Mailman 3 September 2006 - SciPy-User

global fitting of data sets with common parameters
by morovia morovia 26 Sep '06

26 Sep '06

Hello I have data sets and would like to fit them globally with common parameters. Is there a way to do this using existing scipy modules leastsq. Any pointers for algo and suggestions are welcome. Thanks Morovia.

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new SVN build issue?
by Scott Ransom 25 Sep '06

25 Sep '06

Hi All, So I just svn updated to revision 2233 and successfully installed on a 64-bit Debian installation using: rm -rf build ; python setup.py install --prefix=/usr/local However, on a 32-bit Debian machine, I'm getting the following error after doing: rm -rf build ; python setup.py install --prefix=/users/sransom ---------------------------------------- Warning: Inheriting attribute 'description'='image array convolution functions' from 'scipy.stsci.convolve' Warning: Inheriting attribute 'author'='Todd Miller' from 'scipy.stsci.convolve' Warning: Inheriting attribute 'author_email'='help(a)stsci.edu' from 'scipy.stsci.convolve' Warning: Inheriting attribute 'description'='image array convolution functions' from 'scipy.stsci' Warning: Inheriting attribute 'author'='Todd Miller' from 'scipy.stsci' Warning: Inheriting attribute 'author_email'='help(a)stsci.edu' from 'scipy.stsci' Traceback (most recent call last): File "setup.py", line 55, in ? setup_package() File "setup.py", line 47, in setup_package configuration=configuration ) File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/core.py", line 144, in setup config = configuration() File "setup.py", line 19, in configuration config.add_subpackage('Lib') File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/misc_util.py", line 753, in add_subpackage caller_level = 2) File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/misc_util.py", line 736, in get_subpackage caller_level = caller_level + 1) File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/misc_util.py", line 683, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./Lib/setup.py", line 25, in configuration config.make_svn_version_py() # installs __svn_version__.py File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/misc_util.py", line 1298, in make_svn_version_py self.add_data_files(('', generate_svn_version_py())) File "/users/sransom/lib/python2.3/site-packages/numpy/distutils/misc_util.py", line 1281, in generate_svn_version_py assert revision is not None,'hmm, why I am not inside SVN tree???' AssertionError: hmm, why I am not inside SVN tree??? ---------------------------------------- Am I doing something stupid? Thanks, Scott -- Scott M. Ransom Address: NRAO Phone: (434) 296-0320 520 Edgemont Rd. email: sransom(a)nrao.edu Charlottesville, VA 22903 USA GPG Fingerprint: 06A9 9553 78BE 16DB 407B FFCA 9BFA B6FF FFD3 2989

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Summary of SciPy 2006 & Guido's keynote
by Bill Baxter 24 Sep '06

24 Sep '06

I found this decent blog summary of SciPy2006 that I thought other folks might be interested in: http://pyre.third-bit.com/blog/archives/612.html I think it's Greg Wilson's blog. Greg, if you're out there, hope you don't mind me posting this. --bill

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additions to signal.ltisys.lti
by Ryan Krauss 24 Sep '06

24 Sep '06

I don't know if this is a developer question or not. It isn't anything hard core developer-ish, so I will start with the regular list. I would like to propose the addition of the following methods to signal.ltisys.lti. The two lsim ones are just conveinence functions, but I find the Bode method really useful. (I may have had to add an import statement for poly1d). def Bode(self,f): num=poly1d(self.num) den=poly1d(self.den) s=2.0j*pi*f tf=num(s)/den(s) return tf def lsim(self, U, T, X0=None, interp=1): Y=signal.lsim(self, U, T, X0, interp) return Y def lsim2(self, U, T, X0=None): Y=signal.lsim2(self, U, T, X0) return Y Basically, I am teaching a class with some controls/systems modeling and want Python to offer most of the same tools for lti's as Matlab's controls toolbox (eventually). Any thoughts? Ryan

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installing numpy
by Todd Keeler 24 Sep '06

24 Sep '06

Hi, I'm attempting to install numpy/scipy on my computer. I've installed lapack / atlas and have the following libs on my system: atlas-lapack /usr/lib/libatlas.a atlas-lapack /usr/lib/libcblas.a atlas-lapack /usr/lib/libf77blas.a atlas-lapack /usr/lib/liblapack.a The site.cfg reads: [atlas] library_dirs = /usr/lib/ atlas_libs = lapack, blas I'm having serious problems getting the numpy install to find the atlas and blas libraries: Any tips would be greatly appreciated. Thanks Todd heres the output of $ python setup.py config_fc --fcompiler=gnu95 build Running from numpy source directory. F2PY Version 2_3198 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib NOT AVAILABLE /home/todd/pkg/python-numpy/src/numpy-1.0rc1/numpy/distutils/system_info.py:1296: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/lib libraries blas not found in /usr/lib NOT AVAILABLE /home/todd/pkg/python-numpy/src/numpy-1.0rc1/numpy/distutils/system_info.py:1305: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /home/todd/pkg/python-numpy/src/numpy-1.0rc1/numpy/distutils/system_info.py:1308: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable./home/todd/pkg/python-numpy/src/numpy- 1.0rc1/numpy/distutils/system_info.py:1205: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in /usr/local/lib FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 /home/todd/pkg/python-numpy/src/numpy-1.0rc1/numpy/distutils/system_info.py:1229: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /home/todd/pkg/python-numpy/src/numpy-1.0rc1/numpy/distutils/system_info.py:1232: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries lapack,blas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE

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docstring cross-references [PATCH]
by A. M. Archibald 23 Sep '06

23 Sep '06

Hi, I've quickly gone through and done some cross-referencing of docstrings in scipy. Only the modules interpolate, integrate, and optimize have cross-references so far. I looked at special, but there are so many special functions I'm not sure what to do (for example, should the docstring on Bessel functions list modified Bessel functions? spherical Bessel functions?). That's all the packages I've had occasion to use, so the others would take longer. I'm afraid the cross-referencing is not neccessarily very consistent in formatting, but then neither are the docstrings themselves. A. M. Archibald

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Installation problems Mac OS X 10.4.7
by Helmut Strey 22 Sep '06

22 Sep '06

I have been trying to install the SciPy Superpack for Python. I used MacPython2.4. When I try to import pylab the following error message appears: helmut-streys-imac-g5:~ hstrey$ python Python 2.4.3 (#1, Apr 7 2006, 10:54:33) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from pylab import * Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/pylab.py", line 1, in ? from matplotlib.pylab import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/pylab.py", line 200, in ? from axes import Axes, PolarAxes File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/axes.py", line 15, in ? from axis import XAxis, YAxis File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/axis.py", line 25, in ? from font_manager import FontProperties File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/font_manager.py", line 39, in ? from matplotlib import ft2font ImportError: Failure linking new module: /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/matplotlib/ft2font.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/ft2font.so Reason: image not found >>> It seems that the package expects libfreetype6.dylib in /usr/local/lib. I found it in /usr/X11R6/lib. I tried to create a symbolic link but then it says that the compiler versions dont match. What should I do? Everything else works. Thanks Helmut Strey

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on global fitting for sets of data
by morovia morovia 22 Sep '06

22 Sep '06

Hello I have data sets and would like to fit them globally with common parameters. Is there a way to do this using existing scipy modules leastsq. Any pointers for algo and suggestions are welcome. Thanks Morovia.

3 2

matplotlib fails to run with latest scipy/numpy release
by fred 22 Sep '06

22 Sep '06

Hi all, I have just updated scipy (0.5.2.dev2209) and numpy (1.0.dev3204) and now, matplotlib (0.87-4) fails to run :-( ./> python Python 2.4.3 (#1, Aug 10 2006, 09:25:31) [GCC 3.3.5 (Debian 1:3.3.5-13)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import pylab Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.4/site-packages/pylab.py", line 1, in ? from matplotlib.pylab import * File "/usr/local/lib/python2.4/site-packages/matplotlib/pylab.py", line 196, in ? import cm File "/usr/local/lib/python2.4/site-packages/matplotlib/cm.py", line 5, in ? import colors File "/usr/local/lib/python2.4/site-packages/matplotlib/colors.py", line 33, in ? from numerix import array, arange, take, put, Float, Int, where, \ File "/usr/local/lib/python2.4/site-packages/matplotlib/numerix/__init__.py", line 74, in ? Matrix = matrix NameError: name 'matrix' is not defined What's wrong ? Cheers, -- « Python, c'est un peu comme la baïonnette en 14, faut toujours sortir avec, et pas hésiter d'en mettre un coup en cas de besoin. » J.-Ph. D.

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Selecting array elements using other array
by Jose Luis Gomez Dans 22 Sep '06

22 Sep '06

Hi! For the time being, I am still trapped with Numeric, and an old-ish version of Enthought. i am aware that with numpy, this question is trivial, but I need to keep using this version of Enthought. Essentially, I have two arrays: one is X (shape Nxd), and the other is id (shape N). I want to get an array which give me the rows of X where id is equal to some value. I can do this with for loops, but it is quite slow. I am sure there must be a way to do this efficiently. Note that d can vary. I have tried to build a new array and use compress or where. The new array has a new column with the id appended: tmp=c_[X[:,0,NewAxis],X[:,1,NewAxis],X[:,2,NewAxis],id[:,NewAxis]] However, this is just as messy, and i need to hard-code the second dimension of X. There has to be a more elegant solution to this!!! Many thanks! José -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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