Mailman 3 February 2006 - SciPy-User

Confused about enhanced-scalar dtypes
by LATORNELL, Doug Feb. 25, 2006

Feb. 25, 2006

I built NumPy from SVN this morning and got a surprise concerning dtype arguments: In [24]: import numpy In [25]: numpy.__version__ Out[25]: '0.9.6.2165' In [26]: a = numpy.fromfile("profiles-O0", dtype="float", sep=' ') ------------------------------------------------------------------------ --- exceptions.TypeError Traceback (most recent call last) /ocean/dlatorne/SoG/dlatornell06/profiles/<ipython console> TypeError: data type not understood In [27]: a = numpy.fromfile("profiles-O0", dtype="float_", sep=' ') In [28]: a[:5] Out[28]: array([ 282.8318, 27.2176, 20.932 , 5.9051, 0. ]) But on a several week old build on an other machine: In [1]: import numpy In [2]: numpy.__version__ Out[2]: '0.9.3.1868' In [3]: a = numpy.fromfile("test", dtype="float", sep=" ") In [4]: a = numpy.fromfile("test", dtype="float_", sep=" ") ------------------------------------------------------------------------ --- exceptions.TypeError Traceback (most recent call last) /home/doug/<console> TypeError: data type not understood In [5]: Based on the tip in the middle of pg 19 of my copy of the NumPy book, I expected both dtype="float" and dtype="float_" to work. I know there has been a bunch of work lately on things related to dtype, but I don't recall seeing anything about breaking the equivalence of the enhanced-scalar types (like float_) and the corresponding standard Python types (float, in this case). Did I miss, or misunderstand something, get unluck with the timing of my checkout this morning, or is this a bug? Doug This email and any files transmitted with it may contain privileged or confidential information and may be read or used only by the intended recipient. If you are not the intended recipient of the email or any of its attachments, please be advised that you have received this email in error and any use, dissemination, distribution, forwarding, printing or copying of this email or any attached files is strictly prohibited. If you have received this email in error, please immediately purge it and all attachments and notify the sender by reply email or contact the sender at the number listed.

2 1

(no subject)
by Adrián López Feb. 25, 2006

Feb. 25, 2006

Hi people, I use SciPy since a few months ago. I use it mainly to integrate a system of ODEs. Until now this piece of code was running nicely with the previous version of SciPy: from Numeric import * from scipy.integrate import odeint def func(x, t, *args): xdot = [0.0, 5.0, 0.0, 15.0, 0.0, 0.0, 0.0] xdot[0] = + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 xdot[1] = - (x[1] * beta) + x[4] * beta xdot[2] = - (x[2] * beta) + x[5] * beta xdot[3] = + x[6] * beta - (x[3] * beta) xdot[4] = + alpha0 + (alpha + (x[3])**( n) * alpha1) / ((K)** ( n) + (x[3])**( n)) - (k1 * x[4]) xdot[5] = + alpha0 + (alpha + (x[1])**( n) * alpha1) / ((K)** ( n) + (x[1])**( n)) - (k1 * x[5]) xdot[6] = - (k1 * x[6]) + alpha0 + (alpha + (x[2])**( n) * alpha1) / ((K)**( n) + (x[2])**( n)) g.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n'%(t, xdot[0], xdot [1], xdot[2], xdot[3], xdot[4], xdot[5], xdot[6])) return xdot t = arange(0, 100.01, 0.01) alpha0 = 0.0 alpha1 = 0.0 K = 1.0 beta = 5.0 n = 2.1 k1 = 1.0 alpha = 250.0 cell = 1.0 parameters = [alpha0, alpha1, K, beta, n, k1, alpha, cell] x_0 = [0.0, 5.0, 0.0, 15.0, 0.0, 0.0, 0.0] g = open('repressilator.veloc.out', 'w') args = (parameters, g) x = odeint(func, x_0, t, args) But now, with the new version, it is giving me the ugly error of [alopez@thymus tmp]$ python file.py Segmentation fault on a linux machine and Macintosh-3:~/work/tmp adrianlopez$ python test.py Bus error on a mac. There is something wrong on my code? Is there some problem on odeint from scipy.integrate? Could be any trouble calling also Numeric? I will appreciate any comment, Thanks for your help, -- Adrián López García de Lomana, Graduate Student Computational Biochemistry and Biophysics Lab Research Group on Biomedical Informatics (GRIB) - IMIM / UPF c/ Dr. Aiguader, 80; 08003 Barcelona (Spain) http://diana.imim.es

