[igraph] Re: Problem with layouts with GraphML

[Dr Karl]

Hi Gábor,

    Ok, I acnowledge the fact that I can't generate an yFiles
compatible .graphml file just from iGraph. I guess my best option is
to generate the graph and layout in .graphml with iGraph, and later
parse the .graphml file and add the yFiles-specific attributes with
another module.

   I don't know either why they need to extend GraphML format to store
coordinates, but as it is a proprietary software which requires a
license to use, I think that perhaps they think that way they are
forcing people to use their library. We have bought a license for the
yFiles Flex library, for web visualization purposes. For graph and
layout generation they have an yFiles Java and yFiles .NET libraries,
which need an additional license (and it's not cheap), but we chose to
use iGraph for graph generation, metrics and statistics which we think
is a stable, reliable and fast (it's written in C) library.

  So, thank you very much for your help, I didn't find any examples in
the documentation or in the mailing list, or in the net of how to
attach attributes.

On 20 nov, 10:12, Gábor Csárdi <address@hidden> wrote:
> Hi Karl,
>
> the problem is, that the yFiles GraphML extensions are not supported
> by igraph. (Actually I don't really know why they needed to extend
> GraphML to store the coordinates.) There is currently no way to export
> such a file from igraph, and most probably this will not change in the
> near future.
>
> Best,
> Gabor
>
>
>
>
>
> On Fri, Nov 20, 2009 at 9:51 AM, Dr Karl <address@hidden> wrote:
> > Hi Tamas,
>
> >     Thank you for your quick answer!!
>
> >     Well, I have done what you said in your message, and now
> > my .graphml file has two attributes. This is my code, in case someone
> > needs to add attributes as well:
>
> >        igraph_t g;
> >        igraph_matrix_t res;
> >        igraph_vector_t edges;
> >        igraph_vector_t col1;
> >        igraph_vector_t col2;
> >        igraph_i_set_attribute_table(&igraph_cattribute_table);
> >        igraph_vector_init(&edges, 4*relations.size());
> >        igraph_matrix_init(&res, 0, 0);
> >        int i = 0;
> >        for (vector<Relationship>::iterator it = relations.begin(); it!
> > =relations.end(); ++it) {
> >                rel = (Relationship)*it;
> >                if (rel.AtoB>=1 && rel.BtoA>=1 && 
> > (rel.AtoB+rel.BtoA)>=minLevels) {
> >                        if (rel.AtoB>0 || rel.BtoA>0) {
> >                                VECTOR(edges)[i] = rel.nodeA;
> >                                i++;
> >                                VECTOR(edges)[i] = rel.nodeB;
> >                                i++;
> >                        }
> >                }
> >        }
> >        igraph_vector_resize(&edges, i);
> >        igraph_create(&g, &edges, 0, IGRAPH_DIRECTED);
> >        igraph_layout_random(&g, &res);
> >        long size = igraph_matrix_nrow(&res);
> >        igraph_vector_init(&col1, size);
> >        igraph_vector_init(&col2, size);
> >        igraph_matrix_get_col(&res, &col1, 0);
> >        igraph_matrix_get_col(&res, &col2, 1);
> >        igraph_cattribute_VAN_setv(&g, "X", &col1);
> >        igraph_cattribute_VAN_setv(&g, "Y", &col2);
> >        FILE* graphml_file;
> >        graphml_file = fopen("test_graph_layouts_random.graphml","w");
> >        igraph_write_graph_graphml(&g, graphml_file);
> >        igraph_vector_destroy(&edges);
> >        igraph_vector_destroy(&col1);
> >        igraph_vector_destroy(&col2);
> >        igraph_destroy(&g);
> >        igraph_matrix_destroy(&res);
>
> > Ok, now on every node I have two attributes, like this
>
> >   <node id="n0">
> >      <data key="X">-0.378323</data>
> >      <data key="Y">0.89578</data>
> >    </node>
>
> > but on yEd generated graphs, the layout is set like this
