;vsize" property belongs to the original graph, and
hence will have a different number of elements. You need to do:
vsize = gv.own_property(vsize)
before calling graph_draw(). Note that, like GraphView, this does not
duplicate the property map; it is only a "view".
Best,
Tiago
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ocumentation.
https://graph-tool.skewed.de/static/doc/graph_tool.html#how-to-use-the-documentation
In short:
The docstring examples assume that graph_tool.all has been imported as gt:
>>> import graph_tool.all as gt
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heck to test if two vertices are unreachable is:
shortest_distance(g, u, v) >= g.num_vertices()
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On 30.09.2015 19:03, Santiago Videla wrote:
> Hi,
>
> I updated graph-tool to 2.9 and I got an exception from
> find_vertex_range method (see below). Can you confirm this is a bug?
Yes it is. I've just fixed it in git.
Thanks for spotting this.
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Invalid vertex index: 1
Hence you could do:
def vertex_belongs(v, g):
try:
g.vertex(int(v))
return True
except ValueError:
return False
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ou run the script under gdb:
gdb python
(gdb) set args ./script.py
(gdb) run
when the segfault occurs you type
(gdb) bt
and post the _entire_ result.
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ples.
Also, I'm not sure what you mean with "another GTK backend". TKAgg is
not a GTK backend, it is a matplotlib backend.
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llow this issue:
https://git.skewed.de/count0/graph-tool/issues/196
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t;
> Any ideas?
This has already been fixed in the new version, 2.5.
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riation of BFS or DFS. Is
> it possible do use graph_tool.search.bfs_search in some way for this?
Just do:
dist = shortest_distance(g, source=v)
k_disk = GraphView(g, vfilt=dist.fa <= k)
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Descr
es in g and then applies a filter? This is
> rather inefficient, especially when then graph is huge...
You can set "max_dist" in shortest_distance() to limit the search.
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Tiago
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signature
ex between 0 and the highest occurring index in my
> dataset. Is there any way to avoid all these unnecessary vertices?
This is possible, but only in the version in git. You would do simply
g.add_edge_list(edges, hashed=True).
In the current version, you have to do the mapping yourself.
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Tiag
. AFIK there is no algorithm that will find
them in any reasonable time.
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to modify the number of threads during the program, you can
use the the function graph_tool.openmp_set_num_threads().
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be going on.
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/static/doc/generation.html#graph_tool.generation.predecessor_tree
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t.vertex(v) in time O(1), where t is the predecessor
tree.
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), it is not a good
idea, since one would need to parse it by hand. Instead do
print(repr(array)).
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are missing, but I'm pretty sure something's
wrong because I'm not getting the number of edges I expect.)
It is difficult to say anything without a specific example of the
problem. Please post a small, self-contained code where the issue can be
seen.
Best,
Tiago
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that are
chosen at run time. This improves performance, but adds complexity.
(There is also an unmaintained, deprecated but official python
bindings for BGL: https://github.com/erwinvaneijk/bgl-python )
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so that someone down the line
can avoid the terms of the GPL, i.e. turn it into proprietary code. Why
would you do that?
But it is up to you, of course.
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restrictions being imposed.
The LGPL makes an exception for just linking (importing) the library,
which can make strategic sense in some cases, but I judged it not to be
the case for graph-tool.
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Tiago
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On 23.07.2015 08:36, Flavien Lambert wrote:
Hi,
could you tell me how to cite the project in a scientific paper? A
bibTeX entry would be awesome!
You find this in the documentation:
https://graph-tool.skewed.de/static/doc/faq.html#how-do-i-cite-graph-tool
Best,
Tiago
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On 15.07.2015 13:59, François wrote:
The warning causes apt-get update to return a non-zero code. This
sitaution is problematic to me, would it be possible to fix this
problem ?
This should be fixed now.
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Tiago
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to examine each and any edge when the weight parameter is provided.
What is the point of this behavior ? what do I miss ?
There might be parallel edges with different weights.
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for target.
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://downloads.skewed.de/apt/stretch/dists/stretch/main/binary-amd64/Packages
404 Not Found
These are just warnings; it should not affect the installation of the
package.
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Tiago
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-tool binaries with ldd, and also check the output of
configure.log, for more information of what library it is being used.
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?
Yes, use g.add_edge_list() for the edges, and put the weights separately
via the array interface for property maps:
e_weight.a = weight_list
The weight list should have the same ordering as the edges you passed to
g.add_edge_list().
Best,
Tiago
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that if you want to do this type of visualization, it can be done
most easily now with the draw_hierarchy() function:
https://graph-tool.skewed.de/static/doc/draw.html#graph_tool.draw.draw_hierarchy
Best,
Tiago
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, try passing the correct suffix value to --with-boost-python.
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.
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, do I need to
move to unstable?
Hm, it seems that it is a mistake on my part: I've built packages for
testing, which is now called 'stretch', not 'jessie'. I'll fix this in
the repository.