3 11

in-place data permutation
by Brian Hawthorne Feb. 25, 2006

Feb. 25, 2006

Hello, I'm looking for an efficient implementation of permuting the positions of data in an array which doesn't require copying the array. Specifically, I am shifting an array by half its length along the 0th dimension, in order to put "textbook" ordered frequency data into the packed format expected by inverse_fft. I'm surprised this is not already implemented in numpy... seems like it would be a common need. Am I missing something obvious? Brian Hawthorne UC Berkeley Brain Imaging Center

1 0

using tcdf
by Miles Lubin Feb. 24, 2006

Feb. 24, 2006

Hi, I've looked through the documentation and the help for the stats module, but I haven't be able to find any examples of how to use the cdf function. Let's say I want n degrees of freedom, and want the cumulative probability from the left tail to -x (standard deviations) on a t-distribution, how would I generate it? On the TI-83+ there's a simple tcdf() function, but I'm lost on how to do it in scipy. Thanks, Miles

2 1

Do I need to get and install LAPACK if I have ATLAS?
by skip＠pobox.com Feb. 24, 2006

Feb. 24, 2006

I seem to have properly built versions of both ATLAS and numpy. (Thank you Robert and Travis.) On to SciPy. The SciPy installation directions say: * Build ATLAS:: ... * Make optimized LAPACK library:: ... When I look in the lib directory ATLAS created I see a LAPACK library though: % ls -l total 22182 lrwxrwxrwx 1 skipm develop 41 Feb 22 06:29 Make.inc -> ... -rw-r--r-- 1 skipm develop 1529 Feb 22 06:29 Makefile -rw-r--r-- 1 skipm develop 10059380 Feb 22 08:24 libatlas.a -rw-r--r-- 1 skipm develop 274044 Feb 22 08:17 libcblas.a -rw-r--r-- 1 skipm develop 322928 Feb 22 08:23 libf77blas.a -rw-r--r-- 1 skipm develop 340352 Feb 22 08:23 liblapack.a -rw-r--r-- 1 skipm develop 300840 Feb 22 06:35 libtstatlas.a Are the SciPy directions out-of-date or is the ATLAS version of LAPACK incomplete? Thx, Skip

3 5

numpy : Fromfile should trigger an exception
by Xavier Gnata Feb. 24, 2006

Feb. 24, 2006

Hi, Trying to read more value than those that are available in a binary file, numpy fromfile function prints a warning message but no exception is triggered import numpy a=numpy.arange(10) a.tofile('toto.dat') b = numpy.fromfile('toto.dat',numpy.Int32,11) shows 11 items requested but only 10 read But there is no easy way to know that something went wrong (or I'm missing something). Xavier -- ############################################ Xavier Gnata CRAL - Observatoire de Lyon 9, avenue Charles André 69561 Saint Genis Laval cedex Phone: +33 4 78 86 85 58 Fax: +33 4 78 86 83 86 E-mail: gnata(a)obs.univ-lyon1.fr ############################################

2 1

RREF - upper triangular
by Ryan Krauss Feb. 24, 2006

Feb. 24, 2006

Is there a scipy function to find the upper triangular form of a matrix? I need to find the null space or null spaces of a matrix and have messed around with SVD in the past, but it seems like doing row reduction on something like [A]x=[0] has worked well. I have written my own RREF algorithm in Python, but it seems like I have re-invented the wheel and I would prefer to use something someone else already wrote who is smarter about round-off error and I would also prefer something in FORTRAN of C for speed. It seems like linalg.solve almost does what I want except I would need it to return the matrix I assume it is calculating instead of or along with the solution. Thanks, Ryan

