Mailman 3 November 2009 - SciPy-User

scipy.org is down
by Sturla Molden Nov. 10, 2009

Nov. 10, 2009

Someone please restart the web-server. Sturla

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Re: [SciPy-User] poisson distribution in scipy.stats
by Davide Cittaro Nov. 9, 2009

Nov. 9, 2009

On Nov 9, 2009, at 10:03 PM, scipy-user-request(a)scipy.org wrote: > Message: 5 > Date: Mon, 9 Nov 2009 15:00:29 -0600 > From: Robert Kern <robert.kern(a)gmail.com> > Subject: Re: [SciPy-User] poisson distribution in scipy.stats > To: SciPy Users List <scipy-user(a)scipy.org> > Message-ID: > <3d375d730911091300h6d9b4df6u4be1e6ae0811b12(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Mon, Nov 9, 2009 at 14:58, Davide Cittaro > <davide.cittaro(a)ifom-ieo-campus.it> wrote: >> Hi all, >> about the poisson generator... given l (expected) and k (found) I >> guess that >> the way to get the probability of k I have to do this: >> >> d = scipy.stats.poisson(l) >> p = pmf(k) > > Correct. > >> which I found being the same of >> p = scipy.stats.poisson.pmf(l, k) > > Also correct. > Although I've just plotted values and they are sligthly different... the second version does have only a max value at l, whereas the first has two maxima (l and l-1) >> I've here some code in which it is written: >> d = scipy.stats.poisson(l, k) > > That one is completely wrong. > Ok, I see... It looks like it shifts the pmf of k... but how does it works? I mean, how the discrete distribution constructor interprets this kind of declaration? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Distributed computing: running embarrassingly parallel (python/c++) codes over a cluster
by Rohit Garg Nov. 9, 2009

Nov. 9, 2009

Hi all, I have an embarrassingly parallel problem, very nicely suited to parallelization. I am looking for community feedback on how to best approach this matter? Basically, I just setup a bunch of tasks, and the various cpu's will pull data, process it, and send it back. Out of order arrival of results is no problem. The processing times involved are so large that the communication is effectively free, and hence I don't care how fast/slow the communication is. I thought I'll ask in case somebody has done this stuff before to avoid reinventing the wheel. Any other suggestions are welcome too. My only constraint is that it should be able to run a python extension (c++) with minimum of fuss. I want to minimize the headaches involved with setting up/writing the boilerplate code. Which framework/approach/library would you recommend? There is one method mentioned at [1], and of course, one could resort to something like mpi4py. [1] http://docs.python.org/library/multiprocessing.html {see the last example} -- Rohit Garg http://rpg-314.blogspot.com/ Senior Undergraduate Department of Physics Indian Institute of Technology Bombay

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poisson distribution in scipy.stats
by Davide Cittaro Nov. 9, 2009

Nov. 9, 2009

Hi all, about the poisson generator... given l (expected) and k (found) I guess that the way to get the probability of k I have to do this: d = scipy.stats.poisson(l) p = pmf(k) which I found being the same of p = scipy.stats.poisson.pmf(l, k) I've here some code in which it is written: d = scipy.stats.poisson(l, k) p = d.pmf(k) which gives different results. Which is the right way to initialize the distribution (and get the PMF)? Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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characteristic functions of probability distributions
by josef.pktd＠gmail.com Nov. 8, 2009

Nov. 8, 2009

The characteristic function is just the (continuous) fourier transform of the probability density function. I tried to use fft and ifft to convert between the characteristic function and the density function but I don't manage to get the units or discretization correctly. Does anyone have an example script for any distribution. Right now it's mostly a theoretical exercise, but there are some interesting applications in finance. Second related question, since I'm not good with complex numbers. scipy.integrate.quad of a complex function returns the absolute value. Is there a numerical integration function in scipy that returns the complex integral or do I have to integrate the real and imaginary parts separately? Thanks, Josef

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Comparing variable time-shifted two measurements
by Gökhan Sever Nov. 6, 2009

Nov. 6, 2009

Hello, I have two aircraft based aerosol measurements. The first one is dccnConSTP (blue), and the latter is CPCConc (red) as shown in this screen capture. ( http://img513.imageshack.us/img513/7498/ccncpclag.png). My goal is to compare these two measurements. It is expected to see that they must have a positive correlation throughout the flight. However, the instrument that gives CPCConc was experiencing a sampling issue and therefore making a varying time-shifted measurements with respect to the first instrument. (From the first box it is about 20 seconds, 24 from the seconds before the dccnConSTP measurements shows up.) In other words in different altitude levels, I have varying time differences in between these two measurements in terms of their shapes. So, my goal turns to addressing this variable shifting issue before I start doing the comparisons. Is there a known automated approach to correct this mentioned varying-lag issue? If so, how? Thank you. -- Gökhan

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RBF plot in reference/tutorial/interpolate.html
by denis Nov. 6, 2009

