NumPy-Discussion October 2008

numpy-discussion@python.org

144 participants
145 discussions

Bilateral filter
by Nadav Horesh 25 Nov '08

25 Nov '08

Attached here my cython implementation of the bilateral filter, which is my first cython program. I would ask for the following: 1. Is there any way to speed up the code just by "cosmetic" modifications? 2. In particular I use the unportable gcc function __builtin_abs: Is there any way to access this in a portable way? 3. I would like to donate this code to scipy or any other suitable project. What can/should I do to realise it? Remarks: The code contains 3 end-user routines: 1. A pure python implementation: Easy to read and modify --- it can be cut out into a python source code. 2. A straight forward cython implementation: About 4 times as fast as the python implementation. 3. An optimised cython implementation earning another factor of 2 in speed (depends on the parameters used). I see this code as a "research grade" that would evolve in the near future, as I am working on a related project, and hopefully following your comments. Nadav

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can't build numpy 1.2.0 under python 2.6 (windows-amd64) using VS9
by Paul Lucek 20 Nov '08

20 Nov '08

I get the following errors in umathmodule.c.src: D:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\cl.exe /c /nolog o /Ox /MD /W3 /GS- /DNDEBUG -Ibuild\src.win-amd64-2.6\numpy\core\src -Inumpy\cor e\include -Ibuild\src.win-amd64-2.6\numpy\core\include/numpy -Inumpy\core\src -I numpy\core\include -Id:\python26\include -Id:\python26\PC /Tcbuild\src.win-amd64 -2.6\numpy\core\src\umathmodule.c /Fobuild\temp.win-amd64-2.6\Release\build\src. win-amd64-2.6\numpy\core\src\umathmodule.obj umathmodule.c numpy\core\src\umathmodule.c.src(64) : error C2059: syntax error : 'type' numpy\core\src\umathmodule.c.src(70) : error C2059: syntax error : 'type' numpy\core\src\ufuncobject.c(1701) : warning C4244: '=' : conversion from 'npy_i ntp' to 'int', possible loss of data numpy\core\src\ufuncobject.c(2422) : warning C4244: '=' : conversion from 'npy_i ntp' to 'int', possible loss of data error: Command "D:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\BIN\amd64\ cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -Ibuild\src.win-amd64-2.6\numpy\core \src -Inumpy\core\include -Ibuild\src.win-amd64-2.6\numpy\core\include/numpy -In umpy\core\src -Inumpy\core\include -Id:\python26\include -Id:\python26\PC /Tcbui ld\src.win-amd64-2.6\numpy\core\src\umathmodule.c /Fobuild\temp.win-amd64-2.6\Re lease\build\src.win-amd64-2.6\numpy\core\src\umathmodule.obj" failed with exit s tatus 2

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Memmapping .npy
by Gael Varoquaux 19 Nov '08

19 Nov '08

Currently memmapping a .npy file is not implemented. Is there a reason than lack of time for this? Are there any major difficulties? Cheers, Gaël

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About Random Number Generation
by Wu, Kejia 19 Nov '08

19 Nov '08

Hi all, I tried the example code here: http://numpy.scipy.org/numpydoc/numpy-20.html#71863 But failed: -------------------------------------- rng.py, line 5, in <module> import RNG ImportError: No module named RNG -------------------------------------- Any suggestion? Thanks at first. Also, can any body tell me whether the random number algorithm in RNG package is a pseudorandom one or a real-random one? And is there an available implementation for Monte Carlo method in NumPy? Thanks a lot for any reply. Regards, Kejia

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Masked arrays and pickle/unpickle
by Anthony Floyd 07 Nov '08

