def from_networkx(G):
"""
Convert a NetworkX graph into a Zen graph object.
In creating the object, the NetworkX node object and node/edge data will be copied over (a shallow copy).
**Returns**:
The return type depends on the input type.
* :py:class:`zen.Graph` if the input graph was a :py:class:`networkx.Graph`.
* :py:class:`zen.DiGraph` if the input graph was a :py:class:`networkx.DiGraph`.
"""
Gdest = None
if type(G) == networkx.DiGraph:
Gdest = DiGraph()
elif type(G) == networkx.Graph:
Gdest = Graph()
else:
raise Exception('Unable to convert graph object type %s' %
str(type(G)))
# add nodes
for n, nd in G.nodes_iter(data=True):
Gdest.add_node(n, nd)
# add edges
for x, y, ed in G.edges_iter(data=True):
Gdest.add_edge(x, y, ed)
return Gdest
def barabasi_albert(n, m, **kwargs):
"""
Generate a random graph using the Barabasi-Albert preferential attachment model.
**Args**:
* ``n`` (int): the number of nodes to add to the graph
* ``m`` (int): the number of edges a new node will add to the graph
**KwArgs**:
* ``directed [=False]`` (boolean): whether to build the graph directed. If ``True``, then the ``m`` edges created
by a node upon its creation are instantiated as out-edges. All others are in-edges to that node.
* ``seed [=-1]`` (int): a seed for the random number generator
* ``graph [=None]`` (:py:class:`zen.Graph` or :py:class:`zen.DiGraph`): this is the actual graph instance to populate. It must be
empty and its directionality must agree with the value of ``directed``.
**Returns**:
:py:class:`zen.Graph` or :py:class:`zen.DiGraph`. The graph generated. If ``directed = True``, then a :py:class:`DiGraph` will be returned.
.. note::
Source: A. L. Barabasi and R. Albert "Emergence of scaling in random networks", Science 286, pp 509-512, 1999.
"""
seed = kwargs.pop('seed', None)
directed = kwargs.pop('directed', False)
graph = kwargs.pop('graph', None)
if graph is not None:
if len(graph) > 0:
raise ZenException, 'the graph must be empty, if provided'
if graph.is_directed() != directed:
raise ZenException, 'graph and directed arguments must agree'
else:
if directed:
graph = DiGraph()
else:
graph = Graph()
if len(kwargs) > 0:
raise ZenException, 'Unknown arguments: %s' % ', '.join(kwargs.keys())
if seed is None:
seed = -1
if not directed:
return __inner_barabasi_albert_udir(n, m, seed, graph)
else:
return __inner_barabasi_albert_dir(n, m, seed, graph)
def erdos_renyi(n, p, **kwargs):
"""
Generate an Erdos-Renyi graph.
**Args**:
* ``num_nodes`` (int): the number of nodes to populate the graph with.
* ``p`` (0 <= float <= 1): the probability p given to each edge's existence.
**KwArgs**:
* ``directed [=False]`` (boolean): indicates whether the network generated is directed.
* ``self_loops [=False]`` (boolean): indicates whether self-loops are permitted in the generated graph.
* ``seed [=-1]`` (int): the seed provided to the random generator used to drive the graph construction.
* ``graph [=None]`` (:py:class:`zen.Graph` or :py:class:`zen.DiGraph`): this is the actual graph instance to populate. It must be
empty and its directionality must agree with the value of ``directed``.
"""
directed = kwargs.pop('directed', False)
self_loops = kwargs.pop('self_loops', False)
seed = kwargs.pop('seed', None)
graph = kwargs.pop('graph', None)
if graph is not None:
if len(graph) > 0:
raise ZenException, 'the graph must be empty, if provided'
if graph.is_directed() != directed:
raise ZenException, 'graph and directed arguments must agree'
else:
if directed:
graph = DiGraph()
else:
graph = Graph()
if len(kwargs) > 0:
raise ZenException, 'Unknown arguments: %s' % ', '.join(kwargs.keys())
if seed is None:
seed = -1
if directed:
return __erdos_renyi_directed(n, p, self_loops, seed, graph)
else:
return __erdos_renyi_undirected(n, p, self_loops, seed, graph)
def build_graph(graph_tree, weight_fxn):
