graph-tool November 2017

graph-tool@skewed.de

8 participants
15 discussions

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.

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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.

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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.

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assigning vertex properties when adding edges
by m jadidi 04 Mar '20

04 Mar '20

Hi, I was wondering if there is any way to assign vertex properties while adding edges to the graph. for example using "add_edge_list" I can assign edge properties but later I have to iterate through all vertices again to assign their properties. I know this is not a problem when the vertex property is of the type "int" or "float" because then one can use "vprop.a = values", but in case of "string" and "object" this method doesn't work What would be the best/fastest way to handle this situation. I guess it would be very helpful to extend the "add_edge_list" function to accept vertex property in some way. cheers, -- Mohsen

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Nested Block State hierarchy level after mcmc_equilibrate
by ilyco 16 Jan '20

16 Jan '20

I ran mcmc_equilibrate on a nested block state model in a weighted graph. As per instructions, I copied the initially computed state in another object with increased hierarchy depth to 10. However, this fixed the depth to 10. Everything computed afterwards has depth 10 even if is clear that after 3 or 4 levels the nodes converge to one. There are many empty branches and when I try to plot it with empty_branches = False, I get an error stating it is not a tree. RuntimeError: Invalid hierarchical tree: No path from source to target. Did anybody perform any similar analyses? The hierarchy after mcmc_equilibrate: <NestedBlockState object, with base <BlockState object with 24 blocks (24 nonempty), degree-corrected, with 1 edge covariate, for graph <Graph object, undirected, with 230 vertices and 11230 edges, edges filtered by (<PropertyMap object with key type 'Edge' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64911d0>, False), vertices filtered by (<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64912d0>, False) at 0x7fc3a89f1210>, at 0x7fc3a6491950>, and 10 levels of sizes [(230, 24), (24, 5), (5, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1)] at 0x7fc3a6491590> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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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.

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FW: Graphtool: Finding the paths that the maximum flow algorithm produces
by Hobé Alex 25 Jun '18

25 Jun '18

Hi Tiago and everyone else on the list Thank you for your swift reply. The attached png is one example of a max flow calculation result. The flow is limited in four places in this graph. I would like to extract the order of the edges in the four paths I drew. The shortest path solution you described corresponds to path 3 in the drawing. all_shortest_paths gives my path 3 and another completely different path before crashing with a memoryError. Looking forward to hearing from you. Best, Alex ________________________________________ From: Tiago de Paula Peixoto [tiago(a)skewed.de] Sent: Thursday, March 09, 2017 18:43 To: Hobé Alex Subject: Re: Graphtool: Finding the paths that the maximum flow algorithm produces Hi Hobé, I'm not sure I understand what you want. Any path containing edges with positive flow is a "flow path". There are many of them. Which one do you want? If you just want _some_ path, just filter out the edges with zero flow and get the shortest path. But there are many other ways to proceed... Best, Tiago PS. There is a mailing list of the graph-tool project, where questions like this can be posted. It is better to use the list than to ask me directly, since it builds a repository of questions others can consult, and other people can help you as well. On 09.03.2017 17:04, Hobé Alex wrote: > Dear Mr. de Paula Peixoto > > I am using the python graphtool for my master thesis and am enjoying the > beautiful pictures it produces. > When computing the maximum flow I would like to use other edge properties > along the computed path for further calculations. > I am therefore looking for a way to find an array, which contains the edges > along a flow path, similar to the shortest_path result. > I looked through all the pages of the online tutorial, learnt a couple of > new tricks, but haven't found a way to solve this. > > I would be very thankful for any assistance you would be able to provide and > I look forward to hearing from you. > Best wishes, > > Alex Hobé -- Tiago de Paula Peixoto <tiago(a)skewed.de>

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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

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create a multilayer network from a group of data.frames
by Rafael Pereira 23 Nov '17

23 Nov '17

Hi all, Is there a way to create a multilayer network from a group of data.frames? This would make it very easy to import data to create multigraphs in graph-tool. This is possible for example in igrap library and for MuxViz in R( https://github.com/manlius/muxViz). In Muxviz, for example, one can create a multilayer network using three data.frames. I copy some of the explanation below from their documentation: ### Node list One df with following columns : - nodeID: [mandatory] numerical integer id to identify each node - nodeLabel: [optional] string specifying the label attribute - nodeX: [optional] float value specifying the Cartesian coordinate x for the layout - nodeY: [optional] float value specifying the Cartesian coordinate x for the layout - nodeLat: [optional] float value specifying the latitude for the geographic layout - nodeLong: [optional] float value specifying the longitude for the geographic layout ### Edges list One or more df with data on the edges. A typical edges list is expected to be a file with at most three columns, giving the list of edges from a node (first column) to other nodes (second column), possibly weighted by an integer or floating number (third column). For instance: 1 2 0.5 1 3 1.4 ... 18 124 0.1 ### input df Muxviz also uses a third data.frame that brings information on the list of layers to be included in a multiplex, the corresponding labels and the possible layout file to define node properties (e.g., ID, labels, geographic coordinates, etc). best wishes, Rafael H M Pereira

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Is it possible to work with legacy structures
by Anton Daneyko 20 Nov '17

20 Nov '17

I am currently working with a code that has a directed graph structure: an object defines `inputs` and `outputs` which return iterables of the objects with the same interface. Each object has a bunch of useful payload. I am looking for a python libarary that is capable of handling such data structure without the conversion to an intermediate format that is loaded for graph processing algrorithms. So instead of walking the data structure I have and converting it to a list of lists or whatever representation is consumed by the graph library, I would specify an adaptor interface to my own class so the graph library would be able to interact with my hierarchy directly. Is this sort of thing possible? Best regards, Anton

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graph-tool November 2017