Mailman 3 October 2008 - NumPy-Discussion

numpy.random.logseries - incorrect convergence for k=1, k=2
by joep 03 Oct '08

03 Oct '08

random numbers generated by numpy.random.logseries do not converge to theoretical distribution: for probability paramater pr = 0.8, the random number generator converges to a frequency for k=1 at 39.8 %, while the theoretical probability mass is 49.71 k=2 is oversampled, other k's look ok check frequency of k=1 and k=2 at N = 1000000 0.398406 0.296465 pmf at k = 1 and k=2 with formula [ 0.4971 0.1988] for probability paramater pr = 0.3, the results are not as bad, but still off: frequency for k=1 at 82.6 %, while the theoretical probability mass is 84.11 check frequency of k=1 and k=2 at N = 1000000 0.826006 0.141244 pmf at k = 1 and k=2 with formula [ 0.8411 0.1262] below is a quick script for checking this Josef {{{ import numpy as np from scipy import stats pr = 0.8 np.set_printoptions(precision=2, suppress=True) # calculation for N=1million takes some time for N in [1000, 10000, 10000, 1000000]: rvsn=np.random.logseries(pr,size=N) fr=stats.itemfreq(rvsn) pmfs=stats.logser.pmf(fr[:,0],pr)*100 print 'log series sample frequency and pmf (in %) with N = ', N print np.column_stack((fr[:,0],fr[:,1]*100.0/N,pmfs)) np.set_printoptions(precision=4, suppress=True) print 'check frequency of k=1 and k=2 at N = ', N print np.sum(rvsn==1)/float(N), print np.sum(rvsn==2)/float(N) k = np.array([1,2]) print 'pmf at k = 1 and k=2 with formula' print -pr**k * 1.0 / k / np.log(1-pr) }}}

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numpy.random.hypergeometric - strange results
by joep 03 Oct '08

03 Oct '08

In my fuzz testing of scipy stats, I get sometimes a test failure. I think there is something wrong with numpy.random.hypergeometric for some cases: Josef >>> import numpy.random as mtrand >>> mtrand.hypergeometric(3,17,12,size=10) # there are only 3 good balls in urn array([16, 17, 16, 16, 15, 16, 17, 16, 17, 16]) >>> mtrand.hypergeometric(17,3,12,size=10) #negative result array([-3, -4, -3, -4, -3, -3, -4, -4, -5, -4]) >>> mtrand.hypergeometric(4,3,12,size=10) >>> np.version.version '1.2.0rc2' I did not find any clear pattern when trying out different parameter values: >>> mtrand.hypergeometric(10,10,12,size=10) array([5, 6, 4, 4, 8, 5, 4, 6, 7, 4]) >>> mtrand.hypergeometric(10,10,20,size=10) array([10, 10, 10, 10, 10, 10, 10, 10, 10, 10]) >>> mtrand.hypergeometric(10,10,19,size=10) array([10, 9, 9, 9, 9, 9, 10, 9, 9, 9]) >>> mtrand.hypergeometric(10,10,5,size=10) array([3, 5, 2, 2, 1, 2, 2, 4, 3, 1]) >>> mtrand.hypergeometric(10,2,5,size=10) array([4, 5, 4, 5, 5, 5, 4, 3, 4, 4]) >>> mtrand.hypergeometric(2,10,5,size=10) array([0, 2, 1, 0, 2, 2, 1, 1, 1, 1]) >>> mtrand.hypergeometric(17,3,12,size=10) array([-5, -3, -4, -4, -4, -3, -4, -4, -3, -3]) >>> mtrand.hypergeometric(3,17,12,size=10) array([15, 16, 17, 16, 15, 16, 15, 15, 17, 17]) >>> mtrand.hypergeometric(18,3,12,size=10) array([-5, -6, -6, -4, -4, -4, -5, -3, -5, -5]) >>> mtrand.hypergeometric(18,3,5,size=10) array([4, 5, 5, 5, 5, 5, 4, 5, 4, 3]) >>> mtrand.hypergeometric(18,3,19,size=10) array([1, 1, 2, 1, 1, 1, 1, 3, 1, 1])