# What kind of graph is being built?
is_bipartite = bool('bipartite' in graph_tree and graph_tree['bipartite'])
is_directed = bool('directed' in graph_tree and graph_tree['directed'])
if is_bipartite:
G = BipartiteGraph()
elif is_directed:
G = DiGraph()
else:
G = Graph()
# Build the nodes
if 'node' in graph_tree:
# get the list of nodes
nodes = graph_tree['node']
# ensure the node-list is a list (needed if there's only one node)
if not isinstance(nodes, list):
nodes = [nodes]
# Build each node and add to the graph
for node in nodes:
# Does the node have an id?
has_id = True
has_valid_id = True
if 'id' not in node:
has_id = False
has_valid_id = False
# We can only use positive integer node ids as graph idx
# If that's not the case, treat it like any other attribute
elif not isinstance(node['id'], int) or node['id'] < 0:
has_valid_id = False
# Got a valid node id
node_idx = node['id']
# For bipartite graphs determine which node set this belongs to
if is_bipartite:
is_in_U = node['isInU']
# collect and verify all the node properties
standard_keys = set(['id', 'name', 'zenData'])
node_data = {}
node_obj = None
zen_data = None
for key, val in list(node.items()):
if key == 'name':
node_obj = val
# give preference to 'name' as source of node_obj
elif key == 'label' and node_obj is None:
node_obj = val
elif key == 'zenData':
zen_data = val
# node_data is dict of all other attributes
else:
node_data[key] = val
# _set_ to node_data else _append_
if zen_data is not None:
if len(node_data) == 0:
node_data = zen_data
else:
node_data['zenData'] = zen_data
elif len(node_data) == 0:
node_data = None
# make sure that the node object is hashable otherwise put it
if not isinstance(node_obj, str) and node_obj is not None:
if not isinstance(node_obj, Hashable): \
if not isinstance(node_obj, Iterable):
node_obj = None
else:
node_obj = tuple(node_obj)
# For bipartite graph, this insertion method does not guarantee
# that indices will be unchanged after a read-write cycle
if is_bipartite:
G.add_node_by_class(is_in_U, node_obj, node_data)
elif has_id and has_valid_id:
if is_directed:
G.add_node_x(node_idx, G.edge_list_capacity,
G.edge_list_capacity, node_obj, node_data)
else:
G.add_node_x(node_idx, G.edge_list_capacity, node_obj,
node_data)
else:
if G.is_directed:
G.add_node(nobj=node_obj, data=node_data)
else:
G.add_node(nobj=node_obj, data=node_data)
# add edges
if 'edge' in graph_tree:
# ensure edge list is a list (needed if there is only one edge)
edges = graph_tree['edge']
if not isinstance(edges, list):
edges = [edges]
# iterate over the edges, add each one to the graph
for edge in edges:
# make sure source and target are specified
source = None
target = None
if 'source' not in edge:
raise ZenException('Edge is missing the source attribute '
'(edge = %s)' % str(edge))
if 'target' not in edge:
raise ZenException('Edge is missing the target attribute '
'(edge = %s)' % str(edge))
weight = 1
edge_idx = None
zen_data = None
edge_data = {}
for key, val in list(edge.items()):
if key == 'id':
edge_idx = val
if type(val) != int:
raise ZenException('Edge id attribute must be a '
'positive integer (edge = %s)' %
str(edge))
elif key == 'source':
source = val
if type(val) != int or val < 0:
raise ZenException('Edge source attribute must be a '
'positive integer (edge = %s)' %
str(edge))
elif key == 'target':
target = val
if type(val) != int or val < 0:
raise ZenException('Edge target attribute must be a '
'positive integer (edge = %s)' %
str(edge))
elif key == 'weight':
weight = float(val)
elif key == 'zenData':
zen_data = val
# edge_data is dict of all other attributes
else:
edge_data[key] = val
# give precedence to a weight-getting function if provided
if weight_fxn != None:
weight = weight_fxn(edge)
# if zenData is only other attribute aside from those handled above
# _set_ to edge_data else _append_
if zen_data is not None:
if len(edge_data) == 0:
edge_data = zen_data
else:
edge_data['zenData'] = zen_data
elif len(edge_data) == 0:
edge_data = None
if edge_idx != None:
G.add_edge_x(edge_idx, source, target, edge_data, weight)
else:
G.add_edge_(source, target, edge_data, weight)
return G
def duplication_divergence_iky(n, s, **kwargs):
"""
Generate a random graph using the duplication-divergence model proposed by Ispolatov, Krapivski, and Yuryev (2008).
