def main():

	
	parser = argparse.ArgumentParser()
	parser.add_argument('path', help = "target file or directory for summarization")
	parser.add_argument("--posseed", help="boosting seed for biased LexRank", default = None)
	parser.add_argument("--negseed", help="blocking seed for biased LexRank", default = None)
	parser.add_argument("--stopfile", help="file containing custom stopwords")
	parser.add_argument("-o", "--output", help = "output file name")
	parser.add_argument("-l", "--length", help = "summary length in lines", default = 10)
	parser.add_argument("--seed_posweight", help = "Weight for positive seed", default = 3)
	parser.add_argument("--seed_negweight", help = "Weight for negative seed", default = .0001)
	parser.add_argument("--ngrams", help = "N-gram number", default = 1)
	#normalization doesn't work due to being inherent within scoring method
	parser.add_argument("-n", "--is_norm", help = "Boolean flag for normalization", default = True)
	args = parser.parse_args()
	
	input_text = args.path
	pos_seed = args.posseed
	neg_seed = args.negseed
	stopfile = args.stopfile
	out_file = args.output
	sum_length = int(args.length)
	norm_flag = args.is_norm
	pos_weight = float(args.seed_posweight)
	neg_weight = float(args.seed_negweight)
	ngram = int(args.ngrams)
	corpus = Corpus(input_text).documents
	
	output_checker(out_file)

	if pos_seed == None and neg_seed == None:
		LR_method = 'unbiased'
		print LR_method
		[term_matrix, normalized] = TDM(corpus, pos_seed, neg_seed, stopfile, norm_flag, ngram).matrix
		pos_seed_vector = []
		neg_seed_vector = []
		
	else:
		LR_method = 'biased'
		if pos_seed == None:
			pos_seed = ''
		if neg_seed == None:
			neg_seed = ''
		
		[term_matrix, normalized, pos_seed_vector, neg_seed_vector] = TDM(corpus, pos_seed, neg_seed, stopfile, norm_flag, ngram).matrix
		corpus = corpus[2:]
		

	[scores,graph] = Graph(normalized, LR_method, pos_seed_vector, neg_seed_vector, pos_weight, neg_weight).sim_scores 
	#embed()
	largest = networkx.strongly_connected_component_subgraphs(graph)[0]
	A = networkx.to_agraph(largest)
	#A.node_attr.update(shape='point')
	A.node_attr.update(overlap='voronoi')
	A.layout(prog='sfdp')
	networkx.write_dot(largest, 'testgraph.gv')
	A.draw('butterflyv2.png')
	
	print_summary(corpus, scores, out_file, sum_length)

def salva_grafoNX_imagem(G):
    """
    Salva grafos em formato png e dot
    """
    nx.draw_graphviz(G)
    nx.write_dot(G, 'relatorios/grafo_lei_vs_lei.dot')
    P.savefig('relatorios/grafo_lei_vs_lei.png')

def runPRN():
	#DG = readDotFile('/home/loenix/Documents/advogato_graph/advogato-graph-2014-03-16.dot')
	DG = readDotFile('advogato-graph-latest.dot')
	#DG = nx.DiGraph(nx.read_dot('/home/loenix/Documents/advogato_graph/advogato-graph-2014-03-16.dot'))

	Eps = 0.000001  #set up epsilon
	alpha = 0.15  # set alpha

	#pick up a nodes far enough from the seed
	#so that the subgraph on which APPR run will 
	#will be large enough

	numHops = 4
	rand = random.randint(0,len(DG.nodes())-1)
	Seed = DG.nodes()[rand]
	remoteSeed =  getTrustorsOfExactHop(DG, Seed, numHops)


	while remoteSeed == 0 :
	    Seed = DG.nodes()[rand]
	    remoteSeed =  getTrustorsOfExactHop(DG, Seed, numHops)

