1 """ 2 ********** 3 Edge Lists 4 ********** 5 Read and write NetworkX graphs as edge lists. 6 7 The multi-line adjacency list format is useful for graphs with nodes 8 that can be meaningfully represented as strings. With the edgelist 9 format simple edge data can be stored but node or graph data is not. 10 There is no way of representing isolated nodes unless the node has a 11 self-loop edge. 12 13 Format 14 ------ 15 You can read or write three formats of edge lists with these functions. 16 17 Node pairs with no data:: 18 19 1 2 20 21 Python dictionary as data:: 22 23 1 2 {'weight':7, 'color':'green'} 24 25 Arbitrary data:: 26 27 1 2 7 green 28 """ 29 __author__ = """Aric Hagberg (hagberg (at] lanl.gov)\nDan Schult (dschult (at] colgate.edu)""" 30 # Copyright (C) 2004-2011 by 31 # Aric Hagberg <hagberg (at] lanl.gov> 32 # Dan Schult <dschult (at] colgate.edu> 33 # Pieter Swart <swart (at] lanl.gov> 34 # All rights reserved. 35 # BSD license. 36 37 __all__ = ['generate_edgelist', 38 'write_edgelist', 39 'parse_edgelist', 40 'read_edgelist', 41 'read_weighted_edgelist', 42 'write_weighted_edgelist'] 43 44 from networkx.utils import open_file, make_str 45 import networkx as nx 46 47 def generate_edgelist(G, delimiter=' ', data=True): 48 """Generate a single line of the graph G in edge list format. 49 50 Parameters 51 ---------- 52 G : NetworkX graph 53 54 delimiter : string, optional 55 Separator for node labels 56 57 data : bool or list of keys 58 If False generate no edge data. If True use a dictionary 59 representation of edge data. If a list of keys use a list of data 60 values corresponding to the keys. 61 62 Returns 63 ------- 64 lines : string 65 Lines of data in adjlist format. 66 67 Examples 68 -------- 69 >>> G = nx.lollipop_graph(4, 3) 70 >>> G[1][2]['weight'] = 3 71 >>> G[3][4]['capacity'] = 12 72 >>> for line in nx.generate_edgelist(G, data=False): 73 ... print(line) 74 0 1 75 0 2 76 0 3 77 1 2 78 1 3 79 2 3 80 3 4 81 4 5 82 5 6 83 84 >>> for line in nx.generate_edgelist(G): 85 ... print(line) 86 0 1 {} 87 0 2 {} 88 0 3 {} 89 1 2 {'weight': 3} 90 1 3 {} 91 2 3 {} 92 3 4 {'capacity': 12} 93 4 5 {} 94 5 6 {} 95 96 >>> for line in nx.generate_edgelist(G,data=['weight']): 97 ... print(line) 98 0 1 99 0 2 100 0 3 101 1 2 3 102 1 3 103 2 3 104 3 4 105 4 5 106 5 6 107 108 See Also 109 -------- 110 write_adjlist, read_adjlist 111 """ 112 if data is True or data is False: 113 for e in G.edges(data=data): 114 yield delimiter.join(map(make_str,e)) 115 else: 116 for u,v,d in G.edges(data=True): 117 e=[u,v] 118 try: 119 e.extend(d[k] for k in data) 120 except KeyError: 121 pass # missing data for this edge, should warn? 122 yield delimiter.join(map(make_str,e)) 123 124 @open_file(1,mode='wb') 125 def write_edgelist(G, path, comments="#", delimiter=' ', data=True, 126 encoding = 'utf-8'): 127 """Write graph as a list of edges. 128 129 Parameters 130 ---------- 131 G : graph 132 A NetworkX graph 133 path : file or string 134 File or filename to write. If a file is provided, it must be 135 opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed. 136 comments : string, optional 137 The character used to indicate the start of a comment 138 delimiter : string, optional 139 The string used to separate values. The default is whitespace. 140 data : bool or list, optional 141 If False write no edge data. 142 If True write a string representation of the edge data dictionary.. 143 If a list (or other iterable) is provided, write the keys specified 144 in the list. 145 encoding: string, optional 146 Specify which encoding to use when writing file. 147 148 Examples 149 -------- 150 >>> G=nx.path_graph(4) 151 >>> nx.write_edgelist(G, "test.edgelist") 152 >>> G=nx.path_graph(4) 153 >>> fh=open("test.edgelist",'wb') 154 >>> nx.write_edgelist(G, fh) 155 >>> nx.write_edgelist(G, "test.edgelist.gz") 156 >>> nx.write_edgelist(G, "test.edgelist.gz", data=False) 157 158 >>> G=nx.Graph() 159 >>> G.add_edge(1,2,weight=7,color='red') 160 >>> nx.write_edgelist(G,'test.edgelist',data=False) 161 >>> nx.write_edgelist(G,'test.edgelist',data=['color']) 162 >>> nx.write_edgelist(G,'test.edgelist',data=['color','weight']) 163 164 See Also 165 -------- 166 write_edgelist() 167 write_weighted_edgelist() 168 """ 169 170 for line in generate_edgelist(G, delimiter, data): 171 line+='\n' 172 path.write(line.encode(encoding)) 173 174 def parse_edgelist(lines, comments='#', delimiter=None, 175 create_using=None, nodetype=None, data=True): 176 """Parse lines of an edge list representation of a graph. 