Mailman 3 April 2011 - SciPy-Dev

possible bug in register
by 江大伟 April 22, 2011

April 22, 2011

Dear all When I tried to registered an new account in the SciPy dev wiki( http://projects.scipy.org/scipy/register), the webpage always said incorrect captcha input but I could not find where the captcha was. What happened? cheers David

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I want to do some traslation about the SciPy Reference Guide
by 江大伟 April 22, 2011

April 22, 2011

Hi guys I am a Chinese postgraduate student in the Australian National University. And I am using SciPy to develop some machine learning algorithms. But I found I could not use classes and functions smoothly, because I often encountered many technical and mathematical words which I could understand in Chinese but couldn’t in English. So I was often interrupted when I was thinking, which was quite annoying. So I guess it is absolutely a major stumbling block for other Chinese students to use SciPy. You can’t expect them to learn English well as well as mathematics. So I want to translate the SciPy Reference Guide into Chinese. Is it ok? Can you give me some advice or some help?

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calc_lwork.f different from Lapack?
by Josh Lawrence April 13, 2011

April 13, 2011

Hello, After receiving an error in using linalg.lstsq, I started some investigating. I found that scipy/linalg/src/calc_lwork.f is essentially a stripped down version of the appropriate functions in Lapack (for linalg.lstsq using double precision complex numbers, it is ZGELSS). It seems that the portions for gelss in calc_lwork.f do not match the current version of lapack. I believe this is the source of my error (it doesn't occur if I use linalg.pinv2 for least squares instead). Is there a particular rationale for these being different or perhaps an incorrect copy and paste? The relevant portions are shown below (a line of % characters are prepended before the codes from the two locations). For example, the first calculation of MAXWRK under Path 1 uses 3*N in calc_lwork and 2*N in lapack. If things were just being over-estimated, I wouldn't really care, but I was able to isolate down that the variable LWORK (calculated from MINWRK) is too small, which if I read the rest of the code right means that some work arrays are not long enough. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% calc_lwork.f (from scipy trunk on github, lines 191-261): IF( M.GE.N .AND. M.GE.MNTHR ) THEN * * Path 1a - overdetermined, with many more rows than columns * MM = N MAXWRK = MAX( MAXWRK, N+N*ILAENV( 1, prefix // 'GEQRF', ' ', $ M, N, -1, -1 ) ) MAXWRK = MAX( MAXWRK, N+NRHS* $ ILAENV( 1, prefix // 'ORMQR', 'LT', M, NRHS, N, -1 ) ) END IF IF( M.GE.N ) THEN * * Path 1 - overdetermined or exactly determined * * Compute workspace neede for BDSQR * BDSPAC = MAX( 1, 5*N ) MAXWRK = MAX( MAXWRK, 3*N+( MM+N )* $ ILAENV( 1, prefix // 'GEBRD', ' ', MM, N, -1, -1 ) ) MAXWRK = MAX( MAXWRK, 3*N+NRHS* $ ILAENV( 1, prefix // 'ORMBR', 'QLT', MM, NRHS, N, -1 ) ) MAXWRK = MAX( MAXWRK, 3*N+( N-1 )* $ ILAENV( 1, prefix // 'ORGBR', 'P', N, N, N, -1 ) ) MAXWRK = MAX( MAXWRK, BDSPAC ) MAXWRK = MAX( MAXWRK, N*NRHS ) MINWRK = MAX( 3*N+MM, 3*N+NRHS, BDSPAC ) MAXWRK = MAX( MINWRK, MAXWRK ) END IF IF( N.GT.M ) THEN * * Compute workspace neede for DBDSQR * BDSPAC = MAX( 1, 5*M ) MINWRK = MAX( 3*M+NRHS, 3*M+N, BDSPAC ) IF( N.GE.MNTHR ) THEN * * Path 2a - underdetermined, with many more columns * than rows * MAXWRK = M + M*ILAENV( 1, prefix // 'GELQF', ' ', $ M, N, -1, -1 ) MAXWRK = MAX( MAXWRK, M*M+4*M+2*M* $ ILAENV( 1, prefix // 'GEBRD', ' ', M, M, -1, -1 ) ) MAXWRK = MAX( MAXWRK, M*M+4*M+NRHS* $ ILAENV( 1, prefix // 'ORMBR', 'QLT', M, NRHS, M, -1 )) MAXWRK = MAX( MAXWRK, M*M+4*M+( M-1 )* $ ILAENV( 1, prefix // 'ORGBR', 'P', M, M, M, -1 ) ) MAXWRK = MAX( MAXWRK, M*M+M+BDSPAC ) IF( NRHS.GT.1 ) THEN MAXWRK = MAX( MAXWRK, M*M+M+M*NRHS ) ELSE MAXWRK = MAX( MAXWRK, M*M+2*M ) END IF MAXWRK = MAX( MAXWRK, M+NRHS* $ ILAENV( 1, prefix // 'ORMLQ', 'LT', N, NRHS, M, -1 ) ) ELSE * * Path 2 - underdetermined * MAXWRK = 3*M + ( N+M )*ILAENV( 1, prefix // 'GEBRD', ' ', $ M, N, -1, -1 ) MAXWRK = MAX( MAXWRK, 3*M+NRHS* $ ILAENV( 1, prefix // 'ORMBR', 'QLT', M, NRHS, M, -1 ) ) MAXWRK = MAX( MAXWRK, 3*M+M* $ ILAENV( 1, prefix // 'ORGBR', 'P', M, N, M, -1 ) ) MAXWRK = MAX( MAXWRK, BDSPAC ) MAXWRK = MAX( MAXWRK, N*NRHS ) END IF END IF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ZGELSS.F (from LAPACK on netlib, lines 165-236): IF( INFO.EQ.0 ) THEN MINWRK = 1 MAXWRK = 1 IF( MINMN.GT.0 ) THEN MM = M MNTHR = ILAENV( 6, 'ZGELSS', ' ', M, N, NRHS, -1 ) IF( M.GE.N .AND. M.GE.MNTHR ) THEN * * Path 1a - overdetermined, with many more rows than * columns * MM = N MAXWRK = MAX( MAXWRK, N + N*ILAENV( 1, 'ZGEQRF', ' ', M, $ N, -1, -1 ) ) MAXWRK = MAX( MAXWRK, N + NRHS*ILAENV( 1, 'ZUNMQR', 'LC', $ M, NRHS, N, -1 ) ) END IF IF( M.GE.N ) THEN * * Path 1 - overdetermined or exactly determined * MAXWRK = MAX( MAXWRK, 2*N + ( MM + N )*ILAENV( 1, $ 'ZGEBRD', ' ', MM, N, -1, -1 ) ) MAXWRK = MAX( MAXWRK, 2*N + NRHS*ILAENV( 1, 'ZUNMBR', $ 'QLC', MM, NRHS, N, -1 ) ) MAXWRK = MAX( MAXWRK, 2*N + ( N - 1 )*ILAENV( 1, $ 'ZUNGBR', 'P', N, N, N, -1 ) ) MAXWRK = MAX( MAXWRK, N*NRHS ) MINWRK = 2*N + MAX( NRHS, M ) END IF IF( N.GT.M ) THEN MINWRK = 2*M + MAX( NRHS, N ) IF( N.GE.MNTHR ) THEN * * Path 2a - underdetermined, with many more columns * than rows * MAXWRK = M + M*ILAENV( 1, 'ZGELQF', ' ', M, N, -1, $ -1 ) MAXWRK = MAX( MAXWRK, 3*M + M*M + 2*M*ILAENV( 1, $ 'ZGEBRD', ' ', M, M, -1, -1 ) ) MAXWRK = MAX( MAXWRK, 3*M + M*M + NRHS*ILAENV( 1, $ 'ZUNMBR', 'QLC', M, NRHS, M, -1 ) ) MAXWRK = MAX( MAXWRK, 3*M + M*M + ( M - 1 )*ILAENV( 1, $ 'ZUNGBR', 'P', M, M, M, -1 ) ) IF( NRHS.GT.1 ) THEN MAXWRK = MAX( MAXWRK, M*M + M + M*NRHS ) ELSE MAXWRK = MAX( MAXWRK, M*M + 2*M ) END IF MAXWRK = MAX( MAXWRK, M + NRHS*ILAENV( 1, 'ZUNMLQ', $ 'LC', N, NRHS, M, -1 ) ) ELSE * * Path 2 - underdetermined * MAXWRK = 2*M + ( N + M )*ILAENV( 1, 'ZGEBRD', ' ', M, $ N, -1, -1 ) MAXWRK = MAX( MAXWRK, 2*M + NRHS*ILAENV( 1, 'ZUNMBR', $ 'QLC', M, NRHS, M, -1 ) ) MAXWRK = MAX( MAXWRK, 2*M + M*ILAENV( 1, 'ZUNGBR', $ 'P', M, N, M, -1 ) ) MAXWRK = MAX( MAXWRK, N*NRHS ) END IF END IF MAXWRK = MAX( MINWRK, MAXWRK ) END IF WORK( 1 ) = MAXWRK * IF( LWORK.LT.MINWRK .AND. .NOT.LQUERY ) $ INFO = -12 END IF

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tzinfo and scikits.timeseries
by jamil egdemir April 13, 2011

April 13, 2011

Hi, When using scikits.timeseries I'm running into an issue with timezone information. When using a datetime.datetime in the constructor for a scikits.timeseries.Date, the tzinfo is getting dropped. Here's the output I'm getting when working from inside ipython (on windows): In [2]: import datetime In [3]: from pytz import timezone In [4]: eastern = timezone('US/Eastern') In [5]: eastern Out[5]: <DstTzInfo 'US/Eastern' EST-1 day, 19:00:00 STD> In [6]: testing = eastern.localize(datetime.datetime(year = 2010, month = 1, day = 1)) In [7]: testing Out[7]: datetime.datetime(2010, 1, 1, 0, 0, tzinfo=<DstTzInfo 'US/Eastern' EST-1 day, 19:00:00 STD>) In [8]: type(testing) Out[8]: <type 'datetime.datetime'> In [9]: import scikits.timeseries as TS In [10]: aDate = TS.Date('D', datetime = testing) In [11]: aDate Out[11]: <D : 01-Jan-2010> In [13]: after = aDate.datetime In [14]: after Out[14]: datetime.datetime(2010, 1, 1, 0, 0) In [15]: after.tzinfo In [16]: type(after.tzinfo) Out[16]: <type 'NoneType'> What's the best way to deal with this situation? Is there a way to keep hold of the tzinfo while still using scikits.timeseries.Date? -- -j ------------------------------------------------------------- Jamil Egdemir unclejamil(a)gmail.com AIM: unclejamil YahooMessenger: uncle_jamil http://grad.physics.sunysb.edu/~jamil (631) 338-3170 (cell) -------------------------------------------------------------

