Python networkx.read_graphml函数代码示例

def load_graphml(input_data):

    # TODO: allow default properties to be passed in as dicts

    try:
        graph = nx.read_graphml(input_data)
    except IOError, e:
        acceptable_errors = set([2, 36, 63])  # no such file or directory
                                              # input string too long for filename
                                              # input string too long for filename
        if e.errno in acceptable_errors:
            from xml.etree.cElementTree import ParseError

            # try as data string rather than filename string

            try:
                input_pseduo_fh = StringIO(input_data)  # load into filehandle to networkx
                graph = nx.read_graphml(input_pseduo_fh)
            except IOError:
                raise autonetkit.exception.AnkIncorrectFileFormat
            except IndexError:
                raise autonetkit.exception.AnkIncorrectFileFormat
            except ParseError:
                raise autonetkit.exception.AnkIncorrectFileFormat
            except ParseError:
                raise autonetkit.exception.AnkIncorrectFileFormat
        else:
            raise e

def test_real_graph(nparts):
    logging.info('Reading author collab graph')
    author_graph = nx.read_graphml('/home/amir/az/io/spam/mgraph2.gexf')
    author_graph.name = 'author graph'
    logging.info('Reading the full author product graph')
    full_graph = nx.read_graphml('/home/amir/az/io/spam/spam_graph.graphml')
    full_graph.name = 'full graph'

    proper_author_graph = author_graph.subgraph([a for a in author_graph if 'revLen' in author_graph.node[a]
                                                                            and 'hlpful_fav_unfav' in author_graph.node[a]
                                                                            and 'vrf_prchs_fav_unfav' in author_graph.node[a]])
    # features = {'revLen': 0.0, 'hlpful_fav_unfav': False, 'vrf_prchs_fav_unfav': False}
    # for a in author_graph:
    #     for feat, def_val in features.items():
    #         if feat not in author_graph.node[a]:
    #             author_graph.node[a][feat] = def_val

    # sub sample proper_author_graph
    # proper_author_graph.remove_edges_from(random.sample(proper_author_graph.edges(), 2*proper_author_graph.size()/3))
    # degree = proper_author_graph.degree()
    # proper_author_graph.remove_nodes_from([n for n in proper_author_graph if degree[n] == 0])
    # author to the product reviewed by him mapping
    logging.debug('forming the product mapping')
    author_product_mapping = {}
    for a in proper_author_graph:
        author_product_mapping[a] = [p for p in full_graph[a] if 'starRating' in full_graph[a][p] and
                                                                 full_graph[a][p]['starRating'] >= 4]
    logging.debug('Running EM')
    ll, partition = HardEM.run_EM(proper_author_graph, author_product_mapping, nparts=nparts, parallel=True)
    print 'best loglikelihood: %s' % ll
    for n in partition:
        author_graph.node[n]['cLabel'] = int(partition[n])
    nx.write_gexf(author_graph, '/home/amir/az/io/spam/spam_graph_mgraph_sage_labeled.gexf')

def load_graphml(input_data):
    #TODO: allow default properties to be passed in as dicts


    try:
        graph = nx.read_graphml(input_data)
    except IOError, e:
        acceptable_errors = set([
            2, # no such file or directory
            36, # input string too long for filename
            63, # input string too long for filename
            ])
        if e.errno in acceptable_errors:
            # try as data string rather than filename string
            try:
                input_pseduo_fh = StringIO(input_data) # load into filehandle to networkx
                graph = nx.read_graphml(input_pseduo_fh)
            except IOError:
                raise autonetkit.exception.AnkIncorrectFileFormat
            except IndexError:
                raise autonetkit.exception.AnkIncorrectFileFormat
        else:
            try:
                import autonetkit.console_script as cs
                input_data=cs.parse_options().file
                graph = nx.read_graphml(input_data)
            except IOError:
                raise e

