June 2016 - graph-tool - archives.skewed.de

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. Thanks a lot. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 5

Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 3

What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 3

Problem with add_edge_list(eprop=x)
by JHickey 04 Oct '18

04 Oct '18

I'd like to use the "add_edge_list" function to add edges to my graph, and simultaneously assign a value for an edge property map for each of the added edges. When I try the following example (with no edge property map information) works fine: elist1 = np.array([[0,1], [1, 2]]) #edge list with no value for edge property map data (only the source and target for the edges) g = gt.Graph() my_eprop = g.new_edge_property('bool') g.add_edge_list(elist) But with the following example, I get the error below: elist2 = np.array([[0,1, 1], [1, 2, 0]]) #edge list with edge property map value in 3rd column g = gt.Graph() my_eprop = g.new_edge_property('bool') g.add_edge_list(elist2, eprops=my_eprop) Error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-48-6a949ea52c9b> in <module>() ----> 1 g.add_edge_list(elist2, eprops=my_eprop) /usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in add_edge_list(self, edge_list, hashed, string_vals, eprops) 1969 eprops = () 1970 else: -> 1971 convert = [_converter(x.value_type()) for x in eprops] 1972 eprops = [_prop("e", self, x) for x in eprops] 1973 if not isinstance(edge_list, numpy.ndarray): /usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in __getitem__(self, k) 534 kt = "Graph" 535 raise ValueError("invalid key '%s' of type '%s', wanted type: %s" --> 536 % (str(k), str(type(k)), kt) ) 537 538 def __setitem__(self, k, v): ValueError: invalid key '0' of type '<type 'int'>', wanted type: Edge --------------------------------------------------------------------------- Please help! -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

4 9

from graph_tool.all import * gives ImportError
by vineesh vs 21 Jun '18

21 Jun '18

I tried the following command in Python and ipython prompt (2.7 version) --------------------------------------------------------------------------- In [1]: from graph_tool.all import * --------------------------------------------------------------------------- Its giving the following error. How can we solve it? --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-100bbe2bc9d9> in <module>() ----> 1 from graph_tool.all import * /usr/lib/python2.7/dist-packages/graph_tool/__init__.py in <module>() 103 104 from .dl_import import * --> 105 dl_import("from . import libgraph_tool_core as libcore") 106 __version__ = libcore.mod_info().version 107 /usr/lib/python2.7/dist-packages/graph_tool/dl_import.pyc in dl_import(import_expr) 55 56 try: ---> 57 exec(import_expr, local_dict, global_dict) 58 finally: 59 sys.setdlopenflags(orig_dlopen_flags) # reset it to normal case to <string> in <module>() ImportError: /usr/lib/python2.7/dist-packages/graph_tool/libgraph_tool_core.so: undefined symbol: _ZN5boost9iostreams4zlib6finishE --------------------------------------------------------------------------- Thanks

4 5

Debian package and boost at compile-time
by Alcolo Alcolo 12 Mar '17

12 Mar '17

Hi, I have installed the package python3-graph-tool and when I use graph_tool.search.dfs_iterator I got the error: Traceback (most recent call last): File "/home/steph/bin/superGraph.py", line 160, in <module> gg.create_revdep(gg.getPackage('umda')) File "/home/steph/bin/superGraph.py", line 88, in create_revdep for e in bfs_iterator(self.graph, node): File "/usr/lib/python3/dist-packages/graph_tool/search/__init__.py", line 345, in bfs_iterator return libgraph_tool_search.bfs_search_generator(g._Graph__graph, int(source)) RuntimeError: This functionality is not available because boost::coroutine was not found at compile-time Ubuntu: 14.04 python3-graph-tool version 2.12-1 (from deb http://downloads.skewed.de/apt/trusty trusty universe) There is a way to install python3-graph-tool binaries compiled with boost ? Of course I can compile myself graph-tool, but it is not my goal.

