Mailman 3 September 2008 - SciPy-User

Re: [SciPy-user] Illegal instruction
by Bernardo Martins Rocha Sept. 8, 2008

Sept. 8, 2008

Hi.. I running Opensuse 11 in an AMD Opteron x64. So, I think the CPU supports SSE2. I'm using the scipy binaries provided by the opensuse-science repository. The strange thing that I also tried some examples (written by Travis Oliphant) and I´got the same error when I call leastsq. I did the scipy.test(level=1) and I got this error too. Should I try to install the scipy from the svn repository? Thanks! Best regards, Bernardo M. Rocha Message: 3 Date: Mon, 08 Sep 2008 17:03:49 +0200 From: bernardo martins rocha <bernardo.rocha(a)meduni-graz.at> Subject: [SciPy-user] Illegal Instruction To: scipy-user(a)scipy.org Message-ID: <48C53ED5.3060905(a)meduni-graz.at> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Guys, i'm trying to use scipy.optimize.leastsq but whenever I call it I get the following error: /"In [13]: p0 = [0.5,1,0.5,1] # initial guesses In [14]: guessfit = dbexpl(t,p0) In [15]: pbest = leastsq(residuals,p0,args=(data,t),full_output=1) Illegal instruction" /What does this error mean? I don't think it's is a error in the way I'm calling the method because I haven't changed my script that was working fine some weeks ago. Thanks in advance! Bernardo M. Rocha / / ------------------------------ Message: 4 Date: Mon, 8 Sep 2008 10:47:14 -0500 From: "Robert Kern" <robert.kern(a)gmail.com> Subject: Re: [SciPy-user] Illegal Instruction To: "SciPy Users List" <scipy-user(a)scipy.org> Message-ID: <3d375d730809080847j1b0ef3f7ydf26f811784143a6(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Mon, Sep 8, 2008 at 10:03, bernardo martins rocha <bernardo.rocha(a)meduni-graz.at> wrote: > Hi Guys, > > i'm trying to use scipy.optimize.leastsq but whenever I call it I get > the following error: > > /"In [13]: p0 = [0.5,1,0.5,1] # initial guesses > > In [14]: guessfit = dbexpl(t,p0) > > In [15]: pbest = leastsq(residuals,p0,args=(data,t),full_output=1) > Illegal instruction" > > /What does this error mean? I don't think it's is a error in the way I'm > calling the method because I haven't changed my script that was working > fine some weeks ago. Are you on Windows? Which scipy binaries are you using? Does your CPU support SSE2? -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco ------------------------------ _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user End of SciPy-user Digest, Vol 61, Issue 10 ******************************************

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modified bessel function of the 2nd/3rd kind
by David Strozzi Sept. 8, 2008

Sept. 8, 2008

Folks, scipy.special contains these Bessel functions: Bessel Functions ---------------- * jn -- Bessel function of integer order and real argument. * jv -- Bessel function of real-valued order and complex argument. * jve -- Exponentially scaled Bessel function. * yn -- Bessel function of second kind (integer order). * yv -- Bessel function of the second kind (real-valued order). * yve -- Exponentially scaled Bessel function of the second kind. * kn -- Modified Bessel function of the third kind (integer order). * kv -- Modified Bessel function of the third kind (real order). * kve -- Exponentially scaled modified Bessel function of the third kind. As has been noted on this list before, kn, kv are also, in fact much more commonly, referred to as mod. Bess. funcs of the *2nd* kind. Can this info please be updated? Is there any good reason not to have the help message say "of the second kind (sometimes called the third kind)"? As someone who works with these I have never heard them called the 3rd kind, only the 2nd. Thanks, Dave Strozzi

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[ Python(x,y) ] New release : 2.0.5
by Pierre Raybaut Sept. 8, 2008

