Mailman 3 August 2005 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

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

5 5

Array functions
by Howey, David A Oct. 5, 2005

Oct. 5, 2005

I guess this is a numpy question, but how do I do truth tests on arrays? I'm trawling around the documentation but struggling to find an answer.. I want to test if any array contains ONLY zeros. Originally I had: if a == 0: # code in here I need this to be true both for a = 0 # ie a is just a number and for a = array((0,0,0,0,0)) It must return false for any array with any nonzero elements anywhere At the moment python does this (which is wrong): >>> vin = array((1.,0,0)) >>> vin array([ 1., 0., 0.]) >>> if vin == 0: print "yes" yes >>> Thanks Dave

5 4

scipy can't find Numeric header files during install
by Yaroslav Bulatov Sept. 5, 2005

Sept. 5, 2005

I'm trying to install scipy with --prefix=~/usr option I've installed Numeric and headers went to " ~/usr/include/python2.3/Numeric/" But now when I install SciPy by doing "python setup.py install --prefix=~/usr", it says Lib/cluster/src/vq_wrap.cpp:563:33: Numeric/arrayobject.h: No such file or directory How can I tell it to look in "~/usr/include/python2.3/Numeric/" for Numeric headers? -- Yaroslav Bulatov bulatov(a)cs.oregonstate.edu Dearborn 102 Oregon State University Corvallis, OR

2 2

SciPy 2005 Conference: Preliminary Schedule of Presentations
by Travis N. Vaught Sept. 5, 2005

Sept. 5, 2005

All, I've posted a preliminary schedule of presentations at: http://www.scipy.org/wikis/scipy05/ConferenceSchedule Please feel free to provide comments or corrections--either to the list or directly to me. If you haven't registered, you may do so at: https://www.enthought.com/scipy05/ More information about the conference is at: http://www.scipy.org/wikis/scipy05/ Regards, Travis (Vaught)

3 2

getting the "best" two eigenvectors for a PCA analysis with a power method
by Syd Diamond Sept. 1, 2005

Sept. 1, 2005

I'll be honest -- I'm mostly interested in the end not the means right now. I need to find the first and second principal components of a 120x520 matrix. Right now, I'm using the "from LinearAlgebra import eigenvectors" method to find eigenvectors of the covariance matrix. This worked fine for my 120x90 matrix, but it's choking on the 120x520 matrix. When I talked to a friend, he said usually shortcuts were taken... like the power method for computing the dominant eigenpair. I've googled around without any luck. Can anyone please give me some guidance here? In return, I can offer some hilariously inefficient code from a guy who still doesn't know what he's doing... enjoy :) Thank you everyone for your continued help. (And if you can offer guidance on the code as well, by all means be my guest :)) from Numeric import array, zeros, shape, Float from LinearAlgebra import eigenvectors from scipy import mean, std, cov def princomp(X): evals, evecs = eigenvectors(cov(X)) eSorter = {} for index in xrange(len(evals)): eval = evals[index] evec = evecs[index] eSorter[eval] = evec evalsList = eSorter.keys().sort() evecNew = zeros(shape(evecs), typecode=Float) counter = 0 for eval in evals: evec = eSorter[eval] evecNew[counter] = evec counter += 1 return evecNew

4 5

python crashes on scipy testing
by rainman Sept. 1, 2005

Sept. 1, 2005

Hello scipy-user, God, that's one thing I hate about Open Source - having to hunt high and low for binaries... or to face tremendous nightmares of building-from-sources. Let's see. I'm running WinXP on A-64. I have Python 2.4. Some time ago I decided to try SciPy. Aw, hell! No prebuilt binaries for Py2.4. And you need a ton of compilers to "make" sources. But I'm stubborn. I had nerve. I took: MSYS-1.0.10.exe MinGW-3.1.0-1.exe atlas3.6.0_WinNT_PIII.zip SciPy_complete-0.3.2.tar.gz Numeric-23.8.win32-py2.4.exe F2PY-2-latest.win32.exe , then I tuned environment vars and started "setup.py build". Oh! how cute! they forgot to put wgnuplot.exe inside! Let's take it from SciPy_complete-0.3.2.win32-py2.3-num23.5.exe. Trying once more... Tada! Compilation finally finished without error message. Let's run: import scipy scipy.test() Yeah, a lot of "no test file" messages, dots, some cryptic mumbling ending with "zswap:n=3", more dots, WHOOPS! python crashes. So, the question is... WHAT ELSE??? -- Best regards, rainman mailto:rainman.rocks@gmail.com