8 11

'Expected in: dynamic lookup' error for scipy.signal and .fftpack
by David Treadwell Feb. 23, 2006

Feb. 23, 2006

With Robert's help, I got SciPy-0.4.6 to install. See original post: http://www.scipy.net/pipermail/scipy-user/2006-February/007137.html SciPy now works great, with the exception of 'signal' and 'fftpack'. When those packages are imported, an error is thrown: "Expected in: dynamic lookup". See ERROR below. The build looks like it proceeded w/o error, but I could have missed something. The error looks similar to in http://www.scipy.net/pipermail/scipy-user/2005-May/004450.html I suspected a mismatch of using different compilers for fftw2.1.5, NumPy and SciPy, so I removed these three packages and recompiled them with gcc3.3 and the latest release snapshots of NumPy and SciPy. One other possibility Google has suggested is a problem with python- ldap. I'm not too sure what that means. :( http://sourceforge.net/mailarchive/forum.php? forum_id=4346&max_rows=25&style=flat&viewmonth=200506 Any suggestions on this one? --DRT ERROR: >>> import numpy >>> import scipy >>> scipy.test(10,1) import signal -> failed: Failure linking new module: ~/Library/ Python2.4/site-packages/scipy-0.4.6-py2.4-macosx-10.4-ppc.egg/scipy/ fftpack/_fftpack.so: Symbol not found: _fprintf$LDBLStub Referenced from:~/Library/Python2.4/site-packages/scipy-0.4.6- py2.4-macosx-10.4-ppc.egg/scipy/fftpack/_fftpack.so Expected in: dynamic lookup import fftpack -> failed: Failure linking new module: ~/Library/ Python2.4/site-packages/scipy-0.4.6-py2.4-macosx-10.4-ppc.egg/scipy/ fftpack/_fftpack.so: Symbol not found: _fprintf$LDBLStub Referenced from: ~/Library/Python2.4/site-packages/scipy-0.4.6- py2.4-macosx-10.4-ppc.egg/scipy/fftpack/_fftpack.so Expected in: dynamic lookup

1 0

Broken links in WindowsBuild wiki page
by Albert Strasheim Feb. 23, 2006

Feb. 23, 2006

Hello all The WindowsBuild wiki page refers to http://www.scipy.org/download/atlasbinaries/winnt/ which opens up a "page does not exist" wiki page, instead of the directory. On my personal site I use the following .htaccess to prevent this from happening: RewriteEngine On RewriteRule ^$ FrontPage [L] RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule ^(.*)$ /cgi-bin/moin.cgi/$1 [L] Maybe something similar can be done for the SciPy site. Meanwhile, broken links can be found at old.scipy.org, for example: http://old.scipy.org/download/atlasbinaries/winnt/ Regards Albert

2 1

Lib\special\cephes\const.c doesn't compile with Visual Studio
by Albert Strasheim Feb. 22, 2006

Feb. 22, 2006

Hello all I'm having problems recompiling SciPy from SVN with Visual Studio .NET 2003. When compiling Lib\special\cephes\const.c, the following error occurs: Lib\special\cephes\const.c(92) : error C2099: initializer is not a constant Lib\special\cephes\const.c(97) : error C2099: initializer is not a constant This problem was discussed in comp.lang.c as "initializer is not a constant error ??" way back in 2004, when somebody else was also trying to compile some variation on this same code. http://groups.google.com/group/comp.lang.c/browse_thread/thread/23303c76b16… libxml2's trionan.c has some ideas for how to fix this problem. http://cvs.gnome.org/viewcvs/libxml2/trionan.c?rev=1.14&view=markup I added a ticket to Trac: http://projects.scipy.org/scipy/scipy/ticket/12 Regards Albert

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