Mailman 3 December 2006 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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3D plotting
by Robert Cimrman 10 Sep '09

10 Sep '09

Hi, I need to do some simple 3D plots, so I tried the two Cookbook recipes (xplt, mplot3d) and failed: * xplt: does not work when using a custom installation directory such as python setup.py install --root=/home/share/software apparently the gistdata directory path is wrong: gist.error: failed to create drawing -- Gist work.gs style sheet missing * mplot3d: does not work with my version of matplotlib (0.80). I have made the changes mentioned in the Cookbook to no avail. (Axes.__init__() args apparently changed, as well as some other matplotlib object attributes) Any ideas? mplot3d looks great, I would really like to use it! thanks, r.

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clapack and cblas modules are empty
by jrpirone 16 Mar '07

16 Mar '07

Hello, I've installed scipy and numpy from Andrew Straw's repository, all other libraries are from the standard Ubuntu repositories (6.10). When I execute scipy.test(), the following warnings appear: **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** Running the command: ldd /usr/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so Gives me: linux-gate.so.1 => (0xffffe000) liblapack.so.3 => /usr/lib/atlas/sse2/liblapack.so.3 (0xb7958000) libblas.so.3 => /usr/lib/atlas/sse2/libblas.so.3 (0xb7387000) libg2c.so.0 => /usr/lib/libg2c.so.0 (0xb735f000) libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7339000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb732e000) libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb71fa000) /lib/ld-linux.so.2 (0x80000000) Is there a problem with the libraries I have installed? Should I be worried about these warnings, or am I just being compulsive? Thanks for your help, Jason

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problem with lsim
by Ryan Krauss 08 Jan '07

08 Jan '07

I am having a problem with signal.lsim. Here is a script that recreates my problem: from scipy import * from pylab import plot t=arange(0,10,0.01) u=ones(shape(t)) sys=signal.lti([1.0],[1.0,1.0]) out=signal.lsim(sys,u,t) plot(out[0],out[1]) Here is the error message: I:\lsim_test.py 5 u=ones(shape(t)) 6 sys=signal.lti([1.0],[1.0,1.0]) ----> 7 out=signal.lsim(sys,u,t) 8 plot(out[0],out[1]) 9 c:\python24\lib\site-packages\scipy\signal\ltisys.py in lsim(system, U, T, X0, i nterp) 403 vt = transpose(v) 404 vti = linalg.inv(vt) --> 405 GT = dot(dot(vti,diag(numpy.exp(dt*lam))),vt).astype(xout.dtype.char ) 406 ATm1 = linalg.inv(AT) 407 ATm2 = dot(ATm1,ATm1) C:\Python24\Lib\site-packages\numpy\lib\twodim_base.py in diag(v, k) 66 i = arange(0,n+k) 67 fi = i+(i-k)*n ---> 68 res.flat[fi] = v 69 return res 70 elif len(s)==2: TypeError: can't convert complex to float; use abs(z) WARNING: Failure executing file: <lsim_test.py> My script is also attached if someone wants to run it. How do I fix this? Thanks, Ryan

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Indefinite coefficient matrix
by Nils Wagner 02 Jan '07

02 Jan '07

Hi all, I wan't to solve a system of linear equations A x = b, where A is symmetric but indefinite. Thus one cannot use a Cholesky factorization L L^T. AFAIK one can use an L D L^T - factorization, where D is a diagonal matrix. Is this factorization available in numpy/scipy ? Nils

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New user questions
by Niklas Saers 02 Jan '07

02 Jan '07

Hi guys, I'm a new user to SciPy, seeking a Python alternative to MatLab. I'm installing on an OS X box and downloaded and installed the SciPy Superpack with SciPy 0.5.2. I noticed that much of the copyright notices said 2001, 2002. Is SciPy still under active development? When running scipy.test(10) I got: Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/ umfpack.pyc'> Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'> I can import scipy.linsolve and scipy.linsolve.umfpack, though. Should I be worried or not worry about this at all? :-) Cheers Nik

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additional superpak problems
by belinda thom 01 Jan '07

