Mailman 3 December 2007 - 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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Is numpy's argsort lying about its numpy.int32 types?
by Rob Clewley 15 May '09

15 May '09

Hi, I'm having a problem comparing some types when using numpy's argsort. I'm using numpy 1.0.2. I can reproduce it simply: Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] << snip >> In [1]: from numpy import argsort, sort, int32, array In [2]: x=array([1,3,2]) In [3]: aa=argsort(x) In [4]: as=sort(x) In [5]: type(aa[0]) Out[5]: <type 'numpy.int32'> In [6]: type(as[0]) Out[6]: <type 'numpy.int32'> In [7]: int32 Out[7]: <type 'numpy.int32'> In [8]: type(as[0])==int32 Out[8]: True In [9]: type(aa[0])==int32 Out[9]: False Any of the three indices in aa give me the same problem. Can someone explain if I should be doing this a different way, and if this is a bug?! Thanks, Rob

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Installing Scipy
by David Arnold 10 Apr '08

10 Apr '08

All, Mac OS X 10.4.11 PPC. Installed python from this: http://www.python.org/ftp/python/2.5.1/python-2.5.1-macosx.dmg Installation finishes with "There were errors installing the software. Please try installing again." Installing again makes no difference, but Python appears to be running: scipy-0.6.0 $ python Python 2.5.1 (r251:54869, Apr 18 2007, 22:08:04) [GCC 4.0.1 (Apple Computer, Inc. build 5367)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> Downloaded scipy from: http://prdownloads.sourceforge.net/scipy/ scipy-0.6.0.tar.gz?download After unpacking and changing directories, simply did this: scipy-0.6.0 $ sudo python setup.py install Seem to finish OK. Lots of "Warnings.' But testing according to INSTALL.txt resulted in: scipy-0.6.0 $ python Python 2.5.1 (r251:54869, Apr 18 2007, 22:08:04) [GCC 4.0.1 (Apple Computer, Inc. build 5367)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "scipy/__init__.py", line 54, in <module> from __config__ import show as show_config ImportError: No module named __config__ Any ideas or advice? Thanks David.

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illegal instruction error in scipy.linalg.decomp.svd
by Lev Givon 11 Mar '08

11 Mar '08

On a Pentium 4 Linux box running python 2.5.1, scipy 0.6.0, numpy 1.0.4, and lapack 3.0, I recently noticed that scipy.linalg.decomp.svd() fails (and causes python to crash) with an "illegal instruction" error. A bit of debugging revealed that the error occurs in the line lwork = calc_lwork.gesdd(gesdd.prefix,m,n,compute_uv)[1] in scipy/linalg/decomp.py. Interestingly, scipy 0.5.2.1 on the same box (with all of the other software packages unchanged) does not exhibit this problem. Moreover, when I install scipy 0.6.0 along with all of the other packages on a Linux machine containing a Pentium D CPU, I do not observe the problem either. Being that I am running Mandriva Linux, closed scipy bug 540 caught my eye. I'm not sure how it could be related to the above problem, though (and I also do not know what the lapack patch mentioned in the ticket could have been - even though I have been maintaining Mandriva's lapack lately :-). Thoughts? L.G.

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assignment of hours of day in time series
by Tim Michelsen 13 Jan '08

13 Jan '08

Hello, how do I assign the hours of a day in time series? I have hourly measurements where hour 1 represents the end of the period 0:00-1:00, 2 the end of the period 1:00-2:00, ... , 24 the end of the period 23:00 to 24:00. When I plot these hourly time series from February to November the curve is continued into December because of that matter. time series then assumes that the value for hour 0:00 of dec, 01 is 0 which then leads do a wrong plotting behaviour. I want to achieve that hour 24 is accounted as the last measurement period of a day and not as the first measurement of the next day (like 0:00). Please help me out here. Thanks in advance, Timmie

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read_array problem
by Christoph Scheit 08 Jan '08

08 Jan '08

Hello everybody, just for curiosity I have a question regarding read_array. When I use the scipy.io read_array function I observe some behaviour which I don't understand... First I call the function like this: self.varVector = read_array(f, columns=cols, lines=((0, 0 + bsize), )) with cols = ((1,3), ) bsize = 5832 and I get an exception: ValueError: Argument lines must be a sequence of integers and/or range tuples. Calling now read_array like this self.varVector = read_array(f, columns=cols, lines=((0, 0 + 5832), )) works fine to my surprise... cols is here the same like before. Thanks in advance, Christoph

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Would anyone connect fortran constrained linear least squares solver to Python?
by dmitrey 07 Jan '08

