Python json_graph.node_link_data函数代码示例

def build_network(seed_network,utility_params,network_length):
    now_start = datetime.datetime.now()
    start_node = len(seed_network)
    for i in range(len(seed_network),network_length):
        print ("sim network length = " + str(len(seed_network)+1))
        seed_network.expansion_utilities(utility_params)
        if seed_network.expansion_city_ghs:
            new_nodes = {node:data for node,data in seed_network.expansion_cache.items() if node in seed_network.expansion_city_ghs}
            best_node = max(new_nodes, key= lambda x: new_nodes[x][-1])#last value in array
            print (best_node)
        else:
            print ("no expansion cities found at node " + str(i))
            file_name = "simulated_networks/" + str(start_node) + "_" + str(len(seed_network)) + "_" + "_".join([str(param) for param in utility_params.tolist()]) + ".pickle"
            with open(file_name, 'wb') as outfile:
                pickle.dump(seed_network, outfile)
            file_name = "simulated_networks/" + str(start_node) + "_" + str(len(seed_network)) + "_" + "_".join([str(param) for param in utility_params.tolist()]) + ".json"
            with open(file_name, 'w') as outfile:
                json.dump(json_graph.node_link_data(seed_network), outfile)
            return seed_network
        seed_network.add_SC(best_node)
        if len(seed_network[best_node].keys()) == 0:
            print ("added node has no conenctions")
            print (seed_network.expansion_cache[best_node])
    file_name = "simulated_networks/" + str(start_node) + "_" + str(len(seed_network)) + "_" + "_".join([str(param) for param in utility_params.tolist()]) + ".pickle"
    with open(file_name, 'wb') as outfile:
        pickle.dump(seed_network, outfile)
    file_name = "simulated_networks/" + str(start_node) + "_" + str(len(seed_network)) + "_" + "_".join([str(param) for param in utility_params.tolist()]) + ".json"
    with open(file_name, 'w') as outfile:
        json.dump(json_graph.node_link_data(seed_network), outfile)
    now_finish = datetime.datetime.now()
    elapsedTime = now_finish- now_start
    print(elapsedTime / timedelta(minutes=1))
    return seed_network

    def test_job_set_accepted(self):
        # Arrange
        job_id = "1"
        job_name = "new job"
        g = nx.Graph()
        expected_result = {'name': job_name, 'graph': json_graph.node_link_data(g), 'status': "Accepted", 'id': job_id}

        class TestJobManager(object):
            def __init__(self):
                self.job = None

            def get_job(self, job_id):
                return self.job

            def insert_job(self, job_name, graph):
                self.job = {'name': job_name, 'graph': graph, 'status': "Received", "id": job_id}
                return job_id

            def update_job(self, job_id, job):
                self.job['status'] = job['status']

        api.config['REPOSITORY'] = JobManagerRepository(TestJobManager())
        self.app = api.test_client()

        # Act
        data = {'job_name': job_name, 'graph': json_graph.node_link_data(g)}
        rv = self.app.post('/jobs', data=json.dumps(data))
        rv2 = self.app.put('/jobs/' + job_id + '/status', data=json.dumps({'status': 'Accepted'}))
        rv3 = self.app.get('/jobs/' + job_id)

        # Assert
        final_job = json.loads(rv3.data.decode(rv.charset))

        self.assertEqual(expected_result, final_job)

 def send_network(self):
     if self.mininet:
         d = json_graph.node_link_data(self.mininet_to_nx_graph())
     else:
         d = json_graph.node_link_data(self.net.to_nx_graph())
     d['message_type'] = 'network'
     d['mininet'] = bool(self.mininet)
     self.send_to_ws(json.dumps(d))

def computebwmod(graph,path,protlist,path_lenght,alone):
	import itertools 
	fixed=[]
	combination=[]
	betweennees=nx.betweenness_centrality(graph,normalized=True)
	print "------Starting Graph------"
	print nx.info(graph)

	d = json_graph.node_link_data(graph) # node-link format to serialize
# write json
	json.dump(d, open('mcn.json','w'))
	count={}
	for i in graph.nodes():
		if i in protlist:
			continue
		else:
			count[i]=0
	combination=list(itertools.combinations(path,2))
	pa={}
	for i in path:
		pa[i]=[]
		for j in path[i]:
			
