Mailman 3 December 2003 - SciPy-User

Pythonw crashes if I try to plot Complex data points
by Hetal Patel Jan. 14, 2004

Jan. 14, 2004

Whenever I try to plot complex data using either plt or gplt from any pyhton shell(Python,PythonWin,IDLE,PyCrust). windows reports that pythonw has crashed. I know that it's a bit unfair to ask the plot routines to plot complex data but I would expect an error, not python to crash. I'm running the latest SciPy release on Windows XP. Example code below crashes. >>>from scipy import * >>>a = arange(1,10,0.2) >>>b = a + 2.j >>>b array([ 1. +2.j, 1.2+2.j, 1.4+2.j, 1.6+2.j, 1.8+2.j, 2. +2.j, 2.2+2.j, 2.4+2.j, 2.6+2.j, 2.8+2.j, 3. +2.j, 3.2+2.j, 3.4+2.j, 3.6+2.j, 3.8+2.j, 4. +2.j, 4.2+2.j, 4.4+2.j, 4.6+2.j, 4.8+2.j, 5. +2.j, 5.2+2.j, 5.4+2.j, 5.6+2.j, 5.8+2.j, 6. +2.j, 6.2+2.j, 6.4+2.j, 6.6+2.j, 6.8+2.j, 7. +2.j, 7.2+2.j, 7.4+2.j, 7.6+2.j, 7.8+2.j, 8. +2.j, 8.2+2.j, 8.4+2.j, 8.6+2.j, 8.8+2.j, 9. +2.j, 9.2+2.j, 9.4+2.j, 9.6+2.j, 9.8+2.j]) >>>gplt.plot(b) At this point python\pythonw crashes with the following error "python.exe has encountered a problem and needs to close. We are sorry for the inconvenience." If anyone can help me resolve this then I would greatly appreciate it. _________________________________________________________________ Use MSN Messenger to send music and pics to your friends http://www.msn.co.uk/messenger

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weave and Differential Evolution ga code
by zunzun＠zunzun.com Jan. 6, 2004

Jan. 6, 2004

I have used weave to inline my genetic algorithm code for Differential Evolution, and it is b-b-blazing fast. The DE home page is http://www.icsi.berkeley.edu/~storn/code.html which is chock full of source code. My native Python implementation crawls compared to any other language, but I do understand the algorithm now :) I'll put up the source code to my SciPy home page as soon as my membership stuff completes. James Phillips http://zunzun.com

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gcc error Using weave.blitz()
by Joshua Menke Dec. 29, 2003

Dec. 29, 2003

I'm having problems getting weave.blitz() to work. I'm running RedHat 9 with gcc 3.2. I've gotten the latest scipy and weave from cvs. The error seems to manifest whenever I try to pass in a variable from Python to the inline code. For example this works fine: from weave import line code = 'printf("test\n"); inline(code) But this doesn't: a = 1 code = 'a=2' inline(code,['a']) It returns the following (not sure what the "file changed" thing is either): file changed /home/josh/.python22_compiled/sc_83a88ab12cf3296e031df84985733d331.cpp: In function `PyObject* compiled_func(PyObject*, PyObject*)': /home/josh/.python22_compiled/sc_83a88ab12cf3296e031df84985733d331.cpp:650: parse error before `}' token Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 335, in inline auto_downcast = auto_downcast, File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 439, in compile_function verbose=verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/ext_tools.py", line 340, in compile verbose = verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/build_tools.py", line 272, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/lib/python2.2/site-packages/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/lib/python2.2/distutils/core.py", line 157, in setup raise SystemExit, "error: " + str(msg) weave.build_tools.CompileError: error: command 'gcc' failed with exit status 1 Any help would be great. thanks, Josh -- Joshua Menke NNML Lab BYU CS Dept. josh(a)cs.byu.edu

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Re: [SciPy-user] more OSX build problems
by Christopher Fonnesbeck Dec. 28, 2003