01 Jan '07

Again, regarding SciPy Superpack for Python 2.4 (Power PC), PyMC-1.1- py2.4-macosx10.4.mpkg and scipy-0.5.2.dev2095-py2.4-macosx10.4.mpkg are problematic. For example, after installing all the superpack packages, behavior like the following results. A similar error occurs when doing spicy.test(). Only numpy's test worked w/no errors. It seems to me that superpaks with these kind of problems should not be listed as what to download at the Scipy download site. 22 % python Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. history mechanism set up >>> import PyMC Matplotlib module not detected ... plotting disabled. Matplotlib module not detected ... plotting disabled. Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/PyMC/__init__.py", line 19, in ? exec "from %s import *" % mod File "<string>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/PyMC/MCMC.py", line 37, in ? from flib import categor as _categorical ImportError: Failure linking new module: /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/PyMC/ flib.so: Library not loaded: /usr/local/lib/libg2c.0.dylib Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ lib/python2.4/site-packages/PyMC/flib.so Reason: image not found

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mac os x python 2.4 superpak issues
by belinda thom 31 Dec '06

31 Dec '06

Hi, I have been trying to determine the best way to install ipython in the scipy context for the mac. On the http://www.scipy.org/Download website I obtained "SciPy Superpack for Python 2.4 (Power PC)" because I liked the fact that everything came bundled together (and delivers receipts). I've run into a problem though: nowhere can I find an "ipython" executable. In addition, the "/doc" files listed in the "ipython-data" bom are also not present anywhere on my computer (the contents of the 2 bom files related to the ipython mkpg are appended) Have others been able to successfully use this method? Any idea what is wrong? Thanks, --b contents of ipython-data-0.7.2-py2.4-macosx10.4.pkg/Contents/Archive.bom ----------------- /doc /doc/ipython-0.7.2 /doc/ipython-0.7.2/COPYING /doc/ipython-0.7.2/ChangeLog /doc/ipython-0.7.2/README.txt /doc/ipython-0.7.2/README_Windows.txt /doc/ipython-0.7.2/build_doc_instruction.txt /doc/ipython-0.7.2/examples /doc/ipython-0.7.2/examples/example-demo.py /doc/ipython-0.7.2/examples/example-embed-short.py /doc/ipython-0.7.2/examples/example-embed.py /doc/ipython-0.7.2/examples/example-gnuplot.py /doc/ipython-0.7.2/examples/example-magic.py /doc/ipython-0.7.2/examples/magic_grepl.py /doc/ipython-0.7.2/ipnb_google_soc.lyx /doc/ipython-0.7.2/ipython.1 /doc/ipython-0.7.2/ipython.el /doc/ipython-0.7.2/magic.tex /doc/ipython-0.7.2/manual /doc/ipython-0.7.2/manual.lyx /doc/ipython-0.7.2/manual_base.lyx /doc/ipython-0.7.2/nbexample.py /doc/ipython-0.7.2/nbexample_latex.py /doc/ipython-0.7.2/nbexample_output.py /doc/ipython-0.7.2/new_design.lyx /doc/ipython-0.7.2/pycolor.1 /doc/ipython-0.7.2/pycon.ico /doc/ipython-0.7.2/update_manual.py /man /man/man1 /man/man1/ipython.1.gz /man/man1/pycolor.1.gz contents of ipython-purelib-0.7.2-py2.4-macosx10.4.pkg/Contents/Archive.bom ------------------ /ColorANSI.py /ColorANSI.pyc /ColorANSI.pyo /ConfigLoader.py /ConfigLoader.pyc /ConfigLoader.pyo /CrashHandler.py /CrashHandler.pyc /CrashHandler.pyo /DPyGetOpt.py /DPyGetOpt.pyc /DPyGetOpt.pyo /Debugger.py /Debugger.pyc /Debugger.pyo /Extensions /Extensions/InterpreterExec.py /Extensions/InterpreterExec.pyc /Extensions/InterpreterExec.pyo /Extensions/InterpreterPasteInput.py /Extensions/InterpreterPasteInput.pyc /Extensions/InterpreterPasteInput.pyo /Extensions/PhysicalQInput.py /Extensions/PhysicalQInput.pyc /Extensions/PhysicalQInput.pyo /Extensions/PhysicalQInteractive.py /Extensions/PhysicalQInteractive.pyc /Extensions/PhysicalQInteractive.pyo /Extensions/__init__.py /Extensions/__init__.pyc /Extensions/__init__.pyo /Extensions/astyle.py /Extensions/astyle.pyc /Extensions/astyle.pyo /Extensions/clearcmd.py /Extensions/clearcmd.pyc /Extensions/clearcmd.pyo /Extensions/ext_rehashdir.py /Extensions/ext_rehashdir.pyc /Extensions/ext_rehashdir.pyo /Extensions/ext_rescapture.py /Extensions/ext_rescapture.pyc /Extensions/ext_rescapture.pyo /Extensions/ibrowse.py /Extensions/ibrowse.pyc /Extensions/ibrowse.pyo /Extensions/ipipe.py /Extensions/ipipe.pyc /Extensions/ipipe.pyo /Extensions/ipy_defaults.py /Extensions/ipy_defaults.pyc /Extensions/ipy_defaults.pyo /Extensions/ipy_system_conf.py /Extensions/ipy_system_conf.pyc /Extensions/ipy_system_conf.pyo /Extensions/numeric_formats.py /Extensions/numeric_formats.pyc /Extensions/numeric_formats.pyo /Extensions/path.py /Extensions/path.pyc /Extensions/path.pyo /Extensions/pickleshare.py /Extensions/pickleshare.pyc /Extensions/pickleshare.pyo /Extensions/pspersistence.py /Extensions/pspersistence.pyc /Extensions/pspersistence.pyo /Extensions/win32clip.py /Extensions/win32clip.pyc /Extensions/win32clip.pyo /FakeModule.py /FakeModule.pyc /FakeModule.pyo /Gnuplot2.py /Gnuplot2.pyc /Gnuplot2.pyo /GnuplotInteractive.py /GnuplotInteractive.pyc /GnuplotInteractive.pyo /GnuplotRuntime.py /GnuplotRuntime.pyc /GnuplotRuntime.pyo /Itpl.py /Itpl.pyc /Itpl.pyo /Logger.py /Logger.pyc /Logger.pyo /Magic.py /Magic.pyc /Magic.pyo /OInspect.py /OInspect.pyc /OInspect.pyo /OutputTrap.py /OutputTrap.pyc /OutputTrap.pyo /Prompts.py /Prompts.pyc /Prompts.pyo /PyColorize.py /PyColorize.pyc /PyColorize.pyo /Release.py /Release.pyc /Release.pyo /Shell.py /Shell.pyc /Shell.pyo /UserConfig /UserConfig/ipy_profile_sh.py /UserConfig/ipy_profile_sh.pyc /UserConfig/ipy_profile_sh.pyo /UserConfig/ipy_user_conf.py /UserConfig/ipy_user_conf.pyc /UserConfig/ipy_user_conf.pyo /UserConfig/ipythonrc /UserConfig/ipythonrc-math /UserConfig/ipythonrc-numeric /UserConfig/ipythonrc-physics /UserConfig/ipythonrc-pysh /UserConfig/ipythonrc-scipy /UserConfig/ipythonrc-tutorial /__init__.py /__init__.pyc /__init__.pyo /background_jobs.py /background_jobs.pyc /background_jobs.pyo /completer.py /completer.pyc /completer.pyo /deep_reload.py /deep_reload.pyc /deep_reload.pyo /demo.py /demo.pyc /demo.pyo /excolors.py /excolors.pyc /excolors.pyo /genutils.py /genutils.pyc /genutils.pyo /hooks.py /hooks.pyc /hooks.pyo /ipapi.py /ipapi.pyc /ipapi.pyo /iplib.py /iplib.pyc /iplib.pyo /ipmaker.py /ipmaker.pyc /ipmaker.pyo /ipstruct.py /ipstruct.pyc /ipstruct.pyo /irunner.py /irunner.pyc /irunner.pyo /macro.py /macro.pyc /macro.pyo /numutils.py /numutils.pyc /numutils.pyo /platutils.py /platutils.pyc /platutils.pyo /platutils_dummy.py /platutils_dummy.pyc /platutils_dummy.pyo /platutils_posix.py /platutils_posix.pyc /platutils_posix.pyo /platutils_win32.py /platutils_win32.pyc /platutils_win32.pyo /rlineimpl.py /rlineimpl.pyc /rlineimpl.pyo /ultraTB.py /ultraTB.pyc /ultraTB.pyo /upgrade_dir.py /upgrade_dir.pyc /upgrade_dir.pyo /usage.py /usage.pyc /usage.pyo /wildcard.py /wildcard.pyc /wildcard.pyo /winconsole.py /winconsole.pyc /winconsole.pyo bthom(a)tweedledum.local [11:07am] ~/ rcpts 15 %