			if path.has_key(i):
				pa[i].extend(j[1:len(j)-1])
			else:
				pa[i].extend(j[1:len(j)-1])

	for i in path:
		pa[i]=list(set(sum(path[i],[])))


	for i in pa:
		for j in list(set(pa[i])):
			if j in protlist:
				continue
			else:
				count[j]=count[j]+1
	countsort = sorted(count, key=count.get)
	removable=set(countsort).difference(set(protlist))
	print len(protlist)
	graphred=check(graph,path_lenght,removable,protlist,path)
	for i in graphred.nodes():
	
		if i in protlist:
			graphred.node[i]["group"]=5
		else:
			graphred.node[i]["group"]=10
	f1=open("bwmodproteins.txt","w")
	for i in graphred.nodes():	
			f1.write(i+"\n")
	d = json_graph.node_link_data(graphred) # node-link format to serialize
# write json
	json.dump(d, open('filteredgraph.json','w'))
	nx.write_gpickle(graphred,"bwmodfiltgraph.gpickle")

def main():

    Motifset = Motifsets()
    patterns2 = enumerate2()
    output_file1 = "/net/data/graph-models/sim-graphs/approx3-json"
    with open(output_file1, 'w') as fout:
        for item in patterns2:
            string_item = json.dumps(json_graph.node_link_data(item))
            fout.write(string_item + "\n")

    subprocess.check_call("hdfs dfs -put /net/data/graph-models/sim-graphs/approx3-json approx3-json", shell=True)
    approx3Motifs = sc.textFile("hdfs://scrapper/user/xiaofeng/approx3-json", 192)
    #.number of partitions
    collapsed_patterns = approx3Motifs.flatMap(lambda line: worker_all_collapse(Motifset, line))
    subprocess.check_call("hdfs dfs -rm -r patterns_queue", shell=True)
    collapsed_patterns.saveAsTextFile("hdfs://scrapper/user/xiaofeng/patterns_queue")
    #save to HDFS, as a text file, and keep using that RDD

    collapsed_patterns.persist()
    non_iso_set = set()


#    while not collapsed_patterns.isEmpty(): #or use count() != 0 as an alternative

#        povet = collapsed_patterns.take(1)[0]#BROADCAST
#        povet_broad = sc.broadcast(povet)
#        print type(povet)

#        non_iso_set.add(povet)
#        collapsed_patterns = collapsed_patterns.filter(lambda x: not nx.is_isomorphic(x, povet_broad.value))
#


###########write to hard disk the queue of elements waiting to be processed
    while True:
        collapsed_patterns = sc.textFile("hdfs://scrapper/user/xiaofeng/patterns_queue")
        if collapsed_patterns.count() == 0:
            break
        else:
            povet = collapsed_patterns.take(1)[0]#BROADCAST
            povet_broad = sc.broadcast(povet)
            non_iso_set.add(povet)
            collapsed_patterns_new = collapsed_patterns.filter(lambda x: not nx.is_isomorphic(x, povet_broad.value))
            subprocess.check_call("hdfs dfs -rm -r patterns_queue", shell=True)
            collapsed_patterns_new.saveAsTextFile("hdfs://scrapper/user/xiaofeng/patterns_queue")
            print collapsed_patterns.count()



    output_file2 = "/net/data/graph-models/sim-graphs/approx5-json"
    with open(output_file2, 'w') as fout:
        for item in non_iso_set:
            string_item = json.dumps(json_graph.node_link_data(item))
            fout.write(string_item + '\n')