07 Jan '08

Hi all, I had noticed (from traffic statistics): lots of people are interested in linear least squares problems (LLSP). However, scipy has only unconstrained LAPACK dGELSS/sGELSS. Could anyone provide connection of the fortran-written solver to Python (or connect it to scipy)? http://netlib3.cs.utk.edu/toms/587 (that one can handle linear eq and ineq constraints) Then I would gladly provide connection of the one to scikits.openopt. Regards, D. http://scipy.org/scipy/scikits/wiki/Dmitrey

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flagging no data in timeseries
by Tim Michelsen 06 Jan '08

06 Jan '08

Hello, I while ago I was pointed to the timeseries module from sandbox by one of its developers. Thanks again for that. I am still having some troubles and questions: Since I am still very new to the package I need some hints. In my original data nodata values are marked with "-999". How can I import the data or create the time series and exclude these no data points from further processing? I presume it has to do with the mask keyword. But I cannot get it. Here is the code: data = N.loadtxt(mydata_file, comments='#', delimiter='\t', converters=None, skiprows=2, usecols=None, unpack=False) # define start date D_hr = TS.Date(freq='HR', year=1995, month=2, day=1, hour=1) # mask ## prepare time series # take only needed values myvalues = data[:,5] # hourly values myvalues_ts_hourly = TS.time_series(myvalues, start_date=D_hr) I will appreciate every help. For further readability and archivability I write my other questions in separate emails. Kind regards, Timmie

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Mayavi2 installation woes (OS X 10.4.11, Python 2.5)
by William Henney 05 Jan '08

05 Jan '08

Hi list, I have been trying to install MayaVi2 on an intel Mac running 10.4.11, but I am running into a brick wall. I have been trying to follow the instructions I have found in various threads on this list and at https://svn.enthought.com/enthought/wiki/IntelMacPython25. I have managed to install all the dependencies (vtk, pyrex, wxpython, etc) but I just can't get the enthought.traits package to build. I have tried the versions from the SVN repo and also the tar balls from http://code.enthought.com/downloads/source/ets2.6/ but I always get the error when building enthought.traits: TypeError: swig_sources() takes exactly 3 arguments (2 given) An example of a full stack trace is given below. It seems that the problem has something to do with setuptools, and possibly with pyrex. I was initially using setuptools 0.6c7 and Pyrex 0.9.6.4, but after reading negative comments about 0.9.6, I downgraded to 0.9.5.1a, although this makes no difference. I have also tried using the latest development version of setuptools (0.7a1dev-r58661), but this doesn't work at all due to problems with "Namespace Packages" (with 0.6 these just give a warning, as seen in the output below). Does anyone have any idea how to solve this? Cheers Will Henney $ python setup.py build running build running build_py WARNING: enthought is a namespace package, but its __init__.py does not declare_namespace(); setuptools 0.7 will REQUIRE this! (See the setuptools manual under "Namespace Packages" for details.) WARNING: enthought.traits is a namespace package, but its __init__.py does not declare_namespace(); setuptools 0.7 will REQUIRE this! (See the setuptools manual under "Namespace Packages" for details.) WARNING: enthought.traits.ui is a namespace package, but its __init__.py does not declare_namespace(); setuptools 0.7 will REQUIRE this! (See the setuptools manual under "Namespace Packages" for details.) running egg_info writing requirements to enthought.traits.egg-info/requires.txt writing enthought.traits.egg-info/PKG-INFO writing namespace_packages to enthought.traits.egg-info/namespace_packages.txt writing top-level names to enthought.traits.egg-info/top_level.txt writing dependency_links to enthought.traits.egg-info/dependency_links.txt reading manifest file 'enthought.traits.egg-info/SOURCES.txt' writing manifest file 'enthought.traits.egg-info/SOURCES.txt' running build_ext building 'enthought.traits.ctraits' extension Traceback (most recent call last): File "setup.py", line 72, in <module> zip_safe = False, File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/core.py", line 151, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/dist.py", line 994, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/dist.py", line 994, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ site-packages/setuptools-0.6c7-py2.5.egg/setuptools/command/build_ext.py", line 46, in run File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/command/build_ext.py", line 290, in run self.build_extensions() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ site-packages/Pyrex/Distutils/build_ext.py", line 82, in build_extensions self.build_extension(ext) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ site-packages/setuptools-0.6c7-py2.5.egg/setuptools/command/build_ext.py", line 175, in build_extension File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ distutils/command/build_ext.py", line 453, in build_extension sources = self.swig_sources(sources, ext) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ site-packages/setuptools-0.6c7-py2.5.egg/setuptools/command/build_ext.py", line 77, in swig_sources TypeError: swig_sources() takes exactly 3 arguments (2 given)

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