for l_ctr, l in enumerate(LS):
print(l)
for repeat in range(N_REPEATS):
print(repeat)
g = algo(bc.num_brain_nodes,
bc.num_brain_edges_directed,
L=l,
gamma=1,
brain_size=BRAIN_SIZE)[0]
rs[key][l_ctr, repeat] = metrics.reciprocity(g)
rs['rand'] = np.nan * np.zeros((N_REPEATS, ), dtype=float)
for repeat in range(N_REPEATS):
g_rand = random_directed_deg_seq(in_sequence=brain_in_deg,
out_sequence=brain_out_deg,
simplify=True)[0]
rs['rand'][repeat] = metrics.reciprocity(g_rand)
np.save(RECIPROCITY_FILE_NAME, np.array([rs]))
else:
print('Loading previous reciprocity calculations...')
rs = np.load(RECIPROCITY_FILE_NAME)[0]
print('Crunching numbers...')
# get reciprocal/nonreciprocal distance histograms for real brain
r_dists_brain, non_r_dists_brain = metrics.dists_by_reciprocity(
a_brain, d_brain)
# do the same for each of the four graphs
graphss = {key: [] for key in KEYS}
in_degree_brain = G_brain.in_degree().values()
out_degree_brain = G_brain.out_degree().values()
for g_ctr in range(N_GRAPH_SAMPLES):
Gs = {}
# create directed ER graph
Gs['er'] = nx.erdos_renyi_graph(
bc.num_brain_nodes, bc.p_brain_edge_directed, directed=True)
# create directed degree-controlled random graph
Gs['rand'] = random_directed_deg_seq(in_sequence=in_degree_brain,
out_sequence=out_degree_brain,
simplify=True)[0]
# create target attraction graph
Gs['ta'] = ta(N=bc.num_brain_nodes,
N_edges=bc.num_brain_edges_directed, L=L,
brain_size=BRAIN_SIZE,)[0]
# create source growth graph
Gs['sg'] = sg(N=bc.num_brain_nodes,
N_edges=bc.num_brain_edges_directed, L=L,
brain_size=BRAIN_SIZE,)[0]
# create source growth graph with only topo rule
Gs['sg_topo'] = sg(N=bc.num_brain_nodes,
N_edges=bc.num_brain_edges_directed, L=np.inf,
@author: rkp
degree_controlled_random_spurious_edges.py
Calculate how many self/multi-edges are removed on average when making a
directed degree-controlled random graph with degree-distribution fixed to the brain's.
"""
from __future__ import division, print_function
import numpy as np
import networkx as nx
from extract import brain_graph
from random_graph import binary_directed
N_GRAPHS = 30
G_brain_dir, _, _ = brain_graph.binary_directed()
in_degree_seq = G_brain_dir.in_degree().values()
out_degree_seq = G_brain_dir.out_degree().values()
print('Making directed degree-controlled random graphs')
n_edges_lost_dir = []
for ctr in range(N_GRAPHS):
print(ctr)
G_dir, _, _ = binary_directed.random_directed_deg_seq(in_degree_seq,
out_degree_seq,
simplify=True)
n_edges_lost_dir.append(len(G_brain_dir.edges()) - len(G_dir.edges()))
print('Directed: mean edges lost +- std = {} +- {}'.format(
np.mean(n_edges_lost_dir), np.std(n_edges_lost_dir)))
@author: rkp
degree_controlled_random_spurious_edges.py
Calculate how many self/multi-edges are removed on average when making a
directed degree-controlled random graph with degree-distribution fixed to the brain's.