def store_network_as_jason(up_path_edges,down_path_edges,upband=2000,downband=2000):
    '''
        Description:
            This function export the node and link information to the frontend lib, to visiualize the 
            topo and the calculated path between hosts.
    '''
    graph1=nx.DiGraph()
    graph2=nx.DiGraph()
    for edge in edges:
        if edge['localnode'] not in graph1.nodes():
            group=1
            if edge['localaddr'] in ipmap.keys():
                group=0
            graph1.add_node(edge['localnode'],{'localinterface':edge['localifname'],'IPAdd':edge['localaddr'],'group':group})
        if edge['remotenode'] not in graph1.nodes():
            group=1
            if edge['remoteaddr'] in ipmap.keys():
                group=0
            graph1.add_node(edge['remotenode'],{'remoteinterface':edge['remoteifname'],'IPAdd':edge['remoteaddr'],'group':group})
        graph1.add_edge(edge['localnode'],edge['remotenode'],{'AvailableBandwidth':edge['available_bandwidth'],'value':edge['available_bandwidth']})
    for edge in up_path_edges:
        if edge['localnode'] not in graph2.nodes():
            group=1
            if edge['localaddr'] in ipmap.keys():
                group=0
            graph2.add_node(edge['localnode'],{'localinterface':edge['localifname'],'IPAdd':edge['localaddr'],'group':group})
        if edge['remotenode'] not in graph2.nodes():
            group=1
            if edge['remoteaddr'] in ipmap.keys():
                group=0
            graph2.add_node(edge['remotenode'],{'remoteinterface':edge['remoteifname'],'IPAdd':edge['remoteaddr'],'group':group})
        graph2.add_edge(edge['localnode'],edge['remotenode'],{'UpBandwidth':upband,'value':upband})
    for edge in down_path_edges:
        if edge['localnode'] not in graph2.nodes():
            group=1
            if edge['localaddr'] in ipmap.keys():
                group=0
            graph2.add_node(edge['localnode'],{'localinterface':edge['localifname'],'IPAdd':edge['localaddr'],'group':group})
        if edge['remotenode'] not in graph2.nodes():
            group=1
            if edge['remoteaddr'] in ipmap.keys():
                group=0
            graph2.add_node(edge['remotenode'],{'remoteinterface':edge['remoteifname'],'IPAdd':edge['remoteaddr'],'group':group})
        graph2.add_edge(edge['localnode'],edge['remotenode'],{'DownBandwidth':downband,'value':downband})
    for node in host.keys():
        graph1.add_node(host[node],{'IPAdd':node,'group':0})
        graph2.add_node(host[node],{'IPAdd':node,'group':0})
        graph1.add_edge(host[node],ipmap[node])
        graph2.add_edge(host[node],ipmap[node])
    d1=json_graph.node_link_data(graph1)
    d2=json_graph.node_link_data(graph2)
    json.dump(d1,open('/Users/eric/Desktop/topo/1.json','w'))
    json.dump(d2,open('/Users/eric/Desktop/topo/2.json','w'))

def vis_hierarchy(sieve, column_label, max_edges=200, prefix=''):
    """Visualize a hierarchy of representations."""
    import textwrap
    column_label = map(lambda q: '\n'.join(textwrap.wrap(q, width=20)), column_label)

    def f(j):
        if j < sieve.nv:
            return j
        else:
            return (1, j - sieve.nv)

    # Construct non-tree graph
    g = nx.DiGraph()
    max_node_weight = np.max(sieve.tcs)
    for i, c in enumerate(column_label):
        if i < sieve.nv:
            g.add_node(i)
            g.node[i]['weight'] = 1
            g.node[i]['label'] = c
            g.node[i]['name'] = c  # JSON uses this field
        else:
            g.add_node(f(i))
            g.node[f(i)]['weight'] = 0.33 * np.clip(sieve.tcs[i - sieve.nv] / max_node_weight, 0.33, 1)
        if i >= sieve.nv:
            g.add_weighted_edges_from([(f(j), (1, i - sieve.nv), sieve.mi_j(i - sieve.nv)[j]) for j in range(i)])

    # Display pruned version
    h = g.copy()  # trim(g.copy(), max_parents=max_parents, max_children=max_children)
    h.remove_edges_from(sorted(h.edges(data=True), key=lambda q: q[2]['weight'])[:-max_edges])
    edge2pdf(h, prefix + '/graphs/graph_%d' % max_edges, labels='label', directed=True, makepdf=True)

    # Display tree version
    tree = g.copy()
    tree = trim(tree, max_parents=1, max_children=False)
    edge2pdf(tree, prefix + '/graphs/tree', labels='label', directed=True, makepdf=True)

    # Output JSON files
    try:
        import os
        print os.path.dirname(os.path.realpath(__file__))
        copyfile(os.path.dirname(os.path.realpath(__file__)) + '/tests/d3_files/force.html', prefix + '/graphs/force.html')
    except:
        print "Couldn't find 'force.html' file for visualizing d3 output"
    import json
    from networkx.readwrite import json_graph

    mapping = dict([(n, tree.node[n].get('label', str(n))) for n in tree.nodes()])
    tree = nx.relabel_nodes(tree, mapping)
    json.dump(json_graph.node_link_data(tree), safe_open(prefix + '/graphs/force.json', 'w+'))
    json.dump(json_graph.node_link_data(h), safe_open(prefix + '/graphs/force_nontree.json', 'w+'))

    return g

def NetworkAnalysis(jsonGraph):
    """gets graph defined by for export json and computes the top 3
    most connected subgraphs"""

