def add_layer(self, layer, **attr):
if self.num_nodes_in_layers is 0:
self.list_of_layers=[layer]
else:
self.list_of_layers.append(layer)
self.num_layers = len(self.list_of_layers)
self.num_nodes_in_layers = self.list_of_layers[0].number_of_nodes()
for i,j in layer.edges():
self.intra_layer_edges.append((
i+(len(self.list_of_layers)-1)*layer.number_of_nodes(),
j+(len(self.list_of_layers)-1)*layer.number_of_nodes()))
try:
Graph.__init__(self,
Graph(disjoint_union_all(self.list_of_layers),
**attr))
except multinetxError:
raise multinetxError("Multiplex cannot inherit Graph properly")
## Check if all graphs have the same number of nodes
for lg in self.list_of_layers:
try:
assert(lg.number_of_nodes() == self.num_nodes_in_layers)
except AssertionError:
raise multinetxError("Graph at layer does not have the same number of nodes")
def add_layer(self, layer, **attr):
if self.num_nodes_in_layers is 0:
self.list_of_layers = [layer]
else:
self.list_of_layers.append(layer)
self.num_layers = len(self.list_of_layers)
self.num_nodes_in_layers = self.list_of_layers[0].number_of_nodes()
for i, j in layer.edges():
self.intra_layer_edges.append(
(i + (len(self.list_of_layers) - 1) * layer.number_of_nodes(),
j + (len(self.list_of_layers) - 1) * layer.number_of_nodes()))
try:
Graph.__init__(
self, Graph(disjoint_union_all(self.list_of_layers), **attr))
except multinetxError:
raise multinetxError("Multiplex cannot inherit Graph properly")
## Check if all graphs have the same number of nodes
for lg in self.list_of_layers:
try:
assert (lg.number_of_nodes() == self.num_nodes_in_layers)
except AssertionError:
raise multinetxError(
"Graph at layer does not have the same number of nodes")
def add_layer(self, layer, **attr):
if self.num_nodes is 0:
self.list_of_layers = [layer]
else:
self.list_of_layers.append(layer)
self.num_nodes_in_layers.append(layer.number_of_nodes())
self.num_layers = len(self.list_of_layers)
for i, j in layer.edges():
self.intra_layer_edges.append(
(i + (len(self.list_of_layers) - 1) * layer.number_of_nodes(),
j + (len(self.list_of_layers) - 1) * layer.number_of_nodes()))
try:
Graph.__init__(
self, Graph(disjoint_union_all(self.list_of_layers),
**attr))
except multinetxError:
raise multinetxError("Multiplex cannot inherit Graph properly")
def layers_interconnect(self, inter_adjacency_matrix=None):
"""Parameters:
-----------
Examples:
---------
"""
# Make a zero lil matrix for inter_adjacency_matrix
if inter_adjacency_matrix is None:
inter_adjacency_matrix = lil_matrix(
zeros((self.num_nodes, self.num_nodes)))
# Check if the matrix inter_adjacency_matrix is lil
try:
assert (inter_adjacency_matrix.format == "lil")
except AssertionError:
raise multinetxError("interconnecting_adjacency_matrix\
is not scipy.sparse.lil")
for i, row in enumerate(inter_adjacency_matrix.rows):
for pos, j in enumerate(row):
if i > j:
self.inter_layer_edges.append((i, j))
self.add_edges_from(self.inter_layer_edges)
def layers_interconnect(self, inter_adjacency_matrix=None):
"""Parameters:
-----------
Examples:
---------
"""
## Make a zero lil matrix for inter_adjacency_matrix
if inter_adjacency_matrix is None:
inter_adjacency_matrix = \
lil_matrix(zeros(
(self.num_nodes_in_layers*self.num_layers,
self.num_nodes_in_layers*self.num_layers)))
## Check if the matrix inter_adjacency_matrix is lil
try:
assert(inter_adjacency_matrix.format == "lil")
except AssertionError:
raise multinetxError("interconnecting_adjacency_matrix "\
"is not scipy.sparse.lil")
for i,row in enumerate(inter_adjacency_matrix.rows):
for pos,j in enumerate(row):
if i>j:
self.inter_layer_edges.append((i,j))
self.add_edges_from(self.inter_layer_edges)
def __init__(self,
list_of_layers=None,
inter_adjacency_matrix=None,
**attr):
"""Constructor of a MultilayerGraph.
It creates a symmetric (undirected) MultilayerGraph object
inheriting methods from networkx.Graph
Parameters:
-----------
list_of_layers : Python list of networkx.Graph objects
inter_adjacency_matrix : a lil sparse matrix (NxN) with zero
diagonal elements and off-diagonal
block elements defined by the
inter-connectivity architecture.
