[graph-tool] graph-tool Digest, Vol 99, Issue 13

Matyas, Csongor cfm482 at mun.ca
Mon May 9 21:41:04 CEST 2016


Hi Tiago and all

Thank you very much for adding this functionality to graph-tool, I could
use this for sure. The only problem is, that since you've sent this email,
I'm trying to recompile the newest version of graph-tool and after lots of
trouble I managed to get it compiled and working, (without sparsehash
unfortunately) (the bigges problems I faced with not enough memory, but
never mind), now I have the working graph-tool 2.16 and stil if I try to
call the:

planar_position = graph_tool.draw.planar_layout(Graph_of_the_knot, pos=None)

function it prints:

Traceback (most recent call last):
  File "./knot_representations.py", line 1947, in <module>
    Crossings_adjacency_matrix = CrossingsAdjacencyMatrix(Nr_of_crossings,
Nr_of_ropes, Starting_points, Rope_path_length, Crossings_chirality,
Connections_dict_inv, Connections_dict)
  File "./knot_representations.py", line 1526, in CrossingsAdjacencyMatrix
    planar_position = graph_tool.draw.planar_layout(Graph_of_the_knot,
pos=None)
AttributeError: 'module' object has no attribute 'planar_layout'

Am I doing something wrong, or I'm not using the right version?

I've downloaded graph-tool 2.16 from the site.

I would also like to ask something about the sfdp.layout in the draw tool.
Can I set the C parameter,

*C* : float (optional, default: 0.2) Relative strength of repulsive forces.

separately for some vertices? I assume that I can't, because it's not a
property map, but I thought I'll ask.
Thx

Csongor

On Mon, Apr 25, 2016 at 9:30 AM, <graph-tool-request at skewed.de> wrote:

> Send graph-tool mailing list submissions to
>         graph-tool at skewed.de
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.skewed.de/mailman/listinfo/graph-tool
> or, via email, send a message with subject or body 'help' to
>         graph-tool-request at skewed.de
>
> You can reach the person managing the list at
>         graph-tool-owner at skewed.de
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of graph-tool digest..."
>
>
> Today's Topics:
>
>    1. Re: First question - Planarity (Tiago de Paula Peixoto)
>    2. Re: First question - Planarity (Alexandre Hannud Abdo)
>    3. Re: First question - Planarity (Tiago de Paula Peixoto)
>    4. Re: How to see the relations between two groups of blocks in
>       a bipartite network? (Andrea Briega)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 24 Apr 2016 21:48:43 +0200
> From: Tiago de Paula Peixoto <tiago at skewed.de>
> To: graph-tool at skewed.de
> Subject: Re: [graph-tool] First question - Planarity
> Message-ID: <cb99c96b-6dd5-e142-8e14-4efc7f97969b at skewed.de>
> Content-Type: text/plain; charset="utf-8"
>
> On 20.04.2016 17:01, Tiago de Paula Peixoto wrote:
> > On 20.04.2016 14:20, Matyas, Csongor wrote:
> >> I will also post my first question, this was the main reason why I
> registered for this mailing list. The description and examples were usually
> more than enough for me to use graph_tool, nice job ;) I have a question
> though.
> >> In the "|graph_tool.topology.||is_planar|(/g/, /embedding=True///)" how
> do I use the embedding information to print my graphs planar. Do I have to
> do that for myself, or there is a built in function that I didn't find? Do
> I have to add the edges following the order that they come using the
> embedding somehow?
> >
> > Here is one way it can be used to draw the graph:
> >
> >
> http://www.boost.org/doc/libs/1_60_0/libs/graph/doc/straight_line_drawing.html
> >
> > However, this function is not yet implemented in graph-tool.
>
> FYI, I have just added this functionality to graph-tool:
>
>
> https://graph-tool.skewed.de/static/doc/dev/draw.html#graph_tool.draw.planar_layout
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <tiago at skewed.de>
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: signature.asc
> Type: application/pgp-signature
> Size: 819 bytes
> Desc: OpenPGP digital signature
> URL: <
> https://lists.skewed.de/pipermail/graph-tool/attachments/20160424/fc4b50a4/attachment-0001.sig
> >
>
> ------------------------------
>
> Message: 2
> Date: Sun, 24 Apr 2016 23:01:38 +0200
> From: Alexandre Hannud Abdo <abdo at member.fsf.org>
> To: Main discussion list for the graph-tool project
>         <graph-tool at skewed.de>
> Subject: Re: [graph-tool] First question - Planarity
> Message-ID:
>         <
> CANawF5W4H8y4f9SrbU+jJO7A5_DBc6rOUjs3kE4Qf1h+PyCEoQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Cool!
>
> Hey, the link to the boost reference in the documentation doesn't
> work, I think the correct link would be:
>
>
> http://www.boost.org/doc/libs/release/libs/graph/doc/straight_line_drawing.html
>
> Ni!
> ale
>
>
> On Sun, Apr 24, 2016 at 9:48 PM, Tiago de Paula Peixoto <tiago at skewed.de>
> wrote:
> > On 20.04.2016 17:01, Tiago de Paula Peixoto wrote:
> >> On 20.04.2016 14:20, Matyas, Csongor wrote:
> >>> I will also post my first question, this was the main reason why I
> registered for this mailing list. The description and examples were usually
> more than enough for me to use graph_tool, nice job ;) I have a question
> though.
> >>> In the "|graph_tool.topology.||is_planar|(/g/, /embedding=True///)"
> how do I use the embedding information to print my graphs planar. Do I have
> to do that for myself, or there is a built in function that I didn't find?
> Do I have to add the edges following the order that they come using the
> embedding somehow?
> >>
> >> Here is one way it can be used to draw the graph:
> >>
> >>
> http://www.boost.org/doc/libs/1_60_0/libs/graph/doc/straight_line_drawing.html
> >>
> >> However, this function is not yet implemented in graph-tool.
> >
> > FYI, I have just added this functionality to graph-tool:
> >
> >
> https://graph-tool.skewed.de/static/doc/dev/draw.html#graph_tool.draw.planar_layout
> >
> > Best,
> > Tiago
> >
> > --
> > Tiago de Paula Peixoto <tiago at skewed.de>
> >
> >
> > _______________________________________________
> > graph-tool mailing list
> > graph-tool at skewed.de
> > https://lists.skewed.de/mailman/listinfo/graph-tool
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 24 Apr 2016 23:12:50 +0200
> From: Tiago de Paula Peixoto <tiago at skewed.de>
> To: Main discussion list for the graph-tool project
>         <graph-tool at skewed.de>
> Subject: Re: [graph-tool] First question - Planarity
> Message-ID: <4aa2a155-c227-2759-7c87-5f93bf7b84e0 at skewed.de>
> Content-Type: text/plain; charset="utf-8"
>
> On 24.04.2016 23:01, Alexandre Hannud Abdo wrote:
> > Hey, the link to the boost reference in the documentation doesn't
> > work, I think the correct link would be:
> >
> >
> http://www.boost.org/doc/libs/release/libs/graph/doc/straight_line_drawing.html
>
> Thanks! Fixed.
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <tiago at skewed.de>
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: signature.asc
> Type: application/pgp-signature
> Size: 819 bytes
> Desc: OpenPGP digital signature
> URL: <
> https://lists.skewed.de/pipermail/graph-tool/attachments/20160424/36e9db92/attachment-0001.sig
> >
>
> ------------------------------
>
> Message: 4
> Date: Mon, 25 Apr 2016 12:47:08 +0200
> From: Andrea Briega <annbrial at gmail.com>
> To: graph-tool at skewed.de
> Subject: Re: [graph-tool] How to see the relations between two groups
>         of blocks in a bipartite network?
> Message-ID:
>         <CAOhEWiEW36kW+BdROoQmLbrH3s5dR=bM0715S7bCYszHgz=
> m_w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thank you very much for your detailed answer, it has been really helpful.
>
> The point is that I want to know how the relations are beween the two types
> of nodes of my network and with both classifications. Other algorithms,
> such as map equation, classify both types of nodes in the same groups so I
> see this relations directly, althought as you say by this way some
> information is hidden. In this sense I prefer graphtool, but I didn't know
> how to get this relation.
>
> Now I see I can get the partitions network from the BlockState object, I
> didn't know! (as I said, I am new in this, and in python too). I think it
> will be enough with this output.
>
> Thank you again,
>
>
> Andrea
>
>
> 2016-04-22 15:45 GMT+02:00 Andrea Briega <annbrial at gmail.com>:
>
> > Hi,
> >
> >
> > Sorry if I ask basic questions but I'm new in this. I have a bipartite
> > network, with two types of nodes with no connections between the nodes of
> > the same type, only between different types. I have run
> > minimize_blockmodel_dl y minimize_nested_blockmodel_dl with different
> > options but I always get separated blocks for each type of node: some
> > blocks only with nodes of one type and the rest only with nodes of the
> > other type. But I am really interested in the relation between this two
> > groups of blocks. Any idea about how could I get that? Thank you very
> much.
> >
> >
> >
> > Best regards,
> >
> >
> > Andrea
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> https://lists.skewed.de/pipermail/graph-tool/attachments/20160425/214ca2ca/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> graph-tool mailing list
> graph-tool at skewed.de
> https://lists.skewed.de/mailman/listinfo/graph-tool
>
>
> ------------------------------
>
> End of graph-tool Digest, Vol 99, Issue 13
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.skewed.de/pipermail/graph-tool/attachments/20160509/b4b551c5/attachment.htm>


More information about the graph-tool mailing list