def create_joined_multigraph():
    G=nx.DiGraph()
    upp=nx.read_graphml('upperlevel_hashtags.graphml')
    for ed in upp.edges(data=True):
        G.add_edge(ed[0],ed[1],attr_dict=ed[2])
        G.add_edge(ed[1],ed[0],attr_dict=ed[2])
    mid=nx.read_graphml('friendship_graph.graphml')
    for ed in mid.edges(data=True):
        G.add_edge(ed[0],ed[1],attr_dict=ed[2]) 
    inter=nx.read_graphml('interlevel_hashtags.graphml')
    for ed in inter.edges(data=True):
        G.add_edge(ed[0],ed[1],attr_dict=ed[2]) 
        G.add_edge(ed[1],ed[0],attr_dict=ed[2])
    down=nx.read_graphml('retweet.graphml')
    mapping_f={}
    for i,v in enumerate(down.nodes()):
        mapping_f[v]='%iretweet_net' %i
    for ed in down.edges(data=True):
        G.add_edge(mapping_f[ed[0]],mapping_f[ed[1]],attr_dict=ed[2]) 

    for nd in mid.nodes():
        if nd in mapping_f:
            G.add_edge(nd,mapping_f[nd])
            G.add_edge(mapping_f[nd],nd)
    nx.write_graphml(G,'joined_3layerdigraph.graphm')
    return G,upp.nodes(),mid.nodes(),mapping_f.values()

    def test_generate_graphml(self):

        self.ts = pyTripleSimple.SimpleTripleStore()
        f = open("acme.nt")
        self.ts.load_ntriples(f)
        f.close()
        egfrsts_obj = pyTripleSimple.ExtractGraphFromSimpleTripleStore(self.ts)
        egfrsts_obj.register_label()
        egfrsts_obj.register_class()
        egfrsts_obj.add_pattern_for_links([['a','b','c']],[('b','in',['<http://acme.com/rdf#isLabeller>'])],("a","c"), "labeller")
        egfrsts_obj.register_node_predicate("<http://acme.com/rdf#ndc/date_issued>", "date", lambda x : x.upper())
        result_xml = egfrsts_obj.translate_into_graphml_file()

        from xml.etree.ElementTree import XML
        elements = XML(result_xml)
        xml_tags = []

        for element in elements:
            xml_tags.append(element.tag)
        self.assertTrue("{http://graphml.graphdrawing.org/xmlns}key" in xml_tags)
        self.assertTrue("{http://graphml.graphdrawing.org/xmlns}graph" in xml_tags)

        try:
            import networkx
            fo = open("acme.graphml","w")
            fo.write(result_xml)
            fo.close()
            networkx.read_graphml("acme.graphml")
            f.close()
        except ImportError:
            pass

 def graph_from_file(cls, path, file_format=GraphFileFormat.GraphMl):
     if file_format == GraphFileFormat.GraphMl:
         graph = net.read_graphml(path)
     elif file_format == GraphFileFormat.AdjList:
         graph = net.read_adjlist(path)
     elif file_format == GraphFileFormat.Gml:
         graph = net.read_gml(path)
     elif file_format == GraphFileFormat.Yaml:
         graph = net.read_yaml(path)
     else:
         graph = net.read_graphml(path)
     return cls(graph=graph)

 def __init__(self, configurationFilePath, paretoFilePath):
     """
         @param configurationFilePath: path to the file that has information
         about how the experiment was runned: 1) demand center, 
         2) distribution center, 3) objective functions
         
         @param paretoFilePath: path to the file containing the Pareto set.
         This file also has information about the objective function types 
         The pareto was created by running the program facility-location using
         the configurationFilePath  
     """
     self.configurationFilePath = configurationFilePath
     self.paretoFilePath = paretoFilePath
     configurationFile = open(self.configurationFilePath, 'r')
     paretoFile = open(self.paretoFilePath, 'r')
     
     print 'configuration file', self.configurationFilePath
     print 'pareto file', self.paretoFilePath
     tree = ET.parse(self.configurationFilePath)
     #obtain the file path of the distribution centers
     for elem in tree.iter(tag='distributionCenters'):
         self.distributionCentersFilePath = elem.text
     #obtain the file path of the demand centers
     for elem in tree.iter(tag='demandCenters'):
         self.demandCentersFilePath = elem.text
     
     
     os.path.normpath(self.distributionCentersFilePath)
     os.path.normpath(self.demandCentersFilePath)
     
     #load the demand and distribution centers as s
     distributionCenters = nx.read_graphml(self.distributionCentersFilePath, node_type=int)
     demandCenters = nx.read_graphml(self.demandCentersFilePath, node_type=int)
     
