Mailman 3 August 2006 - SciPy-User

weave and numpy
by Sebastian Haase Aug. 8, 2006

Aug. 8, 2006

Hi, if I pass a numpy array 'arr' as argument a) how does the C code get arr.ndim ? b) how does the C code get arr.shape[0],... ? c) if the C code changes elements of arr, are those changes *on the original data* ? In other words, is weave.inline making a copy of arr ? I searched through http://projects.scipy.org/scipy/scipy/browser/trunk/Lib/weave/doc/tutorial.… but did not find a definite answer. From the 'array3d.py' example in weave in looks like Narr would contain the shape !? Thanks, Sebastian Haase

2 2

ga examples broken?
by Jelle Feringa / EZCT Architecture & Design Research Aug. 7, 2006

Aug. 7, 2006

I just checked in the scipy.ga package from the svn server, but failed to run the example: c:\Python24\Lib\site-packages\scipy\ga>python examples.py Warning: The key "migrants" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_devia tion', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] Warning: The key "num_pops" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_devia tion', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] Traceback (most recent call last): File "examples.py", line 64, in ? ex1() File "examples.py", line 60, in ex1 galg.evolve() File "c:\Python24\lib\site-packages\scipy\ga\algorithm.py", line 127, in evolv e self.initialize() File "c:\Python24\lib\site-packages\scipy\ga\algorithm.py", line 60, in initia lize if reseed: rv.initialize(seed = sd, algorithm = alg) AttributeError: 'module' object has no attribute 'initialize' In [2]: sp.__version__ Out[2]: '0.4.9' Might it possible broken, or is something the matter with my setup? Thanks, Jelle

1 0

Re: [SciPy-user] Use of Scipy in a students final year mechanical engineering project
by Alex Liberzon Aug. 7, 2006

Aug. 7, 2006

I'm from mechanical engineering field myself, from the fluid mechanical part of it and I'm working on a project that might be useful for you to see as a 'test case'. The project is about one of the experimental techniques in fluid mechanics, called Particle Image Velocimetry and it is the state-of-the-art method to measure spatial and temporal distribution of the flow velocity fields. You may find thousands of references about the method all around the web. The 'test case' I'm talking about is an algorithm used for analysing the images of particles in the flow. The original project, called URAPIV http://urapiv.wordpress.com was developed (proudly to say among the first) in Matlab, to allow various users to test their commercial software, to compare or to develop further different algorithms for this digital image correlation method. Recently we decided that Mathworks's licensing is too strict and we would like to let the users not only open source, but also a real open source project, one they can use without paying for 'beer'. So, we develop PyPIV, a clone of URAPIV in Python with Scipy/Numpy. We already have one more developer from outside the group, from Australia, a Master student for Aeronautics, and we'd like to have more developers. You can download both packages and demo images and start playing with it. The further development which is necessary: 1) develop drivers and image acquisition to allow this project be complete package, allowing open source and free educational tool for high schools, universities, etc. 2) develop GUI in Python for easy installation, use and analysis 3) develop new algorithms, e.g. iterative, multi-resolution, window shifting, pattern matching, optical flow, etc. 4) develop it into a new package, for strain measurements, using the basic ability to do 2D correlation and followed by a gradients (strain, stress) measurements of tenciles, etc. 5) develop other techniques of the similar kind, e.g. particle tracking velocimetry in three dimensions and similar. ..... The list is actually very long and I'll skip the rest. If you're interested, you can contact us offline (urapiv at gmail dot com) Best regards and good luck with Python/Numpy/Scipy. It does not need the justification, it's great. Alex

1 0

Accelerating the calculation of a function
by Gael Varoquaux Aug. 7, 2006

Aug. 7, 2006

Hi list, I am integrating an ODE. I thus have a complicated function that I call a lot of times. What limits my execution times (currently too high) is the call to this function, which happens a great number of times. I therefore need to speed this up. If it where a simple function I could use weave.inline or weave.blitz but this is a rather complicated function involving a lot of python magic that I would be very happy to keep ( things such as : sum( [F(k) for k in lasers]) ). How can I speed this up without rendering my function unreadable ? Is there a compiler (Just in time, maybe) that could speed this up ? Is psyco of any use ? Is their a way to inline my functions (I would like to keep them as functions for the sake of readability) ? Any tricks or ideas appreciated. Cheers -- Gaël