	#now got a seed which has 4 hop neighbor, run APPR

	#print('seed is:' + Seed)
	#print('nb of seed is: ' + str(DG.neighbors(Seed)))
	#since the algr works on undirected graph
	DG.to_undirected()
	PR = PageRankNibble(DG, Seed, alpha, Eps)
	#using the ranked nodes to form a subgraph. 
	H = DG.subgraph(PR)
	nx.write_dot(H, 'pprResult.dot')
	return H

def main():
    """ Application entry point """
    args = process_arguments()
    print('Loading data...')
    data = load_data(args.infile)
    people = list(set(m['sender'] for m in data) | set(r for m in data for r in m['recipients']))

    counts = defaultdict(Counter)
    for message in data:
        counts[message['sender']].update(message['recipients'])
    for person in people:
        counts[person][person]=0
    df = pd.DataFrame(counts)
    connections = (df * df.T).stack().to_frame()
    connections.index.names=['sender', 'recipient']
    connections.reset_index(inplace=True)
    subset = connections[connections['sender'] < connections['recipient']].copy()
    subset.columns = ['sender', 'recipient', 'product']
    subset['rank'] = subset['product'].rank(method='first', ascending=False)
    ranking = subset.sort_values(by='rank').set_index(['rank'])
    ranking.to_csv(args.outfile)

    gr = nx.Graph()
    for sender, recipient in zip(ranking['sender'], ranking['recipient']):
         gr.add_edge(sender, recipient) 
    nx.write_dot(gr, 'thing.dot')



    args.infile.close()
    args.outfile.close()

	def write_dot_graph(self, dot_adr):
		for n in self.GRAPH.nodes() : 
			self.GRAPH.node[n]["label"] = self.GRAPH.node[n]["contig"]+"_"+str(n)+"_"+self.GRAPH.node[n]["sens"]+"_"+self.GRAPH.node[n]["bi"]+"_"+str(self.GRAPH.node[n]["coords"])
			if self.GRAPH.node[n]["bi"] == "b" :
				self.GRAPH.node[n]["shape"] = "box"
			if self.GRAPH.node[n]["sens"] == "f" :
				self.GRAPH.node[n]["color"] = "green"
			elif self.GRAPH.node[n]["sens"] == "r" : 	
				self.GRAPH.node[n]["color"] = "red"
			if "selected" in self.GRAPH.node[n].keys() :
				self.GRAPH.node[n]["style"] = "filled"
		for e in self.GRAPH.edges() : 
			self.GRAPH.edge[e[0]][e[1]]["label"] = self.GRAPH.edge[e[0]][e[1]]["length"]
			if ((e[0] == "In" or e[0] == "Out") or (e[1] == "Out" or e[1] == "In"))  and (self.GRAPH.edge[e[0]][e[1]]["length"] == 0): 
				self.GRAPH.edge[e[0]][e[1]]["style"] = "dashed"
				self.GRAPH.edge[e[0]][e[1]]["color"] = "grey"
			elif self.GRAPH.node[e[0]]["contig"] == self.GRAPH.node[e[1]]["contig"] and self.GRAPH.node[e[0]]["sens"] == "f" : 
				self.GRAPH.edge[e[0]][e[1]]["color"] = "green"
			elif self.GRAPH.node[e[0]]["contig"] == self.GRAPH.node[e[1]]["contig"] and self.GRAPH.node[e[0]]["sens"] == "r" : 
				self.GRAPH.edge[e[0]][e[1]]["color"] = "red"
			elif ((e[0] == "In" or e[0] == "Out")  and self.GRAPH.node[e[1]]["sens"] == "f") or ((e[1] == "In" or e[1] == "Out")  and self.GRAPH.node[e[0]]["sens"] == "f") :
				self.GRAPH.edge[e[0]][e[1]]["color"] = "green"
			elif ((e[0] == "In" or e[0] == "Out")  and self.GRAPH.node[e[1]]["sens"] == "r") or ((e[1] == "In" or e[1] == "Out")  and self.GRAPH.node[e[0]]["sens"] == "r") :
				self.GRAPH.edge[e[0]][e[1]]["color"] = "red"
		nx.write_dot(self.GRAPH, dot_adr)

    def write_graph(self, filename, problem_edges=[], max_edge=0.99):
        G = nx.DiGraph()
        print 'writing graph!'
        print 'internal edges', self.directed_edges

        for o in self.observations:
            if o in self.anchors.values():
                G.add_node(o, style='filled', color='red')
            else:
                G.add_node(o, style='filled', color='gray')

        for e in self.directed_edges:
            i = e[0]
            j = e[1]
            print ''
            if e in problem_edges:
                G.add_edge(i, j, color='red')
            else:
                G.add_edge(i, j, color='blue')
        for e in self.failures:
            i = e[0]
            j = e[1]
            if self.failures[e] < max_edge:
                G.add_edge(i, j, color='green', weight=(1-self.failures[e])*10)


        nx.write_dot(G, filename)

