"""Read and write graphs in GEXF format.
.. warning::
This parser uses the standard xml library present in Python, which is
insecure - see :external+python:mod:`xml` for additional information.
Only parse GEFX files you trust.
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
undirected edges together).
Format
------
GEXF is an XML format. See http://gexf.net/schema.html for the
specification and http://gexf.net/basic.html for examples.
"""
import itertools
import time
from xml.etree.ElementTree import (
Element,
ElementTree,
SubElement,
register_namespace,
tostring,
)
import networkx as nx
from networkx.utils import open_file
__all__ = ["write_gexf", "read_gexf", "relabel_gexf_graph", "generate_gexf"]
[docs]
@open_file(1, mode="wb")
def write_gexf(G, path, encoding="utf-8", prettyprint=True, version="1.2draft"):
"""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]_.
Node attributes are checked according to the version of the GEXF
schemas used for parameters which are not user defined,
e.g. visualization 'viz' [2]_. See example for usage.
Parameters
----------
G : graph
A NetworkX graph
path : file or string
File or file name to write.
File names ending in .gz or .bz2 will be compressed.
encoding : string (optional, default: 'utf-8')
Encoding for text data.
prettyprint : bool (optional, default: True)
If True use line breaks and indenting in output XML.
version: string (optional, default: '1.2draft')
The version of GEXF to be used for nodes attributes checking
Examples
--------
>>> G = nx.path_graph(4)
>>> nx.write_gexf(G, "test.gexf")
# visualization data
>>> G.nodes[0]["viz"] = {"size": 54}
>>> G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1}
>>> G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256}
Notes
-----
This implementation does not support mixed graphs (directed and undirected
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 File Format, http://gexf.net/
.. [2] GEXF schema, http://gexf.net/schema.html
"""
writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version)
writer.add_graph(G)
writer.write(path)
[docs]
def generate_gexf(G, encoding="utf-8", prettyprint=True, version="1.2draft"):
"""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, default: 'utf-8')
Encoding for text data.
prettyprint : bool (optional, default: True)
If True use line breaks and indenting in output XML.
version : string (default: 1.2draft)
Version of GEFX File Format (see http://gexf.net/schema.html)
Supported values: "1.1draft", "1.2draft"
Examples
--------
>>> G = nx.path_graph(4)
>>> linefeed = chr(10) # linefeed=\n
>>> s = linefeed.join(nx.generate_gexf(G))
>>> for line in nx.generate_gexf(G): # doctest: +SKIP
... print(line)
Notes
-----
This implementation does not support mixed graphs (directed and undirected
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 File Format, https://gephi.org/gexf/format/
"""
writer = GEXFWriter(encoding=encoding, prettyprint=prettyprint, version=version)
writer.add_graph(G)
yield from str(writer).splitlines()
[docs]
@open_file(0, mode="rb")
@nx._dispatchable(graphs=None, returns_graph=True)
def read_gexf(path, node_type=None, relabel=False, version="1.2draft"):
"""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 file name to read.
File names ending in .gz or .bz2 will be decompressed.
node_type: Python type (default: None)
Convert node ids to this type if not None.
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.
version : string (default: 1.2draft)
Version of GEFX File Format (see http://gexf.net/schema.html)
Supported values: "1.1draft", "1.2draft"
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 undirected
edges together).
References
----------
.. [1] GEXF File Format, http://gexf.net/
"""
reader = GEXFReader(node_type=node_type, version=version)
if relabel:
G = relabel_gexf_graph(reader(path))
else:
G = reader(path)
return G
class GEXF:
versions = {
"1.1draft": {
"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",
},
"1.2draft": {
"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",
},
}
def construct_types(self):
types = [
(int, "integer"),
(float, "float"),
(float, "double"),
(bool, "boolean"),
(list, "string"),
(dict, "string"),
(int, "long"),
(str, "liststring"),
(str, "anyURI"),
(str, "string"),
]
# These additions to types allow writing numpy types
try:
import numpy as np
except ImportError:
pass
else:
# prepend so that python types are created upon read (last entry wins)
types = [
(np.float64, "float"),
(np.float32, "float"),
(np.float16, "float"),
(np.int_, "int"),
(np.int8, "int"),
(np.int16, "int"),
(np.int32, "int"),
(np.int64, "int"),
(np.uint8, "int"),
(np.uint16, "int"),
(np.uint32, "int"),
(np.uint64, "int"),
(np.int_, "int"),
(np.intc, "int"),
(np.intp, "int"),
] + types
self.xml_type = dict(types)
self.python_type = dict(reversed(a) for a in types)
# http://www.w3.org/TR/xmlschema-2/#boolean
convert_bool = {
"true": True,
"false": False,
"True": True,
"False": False,
"0": False,
0: False,
"1": True,
1: True,
}
def set_version(self, version):
d = self.versions.get(version)
if d is None:
raise nx.NetworkXError(f"Unknown GEXF version {version}.")