07 Nov '08

We have an application that has previously used masked arrays from Numpy 1.0.3. Part of saving files from that application involved pickling data types that contained these masked arrays. In the latest round of library updates, we've decided to move to the most recent version of matplotlib, which requires Numpy 1.1. Unfortunately, when we try to unpickle the data saved with Numpy 1.0.3 in the new code using Numpy 1.1.0, it chokes because it can't import numpy.core.ma for the masked arrays. A check of Numpy 1.1.0 shows that this is now numpy.ma.core. Does anyone have any advice on how we can unpickle the old data files and update the references to the new classes? Thanks, Anthony. -- Anthony Floyd, PhD Convergent Manufacturing Technologies Inc. 6190 Agronomy Rd, Suite 403 Vancouver BC V6T 1Z3 CANADA Email: Anthony.Floyd(a)convergent.ca | Tel: 604-822-9682 x102 WWW: http://www.convergent.ca | Fax: 604-822-9659 CMT is hiring: See http://www.convergent.ca for details

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Re: [Numpy-discussion] passing a C array to embedded Python fromC code
by Anthony Floyd 06 Nov '08

06 Nov '08

Hi Chris, > Matthieu Brucher wrote: > > If you can > > follow a French tutorial, you can go on > > > http://matthieu-brucher.developpez.com/tutoriels/python/swig-numpy/#LV > > to have a skeletton for your issue. > > That looks very useful -- any chance of an English > translation? My one > year of high school French is proving useless. Otherwise, the code > itself is still quite helpful. > Google does a pretty good job on this one: http://translate.google.com/translate?u=http%3A%2F%2Fmatthieu-brucher.devel… Anthony. -- Anthony Floyd, PhD Convergent Manufacturing Technologies Inc. 6190 Agronomy Rd, Suite 403 Vancouver BC V6T 1Z3 CANADA Email: Anthony.Floyd(a)convergent.ca | Tel: 604-822-9682 x102 WWW: http://www.convergent.ca | Fax: 604-822-9659 CMT is hiring: See http://www.convergent.ca for details

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(Late) summary of PEP-225 discussion at Scipy
by Fernando Perez 05 Nov '08

05 Nov '08

Hi all, much delayed, but here it is, finally. The doc regarding our discussion about PEP 225 is attached, and I'm keeping a public copy for viewing convenience (with html) here: https://cirl.berkeley.edu/fperez/static/numpy-pep225/ Note that, as indicated in the link above, the real doc is in bzr, so you can check it out to generate patches or a branch (the preferred formats for big changes). This is just a first cut, going from memory and notes. I'd appreciate any feedback, corrections, etc. I'm giving a talk at the BayPiggies group Nov 13 about SciPy and will take the opportunity to bring this document up, since that user group has a lot of python people, including some core developers. Since this is from memory and written by me, it's likely pretty biased. But I really want to clarify that I'm trying to act as a scribe here, not to push my own agenda (I do have one :). So please bring up anything you feel is missing/misstated here; I'd really like to have a doc that people feel is a fair representation of the community's views to bring to the core python team. That way we either get our operators or not once and for all, but this issue can be put to rest in the language for good (as of 2.7/3.1, of course). So let's have Nov 11 or so as a wrapup deadline on this discussion, so I can have the summary ready for the Nov 13 talk. Best, f

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Simplifying compiler optimization flags logic (fortran compilers)
by David Cournapeau 03 Nov '08

03 Nov '08

Hi, I was wondering whether it was really worth having a lot of magic going on in fcompilers for flags like -msse2 and co (everything done in get_flags_arch, for example). It is quite fragile (we had several problems wrt buggy compilers, buggy CPU detection), and I am not sure it buys us much anyway. Did some people notice a difference between gfortran -O3 -msse2 and gfortran -O3 ? thanks, David

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Re: [Numpy-discussion] Complete LAPACK needed (Frank Lagor)
by Frank Lagor 01 Nov '08