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Possibly bug in fmin_ncg
by Nils Wagner April 12, 2011

April 12, 2011

Hi all, fmin_cg works fine x_opt, f_opt, func_calls, grad_calls, warnflag, allvecs = fmin_cg(func, x0, fprime=fprime, args=(), gtol=1.0000000000000001e-05, norm=inf, epsilon=1.4901161193847656e-08, maxiter=None, full_output=1, disp=1, retall=1, callback=None) while fmin_ncg fails with x_opt, f_opt, fcalls, gcalls,hcalls,warnflag =fmin_ncg(func, x0, fprime=fprime, fhess_p=None, fhess=None, args=(), avextol=1.0000000000000001e-05, epsilon=1.4901161193847656e-08, maxiter=None, full_output=1, disp=1, retall=1, callback=None) File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/optimize/optimize.py", line 811, in fmin_ncg maggrad = numpy.add.reduce(abs(b)) TypeError: cannot reduce on a scalar Is it possible to replace numpy.add.reduce by numpy.sum ? >>> numpy.add.reduce(abs(numpy.array(([1.,2.])))) 3.0 >>> numpy.sum(abs(numpy.array(([1.,2.])))) 3.0 >>> numpy.add.reduce(abs(1.)) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: cannot reduce on a scalar >>> numpy.sum(abs(1.)) 1.0 Nils

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Re: [SciPy-Dev] [SciPy-User] What "Array" means
by Sturla Molden April 10, 2011

April 10, 2011

Den 08.04.2011 12:14, skrev Timothy Wu: > > File "/usr/lib/python2.6/dist-packages/scipy/stats/mstats_basic.py", > line 1546, in kurtosistest > n = a.count(axis=axis).astype(float) > AttributeError: 'int' object has no attribute 'astype' > > I'm not familiar with numpy nor scipy. What exactly should I put in there? I find multiple cases of code like this: a, axis = _chk_asarray(a, axis) n = a.count(axis) a, axis = _chk_asarray(a, axis) n = a.count(axis=axis) a, axis = _chk_asarray(a, axis) n = a.count(axis) a, axis = _chk_asarray(a, axis) n = a.count(axis=axis).astype(float) All of them are bugs: _chk_asarray sometimes returns an ndarray (due to np.ma.ravel), which does not have a count attribute. Sometimes count returns an int, which does not have an asfloat attribute. Sturla

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scipy.factorial in python 3.2
by josef.pktd＠gmail.com April 10, 2011

April 10, 2011

python 3.2 (64 bit version) doesn't have scipy.factorial anymore, with python 2.7 it's there. Is this intentional? It's easy to work around, I just import it from scipy.misc Python 3.2 (r32:88445, Feb 20 2011, 21:30:00) [MSC v.1500 64 bit (AMD64)] on win32 Type "copyright", "credits" or "license()" for more information. ==== No Subprocess ==== >>> import scipy >>> scipy.factorial Traceback (most recent call last): File "<pyshell#1>", line 1, in <module> scipy.factorial AttributeError: 'module' object has no attribute 'factorial' >>> import scipy.misc >>> scipy.misc.factorial <function factorial at 0x0000000005475CC8> Josef

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OT: bug in matplotlib for py32
by josef.pktd＠gmail.com April 10, 2011

April 10, 2011

I'm going through py23 conversion for statsmodels, using Goehlke's matplotlib we have a function that uses squeeze=False, and get an exception in pyplot.py def subplots(nrows=1, ncols=1, sharex=False, sharey=False, squeeze=True, subplot_kw=None, **fig_kw): doesn't have a ret defined, no return value (Sorry for OT, I'm not setup for reporting matplotlib bugs) Josef

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scipy.io.savemat and sparse matrices
by Nils Wagner April 8, 2011

April 8, 2011

Hi all, I tried to save a sparse matrix savemat('mass.mat',dict(M_sparse)) File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/sparse/base.py", line 109, in __iter__ yield self[r,:] TypeError: 'coo_matrix' object is unsubscriptable >>> type(M_sparse) <class 'scipy.sparse.coo.coo_matrix'> How can I resolve the problem ? Nils

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warnings in quadpack.py are printed, patch linked
by Skipper Seabold April 8, 2011

April 8, 2011

The warnings in quadpack are printed. Does this change look ok? https://github.com/jseabold/scipy/compare/master...quadpack-warn-fix Skipper

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