Mailman 3 March 2010 - SciPy-Dev

Stefan Hannweber
by Bairam Komaki March 20, 2010

March 20, 2010

http://wiaderko.110mb.com/mustapha.html

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Spherical harmonics, convention
by Matthew Brett March 20, 2010

March 20, 2010

Hi, I noticed that scipy.special.sph_harm uses conventions that (on superficial reading) seem to be rather unusual; can I ask for advice whether that is correct? For example; http://en.wikipedia.org/wiki/Spherical_harmonics assumes: theta = polar angle phi = azimuthal angle l (little L) = degree of harmonic but we have: theta = azimuthal angle phi = polar angle n = degree of harmonic I realize that the theta / phi switch is the difference between physics and math conventions of spherical coordinates, but my superficial impression was that there was a rather strong tradition in spherical harmonics to prefer theta = polar, phi = azimuthal; is that correct? Thanks a lot, Matthew

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restarting the discussion about sparse SVD
by David Warde-Farley March 19, 2010

March 19, 2010

A friend of mine yesterday was a bit shocked/annoyed when he realized there was no way currently in SciPy to compute the SVD of a sparse matrix. This has come up a number of times, so maybe we should organize our thoughts and figure out what exactly needs to get done. - I remember hearing that ARPACK contained a sparse SVD routine but I can't seem to find mention of it in the docs. - It also looks like the code in Divisi ( http:// divisi.media.mit.edu ) would be helpful, and looking in the archives it looks like the authors may be receptive to relicensing bits of it for use in SciPy. Other thoughts? David

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Re: [SciPy-Dev] ImportError: No module named ipapp
by Johann Cohen-Tanugi March 14, 2010

March 14, 2010

Hi Brian, thanks for your help, see below my still being confused : <quote author="Brian Granger-3"> Hi, > I have an identical problem : I have a trunk build of ipython, that I > installed with --user, and then today I wanted to have a look at the bundle > EPD distribution. I thought that the whole point was that I could get a > completely "waterproof" distribution with EPD, irrespective of any other > development version of say ipython on my system. > > EPD, is like any other Python installation in terms of how it resolves and finds > Python packages. When you install EPD, it sets your PATH variables to point > to its python, ipython, etc scripts. BUT, Python 2.6 still uses the > --user location > to find packages. Thus, you have the following problem: > > * /home/cohen/sources/python/epd-6.1-1-rh5-x86/bin/ipython is first on your > path, so when you type ipython at the command line, that script starts. > > * But when that script tries to "from IPython.ipapi import launch_new_instance" > Python goes and finds the IPython package in the --user location, which is the > wrong version of IPython (trunk doesn't have launch_new_instance). -> Ok that is where I am being confused. The trunk ipython with the --user has been built/installed with the native python, while the EPD ipython is supposed to call the EPD python shipped in. I was expecting that things would be messed up *if* I had a PYTHONPATH env var installed, because this would be read by either instance. Thus I made sure to unset PYTHONPATH..... but it seems that something else keeps been share.... Isn't there any way to keep these two python instances completely separate within one system? thanks for the clarification, this is a bit disappointing to me :( Johann > So you must: > > * Install trunk IPython into EPD so that its "ipython" script points > to the trunk version. > * Set your PATH differently so that the trunk "ipython" script is > found before the EPD > version. > * Uninstall the trunk version of IPython. > > Hope this helps, > > Cheers, > > Brian > But I get: > [cohen@jarrett ~]$ /home/cohen/sources/python/epd-6.1-1-rh5-x86/bin/ipython > Traceback (most recent call last): > File "/home/cohen/sources/python/epd-6.1-1-rh5-x86/bin/ipython", line 7, > in <module> > from IPython.ipapi import launch_new_instance > ImportError: No module named ipapi > > if I rename .local as local, then the EPD version loads ok.... Isn't there a > way to keep both functioning? > > thanks, > Johann > > On 02/10/2010 05:34 AM, Brian Granger wrote: > > Can you try removing all traces of ipython (both from bin dirs and > site-packages) and reinstall. It looks like you have multiple versions on > your PATH/PYTHONPATH that are conflicting. > > Cheers, > > Brian > > > > On Tue, Feb 9, 2010 at 11:22 AM, Nils Wagner <nwagner(a)iam.uni-stuttgart.de> > wrote: >> >> Hi all, >> >> I have installed ipython from scratch >> >> bzr branch lp:ipython >> cd ipython >> python setup.py install --prefix=$HOME/local >> >> If I start ipython >> >> ipython >> Traceback (most recent call last): >> File "/home/nwagner/local/bin/ipython", line 4, in >> <module> >> from IPython.core.ipapp import launch_new_instance >> ImportError: No module named ipapp >> >> Any idea ? >> >> Nils >> _______________________________________________ >> IPython-dev mailing list >> IPython-dev(a)scipy.org >> http://mail.scipy.org/mailman/listinfo/ipython-dev > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > IPython-dev mailing list > IPython-dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/ipython-dev > > > _______________________________________________ > IPython-dev mailing list > IPython-dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/ipython-dev > > -- Brian E. Granger, Ph.D. Assistant Professor of Physics Cal Poly State University, San Luis Obispo bgranger(a)calpoly.edu ellisonbg(a)gmail.com _______________________________________________ IPython-dev mailing list IPython-dev(a)scipy.org http://mail.scipy.org/mailman/listinfo/ipython-dev </quote>

