import logging
import numpy as np
logger = logging.getLogger(__name__)
[docs]
def network_from_networkx(G):
r"""
Creates an OpenPNM Network from a undirected NetworkX graph object
Parameters
----------
G : networkx.classes.graph.Graph Object
The NetworkX graph. G should be undirected. The numbering of nodes
should be numeric (int's), zero-based and should not contain any
gaps, i.e. ``G.nodes() = [0,1,3,4,5]`` is not allowed and should be
mapped to ``G.nodes() = [0,1,2,3,4]``.
Returns
-------
network : dict
An OpenPNM network dictionary
Notes
-----
1. Each node in a NetworkX object (i.e. ``G``) can be assigned properties
using syntax like ``G.node[n]['diameter'] = 0.5`` where ``n`` is the
node number. There is no need to precede the property name with any
indication that it is pore data such as \'pore\_\'. OpenPNM will prepend
\'pore.\' to each property name.
2. Since \'pore.coords\' is so central to OpenPNM it should be specified
in the NetworkX object as \'coords\', and the [X, Y, Z] coordinates of
each node should be a 1x3 list.
3. Edges in a NetworkX object are accessed using the index numbers of the
two nodes it connects, such as ``G.adj[2][3]['length'] = 0.1``
indicating the edge that connects nodes 2 and 3. There is no need to
precede the property name with any indication that it is throat data such
as \'throat\_\'. OpenPNM will prepend \'throat.\' to each property name.
4. The \'throat.conns\' property is essential to OpenPNM, but this does NOT
need to be specified explicitly as a property in NetworkX. The
connectivity is embedded into the network representation and is extracted
by OpenPNM.
"""
import networkx as nx
from openpnm.network import Network
net = {}
# Ensure G is an undirected networkX graph with numerically numbered
# nodes for which numbering starts at 0 and does not contain any gaps
if not isinstance(G, nx.Graph): # pragma: no cover
raise Exception('Provided object is not a NetworkX graph.')
if nx.is_directed(G): # pragma: no cover
raise Exception('Provided graph is directed. Convert to undirected graph.')
if not all(isinstance(n, int) for n in G.nodes()): # pragma: no cover
raise Exception('Node numbering is not numeric. Convert to int.')
if min(G.nodes()) != 0: # pragma: no cover
raise Exception('Node numbering does not start at zero.')
if max(G.nodes()) + 1 != len(G.nodes()): # pragma: no cover
raise Exception('Node numbering contains gaps. Map nodes to remove gaps.')
# Parsing node data
Np = len(G)
net.update({'pore.all': np.ones((Np,), dtype=bool)})
for n, props in G.nodes(data=True):
for item in props.keys():
val = props[item]
dtype = type(val)
# Remove prepended pore. and pore_ if present
for b in ['pore.', 'pore_']:
item = item.replace(b, '')
# Create arrays for subsequent indexing, if not present already
if 'pore.'+item not in net.keys():
if dtype == str: # handle strings of arbitrary length
net['pore.'+item] = np.ndarray((Np,), dtype='object')
elif dtype is list:
dtype = type(val[0])
if dtype == str:
dtype = 'object'
cols = len(val)
net['pore.'+item] = np.ndarray((Np, cols), dtype=dtype)
else:
net['pore.'+item] = np.ndarray((Np,), dtype=dtype)
net['pore.'+item][n] = val
# Parsing edge data
# Deal with conns explicitly
try:
conns = list(G.edges) # NetworkX V2
except Exception: # pragma: no cover
conns = G.edges() # NetworkX V1
conns.sort()
# Add conns to Network
Nt = len(conns)
net.update({'throat.all': np.ones(Nt, dtype=bool)})
net.update({'throat.conns': np.array(conns)})
# Scan through each edge and extract all its properties
i = 0
for t in conns:
props = G[t[0]][t[1]]
for item in props:
val = props[item]
dtype = type(val)
# Remove prepended throat. and throat_ if present
for b in ['throat.', 'throat_']:
item = item.replace(b, '')
# Create arrays for subsequent indexing, if not present already
if 'throat.'+item not in net.keys():
if dtype == str:
net['throat.'+item] = np.ndarray((Nt,), dtype='object')
if dtype is list:
dtype = type(val[0])
if dtype == str:
dtype = 'object'
cols = len(val)
net['throat.'+item] = np.ndarray((Nt, cols),
dtype=dtype)
else:
net['throat.'+item] = np.ndarray((Nt,), dtype=dtype)
net['throat.'+item][i] = val
i += 1
network = Network()
network.update(net)
return network
[docs]
def network_to_networkx(network):
r"""
Write OpenPNM Network to a NetworkX object.
Parameters
----------
network : dict
The OpenPNM Network to be converted to a NetworkX object
Returns
-------
G : undirected graph object
A NetworkX object with all pore/throat properties attached to it
"""
import networkx as nx
from openpnm.network import Network
# Ensure network is an Network.
if not isinstance(network, Network): # pragma: no cover
raise Exception('Provided network is not an OpenPNM Network.')
G = nx.Graph()
# Extracting node list and connectivity matrix from Network
nodes = map(int, network.Ps)
conns = network['throat.conns']
# Explicitly add nodes and connectivity matrix
G.add_nodes_from(nodes)
G.add_edges_from(conns)
# Attach Network properties to G
for prop in network.props() + network.labels():
if 'pore.' in prop:
if len(network[prop].shape) > 1:
val = {i: list(network[prop][i]) for i in network.Ps}
else:
val = {i: network[prop][i] for i in network.Ps}
nx.set_node_attributes(G, name=prop[5:], values=val)
if 'throat.' in prop:
val = {tuple(conn): network[prop][i] for i, conn
in enumerate(conns)}
nx.set_edge_attributes(G, name=prop[7:], values=val)
return G