5 4

scipy.test() fail
by Ramon Crehuet Aug. 31, 2005

Aug. 31, 2005

Dear all, I have downloaded and installed Scipy but I get a problem running the tests. After a long output I get: >>>import scipy >>>scipy.test() . . . Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. .........................................................................................................................................../usr/lib/python2.3/site-packages/scipy/interpolate/fitpack2.py:412: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) ...................Illegal instruction And I am returned to the shell. This is the output from system_info.py _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libf77blas.a ) ( paths: /usr/lib/libcblas.a ) ( paths: /usr/lib/libatlas.a ) ( paths: /usr/lib/ATLAS ) system_info.atlas_blas_info ( include_dirs = /usr/local/include:/usr/include ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c atlas_blas_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libatlas.a ) system_info.atlas_blas_threads_info NOT AVAILABLE atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libf77blas.a ) ( paths: /usr/lib/libcblas.a ) ( paths: /usr/lib/libatlas.a ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/liblapack.so ) system_info.atlas_info ( include_dirs = /usr/local/include:/usr/include ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 atlas_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libatlas.a ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/libblas.so ) FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 blas_opt_info: running build_src building extension "atlas_version" sources creating build creating build/src adding 'build/src/atlas_version_0x375d48b1.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'atlas_version' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -g -fPIC' creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/build creating build/temp.linux-i686-2.3/build/src compile options: '-I/usr/include/python2.3 -c' gcc: build/src/atlas_version_0x375d48b1.c gcc -pthread -shared build/temp.linux-i686-2.3/build/src/atlas_version_0x375d48b1.o -L/usr/lib -latlas -o build/temp.linux-i686-2.3/atlas_version.so /usr/lib/python2.3/site-packages/scipy_distutils/system_info.py:812: FutureWarning: hex()/oct() of negative int will return a signed string in Python 2.4 and up magic = hex(hash(`config`)) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] blas_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE boost_python_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE dfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE dfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE djbfft_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE freetype2_info: NOT AVAILABLE gdk_2_info: FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_2_INFO', '"\\"2.2.4\\""'), ('GDK_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/include/pango-1.0', '/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_info: FOUND: libraries = ['gdk', 'Xi', 'Xext', 'X11', 'm', 'glib'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('GDK_INFO', '"\\"1.2.10\\""'), ('GDK_VERSION_1_2_10', None)] include_dirs = ['/usr/include/gtk-1.2', '/usr/X11R6/include', '/usr/include/glib-1.2', '/usr/lib/glib/include'] gdk_pixbuf_2_info: FOUND: libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.2.4\\""'), ('GDK_PIXBUF_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_pixbuf_xlib_2_info: FOUND: libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.2.4\\""'), ('GDK_PIXBUF_XLIB_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_x11_2_info: FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_X11_2_INFO', '"\\"2.2.4\\""'), ('GDK_X11_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/include/pango-1.0', '/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GTKP_2_INFO', '"\\"2.2.4\\""'), ('GTK_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_x11_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GTKP_X11_2_INFO', '"\\"2.2.4\\""'), ('GTK_X11_VERSION_2_2_4', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] lapack_atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libf77blas.a ) ( paths: /usr/lib/libcblas.a ) ( paths: /usr/lib/libatlas.a ) system_info.lapack_atlas_info NOT AVAILABLE lapack_atlas_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/ATLAS ) ( paths: /usr/lib/libatlas.a ) system_info.lapack_atlas_threads_info NOT AVAILABLE lapack_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/liblapack.so ) FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0xf2e16eb0.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] lapack_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE numarray_info: NOT AVAILABLE numpy_info: ( include_dirs = /usr/include/python2.3 ) ( paths: /usr/include/python2.3/Numeric/arrayobject.h ) FOUND: define_macros = [('NUMERIC_VERSION', '"\\"23.8\\""')] include_dirs = ['/usr/include/python2.3'] sfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE sfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE wx_info: FOUND: libraries = ['wx_gtk2-2.4'] extra_link_args = ['-pthread'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('WX_INFO', '"\\"2.4.2\\""'), ('WX_VERSION_2_4_2', None), ('WX_RELEASE_2_4', None), ('GTK_NO_CHECK_CASTS', None), ('__WXGTK__', None), ('_FILE_OFFSET_BITS', '64'), ('_LARGE_FILES', None)] include_dirs = ['/usr/lib/wx/include/gtk2-2.4'] x11_info: ( library_dirs = /usr/X11R6/lib:/usr/lib ) ( include_dirs = /usr/X11R6/include:/usr/include ) ( paths: /usr/X11R6/lib/libX11.so ) ( paths: /usr/X11R6/include/X11/X.h ) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] xft_info: FOUND: libraries = ['Xft', 'X11', 'freetype', 'Xrender', 'fontconfig'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('XFT_INFO', '"\\"2.1.2\\""'), ('XFT_VERSION_2_1_2', None)] include_dirs = ['/usr/X11R6/include', '/usr/include/freetype2'] Does anybody have an idea of what is going on? Thanks, Ramon

2 1

scipy.test() fail
by Ramon Crehuet Aug. 31, 2005

Aug. 31, 2005

Dear all, I sent a message a couple of hours ago saying that I got a message with Scipy tests. I recompiles BLAS, LAPACK, ATLAS and Numeric and now everything works fine. I'm looking forward to use this great code! Ramon

1 0

use of rv_continuous "fit"?
by lindeman＠bard.edu Aug. 31, 2005

Aug. 31, 2005

Evidently I haven't grasped the Zen of SciPy's rv_continuous classes. I am trying to compose a simple snippet of code that would fit a normal curve to a vector of data (say, [-2.0, -1.0, -0.5, 0.0, 0.5, 1.0, 2.0]) -- which .fit seems that it ought to do, with about three lines of code, but I can't figure out the three lines. And I can't seem to find a single use of .fit anywhere on the Web. Sigh. Could someone please rescue the newbie? Best, Mark Lindeman

2 6

pygist drivers
by Alan Bromborsky Aug. 30, 2005

Aug. 30, 2005

When plotting I usually have my python program write and execute a gnuplot script. I do this because gnuplot has a LaTeX driver so that I can use all the LaTeX symbols to annotate my graphs. Does pygist have a LaTeX driver?

3 2