def simple_test():
"""run simple test"""
with open("sbm_graph.pkl", "rb") as pickle_file:
graph = pickle.load(pickle_file)
all_results = run(graph)
plotting.plot_scan(all_results, use_plotly=False)
plotting.plot_scan(all_results, use_plotly=True, live=False)
with open("sbm_graph.gpickle", "rb") as pickle_file:
graph = pickle.load(pickle_file)
plotting.plot_communities(graph, all_results)
def simple_test():
"""run simple test"""
with open("sbm_graph.pkl", "rb") as pickle_file:
graph = pickle.load(pickle_file)
all_results = run(graph, n_time=50)
all_results = identify_optimal_scales(all_results, window=2, beta=0.1)
plot_optimal_scales(all_results, use_plotly=True)
plt.show()
with open("sbm_graph.gpickle", "rb") as pickle_file:
graph = pickle.load(pickle_file)
plotting.plot_communities(graph, all_results)
def cluster_signed_modularity(
graph,
times,
kappas,
kappa0=None,
n_louvain=10,
with_VI=True,
n_louvain_VI=10,
with_postprocessing=True,
with_ttprime=True,
n_workers=1,
tqdm_disable=False,
):
"""Cluster using signed modularity of Gomez, Jensen, Arenas PRE 2009.
Args:
graph (networkx): graph to cluster
times (list): markov times to consider
kappas (list): list of corresponding Kappa matrices
kappa0 (float): shift of kappa via the null model
n_louvain (int): number of Louvain evaluations
with_VI (bool): compute the variatio of information between Louvain runs
n_louvain_VI (int): number of randomly chosen Louvain run to estimate VI
with_postprocessing (bool): apply the final postprocessing step
with_ttprime (bool): compute the ttprime matrix
n_workers (int): number of workers for multiprocessing
tqdm_disable (bool): disable progress bars
"""
return run(
graph=None,
constructor=constructor(
nx.adjacency_matrix(graph, weight="weight"),
kappa0=kappa0,
kappas=kappas,
time_dict={time: i
for i, time in enumerate(times)},
row=np.array([e[0] for e in graph.edges]),
col=np.array([e[1] for e in graph.edges]),
),
times=times,
n_louvain=n_louvain,
with_VI=with_VI,
n_louvain_VI=n_louvain_VI,
with_postprocessing=with_postprocessing,
with_ttprime=with_ttprime,
n_workers=n_workers,
tqdm_disable=tqdm_disable,
)