Mailman 3 February 2007 - 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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3D plotting
by Robert Cimrman 10 Sep '09

10 Sep '09

Hi, I need to do some simple 3D plots, so I tried the two Cookbook recipes (xplt, mplot3d) and failed: * xplt: does not work when using a custom installation directory such as python setup.py install --root=/home/share/software apparently the gistdata directory path is wrong: gist.error: failed to create drawing -- Gist work.gs style sheet missing * mplot3d: does not work with my version of matplotlib (0.80). I have made the changes mentioned in the Cookbook to no avail. (Axes.__init__() args apparently changed, as well as some other matplotlib object attributes) Any ideas? mplot3d looks great, I would really like to use it! thanks, r.

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clapack and cblas modules are empty
by jrpirone 16 Mar '07

16 Mar '07

Hello, I've installed scipy and numpy from Andrew Straw's repository, all other libraries are from the standard Ubuntu repositories (6.10). When I execute scipy.test(), the following warnings appear: **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** Running the command: ldd /usr/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so Gives me: linux-gate.so.1 => (0xffffe000) liblapack.so.3 => /usr/lib/atlas/sse2/liblapack.so.3 (0xb7958000) libblas.so.3 => /usr/lib/atlas/sse2/libblas.so.3 (0xb7387000) libg2c.so.0 => /usr/lib/libg2c.so.0 (0xb735f000) libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7339000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb732e000) libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb71fa000) /lib/ld-linux.so.2 (0x80000000) Is there a problem with the libraries I have installed? Should I be worried about these warnings, or am I just being compulsive? Thanks for your help, Jason

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problem with _num.seterr when importing scipy
by Kevin Long 14 Mar '07

14 Mar '07

Hello, I'm getting an error message about "_num.seterr" when importing scipy. Output is below. <diogenes:/home/krlong> python Python 2.4.4 (#1, Feb 9 2007, 14:45:36) [GCC 3.4.6] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.4/site-packages/scipy/__init__.py", line 37, in ? _num.seterr(all='ignore') TypeError: seterr() got an unexpected keyword argument 'all' >>> I've googled the error message, but found no other reports of it. To get past this problem, I commented out line 37 in __init.py__ and pressed bravely (or foolishly) onwards. Things seem to work OK after that, but I'm nervous about commenting something out of your code. This is on SuSE 10.1, but I'm not using the versions of python, gcc, blas, or lapack that were bundled with the system. The python version is 2.4.4. Lapack is the distribution from netlib. The BLAS is the version shipped with netlib's lapack, with srotmg.f, srotm.f, drotm.f, and drotmg.f added (from netlib's blas.tar.gz) to provide the complete BLAS needed by scipy. Everything was built with gcc 3.4.6. Any ideas? Thank you, Kevin Long -- ----------------------------------------------------------------------------- Dr. Kevin Long Computational Science and Mathematics Research Department Sandia National Laboratories MS 9217 krlong(a)sandia.gov Livermore, CA 94551 (925)-294-4910 -----------------------------------------------------------------------------

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Fitting sphere to 3d data points
by James Vincent 02 Mar '07

02 Mar '07

Hello, Is it possible to fit a sphere to 3D data points using scipy.optimize.leastsq? I'd like to minimize the residual for the distance from the actual x,y,z point and the fitted sphere surface. I can see how to minimize for z, but that's not really what I'm looking for. Is there a better way to do this? Thanks for any help. params = a,b,c and r a,b,c are the fitted center point of the sphere, r is the radius err = distance-to-center - radius err = sqrt( x-a)**2 + (y-b)**2 + (z-c)**2) - r ---- James J. Vincent, Ph.D. National Cancer Institute National Institutes of Health Laboratory of Molecular Biology Building 37, Room 5120 37 Convent Drive, MSC 4264 Bethesda, MD 20892 USA 301-451-8755 jjv5(a)nih.gov

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Any Books on SciPy?
by Robert Love 02 Mar '07

02 Mar '07

Are there any good, up to date books that people recommend for numerical work with Python? I see the book Python Scripting for Computational Science Hans Petter Langtangen Does anyone have opinions on this? Is it current? Are there better books? All pointers appreciated.

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scipy and cvxopt
by Emin.shopper Martinian.shopper 01 Mar '07

01 Mar '07

Dear Experts, I need to solve some quadratic programs (and potentially other nonlinear programs). While scipy.optimize.fmin_cobyla seems like it can do this, it seems orders of magnitude slower than cvxopt. Are there plans to merge/include cvxopt in scipy or otherwise improve scipy's quadratic/nonlinear constrained optimization routines? I saw an old response to this question but the response pointed to a non-existent URL. Thanks, -Emin

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NumPy in Teaching
by Steven H. Rogers 01 Mar '07

01 Mar '07

I'm doing an informal survey on the use of Array Programming Languages for teaching. If you're using NumPy in this manner I'd like to hear from you. What subject was/is taught, academic level, results, lessons learned, etc. Regards, Steve

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Using SciPy/NumPy optimization
by Brandon Nuttall 01 Mar '07

01 Mar '07

Folks, The usual confessions: I am relatively new to Python programming and SciPy. I have a problem I'm looking for some help in solving. I have a list of data pairs [[x1,y1], [x2,y2], ..., [xn,yn]] and am trying to find the best fit of that data to an equation: y = a*(1+b*c*y)^(-1/b) The parameters, b and c, are constrained: 1) 0<b<=5 2) -1<=c<=1 Parameter a is only weakly constrained in that x is usually >= max(x1, x2, ... , xn). My "best fit" goal is either to minimize the root mean square deviation (or consequently maximize the r-square value). Any suggestions? Thanks. Brandon C. Nuttall BNUTTALL(a)UKY.EDU Kentucky Geological Survey (859) 257-5500 University of Kentucky (859) 257-1147 (fax) 228 Mining & Mineral Resources Bldg http://www.uky.edu/KGS/home.htm Lexington, Kentucky 40506-0107

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Library Message On Application Start
by Rich Shepard 28 Feb '07

28 Feb '07

Each time I start my application I see this: Overwriting info=<function info at 0xb5fa05dc> from scipy.misc (was <function info at 0xb610d994> from numpy.lib.utils) It does not seem to affect the few functions we use, but I wonder if it's something that should be fixed somewhere. Rich -- Richard B. Shepard, Ph.D. | The Environmental Permitting Applied Ecosystem Services, Inc. | Accelerator(TM) <http://www.appl-ecosys.com> Voice: 503-667-4517 Fax: 503-667-8863

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