""" ***** Pydot ***** Import and export NetworkX graphs in Graphviz dot format using pydot. Either this module or nx_pygraphviz can be used to interface with graphviz. See Also -------- Pydot: http://www.dkbza.org/pydot.html Graphviz: http://www.research.att.com/sw/tools/graphviz/ DOT Language: http://www.graphviz.org/doc/info/lang.html """ __author__ = """Aric Hagberg (hagberg@lanl.gov)""" # Copyright (C) 2004-2008 by # Aric Hagberg # Dan Schult # Pieter Swart # All rights reserved. # BSD license. __all__ = ['write_dot', 'read_dot', 'graphviz_layout', 'pydot_layout', 'to_pydot', 'from_pydot'] import sys from networkx.utils import _get_fh import networkx as nx def write_dot(G,path): """Write NetworkX graph G to Graphviz dot format on path. Path can be a string or a file handle. """ try: import pydot except ImportError: raise ImportError, \ "write_dot() requires pydot http://dkbza.org/pydot.html/" fh=_get_fh(path,'w') P=to_pydot(G) fh.write(P.to_string()) fh.flush() # might be a user filehandle so leave open (but flush) return def read_dot(path): """Return a NetworkX Graph or DiGraph from a dot file on path. Path can be a string or a file handle. """ try: import pydot except ImportError: raise ImportError, \ "read_dot() requires pydot http://dkbza.org/pydot.html/" fh=_get_fh(path,'r') data=fh.read() P=pydot.graph_from_dot_data(data) return from_pydot(P) def from_pydot(P): """Return a NetworkX graph from a Pydot graph. Parameters ---------- P : Pydot graph A graph created with Pydot Examples -------- >>> K5=nx.complete_graph(5) >>> A=nx.to_pydot(K5) >>> G=nx.from_pydot(A) """ if P.get_strict(None): # pydot bug: get_strict() shouldn't take argument multiedges=False else: multiedges=True if P.get_type()=='graph': # undirected if multiedges: create_using=nx.MultiGraph() else: create_using=nx.Graph() else: if multiedges: create_using=nx.MultiDiGraph() else: create_using=nx.DiGraph() # assign defaults N=nx.empty_graph(0,create_using) N.name=P.get_name() node_attr={} # add nodes, attributes to N.node_attr for p in P.get_node_list(): n=p.get_name().strip('"') if n in ('node','graph','edge'): continue N.add_node(n,**p.get_attributes()) # add edges for e in P.get_edge_list(): u=e.get_source().strip('"') v=e.get_destination().strip('"') attr=e.get_attributes() N.add_edge(u,v,**attr) # add default attributes for graph, nodes, edges N.graph['graph']=P.get_attributes() # get atributes not working for these? # get_node_defaults() N.graph['node']={} if 'node' in P.obj_dict['nodes']: N.graph['node']=P.obj_dict['nodes']['node'][0]['attributes'] # get_edge_defaults() N.graph['edge']={} if 'edge' in P.obj_dict['nodes']: N.graph['edge']=P.obj_dict['nodes']['edge'][0]['attributes'] N.node_attr=node_attr return N def to_pydot(N, strict=True): """Return a pydot graph from a NetworkX graph N. Parameters ---------- N : NetworkX graph A graph created with NetworkX Examples -------- >>> K5=nx.complete_graph(5) >>> P=nx.to_pydot(K5) Notes ----- """ try: import pydot except ImportError: raise ImportError, \ "to_pydot() requires pydot http://dkbza.org/pydot.html/" # set Graphviz graph type if N.is_directed(): graph_type='digraph' else: graph_type='graph' strict=N.number_of_selfloops()==0 and not N.is_multigraph() P = pydot.Dot(graph_type=graph_type,strict=strict) for n,nodedata in N.nodes_iter(data=True): str_nodedata=dict((k,str(v)) for k,v in nodedata.iteritems()) p=pydot.Node(str(n),**str_nodedata) P.add_node(p) if N.is_multigraph(): for u,v,key,edgedata in N.edges_iter(data=True,keys=True): str_edgedata=dict((k,str(v)) for k,v in edgedata.iteritems()) edge=pydot.Edge(str(u),str(v),key=str(key),**str_edgedata) P.add_edge(edge) else: for u,v,edgedata in N.edges_iter(data=True): str_edgedata=dict((k,str(v)) for k,v in edgedata.iteritems()) edge=pydot.Edge(str(u),str(v),**str_edgedata) P.add_edge(edge) try: P.obj_dict['attributes'].update(N.graph.get('graph',{})) except: pass try: P.obj_dict['nodes']['node'][0]['attributes'].update(N.graph.get('node',{})) except: pass try: P.obj_dict['nodes']['edge'][0]['attributes'].update(N.graph.get('edge',{})) except: pass return P def pydot_from_networkx(N): """Create a Pydot graph from a NetworkX graph.""" from warnings import warn warn('pydot_from_networkx is replaced by to_pydot', DeprecationWarning) return to_pydot(N) def networkx_from_pydot(D, create_using=None): """Create a NetworkX graph from a Pydot graph.""" from warnings import warn warn('networkx_from_pydot is replaced by from_pydot', DeprecationWarning) return from_pydot(D) def graphviz_layout(G,prog='neato',root=None, **kwds): """Create node positions using Pydot and Graphviz. Returns a dictionary of positions keyed by node. Examples -------- >>> G=nx.complete_graph(4) >>> pos=nx.graphviz_layout(G) >>> pos=nx.graphviz_layout(G,prog='dot') Notes ----- This is a wrapper for pydot_layout. """ return pydot_layout(G=G,prog=prog,root=root,**kwds) def pydot_layout(G,prog='neato',root=None, **kwds): """Create node positions using Pydot and Graphviz. Returns a dictionary of positions keyed by node. Examples -------- >>> G=nx.complete_graph(4) >>> pos=nx.pydot_layout(G) >>> pos=nx.pydot_layout(G,prog='dot') """ try: import pydot except ImportError: raise ImportError, \ "pydot_layout() requires pydot http://dkbza.org/pydot.html/" P=to_pydot(G) if root is not None : P.set("root",str(root)) D=P.create_dot(prog=prog) if D=="": # no data returned print "Graphviz layout with %s failed"%(prog) print print "To debug what happened try:" print "P=pydot_from_networkx(G)" print "P.write_dot(\"file.dot\")" print "And then run %s on file.dot"%(prog) return Q=pydot.graph_from_dot_data(D) node_pos={} for n in G.nodes(): node=Q.get_node(pydot.Node(n).get_name()) pos=node.get_pos()[1:-1] # strip leading and trailing double quotes if pos != None: xx,yy=pos.split(",") node_pos[n]=(float(xx),float(yy)) return node_pos