Mailman 3 October 2007 - SciPy-User

Bug in scipy.sparse
by Olivier Verdier 02 Nov '07

02 Nov '07

The first thing I'm surprised about with scipy.sparse is that it uses the matrix type instead of the array type. This is very unfortunate, in my opinion. The bug is that a sparse matrix won't work correctly with `dot` and `array`: spmat = speye(3,3) vec = array([1,0,0]) dot(spmat, vec) returns: array([ (0, 0) 1.0 (1, 1) 1.0 (2, 2) 1.0, (0, 0) 0.0 (1, 1) 0.0 (2, 2) 0.0, (0, 0) 0.0 (1, 1) 0.0 (2, 2) 0.0], dtype=object) Ouch!! The right result may however be obtained with spmat * vec. This is a pity because any code that works with arrays or matrices in general and uses `dot` to do the matrix vector multiplication will be *broken* with sparse matrices. How reliable is scipy.sparse? Is there any plan to make it more compatible with the array type? Behave like the array type? How can I help? == Olivier

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Generating random variables in a joint normal distribution?
by Parvel Gu 01 Nov '07

01 Nov '07

Hi all, Since I am fresh to use SciPy for simulation, I am not sure about how to get a sequence of pairs of random variables in a joint normal distribution. I have read the info docs in the module scipy.stats. It seems that only the normal distribution rvs for single variable is provided. Thus one sequence of random variables could be get by calling stats.norm.rvs() for times (right?). But if I want pairs of random variables, for example, (p, s), which are expected to be in the joint normal distribution of some given coefficient ro, would there be any routine provided to do this just like stats.norm.rvs? If currently there is no such routine, would there be some workaround to achieve this by combining the existing routines? I am not very good at numerical probabilities... Any suggestions would be much appreciated:) Regards, Parvel

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casting ndarray object to double
by Christopher Clarke 31 Oct '07

31 Oct '07

Hi What's the most efficient way of casting an object array to a double ndarray? other than numpy.array(obj_arr.tolist(),dtype='d') The original data is a list of tuples form a SQL query which could potentially contain None Indeed a masked array would be more ideal where None is replaced by the mask I'm currently using list comprehension to replace the None in the original data with the mask But i wish to eliminate this step if possible Regards Chris

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optimize.fmin_l_bfgs_b and 'ABNORMAL_TERMINATION_IN_LNSRCH',
by Ryan Krauss 30 Oct '07

30 Oct '07

I am using optimize.fmin_l_bfgs_b and getting the following output: (array([ 8142982.47310469, 0. , 614438.11725001]), 1.58474444864e+12, {'funcalls': 21, 'grad': array([ 0. , 952148.4375, 24414.0625]), 'task': 'ABNORMAL_TERMINATION_IN_LNSRCH', 'warnflag': 2}) What does this mean? I am trying to do a least squares curve fit between some noisy data and a nonlinear model. I need to constrain one of my fit parameters to be positive. I do not have an fprime function, so the gradient is being determined numerically. Is there a better routine to use? I get a fairly close answer using my own hacked solution of using optimize.fmin where the cost function adds a gigantic penalty to the cost if the middle coefficient is greater than 0: [ 8.16174249e+06 1.93528613e-10 6.14626152e+05] So, I don't think the answer is bad, I just want to know why it terminated abnormally and whether or not I can trust the result. Thanks, Ryan

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Borda's mouthpiece and signed zero
by Stefan van der Walt 30 Oct '07

30 Oct '07

Hi all, After browsing through Kahan's slides titled "How Java's Floating-Point Hurts Everyone Everywhere" [1], I plotted Borda's Mouthpiece, as illustrated by David Williams [2]. The code is attached. It would also be interesting to simulate the anomaly shown in [2], but I don't know how. Regards Stéfan [1] http://www.cs.berkeley.edu/~wkahan/JAVAhurt.pdf [2] http://www-personal.umich.edu/~williams/archive/forth/complex/borda.html

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MFCC implementation
by Georg Holzmann 29 Oct '07

29 Oct '07

Hallo list! I only wanted to ask if there is already an MFCC implementation as used in speech or audio processing ? Thanks for any hint, LG Georg

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Subject: Re: Scientific Python publications
by Tony Mannucci 28 Oct '07