Nov. 6, 2009

Scipy doc people, in http://docs.scipy.org/doc/scipy/reference/tutorial/interpolate.html#d-examp… last updated Oct 08 the two 1d plots Interpolation using univariate spline Interpolation using RBF - multiquadrics look rather similar, hmm - plt.plot(xi, yi, 'g') + plt.plot(xi, fi, 'g') cheers -- denis

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SciPy installation problems
by Gaston Fiore Nov. 5, 2009

Nov. 5, 2009

Hello, I'm trying to install scipy from the SVN repository but I'm getting an error. I've also discovered that numpy doesn't pass the built-in unit tests, although it did seem to install without problems. Below is all the information that I think it's needed to determine the problem and its solution. Is it the fact that UMFPACK is missing? Thanks a lot, -Gaston gbrain2:~ gafiore$ sw_vers ProductName: Mac OS X ProductVersion: 10.5.8 BuildVersion: 9L30 gbrain2:~ gafiore$ gcc --version i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465) Copyright (C) 2005 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. gbrain2:~ gafiore$ gfortran --version GNU Fortran (GCC) 4.2.3 Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING >>> import numpy >>> numpy.test('1','10') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/__init__.py", line 88, in test return NumpyTest().testall(level, verbosity) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/testing/numpytest.py", line 576, in testall for mthname in self._get_method_names(obj,abs(level)): TypeError: bad operand type for abs(): 'str' dhcp-0011377089-64-8f:scipy gafiore$ python setup.py build Warning: No configuration returned, assuming unavailable. blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/Python.framework/Versions/2.5/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib libraries umfpack not found in /opt/local/lib /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/system_info.py:401: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 152, in setup_package configuration=configuration ) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/core.py", line 144, in setup config = configuration() File "setup.py", line 118, in configuration config.add_subpackage('scipy') File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 765, in add_subpackage caller_level = 2) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 748, in get_subpackage caller_level = caller_level + 1) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 695, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./scipy/setup.py", line 20, in configuration config.add_subpackage('special') File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 765, in add_subpackage caller_level = 2) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 748, in get_subpackage caller_level = caller_level + 1) File "/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/misc_util.py", line 680, in _get_configuration_from_setup_py ('.py', 'U', 1)) File "scipy/special/setup.py", line 7, in <module> from numpy.distutils.misc_util import get_numpy_include_dirs, get_info ImportError: cannot import name get_info

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Troubles with odeint or ode
by ANDREA ARMAROLI Nov. 5, 2009

Nov. 5, 2009

Dear users, I'm trying to solve an ODE system that models a parametric oscillator with complex amplitudes at two freqencies. I'm new to python. This problem is simply solved in matlab using ode45. If I try to use odeint I cannot set parameters like tolerances or max step. The result is constant-valued solutions. Trying with ode class and ZVODE integrator, I have that total intensity is not conserved. I have weird quasi-periodic oscillations. I do know that my equations have excess degrees of freedom and I know from symmetries what the integrals of motion are, but in Matlab this works pretty well. Here is the code with odeint import numpy as N import scipy as S import scipy.integrate import pylab as P def deriv(Y,t): A1 = Y[0] A2 = Y[1] A1d = 1j*A2*N.conj(A1) A2d = 1j*(A1**2/2.0 + dk*A2) return [A1d, A2d] nplot = 10000 zmax = 10.0 zstep = zmax/nplot dk = 0.5 # normalised detuning/dispersion phi0 = 0.0*N.pi # initial dephasing eta0 = 0.3 # initial pump intensity # initial values u20 = N.sqrt(eta0)*N.exp(1j*phi0) u10 = N.sqrt(2*(1-eta0)) H0=dk*eta0+2*N.sqrt(eta0)*(1-eta0)*N.cos(phi0); Y,info = scipy.integrate.odeint(deriv,[u10,u20],N.arange(0,zmax+zstep,zstep),full_output=True,printmessg = True) # are conserved quantities constant? Ptot = N.abs(Y[:,0])**2/2+ N.abs(Y[:,1])**2 P.plot(N.arange(0,zmax+zstep-0.0001,zstep),Ptot) # then Hamiltonian... #... p1 = P.plot(N.arange(0,zmax+zstep-0.0001,zstep),N.abs(Y[:,0])) p2 = P.plot(N.arange(0,zmax+zstep-0.0001,zstep),N.abs(Y[:,1])) Thank you very much for your help. Andrea Armaroli

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iterating in a timeseries
by Zunbeltz Izaola Nov. 5, 2009

Nov. 5, 2009

Hi, I am using scikits.timeseries. I have a time series with daily frequency, with data of 2 years. I have data almost every day, but some days are missing. I want to iterate over the timeseries to get the values of the first and last day of each month. I had tried to convert freq to 'M' and other things, but I can not find an easy way. Any idea? TIA, Zunbeltz

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