01 Nov '08

Hi Everyone, I am trying to give an update here so that maybe it will be easier for someone to help me out now. I have gone through the lapack installation and the atlas installation and everything seems to have worked fine. Everything was compiled using the 'fPIC' option and I figured out how to make shared blas and lapack library files with atlas. Also, I figured out how to tell Atlas that I want a COMPLETE lapack. Now I am having trouble with the numpy install. In the site.cfg file, I included the location where I have the include and lib files for lapack. After install, when I test, I get the following: [dfranci@alpha ~]$ python -c 'import numpy; numpy.test()' Traceback (most recent call last): File "<string>", line 1, in <module> File "/ronaldo/pkg/dfranci/Python-2.5.2/lib/python2.5/site-packages/numpy/__init__.py", line 143, in <module> import linalg File "/ronaldo/pkg/dfranci/Python-2.5.2/lib/python2.5/site-packages/numpy/linalg/__init__.py", line 47, in <module> from linalg import * File "/ronaldo/pkg/dfranci/Python-2.5.2/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 29, in <module> from numpy.linalg import lapack_lite ImportError: liblapack.so: cannot open shared object file: No such file or directory I notice one thing here that concerns me: numpy is trying to import a module that it calls "lapack_lite". Does numpy always build such a module? If I am trying to get the complete lapack, did I do something wrong? Thanks in advance, Frank

3 3

installation problem on Red Hat
by Christoph Göbl 01 Nov '08

01 Nov '08

dear members, I'm very sorry to bother you with a (hopefully) simple problem... I need pyhton and the numerical package to run another program. I installed Python, it works fine. But I can't install the numpy package. To install the oder Numeric package was no problem, but I need the newer numpy... after "python setup.py install" I get an error message after sime while: ... compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-2.5/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/usr/local/include/python2.5 -c' /usr/local/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.5/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.5/numpy/linalg/python_xerbla.o -L/usr/lib -llapack -lblas -lg2c -o build/lib.linux-x86_64-2.5/numpy/linalg/lapack_lite.so /usr/bin/ld: skipping incompatible /usr/lib/liblapack.so when searching for -llapack /usr/bin/ld: skipping incompatible /usr/lib/liblapack.a when searching for -llapack /usr/bin/ld: skipping incompatible /usr/lib/libblas.so when searching for -lblas /usr/bin/ld: skipping incompatible /usr/lib/libblas.a when searching for -lblas /usr/bin/ld: skipping incompatible /usr/lib/libg2c.so when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libg2c.a when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libfrtbegin.a when searching for -lfrtbegin /usr/bin/ld: skipping incompatible /usr/lib/libg2c.so when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libg2c.a when searching for -lg2c /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status /usr/bin/ld: skipping incompatible /usr/lib/liblapack.so when searching for -llapack /usr/bin/ld: skipping incompatible /usr/lib/liblapack.a when searching for -llapack /usr/bin/ld: skipping incompatible /usr/lib/libblas.so when searching for -lblas /usr/bin/ld: skipping incompatible /usr/lib/libblas.a when searching for -lblas /usr/bin/ld: skipping incompatible /usr/lib/libg2c.so when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libg2c.a when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libfrtbegin.a when searching for -lfrtbegin /usr/bin/ld: skipping incompatible /usr/lib/libg2c.so when searching for -lg2c /usr/bin/ld: skipping incompatible /usr/lib/libg2c.a when searching for -lg2c /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status error: Command "/usr/local/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.5/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.5/numpy/linalg/python_xerbla.o -L/usr/lib -llapack -lblas -lg2c -o build/lib.linux-x86_64-2.5/numpy/linalg/lapack_lite.so" failed with exit status 1 ... I don't know, what I can do... On a Suse 10.2 it ran easily, but on the other computer, Red Hat 3.4.3_9, X86_64, gcc 3.4.3 there is always this error message. I read in another forum, that a person solved a similar problem using unsetenv ldflags But - sorry I'm a Newbie in Linux and Python - there the installation was on another platform I think. Anyway, maybe it's a linking problem? thank you very much for any thoughts you may waste on my problems... best regards, Christoph _________________________________________________________________ Hol dir 30 kostenlose Emoticons für deinen Windows Live Messenger http://www.livemessenger-emoticons.com/funfamily/de-at/

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NumPy-Discussion October 2008