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Seeking help/ advice for applying functions
by eat March 13, 2010

March 13, 2010

""" Hi, I would like to ask some advice for a (pretty generic kind of) problem as: I do have some data which I'll like to put trough several (thousands of) functions. I have cooked up a simple demonstration of the problem, and two plausible solutions for it. However I'm not happy with either 'gproc1' or 'gproc2'. So, does someone have a more suitable scipy/ numpy solution for this kind of problem? Regards, eat OK, here is the some code as demonstration: """ import numpy as np data= np.random.random((1, 2)) fncs= np.asarray([np.sin, np.cos, np.tan, np.sinh, np.cosh, np.tanh]) cs= np.asarray(np.random.randint(0, 2, (5, len(fncs))), dtype= bool) def mid(x): return np.round(x, 3) def gcntrl(m, cs): for k in xrange(m): yield cs[k, :] def gproc1(gcntrl, fncs, data): for c in gcntrl: yield np.asarray([mid(f(data)) for f in fncs[c]]) def rr(data): def f(g): return g(data) return f def gproc2(gcntrl, fncs, data): for c in gcntrl: yield mid(np.asarray(map(rr(data), fncs[c]))) def a(g, n): def p(g, c, cs, f, d): for r in g(c(cs.shape[0], cs), f, d): print r.squeeze() print n+ ' approach:'; p(g, gcntrl, cs, fncs, data); print if __name__ == '__main__': a(gproc1, 'firsth') a(gproc2, 'second') #??? a(gproc3, 'third')

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Why does optimize.nonlin take a tuple for func to optimize?
by Skipper Seabold March 11, 2010

March 11, 2010

I am curious why optimize.nonlin expects a tuple for the function to optimize? This seems inconsistent with the other optimize methods I have used in optimize. http://docs.scipy.org/scipy/docs/scipy.optimize.nonlin/ Are there any objections to changing this to be more consistent with the other solvers which take something like (F, x0, args=()) and use optimize.wrap_function for the function to be optimized? Perhaps there is something I am missing. -Skipper

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linalg.solveh_banded => Mac OS BLAS parameter error in DPBSV
by denis March 10, 2010

