graph-tool September 2013

graph-tool@skewed.de

6 participants
14 discussions

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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graph-tool can't find Graphviz renderer
by Mikhail Spivakov 07 Apr '16

07 Apr '16

Hello! I've got graphviz installed with python and python27 bindings. However, when I do: graph_draw(ug, vprops={"label": ug.vertex_index}, output="two-nodes.pdf", layout="fdp") I get the following error: graph G { graph [outputorder=edgesfirst, mode=major, overlap=true, ratio=fill, size="5.905512,5.905512", start=3019255687130444316]; node [label="\N", shape=circle, width="0.105", height="0.105", style=filled, color="#2e3436", fillcolor="#a40000"]; edge [arrowsize="0.3", color="#2e3436", penwidth="1.0"]; graph [bb="0,0,425,425"]; 0 [label=0, width="0.47", height="0.47", pos="330,101"]; 1 [label=1, width="0.47", height="0.47", pos="93,324"]; 0 -- 1 [pos="318,113 277,152 147,274 106,312"]; } Error: renderer for pdf is unavailable Out[8]: <PropertyMap object with key type 'Vertex' and value type 'vector<double>', for Graph 0x5ff3f90, at 0x6001290> At the same time, if I save the above dot expression as test1.dot and run the following command from the command line: $ dot -Tpng test1.dot -o graph1.png I get a beautiful graph1.png. Graphviz is installed in a non-standard location as I don't have admin rights. However, the graphviz folder is in LD_LIBRARY_PATH and gv.py is in PYTHONPATH. Would very much appreciate your advice on what else graph-tool might need to find the libraries and/or how to test it better. Many thanks, Mikhail

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Segmentation fault using shortest_distance
by Juan Manuel Tirado 20 Mar '16

20 Mar '16

Hi Tiago, I am trying to calculate the shortest distances of a graph after applying a filter. I have a code that looks like this: g=gt.load_graph("myGraph.xml",format="xml") #for later use distances = gt.shortest_distance(g) #extract the components of the graph comp = g.label_components(g) #This splits the graph in several components #I want to calculate the shortest distances #for the component 2 for example filtering = g.new_vertex_property("boolean") for v in g.vertices(): if comp[v]==2: filtering[v]=True else: filtering[v]=False #set the vertex filter g.set_vertex_filter(filtering) distances_comp=gt.shortest_distance(g) The last line of code rises a segmentation fault. I have plotted the graph with the filtered graph and its correct, also I can calculate the local_clustering_coefficient without problems. Am I doing something wrong? Is there any other way to filter the graph and calculate the shortest distances? Is this a bug? Thanks so much, Juan

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graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> thanks - -- 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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Undefined symbol drawing function
by sasho.j.markov 20 Apr '15

20 Apr '15

Hi New to the graph-tool. Build it from src on Fedora 16 (64) . Built with cairomm enabled . Try to run as per the quick start , however when executing graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ... output_size=(200, 200), output="two-nodes.pdf") i get undefined symbol _ZN5Cairo7ContextC1EP6_cairob However the symbol above is defined in : libcairomm-1.0.so see below nm command results nm /usr/local/lib/libcairomm-1.0.so | grep -i _ZN5Cairo7ContextC1EP6_cairob 0000000000014b90 T _ZN5Cairo7ContextC1EP6_cairob Interestingly the library libgraph_tool_draw.so has indeed have the undefined symbol U _ZN5Cairo7ContextC1EP6_cairob but does not depend on the cairomm libarary - see the ldd output . unless the library is dynamically load i do not understand why Any advise appreciated- regards Sasho ldd /usr/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so linux-vdso.so.1 => (0x00007fffc46da000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f99fd6cd000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f99fd30e000) libboost_iostreams.so.1.49.0 => /usr/local/lib/libboost_iostreams.so.1.49.0 (0x00007f99fd0f6000) libboost_python.so.1.49.0 => /usr/local/lib/libboost_python.so.1.49.0 (0x00007f99fceaa000) libboost_regex.so.1.49.0 => /usr/local/lib/libboost_regex.so.1.49.0 (0x00007f99fcbc8000) libCGAL.so.9 => /usr/local/lib/libCGAL.so.9 (0x00007f99fc9a5000) libexpat.so.0 => /usr/local/lib/libexpat.so.0 (0x00007f99fc77c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f99fc54d000) libm.so.6 => /lib64/libm.so.6 (0x00007f99fc2c9000) libc.so.6 => /lib64/libc.so.6 (0x00007f99fbf11000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99fbcfb000) /lib64/ld-linux-x86-64.so.2 (0x00000030cea00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99fbadf000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f99fb8db000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f99fb6d7000) libz.so.1 => /lib64/libz.so.1 (0x00007f99fb4c0000) librt.so.1 => /lib64/librt.so.1 (0x00007f99fb2b8000) libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x00007f99fb0b3000) libboost_thread.so.1.49.0 => /usr/local/lib/libboost_thread.so.1.49.0 (0x00007f99fae98000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007f99fac41000) -- 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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Problem importing on Mac OS X 10.8, installed using MacPorts
by Uldis Bojars 07 Mar '14