"""
from __future__ import division, print_function
import numpy as np
import networkx as nx
from extract import brain_graph
from random_graph import binary_directed
N_GRAPHS = 30
G_brain_dir, _, _ = brain_graph.binary_directed()
in_degree_seq = G_brain_dir.in_degree().values()
out_degree_seq = G_brain_dir.out_degree().values()
print("Making directed degree-controlled random graphs")
n_edges_lost_dir = []
for ctr in range(N_GRAPHS):
print(ctr)
G_dir, _, _ = binary_directed.random_directed_deg_seq(in_degree_seq, out_degree_seq, simplify=True)
n_edges_lost_dir.append(len(G_brain_dir.edges()) - len(G_dir.edges()))
print("Directed: mean edges lost +- std = {} +- {}".format(np.mean(n_edges_lost_dir), np.std(n_edges_lost_dir)))
from extract import brain_graph
import networkx as nx
G_brain, _, _ = brain_graph.binary_directed()
p = G_brain.number_of_nodes() / G_brain.number_of_edges()
in_sequence = G_brain.in_degree().values()
out_sequence = G_brain.out_degree().values()
labels = ['Deg. Cont. Rand.', 'ER Rand.', 'Brain']
n_edges_deg_controlled_random = []
n_edges_ER_random = []
for ri in range(N_TRIALS):
G_RAND, _, _ = binary_directed.random_directed_deg_seq(in_sequence,
out_sequence,
simplify=True)
G_ER, _, _ = binary_directed.ER_distance(p=p)
G_ER = nx.DiGraph(G_ER) # Remove parallel
G_ER.remove_edges_from(G_ER.selfloop_edges()) # Remove self-loops
n_edges_deg_controlled_random.append(G_RAND.number_of_edges())
n_edges_ER_random.append(G_ER.number_of_edges())
print('Finished repeat: ' + str(ri + 1) + ' of ' + str(N_TRIALS))
_, ax = plt.subplots(1, 1)
ax.hist(n_edges_deg_controlled_random, color='b', alpha=0.5, label=labels[0])
ax.hist(n_edges_ER_random, color='r', alpha=0.5, label=labels[1])
ax.axvline(len(G_brain.edges()), color='k', label=labels[2])
#ax.legend(['Deg. Cont. Rand', 'ER Rand.', 'Brain'])
ax.legend(loc='best')
G_er = nx.erdos_renyi_graph(bc.num_brain_nodes,
bc.p_brain_edge_directed,
directed=True)
# create sgpa graph
G_sgpa, _, _ = sgpa(N=bc.num_brain_nodes, N_edges=bc.num_brain_edges_directed, L=LENGTH_SCALE)
# create source growth only graph
G_sg, _, _ = sgpa(N=bc.num_brain_nodes, N_edges=bc.num_brain_edges_directed, L=np.inf)
# create target attraction graph
G_ta, _, _ = ta(N=bc.num_brain_nodes, N_edges=bc.num_brain_edges_directed, L=np.inf)
# create directed degree-controlled random graph
G_rand, _, _ = random_directed_deg_seq(in_sequence=in_degree_brain,
out_sequence=out_degree_brain,
simplify=True)
# calculate things for both types of graph
labels = ['er', 'sgpa', 'source-growth', 'target-attraction', 'random']
Gs = [G_er, G_sgpa, G_sg, G_ta, G_rand]
for label, G in zip(labels, Gs):
G.efficiency_matrix = metrics_bd.efficiency_matrix(G)
# calculate nodal efficiency
nodal_efficiency = np.sum(G.efficiency_matrix, axis=1) / (len(G.nodes()) - 1)
G.counts_nodal_efficiency = np.histogram(nodal_efficiency, bins=BINS_NODAL_EFFICIENCY)[0]
if label == 'er':
graphs_er += [G]
elif label == 'sgpa':
print(key)
rs[key] = np.nan * np.zeros((len(LS), N_REPEATS), dtype=float)
for l_ctr, l in enumerate(LS):
print(l)
for repeat in range(N_REPEATS):
print(repeat)
g = algo(bc.num_brain_nodes, bc.num_brain_edges_directed,
L=l, gamma=1, brain_size=BRAIN_SIZE)[0]
rs[key][l_ctr, repeat] = metrics.reciprocity(g)
rs['rand'] = np.nan * np.zeros((N_REPEATS,), dtype=float)
for repeat in range(N_REPEATS):
g_rand = random_directed_deg_seq(in_sequence=brain_in_deg,
out_sequence=brain_out_deg,
simplify=True)[0]
rs['rand'][repeat] = metrics.reciprocity(g_rand)
np.save(RECIPROCITY_FILE_NAME, np.array([rs]))
else:
print('Loading previous reciprocity calculations...')
rs = np.load(RECIPROCITY_FILE_NAME)[0]
print('Crunching numbers...')