    G = json_graph.node_link_graph(jsonGraph)
    graphs = sorted(nx.connected_component_subgraphs(G), key = len, reverse=True)
    (GC1, GC2, GC3, GC4, GC5) = graphs[0:5]
    top5 = nx.compose_all([GC1,GC2,GC3,GC4,GC5])
    deg = top5.degree()
    nx.set_node_attributes(top5, "degree", deg)
    take = {
        "nodes": json_graph.node_link_data(top5)["nodes"],
        "links": json_graph.node_link_data(top5)["links"]
        }
    return take

def vis_hierarchy(corexes, column_label=None, max_edges=100, prefix='topics', n_anchors=0):
    """Visualize a hierarchy of representations."""
    if column_label is None:
        column_label = map(str, range(corexes[0].alpha.shape[1]))

    # make l1 label
    alpha = corexes[0].alpha
    mis = corexes[0].mis
    l1_labels = []
    annotate = lambda q, s: q if s > 0 else '~' + q
    for j in range(corexes[0].n_hidden):
        # inds = np.where(alpha[j] * mis[j] > 0)[0]
        inds = np.where(alpha[j] >= 1.)[0]
        inds = inds[np.argsort(-alpha[j, inds] * mis[j, inds])]
        group_number = u"red_" + unicode(j) if j < n_anchors else unicode(j)
        label = group_number + u':' + u' '.join([annotate(column_label[ind], corexes[0].sign[j,ind]) for ind in inds[:6]])
        label = textwrap.fill(label, width=25)
        l1_labels.append(label)

    # Construct non-tree graph
    weights = [corex.alpha.clip(0, 1) * corex.mis for corex in corexes[1:]]
    node_weights = [corex.tcs for corex in corexes[1:]]
    g = make_graph(weights, node_weights, l1_labels, max_edges=max_edges)

    # Display pruned version
    h = g.copy()  # trim(g.copy(), max_parents=max_parents, max_children=max_children)
    edge2pdf(h, prefix + '/graphs/graph_prune_' + str(max_edges), labels='label', directed=True, makepdf=True)

    # Display tree version
    tree = g.copy()
    tree = trim(tree, max_parents=1, max_children=False)
    edge2pdf(tree, prefix + '/graphs/tree', labels='label', directed=True, makepdf=True)

    # Output JSON files
    try:
        import os
        copyfile(os.path.dirname(os.path.realpath(__file__)) + '/tests/d3_files/force.html', prefix + '/graphs/force.html')
    except:
        print "Couldn't find 'force.html' file for visualizing d3 output"
    import json
    from networkx.readwrite import json_graph

    mapping = dict([(n, tree.node[n].get('label', str(n))) for n in tree.nodes()])
    tree = nx.relabel_nodes(tree, mapping)
    json.dump(json_graph.node_link_data(tree), safe_open(prefix + '/graphs/force.json', 'w+'))
    json.dump(json_graph.node_link_data(h), safe_open(prefix + '/graphs/force_nontree.json', 'w+'))

    return g

def plot_graph(graph, scope=None, parent=None,
               excludes=(), d3page='fixedforce.html', minimal=False):
    """Open up a display of the graph in a browser window."""

    tmpdir = tempfile.mkdtemp()
    fdir = os.path.dirname(os.path.abspath(__file__))
    shutil.copy(os.path.join(fdir, 'd3.js'), tmpdir)
    shutil.copy(os.path.join(fdir, d3page), tmpdir)

    graph = _clean_graph(graph, excludes=excludes,
                         scope=scope, parent=parent, minimal=minimal)
    data = node_link_data(graph)
    tmp = data.get('graph', [])
    data['graph'] = [dict(tmp)]

    startdir = os.getcwd()
    os.chdir(tmpdir)
    try:
        # write out the json as a javascript var
        # so we we're not forced to start our own webserver
        # to avoid cross-site issues
        with open('__graph.js', 'w') as f:
            f.write("__mygraph__json = ")
            json.dump(data, f)
            f.write(";\n")