07 Mar '14

Hi, When trying to import graph-tool the following error message is returned: >>> from graph_tool.all import * Fatal Python error: PyThreadState_Get: no current thread Could you help me solve this problem? graph-tool version py-graph-tool-2.2.18 was successfully installed using MacPorts but it fails during importing. Thanks, Uldis

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Parallel Processing
by Derek Ditch 21 Nov '13

21 Nov '13

I want to use graph-tool using the multiprocessing library in Python 2.6. I keep running into issues though with trying to share a full graph object. I can store the graph in a multiprocessing.Namespace, but it doesn't keep the dicts of properties. Example: def initNS( ns ): _g = Graph( directed = False) ns.graph = _g ns.edge_properties = { 'genres': _g.new_edge_property("vector<string>"), 'movieid': _g.new_edge_property("int"), } ns.vertex_properties = { 'personid': _g.new_vertex_property("int32_t") } """ Build property maps for edges and vertices to hold our data The graph vertices represent actors whereas movies represent edges """ # Edges _g.edge_properties["genres"] = ns.edge_properties['genres'] _g.edge_properties["movieid"] = ns.edge_properties['movieid'] # Vertices _g.vertex_properties["personid"] = ns.vertex_properties['personid'] ns.graph = _g ########## This initializes 'ns', which is a multiprocessing.Namespace. The problem is that for example, ns.edge_properties[ * ] tells me that the type isn't pickle-able. I tried to just skip that and use the _g.edge_properties to access it, but those dicts aren't carried over to the different process in the pool. Presumably b/c they aren't pickle-able. Any thoughts about how to fix this? (For those interested, I'm attempting to use the IMDbPy library to do some graph analysis on the relationships among actors and movies. Each process has it's own db connection and trying to populate the graph with actor and movie information in parallel since it's a pretty large and dense graph. Somewhere in the neighborhood of 250,000+ vertices for just a depth of three relationships) Thanks, -- Derek

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TypeError from purge_vertices()
by Mark Howell 21 Oct '13

21 Oct '13

I am trying to use purge_vertices() with a vertex filter to efficiently remove vertices from a graph. I am seeing different behavior in version 2.2.18 and 2.2.25, both as prebuilt packages for Ubuntu precise (current "graph-tool" and "python-graph-tool" packages, respectively) I have a simple example script attached which shows the behavior. If I run with graph-tool 2.2.18, it works without complaint, e.g.: $ python graph-tool-play2.py graph_tool version 2.2.18 (commit 83bb8a49, Tue Nov 13 00:57:29 2012 +0100) pruning 11 pruning 13 pruning 14 pruning 19 pruning 23 pruning 26 pruning 46 pruning 47 pruning 48 pruning 52 pruning 63 pruning 81 pruning 93 pruning 97 complete If I run with python-graph-tool 2.2.25, I get a TypeError, e.g.: $ python graph-tool-play2.py graph_tool version 2.2.25 (commit feec13d9, Mon Sep 2 00:01:39 2013 +0200) pruning 10 pruning 12 pruning 13 pruning 18 pruning 22 pruning 25 pruning 45 pruning 46 pruning 47 pruning 51 pruning 62 pruning 80 pruning 92 pruning 96 Traceback (most recent call last): File "graph-tool-play2.py", line 59, in <module> g.purge_vertices() # MJH this will die in graph-tool 2.2.25 with a TypeError. Works in 2.2.18. File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1838, in purge_vertices new_g = Graph(self, prune=(True, False, False)) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1109, in __init__ vorder.fa = numpy.arange(gv.num_vertices()) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 561, in <lambda> lambda self, v: self.__get_set_f_array(v, False), File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 556, in __get_set_f_array a[m] = v TypeError: array cannot be safely cast to required type Why would this fail in 2.2.25? It's entirely possible that I am missing something basic about how to fly graph-tool. Any clues appreciated! Cheers, Mark.

