Hi!
I am trying to subset my graph to a smaller graph which I do by making a view of the original graph. Then from that graph I want to keep the largest component. Hence, I do another GraphView of that former GraphView. This does for some reason not work. Aren't graph view supposed to work on graph views themselfes. The solution which is now working for me is:
gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = label_largest_component(gp) path_lc = [] for v in gp.vertices(): if(gpl[v]): path_lc.append(int(v))
The more elegant solution
gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = GraphView(gp, vfilt=label_largest_component(gp)) path_lc = [ int(v) for v in gpl.vertices() ]
fails for some reason I don't see. BTW, in the end I want the vertex indices in the very original graph, which is what I hope to get here, but I am not really sure about that as I could not find anything about how to obtain vertex identifiers of filtered graphs which are good for referring to nodes in the original un-filtered graph. Or I overlooked it somewhere...
BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box.
Cheers,
On 06/21/2011 03:15 PM, Sebastian Weber wrote:
The more elegant solution
gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = GraphView(gp, vfilt=label_largest_component(gp)) path_lc = [ int(v) for v in gpl.vertices() ]fails for some reason I don't see.
I guess the problem is a small quirk with label_largest_component(). The code above removes all but one vertex, which has index gPath_ind, from the graph (is this really what you want, BTW?). The function label_largest_component() marks all the vertices which have the same index as the largest component. Since there is only one vertex, the component index is zero. However, the _unfiltered_ vertices will also have an index of zero, and they will get labelled as well... So your GraphView in the end will contain all the vertices.
I have fixed this now in the git version (now label_largest_component() never labels filtered graphs).
BTW, in the end I want the vertex indices in the very original graph, which is what I hope to get here, but I am not really sure about that as I could not find anything about how to obtain vertex identifiers of filtered graphs which are good for referring to nodes in the original un-filtered graph. Or I overlooked it somewhere...
The vertex index is preserved by filtering. So you could do something like:
v = g.vertex(int(u))
where u belongs to the filtered graph, and g is the unfiltered graph.
BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box.
What do you mean? I haven't included DLFCN.py anywhere... (I can't anyway, since it is platform-dependent code)
Cheers, Tiago
Hi!
gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = GraphView(gp, vfilt=label_largest_component(gp)) path_lc = [ int(v) for v in gpl.vertices() ]fails for some reason I don't see.
I guess the problem is a small quirk with label_largest_component(). The code above removes all but one vertex, which has index gPath_ind, from the graph (is this really what you want, BTW?). The function
gPath_ind is a list of indices of vertices I wanna keep in the filtered view of the graph, i.e. definitely more than one vertex. From that set of vertices I want to extract the largest component.
The vertex index is preserved by filtering. So you could do something like:
v = g.vertex(int(u))
where u belongs to the filtered graph, and g is the unfiltered graph.
That is what I assumed, but good to have that confirmed. Thanks
BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box.
What do you mean? I haven't included DLFCN.py anywhere... (I can't anyway, since it is platform-dependent code)
Hmm, I thought I deleted it manually, but obviously not. Anyway, if one puts the DLFCN.py into the graph-tool directory, it runs fine here. So I guess we should file a bug to macports regarding the python installation (in the meantime I reinstalled Xcode and python such that I have a proper macports installation of python 2.7).
CU,
Sebastian
Cheers, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 06/22/2011 09:15 AM, Sebastian Weber wrote:
Hi!
gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = GraphView(gp, vfilt=label_largest_component(gp)) path_lc = [ int(v) for v in gpl.vertices() ]fails for some reason I don't see.
I guess the problem is a small quirk with label_largest_component(). The code above removes all but one vertex, which has index gPath_ind, from the graph (is this really what you want, BTW?). The function
gPath_ind is a list of indices of vertices I wanna keep in the filtered view of the graph, i.e. definitely more than one vertex. From that set of vertices I want to extract the largest component.
Oh, I see now. I misunderstood the first line of your code. But in any case, I think I had correctly identified the bug, which should always happen when the largest component has an index of zero. Could you see if things work now with the git version?
BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box.
What do you mean? I haven't included DLFCN.py anywhere... (I can't anyway, since it is platform-dependent code)
Hmm, I thought I deleted it manually, but obviously not. Anyway, if one puts the DLFCN.py into the graph-tool directory, it runs fine here. So I guess we should file a bug to macports regarding the python installation (in the meantime I reinstalled Xcode and python such that I have a proper macports installation of python 2.7).
Yes, we should file a bug report. There is no possible workaround we can do from graph-tool, since the contents of DLFCN.py will be different in each platform.
Cheers, Tiago
Hi!
Oh, I see now. I misunderstood the first line of your code. But in any case, I think I had correctly identified the bug, which should always happen when the largest component has an index of zero. Could you see if things work now with the git version?
For some reason ccache is not working; therefore I will tell you later today... argh I hate compiling graph-tool...
BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box.
What do you mean? I haven't included DLFCN.py anywhere... (I can't anyway, since it is platform-dependent code)
Hmm, I thought I deleted it manually, but obviously not. Anyway, if one puts the DLFCN.py into the graph-tool directory, it runs fine here. So I guess we should file a bug to macports regarding the python installation (in the meantime I reinstalled Xcode and python such that I have a proper macports installation of python 2.7).
Yes, we should file a bug report. There is no possible workaround we can do from graph-tool, since the contents of DLFCN.py will be different in each platform.
Yup. Do you go ahead?
CU,
Sebastian
Cheers, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 06/22/2011 09:52 AM, Sebastian Weber wrote:
For some reason ccache is not working; therefore I will tell you later today... argh I hate compiling graph-tool...
It is a python-only modification, so you should be able just to copy the __init__.py file from the topology module to your installation, if you are in a hurry.
Cheers, Tiago
-
Sebastian Weber -
Tiago de Paula Peixoto