Dec. 28, 2003

Make sure the following is in your CFLAGS environmental variable: -framework vecLib in fact, my CFLAGS looks like this: -faltivec -lcc_dynamic -framework vecLib Let me know if this does not help. C. On Dec 19, 2003, at 2:04 PM, John Hunter wrote: >>>>>> "Christopher" == Christopher Fonnesbeck <chris(a)fonnesbeck.org> >>>>>> writes: > > Christopher> The only one you will have to install explicitly is > Christopher> f2py; ATLAS, LAPACK and fftw are available when you > Christopher> install the developer tools. > > > Hi Christopher, > > I've been trying to build scipy on OSX. I am not clear on how the > ATLAS / LAPACK / BLAS thing is supposed to work. I have > /System/Library/Frameworks/vecLib.framework on my system, but do no > see liblapack or libatlas or libblas. If these libs are contained in > vecLib, as was suggested in your post, how do I make scipy aware of > them? > > I have spent a fair amount of time following the links at > http://developer.apple.com/documentation/ReleaseNotes/MacOSX/ > vecLib.html > but do not see anything to download that looks like it has > blas, lapack and atlas. > > Also, > miriam:/System/Library/Frameworks/vecLib.framework> du > 1280 ./Versions/A/Headers > 8 ./Versions/A/Resources/English.lproj > 24 ./Versions/A/Resources > 1928 ./Versions/A > 1936 ./Versions > 1960 . > > is too small to contain atlas, lapack and blas > > On my linux box, liblapack with ATLAS built in is 5MB + . > > Thanks for any help, > JDH > > -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia

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Test for singular matrices
by Nils Wagner Dec. 17, 2003

Dec. 17, 2003

Dear experts, The RQI begins with a fixed square, complex matrix A, an initial estimated eigenvalue \mu_0, and an initial estimated eigenvector x_0, then the algorithm iterates the following steps (a) Solve the system (A-\mu_n I) y = x_n (b) let x_{n+1} be the unit vector in the direction of y (c) \mu_{n+1} = x_{n+1}^H A x_{n+1} I denotes the identity matrix x0 = ones(n) mu0 = rand(1)+rand(1)*1j y = linalg.solve(A-mu0*identity(n),x0) x1 = y/linalg.norm(y) mu1 = dot(conjugate(x1),dot(A,x1)) x0 = x1 mu0 = mu1 The iteration should halt when the system to be solved is singular, up to numerical tolerance. How can I realize this condition in scipy ? Thanks in advance. Nils

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SciPy install
by Carlos Dec. 17, 2003

Dec. 17, 2003

Hi, I'm really interrested in SciPy and tried to install it but it refuses to install with Python ver. 2.3. Do I need to revert back to Python ver 2.2 or is there a new release of SciPy that allows install for Python 2.3? Any work arounds? Thanks ahead. _____________________________ Bill Boykin Software Engineer SoftScience _____________________________ "Only those who will risk going too far can possibly find out how far one can go." --T.S. Eliot

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optimization with bounded parameter values
by Michael Sorich Dec. 16, 2003

Dec. 16, 2003

Hi All, I am trying to solve a nonlinear regression problem with 4 inputs and 8 parameters. I have used the leastsq function, however, the parameter values returned are not realistic and thus I would like to constrain the parameters to be within certain bounds. Is it possible to do this in scipy? If not, I would welcome suggestions of other free code (preferably in python) or software that can. Thanks for your time, Michael Sorich

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ANN: matplotlib-0.40 python plots with matlab syntax
by John Hunter Dec. 15, 2003

Dec. 15, 2003

matplotlib is a pure python 2D plotting library with a matlab syntax which produces publication quality figures using in a variety of hardcopy formats (PNG, JPG, TIFF, PS) and interactive GUI environments (WX, GTK) across platforms. matplotlib can be used in python scripts, interactively from the python shell (ala matlab or mathematica), in web application servers generating dynamic charts, or embedded in GTK or WX applications. http://matplotlib.sourceforge.net What's new WX python backend Jeremy O'Donoghue has done an amazing job implementing the backend for wxpython, with all the features such as interactive navigation that are supported in the GTk backend. matplotlib should not be available with a GUI anywhere wxpython, Numeric and python work, including linux and friends, win32, and Mac OS X. See http://matplotlib.sourceforge.net/matplotlib.backends.backend_wx.html for a summary of known issues. Pseudo color plots The pcolor command generates pseudo color plots. See http://matplotlib.sourceforge.net/screenshots.html#pcolor_demo and http://matplotlib.sourceforge.net/screenshots.html#mri_with_eeg for screenshots and example code New time-series plotting functions * psd - plots the power spectral density of a time series * csd - plots the cross spectral density of two time series * cohere - plots the coherence See the examples dir in the src distro: psd_demo.py and csd_demo.py Substantially improved layout The transform architecture was refactored, allowing much more precise layout. Lines, patches, text, etc... can now be placed and scaled in arbitrary units, relative axes units, or physical size. Applicaiton programmers who want to create lines, patches and text directly using the API should read the transform module docs for more info. See the text help for an example of how to specify text locations in axes coords (0,0 is lower left and 1,1 is upper right) Expanded legend capabilities The legend class is improved, with a more sophisticated layout engine and the ability to accept lines and rectangle patches as an optional first argument to specify which lines/patches make up the legend. There are also additional legend placement locations, like 'upper center'. See http://matplotlib.sourceforge.net/screenshots.html#legend_demo Expanded errorbar capabilities Gary Ruben contributed some code to support x and y errorbars, either symmetrix or asymettric, in one enhanced function 'errorbar'. See the errorbar_demo.py for examples of all the wild and wonderful errorbar styles. Bar charts can now also display errorbars; see http://matplotlib.sourceforge.net/screenshots.html#barchart_demo Figure size and DPI controllable from matlab interface The figure command now takes optional args figsize and dpi to set the figure size and DPI in the matlab interface. This change involved some changes in the way default sizes and resolutions were handled among the various backends, with the effect that figures generated by existing scripts may appear different, eg, in the relative size of text to the figure elements. The advantage is that the current implementation does a better job of computing true sizes with increased fidelity between backends. Apologies for any inconveniences! API changes There have been some minor changes to the API for those using matplotlib embedded in GTK applications. * If you instantiate an Axes of Subplot intace, the first arg to __init__ must be the figure that contains it. * If you instantiate any artists, eg, Line2D, Rectangle, or AxisTextGTk, you must initialize them with their dpi, bbox, and transforms. See the help for the transforms modules and the examples logo.py and mri_with_eeg.py, where the objects are explicity created using the new API. * The only change to the matlab interface is in the signature of the errorbar func, which breaks matlab compatibility for the enhanced ability to do x and y errorbars. * See matplotlib.axes.py for a complete list of API changes John Hunter