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Re: [graph-tool] Subsets of property map values - iterating over vertices
by Rene Pfitzner 30 Sep '13

30 Sep '13

Aha - yeah. Sorry, using arrays works, but not lists. (important to know, though) On 30 September 2013 19:11, Tiago de Paula Peixoto <tiago(a)skewed.de> wrote: > On 09/30/2013 07:09 PM, Rene Pfitzner wrote: > > Thanks Tiago! > > > > Let me just point out that the part > > > > mask.a = g.degree_property_map("out").a > 4 > > > > will (if you are using python 2.x) not give you what you most likely > would like to have, namely a list of boolean values containing the results > of the element wise comparisons of elements > g.degree_property_map("out").a[i]>4. Instead, for some strange reason, > you'll simply get the *value* True back, writing True to all elements in > mask.a ... instead, it seems to me, the only (fastest) way to do it is to > use map > > > > mask.a = map(lambda(x): x > 4, g.degree_property_map("out").a) > > > > .... so be careful. > > Are you sure? > > I get the following with python 2 and numpy 1.7.1: > > In [4]: arange(10) > Out[4]: array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]) > > In [5]: arange(10) > 2 > Out[5]: array([False, False, False, True, True, True, True, True, > True, True], dtype=bool) > > > Cheers, > Tiago > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > > -- René Pfitzner, Dipl. Phys. Scientific assistant / Doctoral candidate ETH Zürich Chair of Systems Design +41-44-63-28478 rpfitzner(a)ethz.ch http://www.sg.ethz.ch/people/prene

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Re: [graph-tool] Subsets of property map values - iterating over vertices
by Rene Pfitzner 30 Sep '13

30 Sep '13

Thanks Tiago! Let me just point out that the part mask.a = g.degree_property_map("out").a > 4 will (if you are using python 2.x) not give you what you most likely would like to have, namely a list of boolean values containing the results of the element wise comparisons of elements g.degree_property_map("out").a[i]>4. Instead, for some strange reason, you'll simply get the *value* True back, writing True to all elements in mask.a ... instead, it seems to me, the only (fastest) way to do it is to use map mask.a = map(lambda(x): x > 4, g.degree_property_map("out").a) .... so be careful. Cheers, René On 30 September 2013 16:13, Tiago de Paula Peixoto <tiago(a)skewed.de> wrote: > Hi René, > > On 09/30/2013 03:57 PM, Rene Pfitzner wrote: > > Hi everyone, > > > > this might be easily solved, but anyways: > > > > I have been thinking whether there is a fast way of retrieving > > property map values of subsets of nodes? I mean the following: let's > > say I have a property map A, defined for all vertices of graph G. Now, > > lets say I have a vertex iterator V that spans a subset of all nodes > > of G. Is there now a fast way, to a) read and b) eventually change the > > values in A of all nodes in V, e.g. to do something like A[V] and to > > get an array back, like in A.a .... > > > > Of course, iterating or map would be obvious options, but take > > eventually a lot of time. Another idea I had was, let's say the > > property map is an internal property map, to use vertex_filter and > > then get A.a. But what if the property map is not internal? > > This is easily done with graph filters, as you suggest. It does not > matter whether or not the property maps are internal. > > For instance, suppose you want to modify the property of all nodes with > a degree larger than four. You could do: > > g = ... # this is your graph > prop = ... # this is your property > > mask = g.new_vertex_property("bool") > mask.a = g.degree_property_map("out").a > 4 > g.set_vertex_filter(mask) > > prop.fa = 42 # this only affects the filtered values > > You can also do it using a graph view: > > u = GraphView(g, vfilt=g.degree_property_map("out").a > 4) > uprop = u.own_property(prop) > uprop.fa = 42 > > I prefer the last one, since it is more compact. > > (Note the use of A.fa instead of A.a) > > Cheers, > Tiago > > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > > -- René Pfitzner, Dipl. Phys. Scientific assistant / Doctoral candidate ETH Zürich Chair of Systems Design +41-44-63-28478 rpfitzner(a)ethz.ch http://www.sg.ethz.ch/people/prene

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graph-tool September 2013