 def printDecoder(self, fileName):
     try:
         NX.write_dot(self.decodingTree, fileName)
     except:
         import traceback
         traceback.print_exc()
         print ('Error in printing the decoding tree on file ' + fileName)

def main():
    if len(sys.argv) < 4:
        print('Usage:')
        print('python graphmaker.py [<input> Newick tree file] [<input> cutoff] [<output> DOT file]')
    treefile = sys.argv[1]
    cutoff = sys.argv[2]
    dotfile = sys.argv[3]
    try:
        cutoff = float(cutoff)
    except:
        print('ERROR: expecting a float value for [cutoff]')
        sys.exit()
    
    try:
        tree = Phylo.read(treefile, 'newick')
    except:
        print('ERROR: tree must be in Newick format')
        sys.exit()
    
    GM = GraphMaker(tree)
    edges = GM.cluster(cutoff)
    
    # generate networkx object
    g = nx.Graph()
    for tip1, neighbours in edges.iteritems():
        for tip2, dist in neighbours.iteritems():
            g.add_edge(tip1, tip2, dist=dist)
    
    # each cluster can be examined using networkx functions; for example,
    # clusters = nx.connected_components(g)
    
    # export as GraphViz file
    nx.write_dot(g, dotfile)

    def graph(end_with, start_with):
        #g = xs.connection_graph()
        g = signals.detailed_connection_graph(start_with=start_with,
                                              end_with=end_with)

        nx.write_dot(g, 'graph.dot')
        fabric_api.local('dot -Tpng graph.dot -o graph.png')

def iterate(n_iters):
    for i in tqdm(xrange(n_iters)):
        sampler.sample()
        likelihoods.append(sampler.tree.marg_log_likelihood())

    plt.figure()
    plt.xlabel("Iterations", fontsize=fontsize)
    plt.ylabel("Data Log Likelihood", fontsize=fontsize)
    plt.plot(likelihoods)
    plt.legend(loc='best', fontsize=12)

    plt.savefig('unconstrained-likelihoods.png', bbox_inches='tight')


    final_tree = sampler.tree.copy()

    plt.figure()
    plot_tree_2d(final_tree, X, pca)

    for node in final_tree.dfs():
        if node.is_leaf():
            node.point = y[node.point]

    plt.figure()
    newick = final_tree.to_newick()
    tree = Phylo.read(StringIO(newick), 'newick')

    Phylo.draw_graphviz(tree, prog='neato')
    plt.savefig('unconstrained-tree.png', bbox_inches='tight')
    graph = Phylo.to_networkx(tree)
    with open('unconstrained-tree.nwk', 'w') as fp:
        print >>fp, newick,
    nx.write_dot(graph, 'unconstrained-tree.dot')
    plt.show()

def sampleNodesFromGraph(inputGraph, proportionToKeep): 
        # 0.9 ... keep 90% of the nodes, remove the rest along with incident edges

        filename = inputGraph+'_sampled_'+str(proportionToKeep)
        if os.path.isfile(filename):
                 G = nx.read_dot(filename)
                 print "Cached %s loaded." % filename
                 return G
                 
        Gorig = nx.read_dot(inputGraph)
        G = nx.read_dot(inputGraph)
        #G = nx.Graph(Gorig)
        print "%s loaded." % inputGraph

        nodes = Gorig.nodes()
        random.shuffle(nodes)
        N = len(nodes)
        # keep k nodes
        k = int(round(N*(1-proportionToKeep)))
        
        for n in range(0,k):
                G.remove_node(nodes[n])

        nx.write_dot(G, filename)
        print "\tGraph sampled. Original graph had %d nodes, sampled graph has %d nodes." % (len(Gorig.nodes()), len(G.nodes())) 

        return G

def main():
    files = []
    for i in range(1,26): files.append("db/Minna_no_nihongo_1.%02d.txt" % i)
    for i in range(26,51): files.append("db/Minna_no_nihongo_2.%02d.txt" % i)


    data = get_words_from_files(files)
    words = [w for w in data]
    #print words
    G=nx.Graph()
    for word1, word2 in itertools.combinations(words,2):
        for w1 in word1[:-1]:
            #print w1.encode('utf-8')
            #print ud.name(w1)
            if "CJK UNIFIED" in ud.name(w1) and w1 in word2:
                #print word1.encode('utf-8'), word2.encode('utf-8')
                G.add_edge(word1, word2)
                break
    
    nx.draw(G)
    nx.write_dot(G, "kanjis.dot")
    nx.write_graphml(G, "kanjis.graphml")
    #plt.show()

