Mailman 3 October 2000 - NumPy-Discussion

simple array help?
by Pete Shinners Sept. 17, 2001

Sept. 17, 2001

i have a simple array with floating values >>> print a array([ 0. , 0.2, 0.4, 0.6, 0.8]) what i need to do is change each index into another dimension with 3 indices. hmm, kind of confusing, an example will explain better >>> b = array(zip(a,a,a)) >>> print b array([[ 0. , 0. , 0. ], [ 0.2, 0.2, 0.2], [ 0.4, 0.4, 0.4], [ 0.6, 0.6, 0.6], [ 0.8, 0.8, 0.8]]) ok, this does the job, but once i start using large arrays, the back-n-forth conversion between arrays and python lists is costing me quite a bit. is there a way i can reshape the array this way without the call to python's 'zip'? (no, 'map' doesn't count either) i've tried much fooling with NewAxis, resize, and friends. but either i haven't stumbled upon the correct combination or i'm not trying the correct tools. i'd like to keep this as quick as possible, so hopefully it can be done without anything too elaborate. thanks (doh, sorry for the previous distutils related post... hit the wrong mailing list)

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Numpy install problems
by Michael D. Risser July 27, 2001

July 27, 2001

When attempting to install Numeric 17.0 with Python 1.5.2 and Distutils 1.0 on Red Hat 7.0, I get the following error after issuing the command 'python setup.py install' Traceback (innermost last): File "setup.py", line 15, in ? vs = map(string.atoi, v.groups()) AttributeError: 'None' object has no attribute 'groups' This error occurs regardless of whether or not I am root. I have also tried uninstalling the Red Hat Python packages and installing all from source, but I get the same error. Any help would be appreciated. Thanks.

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[Q]Best way for an array operation?
by Daehyok Shin May 4, 2001

May 4, 2001

What is the best Numpy way for the following work? for i in range(len(x)): if x[i] > 0: y[i] = v[i] z[i] = u[i]+2 Daehyok Shin (Peter)

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Re: [Numpy-discussion] Da Blas
by Frank Horowitz Jan. 2, 2001

Jan. 2, 2001

At 3:14 PM -0700 14/9/00, <dubois(a)users.sourceforge.net> wrote: >Well, I certainly didn't mean to flame anyone in particular, so I'm sorry >that Frank was offended. Publicly apologized, and publicly accepted. I'm sorry I lost my cool. Ray Beausoleil and I are having a look at this too. He's coming at the problem from a Windows perspective, and I'm coming at it from a Linux/Unix perspective. It's going to be a little slow going for me at first, since it appears that I'm going to have to get my head around the distutils way of doing things.... Just in case it saves anyone else following a false lead, yes, there is a bug in the (Linux Mandrake 7.1; but probably any unix-ish box) compile line for building the lapack_lite.so shared library (i.e. what is generated on my box is "-L/usr/lib-llapack" which obviously is missing a blank before the "-llapack" substring). However, when I coerced the distutils system to get around that bug (by specifying "/usr/lib " with a trailing blank for the BLASLIBDIR and LAPACKLIBDIR variables in setup.py) the same problem (i.e. an "ImportError: /usr/lib/liblapack.so.3: undefined symbol: e_wsfe" in importing lapack_lite) ultimately manifested itself. So my advice is not to bother tracking that one down (although it probably should be reported as a bug in distutils, since adding that trailing blank algorithmically instead of in a user modifiable configuration string is the "right thing to do", TM.). I'm still puzzled by Thomas Breul's report of preloading an f2c library squashing the bug under RedHat 6.2(?). That does not work under Mandrake, although clearly there is some bloody symbol table missing from somewhere. The trouble is to find out where, and then to coerce distutils to deal with that in a portable way... Frank -- -- Frank Horowitz frank(a)ned.dem.csiro.au CSIRO-Exploration & Mining, PO Box 437, Nedlands, WA 6009, AUSTRALIA Direct: +61 8 9284 8431; FAX: +61 8 9389 1906; Reception: +61 8 9389 8421

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quick optimization
by Pete Shinners Nov. 27, 2000

Nov. 27, 2000

i've got a quick optimization for the arrayobject.c source. it speeds my usage of numpy up by about 100%. i've tested with other numpy apps and noticed a minimum of about 20% speed. anyways, in "do_sliced_copy", change out the following block: if (src_nd == 0 && dest_nd == 0) { for(j=0; j<copies; j++) { memcpy(dest, src, elsize); dest += elsize; } return 0; } with this slightly larger one: if (src_nd == 0 && dest_nd == 0) { switch(elsize) { case sizeof(char): memset(dest, *src, copies); break; case sizeof(short): for(j=copies; j; --j, dest += sizeof(short)) *(short*)dest = *(short*)src; break; case sizeof(long): for(j=copies; j; --j, dest += sizeof(int)) *(int*)dest = *(int*)src; break; case sizeof(double): for(j=copies; j; --j, dest += sizeof(double)) *(double*)dest = *(double*)src; break; default: for(j=copies; j; --j, dest += elsize) memcpy(dest, src, elsize); } return 0; } anyways, you can see it's no brilliant algorithm change, but for me, getting a free 2X speedup is a big help. i'm hoping something like this can get merged into the next releases? after walking through the numpy code, i was surprised how almost every function falls back to do_sliced_copy (guess that's why it's at the top of the source?). that made it a quick target for making optimization changes.

