Hi, So I tried to get as close to your setup as possible; I tried it on Ubuntu 12.10 with Python 2.7.3 and igraph 0.6.5 and it seemed to work just fine for me. Are you on a 64-bit platform? Have you compiled igraph yourself or did you use the official packages? If all else fails, I'll try to reproduce your issue in a virtual machine but I have to know exactly how you obtained igraph and its Python interface.
All the best, Tamas On 29 Apr 2013, at 10:35, Gábor Tóth <[email protected]> wrote: > Hi Tamas, > > My Platform is Ubuntu 12.10 > > My python version is : Python 2.7.3 > > My Igraph version is: 0.6.5 > > I did the same commands you did: > > >>> g=load("test_for_igraph.graphml") > >>> g.vertex_attributes() > ['propernoun', 'noun', 'pronoun', 'adverb', 'id', 'number', 'vocid', 'label', > 'adjective', 'verb', 'ambiguity', 'operator', 'other'] > >>> print g.vs["adverb"][:10] > [5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, 5e-324, > 5e-324] > > > Thanks again, > > Gabor > > > > On Mon, Apr 29, 2013 at 9:07 AM, Tamás Nepusz <[email protected]> wrote: > Dear Gábor, > > That's weird, I loaded the GraphML file you sent; all the boolean attributes > came through just fine and they even survive a save-load cycle: > > In [1]: g=load("test_for_igraph.graphml") > In [2]: g.vertex_attributes() > Out[2]: > ['propernoun', > 'noun', > 'pronoun', > 'adverb', > 'id', > 'number', > 'vocid', > 'label', > 'adjective', > 'verb', > 'ambiguity', > 'operator', > 'other'] > In [3]: print g.vs["adverb"][:10] > [False, False, False, False, False, False, False, False, False, False] > In [4]: g.write_graphml("test.graphml") > In [5]: g2=load("test.graphml") > /Users/ntamas/virtualenvs/default/lib/python2.7/site-packages/python_igraph-0.7-py2.7-macosx-10.8-intel.egg/igraph/__init__.py:2130: > RuntimeWarning: Could not add vertex ids, there is already an 'id' vertex > attribute at ../../src/foreign-graphml.c:416 > In [6]: print g2.vs["adverb"][:10] > [False, False, False, False, False, False, False, False, False, False] > > What platform are you running igraph on, which igraph version it is, and in > which version of Python? > > -- > T. > > On 29 Apr 2013, at 09:19, Gábor Tóth <[email protected]> wrote: > > > Dear Tamas, > > > > Thanks for the prompt reply, I am attaching my graphml file in a zipped > > file. > > > > FYI, this is the header of the exported version, it seems that boolean > > value is transformed into double. > > > > <!-- Created by igraph --> > > <key id="v_propernoun" for="node" attr.name="propernoun" > > attr.type="double"/> > > <key id="v_noun" for="node" attr.name="noun" attr.type="double"/> > > <key id="v_pronoun" for="node" attr.name="pronoun" attr.type="double"/> > > <key id="v_adverb" for="node" attr.name="adverb" attr.type="double"/> > > > > > > > > > > Best, > > > > Gabor > > > > > > On Sun, Apr 28, 2013 at 8:02 PM, Tamás Nepusz <[email protected]> wrote: > > Hi, > > > > > By using Igraph python have imported a graphml file that I created with > > > TinkerGraph. First, in the imported graphml file nodes have boolean > > > values, however after the import they don't have them anymore: > > Can you post your GraphML file or any other GraphML file that reproduces > > the issue? I tried the following on my machine and it worked: > > > > In [1]: g=Graph(1) > > In [2]: g.vs[0]["test"] = True > > In [3]: g.write_graphml("test.graphml") > > In [4]: g2=load("test.graphml") > > In [5]: g2.vs[0]["test"] > > Out[5]: True > > > > > How can I import grahml files by keeping boolean values? When I created > > > the graphm file in TinkerGraph I used the id attribute as index. > > > How could Igraph use the id attribute of the node as index after the > > > import? As you can see, the index is 2317 in Igraph, and not 363. > > igraph vertex indices have nothing to do with the indices of the nodes in > > the GraphML file, especially because GraphML node IDs are not guaranteed to > > be integers, so in the vast majority of cases, igraph would have to invent > > its own IDs anyway (since the C core of igraph always uses a range of > > integers from 0 to |V|-1 where |V| is the number of vertices). > > > > > <node id="n2317"> > > > <data key="v_propernoun">4.94066e-324</data> > > > <data key="v_noun">4.94066e-324</data> > > [...snip...] > > > </node> > > > > > > Again, the question, how can I use the original id attribute (363) > > > instead of n2317? > > You can't (for reasons mentioned above) and I don't really see why you > > would want to keep the same ID. The IDs are just internal references within > > the GraphML file with no semantic meaning. If your IDs *do* have some > > semantic meaning, just duplicate them as a vertex attribute and use the > > attribute instead. > > > > > Is there a way not putting v before the name of attributes and n before > > > the id? > > No, there isn't, for different reasons. The v_ prefix before the attribute > > names are required because theoretically you could have a graph where both > > the edges and the vertices have an attribute with the same name. To avoid > > such conflicts, igraph prefixes the identifiers of the vertex attributes > > with v_ and the identifiers of edge attributes with e_. Note, however, that > > this does *not* mean that the attribute itself is renamed since "key" is > > also just an internal reference within the GraphML file. The *name* of the > > attribute corresponding to a specific key is given by the attr.name > > attribute of the corresponding <key> tag in the GraphML file. E.g., in the > > example I listed above, the "test" attribute is declared like this in the > > GraphML file: > > > > <key id="v_test" for="node" attr.name="test" attr.type="boolean"/> > > > > You can see that its internal ID within the GraphML file is "v_test" to > > avoid conflicts with possibly existing edge attributes with the same name, > > but the _name_ in the attr.name attribute of the <key> tag is declared as > > "test", and not "v_test". > > > > As for the "n" prefix before the node IDs, it is also required because IDs > > that start with digits are not valid IDs in XML files (although of course > > many parsers accept them). This is not immediately obvious but it follows > > from the following W3C recommendation: > > > > http://www.w3.org/TR/REC-xml/ > > > > See, in particular, Section 3.3.1 > > (http://www.w3.org/TR/REC-xml/#sec-attribute-types) which says that "Values > > of type ID must match the Name production", and Section 2.3 > > (http://www.w3.org/TR/REC-xml/#NT-Name), which says that "The first > > character of a Name must be a NameStartChar", and the BNF rule for > > NameStartChar is also defined as: > > > > NameStartChar ::= ":" | [A-Z] | "_" | [a-z] | [#xC0-#xD6] | > > [#xD8-#xF6] | [#xF8-#x2FF] | [#x370-#x37D] | [#x37F-#x1FFF] | > > [#x200C-#x200D] | [#x2070-#x218F] | [#x2C00-#x2FEF] | [#x3001-#xD7FF] | > > [#xF900-#xFDCF] | [#xFDF0-#xFFFD] | [#x10000-#xEFFFF] > > > > So, in a nutshell, igraph uses the "n" prefix for node IDs because node IDs > > cannot start with numbers. > > > > All the best, > > Tamas > > _______________________________________________ > > igraph-help mailing list > > [email protected] > > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > <test_for_igraph.graphml.zip>_______________________________________________ > > igraph-help mailing list > > [email protected] > > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