    words = G.nodes()

    with open('kanjis.json', 'w') as f:
        json.dump({'nodes': [{'name': i.encode('utf-8'), 
                              'kana': data[i]['kana'], 
                              'chapter': data[i]['chapter'],
                              'meaning': data[i]['meaning']} for i in G.nodes()], 
                   'links': list(map(lambda u: {'source': words.index(u[0]), 'target': words.index(u[1])}, G.edges()))}, 
              f, indent=2,)

 def build_network(self, nodes, nodesizes, weights,
                   outfile = 'network.dot', nodeprop=None):
     '''
     Not working yet
     Nodes represents the states
     '''
     nodes=np.array(nodes)
     import networkx as nx
     G = nx.Graph()
     
     if nodeprop is not None:
         for i in range(nodes.size):
             G.add_node(int(nodes[i]), size=int(nodesizes[i]),
                         label=int(nodes[i]), prop=nodeprop[i])
     else:
         for i in range(nodes.size):
             G.add_node(int(nodes[i]), size=int(nodesizes[i]),
                         label=int(nodes[i]))
          
     for i in range(weights.shape[0]):
         w = weights[i, 2]
         G.add_edge(int(weights[i, 0]), int(weights[i, 1]),
                     weight=float(w))
         
     nx.write_dot(G, outfile)
     outfile1 = outfile.replace('.dot', '.gml')
     nx.write_gml(G, outfile1)

    def export(self, name=None, valuation=None):
        tmpdir = 'tmp/'
#        dotpgm = 'dot'
        filename = tmpdir + self.automaton.graph['name']
        if name:
            filename = tmpdir + name
        
        dotfile = filename + '.dot'
#        pngfile = filename + '.png'
        
        if valuation:
            # We now want to remove any edges that are not in the valuation 
            for fv, tv, key, dct in self.get_transitions(keys=True):
                if valuation.get_var_val(dct['f_var']) == 0:
                    self.automaton.remove_edge(fv, tv, key=key)
                else:
                    fvar = str(valuation.get_var_val(dct['f_var']))
                    self.automaton.edge[fv][tv][key]['label'] = fvar
            # Now we want to remove any orphaned nodes
            for node, deg in self.automaton.degree().iteritems():
                if deg == 0:
                    self.automaton.remove_node(node)
            
            
        networkx.write_dot(self.automaton, dotfile)

def genome_animation(genomes_files, indir, outdir=None):

    # by default the same 
    if outdir == None :
        outdir = indir
    
    # create dot files 
    last_genome_file = genomes_files[-1]
    last_genome = process_graph(indir+'/'+last_genome_file)
    for gf in genomes_files :
        graph_of_g = graph_from_graph(last_genome, indir+'/'+gf)
        nx.write_dot(graph_of_g, outdir+'/'+gf[:-4]+'.dot')
        
    # create png files 
    png_filenames = generate_fname_seq(len(genomes_files), 'png')
    i=0
    for gf in genomes_files :
        dot2png(outdir+'/'+gf[:-4]+'.dot', outdir+'/'+png_filenames[i])
        i=i+1

    # print the command line to create the movie 
    zpad = len(str(i)) 
    cmd_line = 'ffmpeg -framerate 1 -i '+outdir+'/'+'%0'+str(zpad)+'d.png  -c:v libx264 -pix_fmt yuv420p '+outdir+'/out.mp4';
    print 'To create the movies run the following command:'
    print cmd_line

def create_phylo_tree(fname, save=False, dotfile='philo.dot', xover=False, prune=False): 
    colors = ['chartreuse', 'chocolate', 'cadetblue', 'cornflowerblue', 'cyan',
              'darkorange', 'darkviolet', 'deeppink']
    #TODO check how to define hexadecimal colors for GraphViz
    colorsH = ["#7FFF00", "#D2691E", "#5F9EA0", "#6495ED", "#00FFFF",
              "#FF8C00", "#9400D3", "#F1493"]

    # create a graph
    G=nx.MultiDiGraph()        

    # fill the lists with all the genes 
    gl = process_file(fname)
    # create the phylo-tree
    for n in gl.keys():
        G.add_node(n) # the root node (the initial genome)
        G.node[n]['agent'] = n
        G.node[n]['id']    = n
        G.node[n]['color'] = colors[n%len(colors)]
        trac_genome(gl, n, G, colors)
    
    if xover:
        G=add_dad_links(G,gl)
    
    if prune:
        id_last_epoch= max(G.nodes()) - len(gl.keys()) + 1
        nb_epochs= len(G.nodes())/len(gl.keys())
        G=prune_tree(G,id_last_epoch,nb_epochs)