self.NS_GEXF = d["NS_GEXF"]
self.NS_VIZ = d["NS_VIZ"]
self.NS_XSI = d["NS_XSI"]
self.SCHEMALOCATION = d["SCHEMALOCATION"]
self.VERSION = d["VERSION"]
self.version = version
class GEXFWriter(GEXF):
# class for writing GEXF format files
# use write_gexf() function
def __init__(
self, graph=None, encoding="utf-8", prettyprint=True, version="1.2draft"
):
self.construct_types()
self.prettyprint = prettyprint
self.encoding = encoding
self.set_version(version)
self.xml = Element(
"gexf",
{
"xmlns": self.NS_GEXF,
"xmlns:xsi": self.NS_XSI,
"xsi:schemaLocation": self.SCHEMALOCATION,
"version": self.VERSION,
},
)
# Make meta element a non-graph element
# Also add lastmodifieddate as attribute, not tag
meta_element = Element("meta")
subelement_text = f"NetworkX {nx.__version__}"
SubElement(meta_element, "creator").text = subelement_text
meta_element.set("lastmodifieddate", time.strftime("%Y-%m-%d"))
self.xml.append(meta_element)
register_namespace("viz", self.NS_VIZ)
# counters for edge and attribute identifiers
self.edge_id = itertools.count()
self.attr_id = itertools.count()
self.all_edge_ids = set()
# 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):
# first pass through G collecting edge ids
for u, v, dd in G.edges(data=True):
eid = dd.get("id")
if eid is not None:
self.all_edge_ids.add(str(eid))
# set graph attributes
if G.graph.get("mode") == "dynamic":
mode = "dynamic"
else:
mode = "static"
# Add a graph element to the XML
if G.is_directed():
default = "directed"
else:
default = "undirected"
name = G.graph.get("name", "")
graph_element = Element("graph", defaultedgetype=default, mode=mode, name=name)
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(data=True):
node_data = data.copy()
node_id = str(node_data.pop("id", node))
kw = {"id": node_id}
label = str(node_data.pop("label", node))
kw["label"] = label
try:
pid = node_data.pop("pid")
kw["pid"] = str(pid)
except KeyError:
pass
try:
start = node_data.pop("start")
kw["start"] = str(start)
self.alter_graph_mode_timeformat(start)
except KeyError:
pass
try:
end = node_data.pop("end")
kw["end"] = str(end)
self.alter_graph_mode_timeformat(end)
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(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)
while str(edge_id) in self.all_edge_ids:
edge_id = next(self.edge_id)
self.all_edge_ids.add(str(edge_id))
yield u, v, edge_id, edge_data
else:
for u, v, data in G.edges(data=True):
edge_data = data.copy()
edge_id = edge_data.pop("id", None)
if edge_id is None:
edge_id = next(self.edge_id)
while str(edge_id) in self.all_edge_ids:
edge_id = next(self.edge_id)
self.all_edge_ids.add(str(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": str(key)}
try:
edge_label = edge_data.pop("label")
kw["label"] = str(edge_label)
except KeyError:
pass
try:
edge_weight = edge_data.pop("weight")
kw["weight"] = str(edge_weight)
except KeyError:
pass
try:
edge_type = edge_data.pop("type")
kw["type"] = str(edge_type)
except KeyError:
pass
try:
start = edge_data.pop("start")
kw["start"] = str(start)
self.alter_graph_mode_timeformat(start)
except KeyError:
pass
try:
end = edge_data.pop("end")
kw["end"] = str(end)
self.alter_graph_mode_timeformat(end)
except KeyError:
pass
source_id = str(G.nodes[u].get("id", u))
target_id = str(G.nodes[v].get("id", v))
edge_element = Element("edge", source=source_id, target=target_id, **kw)
default = G.graph.get("edge_default", {})
if self.VERSION == "1.1":
edge_data = self.add_slices(edge_element, edge_data)
else:
edge_data = self.add_spells(edge_element, edge_data)
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
mode = "static"
for k, v in data.items():
# rename generic multigraph key to avoid any name conflict
if k == "key":
k = "networkx_key"
val_type = type(v)
if val_type not in self.xml_type:
raise TypeError(f"attribute value type is not allowed: {val_type}")
if isinstance(v, list):
# dynamic data
for val, start, end in v:
val_type = type(val)
if start is not None or end is not None:
mode = "dynamic"
self.alter_graph_mode_timeformat(start)
self.alter_graph_mode_timeformat(end)
break
attr_id = self.get_attr_id(
str(k), self.xml_type[val_type], node_or_edge, default, mode
