Mailman 3 September 2005 - SciPy-User

SciPy 2005 - thanks, accolades and suggestions
by Simon Hook Sept. 25, 2005

Sept. 25, 2005

Many thanks to Enthought and all the speakers/developers for putting on an excellent SciPy 2005. As a someone who is fairly new to both Python and SciPy, I found this a tremendous opportunity to learn more about what can be done with Python for scientific computing (just about everything!). At the meeting there was a request for suggestions on how increase the usability and audience. Here are more thoughts: 1. The Enthought distribution of Python (Enthon) which includes many of the scientific packages, tested to make sure they work together is extremely valuable to someone like me who does not know what tools are out there and does not want to do dozens of downloads and installs only to find that package "a" conflicts with "b". I realize that such a distribution is a significant contribution and I would be happy to pay a modest sum for such a package. If someone puts together such a package please make the payment easy - i..e. credit card over the net. If you work in/with government there are certain methods that are straighforward to pay for stuff and others that require much more paperwork, e.g. check, paypal, ebay. The best method is credit card over the net. Given the rapid rate of improvement, another approach might be to buy the first distribution, then get free new distributions for a year and then buy the next distribution. Note setting up service contracts is also a hassle so better to have a new distribution to buy once per year or so. 2. I would like to suggest the following packages be added to the Enthon distribution: mxtime (www.egenix.com) ipython (ipython.scipy.org) matplotlib (matplotlib.sourceforge.net) inotebook (shown at scipy - not sure where to download) vision (www.scripps.edu/~sanner/python/viper) 3. Many of the packages have excellent tutorials but they are package centric. What I mean by this is instead of taking a scientific problem and showing how you solve it, each package carefully describes its capabilities largely in isolation. It would be great if there was a simple tutorial(s) that tried to show how the tools could be used together. For example, say you want to read in some air temperature data, produce a plot of the data, create and fit a model to the data, generate an inotebook and then create a vision type model to interact with the data - you would have to know about all the packages and have read all the tutorials for each of the packages - too much time would be spent on the tools and not enough on the problem. Incidentally there is an example of something headed along these lines in the scipy tutorial. I am happy to help try and put something like this together, perhaps it could be a tutorial, perhaps a book - it would benefit from help from each of the people developing the different packages. On that note it would be nice if the package tutorials were on the scipy site under docs and if package developers called their guides "package-name_users_guide" rather than just "users_guide". 4. More examples. I find it much easier to follow examples than read manuals. It would be great if there were more user contributed examples in scipy. Matplotlib does an excellent job with examples. I just sent an example in on using read_array for scipy. 5. If there were some tutorials that showed how the tools could be used to solve scientific problems it may be worthwhile trying to have a morning at scipy for new users that worked them through the tutorials. Alternatively these could be at science conferences. In my research area, before a conference starts there are usually classes which people pay for that teach them new tools. The classes tend to be geared towards a particular research area, in my case geologic remote sensing. I have run a few classes and it would be good way to introduce students to scipy+ in the context of what they need to do. Again many thanks again to the organizers, developers and presenters. Simon -- +++++++++++++++++++++++++++++++++++++++++ Simon J. Hook, MSc, PhD Jet Propulsion Laboratory MS 183-501 Pasadena, CA 91109 Office: 818-354-0974 Fax: 818-354-0966 Email: simon.j.hook(a)jpl.nasa.gov http://asterweb.jpl.nasa.gov http://masterweb.jpl.nasa.gov http://laketahoe.jpl.nasa.gov +++++++++++++++++++++++++++++++++++++++++

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Release of scipy core beta will happen next week.
by Travis Oliphant Sept. 25, 2005

Sept. 25, 2005

At the SciPy 2005 conference I announced that I was hoping to get a beta of the new scipy (core) (aka Numeric3 aka Numeric Next Generation) released by the end of the conference. This did not happen. Some last minute features were suggested by Fernando Perez that I think will be relatively easy to add and make the release that much stronger. Look for the beta announcement next week. For the impatient, the svn server is always available: http://svn.scipy.org/svn/scipy_core/branches/newcore -Travis O.

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os x vga dongle at scipy conference tomorrow
by John Hunter Sept. 22, 2005

Sept. 22, 2005

If anyone is coming to the SciPy conference tomorrow morning and has a 12 inch powerbook dvi->VGA adaptor for the overhead could you bring it along for the morning session? Apple in their infinite wisdom has two sizes on the dvi side depending on the 12 inch model. I have the fat one. Or I should say, I need the fat one. Thanks, JDH

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RE: [SciPy-user] Scipy with Python 2.4 on Windows
by Howey, David A Sept. 21, 2005

Sept. 21, 2005

I just used python 2.3 it works fine on windows. also check out enthought python at http://www.enthought.com/python/ Dave Howey -----Original Message----- From: scipy-user-bounces(a)scipy.net on behalf of Ryan Krauss Sent: Wed 21/09/2005 13:30 To: SciPy Users List Subject: Re: [SciPy-user] Scipy with Python 2.4 on Windows Whenever the question of 2.4 and Windows has come up, the answer has been that no one is doing it yet. Ryan Sylvain Gerbier wrote: > Hi everybody, > > Need help here ... does anybody install scipy on a windows computer with > Python 2.4 ? If yes, can he/she tells me how to do it ? I am not so much > familiar with the build procedure but can learn ... > If nobody have done it, I actually only use the io.savemat function from > the scipy library. Does anybody know how I can find a turnaround to save > a file with the matlab format without using the scipy library ? > Thanks for your help. > > Sylvain > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