3 3

Using Mayavi's tvtk/mlab within pyGTK?
by René Donner Aug. 5, 2006

Aug. 5, 2006

hello, i have found this post http://www.serpia.org/pygtk on how to display a matplotlib figure inside a pyGTK window. Is it somehow possible to do the same with the mlab module from the Mayavi / tvtk visualization toolkit? (http://scipy.org/Cookbook/ MayaVi/mlab) Even a hack to render mlab's output to a png and display this in the pygtk window would be great! Any link or snippet is highly appreciated! Thanks a lot, rene

2 2

global fitting
by morovia morovia Aug. 5, 2006

Aug. 5, 2006

Hello I have data sets and would like to fit them globally with common parameters. Is there a way to do this using scipy. Any pointers for algo and suggestions are welcome. Thanks Morovia.

1 0

jn & lpmn or sph_jn...
by fred Aug. 4, 2006

Aug. 4, 2006

Hi, I like how jn works because I can array as arg (I use jn on 3D array). This is not the case for sph_jn & lpmn :-( I tried to bypass it, with something like def foo(m,n): x = arange(0,Lx,dx) y = arange(0,Ly,dy) z = arange(0,Lz,dz) tab = zeros((len(x), len(y), len(z)), dtype='f') for i in range(0,len(x)): for j in range(0,len(y)): for k in range(0,len(z)): tab[i,j,k] = cos(theta(x[i],y[j],z[k])) # tab[i,j,k] = Ymn_theta_p(x[i],y[j],z[k],m,n)*sph_jn(n,r(x[i],y[j],z[k]))[n][0]*rho(x[i],y[j],z[k]) return (tab) but knowing my arrays have more than hundred of thousand cells, it is _very_ slow. I guess sph_jn & lpmn are written like this because they return arrays (0 to n order, derivative, etc). I wish to have Legendre & spherical Bessel functions which could accept array as arg. I only need the last order (n) and the derivative (which could be called by another func) for the same order. How could I write this ? Or is there another way to do the same thing ? Ex. : In [1]: from scipy.special import * In [2]: x=arange(0,1,0.1) In [3]: print jn(1,x) [ 0. 0.04993753 0.09950083 0.14831882 0.19602658 0.24226846 0.28670099 0.32899574 0.36884205 0.40594955] In [4]: print sph_jn(1,x) --------------------------------------------------------------------------- exceptions.ValueError Traceback (most recent call last) /home/fred/<ipython console> /usr/local/lib/python2.4/site-packages/scipy/special/basic.py in sph_jn(n, z) 212 """ 213 if not (isscalar(n) and isscalar(z)): --> 214 raise ValueError, "arguments must be scalars." 215 if (n!= floor(n)) or (n<0): 216 raise ValueError, "n must be a non-negative integer." ValueError: arguments must be scalars. Cheers, -- Fred.

5 11

scipy site will be back up real soon now
by Jeff Strunk Aug. 4, 2006

Aug. 4, 2006

Hello, The automatic update for apache had different behavior than the previous version. I am compiling a fixed version, so it should work again soon. Sorry for the inconvenience. Jeff Strunk IT Administrator Enthought, Inc.

1 0

Re: [SciPy-user] Pycluster, Numeric, & numpy
by R. Padraic Springuel Aug. 4, 2006

Aug. 4, 2006

I am indeed using a version that used a binary installer. I'm on a Windows machine and have zero experience with compilers, so I always use binary installs. It's a habit I should probably get out of, especially since I'm hoping to switch to a dual boot system soon. For now, however, the alongside install of Numeric seems to work. Thanks. -- R. Padraic Springuel Teaching Assistant Department of Physics and Astronomy University of Maine Bennett 214 Office Hours: By Appointment only during the Summer

1 0

Mesh generator
by Nils Wagner Aug. 4, 2006

Aug. 4, 2006

Hi all, Is there something similar available for scipy ? http://www-math.mit.edu/~persson/mesh/ Nils

6 10