     #load the ids of the distribution centers of the pareto set
     os.path.normpath(self.paretoFilePath)
     pareto = myutils.load_pareto(self.paretoFilePath)
     """
     probabilityFailureProblem = probabilityfailureproblem.ProbabilityFailureProblem(demandCenters=demandCenters,
                                                                                     distributionCenters=distributionCenters,
                                                                                     pareto=pareto
                                                                                     )
     """
     probabilityFailureProblem = probabilityfailureproblem.ProbabilityFailureProblem(demandCentersFilePath=self.demandCentersFilePath,
                                                                                     distributionCentersFilePath=self.distributionCentersFilePath,
                                                                                     pareto=pareto,
                                                                                     configurationFilePath=configurationFilePath
                                                                                     )

def graph_product(G_file):
    
    #TODO: take in a graph (eg when called from graphml) rather than re-reading the graph again
    LOG.info("Applying graph product to %s" % G_file)
    H_graphs = {}
    try:
        G = nx.read_graphml(G_file).to_undirected()
    except IOError:
        G = nx.read_gml(G_file).to_undirected()
        return
    G = remove_yed_edge_id(G)
    G = remove_gml_node_id(G)
#Note: copy=True causes problems if relabelling with same node name -> loses node data
    G = nx.relabel_nodes(G, dict((n, data.get('label', n)) for n, data in G.nodes(data=True)))
    G_path = os.path.split(G_file)[0]
    H_labels  = defaultdict(list)
    for n, data in G.nodes(data=True):
        H_labels[data.get("H")].append(n)

    for label in H_labels.keys():
        try:
            H_file = os.path.join(G_path, "%s.graphml" % label)
            H = nx.read_graphml(H_file).to_undirected()
        except IOError:
            try:
                H_file = os.path.join(G_path, "%s.gml" % label)
                H = nx.read_gml(H_file).to_undirected()
            except IOError:
                LOG.warn("Unable to read H_graph %s, used on nodes %s" % (H_file, ", ".join(H_labels[label])))
                return
        root_nodes = [n for n in H if H.node[n].get("root")]
        if len(root_nodes):
# some nodes have root set
            non_root_nodes = set(H.nodes()) - set(root_nodes)
            H.add_nodes_from( (n, dict(root=False)) for n in non_root_nodes)
        H = remove_yed_edge_id(H)
        H = remove_gml_node_id(H)
        nx.relabel_nodes(H, dict((n, data.get('label', n)) for n, data in H.nodes(data=True)), copy=False)
        H_graphs[label] = H

    G_out = nx.Graph()
    G_out.add_nodes_from(node_list(G, H_graphs))
    G_out.add_nodes_from(propagate_node_attributes(G, H_graphs, G_out.nodes()))
    G_out.add_edges_from(intra_pop_links(G, H_graphs))
    G_out.add_edges_from(inter_pop_links(G, H_graphs))
    G_out.add_edges_from(propagate_edge_attributes(G, H_graphs, G_out.edges()))
#TODO: need to set default ASN, etc?
    return G_out

def igraph_draw_traj(filname,pold,polar=True,layout=None):
    import igraph as ig
    g = ig.read(filname,format="graphml")
    pols=[]
    for i in g.vs:
        pols.append(pold[i['id']])
    # print pols
    if polar:
        rgbs = [(1-(i+1.)/2,(i+1.)/2,0) for i in pols]
    else:
        rgbs = [(1-i,i,0) for i in pols]
    # print filname
    GGG=nx.read_graphml(filname)
    g.vs["label"] = GGG.nodes()
    visual_style = {}
    visual_style["vertex_size"] = 15
    visual_style['vertex_color']=rgbs#'pink'
    visual_style['vertex_label_size']='10'
    visual_style["vertex_label"] = g.vs["label"]
    if layout==None:
        layout=g.layout("kk")
    # else:

    visual_style["layout"] = layout
    visual_style["bbox"] = (700, 700)
    visual_style["margin"] = 100
    return g,visual_style,layout

def draw(args):
    """
    Draw a GraphML with the tribe draw method.
    """
    G = nx.read_graphml(args.graphml[0])
    draw_social_network(G, args.write)
    return ""

def main(args):
    """
    Entry point.
    """
    if len(args) == 0:
        print "Usage: python disease.py <params file>"
        sys.exit(1)

    # Load the simulation parameters.
    params = json.load((open(args[0], "r")))
    network_params = params["network_params"]

