Mailman 3 April 2005 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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pyvtk ?
by Gary Pajer 06 May '05

06 May '05

Pearu, et al, I have been looking at MayaVi, and I want to explore further. pyvtk is suggested (and Pearu's name is attached to it) but ... http://cens.ioc.ee/projects/pyvtk/ has been unresponsive for a few days. Is this a server problem, or has it moved? Or has it been withdrawn? More generally, is MayaVi / pyvtk a recommended or practical way to interactively visualize 3d data sets? By 3d I mean functions of two variables... surface plots. Any other suggestions? Regards, Gary Pajer

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problem with plt.plot
by Fernando Avila Castro 30 Apr '05

30 Apr '05

Hi, i have installed the Scipy packages on Scientific Linux 4 (derived from RHEL 4) with the ATLAS libs, gnuplot.py and wxPython. It rans the test ok, and I can make plots using gplt. The problem is with plt. I can't even run the examples on the plotting tutorial: Python 2.3.4 (#1, Feb 18 2005, 12:15:38) [GCC 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy import * >>> import gui_thread >>> gui_thread.start() Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/gui_thread/__init__.py", line 73, in start wxPython_thread() File "/usr/lib/python2.3/site-packages/gui_thread/wxPython_thread.py", line 160, in wxPython_thread sys.modules[name] = wrap_extmodule(module,call_holder) File "/usr/lib/python2.3/site-packages/gui_thread/wxPython_thread.py", line 61, in wrap_extmodule raise NotImplementedError,`t` NotImplementedError: <type 'PyCObject'> >>> gui_thread.wxPython_thread() Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/gui_thread/wxPython_thread.py", line 156, in wxPython_thread for name in get_extmodules(pexec): File "/usr/lib/python2.3/site-packages/gui_thread/wxPython_thread.py", line 25, in get_extmodules _do_import(pexec) File "/usr/lib/python2.3/site-packages/gui_thread/wxPython_thread.py", line 104, in _do_import assert not sys.modules.has_key('wx'), \ AssertionError: wx is already imported, cannot proceed Any hints on how to solve this?

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Re: SciPy-- convincing my lab to switch to SciPy/Python
by Travis Oliphant 28 Apr '05

28 Apr '05

Josh Tasman wrote: > Python seems like a good choice for our lab, as it's relatively easy > for novice programmers to work with (vs C++ or perl.) More > importantly, it has a large community behind it. > > Specifically, I need to convince my lab (and myself) that Python/SciPy > is a robust replacement for Matlab. Primarily, I need more info > regarding the reliability of numeric computation. Programs like > Matlab and Mathematica go through rigorous mathematical testing. > What's the state of > SciPy in this regard? Would you stand behind it for > publication-quality work? The reliability of SciPy is somewhat mixed. Most of the actual algorithms are based on FORTRAN code that has been around for literally decades and are quite reliable. On the other hand, you may still find bugs in some of the less well-tested and not-as-often-used routines. Most of the time, these bugs are small easy-to-fix Python-interface bugs. Many people use and rely on the numerical algorithms in scipy everyday. Enthought uses scipy to deliver numerical products to their clients. Several researchers use scipy in their publishable work. Many scientists at the national labs (Argonne, Livermore, Sandia, etc.) all use Python for numerical work. I would absolutely stand by SciPy for publication-quality work. I've published using SciPy. I think it's preferrable to proprietary solutions for publications, because it actually allows someone to reproduce your work and even inspect the code used to produce your work. So it is more in keeping with the academic philosophy. > > How would you compare SciPy's signal processing tools vs. Matlab's? > SciPy has quite a few of the tools that Matlab has (but not everything, yet), and adding your own is not difficult. I've found it much easier, for example, to add a tool to scipy then to go back to MATLAB for data processing. Wavelets are missing (but there is interest here and some people are working on it). Look at the docs at http://www.scipy.org/livedocs/ for an overview. If there is something you need that is missing, speak up, maybe somebody can contribute it. -Travis O. P.S. Scipy-Numeric is going through some changes that should be in place in a couple of months. My suggestion is to start using scipy and then make the push to your people in a few months.

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Replacing elements in matrix
by Dimitri D'Or 26 Apr '05

26 Apr '05

Hello, I come from the Matlab world and I'm used to write operations such as: A[indexi,indexj]=A[indexi,indexj]+B where A is a n by n matrix, indexi is i by 1 vector, indexj is a j by 1 vector and B is a i by j matrix. With this operation, some of the elements of A are replaced by their original value augmented by some value coming from B. for example, take A=array([[1,5,7,8,2],[5,3,4,6,7],[9,4,6,7,2],[0,2,0,3,4]]) indexi=array([0,2]) indexj=array([1,2,4]) B=array([[10,20,30],[100,200,300]]) With this, Matlab results would be A[indexi,indexj]=array([[5, 7, 2],[4, 6, 2]]) and A[indexi,indexj]=A[indexi,indexj]+B yields A=array([[1,15,27,8,32],[5,3,4,6,7],[9,104,206,7,302],[0,2,0,3,4]]) I would like to make the same operation with Python. Would you please propose me a compact code for achieving that? Thank you, Dimitri