177 178 179 Returns 180 ------- 181 G: NetworkX Graph 182 The graph corresponding to lines 183 data : bool or list of (label,type) tuples 184 If False generate no edge data or if True use a dictionary 185 representation of edge data or a list tuples specifying dictionary 186 key names and types for edge data. 187 create_using: NetworkX graph container, optional 188 Use given NetworkX graph for holding nodes or edges. 189 nodetype : Python type, optional 190 Convert nodes to this type. 191 comments : string, optional 192 Marker for comment lines 193 delimiter : string, optional 194 Separator for node labels 195 create_using: NetworkX graph container 196 Use given NetworkX graph for holding nodes or edges. 197 198 Examples 199 -------- 200 Edgelist with no data: 201 202 >>> lines = ["1 2", 203 ... "2 3", 204 ... "3 4"] 205 >>> G = nx.parse_edgelist(lines, nodetype = int) 206 >>> G.nodes() 207 [1, 2, 3, 4] 208 >>> G.edges() 209 [(1, 2), (2, 3), (3, 4)] 210 211 Edgelist with data in Python dictionary representation: 212 213 >>> lines = ["1 2 {'weight':3}", 214 ... "2 3 {'weight':27}", 215 ... "3 4 {'weight':3.0}"] 216 >>> G = nx.parse_edgelist(lines, nodetype = int) 217 >>> G.nodes() 218 [1, 2, 3, 4] 219 >>> G.edges(data = True) 220 [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})] 221 222 Edgelist with data in a list: 223 224 >>> lines = ["1 2 3", 225 ... "2 3 27", 226 ... "3 4 3.0"] 227 >>> G = nx.parse_edgelist(lines, nodetype = int, data=(('weight',float),)) 228 >>> G.nodes() 229 [1, 2, 3, 4] 230 >>> G.edges(data = True) 231 [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})] 232 233 See Also 234 -------- 235 read_weighted_edgelist 236 237 """ 238 from ast import literal_eval 239 if create_using is None: 240 G=nx.Graph() 241 else: 242 try: 243 G=create_using 244 G.clear() 245 except: 246 raise TypeError("create_using input is not a NetworkX graph type") 247 248 for line in lines: 249 p=line.find(comments) 250 if p>=0: 251 line = line[:p] 252 if not len(line): 253 continue 254 # split line, should have 2 or more 255 s=line.strip().split(delimiter) 256 if len(s)<2: 257 continue 258 u=s.pop(0) 259 v=s.pop(0) 260 d=s 261 if nodetype is not None: 262 try: 263 u=nodetype(u) 264 v=nodetype(v) 265 except: 266 raise TypeError("Failed to convert nodes %s,%s to type %s." 267 %(u,v,nodetype)) 268 269 if len(d)==0 or data is False: 270 # no data or data type specified 271 edgedata={} 272 elif data is True: 273 # no edge types specified 274 try: # try to evaluate as dictionary 275 edgedata=dict(literal_eval(' '.join(d))) 276 except: 277 raise TypeError( 278 "Failed to convert edge data (%s) to dictionary."%(d)) 279 else: 280 # convert edge data to dictionary with specified keys and type 281 if len(d)!=len(data): 282 raise IndexError( 283 "Edge data %s and data_keys %s are not the same length"% 284 (d, data)) 285 edgedata={} 286 for (edge_key,edge_type),edge_value in zip(data,d): 287 try: 288 edge_value=edge_type(edge_value) 289 except: 290 raise TypeError( 291 "Failed to convert %s data %s to type %s." 292 %(edge_key, edge_value, edge_type)) 293 edgedata.update({edge_key:edge_value}) 294 G.add_edge(u, v, attr_dict=edgedata) 295 return G 296 297 @open_file(0,mode='rb') 298 def read_edgelist(path, comments="#", delimiter=None, create_using=None, 299 nodetype=None, data=True, edgetype=None, encoding='utf-8'): 300 """Read a graph from a list of edges. 301 302 Parameters 303 ---------- 304 path : file or string 305 File or filename to write. If a file is provided, it must be 306 opened in 'rb' mode. 307 Filenames ending in .gz or .bz2 will be uncompressed. 308 comments : string, optional 309 The character used to indicate the start of a comment. 310 delimiter : string, optional 311 The string used to separate values. The default is whitespace. 312 create_using : Graph container, optional, 313 Use specified container to build graph. The default is networkx.Graph, 314 an undirected graph. 