Seconding Jaime; I use this trick in mesh manipulations a lot as well. There are a lot of graph-type manipulations you can express effectively in numpy using np.unique and related functionality.
On Sun, Feb 2, 2014 at 11:57 PM, Jaime Fernández del Río < jaime.f...@gmail.com> wrote: > Cannot test right now, but np.unique(b, return_inverse=True)[1].reshape(2, > -1) should do what you are after, I think. > On Feb 2, 2014 11:58 AM, "Mads Ipsen" <mads.ip...@gmail.com> wrote: > >> Hi, >> >> I have run into a potential 'for loop' bottleneck. Let me outline: >> >> The following array describes bonds (connections) in a benzene molecule >> >> b = [[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 7, >> 8, 9, 10, 11], >> [5, 6, 1, 0, 2, 7, 3, 8, 1, 4, 9, 2, 10, 5, 3, 4, 11, 0, 0, 1, >> 2, 3, 4, 5]] >> >> ie. bond 0 connects atoms 0 and 5, bond 1 connects atom 0 and 6, etc. In >> practical examples, the list can be much larger (N > 100.000 connections. >> >> Suppose atoms with indices a = [1,2,3,7,8] are deleted, then all bonds >> connecting those atoms must be deleted. I achieve this doing >> >> i_0 = numpy.in1d(b[0], a) >> i_1 = numpy.in1d(b[1], a) >> b_i = numpy.where(i_0 | i_1)[0] >> b = b[:,~(i_0 | i_1)] >> >> If you find this approach lacking, feel free to comment. >> >> This results in the following updated bond list >> >> b = [[0, 0, 4, 4, 5, 5, 5, 6, 10, 11] >> [5, 6, 10, 5, 4, 11, 0, 0, 4, 5]] >> >> This list is however not correct: Since atoms [1,2,3,7,8] have been >> deleted, the remaining atoms with indices larger than the deleted atoms >> must be decremented. I do this as follows: >> >> for i in a: >> b = numpy.where(b > i, bonds-1, bonds) (*) >> >> yielding the correct result >> >> b = [[0, 0, 1, 1, 2, 2, 2, 3, 5, 6], >> [2, 3, 5, 2, 1, 6, 0, 0, 1, 2]] >> >> The Python for loop in (*) may easily contain 50.000 iteration. Is there >> a smart way to utilize numpy functionality to avoid this? >> >> Thanks and best regards, >> >> Mads >> >> -- >> +---------------------------------------------------------+ >> | Mads Ipsen | >> +----------------------+----------------------------------+ >> | Gåsebæksvej 7, 4. tv | phone: +45-29716388 | >> | DK-2500 Valby | email: mads.ip...@gmail.com | >> | Denmark | map : www.tinyurl.com/ns52fpa | >> +----------------------+----------------------------------+ >> _______________________________________________ >> NumPy-Discussion mailing list >> NumPy-Discussion@scipy.org >> http://mail.scipy.org/mailman/listinfo/numpy-discussion >> > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > >
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