Best,
Tiago
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*
This is trivial, just compute the avg_neighbour_corr with the reversed
graph:
avg_neighbour_corr(GraphView(g, reversed=True), in, out)
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text shown in a correct orientation. Thanks a lot.
I'm not sure I understand. Can you provide an example?
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, I've never encountered this problem before, and I don't know what
may be causing it. Without a concrete example, I cannot investigate.
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network.
Thanks for this. I have now fixed the bug in git.
I'll make a new release soon with this fix.
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,
eweight=g.edge_properties[weight], multigraph = True)
This looks like a bug. Can you please also change the network which you
are using, so I can debug it?
Thanks!
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convenient mathematically. See for instance Mark Newman's book.
In any case, this an unimportant issue. A matrix transpose can be
obtained trivially in numpy.
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that the documentation of the other
spectral functions were inconsistent with this definition. I have fixed
it now:
https://graph-tool.skewed.de/static/doc/dev/spectral.html#graph_tool.spectral.adjacency
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Tiago
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be a vector
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On 29.05.2015 17:28, Smith, Steven - 1004 - MITLL wrote:
This is python 2.7 and graph-tool 2.2.38_0
This has already been fixed. Please update to the latest version.
Best,
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things
properly but it does not seem to change anything.
Indeed there seems to be a bug with the fit_view option. I'll provide a fix.
In the meantime, the best approach would be to set fit_view=False, and
scale your vertex positions accordingly.
Best,
Tiago
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bfs_search().
(Note that both these functions use BFS internally, but without
Python interference.)
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On 14.05.2015 21:42, dushyanthbn wrote:
Is degree centrality available in graph tool?
Of course. The degree centrality is just the degree of the node.
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/util.html#graph_tool.util.find_edge
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of weights on each node to
be a fixed quantity, you have to use parallel edges (or write your own
code for weighted edges).
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it is stable enough.
I get no segfaults with the git version.
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would access them as:
g = load_graph(mygraph.xml)
size = g.vp[size]
# print all sizes
for v in g.vertices():
print(size[v])
See https://graph-tool.skewed.de/static/doc/quickstart.html#property-maps
for more information.
Best,
Tiago
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a good way to update the drawing? thanks a lot!
Gtk+ and cairo are not thread safe like this! You need to call all
drawing commands from the same thread if they share some state.
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the mapping to ints, but to iterate only through the
individual objects.
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On 27.04.2015 16:29, Tiago de Paula Peixoto wrote:
On 27.04.2015 00:31, desert_rain wrote:
Hi,
I am using graph-tool for my research, thanks for creating graph-tool.
I need to calculate average values from vertex and edge properties.
Property types are vectordouble. When I use
can I calculate averages from vector
property?
Right now you can't, because the sum of two vectors is not defined.
You have to split the vector into two property maps with
ungroup_vector_property() and calculate the averages separately.
Best,
Tiago
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On 22.04.2015 20:01, Jose Albornoz wrote:
Hi there.
I am trying to install Graph-tool on a Linux server with CentOS 6.6, gcc
4.7.2, Boost 1.58.0.
As is stated in the website, you need GCC 4.8 or later.
Best,
Tiago
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if you uncomment the lines, and it
might cause problems. Don't do that; store the edges in a list first.
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?
In any case, if you are getting these missing symbols, something has
gone seriously wrong during compilation.
Could you please send the entire output of the configure command, as
well as the config.log file?
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the graph_tool.draw
module.
Simply avoid doing from graph_tool.all import * and import only the
submodules you need.
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On 19.04.2015 20:40, François Kawala wrote:
I did try to compile my fork, however it fails in a file that I didn't
modified: graph_blockmodel_covariates.
This is a bug when sparse_hash is not enabled. I have fixed it now in
git.
Best,
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/tutorial/doc/html/python/exposing.html
However, in this case a much more straightforward approach is to receive
any python iterable (a generic boost::python::object in C++), and
convert it to an unordered_set in C++, before the algorithm is run.
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difficult.)
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On 13.04.2015 20:23, François Kawala wrote:
I guess that I should update accordingly the *get_dists *function.
Should I submit a pull request once that done ?
Sure, but be careful not to compromise the performance in the case where
there is only a single target.
Best,
Tiago
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gt_bench.py to test performance
Do you use firefox? This might be due to a bug:
https://bugzilla.mozilla.org/show_bug.cgi?id=610679
The file is downloaded correctly if I use wget.
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On 06.04.2015 11:14, Guillaume Gay wrote:
Hope your talk is filmed! Any plan to come to EuroScipPy?
I don't think I will be able to...
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On 28.03.2015 01:13, Johann wrote:
Tiago de Paula Peixoto tiago at skewed.de writes:
On 06.03.2015 01:20, dartdog wrote:
In doing visual exploration it is way helpful to be able to see the
properties of a point in a cluster.. The pretty graphs alone are not
so helpful?