)
for val, start, end in v:
e = Element("attvalue")
e.attrib["for"] = attr_id
e.attrib["value"] = str(val)
# Handle nan, inf, -inf differently
if val_type == float:
if e.attrib["value"] == "inf":
e.attrib["value"] = "INF"
elif e.attrib["value"] == "nan":
e.attrib["value"] = "NaN"
elif e.attrib["value"] == "-inf":
e.attrib["value"] = "-INF"
if start is not None:
e.attrib["start"] = str(start)
if end is not None:
e.attrib["end"] = str(end)
attvalues.append(e)
else:
# static data
mode = "static"
attr_id = self.get_attr_id(
str(k), self.xml_type[val_type], node_or_edge, default, mode
)
e = Element("attvalue")
e.attrib["for"] = attr_id
if isinstance(v, bool):
e.attrib["value"] = str(v).lower()
else:
e.attrib["value"] = str(v)
# Handle float nan, inf, -inf differently
if val_type == float:
if e.attrib["value"] == "inf":
e.attrib["value"] = "INF"
elif e.attrib["value"] == "nan":
e.attrib["value"] = "NaN"
elif e.attrib["value"] == "-inf":
e.attrib["value"] = "-INF"
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 = 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")
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(
f"{{{self.NS_VIZ}}}color",
r=str(color.get("r")),
g=str(color.get("g")),
b=str(color.get("b")),
)
else:
e = Element(
f"{{{self.NS_VIZ}}}color",
r=str(color.get("r")),
g=str(color.get("g")),
b=str(color.get("b")),
a=str(color.get("a", 1.0)),
)
element.append(e)
size = viz.get("size")
if size is not None:
e = Element(f"{{{self.NS_VIZ}}}size", value=str(size))
element.append(e)
thickness = viz.get("thickness")
if thickness is not None:
e = Element(f"{{{self.NS_VIZ}}}thickness", value=str(thickness))
element.append(e)
shape = viz.get("shape")
if shape is not None:
if shape.startswith("http"):
e = Element(
f"{{{self.NS_VIZ}}}shape", value="image", uri=str(shape)
)
else:
e = Element(f"{{{self.NS_VIZ}}}shape", value=str(shape))
element.append(e)
position = viz.get("position")
if position is not None:
e = Element(
f"{{{self.NS_VIZ}}}position",
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_or_edge_element, node_or_edge_data):
slices = node_or_edge_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_or_edge_element.append(slices_element)
return node_or_edge_data
def add_spells(self, node_or_edge_element, node_or_edge_data):
spells = node_or_edge_data.pop("spells", False)
if spells:
spells_element = Element("spells")
for start, end in spells:
e = Element("spell")
if start is not None:
e.attrib["start"] = str(start)
self.alter_graph_mode_timeformat(start)
if end is not None:
e.attrib["end"] = str(end)
self.alter_graph_mode_timeformat(end)
spells_element.append(e)
node_or_edge_element.append(spells_element)
return node_or_edge_data
def alter_graph_mode_timeformat(self, start_or_end):
# If 'start' or 'end' appears, alter Graph mode to dynamic and
# set timeformat
if self.graph_element.get("mode") == "static":
if start_or_end is not None:
if isinstance(start_or_end, str):
timeformat = "date"
elif isinstance(start_or_end, float):
timeformat = "double"
elif isinstance(start_or_end, int):
timeformat = "long"
else:
raise nx.NetworkXError(
"timeformat should be of the type int, float or str"
)
self.graph_element.set("timeformat", timeformat)
self.graph_element.set("mode", "dynamic")
def write(self, fh):
# Serialize graph G in GEXF to the open fh
if self.prettyprint:
self.indent(self.xml)
document = ElementTree(self.xml)
document.write(fh, encoding=self.encoding, xml_declaration=True)
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="1.2draft"):
self.construct_types()
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(f"{{{self.NS_GEXF}}}graph")
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(f"{{{self.NS_GEXF}}}graph")
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):
# 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_name = graph_xml.get("name", "")
if graph_name != "":
G.graph["name"] = graph_name
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
graph_mode = graph_xml.get("mode", "")
if graph_mode == "dynamic":
G.graph["mode"] = "dynamic"
else:
G.graph["mode"] = "static"
# timeformat
self.timeformat = graph_xml.get("timeformat")