6 26

apt-get fail to download index files
by Andy Maloney 10 Mar '17

10 Mar '17

I am trying to install graph-tool on a Trusty Ubuntu virtualbox being hosted on a Mac. I've added the requisite lines deb http://downloads.skewed.de/apt/trusty trusty main deb-src http://downloads.skewed.de/apt/trusty trusty main to my /etc/apt/sources.list, but when I run a sudo apt-get update, I get the following errors: W: Failed to fetch http://downloads.skewed.de/apt/trusty/dists/trusty/Release Unable to find expected entry 'main/source/Sources' in Release file (Wrong sources.list entry or malformed file) E: Some index files failed to download. They have been ignored, or old ones used instead. I have the main, universe, and multiverse repositories available. If any one has come across this problem before, please let me know how to fix it. Thanks. Andy_

4 4

Images in vertices
by Nils Hachmeister 15 Nov '16

15 Nov '16

Hello, I'm using graph_tool in a scenario, in which the meaning of a vertex cannot be easily be explained by a label or a text. To get a meaningful graph I would need to display a image inside the vertices. Has anyone an idea, how could this be achieved? Thanks Soraltan

3 3

Building graph-tool on CentOS 7
by Smith, Steven - 1004 - MITLL 28 Oct '16

28 Oct '16

The graph-tool make command on CentOS 7 fails at this point: $ cd graph-tool-2.2.35 $ ./configure --with-sparsehash-prefix=google $ make make all-recursive make[1]: Entering directory `/home/user/Downloads/graph-tool-2.2.35' Making all in src … make[4]: Entering directory `/home/user/Downloads/graph-tool-2.2.35/src/graph/topology' CXX graph_subgraph_isomorphism.lo graph_subgraph_isomorphism.cc: In instantiation of 'void get_subgraphs::operator()(const Graph1&, const Graph2*, VertexLabel, boost::any, EdgeLabel, boost::any, std::vector<VertexMap>&, size_t, bool, bool) const [with Graph1 = boost::adj_list<long unsigned int>; Graph2 = boost::adj_list<long unsigned int>; VertexLabel = boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >; EdgeLabel = boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >; VertexMap = boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >; size_t = long unsigned int]': /usr/include/c++/4.8.2/functional:1305:50: required from '_Result std::_Bind<_Functor(_Bound_args ...)>::__call_c(std::tuple<_Args2 ...>&&, std::_Index_tuple<_Indexes ...>) const [with _Result = void; _Args = {boost::adj_list<long unsigned int>&, boost::adj_list<long unsigned int>*&, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >&, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >&}; long unsigned int ..._Indexes = {0ul, 1ul, 2ul, 3ul, 4ul, 5ul, 6ul, 7ul, 8ul, 9ul}; _Functor = get_subgraphs; _Bound_args = {std::_Placeholder<1>, std::_Placeholder<2>, std::_Placeholder<3>, boost::any, std::_Placeholder<4>, boost::any, std::reference_wrapper<std::vector<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >, std::allocator<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> > > > >, long unsigned int, bool, bool}]’ … _descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_:: na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_:: na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope vertices_equivalent(make_property_map_equivalent(vertex_label1, vertex_label2))); ^ … , graph_tool::ConstantPropertyMap<bool, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope Any help fixing this would be greatly appreciated. I’m building graph-tool from the latest source, graph-tool-2.2.35.tar.bz2. CGAL is built successfully from source (there aren’t any cgal-devel packages yet in the .el7 repos), and because the .el 7 sparsehash-devel package puts its libraries in /usr/include/google, the specific ./configure command for CentOS 7 above is necessary. This runs successfully, and every compile up to graph_subgraph_isomorphism is successful.

3 13

Re: [graph-tool] Meaning of vertex_corr in block stochastic?
by Tiago Peixoto 03 Oct '16

03 Oct '16

Sorry for the late reply, but there was a problem with the mailing list. ttfoley wrote > I can't figure out the precise meaning of 'proportional' to, and would > like to know where/how it enters into the the actual formulae for > stochastic blocks. I have tried playing with various limits, and of course > tried scaling the 'probability' to account for graph size. For example, > there does not appear to be a limit where all edges are within blocks, > though surely this should be possible(assuming the number of edges fits > within the blocks)? Any help would be greatly appreciated. Proportional means exactly that: The probability will be what you give, up to an overall constant, which is unimportant since the total number of edges is always fixed. To force the edges to always be inside the groups, you should set the probability to zero, whenever r != s. ----- -- Tiago de Paula Peixoto <tiago(a)skewed.de> -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 2