graph-tool September 2013

graph-tool@skewed.de

6 participants
14 discussions

Subsets of property map values - iterating over vertices
by Rene Pfitzner 30 Sep '13

30 Sep '13

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? I am happy about your thoughts. Thanks, René

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Connected components
by Jonny Daenen 25 Sep '13

25 Sep '13

Hi, I'm new to using this library. It seems there is nog direct support for calculating the connected components of a graph, is this correct? Thanks!

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Re: [graph-tool] Best way to store graph 'history'
by Rene Pfitzner 25 Sep '13

25 Sep '13

Hi, I am not sure what exactly you want to achieve and for what reasons you need the "trajectories" (e.g. whether they have to be stored in a text-file format for some other processing step), but having a "dynamic network object", with a property map as you described, sounds like a good idea. Having 5000 nodes, with each having an associated 350 element double list will require roughly 5000*350*8bytes ~ 14MB of memory .... that should fit. For storing, you could pickle the whole graph object.... or/and, as you said, write the property map into a text-file using your format of choice ... René On 25 September 2013 12:47, Guillaume Gay <guillaume(a)mitotic-machine.org>wrote: > Hi, > > I'm using graph tool to represent a mesh of apical junctions > (interconnected cells in a tissue). As my simulation goes, positions of > the graph nodes change. Positions are stored as 3 vertex property maps > with type <double> (i.e. x, y and z). For now, I write a graphxml file > (plus possibliy a .png image of the graph) each time I change the nodes > positions. > > I would like to store the history of each node position, in other terms > its trajectory, but I feel that doing so by assigning a property map > with type vector<double> to each node would produce big files: I > typically have about 5000 vertices, and up to 350 'time points'. I would > also need to store other propery maps (describing each vertex and edge > state in the simulation). A full static view right now gives a 24 Mb xml > file... > > The point is I usually only need the static version, which I tend to > open and close quite often, and that allready takes quite some time to > open. So I thought I could for exemple store the graph's history in a > separate h5 file and access only if needed, for exemple, and only store > a reference to the file in the graph. > > I'd really apreciate to have some insight into that before I go on > coding... > > Cheers, > > Guillaume > _______________________________________________ > graph-tool mailing list > graph-tool(a)skewed.de > http://lists.skewed.de/mailman/listinfo/graph-tool > -- 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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Git repository is no more accessible
by Guillaume Lemaître 06 Sep '13

06 Sep '13

I'm used to stay in sync with git://git.skewed.de/graph-tool But currently I get the following error: $> git fetch fatal: remote error: access denied or repository not exported: /graph-tool $> Is this a problem you are aware of? -- 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 September 2013