Sept. 8, 2008

Hi all, As you may already know, Python(x,y) is a free scientific-oriented Python Distribution based on Qt and Eclipse providing a self-consistent scientific development environment. Release 2.0.5 is now available on http://www.pythonxy.com. (Full Edition, Basic Edition, Light Edition and Update) Changes history Version 2.0.5 (09-06-2008) * Updated: o Enthought Tool Suite 3.0.0(.1) (docs and examples updated) o PyDAP 2.2.6.5 o xy 1.0.5 (New shortcuts and help links) * Corrected: o VTK: VTKData folder was not found by the example scripts (see VTK documentation folder) o Eclipse/Windows Vista: Java RE updated (version 6 Update 7) in Eclipse main installer - the previous version was freezing on some machines under Windows Vista o Console 2 (New settings) o Notepad++ (New Console 2 settings) Regards, Pierre Raybaut

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Illegal Instruction
by bernardo martins rocha Sept. 8, 2008

Sept. 8, 2008

Hi Guys, i'm trying to use scipy.optimize.leastsq but whenever I call it I get the following error: /"In [13]: p0 = [0.5,1,0.5,1] # initial guesses In [14]: guessfit = dbexpl(t,p0) In [15]: pbest = leastsq(residuals,p0,args=(data,t),full_output=1) Illegal instruction" /What does this error mean? I don't think it's is a error in the way I'm calling the method because I haven't changed my script that was working fine some weeks ago. Thanks in advance! Bernardo M. Rocha / /

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segmentation fault in scipy.test()
by gfunch Sept. 7, 2008

Sept. 7, 2008

Hi, I have tried to build SciPy (svn) on an x86_64 system running Linux CentOS5, but ran into a segmentation fault while running the tests. I first compiled and installed Lapack and ATLAS per some instructions I found the web. I then built and installed numpy (which tested fine) and then built scipy. What commands should I run, and output should I generate, to best diagnose the problem, and perhaps seek your kind help? Thanks. -gyro

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[OpenOpt] problem with ralg (latest SVN)
by Emanuele Olivetti Sept. 7, 2008

Sept. 7, 2008

Dear all and Dmitrey, I've just updated to latest openopt (SVN). When using numpy 1.0.3 and scipy 0.5.2 (standard in Ubuntu 7.10 gutsy gibbon) openopt says that "ralg" (NLP) algorithm is missing! With more recent numpy and scipy it seems to work reliably. But what happened with respect to older numpy+scipy? In that case even running examples/nlp_1.py returns: ---- $ python nlp_1.py OpenOpt checks user-supplied gradient df (shape: (150,) ) according to: prob.diffInt = [ 1.00000000e-07] |1 - info_user/info_numerical| <= prob.maxViolation = 0.01 derivatives are equal ======================== OpenOpt checks user-supplied gradient dc (shape: (2, 150) ) according to: prob.diffInt = [ 1.00000000e-07] |1 - info_user/info_numerical| <= prob.maxViolation = 0.01 derivatives are equal ======================== OpenOpt checks user-supplied gradient dh (shape: (2, 150) ) according to: prob.diffInt = [ 1.00000000e-07] |1 - info_user/info_numerical| <= prob.maxViolation = 0.01 derivatives are equal ======================== OO Error:incorrect solver is called, maybe the solver "ralg" is not installed. Maybe setting p.debug=1 could specify the matter more precisely Traceback (most recent call last): File "nlp_1.py", line 110, in <module> r = p.solve('ralg') File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/BaseProblem.py", line 185, in solve return runProbSolver(self, solvers, *args, **kwargs) File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/runProbSolver.py", line 48, in runProbSolver p.err('incorrect solver is called, maybe the solver "' + solver_str +'" is not installed. Maybe setting p.debug=1 could specify the matter more precisely') File "/usr/lib/python2.5/site-packages/scikits/openopt/Kernel/oologfcn.py", line 16, in ooerr raise OpenOptException(msg) scikits.openopt.Kernel.oologfcn.OpenOptException: incorrect solver is called, maybe the solver "ralg" is not installed. Maybe setting p.debug=1 could specify the matter more precisely ---- This did not happen before so I guess it is due to a recent commit. It is possible to solve the problem? Kind Regards, Emanuele