28 Oct '07

Thanks for your comments. It would be a good learning tool to see those two codes side-by-side (matlab and SciPy). I cannot access the article. -Tony >Message: 5 >Date: Tue, 09 Oct 2007 22:24:36 +0200 >From: jaropis <jaropis(a)gazeta.pl> >Subject: Re: [SciPy-user] Scientific Python publications >To: scipy-user(a)scipy.org >Message-ID: <feh65l$9t8$1(a)sea.gmane.org> >Content-Type: text/plain; charset=us-ascii > >> the molecular science group at the university of Bristol on a recent >> scientific paper and thought that I could use the talk as an excuse to >> advertise the wonders of python. > >I use Python a lot - for example this paper: > >http://www.iop.org/EJ/abstract/0967-3334/28/3/005 > >has an animation done in SciPy+pylab, and all the calculations are in >Python. I give Matlab code for the same calculations in an appendix, but >they were originally done in SciPy and then translated to Matlab. > >Jarek P > -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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Thin plates for a 3D deformation field
by Matthieu Brucher 28 Oct '07

28 Oct '07

Hi, I wondered if someone knew of a package that allows the interpolation of a 3D deformation field with thin plates (or in fact with anything) based on a list of points and their associated deformation field. If only 2D deformation field is supported by a package, I'll go for it too ;) -- French PhD student Website : http://miles.developpez.com/ Blogs : http://matt.eifelle.com and http://blog.developpez.com/?blog=92

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ANN: Veusz-1.0 - a scientific plotting package
by Jeremy Sanders 28 Oct '07

28 Oct '07

I'm pleased to announce Veusz-1.0. Linux and Windows binaries are available, with source. For further details see below. Jeremy Veusz 1.0 --------- Velvet Ember Under Sky Zenith ----------------------------- http://home.gna.org/veusz/ Veusz is Copyright (C) 2003-2007 Jeremy Sanders <jeremy(a)jeremysanders.net> Licenced under the GPL (version 2 or greater). Veusz is a scientific plotting package written in Python, using PyQt4 for display and user-interfaces, and numpy for handling the numeric data. Veusz is designed to produce publication-ready Postscript/PDF output. The user interface aims to be simple, consistent and powerful. Veusz provides a GUI, command line, embedding and scripting interface (based on Python) to its plotting facilities. It also allows for manipulation and editing of datasets. Feature changes from 0.99.0: * Import of Text datasets * Labels can be plotted next to X-Y points * Numbers can be directly plotted by entering into X-Y datasets as X and Y * More line styles * Loaded document and functions are checked for unsafe Python features * Contours can be labelled with numbers * 2D dataset creation to make 2D datasets from x, y, z 1D datasets Bug and minor fixes from 0.99.0: * Zooming into X-Y images works now * Contour plots work on datasets with non equal X and Y sizes * Various fixes for datasets including NaN or Inf * Large changes to data import filter to support loading strings (and dates later) * Reduce number of undo levels for memory/speed * Text renderer rewritten to be more simple * Improved error dialogs * Proper error dialog for invalid loading of documents Features of package: * X-Y plots (with errorbars) * Line and function plots * Contour plots * Images (with colour mappings and colorbars) * Stepped plots (for histograms) * Fitting functions to data * Stacked plots and arrays of plots * Plot keys * Plot labels * LaTeX-like formatting for text * EPS/PDF/PNG export * Scripting interface * Dataset creation/manipulation * Embed Veusz within other programs * Text, CSV and FITS importing Requirements: Python (2.3 or greater required) http://www.python.org/ Qt >= 4.3 (free edition) http://www.trolltech.com/products/qt/ PyQt >= 4.3 (SIP is required to be installed first) http://www.riverbankcomputing.co.uk/pyqt/ http://www.riverbankcomputing.co.uk/sip/ numpy >= 1.0 http://numpy.scipy.org/ Microsoft Core Fonts (recommended for nice output) http://corefonts.sourceforge.net/ PyFITS >= 1.1 (optional for FITS import) http://www.stsci.edu/resources/software_hardware/pyfits For documentation on using Veusz, see the "Documents" directory. The manual is in pdf, html and text format (generated from docbook). Issues: * Reqires a rather new version of PyQt, otherwise dialogs don't work. * Can be very slow to plot large datasets if antialiasing is enabled. Right click on graph and disable antialias to speed up output. * The embedding interface appears to crash on exiting. If you enjoy using Veusz, I would love to hear from you. Please join the mailing lists at https://gna.org/mail/?group=veusz to discuss new features or if you'd like to contribute code. The latest code can always be found in the SVN repository. Jeremy Sanders

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Cookbook/InputOutput
by Nils Wagner 27 Oct '07

27 Oct '07

Hi all, I tried to use the home-made function (available at http://www.scipy.org/Cookbook/InputOutput) to read an array from the file topo-28.xohis (See attachment for details). If I run the script (xy.py) I get python -i xy.py Traceback (most recent call last): File "xy.py", line 47, in ? data = readArray("topo-28.xohis") File "xy.py", line 35, in readArray items = split(stripped_line) TypeError: split() takes at least 2 arguments (1 given) How can I fix the problem ? Any pointer would be appreciated. Thanks in advance Nils

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