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FW: Pylab load dates
by Vincent Nijs 30 Dec '06

30 Dec '06

I there someone on this list that can build matplotlib for the mac? I used the matplotlib package in the superpack and also tried the one on macpython to run the example below to read dates from a csv file but it didn't work. Apparently because the pytz module is not available in the matplotlib packages for the mac. I tried compiling matplotlib myself but got the following error on build: gcc: cannot specify -o with -c or -S and multiple compilations Vincent from pylab import figure, show, datestr2num, load dates, closes = load( 'data/msft.csv', delimiter=',', converters={0:datestr2num}, skiprows=1, usecols=(0,2), unpack=True) Date,Open,High,Low,Close,Volume,Adj. Close* 19-Sep-03,29.76,29.97,29.52,29.96,92433800,29.79 18-Sep-03,28.49,29.51,28.42,29.50,67268096,29.34 17-Sep-03,28.76,28.95,28.47,28.50,47221600,28.34 16-Sep-03,28.41,28.95,28.32,28.90,52060600,28.74 15-Sep-03,28.37,28.61,28.33,28.36,41432300,28.20 12-Sep-03,27.48,28.40,27.45,28.34,55777200,28.18 11-Sep-03,27.66,28.11,27.59,27.84,37813300,27.68 10-Sep-03,28.03,28.18,27.48,27.55,54763500,27.40

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Fwd: additional superpak problems
by belinda thom 30 Dec '06

30 Dec '06

Begin forwarded message: > From: Vincent Nijs <v-nijs(a)kellogg.northwestern.edu> > Date: December 30, 2006 4:32:08 PM PST > To: belinda thom <bthom(a)cs.hmc.edu> > Subject: Re: [SciPy-user] additional superpak problems > > g77 was part of the super pack I believe. Perhaps it is important > that you > install that first. > > Ipython -pylab works fine on my laptop (G4) but not on my G5 (same > error you > report). I'll try your fix of using the package from macpython next > week. > > Vincent > > > On 12/30/06 6:13 PM, "belinda thom" <bthom(a)cs.hmc.edu> wrote: > >> And yet more strangeness...the superpack matplotlib breaks the >> ability to use pylab: >> >> running >> ipython -pylab >> >> produces: >> <snip> >> File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ >> python2.4/site-packages/matplotlib/backends/tkagg.py", line 1, in ? >> import _tkagg >> ImportError: Failure linking new module: /Library/Frameworks/ >> Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/ >> backends/_tkagg.so: Library not loaded: /usr/local/lib/libfreetype. >> 6.dylib >> Referenced from: /Library/Frameworks/Python.framework/Versions/ >> 2.4/ >> lib/python2.4/site-packages/matplotlib/backends/_tkagg.so >> Reason: image not found >> >> Reverting back to the matplotlib at http://www.macpython.org/ >> packages/ >> py24-fat/index.html allows ipython -pylab to work. >> >> I have no idea if mixing and matching parts of superpak with other >> packages will cause me later problems. >> >> I'm curious, Vincent, do you run matplotlib interactively with >> ipython? Does that piece installed from the superpack work for you? >> >> Thanks again, >> >> --b >> > > -- > Vincent R. Nijs > Assistant Professor of Marketing > Kellogg School of Management, Northwestern University > 2001 Sheridan Road, Evanston, IL 60208-2001 > Phone: +1-847-491-4574 Fax: +1-847-491-2498 > E-mail: v-nijs(a)kellogg.northwestern.edu > Skype: vincentnijs > > >

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