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 __init__(self, data=None, name='', file=None, **attr):
Graph.__init__(self, data=data, name=name, **attr)
if file is None:
import sys
self.fh = sys.stdout
else:
self.fh = open(file, 'w')
def __init__(self,
environment=None,
channelType=None,
algorithms=(),
networkRouting=True,
propagation_type=2,
**kwargs):
Graph.__init__(self)
self._environment = environment or Environment()
# assert(isinstance(self.environment, Environment))
self.channelType = channelType or ChannelType(self._environment)
if isinstance(self.channelType, Doi):
doi = kwargs.pop('doi', 0)
print "In DOI %s" % doi
self.channelType.set_params(doi=doi)
self.channelType.environment = self._environment
self.propagation = propagation.PropagationModel(
propagation_type=propagation_type)
self.pos = {}
self.ori = {}
self.labels = {}
#self.star = star_graph
self.name = "WSN"
self._algorithms = ()
self.algorithms = algorithms or settings.ALGORITHMS
self.algorithmState = {'index': 0, 'step': 1, 'finished': False}
self.outbox = []
self.networkRouting = networkRouting
self.comm_range = kwargs.pop('commRange', None) or settings.COMM_RANGE
logger.info("Instance of Network has been initialized with %s (%s)" %
(self.propagation, self.comm_range))
def __init__(self, environment=None, channelType=None, algorithms=(),
networkRouting=True, propagation_type=2, **kwargs):
Graph.__init__(self)
self._environment = environment or Environment()
# assert(isinstance(self.environment, Environment))
self.channelType = channelType or ChannelType(self._environment)
if isinstance(self.channelType, Doi):
doi = kwargs.pop('doi', 0)
print "In DOI %s" %doi
self.channelType.set_params(doi=doi)
self.channelType.environment = self._environment
self.propagation = propagation.PropagationModel(propagation_type=propagation_type)
self.pos = {}
self.ori = {}
self.labels = {}
#self.star = star_graph
self.name = "WSN"
self._algorithms = ()
self.algorithms = algorithms or settings.ALGORITHMS
self.algorithmState = {'index': 0, 'step': 1, 'finished': False}
self.outbox = []
self.networkRouting = networkRouting
self.comm_range = kwargs.pop('commRange', None) or settings.COMM_RANGE
logger.info("Instance of Network has been initialized with %s (%s)" % (self.propagation, self.comm_range))
def __init__(self, data=None, name='', file=None, **attr):
Graph.__init__(self, data=data,name=name,**attr)
if file is None:
import sys
self.fh=sys.stdout
else:
self.fh=open(file,'w')
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 __init__(self, input_stream, record_filter=None, node_separator='=', max_nodes=sys.maxint, max_edges=sys.maxint):
"""
Parameters
----------
input_stream: iterator with a next(), should contain list of dicts (records)
record_filter: only use these keys from input_stream
node_separator: separtor between node key and value
max_nodes: stop inserting from stream after max_nodes in graph
max_edges: stop inserting from stream after max_edges in graph
Returns
-------
"""
# constructor fields
self.input_stream = input_stream
self.record_filter = record_filter
self.node_separator = node_separator
self.max_nodes = max_nodes
self.max_edges = max_edges
# stats
self.records_per_second = -1
self.records_processed = 0
# I don't think this is how to handle multiple-inheritance super init, but it seems to work
Graph.__init__(self)
Thread.__init__(self)
self.start()
def __init__(self, data=None, **attr):
Graph.__init__(self, **attr)
if data is not None:
convert.to_networkx_graph(data, create_using=self)
# check if it is a tree.
if not (G.order() == G.size() + 1
and nx.number_connected_components(G) == 1):
raise NetworkXError("Data %s is not a tree" % data)
# load graph attributes (must be after convert)
self.graph.update(attr)
self.edge = self.adj
def __init__(self, environment=None, channelType=None, algorithms=(), networkRouting=True, **kwargs):
self._environment = environment or Environment()
# assert(isinstance(self.environment, Environment))
self.channelType = channelType or ChannelType(self._environment)
self.channelType.environment = self._environment
self.pos = {}
self.ori = {}
self.labels = {}
Graph.__init__(self)
self._algorithms = ()
self.algorithms = algorithms or settings.ALGORITHMS
self.algorithmState = {"index": 0, "step": 1, "finished": False}
self.outbox = []
self.networkRouting = networkRouting
logger.info("Instance of Network has been initialized.")
def __init__(self, environment=None, channelType=None, algorithms=(),
networkRouting=True, **kwargs):
self._environment = environment or Environment()
# assert(isinstance(self.environment, Environment))
self.channelType = channelType or ChannelType(self._environment)
self.channelType.environment = self._environment
self.pos = {}
self.ori = {}
self.labels = {}
Graph.__init__(self)
self._algorithms = ()
self.algorithms = algorithms or settings.ALGORITHMS
self.algorithmState = {'index': 0, 'step': 1, 'finished': False}
self.outbox = []
self.networkRouting = networkRouting
logger.info("Instance of Network has been initialized.")
def __init__(self,sif,labels):
_Graph.__init__(self)
self.labels = {}
with open(labels,'r') as fin:
for f in fin.readlines():
[oid,cell] = f.split('\t')
cell = cell.split(' ')[0]
self.labels[oid] = cell
with open(sif,'r') as fin:
for f in fin.readlines():
[pre,post] = f.split(' pd ')
post = post.split('\n')[0]
pre = self.labels[pre]
post = self.labels[post]
if pre == post: continue
self.add_edge(pre,post)
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 __init__(self, storage, species, aspect=Aspects.BP):
GOGraphBase.__init__(self, storage, species, aspect)
Graph.__init__(self)
def __init__(self, data=None, **keywords):
"""
2013.1.3
wrapper around networkx.Graph
"""
Graph.__init__(self, data=None, **keywords)
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, storage, species, aspect=Aspects.BP):
GOGraphBase.__init__(self, storage, species, aspect)
Graph.__init__(self)
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