Mailman 3 August 2008 - SciPy-User

partially reading a file...
by fred 08 Aug '08

08 Aug '08

Hi, Let's say I want to read a (binary) file which contains a nx*ny*nz array. Is it possible to read a "sub-array" from this file, ie each block of (nx/4, ny/4, nz/4) for instance, without loading the whole file ? TIA. Cheers, -- Fred

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Python tools at the annual SIAM meeting
by Fernando Perez 08 Aug '08

08 Aug '08

Hi all, for those interested, here's a brief report on the recent SIAM meeting where a number of Python-based tools for scientific computing (including ipython, numpy, scipy, sage, and more) were discussed: http://fdoperez.blogspot.com/2008/07/python-tools-for-science-go-to-siam.ht… The punch line is that we got selected for the annual highlights of the conference: http://www.ams.org/ams/siam-2008.html#python Thanks again to all who contributed talks and attended! Cheers, f

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"Use minimum ordering" message
by John Koschwanez 07 Aug '08

07 Aug '08

Simple problem. I'm relatively new to Python, and I'm writing a diffusion simulator using the sparse and linsolve modules. Each time I solve a matrix, I get the following message: "Use minimum degree ordering on A'+A." which results from a printf() in the get_perm_c.c file when a permutation matrix is set up. Questions: 1. Why is this message printed when (I assume) it is not a warning or an error? Any output like this slows down the solver when I'm solving tens of thousands of matrices. 2. Is there a way in Python to selectively ignore output statements like this? I don't want to comment out the source code and recompile. Thanks, John

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scipy.stats.gamma usage.
by cyril giraudon 06 Aug '08

06 Aug '08

Hi, I am not an expert in statistics and had too validate some computations. I currently try to use the scipy.stats.gamma.pdf function. I don't know how to use the function and obtain the results presented in wikipedia http://en.wikipedia.org/wiki/Gamma_distribution. Can anybody help me ? Thanks a lot, Cyril.

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wrong compiler selected?
by Robert Cimrman 06 Aug '08

06 Aug '08

Hi, This is a follow-up to "rev 4595 broken" thread. I got numpy to compile, as I explained (but the e-mail has not arrived yet). Now I have another problem: building 'scipy.sparse.sparsetools._csr' extension compiling C++ sources C compiler: i486-pc-linux-gnu-g++ -pthread -fno-strict-aliasing -DNDEBUG -fPIC creating build/temp.linux-i686-2.4/scipy/sparse creating build/temp.linux-i686-2.4/scipy/sparse/sparsetools compile options: '-I/home/share/software/usr/lib/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c' i486-pc-linux-gnu-g++: scipy/sparse/sparsetools/csr_wrap.cxx scipy/sparse/sparsetools/csr_wrap.cxx: In function 'int require_size(PyArrayObject*, npy_intp*, int)': scipy/sparse/sparsetools/csr_wrap.cxx:2902: error: expected `)' before 'PRIdPTR' scipy/sparse/sparsetools/csr_wrap.cxx:2909: error: expected `)' before 'PRIdPTR' It looks like NPY_USE_C99_FORMATS is set to one, causing 'PRIdPTR' instead of 'd' to be used in NPY_INTP_FMT Is this a problem of numpy compiler selection, or else? SciPy compiles fine when I tweaked this manually. r.

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prefactor response
by Frank Lagor 06 Aug '08

06 Aug '08

Hi Lubos, I don't know a whole lot about transforms however, I do remember one bit of information that may be useful to you: The prefactors in the sine transform (which is of course related to the fourier transform) are actually matters of convention. The sqrt(2/pi) is not always the prefactor! The prefactor is usually chosen to be sqrt(2/pi) so that the inverse transform will also have a prefactor of sqrt(2/pi) and there will be some symmetry in the two formulas so that they look alike and are easier to remember. However, SOMETIMES people chose the transform or inverse transform (I can't recall which) to have a 2/pi prefactor, and the other to have no prefactor. I comes down to a matter of convention and it doesn't matter which one you chose, as long as you are consistent. Please careful and make sure you a certain of the convention chosen and you a consistent in what you code and you will be fine. Hope this helps, Frank PS> Dear Everyone, I am trying to get my email mailing list style fixed so that I don't break mailing list etiquette. Please email me personal to check me if this email sucked. Sorry for my previous mistakes! -- Frank Lagor Ph.D. Candidate Mechanical Engineering and Applied Mechanics University of Pennsylvania

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OpenOpt: ralg crash
by Eli Brosh 06 Aug '08

06 Aug '08

Hello, I encountered problems with the ralg solver in OpenOpt. the example nlp_3.py, supplied with the OpenOpt library crashed on two computers. On an ubuntu linux machine, the program simply stopped without further information. On a windows machine, with entought suite, there was a windows error message "pythonw caused a fatal error and it will be closed". The problem disappeared when I erased ralg from the solvers list. It did not occur with lincher and scipy_cobyla solvers. On both machines, the openopt installation was from the latest tarball (no more than week old). What is the problem ? Can it be corrected ? Another small request concerning OpenOpt. Is it possible to provide an example for use of scipy_tnc and scipy_lbfgsb from openopt ? Can these solvers work with linear equality constraints ? Thanks Eli

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OpenOpt : how to avoid output
by Eli Brosh 06 Aug '08

06 Aug '08

Hello, When OpenOpt is called without graphical output as: r=p.solve('solver',plot=False) I still get lots of output to the screen in the python interpreter. Is it possible to silence this output ? i.e. to cancel the printing of iterations etc. into the interpreter prompt. I only need to get the final result and to put it in other variables like finalf=r.ff finalx=r.xf Thanks Eli

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rev 4595 broken
by Tommy Grav 05 Aug '08

05 Aug '08

I tried to install the current svn trunk and ran into this problem skathi:~] tgrav% python ActivePython 2.5.1.1 (ActiveState Software Inc.) based on Python 2.5.1 (r251:54863, May 1 2007, 17:40:00) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.__version__ '1.1.1' >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/scipy/__init__.py", line 86, in <module> from numpy.testing import Tester ImportError: cannot import name Tester >>> Is the current bleeding edge copy broken? Cheers Tommy Grav + -----------------------------------------------------------------------------------------------------------------+ Associate Research Scientist Dept. of Physics and Astronomy Johns Hopkins University Bloomberg 243 tgrav(a)pha.jhu.edu 3400 N. Charles St. (410) 516-7683 Baltimore, MD21218 + -----------------------------------------------------------------------------------------------------------------+

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Reading Empty Arrays
by Lorenzo Isella 05 Aug '08

05 Aug '08

Dear All, I have a code which saves in files called file001, file002, and so on a set of data. Now, each file contains a record of events which may or may not have occurred. This is to say that, e.g., file004 can be empty. I normally use pylab to read/write files; in my codes I normally use: import scipy as s import pylab as p The problem appears when I try reading one of these arrays. E.g.: my_array=p.load("file004") since then I get an error message. These are my points: (1) I do not know beforehand which files will be empty (2) Since I generate a lot of them which I then post-process automatically, I cannot select by hand which are empty and which are not. (3) Not saving file004 since it is empty would not be a good idea (I read the output files sequentially when postprocessing). If reading this file004 generated a zero-length array like the one you have if you type: f=s.zeros(0) Then I would be probably fine, since in my postprocessing, certain loops depending on the length of the array would be (rightly) skipped if the length of the array is zero. How can I do that? Basically, I may be in trouble if I have to re-write the code generating the results, whereas it would be ideal for me to be able to read empty files as zero-length arrays. Many thanks Lorenzo Isella

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