Mailman 3 April 2001 - NumPy-Discussion

?POOMA and Boost?
by Norman Shelley (rrdn60) 13 Apr '01

13 Apr '01

o How would a Python version of POOMA compare/contrast to Numpy? POOMA (Parallel Object-Oriented Methods and Applications) a C++ high performance simulation infrastructure package http://www.acl.lanl.gov/pooma/ Would boost add anything advantages to the current Numpy methodology? http://www.boost.org/ Thanks, Norman Shelley

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RandArray initialization and docs
by Clay Spence 12 Apr '01

12 Apr '01

Hi, I have occasionally dabbled with numpy in the past, but I'm starting to use it more heavily now. I have two (minor, I think) question/comments: 1) RandomArray seems to be initialized from the time. At least when I repeatedly execute a script that uses RandomArray.uniform, the first number generated changes very little from one invocation to another. For example, with the following file: --------- # testRA.py from RandomArray import * print uniform(-1.0, 1.0) --------- I get: -------- cholla 192% python testRA.py 0.434084415436 cholla 193% python testRA.py 0.433970689774 cholla 194% python testRA.py 0.433856964111 cholla 195% python testRA.py 0.433781266212 -------- Is that really desirable behavior? It is easily fixed in my script; I just generate one random number first and throw it away. (I'm running on a sparc under solaris 2.6.) 2) The example in the documentation on negative strides in slices is incorrect, or old. It says: >>> a = reshape(arrayrange(9),(3,3)) >>> print a[2:-1, 0] [6 3 0] That's not the result I get. I think two colons were wanted there. Clay

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wavelets
by Tariq Rashid 09 Apr '01

09 Apr '01

I'm about to start work on a wavelets module for python... don't know how far i want to go yet.... is there an existsing project? i couldn't find one! tariq

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redirection?
by Paul F. Dubois 09 Apr '01

09 Apr '01

Since I made that typo I have people going to pfdubois.com/numeric when I actually made it /numpy. I can create a numerc -- but I think it would be nicer if I did the automatic redirection trick. So what does one do to get a browser to switch to a different site?

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Nieghbourhood functions
by Robert.Denham＠dnr.qld.gov.au 08 Apr '01

08 Apr '01

I am looking for efficient ways to code neighbourhood functions. For example a neighbourhod add for an element in an array will simply be the sum of the neighbours: 1 0 2 3 x 3 , then x becomes 7 (first order neighbour), 11 (2nd order) etc. 1 1 0 I would be interested in efficient ways of doing this for a whole array, something like a_nsum = neighbour_sum(a, order=1), where each element in a_nsum is the sum of the corresponding element in a. There must be some work done on neighbourhood functions for arrays, so I would be grateful for some pointers. Thanks, Robert Denham ************************************************************************ The information in this e-mail together with any attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any form of review, disclosure, modification, distribution and/or publication of this e-mail message is prohibited. If you have received this message in error, you are asked to inform the sender as quickly as possible and delete this message and any copies of this message from your computer and/or your computer system network. ************************************************************************

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Optimisation of a Numpy set intersection function
by Tim Churches 08 Apr '01

08 Apr '01

I have been trying to optimise a simple set intersection function for a Numpy-based application on which I am working. The function needs to find the common elements (i.e the intersection) of two or more Numpy rank-1 arrays of integers passed to it as arguments - call them array A, array B etc. My first attempt used searchsorted() to see where in array A each element of array B would fit and then check if the element in array A at that position equalled the element in array B - if it did, then that element was part of the intersection: def intersect(A,B): c = searchsorted(A,B) d = compress(less(c,len(A)),B) return compress(equal(take(A,compress(less(c,len(A)),c)),d),d) This works OK but it requires the arrays to be stored in sorted order (which is what we did) or to be sorted by the function (not shown). I should add that the arrays passed to the function may have up to a few million elements each. Ole Nielsen at ANU (Australian National University), who gave a paper on data mining using Python at IPC9, suggested an improvement, shown below. Provided the arrays are pre-sorted, Ole's function is about 40% faster than my attempt, and about the same speed if the arrays aren't pre-sorted. However, Ole's function can be generalised to find the intersection of more than two arrays at a time. Most of the time is spent sorting the arrays, and this increases as N.log(N) as the total size of the concatenated arrays (N) increases (I checked this empirically). def intersect(Arraylist): C = sort(concatenate(Arraylist)) D = subtract(C[0:-n], C[n:]) #or # D = convolve(C,[n,-n]) return compress(equal(D,0),C) #or # return take(C,nonzero(equal(D,0))) Paul Dubois suggested the following elegant alternative: def intersect(x,y): return compress(sum(equal(subtract.outer(x,y),0),1),x) Unfortunately, perhaps due to the overhead of creating the rank-2 array to hold the results of the subtract.outer() method call, it turns out to be slower than Ole's function, as well as using huge tracts of memory. My questions for the list, are: a) can anyone suggest any further optimisation of Ole's function, or some alternative? b) how much do you think would be gained by re-implementing this function in C using the Numpy C API? If such an effort would be worthwhile, are there any things we should consider while tackling this task? Regards, Tim Churches Sydney, Australia