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Re: Legal Notice
by Greg Ball Oct. 31, 2000

Oct. 31, 2000

I think the way Gerard is interpreting this passage > Permission to use, copy, modify, and distribute this software and its > documentation for any purpose and without fee is hereby granted, is that you can DISTRIBUTE the software but you can't CHARGE A FEE. However this appears in the normal python license and many others and I am sure the correct interpretation is that you can USE, DISTRIBUTE, etc the software without PAYING A FEE (to the copyright holders.) It is free software, a XFree86 style license according to RMS, which is BSD-like but with no advertising clause. Gerard, the license is fine for distribution and as Joe said, similar to many other free software packages. -Greg Ball

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Windows zip of Numerical Python 17.1.1 available
by Paul F. Dubois Oct. 31, 2000

Oct. 31, 2000

Numerical 17.1.1 is available in both source and prebuilt Windows versions at: http://sourceforge.net/projects/numpy Windows users, simply extract into your top level Python 2.0 directory, typically c:\python20. Thank you to Pete Shinners for putting the Windows file together. It is too late to change for the 17 series but in future I will make releases that have whole numbers only as names and add files to that release as they become available. That makes it a little clearer that you should take the most recent file of the desired type.

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Re: Legal Notice (Gerard Vermeulen (CRTBT))
by Joe Harrington Oct. 31, 2000

Oct. 31, 2000

Gerard, Could you explain why you think that the phrase you quoted is restrictive? Lots of software comes with that phrase, and it certainly hasn't inhibited its wide promulgation. All it says is that you can't pass off this software as your own, which would be lying anyway. As far as I can tell (I'm not a lawyer, etc.), it's far less restrictive than, say, GPL. It seems very like the BSD license you suggest using instead. If you include the packages in a larger work, you can just say: This work includes the blah blah package, which bears the following license: "Permission to use, copy, modify, and distribute this software for any purpose without fee is hereby granted, provided that this entire notice is included in all copies of any software which is or includes a copy or modification of this software and in all copies of the supporting documentation for such software. " Note that the notice *doesn't* say you have to *copyright* the larger package under the terms of the notice or to the owner of the included package, it just says you have to include the notice, presumably so the recipient knows that the package is in there, who the owner of that component is, and that distributing that part is allowed. If you look at the manuals to most commercial Unices, you'll find several pages of such notices from the owners of the various packages included in the system. What's the problem? --jh--

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Numeric-17.1.1 on IRIX 6.3
by Bernd Weyrauch Oct. 30, 2000

Oct. 30, 2000

Hi, I tried to install Numeric-17.1.1 under IRIX 6.3 after installing Python 2.0 without optimization and the -g workaround. I got this error message: # /usr/local/bin/python setup.py install running install running build running build_py not copying Lib/ArrayPrinter.py (output up-to-date) not copying Lib/Numeric.py (output up-to-date) not copying Lib/Precision.py (output up-to-date) not copying Lib/UserArray.py (output up-to-date) not copying Lib/numeric_version.py (output up-to-date) running build_ext building '_numpy' extension skipping Src/_numpymodule.c (build/temp.irix-6.3-2.0/Src/_numpymodule.o up-to-date) skipping Src/arrayobject.c (build/temp.irix-6.3-2.0/Src/arrayobject.o up-to-date) skipping Src/ufuncobject.c (build/temp.irix-6.3-2.0/Src/ufuncobject.o up-to-date) ld -shared -all build/temp.irix-6.3-2.0/Src/_numpymodule.o build/temp.irix-6.3-2.0/Src/arrayobject.o build/temp.irix-6.3-2.0/Src/ufuncobject.o -o build/lib.irix-6.3-2.0/_numpy.so ld: ERROR 48: Cannot access registry file ./so_locations (No locks available) - ignored. ld: FATAL 51: Can't assign virtual addresses for _numpy.so within specified range. Please check your registry file ./so_locations. error: command 'ld' failed with exit status 4 Has anybody else encountered this problem? Thanks a lot! Bernd -- Bernd Weyrauch Marie-Curie-Str. 9 D-60439 Frankfurt am Main Institute of Biophysical Chemistry Tel. +49-(0)69-798-296-72 Frankfurt J. W. Goethe University Fax +49-(0)69-798-296-32 Biocenter, N230 e-mail bernd(a)bpc.uni-frankfurt.de http://www.biozentrum.uni-frankfurt.de/~bernd http://www.cthulhu.onlinehome.de

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Legal Notice
by Gerard Vermeulen (CRTBT) Oct. 29, 2000

Oct. 29, 2000

I like to propose a numpy-RPM to MandrakeSoft for future inclusion in their contrib-cdroms. Of course, MandrakeSoft requires that all license issues are cleared. I understand that the file Legal.htm applies to the packages MA and RNG. Is this true? I like to point out that the phrase "Permission to use, copy, modify, and distribute this software for any purpose without fee is hereby granted, provided that this entire notice is included in all copies of any software which is or includes a copy or modification of this software and in all copies of the supporting documentation for such software. " is very restrictive. It forbids the inclusion of MA and RNG on a commercial CD rom. Isn't it? It also forbids a consultant to use it for his business. But what about somebody getting paid for his work in a government research laboratory? Could you replace this by something more BSD-like? Best regards -- Gerard Vermeulen

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