        # open URL in web browser
        wb = webbrowser.get()
        wb.open('file://'+os.path.join(tmpdir, d3page))
    except Exception as err:
        print str(err)
    finally:
        os.chdir(startdir)
        print "remember to remove temp directory '%s'" % tmpdir

 def _measurement(self):
     while True:
         print 'ActiveFlows: ', self.active_flows
         print 'FlowRate: ', self.flow_rate
         print 'Graph: ', json.dumps(json_graph.node_link_data(self.graph))
         self._send_measure_request()
         hub.sleep(1)

def draw_to_browser(agents):

    data1 = {}
    data2= []
    for i in range(0,250): #param
        for j in range(20):
            #print graphStrings[i]
            
            G = create_graph_of_agent(agents[str(i)][str(j)])
            d = json_graph.node_link_data(G)
            d["directed"] = 1
            d["multigraph"] = 1
            text= "s " +str(i + 1)+" | " + str(j + 1)
            data1[text] = d
           
            data2.append({"text": text, "value": text})

    data = {"0": data1,
            "codes": data2}

    write_html(data)
    json.dump(data, open('IPD_output/data.json', 'w'))
    print('Wrote node-link JSON data to temp.json')
    # open URL in running web browser
    http_server.load_url('IPD_output/overall.html')
    print('Or copy all files to webserver and load graph.html')

    def generate_weak_links_map(self):
        weak_nodes = self.detect_weak_nodes(-5,25)
        active_weak_nodes = [node[0] for node in weak_nodes if max([l[1] for l in node[1]]) > 10]
        ap_nodes = [node for node in self.g.nodes() if self.g.in_degree(node) > 0]

        edges = self.g.edges(active_weak_nodes)
        snr_g = nx.DiGraph()
        snr_g.add_nodes_from(active_weak_nodes + ap_nodes)
        snr_g.add_edges_from(edges)
        
        for node in active_weak_nodes:
            snr_g.node[node]['type'] = 'sta'
        for node in ap_nodes:
            snr_g.node[node]['type'] = 'ap'
                

        nx.write_gpickle(snr_g,'graph_pickle_connectivity_%d.pkl' % time.time())
        #nx.draw(snr_g,with_labels=False)
        #pylab.savefig("connectivity-graph-%d.png" % (int(time.time())))

        d = json_graph.node_link_data(snr_g) # node-link format to serialize
        # write json 
        json.dump(d, open('force/force.json','w'))


        print ap_nodes

    def _install_one_route(self, chain_graph, res_graph, s, t, backroute=False):
        self._debug('Install route between %s - %s (backroute=%s)' %
                        (s, t, backroute))

        route_id = self.next_route_id()
        self.routes[route_id] = { 'chain': [],
                                  'res': [],
                                  'status': RouteChanged.PENDING,
                                  'res_graph': res_graph,
                                  }

        if backroute:
            #route_search = DefaultRouteAlgorithm()
            #route_search.graph(json_graph.node_link_data(res_graph))

            # send backward traffic directly to the source:
            chain_hops = [(s, t)]
        else:
            route_search = self.chain_route_search
            route_search.graph(json_graph.node_link_data(chain_graph))
            chain_hops = route_search.chain_hops(s, t)

        self.routes[route_id]['chain'] = chain_hops
        self._fire_route_state_change(None, route_id)
        self.install_pending_routes(res_graph)

def simpleDisplay(ipaddress = "localhost",port = "9999"):
    '''
    利用每次处理后保存的图来进行恢复展示
    :return:
    '''
    # client,repo,stargazers,user = getRespond()
    # g = addTOGraph(repo,stargazers,user)
    # addEdge(stargazers,client,g)
    # getPopular(g)
    # savaGraph1(g)
    # top10(g)
    g = nx.read_gpickle("data/github.1")
    print nx.info(g)
    print

    mtsw_users = [n for n in g if g.node[n]['type'] == 'user']
    h = g.subgraph(mtsw_users)

    print nx.info(h)
    print
    d = json_graph.node_link_data(h)
    json.dump(d, open('data/githubRec.json', 'w'))
    cmdstr = "python3 -m http.server %s" % port
    webbrowser.open_new_tab("http://%s:%s/%s.html"%(ipaddress,port, "display_githubRec"))
    os.system(cmdstr)