On Tue, Dec 29, 2009 at 7:58 AM, Eric Emsellem <emsel...@obs.univ-lyon1.fr> wrote: > Hi (sorry if you receive this twice, but I did not see the first post appear) > > I have a nagging problem which I think could be solved nicely with numpy > indexing but I cannot find the solution, except by invoking a stupid > loop. I would like to do this with some numpy item. > > Problem > ======== > I have a 2D array which is let's say 1000 x 100. > This represents 100 1D spectra, each one containing 1000 datapoints. For > example: > > startarray = random((1000,100)) > > Assuming I have a list of indices, for example: > > ind = [1,2,5,6,1,2] > > and a corresponding list of integer shifts let's say between -100 and 100: > > shift = [10,20,34,-10,22,-20] > > I would like to do the following sum > > result = stararray[100+shift[0]:-100+shift[0],ind[0]] > + stararray[100+shift[1]:-100+shift[0],ind[0]] > + ... > > Basically: I would like to sum some extracted 1D line after they have been > shifted by some amount. Note that I would like to be able to use each line > several times (with different shifts). > > At the moment, I am using "take" to extract from this array some of these > spectra, so let's start from scratch here: > > import numpy as num > startarray = random((1000,100)) > take_sample = [1,2,5,6,1,2] > temp = num.take(startarray,take_sample,axis=1)
Would it help to make temp a 1000x4 array instead of 1000x6? Could you do that by changing take_sample to [1,2,5,6] and multiplying columns 1 and 2 by a factor of 2? That would slow down the construction of temp but speed up the addition (and slicing?) in the loop below. > > # and to do the sum after shifting I need a loop > > shift = [10,20,34,-10,22,-20] > result = num.zeros(900) # shorter than initial because of the shift > for i in range(len(shift)) : > result += temp[100+shift[i]:-100+shift[1]] This looks fast to me. The slicing doesn't make a copy nor does the addition. I've read that cython does fast indexing but I don't know if that applies to slicing as well. I assume that shift[1] is a typo and should be shift[i]. > > Is there a way to do this without invoking a loop? Is there also a FAST > solution which makes the shifts at the same time than the "take" (that would > then prevent the use of the "temp" array)? > > Of course the arrays I am using are much BIGGER than these, so I really need > an > efficient way to do all this. > > thanks! > > Eric > > > -- > > > -------------------------------------------------------------------------- > Ce message a été envoyé depuis le webmail IMP (Internet Messaging Program) > _______________________________________________ > 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