315 nodetype : int, float, str, Python type, optional 316 Convert node data from strings to specified type 317 data : bool or list of (label,type) tuples 318 Tuples specifying dictionary key names and types for edge data 319 edgetype : int, float, str, Python type, optional OBSOLETE 320 Convert edge data from strings to specified type and use as 'weight' 321 encoding: string, optional 322 Specify which encoding to use when reading file. 323 324 Returns 325 ------- 326 G : graph 327 A networkx Graph or other type specified with create_using 328 329 Examples 330 -------- 331 >>> nx.write_edgelist(nx.path_graph(4), "test.edgelist") 332 >>> G=nx.read_edgelist("test.edgelist") 333 334 >>> fh=open("test.edgelist", 'rb') 335 >>> G=nx.read_edgelist(fh) 336 >>> fh.close() 337 338 >>> G=nx.read_edgelist("test.edgelist", nodetype=int) 339 >>> G=nx.read_edgelist("test.edgelist",create_using=nx.DiGraph()) 340 341 Edgelist with data in a list: 342 343 >>> textline = '1 2 3' 344 >>> fh = open('test.edgelist','w') 345 >>> d = fh.write(textline) 346 >>> fh.close() 347 >>> G = nx.read_edgelist('test.edgelist', nodetype=int, data=(('weight',float),)) 348 >>> G.nodes() 349 [1, 2] 350 >>> G.edges(data = True) 351 [(1, 2, {'weight': 3.0})] 352 353 See parse_edgelist() for more examples of formatting. 354 355 See Also 356 -------- 357 parse_edgelist 358 359 Notes 360 ----- 361 Since nodes must be hashable, the function nodetype must return hashable 362 types (e.g. int, float, str, frozenset - or tuples of those, etc.) 363 """ 364 lines = (line.decode(encoding) for line in path) 365 return parse_edgelist(lines,comments=comments, delimiter=delimiter, 366 create_using=create_using, nodetype=nodetype, 367 data=data) 368 369 370 def write_weighted_edgelist(G, path, comments="#", 371 delimiter=' ', encoding='utf-8'): 372 """Write graph G as a list of edges with numeric weights. 373 374 Parameters 375 ---------- 376 G : graph 377 A NetworkX graph 378 path : file or string 379 File or filename to write. If a file is provided, it must be 380 opened in 'wb' mode. 381 Filenames ending in .gz or .bz2 will be compressed. 382 comments : string, optional 383 The character used to indicate the start of a comment 384 delimiter : string, optional 385 The string used to separate values. The default is whitespace. 386 encoding: string, optional 387 Specify which encoding to use when writing file. 388 389 Examples 390 -------- 391 >>> G=nx.Graph() 392 >>> G.add_edge(1,2,weight=7) 393 >>> nx.write_weighted_edgelist(G, 'test.weighted.edgelist') 394 395 See Also 396 -------- 397 read_edgelist() 398 write_edgelist() 399 write_weighted_edgelist() 400 401 """ 402 write_edgelist(G,path, comments=comments, delimiter=delimiter, 403 data=('weight',), encoding = encoding) 404 405 def read_weighted_edgelist(path, comments="#", delimiter=None, 406 create_using=None, nodetype=None, encoding='utf-8'): 407 408 """Read a graph as list of edges with numeric weights. 409 410 Parameters 411 ---------- 412 path : file or string 413 File or filename to write. If a file is provided, it must be 414 opened in 'rb' mode. 415 Filenames ending in .gz or .bz2 will be uncompressed. 416 comments : string, optional 417 The character used to indicate the start of a comment. 418 delimiter : string, optional 419 The string used to separate values. The default is whitespace. 420 create_using : Graph container, optional, 421 Use specified container to build graph. The default is networkx.Graph, 422 an undirected graph. 423 nodetype : int, float, str, Python type, optional 424 Convert node data from strings to specified type 425 encoding: string, optional 426 Specify which encoding to use when reading file. 427 428 Returns 429 ------- 430 G : graph 431 A networkx Graph or other type specified with create_using 432 433 Notes 434 ----- 435 Since nodes must be hashable, the function nodetype must return hashable 436 types (e.g. int, float, str, frozenset - or tuples of those, etc.) 437 438 Example edgelist file format. 439 440 With numeric edge data:: 441 442 # read with 443 # >>> G=nx.read_weighted_edgelist(fh) 444 # source target data 445 a b 1 446 a c 3.14159 447 d e 42 448 """ 449 return read_edgelist(path, 450 comments=comments, 451 delimiter=delimiter, 452 create_using=create_using, 453 nodetype=nodetype, 454 data=(('weight',float),), 455 encoding = encoding 456 ) 457 458 459 # fixture for nose tests 460 def teardown_module(module): 461 import os 462 os.unlink('test.edgelist') 463 os.unlink('test.edgelist.gz') 464 os.unlink('test.weighted.edgelist') 465