    # Setup the network.
    if network_params["name"] == "read_graphml":
        G = networkx.read_graphml(network_params["args"]["path"])
        G = networkx.convert_node_labels_to_integers(G)
    else:
        G = getattr(networkx, network_params["name"])(**network_params["args"])

    # Carry out the requested number of trials of the disease dynamics and 
    # average the results.
    Sm, Im, Rm, Rv = 0.0, 0.0, 0.0, 0.0
    for t in range(1, params["trials"] + 1):
        S, I, R = single_trial(G, params)
        Rm_prev = Rm
        Sm += (S - Sm) / t
        Im += (I - Im) / t
        Rm += (R - Rm) / t
        Rv += (R - Rm) * (R - Rm_prev)

    # Print the average
    print("%.3f\t%.3f\t%.3f\t%.3f" \
          %(Sm, Im, Rm, (Rv / params["trials"]) ** 0.5))

def main():
    project = sys.argv[1]

    if project[-1] != "/":
        project += "/"

    usegraphs = []

    #Get usefull graphs

    if "--usegraph" in sys.argv:
        usegraphs.append("{0}{1}".format(project, sys.argv[sys.argv.index("--usegraph") + 1]))
    else:
        for f in os.listdir(project):
            if "usegraph" in f:
                usegraphs.append("{0}{1}".format(project, f))

    for ug in usegraphs:
        print("READ {0}".format(ug))

        g = nx.read_graphml(ug)

        nb_nodes = g.number_of_nodes()
        nb_edges = g.number_of_edges()

        nb_paths = compute_paths(project, g)

        print("Stats for {0}:".format(ug))
        print("\tnumber of nodes : {0}".format(nb_nodes))
        print("\tnumber of edges : {0}".format(nb_edges))
        print("\tnumber of paths : {0}".format(nb_paths))

    print("Done!")

def main(args):
    """
    Entry point.
    """
    if len(args) != 2:
        sys.exit(__doc__ %{"script_name" : args[0].split("/")[-1]})

    # Load the simulation parameters.
    params = json.load((open(args[1], "r")))
    network_params = params["network_params"]

    # Setup the network.
    G = networkx.read_graphml(network_params["args"]["path"])
    G = networkx.convert_node_labels_to_integers(G)

    # Load the attack sequences.
    fname = network_params["args"]["path"].replace(".graphml", ".pkl")
    attack_sequences = pickle.load(open(fname, "rb"))
    
    # Carry out the requested number of trials of the disease dynamics and 
    # average the results.
    Sm, Im, Rm, Rv = 0.0, 0.0, 0.0, 0.0
    for t in range(1, params["trials"] + 1):
        S, I, R = single_trial(G, params, attack_sequences)
        Rm_prev = Rm
        Sm += (S - Sm) / t
        Im += (I - Im) / t
        Rm += (R - Rm) / t
        Rv += (R - Rm) * (R - Rm_prev)

    # Print the average
    print("%.3f\t%.3f\t%.3f\t%.3f" \
          %(Sm, Im, Rm, (Rv / params["trials"]) ** 0.5))

def main():
    arg_parser = ArgumentParser(description='add edge weights to tree')
    arg_parser.add_argument('--input', required=True,
                            help='inpput file')
    arg_parser.add_argument('--output', required=True,
                            help='outpput file')
    arg_parser.add_argument('--seed', type=int, default=None,
                            help='seed for random number generator')
    arg_parser.add_argument('--delim', dest='delimiter', default=' ',
                            help='delimiter for edge list')
    arg_parser.add_argument('--no-data', action='store_true',
                            dest='no_data', help='show edge data')
    arg_parser.add_argument('--edge-list', action='store_true',
                            help='generate edge list output')
    options = arg_parser.parse_args()
    random.seed(options.seed)
    tree = nx.read_graphml(options.input)
    add_edge_weights(tree)
    if options.edge_list:
        nx.write_edgelist(tree, options.output,
                          delimiter=options.delimiter,
                          data=not options.no_data)
    else:
        nx.write_graphml(tree, options.output)
    return 0

def showXY(fnm, x="kx", y="ky"):
    g = nx.read_graphml(fnm)
    x = nx.get_node_attributes(g, x)
    y = nx.get_node_attributes(g, y)
    coords = zip(x.values(),y.values())
    pos = dict(zip(g.nodes(), coords))
    nx.draw(g,pos)