    # write the file 
    if save :
        nx.write_dot(G, dotfile)
    
    return G

def writeExprTree(G,filename='ExprTree.dot'):
    """
    Writes a tree in the DOT format:
        - http://en.wikipedia.org/wiki/DOT_language
        - http://www.graphviz.org/
    """
    nx.write_dot(G,filename)

 def to_dot_file(self, filename):
     '''把图写入到dot文件中，不对原图做什么改变
         新图的节点只是字符串。
     '''
     new_graph = nx.DiGraph()
     for start, end, data  in self.edges_iter(data = True):
         port_pair = data['port_pair']
         connection = data['connection']
         edge = [start, end] # 存储边的起点和终点
         node_id =['','']    # 存储节点的名称
         node_data =[{},{}]  # 存储要打印到dot中的信息
         for i in range(2):
             # 当前节点是prim 或者是 port
             is_prim = True if isinstance(edge[i], cc.circut_module) else False
             # prim和port的数据属性不同，根据判断为生成dot节点的名称，和节点附属的['shape']数据
             node_name = '_d_'+edge[i].name[1:] if edge[i].name[0]=='\\' else edge[i].name 
             node_id[i] = edge[i].cellref+node_name if is_prim else\
                          edge[i].port_type+node_name
             # prim为box形状（盒子），port为invtriangle形状（倒三角）
             node_data[i]['shape'] = 'box' if is_prim else 'invtriangle' 
             new_graph.add_node(node_id[i],node_data[i])
         new_graph.add_edge(node_id[0], node_id[1])
     try:
         nx.write_dot(new_graph, filename)
     except Exception, e:
         print "Warning: Cannot write dot file", e

def export_graph(
    graph_in,
    base_dir=None,
    show=False,
    use_execgraph=False,
    show_connectinfo=False,
    dotfilename="graph.dot",
    format="png",
    simple_form=True,
):
    """ Displays the graph layout of the pipeline

    This function requires that pygraphviz and matplotlib are available on
    the system.

    Parameters
    ----------

    show : boolean
    Indicate whether to generate pygraphviz output fromn
    networkx. default [False]

    use_execgraph : boolean
    Indicates whether to use the specification graph or the
    execution graph. default [False]

    show_connectioninfo : boolean
    Indicates whether to show the edge data on the graph. This
    makes the graph rather cluttered. default [False]
    """
    graph = deepcopy(graph_in)
    if use_execgraph:
        graph = generate_expanded_graph(graph)
        logger.debug("using execgraph")
    else:
        logger.debug("using input graph")
    if base_dir is None:
        base_dir = os.getcwd()
    if not os.path.exists(base_dir):
        os.makedirs(base_dir)
    outfname = fname_presuffix(dotfilename, suffix="_detailed.dot", use_ext=False, newpath=base_dir)
    logger.info("Creating detailed dot file: %s" % outfname)
    _write_detailed_dot(graph, outfname)
    cmd = "dot -T%s -O %s" % (format, outfname)
    res = CommandLine(cmd, terminal_output="allatonce").run()
    if res.runtime.returncode:
        logger.warn("dot2png: %s", res.runtime.stderr)
    pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form)
    outfname = fname_presuffix(dotfilename, suffix=".dot", use_ext=False, newpath=base_dir)
    nx.write_dot(pklgraph, outfname)
    logger.info("Creating dot file: %s" % outfname)
    cmd = "dot -T%s -O %s" % (format, outfname)
    res = CommandLine(cmd, terminal_output="allatonce").run()
    if res.runtime.returncode:
        logger.warn("dot2png: %s", res.runtime.stderr)
    if show:
        pos = nx.graphviz_layout(pklgraph, prog="dot")
        nx.draw(pklgraph, pos)
        if show_connectinfo:
            nx.draw_networkx_edge_labels(pklgraph, pos)

	def testDot(self):
		self.assertEqual( self.g.number_of_edges(), 4 )	
		self.assertEqual( self.g.number_of_edges(), 4 )	
		nx.write_dot( self.g, './test.dot' )
		g1 = nx.read_dot( './test.dot' )
		self.assertEqual( g1.number_of_edges(), self.g.number_of_edges() )
		self.assertEqual( g1.number_of_edges(), 4 )