NetworkX

Source code for networkx.readwrite.gexf

"""
****
GEXF
****
Read and write graphs in GEXF format.

GEXF (Graph Exchange XML Format) is a language for describing complex
network structures, their associated data and dynamics.

This implementation does not support mixed graphs (directed and
unidirected edges together).

Format
------
GEXF is an XML format.  See http://gexf.net/format/schema.html for the
specification and http://gexf.net/format/basic.html for examples.
"""
# Based on GraphML NetworkX GraphML reader
import itertools
import networkx as nx
from networkx.utils import open_file, make_str
try:
    from xml.etree.cElementTree import Element, ElementTree, tostring
except ImportError:
    try:
        from xml.etree.ElementTree import Element, ElementTree, tostring
    except ImportError:
        pass
__author__ = """\n""".join(['Aric Hagberg (hagberg@lanl.gov)'])
__all__ = ['write_gexf', 'read_gexf', 'relabel_gexf_graph', 'generate_gexf']


@open_file(1,mode='wb')
[docs]def write_gexf(G, path, encoding='utf-8',prettyprint=True,version='1.1draft'): """Write G in GEXF format to path. "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Parameters ---------- G : graph A NetworkX graph path : file or string File or filename to write. Filenames ending in .gz or .bz2 will be compressed. encoding : string (optional) Encoding for text data. prettyprint : bool (optional) If True use line breaks and indenting in output XML. Examples -------- >>> G=nx.path_graph(4) >>> nx.write_gexf(G, "test.gexf") Notes ----- This implementation does not support mixed graphs (directed and unidirected edges together). The node id attribute is set to be the string of the node label. If you want to specify an id use set it as node data, e.g. node['a']['id']=1 to set the id of node 'a' to 1. References ---------- .. [1] GEXF graph format, http://gexf.net/format/ """ writer = GEXFWriter(encoding=encoding,prettyprint=prettyprint, version=version) writer.add_graph(G) writer.write(path)
def generate_gexf(G, encoding='utf-8',prettyprint=True,version='1.1draft'): """Generate lines of GEXF format representation of G" "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Parameters ---------- G : graph A NetworkX graph encoding : string (optional) Encoding for text data. prettyprint : bool (optional) If True use line breaks and indenting in output XML. Examples -------- >>> G=nx.path_graph(4) >>> linefeed=chr(10) # linefeed=\n >>> s=linefeed.join(nx.generate_gexf(G)) # doctest: +SKIP >>> for line in nx.generate_gexf(G): # doctest: +SKIP ... print line Notes ----- This implementation does not support mixed graphs (directed and unidirected edges together). The node id attribute is set to be the string of the node label. If you want to specify an id use set it as node data, e.g. node['a']['id']=1 to set the id of node 'a' to 1. References ---------- .. [1] GEXF graph format, http://gexf.net/format/ """ writer = GEXFWriter(encoding=encoding,prettyprint=prettyprint, version=version) writer.add_graph(G) for line in str(writer).splitlines(): yield line @open_file(0,mode='rb')
[docs]def read_gexf(path,node_type=str,relabel=False,version='1.1draft'): """Read graph in GEXF format from path. "GEXF (Graph Exchange XML Format) is a language for describing complex networks structures, their associated data and dynamics" [1]_. Parameters ---------- path : file or string File or filename to write. Filenames ending in .gz or .bz2 will be compressed. node_type: Python type (default: str) Convert node ids to this type relabel : bool (default: False) If True relabel the nodes to use the GEXF node "label" attribute instead of the node "id" attribute as the NetworkX node label. Returns ------- graph: NetworkX graph If no parallel edges are found a Graph or DiGraph is returned. Otherwise a MultiGraph or MultiDiGraph is returned. Notes ----- This implementation does not support mixed graphs (directed and unidirected edges together). References ---------- .. [1] GEXF graph format, http://gexf.net/format/ """ reader = GEXFReader(node_type=node_type,version=version) if relabel: G=relabel_gexf_graph(reader(path)) else: G=reader(path) return G
