Mailman 3 July 2005 - NumPy-Discussion

loading Numeric module
by Daniel Sheltraw 27 Jul '05

27 Jul '05

Hello all When I try doing a "from Numeric import *" at the Python command line I get the error message "ImportError: No module named Numeric" so obviously the module is not in the path known to command line Python. However when the same import statement is part of a Python script file the module is found correctly. How do I fix this? Is there a way to give the full path within the import statement (when I try I get a syntax error message)? Thanks, Daniel

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Re: [Numpy-discussion] convolve
by Alan G Isaac 27 Jul '05

27 Jul '05

On Tue, 26 Jul 2005, René Bastian apparently wrote: > convolve(a,b)==convolve(b,a)[::-1] I do not see this behavior. Can you post a self-contained example? Thanks, Alan Isaac

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"Using Python for Interactive Data Analysis" tutorial available
by Perry Greenfield 27 Jul '05

27 Jul '05

A tutorial that illustrates how Python can be used to analyze and visualize astronomical data (much like one can do in IDL) has been written and now is available at: http://www.scipy.org/wikis/topical_software/Tutorial While much of the focus is on astronomical data, most of it probably could serve as a general tutorial as well if sections on more advanced pyfits usage are skipped (only a few pages). There are appendices that contrast Python/numarray with IDL, I'd be happy to include the equivalent for Matlab if anyone who is familiar with both would like to write such appendices. Suggestions for improvements are welcome. Perry

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convolve
by René Bastian 26 Jul '05

26 Jul '05

Hello, in the actual form convolve(a,b)==convolve(b,a)[::-1] but following the mathematics, one should obtain convolve(a,b)==convolve(b,a) can anyone explain me the reason ? thanks -- René Bastian http://www.musiques-rb.org

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fft output and input storage
by Daniel Sheltraw 26 Jul '05

26 Jul '05

Hello all Would someone please tell me how negative and positive frequencies are stored in the output of the Numerical Python fft? Cheers, Daniel

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is numerical python only for prototyping ?
by Sebastian Haase 26 Jul '05

26 Jul '05

Hi, This is not sopposed to be an evil question; instead I'm hoping for the answer: "No, generally we get >=95% the speed of a pure C/fortran implementation" ;-) But as I am the strongest Python/numarray advocate in our group I get often the answer that Matlab is (of course) also very convenient but generally memory handling and overall execution performance is so bad that for final implementation one would generally have to reimplement in C. We are a bio-physics group at UCSF developping new algorithms for deconvolution (often in 3D). Our data sets are regularly bigger than several 100MB. When deciding for numarray I was assuming that the "Hubble Crowd" had a similar situation and all the operations are therefore very much optimized for this type of data. Is 95% a reasonable number to hope for ? I did wrap my own version of FFTW (with "plan-caching"), which should give 100% of the C-speed. But concerns arise from expression like "a=b+c*a" (think "convenience"!): If a,b,c are each 3D-datastacks creation of temporary data-arrays for 'c*a' AND then also for 'b+...' would have to be very costly. (I think this is at least happening for Numeric - I don't know about Matlab and numarray) Hoping for comments, Thanks Sebastian Haase UCSF, Sedat Lab

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C API function to get the shape of an array ?
by Soeren Sonnenburg 23 Jul '05

23 Jul '05

Hi, I just want to use NA_get1_Int64 etc but I couldn't find a way to 'cleanly' find out about the size of an array, i.e. I always have to access raw fields in the PyArrayObject structure like: PyArrayObject* a; if (a->nd == 2) { if (a->dimensions[0] == m && b->dimensions[1] == n) ... Is this the intended way ? I hope not... Best, Soeren

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Re: [Numpy-discussion] Biulding Numarray with atlas.
by Chris Barker 21 Jul '05

21 Jul '05

Nadav Horesh wrote: > Whenever you need a patch to compile numarray with lapack/atlas, you > should check if the linear_algebra module works. Of course. And test I have, and no, it doesn't work: ImportError: /usr/lib/python2.4/site-packages/numarray/linear_algebra/lapack_lite2.so: undefined symbol: dgesdd_ I'm guessing this is a symbol mangling mismatch between what lapack_lite2 is expecting and what my atlas install used (i.e. too many or not enough underscores) For what it's worth, I get the same error with Numeric. which brings me back to my first question: Where should I get a good lapack/blas for Fedora core 4? There are lapack and blas rpms, but there is no indication of whether they are optimized or not. -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/OR&R/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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Biulding Numarray with atlas.
by Chris Barker 21 Jul '05

21 Jul '05

Hi all, I'm working on building numarray with atlas on a Fedora core 4 system. I installed atlas by downloading a binary from the atlas sourceforge site, and copying stuff into /usr/local/... Then in cfc_packages.py, I added: USE_LAPACK = True at the top. That doesn't seem like where I should do it, but it works. then I got: Src/_dotblas.c:15:19: error: cblas.h: No such file or directory So I looked and saw: else: lapack_dirs = ['/usr/local/lib/atlas'] lapack_libs = ['lapack', 'cblas', 'f77blas', 'atlas', 'g2c', 'm'] which makes sense, we haven't added the include directory that cblas.h is in. So I added: lapack_include_dirs += ['/usr/local/include/atlas/'] and now it seems to work. Perhaps an include line should be added to the stock cfc_packages.py -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/OR&R/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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unexpected behavior of na.where (no short-circuiting)
by Sebastian Haase 20 Jul '05

20 Jul '05

Hi, I was very surprised when I got this warning: >>> a = na.arange(4)-2 >>> na.where(a != 0,1./a, 999) Warning: Encountered divide by zero(s) in divide [ -0.5 -1. 999. 1. ] Then I realized that this is generally referred to as (not) "short circuiting" (e.g. in the case of the '?:'-C-operator, the middle part never gets evaluated at all if the first part evals to 0 ) Especially annoying was this because (for debugging) I had set this error-mode: >>> na.Error.setMode(dividebyzero="error") My questions are: a) Did other people encounter this problem ? b) What is the general feeling about this actually being a "problem" ? c) Could this (at all possible) be implemented differently ? Thanks, Sebastian Haase

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