Return: a MultilayerGraph object
Examples:
---------
import multinetx as mx
N = 10
g1 = mx.erdos_renyi_graph(N,0.07,seed=218)
g2 = mx.erdos_renyi_graph(N,0.07,seed=211)
g3 = mx.erdos_renyi_graph(N,0.07,seed=211)
adj_block = mx.lil_matrix(np.zeros((N*3,N*3)))
adj_block[0: N, N:2*N] = np.identity(N) # L_12
adj_block[0: N,2*N:3*N] = np.identity(N) # L_13
#adj_block[N:2*N,2*N:3*N] = np.identity(N) # L_23
adj_block += adj_block.T
mg = mx.MultilayerGraph(list_of_layers=[g1,g2,g3],
inter_adjacency_matrix=adj_block)
mg.set_edges_weights(inter_layer_edges_weight=4)
mg.set_intra_edges_weights(layer=0,weight=1)
mg.set_intra_edges_weights(layer=1,weight=2)
mg.set_intra_edges_weights(layer=2,weight=3)
"""
## Give an empty graph in the list_of_layers
if list_of_layers is None:
self.list_of_layers = [Graph()]
else:
self.list_of_layers = list_of_layers
## Number of layers
self.num_layers = len(self.list_of_layers)
## Number of nodes in each layer
self.num_nodes_in_layers = self.list_of_layers[0].number_of_nodes()
## Create the MultilayerGraph without inter-layer links.
try:
Graph.__init__(self,
Graph(disjoint_union_all(self.list_of_layers),
**attr))
except multinetxError:
raise multinetxError("Multiplex cannot inherit Graph properly")
## Check if all graphs have the same number of nodes
for lg in self.list_of_layers:
try:
assert(lg.number_of_nodes() == self.num_nodes_in_layers)
except AssertionError:
raise multinetxError("Graph at layer does not have")
## Make a zero lil matrix for inter_adjacency_matrix
if inter_adjacency_matrix is None:
inter_adjacency_matrix = \
lil_matrix(zeros(
(self.num_nodes_in_layers*self.num_layers,
self.num_nodes_in_layers*self.num_layers)))
## Check if the matrix inter_adjacency_matrix is lil
try:
assert(inter_adjacency_matrix.format == "lil")
except AssertionError:
raise multinetxError("interconnecting_adjacency_matrix "\
"is not scipy.sparse.lil")
## Lists for intra-layer and inter-layer edges
if list_of_layers is None:
self.intra_layer_edges = []
else:
self.intra_layer_edges = self.edges()
self.inter_layer_edges = []
## Inter-layer connection
self.layers_interconnect(inter_adjacency_matrix)
## MultiNetX name
self.name = "multilayer"
for layer in self.list_of_layers:
self.name += "_" + layer.name
def __init__(self,
list_of_layers=None,
inter_adjacency_matrix=None,
**attr):
"""Constructor of a MultilayerGraph.
It creates a symmetric (undirected) MultilayerGraph object
inheriting methods from networkx.Graph
Parameters:
-----------
list_of_layers : Python list of networkx.Graph objects
inter_adjacency_matrix : a lil sparse matrix (NxN) with zero
diagonal elements and off-diagonal
block elements defined by the
inter-connectivity architecture.
Return: a MultilayerGraph object
Examples:
---------
import multinetx as mx
N = 10
g1 = mx.erdos_renyi_graph(N,0.07,seed=218)
g2 = mx.erdos_renyi_graph(N,0.07,seed=211)
g3 = mx.erdos_renyi_graph(N,0.07,seed=211)
adj_block = mx.lil_matrix(np.zeros((N*3,N*3)))
adj_block[0: N, N:2*N] = np.identity(N) # L_12
adj_block[0: N,2*N:3*N] = np.identity(N) # L_13
#adj_block[N:2*N,2*N:3*N] = np.identity(N) # L_23
adj_block += adj_block.T
mg = mx.MultilayerGraph(list_of_layers=[g1,g2,g3],
inter_adjacency_matrix=adj_block)
mg.set_edges_weights(inter_layer_edges_weight=4)
mg.set_intra_edges_weights(layer=0,weight=1)
mg.set_intra_edges_weights(layer=1,weight=2)
mg.set_intra_edges_weights(layer=2,weight=3)
"""
## Give an empty graph in the list_of_layers
if list_of_layers is None:
self.list_of_layers = [Graph()]
else:
self.list_of_layers = list_of_layers
## Number of layers
self.num_layers = len(self.list_of_layers)
## Number of nodes in each layer
self.num_nodes_in_layers = self.list_of_layers[0].number_of_nodes()
## Create the MultilayerGraph without inter-layer links.
try:
Graph.__init__(
self, Graph(disjoint_union_all(self.list_of_layers), **attr))
except multinetxError:
raise multinetxError("Multiplex cannot inherit Graph properly")
## Check if all graphs have the same number of nodes
for lg in self.list_of_layers:
try:
assert (lg.number_of_nodes() == self.num_nodes_in_layers)
except AssertionError:
raise multinetxError("Graph at layer does not have")
## Make a zero lil matrix for inter_adjacency_matrix
if inter_adjacency_matrix is None:
inter_adjacency_matrix = \
lil_matrix(zeros(
(self.num_nodes_in_layers*self.num_layers,
self.num_nodes_in_layers*self.num_layers)))
## Check if the matrix inter_adjacency_matrix is lil
try:
assert (inter_adjacency_matrix.format == "lil")
except AssertionError:
raise multinetxError("interconnecting_adjacency_matrix "\
"is not scipy.sparse.lil")
## Lists for intra-layer and inter-layer edges
if list_of_layers is None:
self.intra_layer_edges = []
else:
self.intra_layer_edges = self.edges()
self.inter_layer_edges = []
## Inter-layer connection
self.layers_interconnect(inter_adjacency_matrix)
## MultiNetX name
self.name = "multilayer"
for layer in self.list_of_layers:
self.name += "_" + layer.name