# get reciprocal/nonreciprocal distance histograms for real brain
r_dists_brain, non_r_dists_brain = metrics.dists_by_reciprocity(a_brain,
d_brain)
# do the same for each of the four graphs
NBINS = 15
###############################
# Create graph/ compute metrics
###############################
# Extract brain graph
G_brain, _, _ = extract.brain_graph.binary_directed()
# Error check that keys all match (in_seq is in the same order as out_seq)
assert G_brain.in_degree().keys() == G_brain.out_degree().keys()
# Get in and out degree for each node and construct constrained random graph
brain_indeg = G_brain.in_degree().values()
brain_outdeg = G_brain.out_degree().values()
G, _, _ = binary_directed.random_directed_deg_seq(brain_indeg, brain_outdeg,
simplify=True)
# Get in & out degree of random directed graph (both should match brain)
indeg = np.array(G.in_degree().values())
outdeg = np.array(G.out_degree().values())
deg = indeg + outdeg
# Calculate proportion in degree
proportion_indeg = indeg / deg.astype(float)
###########
# Plotting
###########
# Create figure
fig = plt.figure(figsize=cf.FIGSIZE, facecolor=cf.FACECOLOR, tight_layout=True)
graphss = {key: [] for key in KEYS}
in_degree_brain = G_brain.in_degree().values()
out_degree_brain = G_brain.out_degree().values()
for g_ctr in range(N_GRAPH_SAMPLES):
Gs = {}
# create directed ER graph
Gs['er'] = nx.erdos_renyi_graph(bc.num_brain_nodes,
bc.p_brain_edge_directed,
directed=True)
# create directed degree-controlled random graph
Gs['rand'] = random_directed_deg_seq(in_sequence=in_degree_brain,
out_sequence=out_degree_brain,
simplify=True)[0]
# create target attraction graph
Gs['ta'] = ta(
N=bc.num_brain_nodes,
N_edges=bc.num_brain_edges_directed,
L=L,
brain_size=BRAIN_SIZE,
)[0]
# create source growth graph
Gs['sg'] = sg(
N=bc.num_brain_nodes,
N_edges=bc.num_brain_edges_directed,
L=L,
met_arr[graph_names.index('Mouse Connectome'), :, met_i] = bm(G_brain)
for rep in np.arange(repeats):
#TODO: recheck for correct brain model
# Pref. Growth, Prox. Attachment model
if 'Pref. Growth, Prox. Attachment' in graph_names:
G_Bio, _, _ = bio_dir.biophysical_reverse_outdegree(n_nodes, n_edges,
L=np.inf,
brain_size=brain_size)
met_arr[graph_names.index('Pref. Growth, Prox. Attachment'), rep, :] =\
calc_metrics(G_Bio, metrics)
# Random Configuration model (random with fixed degree sequence)
if 'Random' in graph_names:
G_CM, _, _ = bio_dir.random_directed_deg_seq(brain_indegree,
brain_outdegree,
simplify=True,
brain_size=brain_size)
met_arr[graph_names.index('Random'), rep, :] = calc_metrics(G_CM,
metrics)
# Scale-Free Price's model
if 'Scale-Free' in graph_names:
pass
##########################
# Save metrics
##########################
# Save original array and version averaged across repeats
fname = op.join(save_dir, 'directed_metrics')
np.save(fname + '_orig.npy', met_arr)