March 10, 2010

Folks, has anyone run solveh_banded on a mac ppc ? My versions: scipy 0.7.1 numpy 1.3.0 py 2.6.4 macosx 10.4.11 If this is the wrong place or wrong form, please correct me. # scipy.linalg.solveh_banded => # Parameter 8 to routine DPBSV was incorrect # Mac OS BLAS parameter error in DPBSV , parameter #0, (unavailable), is 0 # 144208 26 Jun 2009 _flinalg.so # (solve_banded is in scipy/linalg/tests, solveh_banded not ...) import sys import numpy as np from scipy.linalg import solve_banded, solveh_banded N = 10 exec "\n".join( sys.argv[1:] ) # N= ... np.random.seed(1) np.set_printoptions( 2, threshold=100, suppress=True ) # .2f ones = np.ones(N) ab = np.array(( ones, 2*ones )) / 4 # ab = np.array(( ones, 2*ones, ones )) / 4 b = np.random.normal( 0, 1, N ) print "ab:", ab print "b:", b c, x = solveh_banded( ab, b ) # , lower=1 ) # x = solve_banded( (1,1), ab, b ) # ok print "x:", x Thanks, cheers -- denis

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lfilter segfault with initial condition on windows
by Oscar Benjamin March 5, 2010

March 5, 2010

Hi, I've just discovered that a program of mine (which works on my ubuntu karmic machine at home) segfaults on win32 at work. I've made a short test case: > #!/usr/bin/env python > > from numpy import ones > from scipy.signal import lfilter > > x = ones(100) > a = ones(5) > b = ones(5) > zi = ones(4) > #xf = lfilter(b, a, x) > xf, zf = lfilter(b, a, x, zi=zi) Swap the comment on the last two lines to prevent segfault. On my machine I get the "Unhandled Exception in python.exe" message box (I assume this is a segfault). versions: python 2.6.4 numpy 1.3.0 scipy 0.7.1 I can see a few tickets about problems with memory leaks and segfaults with lfilter but they seem to be old and marked as closed. Should I expect the above to work? Is this a known issue that's already fixed? Thanks, Oscar.

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FW: Scipy failing -- undefined symbol: _ZNSt8ios_base4InitD1Ev
by Baker D.J. March 4, 2010

March 4, 2010

Hello, I'm just wondering if anyone on this mailing list can help, please. I've just installed scipy on our Linux x86_64 machine using the Intel compilers and MKL. All is not well, however, since when I try to use scipy, for example... from scipy import linsolve, sparse I find that there is an unresolved symbol. That is, _ZNSt8ios_base4InitD1Ev. Using c++filt would appear to suggest that I need to add "-lstdc++" to my loader command. c++filt _ZNSt8ios_base4InitD1Ev std::ios_base::Init::~Init() I'm new to numpy and scipy, and so I'm working in the dark to some degree. I've tried modifying intelccompiler.py in the following way, and recompiling numpy and scipy (the idea being that some of the programs in the scipy build are cxx files) compiler_type = 'intel' cc_exe = 'icc -O3 -fPIC' cxx_exe = 'icpc -O3 -fPIC' def __init__ (self, verbose=0, dry_run=0, force=0): UnixCCompiler.__init__ (self, verbose,dry_run, force) compiler = self.cc_exe compiler_cxx = self.cxx_exe self.set_executables(compiler=compiler, compiler_so=compiler, compiler_cxx=compiler_cxx, linker_exe=compiler, linker_so=compiler_cxx + ' -shared -lstdc++') I rebuild scipy using the following command, however the above hasn't helped: python setup.py config --compiler=intel config_fc --fcompiler=intelem install --prefix=/local/software/rh53/scipy/0.7.1/intel Could someone please advise me how to ensure that the "-lstdc++" is successfully passed to the linker as and when I build scipy. This would really be appreciated. Best -- David.

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N.angle(nan)
by David Goldsmith March 3, 2010

March 3, 2010

Hi! N.angle(z) returns nan if either z.real or z.imag is nan; presently, this is not documented in its docstring, but it is traceable to the low-level c functions N.angle uses to do its work, so I'm assuming it's a bug in the doc, not in the code, i.e., is intended behavior, correct? DG

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