Python nx_agraph.graphviz_layout函数代码示例

def main():
    # Create a directed graph
    G = nx.DiGraph()

    # An example
    l=[ ('a','b'),
        ('b','c'),
        ('c','d'),
        ('d','e'),
        ('e','f'),
        ('w','x'),
        ('w','t'),
        ('t','q'),
        ('q','r'),
        ('q','u')]

    # Build up a graph
    for t in l:
        G.add_edge(t[0], t[1])

    # Plot trees
    pos = graphviz_layout(G, prog='dot')
    nx.draw(G, pos, with_labels=True, arrows=False)

    plt.savefig('draw_trees_with_pygraphviz.png', bbox_inches='tight')   
    plt.show()

def draw_graph(nodes, edges, graphs_dir, default_lang='all'):
    lang_graph = nx.MultiDiGraph()
    lang_graph.add_nodes_from(nodes)
    for edge in edges:
        if edges[edge] == 0:
            lang_graph.add_edge(edge[0], edge[1])
        else:
            lang_graph.add_edge(edge[0], edge[1], weight=float(edges[edge]), label=str(edges[edge]))

    # print graph info in stdout
    # degree centrality
    print('-----------------\n\n')
    print(default_lang)
    print(nx.info(lang_graph))
    try:
        # When ties are associated to some positive aspects such as friendship or collaboration,
        #  indegree is often interpreted as a form of popularity, and outdegree as gregariousness.
        DC = nx.degree_centrality(lang_graph)
        max_dc = max(DC.values())
        max_dc_list = [item for item in DC.items() if item[1] == max_dc]
    except ZeroDivisionError:
        max_dc_list = []
    # https://ru.wikipedia.org/wiki/%D0%9A%D0%BE%D0%BC%D0%BF%D0%BB%D0%B5%D0%BA%D1%81%D0%BD%D1%8B%D0%B5_%D1%81%D0%B5%D1%82%D0%B8
    print('maxdc', str(max_dc_list), sep=': ')
    # assortativity coef
    AC = nx.degree_assortativity_coefficient(lang_graph)
    print('AC', str(AC), sep=': ')
    # connectivity
    print("Слабо-связный граф: ", nx.is_weakly_connected(lang_graph))
    print("количество слабосвязанных компонент: ", nx.number_weakly_connected_components(lang_graph))
    print("Сильно-связный граф: ", nx.is_strongly_connected(lang_graph))
    print("количество сильносвязанных компонент: ", nx.number_strongly_connected_components(lang_graph))
    print("рекурсивные? компоненты: ", nx.number_attracting_components(lang_graph))
    print("число вершинной связности: ", nx.node_connectivity(lang_graph))
    print("число рёберной связности: ", nx.edge_connectivity(lang_graph))
    # other info
    print("average degree connectivity: ", nx.average_degree_connectivity(lang_graph))
    print("average neighbor degree: ", sorted(nx.average_neighbor_degree(lang_graph).items(),
                                              key=itemgetter(1), reverse=True))
    # best for small graphs, and our graphs are pretty small
    print("pagerank: ", sorted(nx.pagerank_numpy(lang_graph).items(), key=itemgetter(1), reverse=True))

    plt.figure(figsize=(16.0, 9.0), dpi=80)
    plt.axis('off')
    pos = graphviz_layout(lang_graph)
    nx.draw_networkx_edges(lang_graph, pos, alpha=0.5, arrows=True)
    nx.draw_networkx(lang_graph, pos, node_size=1000, font_size=12, with_labels=True, node_color='green')
    nx.draw_networkx_edge_labels(lang_graph, pos, edges)

    # saving file to draw it with dot-graphviz
    # changing overall graph view, default is top-bottom
    lang_graph.graph['graph'] = {'rankdir': 'LR'}
    # marking with blue nodes with maximum degree centrality
    for max_dc_node in max_dc_list:
        lang_graph.node[max_dc_node[0]]['fontcolor'] = 'blue'
    write_dot(lang_graph, os.path.join(graphs_dir, default_lang + '_links.dot'))