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f2py IS NOW WORKING
by Blubaugh, David A. 03 Oct '08

03 Oct '08

To all, I have now been able to develop a stable file via f2py!! However, I had to execute the following: 1.) First, I had to copy all required library files from my selected Compaq visual Fortran compiler under python's scripts directory along with f2py itself. 2.) I also had to include a dll from my compiler under python's dll directory as well. I know that the reason as to why I needed to execute these actions, is that I do not know as to what should be my correct environmental variables within windows XP running Compaq Visual Fortran 6.6. Once again, I would appreciate to know as to what are the correct environmental variables should I set my windows xp under, given that the compiler I must utilize is a Compaq Visual Fortran Compiler 6.6??? Thanks, David Blubaugh This e-mail transmission contains information that is confidential and may be privileged. It is intended only for the addressee(s) named above. If you receive this e-mail in error, please do not read, copy or disseminate it in any manner. If you are not the intended recipient, any disclosure, copying, distribution or use of the contents of this information is prohibited. Please reply to the message immediately by informing the sender that the message was misdirected. After replying, please erase it from your computer system. Your assistance in correcting this error is appreciated.

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nan, sign, and all that
by Charles R Harris 03 Oct '08

03 Oct '08

Hi All, I've added ufuncs fmin and fmax that behave as follows: In [3]: a = array([NAN, 0, NAN, 1]) In [4]: b = array([0, NAN, NAN, 0]) In [5]: fmax(a,b) Out[5]: array([ 0., 0., NaN, 1.]) In [6]: fmin(a,b) Out[6]: array([ 0., 0., NaN, 0.]) In [7]: fmax.reduce(a) Out[7]: 1.0 In [8]: fmin.reduce(a) Out[8]: 0.0 In [9]: fmax.reduce([NAN,NAN]) Out[9]: nan In [10]: fmin.reduce([NAN,NAN]) Out[10]: nan I also made the sign ufunc return the sign of nan. That works, but I'm not sure it is the way to go because there doesn't seem to be any spec as to what sign nan takes. The current np.nan on my machine is negative and 0/0, inf/inf all return negative nan. So it doesn't look like the actual sign of nan makes any sense. Currently sign(NAN) returns 0, which doesn't look right either, so I think the thing to do is return nan but this will be a change in numpy behavior. Any thoughts? Chuck

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Texas Python Regional Unconference Reminders
by Travis Vaught 03 Oct '08

03 Oct '08

Greetings, The Texas Python Regional Unconference is coming up this weekend (October 4-5) and I wanted to send out some more details of the meeting. The web page for the meeting is here: http://www.scipy.org/TXUncon2008 The meeting is _absolutely free_, so please add yourself to the Attendees page if you're able to make it. Also, if you're planning to attend, please send me the following information (to travis(a)enthought.com ) so I can request wireless access for you during the meeting: - Full Name - Phone or email - Address - Affiliation There are still opportunities to present your pet projects at the meeting, so feel free to sign up on the presentation schedule here: http://www.scipy.org/TXUncon2008Schedule For those who are in town Friday evening, we're planning to get together for a casual dinner in downtown Austin that night. We'll meet at Enthought offices (http://www.enthought.com/contact/map-directions.php ) and walk to a casual restaurant nearby. Show up as early as 5:30pm and you can hang out and tour the Enthought offices--we'll head out to eat at 7:00pm sharp. Best, Travis

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Portable functions for nans, signbit, etc.
by Charles R Harris 02 Oct '08

02 Oct '08

The normal signbit function of gcc without the -std=c99 flag doesn't work correctly for nans and infs. I found the following code on a boost mailing list and it might be helpful here for portability. const boost::uint32_t signbit_mask = binary_cast<boost::uint32_t>(1.0f) ^ binary_cast<boost::uint32_t>(-1.0f); inline bool signbit(float x) { return binary_cast<boost::uint32_t>(x) & signbit_mask; } inline bool signbit(double x) { return signbit(static_cast<float>(x)); } inline bool signbit(long double x) { return signbit(static_cast<float>(x)); } Which is rather clever. I think binary_cast will require some pointer abuse. There are a bunch of other boost functions here <http://tinyurl.com/3tvj9u>that might prove useful. This file <goog_1222871357985>floating_point_utilities_v3.zip <http://www.boostpro.com/vault/index.php?action=downloadfile&filename=floati…> portable isnan, fpclassify, signbit etc. + facets for portable handling of infinity and NaN in text streams Looks particularly interesting. It's a bit large for the mailing list so I won't attach it. The Boost license should be compatible with numpy. Chuck