**Args**:
* ``n`` (int): the target size of the network.
* ``s`` (float): the probability that a link connected to a newly duplicated node will exist
**KwArgs**:
* ``directed [=False]`` (boolean): whether to build the graph directed. If ``True``, then the ``m`` edges created
by a node upon its creation are instantiated as out-edges. All others are in-edges to that node.
* ``seed [=-1]`` (int): a seed for the random number generator
* ``graph [=None]`` (:py:class:`zen.Graph` or :py:class:`zen.DiGraph`): this is the actual graph instance to populate. It must be
empty and its directionality must agree with the value of ``directed``.
**Returns**:
:py:class:`zen.Graph` or :py:class:`zen.DiGraph`. The graph generated. If ``directed = True``, then a :py:class:`DiGraph` will be returned.
.. note::
Source: I. Ispolatov, P. L. Krapivski, and A. Yuryev "Duplication-divergence model of protein interaction network", ??, 2008.
"""
seed = kwargs.pop('seed', None)
directed = kwargs.pop('directed', False)
graph = kwargs.pop('graph', None)
if graph is not None:
if len(graph) > 0:
raise ZenException, 'the graph must be empty, if provided'
if graph.is_directed() != directed:
raise ZenException, 'graph and directed arguments must agree'
if len(kwargs) > 0:
raise ZenException, 'Unknown arguments: %s' % ', '.join(kwargs.keys())
if seed is None:
seed = -1
# initialize the random number generator
if seed >= 0:
random.seed(seed)
if type(n) != int:
raise ZenException, 'Parameter n must be an integer'
if type(s) != float and type(s) != int and type(s) != double:
print type(s)
raise ZenException, 'Parameter s must be a float, double, or an int'
G = graph
if graph is None:
if directed:
G = DiGraph()
else:
G = Graph()
# initialize the graph with two connected nodes
G.add_edge(0, 1)
# build the rest of the graph
i = 2
while i < n:
# pick an existing node to copy
cn_seed = random.randint(0, 100000)
u = choose_node(G, seed=cn_seed)
#####
# create the partial copy
G.add_node(i)
# copy edges
if not directed:
for w in G.neighbors(u):
if random.random() <= s:
G.add_edge(i, w)
else:
for w in G.in_neighbors(u):
if random.random() <= s:
G.add_edge(w, i)
for w in G.out_neighbors(u):
if random.random() <= s:
G.add_edge(i, w)
# if the node doesn't have any connections, then ditch it
if G.degree(i) == 0:
G.rm_node(i)
else:
i += 1
# done!
return G
if random.random() <= s:
G.add_edge(w, i)
for w in G.out_neighbors(u):
if random.random() <= s:
G.add_edge(i, w)
# if the node doesn't have any connections, then ditch it
if G.degree(i) == 0:
G.rm_node(i)
else:
i += 1
# done!
return G
####
# TODO: Implement duplication_divergence_wagner
###
# TODO: Implement duplication_mutation
if __name__ == '__main__':
from zen.drawing import UbigraphRenderer
G = DiGraph()
ur = UbigraphRenderer('http://localhost:20738/RPC2',
event_delay=1,
graph=G)
G = duplication_divergence_iky(10, 0.4, directed=True, graph=G)
def build_graph(graph_data, weight_fxn):
is_directed = False
if 'directed' in graph_data:
is_directed = graph_data['directed'] == 1
# TODO detect if graphs are bipartite and support that
G = None
if is_directed:
G = DiGraph()
else:
G = Graph()
# TODO: Load graph attributes
# add nodes
if 'node' in graph_data:
nodes = graph_data['node']
if type(nodes) != list:
raise ZenException, 'The node attribute of a graph must be a list'
for node in nodes:
# node must have an 'id'
if 'id' not in node:
raise ZenException, 'Node is missing the id attribute (node = %s)' % str(
node)
node_idx = node['id']
# collect and verify all the node properties
standard_keys = set(['id', 'name', 'zenData'])
node_data = {}
node_obj = None
zen_data = None
for key, val in node.items():
if key == 'id':
node_idx = val
if type(val) != int or val < 0:
raise ZenException, 'Node id attribute must be a positive integer (node = %s)' % str(
node)
elif key == 'name':
node_obj = val
if type(val
) != str: # enforce types on standard attributes
raise ZenException, 'Node name attribute must be a string (node = %s)' % str(
node)
elif key == 'label':
if node_obj is None: # give preference to 'name' as source of node_obj
node_obj = val
if type(val) != str:
raise ZenException, 'Node label attribute must be a string (node = %s)' % str(
node)
elif key == 'zenData':
zen_data = val
else:
node_data[
key] = val # node_data is dict of all other attributes
# if zenData is only other attribute aside from those handled above _set_ to node_data else _append_
if zen_data is not None:
if len(node_data) == 0:
node_data = zen_data
else:
node_data['zenData'] = zen_data
elif len(node_data) == 0:
node_data = None
if is_directed:
G.add_node_x(node_idx, G.edge_list_capacity,
G.edge_list_capacity, node_obj, node_data)
else:
G.add_node_x(node_idx, G.edge_list_capacity, node_obj,
node_data)
# add edges
if 'edge' in graph_data:
edges = graph_data['edge']
if type(edges) != list:
raise ZenException, 'The edge attibute of a graph must be a list'
for edge in edges:
# make sure source and target are specified
source = None
target = None
if 'source' not in edge:
raise ZenException, 'Edge is missing the source attribute (edge = %s)' % str(
edge)
if 'target' not in edge:
raise ZenException, 'Edge is missing the target attribute (edge = %s)' % str(
edge)
weight = 1
edge_idx = None
zen_data = None
edge_data = {}
for key, val in edge.items():
if key == 'id':
edge_idx = val
if type(val) != int:
raise ZenException, 'Edge id attribute must be a positive integer (edge = %s)' % str(
edge)
elif key == 'source':
source = val
if type(val) != int or val < 0:
raise ZenException, 'Edge source attribute must be a positive integer (edge = %s)' % str(
edge)
elif key == 'target':
target = val
if type(val) != int or val < 0:
raise ZenException, 'Edge target attribute must be a positive integer (edge = %s)' % str(
edge)
elif key == 'weight':
weight = float(val)
elif key == 'zenData':
zen_data = val
else:
edge_data[
key] = val # edge_data is dict of all other attributes
# give precedence to a weight-getting function if provided
if weight_fxn != None:
weight = weight_fxn(edge)
# if zenData is only other attribute aside from those handled above _set_ to edge_data else _append_
if zen_data is not None:
if len(edge_data) == 0:
edge_data = zen_data
else:
edge_data['zenData'] = zen_data
elif len(edge_data) == 0:
edge_data = None
if edge_idx != None:
G.add_edge_x(edge_idx, source, target, edge_data, weight)
else:
G.add_edge_(source, target, edge_data, weight)
return G
def read_str(sbuffer, **kwargs):
"""
Read graph data from the ascii string in the binary edge list format.
**Args**:
``sbuffer`` is the string from which the network data will be read.
**KwArgs**:
* ``node_obj_fxn [= str]``: unlike the default definition, this function accepts integers and returns the node object
* ``directed [= False]`` (boolean): indicates whether the data is read as directed
* ``ignore_duplicate_edges [= False]`` (boolean): applies only when loading an undirected graph. If True, then a check will be made to ensure that
no duplicate edges are attempted to be added (in case the underlying graph was originally directed). Checking incurs a small
performance cost due to the check.
**Returns**:
:py:class:`zen.Graph` or :py:class:`zen.DiGraph`. The graph read from the input string. The ``directed`` parameter decides
whether a directed or undirected graph is constructed.
"""
# handle the keyword arguments
node_obj_fxn = kwargs.pop('node_obj_fxn', str)
directed = kwargs.pop('directed', False)
check_for_duplicates = kwargs.pop('ignore_duplicate_edges', False)
if len(kwargs) > 0:
raise ZenException, 'Unknown keyword arguments: %s' % ', '.join(
kwargs.keys())
if check_for_duplicates and directed:
raise ZenException, 'ignore_duplicate_edges can only be set when directed = False'
# build the graph
G = None
if directed == True:
G = DiGraph()
elif directed == False:
G = Graph()
else:
raise ZenException, 'directed must be either True or False.'