    # plt.show()
    plt.savefig(os.path.join(graphs_dir, 'python_' + default_lang + '_graph.png'), dpi=100)
    plt.close()

    def draw(self, zscale=1):
        for n in self.history:
            if len(self.history[n]) % 2 != 0:
                self.history[n].append(self.turn)
        pos = graphviz_layout(self.wot, "twopi")

        for n in self.history:
            periods = list(zip(self.history[n], self.history[n][1:]))
            for i, p in enumerate(periods):
                nbpoints = abs(p[1] - p[0])*zscale
                zline = linspace(p[0]*zscale, p[1]*zscale, nbpoints)
                xline = linspace(pos[n][0], pos[n][0], nbpoints)
                yline = linspace(pos[n][1], pos[n][1], nbpoints)
                plot = self.ax.plot(xline, zline, yline, zdir='y', color=self.colors[n][0], alpha=1/(i % 2 + 1))

        for link in self.past_links:
            nbpoints = abs(pos[link[2]][0] - pos[link[1]][1])*zscale
            zline = linspace(link[0]*zscale, link[0]*zscale, nbpoints)
            xline = linspace(pos[link[2]][0], pos[link[1]][0], nbpoints)
            yline = linspace(pos[link[2]][1], pos[link[1]][1], nbpoints)
            if link[1] in self.colors:
                self.ax.plot(xline, zline, yline, zdir='y', color=self.colors[link[1]][0], alpha=0.1)

            #txt = self.ax.text(pos[n][0], pos[n][1], self.history[n][0]*zscale, n[:5], 'z')

        self.ax.set_xlim3d(-5, max([p[0] for p in pos.values()]))
        self.ax.set_ylim3d(-5, max([p[1] for p in pos.values()]))
        self.ax.set_zlim3d(-5, (self.turn+1)*zscale)

def main( ):
    g = nx.DiGraph( )
    # Add x nodes.
    xs = np.arange(0, 11)
    ys = np.arange(0, 11)

    [ g.add_node( 'x=%d' % i, w = i ) for i in xs ]
    [ g.add_node( 'y=%d' % i, w = i ) for i in ys ]

    # Now add edges.
    img = { }
    for x in xs:
        for z in [1,2,3]:
            y = (x + z) % 11
            g.add_edge( 'x=%d' % x, 'y=%d' % y, label='z=%d' % z, prob=1/3)
            print( '%d + %d -> %d' % (x, z, y) )
            img[ (x, y) ] = 1/3

    mat = np.zeros( shape=(11,11) )
    for k, v in img.items( ):
        mat[ k ] = v

    nx.draw_networkx( g, pos = graphviz_layout( g, 'dot' ) )
    nx.drawing.nx_agraph.write_dot( g, 'network.dot' )
    plt.savefig( 'graph.png' )

    def drawTrie(trie_dict):
        """
        Draws the trie structure of the PHT from dictionnary.

        @param trie_dict: Dictionnary of index entries (prefix -> entry).
        @type  trie_dict: dict
        """
        prefixes = list(trie_dict.keys())
        if len(prefixes) == 0:
            return

        edges = list([])
        for prefix in prefixes:
            for i in range(-1, len(prefix)-1):
                u = prefix[:i+1]
                x = ("." if i == -1 else u, u+"0")
                y = ("." if i == -1 else u, u+"1")
                if x not in edges:
                    edges.append(x)
                if y not in edges:
                    edges.append(y)

        # TODO: use a binary tree position layout...
        #   UPDATE : In a better way [change lib]
        G = nx.Graph(sorted(edges, key=lambda x: len(x[0])))
        plt.title("PHT: Tree")
        pos=graphviz_layout(G,prog='dot')
        nx.draw(G, pos, with_labels=True, node_color='white')
        plt.show()

def visualize(graphs, viz_path, args_viz_format):
  import matplotlib
  from networkx.drawing.nx_agraph import graphviz_layout
  meta_graph = networkx.Graph()
  for graph in graphs:
    add_graph(meta_graph, graph)
  pos = graphviz_layout(meta_graph)
  networkx.draw(meta_graph, pos)
  if viz_path:
    ext = os.path.splitext(viz_path)[1]
    if ext == '.dot':
      viz_format = 'graphviz'
    elif ext == '.png':
      viz_format = 'png'
  else:
    viz_format = args_viz_format
  if viz_format == 'graphviz':
    from networkx.drawing.nx_pydot import write_dot
    assert viz_path is not None, 'Must provide a filename to --visualize if using --viz-format "graphviz".'
    base_path = os.path.splitext(viz_path)
    write_dot(meta_graph, base_path+'.dot')
    run_command('dot', '-T', 'png', '-o', base_path+'.png', base_path+'.dot')
    logging.info('Wrote image of graph to '+base_path+'.dot')
  elif viz_format == 'png':
    if viz_path is None:
      matplotlib.pyplot.show()
    else:
      matplotlib.pyplot.savefig(viz_path)

    def get_tree_layout(self, connected_component):
        layout = None
        tree = self.get_underlying_tree(connected_component)
        try:
            # Nice circular layout if you have graphviz
            from networkx.drawing.nx_agraph import graphviz_layout
            layout = graphviz_layout(tree, prog='twopi', root=str(tree.root))