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loadtxt
by Nils Wagner 02 Oct '08

02 Oct '08

Hi all, how can I load ASCII data if the file contains characters instead of floats Traceback (most recent call last): File "test_csv.py", line 2, in <module> A = loadtxt('ca6_sets.csv',dtype=char ,delimiter=';') NameError: name 'char' is not defined Nils

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complex numpy.ndarray dtypes
by John Gu 02 Oct '08

02 Oct '08

Hello, I am using numpy in conjunction with pyTables. The data that I read in from pyTables seem to have the following dtype: p = hdf5.root.myTable.read() p.__class__ <type 'numpy.ndarray'> p[0].__class__ <type 'numpy.void'> p.dtype dtype([('time', '<f4'), ('obs1', '<f4'), ('obs2', '<f8'), ('obs3', '<f4')]) p.shape (61230,) The manner in which I access a particular column is p['time'] or p['obs1']. I have a couple of questions regarding this data structure: 1) how do I restructure the array into a 61230 x 4 array that can be indexed using [r,c] notation? 2) What kind of dtype is pyTables using? How do I create a similar array that can be indexed by a named column? I tried various ways: a = array([[1,2],[3,4]], dtype=dtype([('obs1','<f4'),('obs2','<f4')])) --------------------------------------------------------------------------- <type 'exceptions.TypeError'> Traceback (most recent call last) p:\AsiaDesk\johngu\projects\deltaForce\<ipython console> in <module>() <type 'exceptions.TypeError'>: expected a readable buffer object I did find some documentation about array type descriptors when reading from files... it seems like these array types are specific to arrays created when reading from some sort of file / buffer? Any help is appreciated. Thanks! John

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Re: [Numpy-discussion] Vectorization of the product of several matrices ?
by oc-spam66 02 Oct '08

02 Oct '08

Hello and thank you for your answer. > There are at least three methods I can think of, but choosing the best one > requires more information. How long are the lists? Do the arrays have > variable dimensions? The simplest and most adaptable method is probably The lists would be made of 4x4 matrices : LM = [M_i, i=1..N], M_i 4x4 matrix LN = [N_i, i=1..N], N_i 4x4 matrix. N would be 1000 or more (why not 100000... if the computation is not too long) > In [3]: P = [m*n for m,n in zip(M,N)] Thank you for this one. I am curious about other possibilities. And also : is there a document about how the python interpreter works ? (order of the operations, typical timings, ...) Regards, O.C. Créez votre adresse électronique prenom.nom(a)laposte.net 1 Go d'espace de stockage, anti-spam et anti-virus intégrés.

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f2py IS NOW WORKING
by Blubaugh, David A. 02 Oct '08

02 Oct '08

To all, I have now been able to develop a stable file via f2py!! However, I had to execute the following: 1.) First, I had to copy all required library files from my selected Compaq visual Fortran compiler under python's scripts directory along with f2py itself. 2.) I also had to include a dll from my compiler under python's dll directory as well. I know that the reason as to why I needed to execute these actions, is that I do not know as to what should be my correct environmental variables within windows XP running Compaq Visual Fortran 6.6. Once again, I would appreciate to know as to what are the correct environmental variables should I set my windows xp under, given that the compiler I must utilize is a Compaq Visual Fortran Compiler 6.6??? Thanks, David Blubaugh This e-mail transmission contains information that is confidential and may be privileged. It is intended only for the addressee(s) named above. If you receive this e-mail in error, please do not read, copy or disseminate it in any manner. If you are not the intended recipient, any disclosure, copying, distribution or use of the contents of this information is prohibited. Please reply to the message immediately by informing the sender that the message was misdirected. After replying, please erase it from your computer system. Your assistance in correcting this error is appreciated.

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