You can place
ns, total: 270 ms
Wall time: 260 ms
Which is around 10 times slower... So thing are indeed faster if
max_dist is specified, but the algorithm will still depend on the total
size of the graph.
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Tiago
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it is not possible to distinguish between O(V),
O(V log V), O(V ^ 2) or anything else.
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)
where 'labels' is some property map.
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are clearly not isomorphic. Do you know if this is
the case for your graphs?
What happens to the time difference if all the graphs tested are
isomorphic?
I can easily implement these shortcuts in graph-tool as well, if they
happen to be the source of the discrepancy.
Best,
Tiago
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to be closer in the
layout. When you leave 'groups' alone, but change 'mu', the effect is
that you add an additional global _attractive_ force between all nodes
in the graph, and hence you get the effect you are seeing: A reduced
clustering.
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, but this is difficult since I don't even
have Mac OS or Windows installed anywhere.
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On 11.02.2015 13:57, podro182 wrote:
Thank you very much for your reply!
I cannot find the demo though!
What do you mean? It is in the link I gave you:
https://graph-tool.skewed.de/static/doc/dev/demos/animation.html#interactive-visualizations
Best,
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be prepared to explain your problem in detail. Asking one-line
questions about how to do this or that, specially when the task in
question is documented, is not going to elicit detailed responses.
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was not uploaded. It is
available now.
Thanks for the heads-up!
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On 29.01.2015 10:31, graph-t...@v6y.net wrote:
Quoting Tiago de Paula Peixoto (2015-01-29 01:14:36)
Is the GDB backtrace the same as before? Is the missing symbol also the same?
Yes, with the patch applied, and sparsehash enabled, the backtrace is the
same (minor change in the segfault
by the subgraph_isomorphism()
function are vertex indexes. You can get a vertex object corresponding
to an index as follows:
v = g.vertex(idx)
where 'idx' is the index value.
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Tiago
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On 28.01.2015 10:26, graph-t...@v6y.net wrote:
Quoting Tiago de Paula Peixoto (2015-01-28 02:11:19)
Do you have sparsehash enabled?
sparsehash 2.0.2 is installed at:
/usr/include/sparsehash
and the graph-tool configure log indicates it found it:
checking whether to enable sparsehash
only. Same issue.
Do you have sparsehash enabled?
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On 28.01.2015 19:42, graph-t...@v6y.net wrote:
Quoting Tiago de Paula Peixoto (2015-01-28 04:47:21)
Can you try disabling sparsehash, with --disable-sparsehash, and see if
the problem persists? This should get rid of any tr1 references.
That did it!
$/usr/bin/python3.3 -c 'import
:
https://graph-tool.skewed.de/static/doc/dev/demos/animation.html#interactive-visualizations
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-tool.
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the full output and logs from the port install command.
But since you are using macports, you are better off opening a ticket at
their website. They are usually quick to respond:
https://trac.macports.org/newticket
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Tiago
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by itself does not say much...
I recommend you install graph-tool with macports, since it requires less
manual intervention.
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, thanks a lot for your work!
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Guillaume
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On 22.01.2015 15:50, malwanain wrote:
Thank,
just quick question, does this tool graph-tool able to check the isomorphism
of graphs which written in .dot(graphviz) which produced from other tool?
Yes.
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Tiago
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is to install two versions of
each library.
Best,
Tiago
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the option --with-boost-python=-3-mt to the configure
script, telling it what suffix should be used.
There is no standard naming across systems, and the configure script
tries some common ones, but it seems to be failing in this case.
Best,
Tiago
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Tiago de Paula Peixoto ti...@skewed.de
#graph_tool.topology.shortest_distance
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.
On an unrelated note: thanks for graph-tool! It is well-crafted and has
brought me much joy :)
You're welcome!
Best,
Tiago
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of a November release but it looks like that didn't work out
(no worries, things come up) so I thought I'd ping again.
A release has finally been made!
Best,
Tiago
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= g.new_vertex_property(double)
y = g.new_vertex_property(double)
x.a = idx.a % 50
y.a = idx.a // 50
pos = group_vector_property([x,y])
graph_draw(g, pos)
Best,
Tiago
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Best,
Tiago
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is it the right way?
No, you have to run 'make install'. Read the documentation in the CGAL
website.
2. I set environment variable: CXXFLAGS=-L/usr/include is it ok?
This is OK, but totally unnecessary.
Best,
Tiago
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configuration?
Best,
Tiago
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/pixman-1
-I/usr/include/freetype2 -I/usr/include/libpng12
cairommconfig.h is included, when the correct path is cairomm/cairommconfig.h.
For me the cairommconfig.h file is included in
/usr/lib/cairomm-1.0/include/cairommconfig.h
so, the is no cairomm prefix...
Best,
Tiago
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an integer-valued map, you should use
something like infinity=((1 31) - 1).
Best,
Tiago
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