            # Scale to fit grid, since twopi seems to ignore the size option
            min_x = min(pos[0] for pos in layout.values())
            max_x = max(pos[0] for pos in layout.values())
            min_y = min(pos[1] for pos in layout.values())
            max_y = max(pos[1] for pos in layout.values())

            center_x = min_x + (max_x - min_x) / 2
            center_y = min_y + (max_y - min_y) / 2
            # Re-center, scale and shift to fit the desired bounding box
            try:
                x_scale = (0.5 - self.layout_margin - 0.005) / (center_x - min_x)
            except ZeroDivisionError:
                x_scale = 1
            try:
                y_scale = (0.5 - self.layout_margin - 0.005) / (center_y - min_y)
            except ZeroDivisionError:
                y_scale = 1
            for vert, pos in layout.iteritems():
                layout[vert] = ((pos[0] - center_x) * x_scale + 0.5,
                        (pos[1] - center_y) * y_scale + 0.5)

        except ImportError:
            # Spring layout if you do not have grahpviz
            layout = nx.spring_layout(tree, scale=1-2*self.layout_margin-0.01,
                    center=(0.5, 0.5))
        return layout

def plot_graph(graph):
    from networkx.drawing.nx_agraph import graphviz_layout
    pos = graphviz_layout(graph, prog='dot')

    for h in nx.connected_component_subgraphs(graph.to_undirected()):
        nx.draw(h, pos, with_labels=True)

    plt.show()

def plot_nx(bn,**kwargs):
	"""
	Draw BayesNet object from networkx engine
	"""
	g = nx.DiGraph(bn.E)
	pos = graphviz_layout(g,'dot')
	#node_size=600,node_color='w',with_labels=False
	nx.draw_networkx(g,pos=pos, **kwargs)
	plt.axis('off')
	plt.show()

    def graph_traditional_object_file(self, nodes_to_ignore):
        if len(self.object_list) == 0:
            return

        G = nx.DiGraph()

        node_rooms_list = []
        node_labels = {}

        for o in self.object_list:
            if o.parent_id in nodes_to_ignore:
                nodes_to_ignore.append(o.object_id)
                continue
            elif o.object_id in nodes_to_ignore:
                continue

            G.add_node(o.object_key())

            if ROOM_ATTRIBUTE_KEY in (int(attribute) for attribute in o.attributes):
                node_rooms_list.append(o.object_key())
                node_labels[o.object_key()] = o.description

        for o in self.object_list:
            if o.object_key() not in G.nodes():
                continue

            if o.parent_id != 0 and o.object_id not in nodes_to_ignore:
                parent_key = self.object_list[o.parent_id - 1].object_key()

                node_key_to_get = node_labels.get(parent_key, "")
                if node_key_to_get is not "":
                    node_labels[parent_key] = node_key_to_get + '\n\t' + o.description
                else:
                    node_labels[parent_key] = o.description

            for direction, node in o.directions.items():
                if node < len(self.object_list):
                    G.add_edge(self.object_list[node-1].object_key(), o.object_key(), direction=direction)

        pos = graphviz_layout(G, prog='dot')

        edge_labels = dict([((u, v,), d['direction'])
                            for u, v, d in G.edges(data=True)])

        nx.draw_networkx_nodes(G, pos, nodelist=node_rooms_list,
                               node_color="b", node_size=5000, alpha=0.8)

        nx.draw_networkx_edges(G, pos)

        nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8)

        nx.draw_networkx_edge_labels(G, pos, edge_labels=edge_labels, font_size=8, alpha=0.5)

        plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=None, hspace=None)
        plt.show()

 def one_layout(self, func, kwargs):
     """Calculates one arbitrary layout"""
     if 'fixed' in kwargs.keys():
         if not kwargs['fixed'] is None:
             kwargs['pos'] = nx.random_layout(self.G, dim=kwargs['dim'])
     if func == 'dh_spring_layout':
         return self.dh_spring_layout(self.G, **kwargs)
     elif func == 'draw_graphviz':
         return graphviz_layout(self.G, **kwargs)
     else:
         return getattr(nx, func)(self.G, **kwargs)