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Citing NumPy
by Konrad Hinsen 05 Apr '01

05 Apr '01

I am just working on an article describing a program which makes heavy use of NumPy, so I should cite some reference to it. Did anyone do this before? What is the most appropriate reference? I think URLs are acceptable these days, but it should be a rather stable one. Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen(a)cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------

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Documentation typos
by Christos Siopis <siopis＠astro.ufl.edu> 03 Apr '01

03 Apr '01

I was reading some sections of the latest NumPy tutorial (the one currently listed as http://pfdubois.com/numpy/numdoc.pdf ) and spotted these typos, listed below in case you want to fix them. Page numbers refer to the actual page numbers printed on the page (not the PDF document's numbers). - p.14: "A very useful features of arrays..." (should be "feature"). - p.15, top-of-page NumPy example: arrays are shown printed before the corresponding "print" command (see "print a" and "print b"). - p.17: in the "Advanced Users" section: the explanation of what these sections are for should perhaps be included in the previous page's "Advanced Users" section, since that one is the first such occurrence in the tutorial. - p.19, near the end: Above "identity": "The first example BELOW satisfies... while the second array ...": there is only one example "below", the buggy example. The first, correct example is probably the one given previously on the same page. Christos

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Using Numpy inside an application...
by Karl Bellve 03 Apr '01

03 Apr '01

Since I can't search the web site, here is a question... I am using the following calls inside my C++ app: import_array(); a=PyRun_SimpleString("from image_module import *"); // my module for wrapping a C++ class a=PyRun_SimpleString("image=imagemanager()\n"); // load a new instance of the class into Python a=PyRun_SimpleString("a=image.GetImage(0)"); // assign image 0 to a Basically, GetImage() returns a numpy Array Object for image 0, properly initialized by PyArray_FromDimsAndData(). I can't return all the images because they might not be sequential in memory (off loaded to the filesystem). "a" appears to be an list of numbers. I am not sure if Python knows it is a PyArrayObject. This is where I am getting into trouble. I can't do something like a=PyRun_SimpleString("a = a + 100"); I get an error "Value Error: Function not Supported". I am trying to figure out what namespace did "import_array()" import Numeric into. Also, I am using _numpy_d.pyd that I compiled under Windows NT and MSVC 6.0. -- Cheers, Karl Bellve, Ph.D. ICQ # 13956200 Biomedical Imaging Group TLCA# 7938 University of Massachusetts Email: Karl.Bellve(a)umassmed.edu Phone: (508) 856-6514 Fax: (508) 856-1840 PGP Public key: finger kdb(a)molmed.umassmed.edu

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numpy newbie question
by Michael Drumheller 03 Apr '01

03 Apr '01

Hi, I am pretty new to numpy and am using it for image processing. (Also, I am not 100% sure that this is the appropriate email address for this question--feel free to redirect me.) My problem is that I would like to be able to dive down into C and write my own filters etc., but I do not want to have to surmount the somewhat daunting Python/C-extension learning curve if that is at all possible. I am wondering if anybody has "packaged" this ability anywhere, sort of like Perl's Inline.pm. Thanks, Mike Drumheller ===== Michael Drumheller 2735 NE 87th Street, Seattle, Washington 98115 206/523-7865 drumheller(a)alum.mit.edu __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/

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