class GEXF(object): # global register_namespace versions={} d={'NS_GEXF':"http://www.gexf.net/1.1draft", 'NS_VIZ':"http://www.gexf.net/1.1draft/viz", 'NS_XSI':"http://www.w3.org/2001/XMLSchema-instance", 'SCHEMALOCATION':' '.join(['http://www.gexf.net/1.1draft', 'http://www.gexf.net/1.1draft/gexf.xsd' ]), 'VERSION':'1.1' } versions['1.1draft']=d d={'NS_GEXF':"http://www.gexf.net/1.2draft", 'NS_VIZ':"http://www.gexf.net/1.2draft/viz", 'NS_XSI':"http://www.w3.org/2001/XMLSchema-instance", 'SCHEMALOCATION':' '.join(['http://www.gexf.net/1.2draft', 'http://www.gexf.net/1.2draft/gexf.xsd' ]), 'VERSION':'1.2' } versions['1.2draft']=d types=[(int,"integer"), (float,"float"), (float,"double"), (bool,"boolean"), (list,"string"), (dict,"string"), ] try: # Python 3.x blurb = chr(1245) # just to trigger the exception types.extend([ (str,"liststring"), (str,"anyURI"), (str,"string")]) except ValueError: # Python 2.6+ types.extend([ (str,"liststring"), (str,"anyURI"), (str,"string"), (unicode,"liststring"), (unicode,"anyURI"), (unicode,"string")]) xml_type = dict(types) python_type = dict(reversed(a) for a in types) convert_bool={'true':True,'false':False} # try: # register_namespace = ET.register_namespace # except AttributeError: # def register_namespace(prefix, uri): # ET._namespace_map[uri] = prefix def set_version(self,version): d=self.versions.get(version) if d is None: raise nx.NetworkXError('Unknown GEXF version %s'%version) self.NS_GEXF = d['NS_GEXF'] self.NS_VIZ = d['NS_VIZ'] self.NS_XSI = d['NS_XSI'] self.SCHEMALOCATION = d['NS_XSI'] self.VERSION=d['VERSION'] self.version=version # register_namespace('viz', d['NS_VIZ']) class GEXFWriter(GEXF): # class for writing GEXF format files # use write_gexf() function def __init__(self, graph=None, encoding="utf-8", mode='static',prettyprint=True, version='1.1draft'): try: import xml.etree.ElementTree except ImportError: raise ImportError('GEXF writer requires ' 'xml.elementtree.ElementTree') self.prettyprint=prettyprint self.mode=mode self.encoding = encoding self.set_version(version) self.xml = Element("gexf", {'xmlns':self.NS_GEXF, 'xmlns:xsi':self.NS_XSI, 'xmlns:viz':self.NS_VIZ, 'xsi:schemaLocation':self.SCHEMALOCATION, 'version':self.VERSION}) # counters for edge and attribute identifiers self.edge_id=itertools.count() self.attr_id=itertools.count() # default attributes are stored in dictionaries self.attr={} self.attr['node']={} self.attr['edge']={} self.attr['node']['dynamic']={} self.attr['node']['static']={} self.attr['edge']['dynamic']={} self.attr['edge']['static']={} if graph is not None: self.add_graph(graph) def __str__(self): if self.prettyprint: self.indent(self.xml) s=tostring(self.xml).decode(self.encoding) return s def add_graph(self, G): # Add a graph element to the XML if G.is_directed(): default='directed' else: default='undirected' graph_element = Element("graph",defaultedgetype=default,mode=self.mode) self.graph_element=graph_element self.add_nodes(G,graph_element) self.add_edges(G,graph_element) self.xml.append(graph_element) def add_nodes(self, G, graph_element): nodes_element = Element('nodes') for node,data in G.nodes_iter(data=True): node_data=data.copy() node_id = make_str(node_data.pop('id', node)) kw={'id':node_id} label = make_str(node_data.pop('label', node)) kw['label']=label try: pid=node_data.pop('pid') kw['pid'] = make_str(pid) except KeyError: pass # add node element with attributes node_element = Element("node", **kw) # add node element and attr subelements default=G.graph.get('node_default',{}) node_data=self.add_parents(node_element, node_data) if self.version=='1.1': node_data=self.add_slices(node_element, node_data) else: node_data=self.add_spells(node_element, node_data) node_data=self.add_viz(node_element,node_data) node_data=self.add_attributes("node", node_element, node_data, default) nodes_element.append(node_element) graph_element.append(nodes_element) def