def desenhaGrafo(G,pngfilename): # desenha o grafo e salva numa imagem png
    edge_labels=dict([((u,v,),d['weight']) # gera os labels das arestas
                    for u,v,d in G.edges(data=True)])
    colors = [G[u][v]['color'] for u,v in G.edges()]
    pos = graphviz_layout(G,prog='neato') # obtem a posicao dos nos (para desenhalo) # TODO: desativar isso?
    nx.draw_networkx_edges(G,pos, edge_color=colors) # desenha as arestas
    nx.draw_networkx_labels(G,pos) # desenha os labels das arestas
    nx.draw_networkx_edge_labels(G,pos,edge_labels=edge_labels) # desenha os labels dos nos
    nx.draw_networkx_nodes(G,pos,node_color='w') # desenha os nos
    plt.axis('off') # desativa os eixos
    plt.savefig(pngfilename)
    plt.close("all")

    def plot(self, savepath=None):
        """
        Draw this individual.
        """

        from networkx.drawing.nx_agraph import graphviz_layout

        fig = plt.figure(figsize=(40, 30))

        tree = self.tree  # type: nx.DiGraph
        pos = graphviz_layout(tree, root=0, prog='dot')

        node_list = tree.nodes(data=True)
        edge_list = tree.edges(data=True)

        node_labels = {
            x[0]: '%s: %s\n%s' % (str(x[1]['node_id']), str(x[1]['label']), '%s/%s' % (
                str(x[1]['inst_correct']), str(x[1]['inst_total'])) if x[1]['terminal'] else '')
            for x in node_list
        }
        node_colors = [x[1]['color'] for x in node_list]
        edge_labels = {(x1, x2): d['threshold'] for x1, x2, d in edge_list}

        nx.draw_networkx_nodes(tree, pos, node_size=1000, node_color=node_colors)  # nodes
        nx.draw_networkx_edges(tree, pos, edgelist=edge_list, style='dashed')  # edges
        nx.draw_networkx_labels(tree, pos, node_labels, font_size=16)  # node labels
        nx.draw_networkx_edge_labels(tree, pos, edge_labels=edge_labels, font_size=16)

        plt.text(
            0.2,
            0.9,
            '\n'.join([
                'individual id: %03.d' % self.ind_id,
                'height: %d' % self.height,
                'n_nodes: %d' % self.n_nodes,
                'train accuracy: %0.4f' % self.train_acc_score,
                'val accuracy: %0.4f' % self.val_acc_score,
                'test accuracy: %0.4f' % self.test_acc_score if self.test_acc_score is not None else '',
                'iteration: %d' % self.iteration if self.iteration is not None else ''

            ]),
            fontsize=15,
            horizontalalignment='right',
            verticalalignment='top',
            transform=fig.transFigure
        )

        plt.axis('off')

        if savepath is not None:
            plt.savefig(savepath, bbox_inches='tight', format='pdf')
            plt.close()

    def draw_circular_graph(self):
        """ Draws a circular graph from the previously computed graph
        :return: None
        """

        pos = graphviz_layout(self.graph, prog="twopi", args="")
        plt.figure(figsize=(8, 8))
        nx.draw(self.graph, pos, node_size=20, alpha=0.5, node_color="blue", with_labels=False)
        nx.draw_networkx_labels(self.graph, pos, self.labels, font_size=6)

        plt.axis("equal")
        plt.savefig("circular_tree.png")
        plt.show()

    def draw_lanl_graph(self):
        """ Draws a lanl graph from the previously computed graph.
        :return: None
        """
        lanl_graph = sorted(nx.connected_component_subgraphs(self.graph), key=len, reverse=True)[0]

        plt.figure(figsize=(8, 8))
        # use graphviz to find radial layout
        pos = graphviz_layout(self.graph, prog="twopi", root=self.root)
        # draw nodes, coloring by rtt ping time
        nx.draw(self.graph, pos, with_labels=False, alpha=0.5, node_size=15)
        # adjust the plot limits
        xmax = 1.02 * max(xx for xx, yy in pos.values())
        ymax = 1.02 * max(yy for xx, yy in pos.values())
        plt.xlim(0, xmax)
        plt.ylim(0, ymax)
        # plt.show()
        plt.savefig("lanl_routes.png")