view convert_graph.py @ 0:fe01a054a6b2 draft

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author bernhardlutz
date Fri, 28 Feb 2014 08:57:44 -0500
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#!/usr/bin/env python
# Aufruf convert_graph.py --infile datei --informat typ --outfile ausgabedatei --outformat ausgabetyp

import sys, os
import networkx as nx
import argparse
import json

from xgmml_networkx import XGMMLParserHelper, XGMMLWriter
from networkx.readwrite import json_graph

#supported graph_types
graph_types = ["gml", "yaml", "gspan", "xgmml", "gexf", "graphml", "json", "pajek"]

func_dic_read= {'gml': nx.read_gml, 'yaml':nx.read_yaml, 'gexf': nx.read_gexf,
    'graphml': nx.read_graphml, 'pajek': nx.read_pajek}
    
func_dic_write= {'gml': nx.write_gml, 'yaml':nx.write_yaml, 'gexf': nx.write_gexf,
    'graphml': nx.write_graphml, 'pajek': nx.write_pajek}

#completely supported types by networkx
completely_supported_types = ["gml", "gexf", "yaml", "graphml", "pajek"]

def read_gspan(infile):
    G = nx.Graph()
    idoffset=0
    old_id_start=0
    for line in infile:
        line_split=line.split(" ")
        if line[0] == "v":
            G.add_node(idoffset, label=line_split[2].strip())
            idoffset+=1
        elif line[0] == "e":
            G.add_edge(old_id_start+int(line_split[1]), old_id_start+int(line_split[2]), label=line_split[3].strip())
        elif line[0] == "t":
        # its a new subgraph
            #idoffset*=1
            old_id_start=idoffset
    #print(nx.is_connected(G))
    return G
    

def write_gspan(graph, outfile):
    # get all subgraphs only works with undirected
    subgraphs=nx.connected_components(graph.to_undirected())
    id_count=1
    node_count=0
    #get labels
    label_dic=nx.get_node_attributes(graph,'label')
    for s in subgraphs:
        node_count_tree=0
        node_dict={}
        outfile.write("t # id "+str(id_count)+"\n")
        # for every node in subgraph
        for v in sorted(s):
        # node id restart from 0 for every sub graph
            node_dict[v]=node_count_tree
            outfile.write("v "+str(node_count_tree)+" "+label_dic[v]+" \n")
            node_count_tree+=1
            node_count+=1
            
        # all edges adjacent to a node of s
        edges=nx.edges(graph, s)
        for e in sorted(edges):
            #print(graph[e[0]][e[1]])
            outfile.write("e "+str(node_dict[e[0]])+" "+str(node_dict[e[1]])+" "+graph[e[0]][e[1]]['label']+"\n")
            
        id_count+=1
def read_json(file):
    json_string=file.read()
    print(json_string)
    json_dict=json.loads(json_string)
    print(json_dict)
    return nx.Graph()
    
def write_json(graph, outfile):
    json_dict=json_graph.node_link_data(graph)
    json_string=json.dumbs(json_dict)
    outfile.write(json_string)
    print("did it")
    
def main( args ):

    if args.informat not in graph_types:
        print "EXCEPTION COMPUTER EXPLODING"
    # everything networkx can do by itself ;)
    elif args.informat in completely_supported_types:
        function = func_dic_read[args.informat]
        graph = function(args.infile)
    elif args.informat == "gspan":
        graph = read_gspan(args.infile)
    elif args.informat == "json":
        graph = read_json(args.infile)
    elif args.informat == "xgmml":
        xgmml=XGMMLParserHelper()
        xgmml.parseFile(args.infile)
        graph=xgmml.graph()



    if args.outformat in completely_supported_types:
        function = func_dic_write[args.outformat]
        function(graph, args.outfile)
    elif args.outformat == "gspan":
        write_gspan(graph, args.outfile)
    elif args.outformat == "json":
        write_json(graph, args.outfile)
    elif args.outformat == "xgmml":  
    #xgmml=XGMMLParserHelper(graph)
    #xgmml.parseFile(open(sys.argv[1]))
        a=XGMMLWriter(args.outfile, graph, "MyGraph")
    
if __name__ == "__main__":
    
    parser = argparse.ArgumentParser()
    parser.add_argument('--infile', type=argparse.FileType('r'),
        help="Specify the input file representing a graph")
    parser.add_argument('--outfile', type=argparse.FileType('w'),
        help="Specify one output file")
    parser.add_argument('--informat', type=str,
        help="Specify the format of the input graph", choices = graph_types)
    parser.add_argument('--outformat', type=str,
        help="Specify the format of the output graph", choices = graph_types)
    if len(sys.argv) < 8:
        print "Too few arguments..."
        parser.print_help()
        exit(1)
    args = parser.parse_args()
    main( args )