeros((iterations, 1))
cost = np.zeros((iterations, 1))
for i in range(iterations):
tmp_binary = np.zeros_like(binary_mtx)
for k in range(N):
for l in range(k + 1, N):
if mtx[k, l] > thresholds[i]:
tmp_binary[k, l] = 1
tmp_binary[l, k] = 1
global_eff = bct.efficiency_bin(tmp_binary)
degree = bct.degrees_und(tmp_binary)
total_degree = np.sum(degree)
cost[i] = (0.5 * total_degree) / num_connections
global_cost_eff[i] = global_eff - cost[i]
indx_max = np.argmax(global_cost_eff)
threshold = thresholds[indx_max]
for k in range(N):
for l in range(k + 1, N):
if mtx[k, l] >= threshold:
binary_mtx[k, l] = 1
binary_mtx[l, k] = 1
cost_max = cost[indx_max]
global_cost_eff_max = global_cost_eff[indx_max]
efficiency = bct.efficiency_bin(binary_mtx)
# import matplotlib.pyplot as plt
# plt.figure()
# plt.plot(cost, global_cost_eff)
# plt.plot(cost_max, global_cost_eff_max, 'b*', label='Max Global Cost Efficiency')
# plt.title('Economical small-world network at max Global Cost Efficiency')
# plt.xlabel('Cost')
# plt.ylabel('Global Cost Efficiency')
# plt.legend()
# plt.show()
return binary_mtx, threshold, global_cost_eff_max, efficiency, cost_max