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Vector mean calculation?
by Thomas Davidoff 26 Apr '05

26 Apr '05

I have a vector with min equal to 412. Why am I getting a negative mean? -- Thomas Davidoff Assistant Professor Haas School of Business UC Berkeley Berkeley, CA 94618 Phone: (510) 643-1425 Fax: (510) 643-7357 email: davidoff(a)haas.berkeley.edu web: http://faculty.haas.berkeley.edu/davidoff/

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modified bessel fn of second kind K(n,z)
by r help 25 Apr '05

25 Apr '05

hi i am trying to use the modified bessel function of the second kind, K_n(z) K is called the mod. bes. fn of second kind on mathworld; K is called the mod. bes. fn of third kind in scipy. the integer order function special.kn(-20,3) gives the same result on both mathematica and scipy: In [3]: special.kn(-20,3) Out[3]: 16254643952204.371 however the real valued special.kv(-20,3) gives different answers each time i call it: In [2]: special.kv(-20,3) Out[2]: -1.9924087524414062 In [4]: special.kv(-20,3) Out[4]: 166558.53135225689 In [5]: special.kv(-20,3) Out[5]: 166541.5313522513 In [6]: special.kv(-20,3) Out[6]: 166541.53135221289 In [7]: special.kv(-20,3) Out[7]: 166592.53135221568 In [8]: special.kv(-20,3) Out[8]: 166541.5313522506 In [9]: special.kv(-20,3) Out[9]: 166592.53135226108 In [10]: special.kv(-20,3) Out[10]: 166541.53135219333 In [11]: special.kv(-20,3) Out[11]: 166592.53135221079 In [19]: print scipy.scipy_version.scipy_version 0.3.2 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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scipy.test() failures on SuSE9.3
by Nils Wagner 25 Apr '05

25 Apr '05

Hi all, I have installed SuSE9.3 and scipy, Numerical, f2py via cvs. scipy.test() results in 26 failures and 3 errors. LAPACK and BLAS are available via ( ~/src/blas ~/src/LAPACK ====================================================================== FAIL: check_syevr_vrange_mid (scipy.lib.lapack.test_lapack.test_flapack_float) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 98, in check_syevr_vrange_mid def check_syevr_vrange_mid(self): self.check_syevr_vrange(vrange=[0,1]) File "/usr/lib/python2.4/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 91, in check_syevr_vrange assert_array_almost_equal(w,ew) File "/usr/lib/python2.4/site-packages/scipy_test/testing.py", line 740, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 100.0%): Array 1: [ 0.5] Array 2: [ 0.4876939] ---------------------------------------------------------------------- Ran 1173 tests in 2.122s FAILED (failures=26, errors=3) Python 2.4 (#1, Mar 22 2005, 21:42:42) [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2 f2py : 2.46.243_1966 Numeric : '24.0b2' Any pointer would be appreciated. Thanks in advance Nils

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mid-size outerproduct too big for memory
by Thomas Davidoff 25 Apr '05

25 Apr '05

I tried to get the outerproduct(a,b) where a is a 23,297 by 15 matrix and b is a 15 element row vector. This led to a memory error. This is a pretty small dataset for empirical economics - is there a way around this? Will I ever be able to do something like 1 million by 100 or is it back to Stata for me? I don't think the issue is other stuff in the program because nothing should be eating a lot of memory. I noticed I get the same problem in command line python just trying a 100,000 by 100 matrix and a 1 by 100 row vector. I am on a new G5 PowerMac with lots of new memory installed. -- Thomas Davidoff Assistant Professor Haas School of Business UC Berkeley Berkeley, CA 94618 Phone: (510) 643-1425 Fax: (510) 643-7357 email: davidoff(a)haas.berkeley.edu web: http://faculty.haas.berkeley.edu/davidoff/

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Python program failure caused by fastumath *FIXED*
by R. Padraic Springuel 25 Apr '05

25 Apr '05

When attempting to evaluate certain functions for which the expected range of the function is complex, fastumath (what scipy uses to define these universal functions) causes a program fatal error in python (at least under Windows XP, which I run). After some experimenting with the problem, I have come up with a work around solution. By rewriting the wrapper functions in scimath (found in the scipy_base folder) so that these functions use Numeric's umath functions instead, the functions work as expected (including the automatic domain change that the wrapper functions in scimath were originally intended for). The only remaining bug is that the fix requires importing Numeric before importing scipy. Any help with this last bug would be appreciated, as I cannot determine why this makes a difference. My rewritten version of scimath can be downloaded from the following address: http://www.umit.maine.edu/~r.springuel/000CCFE8-80000018/ Note: In addition to the above described fix, my rewritten scimath also contains definitions for several trig functions and hyperbolic trig functions which were not previously defined by either numeric or scipy. These functions are also handled appropriately under the above fix where necessary with the following exceptions: arcsec(0), arccsc(0), & arccoth(0), which still return math domain errors (again, suggestions on how to handle these special cases is appreciated). -- R. Padraic Springuel

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