>
> >   <node id="n0">
> >      <data key="d0"/>
> >      <data key="d1">
> >        <y:ShapeNode>
> >          <y:Geometry height="30.0" width="30.0" x="25.0" y="0.0"/>
> >          <y:Fill color="#CCCCFF" transparent="false"/>
> >          <y:BorderStyle color="#000000" type="line" width="1.0"/>
> >          <y:NodeLabel alignment="center" autoSizePolicy="content"
> > fontFamily="Dialog" fontSize="12" fontStyle="plain"
> > hasBackgroundColor="false" hasLineColor="false" height="4.0"
> > modelName="internal" modelPosition="c" textColor="#000000"
> > visible="true" width="4.0" x="13.0" y="13.0"/>
> >          <y:Shape type="rectangle"/>
> >        </y:ShapeNode>
> >      </data>
> >    </node>
>
> > and before the <graph ...> tag
>
> >  <key attr.name="description" attr.type="string" for="node" id="d0"/>
> >  <key for="node" id="d1" yfiles.type="nodegraphics"/>
> >  <key attr.name="description" attr.type="string" for="edge" id="d2"/>
> >  <key for="edge" id="d3" yfiles.type="edgegraphics"/>
> >  <key for="graphml" id="d4" yfiles.type="resources"/>
>
> > I only use yEd for quick viewing of the graph, but I assume that if a
> > graph doesn't display correctly on yEd, it won't display correctly on
> > my Flex web application based on yFiles either.
>
> > So, is there a way I can attach something like <y:Geometry
> > height="30.0" width="30.0" x="25.0" y="0.0"/> inside the <data
> > key="d1"> attribute?? this is like nested attributes, whick I don't
> > know if are supported by iGraph.
>
> > Thank you very much.
>
> > On 19 nov, 18:57, Tamas Nepusz <address@hidden> wrote:
> >> Hi Karl,
>
> >> > My problem is that if I open the resulting .graphml files with
> >> > yEd (by yWorks), all the vertices are centered and it is impossible to
> >> > see the graph.
>
> >> This is  because no layout information is saved in the GraphML file when
> >> you export a graph from igraph. If you want to calculate a layout in
> >> igraph and then store it in the GraphML file, you will need two things:
>
> >> 1. Attach the (experimental) C attribute handler to igraph; these set
> >>    of functions are responsible for storing attributes properly in the
> >>    C layer. (The R and the Python interfaces use different attribute
> >>    handlers, that's why you have to attach the attribute handler
> >>    manually). See:http://igraph.sourceforge.net/doc/html/ch09s02.html
>
> >> 2. Calculate a layout using some of the layout functions in igraph
> >>    and save the layout in an igraph_matrix_t.
>
> >> 3. Extract the first and the second column of the matrix to two
> >>    igraph_vector_t variables.
>
> >> 4. Copy the calculated coordinates from the vectors to two node
> >>    attributes (say, X and Y) using igraph_cattribute_VAN_setv or its
> >>    associated macro version called SETVANV.
>
> >> 5. Save your graph into GraphML as you did before.
>
> >> If you do this, the saved GraphML file will contain the calculated
> >> layout information using the two node attributes. However, I don't know
> >> whether yEd can be "convinced" to use these attributes for setting up
> >> the layout in the graph view. When you save a graph from yEd into
> >> GraphML format, yEd uses its own XML schema extensions to store the
> >> layout and other visual properties of nodes and edges, and you cannot
> >> reproduce that from igraph.
>
> >> --
> >> Tamas
>
> >> _______________________________________________
> >> igraph-help mailing list
> >> address@hidden://lists.nongnu.org/mailman/listinfo/igraph-help
>
> > _______________________________________________
> > igraph-help mailing list
> > address@hidden
> >http://lists.nongnu.org/mailman/listinfo/igraph-help
>
> --
> Gabor Csardi <address@hidden>     UNIL DGM
>
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