#####
# convert the string into a bitvector
bv = BitVector(size=len(sbuffer) * 8)
offset = 0
for c in sbuffer:
v = ord(c)
dec2bv(v, bv, offset, 8)
offset += 8
#####
# read the header
offset = 0
# read the version
version = bv2dec(bv, offset, VERSION_LEN)
offset += VERSION_LEN
if version != 1:
raise Exception, 'Invalid file format or version number'
# read the num of indexes
last_idx = bv2dec(bv, offset, NUM_INDEX_LEN)
idx_size = int(math.ceil(math.log(last_idx + 1, 2)))
offset += NUM_INDEX_LEN
idx2node = [None] * (last_idx + 1)
# build all nodes right now
if node_obj_fxn is not None:
for x in xrange(last_idx + 1):
n = node_obj_fxn(x)
G.add_node(n)
else:
G.add_nodes(last_idx + 1)
# read the number of edges
num_edges = bv2dec(bv, offset, NUM_EDGES_LEN)
offset += NUM_EDGES_LEN
#####
# Read the content: every edge
if directed:
for ei in xrange(num_edges):
idx1 = bv2dec(bv, offset, idx_size)
offset += idx_size
idx2 = bv2dec(bv, offset, idx_size)
offset += idx_size
G.add_edge_(idx1, idx2)
else:
for ei in xrange(num_edges):
idx1 = bv2dec(bv, offset, idx_size)
offset += idx_size
idx2 = bv2dec(bv, offset, idx_size)
offset += idx_size
if check_for_duplicates and G.has_edge_(idx1, idx2):
continue
G.add_edge_(idx1, idx2)
# done!
return G
def local_attachment(n, m, r, **kwargs):
"""
Generate a random graph using the local attachment model.
**Args**:
* ``n`` (int): the number of nodes to add to the graph
* ``m`` (int): the number of edges a new node will add to the graph
* ``r`` (int): the number of edges (of the ``m``) that a node will add to uniformly selected random nodes.
All others will be added to neighbors of the ``r`` selected nodes.
**KwArgs**:
* ``seed [=-1]`` (int): a seed for the random number generator
* ``graph [=None]`` (:py:class:`zen.DiGraph`): the graph that will be populated. If the graph is ``None``,
then a new graph will be created.
**Returns**:
:py:class:`zen.DiGraph`. The graph generated.
.. note::
Source: M. O. Jackson and B. O. Rogers "Meeting strangers and friends of friends: How random are social networks?" The American Economic Review, 2007.
"""
seed = kwargs.pop('seed', None)
graph = kwargs.pop('graph', None)
if graph is not None and not graph.is_directed():
raise ZenException, 'The graph provided must be directed'
if graph is not None and len(graph) > 0:
raise ZenException, 'The graph provided is not empty'
if len(kwargs) > 0:
raise ZenException, 'Unknown arguments: %s' % ', '.join(kwargs.keys())
if type(r) != int:
raise ZenException, 'r must be an integer'
elif r < 1:
raise ZenException, 'r must be 1 or larger'
if seed is None:
seed = -1
if seed >= 0:
random.seed(seed)
#####
# build the initial graph
G = graph
if G is None:
G = DiGraph()
# populate with nodes
for i in range(m + 1):
G.add_node(i)
# according to Jackson's paper, all initial nodes have m neighbors.
for i in range(m + 1):
for j in range(m + 1):
if j != i:
G.add_edge(j, i)
######
# Build the rest of the graph
node_list = list(range(m + 1))
for i in range(m + 1, n):
G.add_node(i)
# pick random neighbors (the parents)
parents = random.sample(node_list, r)
# pick neighbors from the parents' neighborhoods
potentials = set()
for n in parents:
potentials.update(G.out_neighbors(n))
potentials.difference_update(parents)
nsize = min([m - r, len(potentials)])
neighbors = random.sample(potentials, nsize)
# connect
for v in (parents + neighbors):
G.add_edge(i, v)
node_list.append(i)
# done
return G