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plotting questions (gplt and plt)
by Ruben Charles Sept. 20, 2005

Sept. 20, 2005

Hi, I'm using Scipy on Debian Gnu/Linux. (python2.3-scipy) in a program that have to show plots but while i'm testing capabilities of the three possible options (gplt, plt an xplt) a couple of questions comes up. -------------------------------------------------------------------------------------------------------------- plt: If a follow the steps of the plotting tutorial everything seems ok in the first try. >>> import gui_thread >>> gui_thread.start() # or gui_thread.wxPython_thread() >>> from scipy import plt >>> plt.plot((1,2,3)) But if i close the Plot frame (manually with the cursor) and try to plot again >>> plt.plot((1,2,3)) The interpreter shows a message: "The C++ part of the code has been deleted" and i can´t plot again without exit the interpreter and back again. How i can solve that? ---------------------------------------------------------------------------------------------------------------- gplt (gnuplot): If i create a plot with the Gnuplot program the resulting plot has responses to mouse events and shows coordinates in the window but if i create a plot in python gplt.plot((1,2,3)) The window have not the same response to mouse events (no response at all). How i can give the same responses? ___________________________________________________________________ Thanks

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using odeint
by LOPEZ GARCIA DE LOMANA, ADRIAN Sept. 18, 2005

Sept. 18, 2005

Hi people, I'm using odeint from SciPy to solve a a system of ordinary differential equations. I've found a quite a strange error while taking different parameters on the equations: 0.0 0.0 0.0 0.0 0.0 Traceback (most recent call last): File "/home/alopez/tmp/news/output/scratch/modelF.integ.py", line 23, in func xdot[7] = + (v_NACT * x[5]**m_NACT) / (x[5]**m_NACT + k_NACT**m_NACT) - k_deg_h * x[7] ValueError: negative number cannot be raised to a fractional power odepack.error: Error occured while calling the Python function named func 0.0 Traceback (most recent call last): File "/home/alopez/tmp/news/output/scratch/modelF.integ.py", line 23, in func xdot[7] = + (v_NACT * x[5]**m_NACT) / (x[5]**m_NACT + k_NACT**m_NACT) - k_deg_h * x[7] ValueError: negative number cannot be raised to a fractional power odepack.error: Error occured while calling the Python function named func 5.03700957163e-99 Traceback (most recent call last): File "/home/alopez/tmp/news/output/scratch/modelF.integ.py", line 23, in func xdot[7] = + (v_NACT * x[5]**m_NACT) / (x[5]**m_NACT + k_NACT**m_NACT) - k_deg_h * x[7] ValueError: negative number cannot be raised to a fractional power odepack.error: Error occured while calling the Python function named func 7.37964481865e-99 Traceback (most recent call last): those numbers in between the error messages are prints of x[5]. Why is telling me about negative numbers? It's not, actually, close to zero, but positive. k_NACT is also positive. k_NACT = 2.994997603 Some ideas? Thanks for your time, Adrián.

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licence: GNU or not GNU for new image analysis platform
by Sebastian Haase Sept. 17, 2005

Sept. 17, 2005

Prabhu, I noticed that you changed MayaVi's license from GPL to BSD. Why did you think this was needed ? I have developed (rather: put together) a platform for (interactive) multidimensional image analysis and algorithm development. It's a graphical shell window based on wxPython's PyShell where I added a nice, fast OpenGL-based 2d image viewer. But the main aspect of all this was that it comes pre-compiled and ready to use ! (Including numarray, wxPython ... for Linux or Windows or Mac-OSX) Now: before I can give this to anyone my university requires me to attach a license to this. I think I like the "copyleft" idea of GPL or maybe better LGPL. My understanding is that this would allow a company to sell it, but they would have "make their changes publicly available" (under LGPL again) I think Fernando's IPython is LGPL - and I think my "platform" is quite a similar spirit... All comments are most welcome Thanks, Sebastian Haase UCSF, Sedat Lab

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relaxation solver
by Mark Alford Sept. 16, 2005

Sept. 16, 2005

I want to solve a boundary value ODE problem, where I know some boundary conditions at each end of the interval. As far as I know, odeint is just for initial value problems where you know boundary conditions at one end of the interval. Is there a relaxation solver in SciPy?

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scipy.gplt PNG output without plotting on screen
by Johann Rohwer Sept. 16, 2005

Sept. 16, 2005

Hi Is there a way using scipy.gplt to output your graphs to files without having them plotted to screen first? I have a script that generates lots of plots, and currently run a whole sequence of commands to build up every plot, e.g.: >>> scipy.gplt.plot(x,y) >>> scipy.gplt.xtitle('xxx') >>> scipy.gplt.ytitle('yyy') >>> scipy.gplt.logx('on') >>> scipy.gplt.save('file.png') I find that updating the plot on screen takes up a lot of time which almost doubles the total execution time of my script. Johann

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io.read_array slow
by Christian Kristukat Sept. 16, 2005

Sept. 16, 2005

Hi, I noticed that io.read_array is really slow compared to a python while/readline/split loop (about 5 times slower). I believe to remember that at some time it was written in C but when I looked at the source of scipy 0.3.2 it seems to be pure python. Is there a evident reason why it must be that slow or are there maybe plans to rewrite it in C? Regards, Christian

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