add_edges(self, G, graph_element): def edge_key_data(G): # helper function to unify multigraph and graph edge iterator if G.is_multigraph(): for u,v,key,data in G.edges_iter(data=True,keys=True): edge_data=data.copy() edge_data.update(key=key) edge_id=edge_data.pop('id',None) if edge_id is None: edge_id=next(self.edge_id) yield u,v,edge_id,edge_data else: for u,v,data in G.edges_iter(data=True): edge_data=data.copy() edge_id=edge_data.pop('id',None) if edge_id is None: edge_id=next(self.edge_id) yield u,v,edge_id,edge_data edges_element = Element('edges') for u,v,key,edge_data in edge_key_data(G): kw={'id':make_str(key)} try: edge_weight=edge_data.pop('weight') kw['weight']=make_str(edge_weight) except KeyError: pass try: edge_type=edge_data.pop('type') kw['type']=make_str(edge_type) except KeyError: pass edge_element = Element("edge", source=make_str(u),target=make_str(v), **kw) default=G.graph.get('edge_default',{}) edge_data=self.add_viz(edge_element,edge_data) edge_data=self.add_attributes("edge", edge_element, edge_data, default) edges_element.append(edge_element) graph_element.append(edges_element) def add_attributes(self, node_or_edge, xml_obj, data, default): # Add attrvalues to node or edge attvalues=Element('attvalues') if len(data)==0: return data if 'start' in data or 'end' in data: mode='dynamic' else: mode='static' for k,v in data.items(): # rename generic multigraph key to avoid any name conflict if k == 'key': k='networkx_key' attr_id = self.get_attr_id(make_str(k), self.xml_type[type(v)], node_or_edge, default, mode) if type(v)==list: # dynamic data for val,start,end in v: e=Element("attvalue") e.attrib['for']=attr_id e.attrib['value']=make_str(val) e.attrib['start']=make_str(start) e.attrib['end']=make_str(end) attvalues.append(e) else: # static data e=Element("attvalue") e.attrib['for']=attr_id e.attrib['value']=make_str(v) attvalues.append(e) xml_obj.append(attvalues) return data def get_attr_id(self, title, attr_type, edge_or_node, default, mode): # find the id of the attribute or generate a new id try: return self.attr[edge_or_node][mode][title] except KeyError: # generate new id new_id=str(next(self.attr_id)) self.attr[edge_or_node][mode][title] = new_id attr_kwargs = {"id":new_id, "title":title, "type":attr_type} attribute=Element("attribute",**attr_kwargs) # add subelement for data default value if present default_title=default.get(title) if default_title is not None: default_element=Element("default") default_element.text=make_str(default_title) attribute.append(default_element) # new insert it into the XML attributes_element=None for a in self.graph_element.findall("attributes"): # find existing attributes element by class and mode a_class=a.get('class') a_mode=a.get('mode','static') # default mode is static if a_class==edge_or_node and a_mode==mode: attributes_element=a if attributes_element is None: # create new attributes element attr_kwargs = {"mode":mode,"class":edge_or_node} attributes_element=Element('attributes', **attr_kwargs) self.graph_element.insert(0,attributes_element) attributes_element.append(attribute) return new_id def add_viz(self,element,node_data): viz=node_data.pop('viz',False) if viz: color=viz.get('color') if color is not None: if self.VERSION=='1.1': e=Element("{%s}color"%self.NS_VIZ, r=str(color.get('r')), g=str(color.get('g')), b=str(color.get('b')), ) else: e=Element("{%s}color"%self.NS_VIZ, r=str(color.get('r')), g=str(color.get('g')), b=str(color.get('b')), a=str(color.get('a')), ) element.append(e) size=viz.get('size') if size is not None: e=Element("{%s}size"%self.NS_VIZ,value=str(size)) element.append(e) thickness=viz.get('thickness') if thickness is not None: e=Element("{%s}thickness"%self.NS_VIZ,value=str(thickness)) element.append(e) shape=viz.get('shape') if shape is not None: if shape.startswith('http'): e=Element("{%s}shape"%self.NS_VIZ, value='image',uri=str(shape)) else: e=Element("{%s}shape"%self.NS_VIZ,value=str(shape.get)) element.append(e) position=viz.get('position') if position is not None: e=Element("{%s}position"%self.NS_VIZ, x=str(position.get('x')), y=str(position.get('y')), z=str(position.get('z')), ) element.append(e) return node_data def add_parents(self,node_element,node_data): parents=node_data.pop('parents',False) if parents: parents_element=Element('parents') for p in parents: e=Element('parent') e.attrib['for']=str(p) parents_element.append(e) node_element.append(parents_element) return node_data def add_slices(self,node_element,node_data): slices=node_data.pop('slices',False) if slices: slices_element=Element('slices') for start,end in slices: e=Element('slice',start=str(start),end=str(end)) slices_element.append(e) node_element.append(slices_element) return node_data def add_spells(self,node_element,node_data): spells=node_data.pop('spells',False) if spells: spells_element=Element('spells') for start,end in spells: e=Element('spell',start=str(start),end=str(end)) spells_element.append(e) node_element.append(spells_element) return node_data def write(self, fh): # Serialize graph G in GEXF to the open fh if self.prettyprint: self.indent(self.xml) document = ElementTree(self.xml) header='<?xml version="1.0" encoding="%s"?>'%self.encoding fh.write(header.encode(self.encoding)) document.write(fh, encoding=self.encoding) def indent(self, elem, level=0): # in-place prettyprint formatter i = "\n" + level*" " if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for elem in elem: self.indent(elem, level+1) if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i class GEXFReader(GEXF): # Class to read GEXF format files # use read_gexf() function def __init__(self, node_type=None,version='1.1draft'): try: import xml.etree.ElementTree except ImportError: raise ImportError('GEXF reader requires ' 'xml.elementtree.ElementTree') self.node_type=node_type # assume simple graph and test for multigraph on read self.simple_graph=True self.set_version(version) def __call__(self, stream): self.xml = ElementTree(file=stream) g=self.xml.find("{%s}graph" % self.NS_GEXF) if g is not None: return self.make_graph(g) # try all the versions for version in self.versions: self.set_version(version) g=self.xml.find("{%s}graph" % self.NS_GEXF) if g is not None: return self.make_graph(g) raise nx.NetworkXError("No <graph> element in GEXF file") def make_graph(self, graph_xml): # mode is "static" or "dynamic" graph_mode = graph_xml.get("mode", "") self.dynamic=(graph_mode=='dynamic') # start with empty DiGraph or MultiDiGraph edgedefault = graph_xml.get("defaultedgetype", None) if edgedefault=='directed': G=nx.MultiDiGraph() else: G=nx.MultiGraph() # graph attributes graph_start=graph_xml.get('start') if graph_start is not None: G.graph['start']=graph_start graph_end=graph_xml.get('end') if graph_end is not None: G.graph['end']=graph_end # node and edge attributes attributes_elements=graph_xml.findall("{%s}attributes"%self.NS_GEXF) # dictionaries to hold attributes and attribute defaults node_attr={} node_default={} edge_attr={} edge_default={} for a in attributes_elements: attr_class = a.get("class") if attr_class=='node': na,nd = self.find_gexf_attributes(a) node_attr.update(na) node_default.update(nd) G.graph['node_default']=node_default elif attr_class=='edge': ea,ed = self.find_gexf_attributes(a) edge_attr.update(ea) edge_default.update(ed) G.graph['edge_default']=edge_default else: raise # unknown attribute class # Hack to handle Gephi0.7beta bug # add weight attribute ea={'weight':{'type': 'double', 'mode': 'static', 'title': 'weight'}} ed={} edge_attr.update(ea) edge_default.update(ed) G.graph['edge_default']=edge_default # add nodes nodes_element=graph_xml.find("{%s}nodes" % self.NS_GEXF) if nodes_element is not None: for node_xml in nodes_element.findall("{%s}node" % self.NS_GEXF): self.add_node(G, node_xml, node_attr) # add edges