if self.timeformat == "date":
self.timeformat = "string"
# node and edge attributes
attributes_elements = graph_xml.findall(f"{{{self.NS_GEXF}}}attributes")
# 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(f"{{{self.NS_GEXF}}}nodes")
if nodes_element is not None:
for node_xml in nodes_element.findall(f"{{{self.NS_GEXF}}}node"):
self.add_node(G, node_xml, node_attr)
# add edges
edges_element = graph_xml.find(f"{{{self.NS_GEXF}}}edges")
if edges_element is not None:
for edge_xml in edges_element.findall(f"{{{self.NS_GEXF}}}edge"):
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(f"{{{self.NS_GEXF}}}nodes")
if subnodes is not None:
for node_xml in subnodes.findall(f"{{{self.NS_GEXF}}}node"):
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
ttype = self.timeformat
node_start = xml.get("start")
if node_start is not None:
data["start"] = self.python_type[ttype](node_start)
node_end = xml.get("end")
if node_end is not None:
data["end"] = self.python_type[ttype](node_end)
return data
def add_viz(self, data, node_xml):
# add viz element for node
viz = {}
color = node_xml.find(f"{{{self.NS_VIZ}}}color")
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", 1)),
}
size = node_xml.find(f"{{{self.NS_VIZ}}}size")
if size is not None:
viz["size"] = float(size.get("value"))
thickness = node_xml.find(f"{{{self.NS_VIZ}}}thickness")
if thickness is not None:
viz["thickness"] = float(thickness.get("value"))
shape = node_xml.find(f"{{{self.NS_VIZ}}}shape")
if shape is not None:
viz["shape"] = shape.get("shape")
if viz["shape"] == "image":
viz["shape"] = shape.get("uri")
position = node_xml.find(f"{{{self.NS_VIZ}}}position")
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(f"{{{self.NS_GEXF}}}parents")
if parents_element is not None:
data["parents"] = []
for p in parents_element.findall(f"{{{self.NS_GEXF}}}parent"):
parent = p.get("for")
data["parents"].append(parent)
return data
def add_slices(self, data, node_or_edge_xml):
slices_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}slices")
if slices_element is not None:
data["slices"] = []
for s in slices_element.findall(f"{{{self.NS_GEXF}}}slice"):
start = s.get("start")
end = s.get("end")
data["slices"].append((start, end))
return data
def add_spells(self, data, node_or_edge_xml):
spells_element = node_or_edge_xml.find(f"{{{self.NS_GEXF}}}spells")
if spells_element is not None:
data["spells"] = []
ttype = self.timeformat
for s in spells_element.findall(f"{{{self.NS_GEXF}}}spell"):
start = self.python_type[ttype](s.get("start"))
end = self.python_type[ttype](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)
if self.VERSION == "1.1":
data = self.add_slices(data, edge_element) # add slices
else:
data = self.add_spells(data, edge_element) # add spells
# 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(f"{{{self.NS_GEXF}}}attvalues")
if attr_element is not None:
# loop over <attvalue> elements
for a in attr_element.findall(f"{{{self.NS_GEXF}}}attvalue"):
key = a.get("for") # for is required
try: # should be in our gexf_keys dictionary
title = gexf_keys[key]["title"]
except KeyError as err:
raise nx.NetworkXError(f"No attribute defined for={key}.") from err
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]
ttype = self.timeformat
start = self.python_type[ttype](a.get("start"))
end = self.python_type[ttype](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(f"{{{self.NS_GEXF}}}attribute"):
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(f"{{{self.NS_GEXF}}}default")
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 relabeled nodes
Raises
------
NetworkXError
If node labels are missing or not unique while relabel=True.
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.nodes[u]["label"]) for u in G]
except KeyError as err:
raise nx.NetworkXError(
"Failed to relabel nodes: missing node labels found. Use relabel=False."
) from err
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.nodes[m]["id"] = n
H.nodes[m].pop("label")
if "pid" in H.nodes[m]:
H.nodes[m]["pid"] = mapping[G.nodes[n]["pid"]]
if "parents" in H.nodes[m]:
H.nodes[m]["parents"] = [mapping[p] for p in G.nodes[n]["parents"]]
return H