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Problem with plt.plot()
by Boris Breidenbach Dec. 11, 2003

Dec. 11, 2003

Hello! I am new to scipy. I tried the example given in the plotting tutorial (http://www.scipy.org/site_content/tutorials/plot_tutorial, section "Starting plt"). First, I imported gui_thread. But I did not get any message of the kind "<wxPython imported>". But I did not get any error message either. Then I did: >>> from scipy import plt and >>> plt.plot((1,2,3)) After that I get a message like <scipy.plt.wxplt.plot_frame instance; proxy of C++ wxFrame instance at _8259b50_wxFrame_p> but no window appears. Any idea why? On ending python, a window seems to pop up, just for a split second. It is not displayed long enough to recognize any content. Did anyone experience similar problems? Any suggestions what might be wrong? Cheers, Boris

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RE: [SciPy-user] Problem with plt.plot()
by Simon Duane Dec. 11, 2003

Dec. 11, 2003

Any chance of releasing a build of scipy that will install over standard Python 2.3, as opposed to the Enthought edition? Cheers Simon > -----Original Message----- > From: Travis N. Vaught [mailto:travis@enthought.com] > Sent: 10 December 2003 14:51 > To: 'SciPy Users List' > Subject: RE: [SciPy-user] Problem with plt.plot() > > > > > > -----Original Message----- > > From: scipy-user-bounces(a)scipy.net > [mailto:scipy-user-bounces@scipy.net] > > On Behalf Of Pearu Peterson > > Sent: Wednesday, December 10, 2003 7:57 AM > > To: SciPy Users List > > Subject: Re: [SciPy-user] Problem with plt.plot() > > > <snip> > > > > Try: > > > > >>> from gui_thread import wxPython_thread > > >>> wxPython_thread() > > >>> from scipy import plt > > >>> plt.plot((1,2,3)) > > > > The plotting tutorial needs to be updated... > > > > Pearu > > > > > I was just about to update the tutorial and noticed that the > wxPython_thread import doesn't work with Python 2.3 for Windows - > Enthought Edition build 1028 (the current download from > http://www.enthought.com/python ): > > C:\>python > Enthought Edition build 1028 > Python 2.3 (#46, Aug 11 2003, 09:34:05) [MSC v.1200 32 bit (Intel)] on > win32 > Type "help", "copyright", "credits" or "license" for more information. > >>> from gui_thread import wxPython_thread > Traceback (most recent call last): > File "<stdin>", line 1, in ? > File ".\site-packages\gui_thread\wxPython_thread.py", line 17, in ? > ImportError: cannot import name ParallelExec > > I'm going to test with a more recent build (not yet released) shortly, > but I wanted to point this out. > > > _______________________________________________ > > 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 > ------------------------------------------------------------------- This e-mail and any attachments may contain confidential and/or privileged material; it is for the intended addressee(s) only. If you are not a named addressee, you must not use, retain or disclose such information. NPL Management Ltd cannot guarantee that the e-mail or any attachments are free from viruses. NPL Management Ltd. Registered in England and Wales. No: 2937881 Registered Office: Teddington, Middlesex, United Kingdom TW11 0LW. -------------------------------------------------------------------

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