edges_element=graph_xml.find("{%s}edges" % self.NS_GEXF) if edges_element is not None: for edge_xml in edges_element.findall("{%s}edge" % self.NS_GEXF): self.add_edge(G, edge_xml, edge_attr) # switch to Graph or DiGraph if no parallel edges were found. if self.simple_graph: if G.is_directed(): G=nx.DiGraph(G) else: G=nx.Graph(G) return G def add_node(self, G, node_xml, node_attr, node_pid=None): # add a single node with attributes to the graph # get attributes and subattributues for node data = self.decode_attr_elements(node_attr, node_xml) data = self.add_parents(data, node_xml) # add any parents if self.version=='1.1': data = self.add_slices(data, node_xml) # add slices else: data = self.add_spells(data, node_xml) # add spells data = self.add_viz(data, node_xml) # add viz data = self.add_start_end(data, node_xml) # add start/end # find the node id and cast it to the appropriate type node_id = node_xml.get("id") if self.node_type is not None: node_id=self.node_type(node_id) # every node should have a label node_label = node_xml.get("label") data['label']=node_label # parent node id node_pid = node_xml.get("pid", node_pid) if node_pid is not None: data['pid']=node_pid # check for subnodes, recursive subnodes=node_xml.find("{%s}nodes" % self.NS_GEXF) if subnodes is not None: for node_xml in subnodes.findall("{%s}node" % self.NS_GEXF): self.add_node(G, node_xml, node_attr, node_pid=node_id) G.add_node(node_id, data) def add_start_end(self, data, xml): # start and end times node_start = xml.get("start") if node_start is not None: data['start']=node_start node_end = xml.get("end") if node_end is not None: data['end']=node_end return data def add_viz(self, data, node_xml): # add viz element for node viz={} color=node_xml.find("{%s}color"%self.NS_VIZ) if color is not None: if self.VERSION=='1.1': viz['color']={'r':int(color.get('r')), 'g':int(color.get('g')), 'b':int(color.get('b'))} else: viz['color']={'r':int(color.get('r')), 'g':int(color.get('g')), 'b':int(color.get('b')), 'a':float(color.get('a')), } size=node_xml.find("{%s}size"%self.NS_VIZ) if size is not None: viz['size']=float(size.get('value')) thickness=node_xml.find("{%s}thickness"%self.NS_VIZ) if thickness is not None: viz['thickness']=float(thickness.get('value')) shape=node_xml.find("{%s}shape"%self.NS_VIZ) if shape is not None: viz['shape']=shape.get('shape') if viz['shape']=='image': viz['shape']=shape.get('uri') position=node_xml.find("{%s}position"%self.NS_VIZ) if position is not None: viz['position']={'x':float(position.get('x',0)), 'y':float(position.get('y',0)), 'z':float(position.get('z',0))} if len(viz)>0: data['viz']=viz return data def add_parents(self, data, node_xml): parents_element=node_xml.find("{%s}parents"%self.NS_GEXF) if parents_element is not None: data['parents']=[] for p in parents_element.findall("{%s}parent"%self.NS_GEXF): parent=p.get('for') data['parents'].append(parent) return data def add_slices(self, data, node_xml): slices_element=node_xml.find("{%s}slices"%self.NS_GEXF) if slices_element is not None: data['slices']=[] for s in slices_element.findall("{%s}slice"%self.NS_GEXF): start=s.get('start') end=s.get('end') data['slices'].append((start,end)) return data def add_spells(self, data, node_xml): spells_element=node_xml.find("{%s}spells"%self.NS_GEXF) if spells_element is not None: data['spells']=[] for s in spells_element.findall("{%s}spell"%self.NS_GEXF): start=s.get('start') end=s.get('end') data['spells'].append((start,end)) return data def add_edge(self, G, edge_element, edge_attr): # add an edge to the graph # raise error if we find mixed directed and undirected edges edge_direction = edge_element.get("type") if G.is_directed() and edge_direction=='undirected': raise nx.NetworkXError(\ "Undirected edge found in directed graph.") if (not G.is_directed()) and edge_direction=='directed': raise nx.NetworkXError(\ "Directed edge found in undirected graph.") # Get source and target and recast type if required source = edge_element.get("source") target = edge_element.get("target") if self.node_type is not None: source=self.node_type(source) target=self.node_type(target) data = self.decode_attr_elements(edge_attr, edge_element) data = self.add_start_end(data,edge_element) # GEXF stores edge ids as an attribute # NetworkX uses them as keys in multigraphs # if networkx_key is not specified as an attribute edge_id = edge_element.get("id") if edge_id is not None: data["id"] = edge_id # check if there is a 'multigraph_key' and use that as edge_id multigraph_key = data.pop('networkx_key',None) if multigraph_key is not None: edge_id=multigraph_key weight = edge_element.get('weight') if weight is not None: data['weight']=float(weight) edge_label = edge_element.get("label") if edge_label is not None: data['label']=edge_label if G.has_edge(source,target): # seen this edge before - this is a multigraph self.simple_graph=False G.add_edge(source, target, key=edge_id, **data) if edge_direction=='mutual': G.add_edge(target, source, key=edge_id, **data) def decode_attr_elements(self, gexf_keys, obj_xml): # Use the key information to decode the attr XML attr = {} # look for outer "<attvalues>" element attr_element=obj_xml.find("{%s}attvalues" % self.NS_GEXF) if attr_element is not None: # loop over <attvalue> elements for a in attr_element.findall("{%s}attvalue" % self.NS_GEXF): key = a.get('for') # for is required try: # should be in our gexf_keys dictionary title=gexf_keys[key]['title'] except KeyError: raise nx.NetworkXError("No attribute defined for=%s"%key) atype=gexf_keys[key]['type'] value=a.get('value') if atype=='boolean': value=self.convert_bool[value] else: value=self.python_type[atype](value) if gexf_keys[key]['mode']=='dynamic': # for dynamic graphs use list of three-tuples # [(value1,start1,end1), (value2,start2,end2), etc] start=a.get('start') end=a.get('end') if title in attr: attr[title].append((value,start,end)) else: attr[title]=[(value,start,end)] else: # for static graphs just assign the value attr[title] = value return attr def find_gexf_attributes(self, attributes_element): # Extract all the attributes and defaults attrs = {} defaults = {} mode=attributes_element.get('mode') for k in attributes_element.findall("{%s}attribute" % self.NS_GEXF): attr_id = k.get("id") title=k.get('title') atype=k.get('type') attrs[attr_id]={'title':title,'type':atype,'mode':mode} # check for the "default" subelement of key element and add default=k.find("{%s}default" % self.NS_GEXF) if default is not None: if atype=='boolean': value=self.convert_bool[default.text] else: value=self.python_type[atype](default.text) defaults[title]=value return attrs,defaults
[docs]def relabel_gexf_graph(G): """Relabel graph using "label" node keyword for node label. Parameters ---------- G : graph A NetworkX graph read from GEXF data Returns ------- H : graph A NetworkX graph with relabed nodes Notes ----- This function relabels the nodes in a NetworkX graph with the "label" attribute. It also handles relabeling the specific GEXF node attributes "parents", and "pid". """ # build mapping of node labels, do some error checking try: mapping=[(u,G.node[u]['label']) for u in G] except KeyError: raise nx.NetworkXError('Failed to relabel nodes: ' 'missing node labels found. ' 'Use relabel=False.') x,y=zip(*mapping) if len(set(y))!=len(G): raise nx.NetworkXError('Failed to relabel nodes: ' 'duplicate node labels found. ' 'Use relabel=False.') mapping=dict(mapping) H=nx.relabel_nodes(G,mapping) # relabel attributes for n in G: m=mapping[n] H.node[m]['id']=n if 'pid' in H.node[m]: H.node[m]['pid']=mapping[G.node[n]['pid']] if 'parents' in H.node[m]: H.node[m]['parents']=[mapping[p] for p in G.node[n]['parents']] return H # fixture for nose tests
def setup_module(module): from nose import SkipTest try: import xml.etree.cElementTree except: raise SkipTest("xml.etree.cElementTree not available") # fixture for nose tests def teardown_module(module): import os try: os.unlink('test.gexf') except: pass