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how to plot the result of histogram2d
by Johann Cohen-Tanugi Sept. 5, 2008

Sept. 5, 2008

hi, I hope someone can quickly point me to some doc. I can do imshow(histogram2d(x,y)[0]) but then I miss the x and y binning correct labels. If I do imshow(histogram2d(x,y)) I get: ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (115, 0)) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/cohen/data1/WORK/GRB/data/GRB080904886/<ipython console> in <module>() /data1/GLAST/GLAST_EXT/python/2.5.1/lib/python2.5/site-packages/matplotlib/pyplot.pyc in imshow(*args, **kwargs) 1673 hold(h) 1674 try: -> 1675 ret = gca().imshow(*args, **kwargs) 1676 draw_if_interactive() 1677 except: /data1/GLAST/GLAST_EXT/python/2.5.1/lib/python2.5/site-packages/matplotlib/axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, **kwargs) 4432 filterrad=filterrad, **kwargs) 4433 -> 4434 im.set_data(X) 4435 im.set_alpha(alpha) 4436 self._set_artist_props(im) /data1/GLAST/GLAST_EXT/python/2.5.1/lib/python2.5/site-packages/matplotlib/image.pyc in set_data(self, A, shape) 232 X = pil_to_array(A) 233 else: --> 234 X = ma.asarray(A) # assume array 235 self._A = X 236 /data1/GLAST/GLAST_EXT/python/2.5.1/lib/python2.5/site-packages/numpy/core/ma.pyc in asarray(data, dtype) 2121 (dtype is None or dtype == data.dtype): 2122 return data -> 2123 return array(data, dtype=dtype, copy=0) 2124 2125 # Add methods to support ndarray interface /data1/GLAST/GLAST_EXT/python/2.5.1/lib/python2.5/site-packages/numpy/core/ma.pyc in __init__(self, data, dtype, copy, order, mask, fill_value) 565 else: 566 need_data_copied = False #because I'll do it now --> 567 c = numeric.array(data, dtype=tc, copy=True, order=order) 568 tc = c.dtype 569 ValueError: setting an array element with a sequence. so something gets awry. thanks in advance

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ANN: SfePy-00.50.00
by Robert Cimrman Sept. 3, 2008

Sept. 3, 2008

I am pleased announce the release of SfePy 00.50.00. SfePy is a finite element analysis software in Python, based primarily on Numpy and SciPy. Mailing lists, issue tracking, mercurial repository: http://sfepy.org Home page: http://sfepy.kme.zcu.cz People who contributed to this release: Ondrej Certik, Ryan Krauss, Vladimir Lukes. Major improvements: - finite strain elasticity: neo-Hookean, Mooney-Rivlin materials in the total Lagrangian (TL) formulation - solving problems in complex numbers - generalized equations to allow linear combination of terms - run-time type of state term arguments - refactoring to follow Python coding style guidelines - new terms For more information on this release, see http://sfepy.googlecode.com/svn/web/releases/005000_RELEASE_NOTES.txt Best regards, Robert Cimrman

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matplotlib - axis and zoom
by bernardo martins rocha Sept. 2, 2008

Sept. 2, 2008

Hi Guys, how can I maintain zoom in the horizontal axis and keep the vertical axis unchanged using the zoom tool provided by matplotlib? Bernardo M. Rocha

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Create a spectrogram from a waveform
by Ed McCaffrey Sept. 1, 2008

Sept. 1, 2008

Hello, I wrote a program in C# that creates a spectrogram from the waveform of a .wav music file. I now want to port it to Python, and I want to try to use SciPy instead of a direct port of the existing code, because I am not sure that it is perfectly accurate, and it is probably slow. I am having a hard time finding out how to do this with SciPy. With my code, I had a FFT function that took an array of real and imaginary components for each sample, and a second function taking both that produced the amplitude. The FFT function in SciPy just takes one array. Has anyone done this task in SciPy? Thanks.

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