Edge properties

Flavien_Lambert · May 29, 2014, 1:43pm

Hi, is there a way to get the key 'id' of edges in the spirit of the
vertices one like the following? _vertexIds works but not _edgeIds.

g=load_graph(dataFolder+'networkFullyConnected.xml')
_vertexIds = g.vertex_properties["_graphml_vertex_id"]
_edgeIds = g.edge_properties["_graphml_edge_id"]

The result is
Traceback (most recent call last):
  File "edgesProperties.py", line 18, in <module>
    _edgeIds = g.edge_properties["_graphml_edge_id"]
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line 995,
in __getitem__
    val = self.get_func(self.g, key)
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line
1469, in <lambda>
    lambda g, k: g.__properties[("e", k)],
KeyError: ('e', '_graphml_edge_id')

And the network in graphml framework reads as
<edge id="1" source="65091" target="65221">
<data key="w">192.49624317</data>
</edge>
<node id="16071">
<data key="o">5.41539461304e-05</data>
<data key="d">2.03027821579e-05</data>
</node>

Thanks,
F.

attachment.html (1.38 KB)

tiago · May 29, 2014, 3:32pm

The edge property will be there if the edge labeling in the file is not
canonical. I.e., if in the beginning of the file you have something like

that means that both the edge and node ids are canonical, and in that
case the properties will not be available.

I've tested with non-canonical labellings and I see both properties. If
you see otherwise, please provide a short example.

Best,
Tiago

Flavien_Lambert · May 29, 2014, 6:10pm

*Here is a minimal example :*
from graph_tool.all import *
g=load_graph('test.xml')
_vertexIds = g.vertex_properties["_graphml_vertex_id"]
_edgeIds = g.edge_properties["_graphml_edge_id"]

*test.xml:*
<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="
http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="o" for="node" attr.name="origin" attr.type="double"/>
<key id="d" for="node" attr.name="destination" attr.type="double"/>
<key id="w" for="edge" attr.name="weight" attr.type="double"/>
<key id="n" for="edge" attr.name="name" attr.type="int"/>
<graph id="G" edgedefault="directed">
<node id="65091">
<data key="o">0.0</data>
<data key="d">6.76759405264e-06</data>
</node>
<edge id="1" source="65091" target="65221">
<data key="w">192.49624317</data>
<data key="n">1</data>
</edge>
<node id="16071">
<data key="o">5.41539461304e-05</data>
<data key="d">2.03027821579e-05</data>
</node>
<edge id="2" source="16071" target="16081">
<data key="w">269.676249521</data>
<data key="n">2</data>
</edge>
<edge id="3" source="16071" target="16061">
<data key="w">299.894548773</data>
<data key="n">3</data>
</edge>
</graph>
</graphml>

*The error message:*
Traceback (most recent call last):
  File "test.py", line 4, in <module>
    _edgeIds = g.edge_properties["_graphml_edge_id"]
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line 995,
in __getitem__
    val = self.get_func(self.g, key)
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line
1469, in <lambda>
    lambda g, k: g.__properties[("e", k)],
KeyError: ('e', '_graphml_edge_id')

attachment.html (4.81 KB)

tiago · May 29, 2014, 6:43pm

I can't reproduce this. For me, the "_graphml_edge_id" property is
present with the example you provided.

What graph-tool version are you using?

Best,
Tiago

Flavien_Lambert · May 29, 2014, 6:50pm

Damned!

2.2.31

attachment.html (1.69 KB)

tiago · May 29, 2014, 7:06pm

This is very strange... What OS are you using?
Do you see the same problem with the git version?

Best,
Tiago

Flavien_Lambert · May 29, 2014, 7:34pm

I am running it on Fedora 20 and compiled the version on my machine.
For the git version, do I have to download it and recompile the whole stuff?

attachment.html (1.17 KB)

tiago · May 29, 2014, 8:43pm

Yes.

Best,
Tiago

Flavien_Lambert · July 15, 2014, 5:58am

Hi, digging to this old question, I eventualy installed the git version
and, unfortunately, I still have the problem of edge id...

from graph_tool.all import *
g=load_graph('test.xml')

_vertexIds = g.vertex_properties["_graphml_vertex_id"]
_edgeIds = g.edge_properties["_graphml_edge_id"]

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line
1049, in __getitem__
    val = self.get_func(self.g, key)
  File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line
1542, in <lambda>
    lambda g, k: g.__properties[("e", k)],
KeyError: ('e', '_graphml_edge_id')

g.list_properties()

destination (vertex) (type: long double)
origin (vertex) (type: long double)
_graphml_vertex_id (vertex) (type: string)
name (edge) (type: int32_t)
weight (edge) (type: long double)

*test.xml:*
<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="
http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="o" for="node" attr.name="origin" attr.type="double"/>
<key id="d" for="node" attr.name="destination" attr.type="double"/>
<key id="w" for="edge" attr.name="weight" attr.type="double"/>
<key id="n" for="edge" attr.name="name" attr.type="int"/>
<graph id="G" edgedefault="directed">
<node id="65091">
<data key="o">0.0</data>
<data key="d">6.76759405264e-06</

</node>

</edge>
<node id="16071">
<data key="o">5.41539461304e-05</data>
<data key="d">2.03027821579e-05</data>
</node>
<edge id="2" source="16071" target="16081">
<data key="w">269.676249521</data>
<data key="n">2</data>
</edge>
<edge id="3" source="16071" target="16061">
<data key="w">299.894548773</data>
<data key="n">3</data>
</edge>
</graph>
</graphml>

attachment.html (4.65 KB)

Flavien_Lambert · July 15, 2014, 6:10am

I found a funny fact. If I load twice the network, then I can see the edge
ids!

[Flavien(a)localhost tmp]$ ipython
Python 2.7.5 (default, Jun 25 2014, 10:19:55)
Type "copyright", "credits" or "license" for more information.

IPython 2.1.0 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.

In [1]: import graph_tool as gt

In [2]: g = gt.load_graph('test.xml')

In [3]: g.list_properties()
_graphml_vertex_id (vertex) (type: string)

In [4]: g = gt.load_graph('test.xml')

In [5]: g.list_properties()
_graphml_vertex_id (vertex) (type: string)
_graphml_edge_id (edge) (type: string)

with

test.xml

<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="
http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="undirected">
<edge id="1" source="65091" target="65221">
</edge>
</graph>
</graphml>

attachment.html (6.93 KB)

tiago · July 18, 2014, 1:14pm

This has been fixed now in git.

Best,
Tiago